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IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma

Mutations in isocitrate dehydrogenase 1 and 2 ( IDH1 and IDH2 ), are present in most gliomas. IDH1 mutation is an important prognostic marker in glioma. However, its regulatory mechanism in glioma remains incomplet...

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Therapeutic potential of oleic acid supplementation in myotonic dystrophy muscle cell models

We recently reported that upregulation of Musashi 2 (MSI2) protein in the rare neuromuscular disease myotonic dystrophy type 1 contributes to the hyperactivation of the muscle catabolic processes autophagy and...

Dorsal root ganglion-derived exosomes deteriorate neuropathic pain by activating microglia via the microRNA-16-5p/HECTD1/HSP90 axis

The activated microglia have been reported as pillar factors in neuropathic pain (NP) pathology, but the molecules driving pain-inducible microglial activation require further exploration. In this study, we in...

MicroRNA-721 regulates gluconeogenesis via KDM2A-mediated epigenetic modulation in diet-induced insulin resistance in C57BL/6J mice

Aberrant gluconeogenesis is considered among primary drivers of hyperglycemia under insulin resistant conditions, with multiple studies pointing towards epigenetic dysregulation. Here we examine the role of mi...

Combined transcriptomics and proteomics unveil the impact of vitamin C in modulating specific protein abundance in the mouse liver

Vitamin C (ascorbate) is a water-soluble antioxidant and an important cofactor for various biosynthetic and regulatory enzymes. Mice can synthesize vitamin C thanks to the key enzyme gulonolactone oxidase (Gul...

Novel role of LLGL2 silencing in autophagy: reversing epithelial-mesenchymal transition in prostate cancer

Prostate cancer (PCa) is a major urological disease that is associated with significant morbidity and mortality in men. LLGL2 is the mammalian homolog of Lgl. It acts as a tumor suppressor in breast and hepati...

Rapid development and mass production of SARS-CoV-2 neutralizing chicken egg yolk antibodies with protective efficacy in hamsters

Despite the record speed of developing vaccines and therapeutics against the SARS-CoV-2 virus, it is not a given that such success can be secured in future pandemics. In addition, COVID-19 vaccination and appl...

High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats

Obesity, associated with the intake of a high-fat diet (HFD), and anxiety are common among those living in modern urban societies. Recent studies suggest a role of microbiome-gut-brain axis signaling, includin...

General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex

Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regula...

Establishment of primary prostate epithelial and tumorigenic cell lines using a non-viral immortalization approach

Research on prostate cancer is mostly performed using cell lines derived from metastatic disease, not reflecting stages of tumor initiation or early progression. Establishment of cancer cell lines derived from...

The effect of diabetes mellitus on differentiation of mesenchymal stem cells into insulin-producing cells

Diabetes mellitus (DM) is a global epidemic with increasing incidences. DM is a metabolic disease associated with chronic hyperglycemia. Aside from conventional treatments, there is no clinically approved cure...

Control of astrocytic Ca 2+ signaling by nitric oxide-dependent S-nitrosylation of Ca 2+ homeostasis modulator 1 channels

Astrocytes Ca 2+ signaling play a central role in the modulation of neuronal function. Activation of metabotropic glutamate receptors (mGluR) by glutamate released during an increase in synaptic activity triggers ...

Increased levels and activation of the IL-17 receptor in microglia contribute to enhanced neuroinflammation in cerebellum of hyperammonemic rats

Patients with liver cirrhosis may show minimal hepatic encephalopathy (MHE) with mild cognitive impairment and motor incoordination. Rats with chronic hyperammonemia reproduce these alterations. Motor incoordi...

Identification and expression analysis of two steamer-like retrotransposons in the Chilean blue mussel ( Mytilus chilensis )

Disseminated neoplasia (DN) is a proliferative cell disorder of the circulatory system of bivalve mollusks. The disease is transmitted between individuals and can also be induced by external chemical agents su...

Noncoding RNAs in skeletal development and disorders

Protein-encoding genes only constitute less than 2% of total human genomic sequences, and 98% of genetic information was previously referred to as “junk DNA”. Meanwhile, non-coding RNAs (ncRNAs) consist of app...

Cx43 hemichannels and panx1 channels contribute to ethanol-induced astrocyte dysfunction and damage

Alcohol, a widely abused drug, significantly diminishes life quality, causing chronic diseases and psychiatric issues, with severe health, societal, and economic repercussions. Previously, we demonstrated that...

Galectins in epithelial-mesenchymal transition: roles and mechanisms contributing to tissue repair, fibrosis and cancer metastasis

Galectins are soluble glycan-binding proteins that interact with a wide range of glycoproteins and glycolipids and modulate a broad spectrum of physiological and pathological processes. The expression and subc...

Glutaminolysis regulates endometrial fibrosis in intrauterine adhesion via modulating mitochondrial function

Endometrial fibrosis, a significant characteristic of intrauterine adhesion (IUA), is caused by the excessive differentiation and activation of endometrial stromal cells (ESCs). Glutaminolysis is the metabolic...

The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans

Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the...

MicroRNA-148b secreted by bovine oviductal extracellular vesicles enhance embryo quality through BPM/TGF-beta pathway

Extracellular vesicles (EVs) and their cargoes, including MicroRNAs (miRNAs) play a crucial role in cell-to-cell communication. We previously demonstrated the upregulation of bta-mir-148b in EVs from oviductal...

YME1L-mediated mitophagy protects renal tubular cells against cellular senescence under diabetic conditions

The senescence of renal tubular epithelial cells (RTECs) is crucial in the progression of diabetic kidney disease (DKD). Accumulating evidence suggests a close association between insufficient mitophagy and RT...

Effects of latroeggtoxin-VI on dopamine and α-synuclein in PC12 cells and the implications for Parkinson’s disease

Parkinson’s disease (PD) is characterized by death of dopaminergic neurons leading to dopamine deficiency, excessive α-synuclein facilitating Lewy body formation, etc. Latroeggtoxin-VI (LETX-VI), a proteinaceo...

Glial-restricted progenitor cells: a cure for diseased brain?

The central nervous system (CNS) is home to neuronal and glial cells. Traditionally, glia was disregarded as just the structural support across the brain and spinal cord, in striking contrast to neurons, alway...

Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile

The convergence of hypervirulence and carbapenem resistance in the bacterial pathogen Klebsiella pneumoniae represents a critical global health concern. Hypervirulent K. pneumoniae (hvKp) strains, frequently from...

Endometrial mesenchymal stromal/stem cells improve regeneration of injured endometrium in mice

The monthly regeneration of human endometrial tissue is maintained by the presence of human endometrial mesenchymal stromal/stem cells (eMSC), a cell population co-expressing the perivascular markers CD140b an...

Embryo development is impaired by sperm mitochondrial-derived ROS

Basal energetic metabolism in sperm, particularly oxidative phosphorylation, is known to condition not only their oocyte fertilising ability, but also the subsequent embryo development. While the molecular pat...

Fibroblasts inhibit osteogenesis by regulating nuclear-cytoplasmic shuttling of YAP in mesenchymal stem cells and secreting DKK1

Fibrous scars frequently form at the sites of bone nonunion when attempts to repair bone fractures have failed. However, the detailed mechanism by which fibroblasts, which are the main components of fibrous sc...

MSC-derived exosomes protect auditory hair cells from neomycin-induced damage via autophagy regulation

Sensorineural hearing loss (SNHL) poses a major threat to both physical and mental health; however, there is still a lack of effective drugs to treat the disease. Recently, novel biological therapies, such as ...

Alpha-synuclein dynamics bridge Type-I Interferon response and SARS-CoV-2 replication in peripheral cells

Increasing evidence suggests a double-faceted role of alpha-synuclein (α-syn) following infection by a variety of viruses, including SARS-CoV-2. Although α-syn accumulation is known to contribute to cell toxic...

Lactadherin immunoblockade in small extracellular vesicles inhibits sEV-mediated increase of pro-metastatic capacities

Tumor-derived small extracellular vesicles (sEVs) can promote tumorigenic and metastatic capacities in less aggressive recipient cells mainly through the biomolecules in their cargo. However, despite recent ad...

Integration of ATAC-seq and RNA-seq identifies MX1-mediated AP-1 transcriptional regulation as a therapeutic target for Down syndrome

Growing evidence has suggested that Type I Interferon (I-IFN) plays a potential role in the pathogenesis of Down Syndrome (DS). This work investigates the underlying function of MX1, an effector gene of I-IFN,...

The novel roles of YULINK in the migration, proliferation and glycolysis of pulmonary arterial smooth muscle cells: implications for pulmonary arterial hypertension

Abnormal remodeling of the pulmonary vasculature, characterized by the proliferation and migration of pulmonary arterial smooth muscle cells (PASMCs) along with dysregulated glycolysis, is a pathognomonic feat...

Electroacupuncture promotes neurogenesis in the dentate gyrus and improves pattern separation in an early Alzheimer's disease mouse model

Impaired pattern separation occurs in the early stage of Alzheimer’s disease (AD), and hippocampal dentate gyrus (DG) neurogenesis participates in pattern separation. Here, we investigated whether spatial memo...

Role of SYVN1 in the control of airway remodeling in asthma protection by promoting SIRT2 ubiquitination and degradation

Asthma is a heterogenous disease that characterized by airway remodeling. SYVN1 (Synoviolin 1) acts as an E3 ligase to mediate the suppression of endoplasmic reticulum (ER) stress through ubiquitination and de...

Advances towards the use of gastrointestinal tumor patient-derived organoids as a therapeutic decision-making tool

In December 2022 the US Food and Drug Administration (FDA) removed the requirement that drugs in development must undergo animal testing before clinical evaluation, a declaration that now demands the establish...

Melatonin alleviates pyroptosis by regulating the SIRT3/FOXO3α/ROS axis and interacting with apoptosis in Atherosclerosis progression

Atherosclerosis (AS), a significant contributor to cardiovascular disease (CVD), is steadily rising with the aging of the global population. Pyroptosis and apoptosis, both caspase-mediated cell death mechanism...

Prenatal ethanol exposure and changes in fetal neuroendocrine metabolic programming

Prenatal ethanol exposure (PEE) (mainly through maternal alcohol consumption) has become widespread. However, studies suggest that it can cause intrauterine growth retardation (IUGR) and multi-organ developmen...

Autologous non-invasively derived stem cells mitochondria transfer shows therapeutic advantages in human embryo quality rescue

The decline in the quantity and quality of mitochondria are closely associated with infertility, particularly in advanced maternal age. Transferring autologous mitochondria into the oocytes of infertile female...

Development of synthetic modulator enabling long-term propagation and neurogenesis of human embryonic stem cell-derived neural progenitor cells

Neural progenitor cells (NPCs) are essential for in vitro drug screening and cell-based therapies for brain-related disorders, necessitating well-defined and reproducible culture systems. Current strategies em...

Heat-responsive microRNAs participate in regulating the pollen fertility stability of CMS-D2 restorer line under high-temperature stress

Anther development and pollen fertility of cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) restorer lines are susceptible to continuous high-temperature (HT) stress in sum...

Chemogenetic inhibition of NTS astrocytes normalizes cardiac autonomic control and ameliorate hypertension during chronic intermittent hypoxia

Obstructive sleep apnea (OSA) is characterized by recurrent episodes of chronic intermittent hypoxia (CIH), which has been linked to the development of sympathoexcitation and hypertension. Furthermore, it has ...

SARS-CoV-2 spike protein S1 activates Cx43 hemichannels and disturbs intracellular Ca 2+ dynamics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the ongoing coronavirus disease 2019 (COVID-19). An aspect of high uncertainty is whether the SARS-CoV-2 per se or the systemic inflammation ...

The effect of zofenopril on the cardiovascular system of spontaneously hypertensive rats treated with the ACE2 inhibitor MLN-4760

Angiotensin converting enzyme 2 (ACE2) plays a crucial role in the infection cycle of SARS-CoV-2 responsible for formation of COVID-19 pandemic. In the cardiovascular system, the virus enters the cells by bind...

Two murine models of sepsis: immunopathological differences between the sexes—possible role of TGFβ1 in female resistance to endotoxemia

Endotoxic shock (ExSh) and cecal ligature and puncture (CLP) are models that induce sepsis. In this work, we investigated early immunologic and histopathologic changes induced by ExSh or CLP models in female a...

An intracellular, non-oxidative factor activates in vitro chromatin fragmentation in pig sperm

In vitro incubation of epididymal and vas deferens sperm with Mn 2+ induces Sperm Chromatin Fragmentation (SCF), a mechanism that causes double-stranded breaks in toroid-linker regions (TLRs). Whether this mechani...

Focal ischemic stroke modifies microglia-derived exosomal miRNAs: potential role of mir-212-5p in neuronal protection and functional recovery

Ischemic stroke is a severe type of stroke with high disability and mortality rates. In recent years, microglial exosome-derived miRNAs have been shown to be promising candidates for the treatment of ischemic ...

S -Nitrosylation in endothelial cells contributes to tumor cell adhesion and extravasation during breast cancer metastasis

Nitric oxide is produced by different nitric oxide synthases isoforms. NO activates two signaling pathways, one dependent on soluble guanylate cyclase and protein kinase G, and other where NO post-translationa...

Identifying pyroptosis- and inflammation-related genes in intracranial aneurysms based on bioinformatics analysis

Intracranial aneurysm (IA) is the most common cerebrovascular disease, and subarachnoid hemorrhage caused by its rupture can seriously impede nerve function. Pyroptosis is an inflammatory mode of cell death wh...

Drosophila Atlastin regulates synaptic vesicle mobilization independent of bone morphogenetic protein signaling

The endoplasmic reticulum (ER) contacts endosomes in all parts of a motor neuron, including the axon and presynaptic terminal, to move structural proteins, proteins that send signals, and lipids over long dist...

Mucin1 induced trophoblast dysfunction in gestational diabetes mellitus via Wnt/β-catenin pathway

To elucidate the role of Mucin1 (MUC1) in the trophoblast function (glucose uptake and apoptosis) of gestational diabetes mellitus (GDM) women through the Wnt/β-catenin pathway.

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Biological Research

ISSN: 0717-6287

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Plos biology article types.

PLOS Biology considers works of exceptional significance, originality, and relevance in all areas of biological science, including both primary research, meta-analyses and Magazine articles . Our publication options are outlined below.

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PLOS Biology publishes seven different types of research reports. All research articles are compatible with our easy, format-free submission process, and offer options for preprints, published peer review history, and publishing uncorrected proofs. Most, with rare exception, are also protected by our scooping policy , ensuring that your research will not be rejected for novelty within six-months of the publication of a complementary or confirmatory research publication. We evaluate all research based on the important questions it answers and its potential to impact an international scientific community as well as educators, policy makers, patient advocacy groups, and society more broadly.

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Our magazine section is divided into Front Matter and In-depth Analysis subsections. Front Matter articles are short, focussed and provide opinion on topical issues, community resources or commentary on PLOS Biology articles. In-depth Analyses are long-form articles providing forward-looking analysis of a given topic, highlighting gaps in our current understanding or putting forward community recommendations or guidelines. We do not publish traditional review articles.

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Front Matter

Editorials are written in-house by members of the editorial staff or by members of the Editorial Board.

Perspectives

The Perspectives section provides experts with a forum to comment on topical or controversial issues of broad interest. They address controversial issues or those at the interface between science and policy or science and society; present a policy position aimed at influencing policy decisions; examine and make recommendations on scientific and publishing practices. These are meant to be short, opinionated, Op-ed type of pieces.

The ideal Perspective conveys a sense of urgency. Some things to think about would be:

• Is this topic of immediate concern?
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• Does the piece offer a novel point of view on a scientific or policy issue, or on topical events?
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Controversial articles are welcomed, but the text should acknowledge that a position is in fact controversial and provide readers with enough background on the differing views.

Our Perspectives aim to engage a broad and diverse audience—it is therefore important to ensure that they are written in an accessible, persuasive, and stimulating style that appeals to both specialists and non-specialist readers. Perspectives are usually assessed in-house with our Editorial Board, but we reserve the right to peer-review them if needed. Commissioning does not guarantee publication. Editors work closely with authors to ensure that articles are written in an engaging, succinct, yet rigorous manner.

Guidelines for a Perspective

Example perspectives.

Lowe-Power T, Dyson L, Polter AM (2021) A generation of junior faculty is at risk from the impacts of COVID-19. PLoS Biol 19(5): e3001266. https://doi.org/10.1371/journal.pbio.3001266

Bourne PE (2021) Is “bioinformatics” dead? PLoS Biol 19(3): e3001165. https://doi.org/10.1371/journal.pbio.3001165

Primers provide concise and accessible context to a PLOS Biology research article of broad and current interest. Primers are commissioned and published alongside a research article that would benefit from additional context and/or explanation.

Above all, Primers should demystify an area of biology, avoid and/or explain technical jargon and provide critical and forward-thinking analysis about how the research article fits into the current state of the field and its future. A good Primer will briefly discuss (but not exhaustively review) what we know and what questions we have yet to answer for a particular field. It will then introduce the new findings and describe in roughly three paragraphs the advance represented in the related research article, highlighting its significance, not only for the discipline in question, but across disciplines. The Primer should then explain what the findings suggest in terms of next steps: what new avenues of investigation are opened, what new experiments can be tried, what new ideas can now be tested going forward? Ideally, Primers also offer insight into what big questions are likely to remain unanswered for many years (for whatever reasons).

We encourage the use of a figure to illustrate key concepts/mechanism/conclusions in an informative, easy-to-understand manner.

Primers are usually assessed by our Editorial Board, but we reserve the right to peer-review externally if needed. Commissioning does not guarantee publication. Editors work closely with authors to ensure that articles are written in an engaging, succinct, yet rigorous manner.

Guidelines for a Primer

Example primer.

Kazanova A, Rudd CE (2021) Programmed cell death 1 ligand (PD-L1) on T cells generates Treg suppression from memory. PLoS Biol 19(5): e3001272. https://doi.org/10.1371/journal.pbio.3001272

Guizetti J, Frischknecht F (2021) Apicomplexans: A conoid ring unites them all. PLoS Biol 19(3): e3001105. https://doi.org/10.1371/journal.pbio.3001105

Community Pages

Community Pages provide individuals, networks and organizations with the opportunity to highlight resources, tools, or initiatives of benefit to the scientific community and beyond (including science education and public engagement in science). All resources or tools, and the outputs of initiatives must be open and accessible to all.

Contributors must resist the temptation of self-promotion and instead focus on conveying information to a diverse audience.Community Pages should be written in a succinct, accessible, semi-journalistic style that captures the interest of both specialists and non-specialist readers. We encourage the use of 1-2 figures to illustrate key concepts in an informative, easy to grasp manner; or the use of text boxes for background, self-contained information.

Community Pages are peer-reviewed and commissioning does not guarantee publication. Editors work closely with authors to ensure that articles are written in an engaging, succinct, yet rigorous manner.

Guidelines for a Community Page

Example Community Pages

Weissgerber TL (2021) Training early career researchers to use meta-research to improve science: A participant-guided “learn by doing” approach. PLoS Biol 19(2): e3001073. https://doi.org/10.1371/journal.pbio.3001073

McCullagh EA, Nowak K, Pogoriler A, Metcalf JL, Zaringhalam M, Zelikova TJ (2019) Request a woman scientist: A database for diversifying the public face of science. PLoS Biol 17 (4): e3000212. https://doi.org/10.1371/journal. pbio.3000212

Formal Comments

Formal Comments are intended to provide a formal outlet for the discussion and interpretation of research findings associated with specific articles published in PLOS Biology . They are designed to ensure that readers obtain a balanced view of a scientific or meta-scientific/policy question, especially in areas of debate/controversy. Formal Comments are peer-reviewed and indexed in PubMed.

Formal Comments must be coherent, concise, and well-argued, and are subject to the PLOS Biology criteria for publication . Editors will, as a matter of course, invite the authors of the original article to submit a response to the Formal Comment. Any revisions (of the Formal Comment or the response) will be shared with the authors of the associated comment.

Guidelines for Formal Comments

Example formal comment.

Rees WE, Wackernagel M (2013) The Shoe Fits, but the Footprint is Larger than Earth. PLoS Biol 11(11): e1001701. https://doi.org/10.1371/journal.pbio.1001701​ ​

Example Formal Comment - Response

Blomqvist L, Brook BW, Ellis EC, Kareiva PM, Nordhaus T, Shellenberger M (2013) The Ecological Footprint Remains a Misleading Metric of Global Sustainability. PLoS Biol 11(11): e1001702. https://doi.org/10.1371/journal.pbio.1001702

In-Depth Analysis

Essays are opinionated articles on a topic of interest to scientists and to a broader audience, including the general public. Unlike traditional review articles, which include a comprehensive account of a field, Essays take an imaginative approach to a provocative question, with an engaging but rigorous investigation of the problem. We encourage authors of Essays to select the most representative references to convey their points and avoid exhaustively covering the relevant literature.

The remit of Essays is very broad. They might:

• take stock of progress in a field from a personal point of view
• explore the implications of recent advances that promise to have broad-ranging consequences on a field
• comment on a topical or controversial area of research
• discuss key ideas or educational strategies to enhance understanding of fundamental biological questions
• offer historical/philosophical reflections on contemporary biology
• analyze scientific issues with policy implications

Our Essays aim to engage a broad and diverse audience—it is therefore important to ensure that they are written in an accessible, semi-journalistic style that captures the interest of both specialists and non-specialist readers. We encourage the use of figures to illustrate key concepts in an informative, easy to grasp manner; as well as the use of text boxes for background, self-contained information.

Essays are peer-reviewed and commissioning does not guarantee publication.

Guidelines for an Essay

Example essays.

Rees T, Bosch T, Douglas AE (2018) How the microbiome challenges our concept of self. PLoS Biol 16(2): e2005358. https://doi.org/10.1371/journal.pbio.2005358 Konig C, Weigelt P, Schrader J, Taylor A, Kattge J, Kreft H (2019) Biodiversity data integration—the significance of data resolution and domain. PLoS Biol 17(3): e3000183. https://doi.org/10.1371/journal.pbio.3000183

Unsolved Mysteries

Unsolved Mysteries discuss a topic of biological or medical importance that is poorly understood and in need of research attention—e.g., an unexplored or challenging question, an emerging opportunity, or a recent puzzling phenomenon. The articles are intended to stimulate the scientific community to think about future research possibilities outside their areas of expertise. The articles should be aimed at a very broad audience of biologists—an unsolved mystery in a neuroscience topic should be accessible to ecologists and biophysicists, for example.   The article should include a discussion of the basic science relevant to the topic, why it is biologically or medically important, what work has been done on the topic (if any), major challenges to understanding the question at hand, competing hypotheses, and what advances would be necessary to shed light on the problem. Ideally the structure of the article should reflect the mystery (e.g. subsections with questions as headings). The article should end with a discussion of possible means to a solution

Unsolved Mysteries are peer-reviewed and commissioning does not guarantee publication. Editors work closely with authors to ensure that articles are written in an engaging, succinct, yet rigorous manner.

Guidelines for an Unsolved Mystery

Example unsolved mysteries.

Margolis L, Sadovsky Y (2019) The biology of extracellular vesicles: The known unknowns. PLoS Biol 17(7): e3000363. https://doi.org/10.1371/journal.pbio.3000363

Vogels CBF, Ru¨ckert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND (2019) Arbovirus coinfection and co-transmission: A neglected public health concern? PLoS Biol 17(1): e3000130. https://doi.org/10.1371/journal.pbio.3000130

Consensus View

Consensus View articles present a comprehensive analysis by an independent and usually multidisciplinary panel of experts who make specific recommendations on important scientific, publishing or policy issues.

Consensus Views are peer-reviewed and commissioning does not guarantee publication. Editors work closely with authors to ensure that articles are written in an engaging, succinct, yet rigorous manner.

Guidelines for a Consensus View

Example consensus view.

Brown TM, Brainard GC, Cajochen C, Czeisler CA, Hanifin JP, Lockley SW, et al. (2022) Recommendations for daytime, evening, and nighttime indoor light exposure to best support physiology, sleep, and wakefulness in healthy adults. PLoS Biol 20(3): e3001571. https://doi.org/10.1371/journal.pbio.3001571

Kent BA, Holman C, Amoako E, Antonietti A, Azam JM, Ballhausen H, et al. (2022) Recommendations for empowering early career researchers to improve research culture and practice. PLoS Biol 20(7): e3001680. https://doi.org/10.1371/journal.pbio.3001680

Vimercati G, Probert AF, Volery L, Bernardo-Madrid R, Bertolino S, Céspedes V, et al. (2022) The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity. PLoS Biol 20(8): e3001729. https://doi.org/10.1371/journal.pbio.3001729

Retired Article Types

Book Review/Science in the Media. These short reviews critiqued books, films, plays, and other media that deal with some aspect of the biological sciences.  

• Education. Although we no longer publish Education articles as a separate article type, we continue publishing them as part of the Education Series. The format selected (Essay, Perspective, or Community Page) depends on the aims of each article.
• Historical and Philosophical Perspectives. The Historical and Philosophical Perspectives section provided professional historians and philosophers of science with a forum to reflect on topical issues in contemporary biology.
• Obituaries.
• Open Highlights. Written in-house by members of the editorial staff, Open Highlights used recent publication as keystones around which to nucleate a short synthesis of several related research articles from PLOS and the wider Open Access corpus.
• Research Matters. Brief pieces by leading scientists explaining why the research carried out in their laboratories - and those of their collaborators and their colleagues - matters to lay audiences. 
• Series. Series were recurrent themed articles on specific topics, including Education, Public Engagement with Science, Cool Tools, and Where Next?
• Synopses. Selected PLOS Biology research articles are accompanied by a synopsis written for a general audience to provide non-experts with insight into the significance of the published work. They are commissioned only.

Post-Publication Notices

PLOS publishes Editorial Notes, Corrections, Expressions of Concern, and Retraction notices, as needed, to address issues that arise after a PLOS article has been published.

Secondary Menu

• Research Articles & Papers

Korunes, KL; Myers, RB; Hardy, R; Noor, MAF

Drosophila pseudoobscura is a classic model system for the study of evolutionary genetics and genomics. Given this long-standing interest, many genome sequences have accumulated for D. pseudoobscura and closely related species D. persimilis, D. miranda, and D. lowei. To facilitate the exploration… read more about this publication  »

Zipple, MN; Roberts, EK; Alberts, SC; Beehner, JC

Bartoš et al. (2021; Mammal Review 51: 143–153; https://doi.org/10.1111/mam.12219) reviewed the mechanisms involved in the ‘Bruce effect’ – a phenomenon originally documented in inseminated female house mice Mus musculus, who block pregnancy following exposure to a novel (non-sire) male. They argue… read more about this publication  »

Byrne, M; Koop, D; Strbenac, D; Cisternas, P; Yang, JYH; Davidson, PL; Wray, G

The molecular mechanisms underlying development of the pentameral body of adult echinoderms are poorly understood but are important to solve with respect to evolution of a unique body plan that contrasts with the bilateral body plan of other deuterostomes. As Nodal and BMP2/4 signalling is involved… read more about this publication  »

Wang, Q; Xu, P; Sanchez, S; Duran, P; Andreazza, F; Isaacs, R; Dong, K

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Bibliometric Analysis of Edible Insects from Entomology Category Based on Web of Science

• Published: 16 May 2024

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• Bao-Zhong Yuan   ORCID: orcid.org/0000-0003-2353-3873 1 &
• Jie Sun 2  

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Based on Web of Science database and using the bibliometric analysis method, the 3591 papers were analyzed in the field of edible insects topic research from Entomology category during of 1942 to December 18, 2022. All papers written most in English (98.134%), were from 11,742 authors, 2841 affiliation and 132 countries or territories, and published in 127 journals and book series. The top five journals are Insects (290, 8.076%), Journal of Insects as Food and Feed (285, 7.853%), Entomologia Experimentalis et Applicata (194, 5.402%), Journal of Economic Entomology (172, 4.79%) and Journal of Stored Products Research (159, 4.428%), each journal published more than 159 papers. Top five countries were USA, Peoples R China, Brazil, Germany, England. Top four organizations were United States Department of Agriculture (USDA), State University System of Florida, Wageningen University Research, Kansas State University, each with more than 73 papers. The top five authors were Arthur FH, Athanassiou CG, Phillips TW, Campbell JF, Subramanyam B, each published more than 18 papers. All keywords were separated into seven clusters for different research topics. Based on ESI database, there were twenty-eight top papers both twenty-eight highly cited paper and two front papers. Visualizations offer exploratory information on the current state in a scientific field or discipline as well as indicate possible developments in the future.

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The present study reports the bibliometric analysis of edible insects from entomology category based on web of science during of 1942 to December 18, 2022. All papers written most in English (98.134 %), were from 11,742 authors, 2841 affiliation and 132 countries or territories, and published in 127 journals and book series. All keywords were separated into seven clusters for different research topics. The recent or front research topic were edible insects. Visualizations offer exploratory information on the current state in a scientific field or discipline as well as indicate possible developments in the future. We expect the results of this study to help researchers and communities better align their present and future work.

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Yuan, BZ., Sun, J. Bibliometric Analysis of Edible Insects from Entomology Category Based on Web of Science. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. (2024). https://doi.org/10.1007/s40011-024-01570-y

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DOI : https://doi.org/10.1007/s40011-024-01570-y

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NMR study of the structure and dynamics of the BRCT domain from the kinetochore protein KKT4

Akiyoshi Lab - Springer

Ludzia, P., Hayashi, H., Robinson, T., Akiyoshi, B., and Redfield, C.

Summary of Paper by Eleanor Casey, Marston Lab

The kinetochore is a large protein complex which physically links the spindle microtubule to the chromosome during mitosis. Mutations in kinetochore proteins prevent accurate segregation of the chromosomes. This causes growth defects in lower eukaryotes, and diseases in higher organisms. Due to their essentiality in ensuring proper genetic inheritance, kinetochores and kinetochore proteins are highly conserved among most eukaryotes. However, an evolutionarily divergent group of organisms called kinetoplastids have a compositionally and structurally unique kinetochore which bears very little similarity to most eukaryotes. The kinetoplastid group includes the parasite Trypanosoma brucei which causes sleeping sickness in infected individuals. A better understanding of the unique kinetochore structure of T. brucei parasites would provide novel therapeutic targets to treat sleeping sickness.

In this paper, Ludzia and colleagues use nuclear magnetic resonance (NMR) spectroscopy to understand the structure the T. brucei kinetochore protein KKT4. The researchers had previously characterized the structure of the KKT4 C terminus by X ray crystallography, although the functional significance of this structure remained unknown. NMR allowed the structure of KKT4 to be observed in solution, and showed that the protein was able to bind phosphate ions through 3 key amino acid residues in a sulphate ion binding site. When these 3 amino acids were mutated in live T. brucei cells to disrupt phosphate ion binding, there was a severe growth defect. This demonstrated the importance of KKT4 binding to phosphorylated proteins in maintaining the T. brucei kinetochore structure, and highlights this binding pocket as a potential target for drug discovery.

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AlphaFold 3 can predict how DNA, RNA, and other molecules interact, further cementing its leading role in drug discovery and research. Who will benefit?

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Google DeepMind has released an improved version of its biology prediction tool, AlphaFold, that can predict the structures not only of proteins but of nearly all the elements of biological life.

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AlQuraishi says the release marks a big leap forward. But there are caveats.

“It makes the system much more general, and in particular for drug discovery purposes (in early-stage research), it’s far more useful now than AlphaFold 2,” he says. But as with most models, the impact of AlphaFold will depend on how accurate its predictions are. For some uses, AlphaFold 3 has double the success rate of similar leading models like RoseTTAFold. But for others, like protein-RNA interactions, AlQuraishi says it’s still very inaccurate. 

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Standardized metadata for biological samples could unlock the potential of collections

by Charles University

Vojtěch Brlík from the Department of Ecology, Faculty of Science, Charles University and the Institute of Vertebrate Biology, Czech Academy of Sciences calls on scientists to share basic information about biological samples (metadata) to ensure their effective repurposing across biological disciplines.

The call to the scientific community, published in the journal Nature , is based on the experience gained from coordinating the AviSample Network metadata repository, which currently holds the metadata of more than 35,000 samples of almost 500 bird species.

Scientific community has been systematically optimizing research activities, and there are a number of initiatives actively pursuing this goal. The project led by Brlík pushes these efforts even further, "Our initiative demonstrates that the availability and traceability of basic information about samples (so-called metadata) has the potential to make scientific research more efficient, save financial and human resources and diversify research teams on a global level."

He adds, "This initiative is not concerned with the storage of the physical samples or the data. We are only interested in basic information about biological samples , simply put, when, where and how the samples were collected and how they are preserved. Sharing these metadata is inexpensive, applicable on a global level, and facilitates the use of already collected samples, which benefits both the sample owners and the researchers who will use them."

The principle of sharing sample metadata and repurposing existing samples is beneficial in many ways. Centralized and standardized reporting of sample metadata makes it easy to see what samples are currently available without demanding communication with colleagues or costly collection of new samples.

Sharing metadata could therefore streamline scientific activities, especially in less explored areas that are difficult to access, while strengthening key collaborations with local scientists. Similarly, reporting sample metadata would help scientists whose research focuses on endangered species or large spatial scales.

"The initial idea for this initiative was conceived during my Ph.D. studies, when I was looking for feather samples originating from a large area of sub-Saharan Africa. I had samples from our research group, but I needed to expand the dataset considerably.

"We wrote to colleagues in Sweden and Switzerland who we suspected had similar samples from other locations in Africa. And fortunately, it turned out that they did indeed have them. Although they primarily collected the samples for a completely different purpose, we have managed to cover a huge part of the sub-Saharan Africa region through this joint effort, which would not have been possible without a cooperation with colleagues," says Brlík, describing the origins of the current project.

In 2022, Brlík and a team of colleagues (in particular Pavel Pipek from the Department of Ecology, Faculty of Science, Charles University and Petr Procházka from the Institute of Vertebrate Biology of the CAS) created the AviSample Network metadata repository. In this database, ornithologists can now enter metadata of bird samples, i.e. where, when, and how the sample was collected, from which bird species and how these samples are stored.

The database currently includes information on nearly 500 bird species and metadata for more than 35,000 samples are available. The repository has a number of ambassadors who are involved in spreading the initiative in their regions.

"One of the examples of the repurposing of existing samples enabled by sharing metadata is the B10K project. This project aims to survey the genomes of all 10,000 bird species , which the project coordinators are collecting primarily from museums.

"However, for rare species and species occurring in understudied areas (e.g. tropics) it is not easy to obtain samples. Sharing metadata of samples stored in researchers' collections has made it possible to use existing samples collected in Africa and Europe, for this large-scale project," describes Brlík.

In a correspondence published in his article, Brlík shows, using the AviSample Network as an example, that sharing metadata facilitates repurposing existing samples stored in researchers' collections and has thus a huge potential.

"I aim to take this initiative and change in perception to a global level and show that sharing sample metadata has the potential to advance the efficiency of scientific activities across biological disciplines," concludes Brlík.

Journal information: Nature

Provided by Charles University

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Science is making anti-aging progress. But do we want to live forever?

Nobel laureate details new book, which surveys research, touches on larger philosophical questions

Anne J. Manning

Harvard Staff Writer

Mayflies live for only a day. Galapagos tortoises can reach up to age 170. The Greenland shark holds the world record at over 400 years of life. 

Venki Ramakrishnan, Nobel laureate and author of the newly released “ Why We Die: The New Science of Aging and the Quest for Immortality ,” opened his packed Harvard Science Book Talk last week by noting the vast variabilities of lifespans across the natural world. Death is certain, so far as we know. But there’s no physical or chemical law that says it must happen at a fixed time, which raises other, more philosophical issues.

The “why” behind these enormous swings, and the quest to harness longevity for humans, have driven fevered attempts (and billions of dollars in research spending) to slow or stop aging. Ramakrishnan’s book is a dispassionate journey through current scientific understanding of aging and death, which basically comes down to an accumulation of chemical damage to molecules and cells.

“The question is whether we can tackle aging processes, while still keeping us who we are as humans,” said Ramakrishnan during his conversation with Antonio Regalado, a writer for the MIT Technology Review. “And whether we can do that in a safe and effective way.”

Even if immortality — or just living for a very, very long time — were theoretically possible through science, should we pursue it? Ramakrishnan likened the question to other moral ponderings.

“There’s no physical or chemical law that says we can’t colonize other galaxies, or outer space, or even Mars,” he said. “I would put it in that same category. And it would require huge breakthroughs, which we haven’t made yet.”

In fact, we’re a lot closer to big breakthroughs when it comes to chasing immortality. Ramakrishnan noted the field is moving so fast that a book like his can capture but a snippet. He then took the audience on a brief tour of some of the major directions of aging research. And much of it, he said, started in unexpected places.

Take rapamycin, a drug first isolated in the 1960s from a bacterium on Easter Island found to have antifungal, immunosuppressant, and anticancer properties. Rapamycin targets the TOR pathway, a large molecular signaling cascade within cells that regulates many functions fundamental to life. Rapamycin has garnered renewed attention for its potential to reverse the aging process by targeting cellular signaling associated with physiological changes and diseases in older adults.

Other directions include mimicking the anti-aging effects of caloric restriction shown in mice, as well as one particularly exciting area called cellular reprogramming. That means taking fully developed cells and essentially turning back the clock on their development.

The most famous foundational experiment in this area was by Kyoto University scientist and Nobel laureate Shinya Yamanaka, who showed that just four transcription factors could revert an adult cell all the way back to a pluripotent stem cell, creating what are now known as induced pluripotent stem cells.

Ramakrishnan , a scientist at England’s MRC Laboratory of Molecular Biology, won the 2009 Nobel Prize in chemistry for uncovering the structure of the ribosome. He said he felt qualified to write the book because he has “no skin in the game” of aging research. As a molecular biologist who has studied fundamental processes of how cells make proteins, he had connections in the field but wasn’t too close to any of it.

While researching the book, he took pains to avoid interviewing scientists with commercial ventures tied to aging.

The potential for conflicts of interest abound.

The world has seen an explosion in aging research in recent decades, with billions of dollars spent by government agencies and private companies . And the consumer market for products is forecast to hit $93 billion by 2027 .

As a result, false or exaggerated claims by companies promising longer life are currently on the rise, Ramakrishnan noted. He shared one example: Supplements designed to lengthen a person’s telomeres, or genetic segments that shrink with age, are available on Amazon.

“Of course, these are not FDA approved. There are no clinical trials, and it’s not clear what their basis is,” he said.

But still there appears to be some demand.

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Biological, Psychological, and Social Determinants of Depression: A Review of Recent Literature

Olivia remes.

1 Institute for Manufacturing, University of Cambridge, Cambridge CB3 0FS, UK

João Francisco Mendes

2 NOVA Medical School, Universidade NOVA de Lisboa, 1099-085 Lisbon, Portugal; ku.ca.mac@94cfj

Peter Templeton

3 IfM Engage Limited, Institute for Manufacturing, University of Cambridge, Cambridge CB3 0FS, UK; ku.ca.mac@32twp

4 The William Templeton Foundation for Young People’s Mental Health (YPMH), Cambridge CB2 0AH, UK

Associated Data

Depression is one of the leading causes of disability, and, if left unmanaged, it can increase the risk for suicide. The evidence base on the determinants of depression is fragmented, which makes the interpretation of the results across studies difficult. The objective of this study is to conduct a thorough synthesis of the literature assessing the biological, psychological, and social determinants of depression in order to piece together the puzzle of the key factors that are related to this condition. Titles and abstracts published between 2017 and 2020 were identified in PubMed, as well as Medline, Scopus, and PsycInfo. Key words relating to biological, social, and psychological determinants as well as depression were applied to the databases, and the screening and data charting of the documents took place. We included 470 documents in this literature review. The findings showed that there are a plethora of risk and protective factors (relating to biological, psychological, and social determinants) that are related to depression; these determinants are interlinked and influence depression outcomes through a web of causation. In this paper, we describe and present the vast, fragmented, and complex literature related to this topic. This review may be used to guide practice, public health efforts, policy, and research related to mental health and, specifically, depression.

1. Introduction

Depression is one of the most common mental health issues, with an estimated prevalence of 5% among adults [ 1 , 2 ]. Symptoms may include anhedonia, feelings of worthlessness, concentration and sleep difficulties, and suicidal ideation. According to the World Health Organization, depression is a leading cause of disability; research shows that it is a burdensome condition with a negative impact on educational trajectories, work performance, and other areas of life [ 1 , 3 ]. Depression can start early in the lifecourse and, if it remains unmanaged, may increase the risk for substance abuse, chronic conditions, such as cardiovascular disease, and premature mortality [ 4 , 5 , 6 , 7 , 8 ].

Treatment for depression exists, such as pharmacotherapy, cognitive behavioural therapy, and other modalities. A meta-analysis of randomized, placebo-controlled trials of patients shows that 56–60% of people respond well to active treatment with antidepressants (selective serotonin reuptake inhibitors, tricyclic antidepressants) [ 9 ]. However, pharmacotherapy may be associated with problems, such as side-effects, relapse issues, a potential duration of weeks until the medication starts working, and possible limited efficacy in mild cases [ 10 , 11 , 12 , 13 , 14 ]. Psychotherapy is also available, but access barriers can make it difficult for a number of people to get the necessary help.

Studies on depression have increased significantly over the past few decades. However, the literature remains fragmented and the interpretation of heterogeneous findings across studies and between fields is difficult. The cross-pollination of ideas between disciplines, such as genetics, neurology, immunology, and psychology, is limited. Reviews on the determinants of depression have been conducted, but they either focus exclusively on a particular set of determinants (ex. genetic risk factors [ 15 ]) or population sub-group (ex. children and adolescents [ 16 ]) or focus on characteristics measured predominantly at the individual level (ex. focus on social support, history of depression [ 17 ]) without taking the wider context (ex. area-level variables) into account. An integrated approach paying attention to key determinants from the biological, psychological, and social spheres, as well as key themes, such as the lifecourse perspective, enables clinicians and public health authorities to develop tailored, person-centred approaches.

The primary aim of this literature review: to address the aforementioned challenges, we have synthesized recent research on the biological, psychological, and social determinants of depression and we have reviewed research from fields including genetics, immunology, neurology, psychology, public health, and epidemiology, among others.

The subsidiary aim: we have paid special attention to important themes, including the lifecourse perspective and interactions between determinants, to guide further efforts by public health and medical professionals.

This literature review can be used as an evidence base by those in public health and the clinical setting and can be used to inform targeted interventions.

2. Materials and Methods

We conducted a review of the literature on the biological, psychological, and social determinants of depression in the last 4 years. We decided to focus on these determinants after discussions with academics (from the Manchester Metropolitan University, University of Cardiff, University of Colorado, Boulder, University of Cork, University of Leuven, University of Texas), charity representatives, and people with lived experience at workshops held by the University of Cambridge in 2020. In several aspects, we attempted to conduct this review according to PRISMA guidelines [ 18 ].

The inclusion and exclusion criteria are the following:

• - We included documents, such as primary studies, literature reviews, systematic reviews, meta-analyses, reports, and commentaries on the determinants of depression. The determinants refer to variables that appear to be linked to the development of depression, such as physiological factors (e.g., the nervous system, genetics), but also factors that are further away or more distal to the condition. Determinants may be risk or protective factors, and individual- or wider-area-level variables.
• - We focused on major depressive disorder, treatment-resistant depression, dysthymia, depressive symptoms, poststroke depression, perinatal depression, as well as depressive-like behaviour (common in animal studies), among others.
• - We included papers regardless of the measurement methods of depression.
• - We included papers that focused on human and/or rodent research.
• - This review focused on articles written in the English language.
• - Documents published between 2017–2020 were captured to provide an understanding of the latest research on this topic.
• - Studies that assessed depression as a comorbidity or secondary to another disorder.
• - Studies that did not focus on rodent and/or human research.
• - Studies that focused on the treatment of depression. We made this decision, because this is an in-depth topic that would warrant a separate stand-alone review.
• Next, we searched PubMed (2017–2020) using keywords related to depression and determinants. Appendix A contains the search strategy used. We also conducted focused searches in Medline, Scopus, and PsycInfo (2017–2020).
• Once the documents were identified through the databases, the inclusion and exclusion criteria were applied to the titles and abstracts. Screening of documents was conducted by O.R., and a subsample was screened by J.M.; any discrepancies were resolved through a communication process.
• The full texts of documents were retrieved, and the inclusion and exclusion criteria were again applied. A subsample of documents underwent double screening by two authors (O.R., J.M.); again, any discrepancies were resolved through communication.
• a. A data charting form was created to capture the data elements of interest, including the authors, titles, determinants (biological, psychological, social), and the type of depression assessed by the research (e.g., major depression, depressive symptoms, depressive behaviour).
• b. The data charting form was piloted on a subset of documents, and refinements to it were made. The data charting form was created with the data elements described above and tested in 20 studies to determine whether refinements in the wording or language were needed.
• c. Data charting was conducted on the documents.
• d. Narrative analysis was conducted on the data charting table to identify key themes. When a particular finding was noted more than once, it was logged as a potential theme, with a review of these notes yielding key themes that appeared on multiple occasions. When key themes were identified, one researcher (O.R.) reviewed each document pertaining to that theme and derived concepts (key determinants and related outcomes). This process (a subsample) was verified by a second author (J.M.), and the two authors resolved any discrepancies through communication. Key themes were also checked as to whether they were of major significance to public mental health and at the forefront of public health discourse according to consultations we held with stakeholders from the Manchester Metropolitan University, University of Cardiff, University of Colorado, Boulder, University of Cork, University of Leuven, University of Texas, charity representatives, and people with lived experience at workshops held by the University of Cambridge in 2020.

We condensed the extensive information gleaned through our review into short summaries (with key points boxes for ease of understanding and interpretation of the data).

Through the searches, 6335 documents, such as primary studies, literature reviews, systematic reviews, meta-analyses, reports, and commentaries, were identified. After applying the inclusion and exclusion criteria, 470 papers were included in this review ( Supplementary Table S1 ). We focused on aspects related to biological, psychological, and social determinants of depression (examples of determinants and related outcomes are provided under each of the following sections.

3.1. Biological Factors

The following aspects will be discussed in this section: physical health conditions; then specific biological factors, including genetics; the microbiome; inflammatory factors; stress and hypothalamic–pituitary–adrenal (HPA) axis dysfunction, and the kynurenine pathway. Finally, aspects related to cognition will also be discussed in the context of depression.

3.1.1. Physical Health Conditions

Studies on physical health conditions—key points:

• The presence of a physical health condition can increase the risk for depression
• Psychological evaluation in physically sick populations is needed
• There is large heterogeneity in study design and measurement; this makes the comparison of findings between and across studies difficult

A number of studies examined the links between the outcome of depression and physical health-related factors, such as bladder outlet obstruction, cerebral atrophy, cataract, stroke, epilepsy, body mass index and obesity, diabetes, urinary tract infection, forms of cancer, inflammatory bowel disorder, glaucoma, acne, urea accumulation, cerebral small vessel disease, traumatic brain injury, and disability in multiple sclerosis [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ]. For example, bladder outlet obstruction has been linked to inflammation and depressive behaviour in rodent research [ 24 ]. The presence of head and neck cancer also seemed to be related to an increased risk for depressive disorder [ 45 ]. Gestational diabetes mellitus has been linked to depressive symptoms in the postpartum period (but no association has been found with depression in the third pregnancy trimester) [ 50 ], and a plethora of other such examples of relationships between depression and physical conditions exist. As such, the assessment of psychopathology and the provision of support are necessary in individuals of ill health [ 45 ]. Despite the large evidence base on physical health-related factors, differences in study methodology and design, the lack of standardization when it comes to the measurement of various physical health conditions and depression, and heterogeneity in the study populations makes it difficult to compare studies [ 50 ].

The next subsections discuss specific biological factors, including genetics; the microbiome; inflammatory factors; stress and hypothalamic–pituitary–adrenal (HPA) axis dysfunction, and the kynurenine pathway; and aspects related to cognition.

3.1.2. Genetics

Studies on genetics—key points:

There were associations between genetic factors and depression; for example:

• The brain-derived neurotrophic factor (BDNF) plays an important role in depression
• Links exist between major histocompatibility complex region genes, as well as various gene polymorphisms and depression
• Single nucleotide polymorphisms (SNPs) of genes involved in the tryptophan catabolites pathway are of interest in relation to depression

A number of genetic-related factors, genomic regions, polymorphisms, and other related aspects have been examined with respect to depression [ 61 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 , 135 , 136 , 137 , 138 , 139 , 140 ]. The influence of BDNF in relation to depression has been amply studied [ 117 , 118 , 141 , 142 , 143 ]. Research has shown associations between depression and BDNF (as well as candidate SNPs of the BDNF gene, polymorphisms of the BDNF gene, and the interaction of these polymorphisms with other determinants, such as stress) [ 129 , 144 , 145 ]. Specific findings have been reported: for example, a study reported a link between the BDNF rs6265 allele (A) and major depressive disorder [ 117 ].

Other research focused on major histocompatibility complex region genes, endocannabinoid receptor gene polymorphisms, as well as tissue-specific genes and gene co-expression networks and their links to depression [ 99 , 110 , 112 ]. The SNPs of genes involved in the tryptophan catabolites pathway have also been of interest when studying the pathogenesis of depression.

The results from genetics studies are compelling; however, the findings remain mixed. One study indicated no support for depression candidate gene findings [ 122 ]. Another study found no association between specific polymorphisms and major depressive disorder [ 132 ]. As such, further research using larger samples is needed to corroborate the statistically significant associations reported in the literature.

3.1.3. Microbiome

Studies on the microbiome—key points:

• The gut bacteria and the brain communicate via both direct and indirect pathways called the gut-microbiota-brain axis (the bidirectional communication networks between the central nervous system and the gastrointestinal tract; this axis plays an important role in maintaining homeostasis).
• A disordered microbiome can lead to inflammation, which can then lead to depression
• There are possible links between the gut microbiome, host liver metabolism, brain inflammation, and depression

The common themes of this review have focused on the microbiome/microbiota or gut metabolome [ 146 , 147 , 148 , 149 , 150 , 151 , 152 , 153 , 154 , 155 , 156 , 157 , 158 , 159 , 160 , 161 ], the microbiota-gut-brain axis, and related factors [ 152 , 162 , 163 , 164 , 165 , 166 , 167 ]. When there is an imbalance in the intestinal bacteria, this can interfere with emotional regulation and contribute to harmful inflammatory processes and mood disorders [ 148 , 151 , 153 , 155 , 157 ]. Rodent research has shown that there may be a bidirectional association between the gut microbiota and depression: a disordered gut microbiota can play a role in the onset of this mental health problem, but, at the same time, the existence of stress and depression may also lead to a lower level of richness and diversity in the microbiome [ 158 ].

Research has also attempted to disentangle the links between the gut microbiome, host liver metabolism, brain inflammation, and depression, as well as the role of the ratio of lactobacillus to clostridium [ 152 ]. The literature has also examined the links between medication, such as antibiotics, and mood and behaviour, with the findings showing that antibiotics may be related to depression [ 159 , 168 ]. The links between the microbiome and depression are complex, and further studies are needed to determine the underpinning causal mechanisms.

3.1.4. Inflammation

Studies on inflammation—key points:

• Pro-inflammatory cytokines are linked to depression
• Pro-inflammatory cytokines, such as the tumour necrosis factor (TNF)-alpha, may play an important role
• Different methods of measurement are used, making the comparison of findings across studies difficult

Inflammation has been a theme in this literature review [ 60 , 161 , 164 , 169 , 170 , 171 , 172 , 173 , 174 , 175 , 176 , 177 , 178 , 179 , 180 , 181 , 182 , 183 , 184 ]. The findings show that raised levels of inflammation (because of factors such as pro-inflammatory cytokines) have been associated with depression [ 60 , 161 , 174 , 175 , 178 ]. For example, pro-inflammatory cytokines, such as tumour necrosis factor (TNF)-alpha, have been linked to depression [ 185 ]. Various determinants, such as early life stress, have also been linked to systemic inflammation, and this can increase the risk for depression [ 186 ].

Nevertheless, not everyone with elevated inflammation develops depression; therefore, this is just one route out of many linked to pathogenesis. Despite the compelling evidence reported with respect to inflammation, it is difficult to compare the findings across studies because of different methods used to assess depression and its risk factors.

3.1.5. Stress and HPA Axis Dysfunction

Studies on stress and HPA axis dysfunction—key points:

• Stress is linked to the release of proinflammatory factors
• The dysregulation of the HPA axis is linked to depression
• Determinants are interlinked in a complex web of causation

Stress was studied in various forms in rodent populations and humans [ 144 , 145 , 155 , 174 , 176 , 180 , 185 , 186 , 187 , 188 , 189 , 190 , 191 , 192 , 193 , 194 , 195 , 196 , 197 , 198 , 199 , 200 , 201 , 202 , 203 , 204 , 205 , 206 , 207 , 208 , 209 , 210 , 211 ].

Although this section has some overlap with others (as is to be expected because all of these determinants and body systems are interlinked), a number of studies have focused on the impact of stress on mental health. Stress has been mentioned in the literature as a risk factor of poor mental health and has emerged as an important determinant of depression. The effects of this variable are wide-ranging, and a short discussion is warranted.

Stress has been linked to the release of inflammatory factors, as well as the development of depression [ 204 ]. When the stress is high or lasts for a long period of time, this may negatively impact the brain. Chronic stress can impact the dendrites and synapses of various neurons, and may be implicated in the pathway leading to major depressive disorder [ 114 ]. As a review by Uchida et al. indicates, stress may be associated with the “dysregulation of neuronal and synaptic plasticity” [ 114 ]. Even in rodent studies, stress has a negative impact: chronic and unpredictable stress (and other forms of tension or stress) have been linked to unusual behaviour and depression symptoms [ 114 ].

The depression process and related brain changes, however, have also been linked to the hyperactivity or dysregulation of the HPA axis [ 127 , 130 , 131 , 182 , 212 ]. One review indicates that a potential underpinning mechanism of depression relates to “HPA axis abnormalities involved in chronic stress” [ 213 ]. There is a complex relationship between the HPA axis, glucocorticoid receptors, epigenetic mechanisms, and psychiatric sequelae [ 130 , 212 ].

In terms of the relationship between the HPA axis and stress and their influence on depression, the diathesis–stress model offers an explanation: it could be that early stress plays a role in the hyperactivation of the HPA axis, thus creating a predisposition “towards a maladaptive reaction to stress”. When this predisposition then meets an acute stressor, depression may ensue; thus, in line with the diathesis–stress model, a pre-existing vulnerability and stressor can create fertile ground for a mood disorder [ 213 ]. An integrated review by Dean and Keshavan [ 213 ] suggests that HPA axis hyperactivity is, in turn, related to other determinants, such as early deprivation and insecure early attachment; this again shows the complex web of causation between the different determinants.

3.1.6. Kynurenine Pathway

Studies on the kynurenine pathway—key points:

• The kynurenine pathway is linked to depression
• Indolamine 2,3-dioxegenase (IDO) polymorphisms are linked to postpartum depression

The kynurenine pathway was another theme that emerged in this review [ 120 , 178 , 181 , 184 , 214 , 215 , 216 , 217 , 218 , 219 , 220 , 221 ]. The kynurenine pathway has been implicated not only in general depressed mood (inflammation-induced depression) [ 184 , 214 , 219 ] but also postpartum depression [ 120 ]. When the kynurenine metabolism pathway is activated, this results in metabolites, which are neurotoxic.

A review by Jeon et al. notes a link between the impairment of the kynurenine pathway and inflammation-induced depression (triggered by treatment for various physical diseases, such as malignancy). The authors note that this could represent an important opportunity for immunopharmacology [ 214 ]. Another review by Danzer et al. suggests links between the inflammation-induced activation of indolamine 2,3-dioxegenase (the enzyme that converts tryptophan to kynurenine), the kynurenine metabolism pathway, and depression, and also remarks about the “opportunities for treatment of inflammation-induced depression” [ 184 ].

3.1.7. Cognition

Studies on cognition and the brain—key points:

• Cognitive decline and cognitive deficits are linked to increased depression risk
• Cognitive reserve is important in the disability/depression relationship
• Family history of cognitive impairment is linked to depression

A number of studies have focused on the theme of cognition and the brain. The results show that factors, such as low cognitive ability/function, cognitive vulnerability, cognitive impairment or deficits, subjective cognitive decline, regression of dendritic branching and hippocampal atrophy/death of hippocampal cells, impaired neuroplasticity, and neurogenesis-related aspects, have been linked to depression [ 131 , 212 , 222 , 223 , 224 , 225 , 226 , 227 , 228 , 229 , 230 , 231 , 232 , 233 , 234 , 235 , 236 , 237 , 238 , 239 ]. The cognitive reserve appears to act as a moderator and can magnify the impact of certain determinants on poor mental health. For example, in a study in which participants with multiple sclerosis also had low cognitive reserve, disability was shown to increase the risk for depression [ 63 ]. Cognitive deficits can be both causal and resultant in depression. A study on individuals attending outpatient stroke clinics showed that lower scores in cognition were related to depression; thus, cognitive impairment appears to be associated with depressive symptomatology [ 226 ]. Further, Halahakoon et al. [ 222 ] note a meta-analysis [ 240 ] that shows that a family history of cognitive impairment (in first degree relatives) is also linked to depression.

In addition to cognitive deficits, low-level cognitive ability [ 231 ] and cognitive vulnerability [ 232 ] have also been linked to depression. While cognitive impairment may be implicated in the pathogenesis of depressive symptoms [ 222 ], negative information processing biases are also important; according to the ‘cognitive neuropsychological’ model of depression, negative affective biases play a central part in the development of depression [ 222 , 241 ]. Nevertheless, the evidence on this topic is mixed and further work is needed to determine the underpinning mechanisms between these states.

3.2. Psychological Factors

Studies on psychological factors—key points:

• There are many affective risk factors linked to depression
• Determinants of depression include negative self-concept, sensitivity to rejection, neuroticism, rumination, negative emotionality, and others

A number of studies have been undertaken on the psychological factors linked to depression (including mastery, self-esteem, optimism, negative self-image, current or past mental health conditions, and various other aspects, including neuroticism, brooding, conflict, negative thinking, insight, cognitive fusion, emotional clarity, rumination, dysfunctional attitudes, interpretation bias, and attachment style) [ 66 , 128 , 140 , 205 , 210 , 228 , 235 , 242 , 243 , 244 , 245 , 246 , 247 , 248 , 249 , 250 , 251 , 252 , 253 , 254 , 255 , 256 , 257 , 258 , 259 , 260 , 261 , 262 , 263 , 264 , 265 , 266 , 267 , 268 , 269 , 270 , 271 , 272 , 273 , 274 , 275 , 276 , 277 , 278 , 279 , 280 , 281 , 282 , 283 , 284 , 285 , 286 , 287 , 288 , 289 , 290 ]. Determinants related to this condition include low self-esteem and shame, among other factors [ 269 , 270 , 275 , 278 ]. Several emotional states and traits, such as neuroticism [ 235 , 260 , 271 , 278 ], negative self-concept (with self-perceptions of worthlessness and uselessness), and negative interpretation or attention biases have been linked to depression [ 261 , 271 , 282 , 283 , 286 ]. Moreover, low emotional clarity has been associated with depression [ 267 ]. When it comes to the severity of the disorder, it appears that meta-emotions (“emotions that occur in response to other emotions (e.g., guilt about anger)” [ 268 ]) have a role to play in depression [ 268 ].

A determinant that has received much attention in mental health research concerns rumination. Rumination has been presented as a mediator but also as a risk factor for depression [ 57 , 210 , 259 ]. When studied as a risk factor, it appears that the relationship of rumination with depression is mediated by variables that include limited problem-solving ability and insufficient social support [ 259 ]. However, rumination also appears to act as a mediator: for example, this variable (particularly brooding rumination) lies on the causal pathway between poor attention control and depression [ 265 ]. This shows that determinants may present in several forms: as moderators or mediators, risk factors or outcomes, and this is why disentangling the relationships between the various factors linked to depression is a complex task.

The psychological determinants are commonly researched variables in the mental health literature. A wide range of factors have been linked to depression, such as the aforementioned determinants, but also: (low) optimism levels, maladaptive coping (such as avoidance), body image issues, and maladaptive perfectionism, among others [ 269 , 270 , 272 , 273 , 275 , 276 , 279 , 285 , 286 ]. Various mechanisms have been proposed to explain the way these determinants increase the risk for depression. One of the underpinning mechanisms linking the determinants and depression concerns coping. For example, positive fantasy engagement, cognitive biases, or personality dispositions may lead to emotion-focused coping, such as brooding, and subsequently increase the risk for depression [ 272 , 284 , 287 ]. Knowing the causal mechanisms linking the determinants to outcomes provides insight for the development of targeted interventions.

3.3. Social Determinants

Studies on social determinants—key points:

• Social determinants are the conditions in the environments where people are born, live, learn, work, play, etc.; these influence (mental) health [ 291 ]
• There are many social determinants linked to depression, such as sociodemographics, social support, adverse childhood experiences
• Determinants can be at the individual, social network, community, and societal levels

Studies also focused on the social determinants of (mental) health; these are the conditions in which people are born, live, learn, work, play, and age, and have a significant influence on wellbeing [ 291 ]. Factors such as age, social or socioeconomic status, social support, financial strain and deprivation, food insecurity, education, employment status, living arrangements, marital status, race, childhood conflict and bullying, violent crime exposure, abuse, discrimination, (self)-stigma, ethnicity and migrant status, working conditions, adverse or significant life events, illiteracy or health literacy, environmental events, job strain, and the built environment have been linked to depression, among others [ 52 , 133 , 235 , 236 , 239 , 252 , 269 , 280 , 292 , 293 , 294 , 295 , 296 , 297 , 298 , 299 , 300 , 301 , 302 , 303 , 304 , 305 , 306 , 307 , 308 , 309 , 310 , 311 , 312 , 313 , 314 , 315 , 316 , 317 , 318 , 319 , 320 , 321 , 322 , 323 , 324 , 325 , 326 , 327 , 328 , 329 , 330 , 331 , 332 , 333 , 334 , 335 , 336 , 337 , 338 , 339 , 340 , 341 , 342 , 343 , 344 , 345 , 346 , 347 , 348 , 349 , 350 , 351 , 352 , 353 , 354 , 355 , 356 , 357 , 358 , 359 , 360 , 361 , 362 , 363 , 364 , 365 , 366 , 367 , 368 , 369 , 370 , 371 ]. Social support and cohesion, as well as structural social capital, have also been identified as determinants [ 140 , 228 , 239 , 269 , 293 , 372 , 373 , 374 , 375 , 376 , 377 , 378 , 379 ]. In a study, part of the findings showed that low levels of education have been shown to be linked to post-stroke depression (but not severe or clinical depression outcomes) [ 299 ]. A study within a systematic review indicated that having only primary education was associated with a higher risk of depression compared to having secondary or higher education (although another study contrasted this finding) [ 296 ]. Various studies on socioeconomic status-related factors have been undertaken [ 239 , 297 ]; the research has shown that a low level of education is linked to depression [ 297 ]. Low income is also related to depressive disorders [ 312 ]. By contrast, high levels of education and income are protective [ 335 ].

A group of determinants touched upon by several studies included adverse childhood or early life experiences: ex. conflict with parents, early exposure to traumatic life events, bullying and childhood trauma were found to increase the risk of depression (ex. through pathways, such as inflammation, interaction effects, or cognitive biases) [ 161 , 182 , 258 , 358 , 362 , 380 ].

Gender-related factors were also found to play an important role with respect to mental health [ 235 , 381 , 382 , 383 , 384 , 385 ]. Gender inequalities can start early on in the lifecourse, and women were found to be twice as likely to have depression as men. Gender-related factors were linked to cognitive biases, resilience and vulnerabilities [ 362 , 384 ].

Determinants can impact mental health outcomes through underpinning mechanisms. For example, harmful determinants can influence the uptake of risk behaviours. Risk behaviours, such as sedentary behaviour, substance abuse and smoking/nicotine exposure, have been linked to depression [ 226 , 335 , 355 , 385 , 386 , 387 , 388 , 389 , 390 , 391 , 392 , 393 , 394 , 395 , 396 , 397 , 398 , 399 , 400 , 401 ]. Harmful determinants can also have an impact on diet. Indeed, dietary aspects and diet components (ex. vitamin D, folate, selenium intake, iron, vitamin B12, vitamin K, fiber intake, zinc) as well as diet-related inflammatory potential have been linked to depression outcomes [ 161 , 208 , 236 , 312 , 396 , 402 , 403 , 404 , 405 , 406 , 407 , 408 , 409 , 410 , 411 , 412 , 413 , 414 , 415 , 416 , 417 , 418 , 419 , 420 , 421 , 422 , 423 , 424 , 425 , 426 , 427 , 428 ]. A poor diet has been linked to depression through mechanisms such as inflammation [ 428 ].

Again, it is difficult to constrict diet to the ‘social determinants of health’ category as it also relates to inflammation (biological determinants) and could even stand alone as its own category. Nevertheless, all of these factors are interlinked and influence one another in a complex web of causation, as mentioned elsewhere in the paper.

Supplementary Figure S1 contains a representation of key determinants acting at various levels: the individual, social network, community, and societal levels. The determinants have an influence on risk behaviours, and this, in turn, can affect the mood (i.e., depression), body processes (ex. can increase inflammation), and may negatively influence brain structure and function.

3.4. Others

Studies on ‘other’ determinants—key points:

• A number of factors are related to depression
• These may not be as easily categorized as the other determinants in this paper

A number of factors arose in this review that were related to depression; it was difficult to place these under a specific heading above, so this ‘other’ category was created. A number of these could be sorted under the ‘social determinants of depression’ category. For example, being exposed to deprivation, hardship, or adversity may increase the risk for air pollution exposure and nighttime shift work, among others, and the latter determinants have been found to increase the risk for depression. Air pollution could also be regarded as an ecologic-level (environmental) determinant of mental health.

Nevertheless, we have decided to leave these factors in a separate category (because their categorization may not be as immediately clear-cut as others), and these factors include: low-level light [ 429 ], weight cycling [ 430 ], water contaminants [ 431 ], trade [ 432 ], air pollution [ 433 , 434 ], program-level variables (ex. feedback and learning experience) [ 435 ], TV viewing [ 436 ], falls [ 437 ], various other biological factors [ 116 , 136 , 141 , 151 , 164 , 182 , 363 , 364 , 438 , 439 , 440 , 441 , 442 , 443 , 444 , 445 , 446 , 447 , 448 , 449 , 450 , 451 , 452 , 453 , 454 , 455 , 456 , 457 , 458 , 459 , 460 , 461 , 462 , 463 , 464 , 465 , 466 , 467 , 468 , 469 ], mobile phone use [ 470 ], ultrasound chronic exposure [ 471 ], nighttime shift work [ 472 ], work accidents [ 473 ], therapy enrollment [ 226 ], and exposure to light at night [ 474 ].

4. Cross-Cutting Themes

4.1. lifecourse perspective.

Studies on the lifecourse perspective—key points:

• Early life has an importance on mental health
• Stress has been linked to depression
• In old age, the decline in social capital is important

Trajectories and life events are important when it comes to the lifecourse perspective. Research has touched on the influence of prenatal or early life stress on an individual’s mental health trajectory [ 164 , 199 , 475 ]. Severe stress that occurs in the form of early-life trauma has also been associated with depressive symptoms [ 362 , 380 ]. It may be that some individuals exposed to trauma develop thoughts of personal failure, which then serve as a catalyst of depression [ 380 ].

At the other end of the life trajectory—old age—specific determinants have been linked to an increased risk for depression. Older people are at a heightened risk of losing their social networks, and structural social capital has been identified as important in relation to depression in old age [ 293 ].

4.2. Gene–Environment Interactions

Studies on gene–environment interactions—key points:

• The environment and genetics interact to increase the risk of depression
• The etiology of depression is multifactorial
• Adolescence is a time of vulnerability

A number of studies have touched on gene–environment interactions [ 72 , 77 , 82 , 119 , 381 , 476 , 477 , 478 , 479 , 480 , 481 ]. The interactions between genetic factors and determinants, such as negative life events (ex. relationship and social difficulties, serious illness, unemployment and financial crises) and stressors (ex. death of spouse, minor violations of law, neighbourhood socioeconomic status) have been studied in relation to depression [ 82 , 135 , 298 , 449 , 481 ]. A study reported an interaction of significant life events with functional variation in the serotonin-transporter-linked polymorphic region (5-HTTLPR) allele type (in the context of multiple sclerosis) and linked this to depression [ 361 ], while another reported an interaction between stress and 5-HTTLPR in relation to depression [ 480 ]. Other research reported that the genetic variation of HPA-axis genes has moderating effects on the relationship between stressors and depression [ 198 ]. Another study showed that early-life stress interacts with gene variants to increase the risk for depression [ 77 ].

Adolescence is a time of vulnerability [ 111 , 480 ]. Perceived parental support has been found to interact with genes (GABRR1, GABRR2), and this appears to be associated with depressive symptoms in adolescence [ 480 ]. It is important to pay special attention to critical periods in the lifecourse so that adequate support is provided to those who are most vulnerable.

The etiology of depression is multifactorial, and it is worthwhile to examine the interaction between multiple factors, such as epigenetic, genetic, and environmental factors, in order to truly understand this mental health condition. Finally, taking into account critical periods of life when assessing gene–environment interactions is important for developing targeted interventions.

5. Discussion

Depression is one of the most common mental health conditions, and, if left untreated, it can increase the risk for substance abuse, anxiety disorders, and suicide. In the past 20 years, a large number of studies on the risk and protective factors of depression have been undertaken in various fields, such as genetics, neurology, immunology, and epidemiology. However, there are limitations associated with the extant evidence base. The previous syntheses on depression are limited in scope and focus exclusively on social or biological factors, population sub-groups, or examine depression as a comorbidity (rather than an independent disorder). The research on the determinants and causal pathways of depression is fragmentated and heterogeneous, and this has not helped to stimulate progress when it comes to the prevention and intervention of this condition—specifically unravelling the complexity of the determinants related to this condition and thus refining the prevention and intervention methods.

The scope of this paper was to bring together the heterogeneous, vast, and fragmented literature on depression and paint a picture of the key factors that contribute to this condition. The findings from this review show that there are important themes when it comes to the determinants of depression, such as: the microbiome, dysregulation of the HPA axis, inflammatory reactions, the kynurenine pathway, as well as psychological and social factors. It may be that physical factors are proximal determinants of depression, which, in turn, are acted on by more distal social factors, such as deprivation, environmental events, and social capital.

The Marmot Report [ 291 ], the World Health Organization [ 482 ], and Compton et al. [ 483 ] highlight that the most disadvantaged segments of society are suffering (the socioeconomic context is important), and this inequality in resources has translated to inequality in mental health outcomes [ 483 ]. To tackle the issue of egalitarianism and restore equality in the health between the groups, the social determinants need to be addressed [ 483 ]. A wide range of determinants of mental health have been identified in the literature: age, gender, ethnicity, family upbringing and early attachment patterns, social support, access to food, water and proper nutrition, and community factors. People spiral downwards because of individual- and societal-level circumstances; therefore, these circumstances along with the interactions between the determinants need to be considered.

Another important theme in the mental health literature is the lifecourse perspective. This shows that the timing of events has significance when it comes to mental health. Early life is a critical period during the lifespan at which cognitive processes develop. Exposure to harmful determinants, such as stress, during this period can place an individual on a trajectory of depression in adulthood or later life. When an individual is exposed to harmful determinants during critical periods and is also genetically predisposed to depression, the risk for the disorder can be compounded. This is why aspects such as the lifecourse perspective and gene–environment interactions need to be taken into account. Insight into this can also help to refine targeted interventions.

A number of interventions for depression have been developed or recommended, addressing, for example, the physical factors described here and lifestyle modifications. Interventions targeting various factors, such as education and socioeconomic status, are needed to help prevent and reduce the burden of depression. Further research on the efficacy of various interventions is needed. Additional studies are also needed on each of the themes described in this paper, for example: the biological factors related to postpartum depression [ 134 ], and further work is needed on depression outcomes, such as chronic, recurrent depression [ 452 ]. Previous literature has shown that chronic stress (associated with depression) is also linked to glucocorticoid receptor resistance, as well as problems with the regulation of the inflammatory response [ 484 ]. Further work is needed on this and the underpinning mechanisms between the determinants and outcomes. This review highlighted the myriad ways of measuring depression and its determinants [ 66 , 85 , 281 , 298 , 451 , 485 ]. Thus, the standardization of the measurements of the outcomes (ex. a gold standard for measuring depression) and determinants is essential; this can facilitate comparisons of findings across studies.

5.1. Strengths

This paper has important strengths. It brings together the wide literature on depression and helps to bridge disciplines in relation to one of the most common mental health problems. We identified, selected, and extracted data from studies, and provided concise summaries.

5.2. Limitations

The limitations of the review include missing potentially important studies; however, this is a weakness that cannot be avoided by literature reviews. Nevertheless, the aim of the review was not to identify each study that has been conducted on the risk and protective factors of depression (which a single review is unable to capture) but rather to gain insight into the breadth of literature on this topic, highlight key biological, psychological, and social determinants, and shed light on important themes, such as the lifecourse perspective and gene–environment interactions.

6. Conclusions

We have reviewed the determinants of depression and recognize that there are a multitude of risk and protective factors at the individual and wider ecologic levels. These determinants are interlinked and influence one another. We have attempted to describe the wide literature on this topic, and we have brought to light major factors that are of public mental health significance. This review may be used as an evidence base by those in public health, clinical practice, and research.

This paper discusses key areas in depression research; however, an exhaustive discussion of all the risk factors and determinants linked to depression and their mechanisms is not possible in one journal article—which, by its very nature, a single paper cannot do. We have brought to light overarching factors linked to depression and a workable conceptual framework that may guide clinical and public health practice; however, we encourage other researchers to continue to expand on this timely and relevant work—particularly as depression is a top priority on the policy agenda now.

Acknowledgments

Thank you to Isla Kuhn for the help with the Medline, Scopus, and PsycInfo database searches.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/brainsci11121633/s1 , Figure S1: Conceptual framework: Determinants of depression, Table S1: Data charting—A selection of determinants from the literature.

Appendix A.1. Search Strategy

Search: ((((((((((((((((“Gene-Environment Interaction”[Majr]) OR (“Genetics”[Mesh])) OR (“Genome-Wide Association Study”[Majr])) OR (“Microbiota”[Mesh] OR “Gastrointestinal Microbiome”[Mesh])) OR (“Neurogenic Inflammation”[Mesh])) OR (“genetic determinant”)) OR (“gut-brain-axis”)) OR (“Kynurenine”[Majr])) OR (“Cognition”[Mesh])) OR (“Neuronal Plasticity”[Majr])) OR (“Neurogenesis”[Mesh])) OR (“Genes”[Mesh])) OR (“Neurology”[Majr])) OR (“Social Determinants of Health”[Majr])) OR (“Glucocorticoids”[Mesh])) OR (“Tryptophan”[Mesh])) AND (“Depression”[Mesh] OR “Depressive Disorder”[Mesh]) Filters: from 2017—2020.

Ovid MEDLINE(R) and Epub Ahead of Print, In-Process, In-Data-Review & Other Non-Indexed Citations, Daily and Versions(R)

• exp *Depression/
• exp *Depressive Disorder/
• exp *”Social Determinants of Health”/
• exp *Tryptophan/
• exp *Glucocorticoids/
• exp *Neurology/
• exp *Genes/
• exp *Neurogenesis/
• exp *Neuronal Plasticity/
• exp *Kynurenine/
• exp *Genetics/
• exp *Neurogenic Inflammation/
• exp *Gastrointestinal Microbiome/
• exp *Genome-Wide Association Study/
• exp *Gene-Environment Interaction/
• exp *Depression/et [Etiology]
• exp *Depressive Disorder/et
• or/4-16   637368
• limit 22 to yr = “2017–Current”
• “cause* of depression”.mp.
• “cause* of depression”.ti.
• (cause adj3 (depression or depressive)).ti.
• (caus* adj3 (depression or depressive)).ti.

Appendix A.2. PsycInfo

(TITLE ( depression OR “ Depressive Disorder ”) AND TITLE (“ Social Determinants of Health ” OR tryptophan OR glucocorticoids OR neurology OR genes OR neurogenesis OR “ Neuronal Plasticity ” OR kynurenine OR genetics OR “ Neurogenic Inflammation ” OR “ Gastrointestinal Microbiome ” OR “ Genome-Wide Association Study ” OR “ Gene-Environment Interaction ” OR aetiology OR etiology )) OR TITLE ( cause* W/3 ( depression OR depressive )).

Author Contributions

O.R. was responsible for the design of the study and methodology undertaken. Despite P.T.’s involvement in YPMH, he had no role in the design of the study; P.T. was responsible for the conceptualization of the study. Validation was conducted by O.R. and J.F.M. Formal analysis (data charting) was undertaken by O.R. O.R. and P.T. were involved in the investigation, resource acquisition, and data presentation. The original draft preparation was undertaken by O.R. The writing was conducted by O.R., with review and editing by P.T. and J.F.M. Funding acquisition was undertaken by O.R. and P.T. All authors have read and agreed to the published version of the manuscript.

This research was funded by The William Templeton Foundation for Young People’s Mental Health, Cambridge Philosophical Society, and the Aviva Foundation.

Conflicts of Interest

The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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The beauty of biology

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When Hanjun Lee arrived at MIT, he was set on becoming a Course 5 chemistry student. Based on his experience in high school, biology was all about rote memorization.

That changed when he took course  7.03 (Genetics) , taught by then-professor  Aviv Regev , now head and executive vice president of research and early development at Genentech, and  Peter Reddien , professor of biology and core member and associate director of the Whitehead Institute for Biomedical Research.

He notes that friends from other schools don’t cite a single course that changed their major, but he’s not alone in choosing Course 7 because of 7.03.

“Genetics has this interesting force, especially in MIT biology. The department’s historical — and active — role in genetics research ties directly into the way the course is taught,” Lee says. “Biology is about logic, scientific reasoning, and posing the right questions.”

A few years later, as a teaching assistant for class  7.002 (Fundamentals of Experimental Molecular Biology ), he came to value how much care MIT biology professors take in presenting the material for all offered courses.

“I really appreciate how much effort MIT professors put into their teaching,” Lee says. “As a TA, you realize the beauty of how the professors organize these things — because they’re teaching you in a specific way, and you can grasp the beauty of it — there’s a beauty in studying and finding the patterns in nature.”

An undertaking to apply

To attend MIT at all hadn’t exactly been a lifelong dream. In fact, it didn’t occur to Lee that he could or should apply until he represented South Korea at the 49th International Chemistry Olympiad, where he won a Gold Medal in 2017. There, he had the chance to speak with MIT alumni, as well as current and aspiring students. More than half of those aspiring students eventually enrolled, Lee among them.

“Before that, MIT was this nearly mythical institution, so that experience really changed my life,” Lee recalls. “I heard so many different stories from people with so many different backgrounds — all converging towards the same enthusiasm towards science.” 

At the time, Lee was already attending medical school — a six-year undergraduate program in Korea — that would lead to a stable career in medicine. Attending MIT would involve both changing his career plans and uprooting his life, leaving all his friends and family behind.

His parents weren’t especially enthusiastic about his desire to study at MIT, so it was up to Lee to meet the application requirements. He woke up at 3 a.m. to find his own way to the only SAT testing site in South Korea — an undertaking he now recalls with a laugh. In just three months, he had gathered everything he needed; MIT was the only institution in the United States Lee applied to.

He arrived in Cambridge, Massachusetts, in 2018 but attended MIT only for a semester before returning to Korea for his two years of mandatory military service.

“During military service, my goal was to read as many papers as possible, because I wondered what topic of science I’m drawn to — and many of the papers I was reading were authored by people I recognized, people who taught biology at MIT,” Lee says. “I became really interested in cancer biology.”

Return to MIT

When he returned to campus, Lee pledged to do everything he could to meet with faculty and discuss their work. To that end, he joined the MIT Undergraduate Research Journal , allowing him to interview professors. He notes that most MIT faculty are enthusiastic about being contacted by undergraduate students.

Stateside, Lee also reached out to Michael Lawrence , an assistant professor of pathology at Harvard Medical School and assistant geneticist at Mass General Cancer Center, about a preprint concerning APOBEC, an enzyme Lee had studied at Seoul National University. Lawrence’s lab was looking into APOBEC and cancer evolution — and the idea that the enzyme might drive drug resistance to cancer treatment.

“Since he joined my lab, I’ve been absolutely amazed by his scientific talents,” Lawrence says. “Hanjun’s scientific maturity and achievements are extremely rare, especially in an undergraduate student.”

Lee has made new discoveries from genomic data and was involved in publishing  a paper in Molecular Cell and  a paper in Nature Genetics . In the latter, the lab identified the source of background noise in chromosome conformation capture experiments, a technique for analyzing chromatin in cells.

Lawrence thinks Lee “is destined for great leadership in science.” In the meantime, Lee has gained valuable insights into how much work these types of achievements require.

“Doing research has been rewarding, but it also taught me to appreciate that science is almost 100 percent about failures,” Lee says. “It is those failures that end up leading you to the path of success.”

Widening the scope

Lee’s personal motto is that to excel in a specific field, one must have a broad sense of what the entire field looks like, and suggests other budding scientists enroll in courses distant from their research area. He also says it was key to see his peers as collaborators rather than competitors, and that each student will excel in their own unique way.

“Your MIT experience is defined by interactions with others,” Lee says. “They will help identify and shape your path.”

For his accomplishments, Lee was recently named an  American Association for Cancer Research Undergraduate Scholar . Last year, he also spoke at the Gordon Research Conference on Cell Growth and Proliferation about his work on the retinoblastoma gene product RB. Lee was also among the 2024 Biology Undergraduate Award Winners, recognized with the Salvador E. Luria Prize for outstanding scholarship and research of publication quality.

Encouraged by positive course evaluations during his time as a TA, Lee hopes to inspire other students in the future through teaching. Lee has recently decided to pursue a PhD in cancer biology at Harvard Medical School, although his interests remain broad.

“I want to explore other fields of biology as well,” he says. “I have so many questions that I want to answer.”

Although initially resistant, Lee’s mother and father are now “immensely proud to be MIT parents” and will be coming to Cambridge in May to celebrate Lee’s graduation.

“Throughout my years here, they’ve been able to see how I’ve changed,” he says. “I don’t think I’m a great scientist, yet, but I now have some sense of how to become one.” 

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First 'warm-blooded' dinosaurs may have emerged 180 million years ago

The ability to regulate body temperature, a trait all mammals and birds have today, may have evolved among some dinosaurs early in the Jurassic period about 180 million years ago, suggests a new study led by UCL and University of Vigo researchers.

In the early 20 th century, dinosaurs were considered slow-moving, "cold-blooded" animals like modern-day reptiles, relying on heat from the sun to regulate their temperature. Newer discoveries indicate some dinosaur types were likely capable of generating their own body heat but when this adaptation occurred is unknown.

The new study, published in the journal Current Biology , looked at the spread of dinosaurs across different climates on Earth throughout the Mesozoic Era (the dinosaur era lasting from 230 to 66 million years ago), drawing on 1,000 fossils, climate models and the geography of the period, and dinosaurs' evolutionary trees.

The research team found that two of the three main groupings of dinosaurs, theropods (such as T. rex and Velociraptor ) and ornithischians (including relatives of the plant eaters Stegosaurus and Triceratops ), moved to colder climates during the Early Jurassic, suggesting they may have developed endothermy (the ability to internally generate heat) at this time. In contrast, sauropods, the other main grouping which includes the Brontosaurus and the Diplodocus , kept to warmer areas of the planet.

Previous research has found traits linked to warm-bloodedness among ornithischians and theropods, with some known to have had feathers or proto-feathers, insulating internal heat.

First author Dr Alfio Alessandro Chiarenza, of UCL Earth Sciences, said: "Our analyses show that different climate preferences emerged among the main dinosaur groups around the time of the Jenkyns event 183 million years ago, when intense volcanic activity led to global warming and extinction of plant groups.

"At this time, many new dinosaur groups emerged. The adoption of endothermy, perhaps a result of this environmental crisis, may have enabled theropods and ornithischians to thrive in colder environments, allowing them to be highly active and sustain activity over longer periods, to develop and grow faster and produce more offspring."

Co-author Dr Sara Varela, of the Universidade de Vigo, Spain, said: "Theropods also include birds and our study suggests that birds' unique temperature regulation may have had its origin in this Early Jurassic epoch.

"Sauropods, on the other hand, which stayed in warmer climates, grew to a gigantic size at around this time -- another possible adaptation due to environmental pressure. Their smaller surface area to volume ratio would have meant these larger creatures would lose heat at a reduced rate, allowing them to stay active for longer."

In the paper, the researchers also investigated if sauropods might have stayed at lower latitudes to eat richer foliage unavailable in colder polar regions. Instead, they found sauropods seemed to thrive in arid, savannah-like environments, supporting the idea that their restriction to warmer climates was more related to higher temperature and then to a more cold-blooded physiology. During that time, polar regions were warmer, with abundant vegetation.

The Jenkyns event occurred after lava and volcanic gasses erupted from long fissures in the Earth's surface, covering large areas of the planet.

Co-author Dr Juan L. Cantalapiedra, of the Museo Nacional de Ciencias Naturales, Madrid, Spain, said: "This research suggests a close connection between climate and how dinosaurs evolved. It sheds new light on how birds might have inherited a unique biological trait from dinosaur ancestors and the different ways dinosaurs adapted to complex and long-term environmental changes."

The study involved researchers from UCL, University of Vigo, the University of Bristol and the Museo Nacional de Ciencias Naturales in Madrid, and received funding from the European Research Council, the Spanish Ministry of Research, the Natural Environment Research Council and the Royal Society.

• Extreme Survival
• Evolutionary Biology
• Paleontology
• Early Birds
• Ichthyosaur
• Feathered dinosaurs
• Brachiosaurus
• Precambrian

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Materials provided by University College London . Note: Content may be edited for style and length.

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• Artist’s impression of a dromaeosaur

Journal Reference :

• Alfio Alessandro Chiarenza, Juan L. Cantalapiedra, Lewis A. Jones, Sara Gamboa, Sofía Galván, Alexander J. Farnsworth, Paul J. Valdes, Graciela Sotelo, Sara Varela. Early Jurassic origin of avian endothermy and thermophysiological diversity in dinosaurs . Current Biology , 2024; DOI: 10.1016/j.cub.2024.04.051

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