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Collection  12 March 2020

Top 50 Life and Biological Sciences Articles

We are pleased to share with you the 50 most read Nature Communications  articles* in life and biological sciences published in 2019. Featuring authors from around the world, these papers highlight valuable research from an international community.

Browse all Top 50 subject area collections here .

*Based on data from Google Analytics, covering January-December 2019 (data has been normalised to account for articles published later in the year)

research paper for biological sciences

Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income

Household income is used as a marker of socioeconomic position, a trait that is associated with better physical and mental health. Here, Hill et al. report a genome-wide association study for household income in the UK and explore its relationship with intelligence in post-GWAS analyses including Mendelian randomization.

  • W. David Hill
  • Neil M. Davies
  • Ian J. Deary

research paper for biological sciences

A 5700 year-old human genome and oral microbiome from chewed birch pitch

Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

  • Theis Z. T. Jensen
  • Jonas Niemann
  • Hannes Schroeder

research paper for biological sciences

A short translational ramp determines the efficiency of protein synthesis

Several factors contribute to the efficiency of protein expression. Here the authors show that the identity of amino acids encoded by codons at position 3–5 significantly impact translation efficiency and protein expression levels.

  • Manasvi Verma
  • Junhong Choi
  • Sergej Djuranovic

research paper for biological sciences

Early coauthorship with top scientists predicts success in academic careers

By examining publication records of scientists from four disciplines, the authors show that coauthoring a paper with a top-cited scientist early in one's career predicts lasting increases in career success, especially for researchers affiliated with less prestigious institutions.

  • Tomaso Aste
  • Giacomo Livan

research paper for biological sciences

Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India

Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.

  • Éadaoin Harney
  • Ayushi Nayak

research paper for biological sciences

Ketamine can reduce harmful drinking by pharmacologically rewriting drinking memories

Memories linking environmental cues to alcohol reward are involved in the development and maintenance of heavy drinking. Here, the authors show that a single dose of ketamine, given after retrieval of alcohol-reward memories, disrupts the reconsolidation of these memories and reduces drinking in humans.

  • Ravi K. Das
  • Sunjeev K. Kamboj

research paper for biological sciences

Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice

Here, the authors show that sequential treatment with long-acting slow-effective release ART and AAV9- based delivery of CRISPR-Cas9 results in undetectable levels of virus and integrated DNA in a subset of humanized HIV-1 infected mice. This proof-of-concept study suggests that HIV-1 elimination is possible.

  • Prasanta K. Dash
  • Rafal Kaminski
  • Howard E. Gendelman

research paper for biological sciences

XX sex chromosome complement promotes atherosclerosis in mice

Men and women differ in their risk of developing coronary artery disease, in part due to differences in their levels of sex hormones. Here, AlSiraj et al. show that the XX sex genotype regulates lipid metabolism and promotes atherosclerosis independently of sex hormones in mice.

  • Yasir AlSiraj
  • Lisa A. Cassis

research paper for biological sciences

Early-career setback and future career impact

Little is known about the long-term effects of early-career setback. Here, the authors compare junior scientists who were awarded a NIH grant to those with similar track records, who were not, and find that individuals with the early setback systematically performed better in the longer term.

  • Benjamin F. Jones
  • Dashun Wang

research paper for biological sciences

Ideological differences in the expanse of the moral circle

How do liberals and conservatives differ in their expression of compassion and moral concern? The authors show that conservatives tend to express concern toward smaller, more well-defined, and less permeable social circles, while liberals express concern toward larger, less well-defined, and more permeable social circles.

  • Jesse Graham

research paper for biological sciences

A metabolic profile of all-cause mortality risk identified in an observational study of 44,168 individuals

Biomarkers that predict mortality are of interest for clinical as well as research applications. Here, the authors analyze metabolomics data from 44,168 individuals and identify key metabolites independently associated with all-cause mortality risk.

  • Joris Deelen
  • Johannes Kettunen
  • P. Eline Slagboom

research paper for biological sciences

New insects feeding on dinosaur feathers in mid-Cretaceous amber

Numerous feathered dinosaurs and early birds have been discovered from the Jurassic and Cretaceous, but the early evolution of feather-feeding insects is not clear. Here, Gao et al. describe a new family of ectoparasitic insects from 10 specimens found associated with feathers in mid-Cretaceous amber.

  • Taiping Gao
  • Xiangchu Yin

research paper for biological sciences

Acoustic enrichment can enhance fish community development on degraded coral reef habitat

Healthy coral reefs have an acoustic signature known to be attractive to coral and fish larvae during settlement. Here the authors use playback experiments in the field to show that healthy reef sounds can increase recruitment of juvenile fishes to degraded coral reef habitat, suggesting that acoustic playback could be used as a reef management strategy.

  • Timothy A. C. Gordon
  • Andrew N. Radford
  • Stephen D. Simpson

research paper for biological sciences

Phagocytosis-like cell engulfment by a planctomycete bacterium

Phagocytosis is a typically eukaryotic feature that could be behind the origin of eukaryotic cells. Here, the authors describe a bacterium that can engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism.

  • Takashi Shiratori
  • Shigekatsu Suzuki
  • Ken-ichiro Ishida

research paper for biological sciences

Hippocampal clock regulates memory retrieval via Dopamine and PKA-induced GluA1 phosphorylation

The neural mechanisms that lead to a relative deficit in memory retrieval in the afternoon are unclear. Here, the authors show that the circadian - dependent transcription factor BMAL1 regulates retrieval through dopamine and glutamate receptor phosphorylation.

  • Shunsuke Hasegawa
  • Hotaka Fukushima
  • Satoshi Kida

research paper for biological sciences

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

Integrating independent large-scale pharmacogenomic screens can enable unprecedented characterization of genetic vulnerabilities in cancers. Here, the authors show that the two largest independent CRISPR-Cas9 gene-dependency screens are concordant, paving the way for joint analysis of the data sets.

  • Joshua M. Dempster
  • Clare Pacini
  • Francesco Iorio

research paper for biological sciences

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

The authors build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on 381 markers. The results indicate a remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that used fewer “core” genes, such as the ribosomal proteins.

research paper for biological sciences

Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers

Mass-spectrometry-based profiling can be used to stratify tumours into molecular subtypes. Here, by classifying over 500 tumours, the authors show that this approach reveals proteomic subgroups which cut across tumour types.

  • Fengju Chen
  • Darshan S. Chandrashekar
  • Chad J. Creighton

research paper for biological sciences

CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci

Inducible genome editing systems often suffer from leakiness or reduced activity. Here the authors develop CRISPR-Switch, a Cre recombinase ON/OFF-controlled sgRNA cassette that allows consecutive editing of two loci.

  • Krzysztof Chylinski
  • Maria Hubmann
  • Ulrich Elling

research paper for biological sciences

CRISPR-Cas3 induces broad and unidirectional genome editing in human cells

Class 1 CRISPR systems are not as developed for genome editing as Class 2 systems are. Here the authors show that Cas3 can be used to generate functional knockouts and knock-ins, as well as Cas3-mediated exon-skipping in DMD cells.

  • Hiroyuki Morisaka
  • Kazuto Yoshimi
  • Tomoji Mashimo

research paper for biological sciences

Genetic evidence for assortative mating on alcohol consumption in the UK Biobank

From observational studies, alcohol consumption behaviours are known to be correlated in spouses. Here, Howe et al. use partners’ genotypic information in a Mendelian randomization framework and show that a SNP in the ADH1B gene associates with partner’s alcohol consumption, suggesting that alcohol consumption affects mate choice.

  • Laurence J. Howe
  • Daniel J. Lawson
  • Gibran Hemani

research paper for biological sciences

The autophagy receptor p62/SQST-1 promotes proteostasis and longevity in C. elegans by inducing autophagy

While the cellular recycling process autophagy has been linked to aging, the impact of selective autophagy on lifespan remains unclear. Here Kumsta et al. show that the autophagy receptor p62/SQSTM1 is required for hormetic benefits and p62/SQSTM1 overexpression is sufficient to extend C. elegans lifespan and improve proteostasis.

  • Caroline Kumsta
  • Jessica T. Chang
  • Malene Hansen

research paper for biological sciences

The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes

Recent studies have suggested that hybridization can facilitate adaptive radiations. Here, the authors show that opportunity for hybridization differentiates Lake Mweru, where cichlids radiated, and Lake Bangweulu, where cichlids did not radiate despite ecological opportunity in both lakes.

  • Joana I. Meier
  • Rike B. Stelkens
  • Ole Seehausen

research paper for biological sciences

Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases

Gut microbiota alterations, including enrichment of flagellated bacteria, are associated with metabolic syndrome and chronic inflammatory diseases. Here, Tran et al. show, in mice, that elicitation of mucosal anti-flagellin antibodies protects against experimental colitis and ameliorates diet-induced obesity.

  • Hao Q. Tran
  • Ruth E. Ley
  • Benoit Chassaing

research paper for biological sciences

Possible role of L-form switching in recurrent urinary tract infection

The reservoir for recurrent urinary tract infection in humans is unclear. Here, Mickiewicz et al. detect cell-wall deficient (L-form) E. coli in fresh urine from patients, and show that the isolated bacteria readily switch between walled and L-form states.

  • Katarzyna M. Mickiewicz
  • Yoshikazu Kawai
  • Jeff Errington

research paper for biological sciences

Dual microglia effects on blood brain barrier permeability induced by systemic inflammation

Although it is known that microglia respond to injury and systemic disease in the brain, it is unclear if they modulate blood–brain barrier (BBB) integrity, which is critical for regulating neuroinflammatory responses. Here authors demonstrate that microglia respond to inflammation by migrating towards and accumulating around cerebral vessels, where they initially maintain BBB integrity via expression of the tight-junction protein Claudin-5 before switching, during sustained inflammation, to phagocytically remove astrocytic end-feet resulting in impaired BBB function

  • Koichiro Haruwaka
  • Ako Ikegami
  • Hiroaki Wake

research paper for biological sciences

Mice with hyper-long telomeres show less metabolic aging and longer lifespans

Telomere shortening is associated with aging. Here the authors analyze mice with hyperlong telomeres and demonstrate that longer telomeres than normal have beneficial effects such as delayed metabolic aging, increased longevity and less incidence of cancer.

  • Miguel A. Muñoz-Lorente
  • Alba C. Cano-Martin
  • Maria A. Blasco

research paper for biological sciences

Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture

Organoid cultures have been developed from multiple tissues, opening new possibilities for regenerative medicine. Here the authors demonstrate the derivation of GMP-compliant hydrogels from decellularized porcine small intestine which support formation and growth of human gastric, liver, pancreatic and small intestinal organoids.

  • Giovanni Giuseppe Giobbe
  • Claire Crowley
  • Paolo De Coppi

research paper for biological sciences

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut

Anti-inflammatory treatments for gastrointestinal diseases can often have detrimental side effects. Here the authors engineer E. coli Nissle 1917 to create a fibrous matrix that has a protective effect in DSS-induced colitis mice.

  • Pichet Praveschotinunt
  • Anna M. Duraj-Thatte
  • Neel S. Joshi

research paper for biological sciences

Ambient black carbon particles reach the fetal side of human placenta

Exposure to air pollution during pregnancy has been associated with impaired birth outcomes. Here, Bové et al. report evidence of black carbon particle deposition on the fetal side of human placentae, including at early stages of pregnancy, suggesting air pollution could affect birth outcome through direct effects on the fetus.

  • Hannelore Bové
  • Eva Bongaerts
  • Tim S. Nawrot

research paper for biological sciences

Real-time decoding of question-and-answer speech dialogue using human cortical activity

Speech neuroprosthetic devices should be capable of restoring a patient’s ability to participate in interactive dialogue. Here, the authors demonstrate that the context of a verbal exchange can be used to enhance neural decoder performance in real time.

  • David A. Moses
  • Matthew K. Leonard
  • Edward F. Chang

research paper for biological sciences

In-cell identification and measurement of RNA-protein interactions

RNA-interacting proteome can be identified by RNA affinity purification followed by mass spectrometry. Here the authors developed a different RNA-centric technology that combines high-throughput immunoprecipitation of RNA binding proteins and luciferase-based detection of their interaction with the RNA.

  • Antoine Graindorge
  • Inês Pinheiro
  • Alena Shkumatava

research paper for biological sciences

A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus

Genedrives bias the inheritance of alleles in diploid organisms. Here, the authors develop a gene-drive analogous system for bacteria, selectively editing and clearing plasmids.

  • J. Andrés Valderrama
  • Surashree S. Kulkarni

research paper for biological sciences

Flavonoid intake is associated with lower mortality in the Danish Diet Cancer and Health Cohort

The studies showing health benefits of flavonoids and their impact on cancer mortality are incomplete. Here, the authors perform a prospective cohort study in Danish participants and demonstrate an inverse association between regular flavonoid intake and both cardiovascular and cancer related mortality.

  • Nicola P. Bondonno
  • Frederik Dalgaard
  • Jonathan M. Hodgson

research paper for biological sciences

Senescent cell turnover slows with age providing an explanation for the Gompertz law

One of the underlying causes of aging is the accumulation of senescent cells, but their turnover rates and dynamics during ageing are unknown. Here the authors measure and model senescent cell production and removal and explore implications for mortality.

  • Amit Agrawal

research paper for biological sciences

Optimizing agent behavior over long time scales by transporting value

People are able to mentally time travel to distant memories and reflect on the consequences of those past events. Here, the authors show how a mechanism that connects learning from delayed rewards with memory retrieval can enable AI agents to discover links between past events to help decide better courses of action in the future.

  • Chia-Chun Hung
  • Timothy Lillicrap

research paper for biological sciences

Mutant p53 drives clonal hematopoiesis through modulating epigenetic pathway

Ageing is associated with clonal hematopoiesis of indeterminate potential (CHIP), which is linked to increased risks of hematological malignancies. Here the authors uncover an epigenetic mechanism through which mutant p53 drives clonal hematopoiesis through interaction with EZH2.

research paper for biological sciences

A systematic evaluation of single cell RNA-seq analysis pipelines

There has been a rapid rise in single cell RNA-seq methods and associated pipelines. Here the authors use simulated data to systematically evaluate the performance of 3000 possible pipelines to derive recommendations for data processing and analysis of different types of scRNA-seq experiments.

  • Beate Vieth
  • Swati Parekh
  • Ines Hellmann

research paper for biological sciences

Cryo-EM structure and polymorphism of Aβ amyloid fibrils purified from Alzheimer’s brain tissue

Alzheimer’s disease is characterised by the deposition of Aβ amyloid fibrils and tau protein neurofibrillary tangles. Here the authors use cryo-EM to structurally characterise brain derived Aβ amyloid fibrils and find that they are polymorphic and right-hand twisted, which differs from in vitro generated Aβ fibrils.

  • Marius Kollmer
  • William Close
  • Marcus Fändrich

research paper for biological sciences

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

Culturing transposon-mutant libraries in pools can mask complex phenotypes. Here the authors present microfluidics mediated droplet Tn-Seq, which encapsulates individual mutants, promotes isolated growth and enables cell-cell interaction analyses.

  • Derek Thibault
  • Paul A. Jensen
  • Tim van Opijnen

research paper for biological sciences

An artificial metalloenzyme biosensor can detect ethylene gas in fruits and Arabidopsis leaves

Existing methods to detect ethylene in plant tissue typically require gas chromatography or use ethylene-dependent gene expression as a proxy. Here Vong et al . show that an artificial metalloenzyme-based ethylene probe can be used to detect ethylene in plants with improved spatiotemporal resolution.

  • Kenward Vong
  • Katsunori Tanaka

research paper for biological sciences

Artificially cloaked viral nanovaccine for cancer immunotherapy

Cancer therapy using oncolytic virus has shown pre-clinical and clinical efficacy. Here, the authors report ExtraCRAd, an oncolytic virus cloaked with tumour cell membrane and report its therapeutic effects in vitro and in vivo in multiple mouse tumour models.

  • Manlio Fusciello
  • Flavia Fontana
  • Vincenzo Cerullo

research paper for biological sciences

A transposable element insertion is associated with an alternative life history strategy

Tradeoffs are central to life history theory and evolutionary biology, yet almost nothing is known about their mechanistic basis. Here the authors characterize one such mechanism and find a transposable element insertion is associated with the switch between alternative life history strategies.

  • Alyssa Woronik
  • Kalle Tunström
  • Christopher W. Wheat

research paper for biological sciences

Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

The Iberian Peninsula has a complex history. Here, the authors analyse the genetic structure of the modern Iberian population at fine scale, revealing historical population movements associated with the time of Muslim rule.

  • Clare Bycroft
  • Ceres Fernandez-Rozadilla
  • Simon Myers

research paper for biological sciences

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

Immune cells are shaped by the tissue environment, yet the states of healthy human T cells are mainly studied in the blood. Here, the authors perform single cell RNA-seq of T cells from tissues and blood of healthy donors and show its utility as a reference map for comparison of human T cell states in disease.

  • Peter A. Szabo
  • Hanna Mendes Levitin
  • Peter A. Sims

research paper for biological sciences

Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke

Stroke risk is influenced by genetic and lifestyle factors and previously a genomic risk score (GRS) for stroke was proposed, albeit with limited predictive power. Here, Abraham et al. develop a metaGRS that is composed of several stroke-related GRSs and demonstrate improved predictive power compared with individual GRS or classic risk factors.

  • Gad Abraham
  • Rainer Malik
  • Martin Dichgans

research paper for biological sciences

Mitochondrial oxidative capacity and NAD + biosynthesis are reduced in human sarcopenia across ethnicities

Sarcopenia is the loss of muscle mass and strength associated with physical disability during ageing. Here, the authors analyse muscle biopsies from 119 patients with sarcopenia and age-matched controls of different ethnic groups and find transcriptional signatures indicating mitochondrial dysfunction, associated with reduced mitochondria numbers and lower NAD +  levels in older individuals with sarcopenia.

  • Eugenia Migliavacca
  • Stacey K. H. Tay
  • Jerome N. Feige

research paper for biological sciences

NAD + augmentation restores mitophagy and limits accelerated aging in Werner syndrome

The molecular mechanisms of mitochondrial dysfunction in the premature ageing Werner syndrome were elusive. Here the authors show that NAD + depletion-induced impaired mitophagy contributes to this phenomenon, shedding light on potential therapeutics.

  • Evandro F. Fang
  • Vilhelm A. Bohr

research paper for biological sciences

Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

Single strand breaks represent the most common form of DNA damage yet no methods to map them in a genome-wide fashion at single nucleotide resolution exist. Here the authors develop such a method and apply to uncover patterns of single-strand DNA “breakome” in different biological conditions.

  • Lorena Salazar-García
  • Philipp Kapranov

research paper for biological sciences

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Here, the authors explore the potential of the 16S gene for discriminating bacterial taxa and show that full-length sequencing combined with appropriate clustering of intragenomic sequence variation can provide accurate representation of bacterial species in microbiome datasets.

  • Jethro S. Johnson
  • Daniel J. Spakowicz
  • George M. Weinstock

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

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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.

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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.

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Our biological science research journals cover a broad range of topics, from animal biology and plant science to genetic engineering, immunology, and microbiology. Read some of the latest and most talked about research from across our portfolio.

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The manifold costs of being a non-native English speaker in science , PLOS Biology

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva , PLOS Genetics

Time-travelling pathogens and their risk to ecological communities , PLOS Computational Biology

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From PLOS Pathogens , Divergence of TORC1-mediated stress response leads to novel acquired stress resistance in a pathogenic yeast

From PLOS Genetics , Wolbachia infection at least partially rescues the fertility and ovary defects of several new Drosophila melanogaster bag of marbles protein-coding mutants

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Contribution of extracellular vesicles for the pathogenesis of retinal diseases: shedding light on blood-retinal barrier dysfunction

Retinal degenerative diseases, including diabetic retinopathy (DR) and age-related macular degeneration (AMD), loom as threats to vision, causing detrimental effects on the structure and function of the retina...

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Exploiting urine-derived induced pluripotent stem cells for advancing precision medicine in cell therapy, disease modeling, and drug testing

The field of regenerative medicine has witnessed remarkable advancements with the emergence of induced pluripotent stem cells (iPSCs) derived from a variety of sources. Among these, urine-derived induced pluri...

Targeting cathepsin S promotes activation of OLF1-BDNF/TrkB axis to enhance cognitive function

Cathepsin S (CTSS) is a cysteine protease that played diverse roles in immunity, tumor metastasis, aging and other pathological alterations. At the cellular level, increased CTSS levels have been associated wi...

Campylobacter jejuni virulence factors: update on emerging issues and trends

Campylobacter jejuni is a very common cause of gastroenteritis, and is frequently transmitted to humans through contaminated food products or water. Importantly, C. jejuni infections have a range of short- and l...

Membrane lipid remodeling eradicates Helicobacter pylori by manipulating the cholesteryl 6'-acylglucoside biosynthesis

Helicobacter pylori , the main cause of various gastric diseases, infects approximately half of the human population. This pathogen is auxotrophic for cholesterol which it converts to various cholesteryl α-glucosi...

research paper for biological sciences

Dengue virus pathogenesis and host molecular machineries

Dengue viruses (DENV) are positive-stranded RNA viruses belonging to the Flaviviridae family. DENV is the causative agent of dengue, the most rapidly spreading viral disease transmitted by mosquitoes. Each yea...

Targeting NLRP3 signaling reduces myocarditis-induced arrhythmogenesis and cardiac remodeling

Myocarditis substantially increases the risk of ventricular arrhythmia. Approximately 30% of all ventricular arrhythmia cases in patients with myocarditis originate from the right ventricular outflow tract (RV...

T cell expressions of aberrant gene signatures and Co-inhibitory receptors (Co-IRs) as predictors of renal damage and lupus disease activity

Systemic lupus erythematosus (SLE) is distinguished by an extensive range of clinical heterogeneity with unpredictable disease flares and organ damage. This research investigates the potential of aberrant sign...

Applications of peptides in nanosystems for diagnosing and managing bacterial sepsis

Sepsis represents a critical medical condition stemming from an imbalanced host immune response to infections, which is linked to a significant burden of disease. Despite substantial efforts in laboratory and ...

research paper for biological sciences

Enhancement of NETosis by ACE2-cross-reactive anti-SARS-CoV-2 RBD antibodies in patients with COVID-19

High levels of neutrophil extracellular trap (NET) formation or NETosis and autoantibodies are related to poor prognosis and disease severity of COVID-19 patients. Human angiotensin-converting enzyme 2 (ACE2) ...

Attenuating mitochondrial dysfunction and morphological disruption with PT320 delays dopamine degeneration in MitoPark mice

Mitochondria are essential organelles involved in cellular energy production. Changes in mitochondrial function can lead to dysfunction and cell death in aging and age-related disorders. Recent research sugges...

research paper for biological sciences

Longitudinal alterations in brain perfusion and vascular reactivity in the zQ175DN mouse model of Huntington’s disease

Huntington’s disease (HD) is marked by a CAG-repeat expansion in the huntingtin gene that causes neuronal dysfunction and loss, affecting mainly the striatum and the cortex. Alterations in the neurovascular co...

Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model

This study addresses the urgent need for infection control agents driven by the rise of drug-resistant pathogens such as Acinetobacter baumannii . Our primary aim was to develop and assess a novel endolysin, Tha-P...

Correction: A novel HIF1α-STIL-FOXM1 axis regulates tumor metastasis

The original article was published in Journal of Biomedical Science 2022 29 :24

Significance of hepatitis B virus capsid dephosphorylation via polymerase

It is generally believed that hepatitis B virus (HBV) core protein (HBc) dephosphorylation (de-P) is important for viral DNA synthesis and virion secretion. HBV polymerase contains four domains for terminal pr...

Association of TRAIL receptor with phosphatase SHP-1 enables repressing T cell receptor signaling and T cell activation through inactivating Lck

T cell receptor (TCR) signaling and T cell activation are tightly regulated by gatekeepers to maintain immune tolerance and avoid autoimmunity. The TRAIL receptor (TRAIL-R) is a TNF-family death receptor that ...

Improving CRISPR–Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration

The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR–Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for g...

A matter of new life and cell death: programmed cell death in the mammalian ovary

The mammalian ovary is a unique organ that displays a distinctive feature of cyclic changes throughout the entire reproductive period. The estrous/menstrual cycles are associated with drastic functional and mo...

Engineered extracellular vesicles carrying let-7a-5p for alleviating inflammation in acute lung injury

Acute lung injury (ALI) is a life-threatening respiratory condition characterized by severe inflammation and lung tissue damage, frequently causing rapid respiratory failure and long-term complications. The mi...

The rise of big data: deep sequencing-driven computational methods are transforming the landscape of synthetic antibody design

Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, st...

Tick-borne encephalitis virus transmitted singly and in duo with Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum bacteria by ticks as pathogens modifying lipid metabolism in human blood

Ticks are vectors of various pathogens, including tick-borne encephalitis virus causing TBE and bacteria such as Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum causing e.g. viral-bacterial co-infec...

Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6’s role in hematopoietic differentiation and leukemia

Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional ...

Reduced interleukin-18 secretion by human monocytic cells in response to infections with hyper-virulent Streptococcus pyogenes

Streptococcus pyogenes (group A streptococcus, GAS) causes a variety of diseases ranging from mild superficial infections of the throat and skin to severe invasive infections, such as necrotizing soft tissue infe...

Metabolism-regulating non-coding RNAs in breast cancer: roles, mechanisms and clinical applications

Breast cancer is one of the most common malignancies that pose a serious threat to women's health. Reprogramming of energy metabolism is a major feature of the malignant transformation of breast cancer. Compar...

Genetic and pharmacologic p32-inhibition rescue CHCHD2-linked Parkinson’s disease phenotypes in vivo and in cell models

Mutations in CHCHD2 have been linked to Parkinson’s disease, however, their exact pathophysiologic roles are unclear. The p32 protein has been suggested to interact with CHCHD2, however, the physiological functio...

The role of pregnancy associated plasma protein-A in triple negative breast cancer: a promising target for achieving clinical benefits

Pregnancy associated plasma protein-A (PAPP-A) plays an integral role in breast cancer (BC), especially triple negative breast cancer (TNBC). This subtype accounts for the most aggressive BC, possesses high tu...

Translational research on drug development and biomarker discovery for hepatocellular carcinoma

Translational research plays a key role in drug development and biomarker discovery for hepatocellular carcinoma (HCC). However, unique challenges exist in this field because of the limited availability of hum...

Germline mutations of homologous recombination genes and clinical outcomes in pancreatic cancer: a multicenter study in Taiwan

Cancer susceptibility germline mutations are associated with pancreatic ductal adenocarcinoma (PDAC). However, the hereditary status of PDAC and its impact on survival is largely unknown in the Asian population.

Rab37 mediates trafficking and membrane presentation of PD-1 to sustain T cell exhaustion in lung cancer

Programmed cell death protein 1 (PD-1) is an immune checkpoint receptor expressed on the surface of T cells. High expression of PD-1 leads to T-cell dysfunction in the tumor microenvironment (TME). However, th...

FLT3L-induced virtual memory CD8 T cells engage the immune system against tumors

Previous research in FMS-like tyrosine kinase 3 ligands (FLT3L) has primarily focused on their potential to generate dendritic cells (DCs) from bone marrow progenitors, with a limited understanding of how thes...

Promising antibacterial efficacy of arenicin peptides against the emerging opportunistic pathogen Mycobacterium abscessus

Mycobacterium abscessus , a fast-growing non-tuberculous mycobacterium, is an emerging opportunistic pathogen responsible for chronic bronchopulmonary infections in people with respiratory diseases such as cystic ...

Targeting MDM2 in malignancies is a promising strategy for overcoming resistance to anticancer immunotherapy

MDM2 has been established as a biomarker indicating poor prognosis for individuals undergoing immune checkpoint inhibitor (ICI) treatment for different malignancies by various pancancer studies. Specifically, ...

Mechanisms and functions of SUMOylation in health and disease: a review focusing on immune cells

SUMOylation, which is a type of post-translational modification that involves covalent conjugation of small ubiquitin-like modifier (SUMO) proteins to target substrates, regulates various important molecular a...

Hesperetin activates CISD2 to attenuate senescence in human keratinocytes from an older person and rejuvenates naturally aged skin in mice

CDGSH iron-sulfur domain-containing protein 2 (CISD2), a pro-longevity gene, mediates healthspan in mammals. CISD2 is down-regulated during aging. Furthermore, a persistently high level of CISD2 promotes longe...

Plectin plays a role in the migration and volume regulation of astrocytes: a potential biomarker of glioblastoma

The expression of aquaporin 4 (AQP4) and intermediate filament (IF) proteins is altered in malignant glioblastoma (GBM), yet the expression of the major IF-based cytolinker, plectin (PLEC), and its contributio...

Modelling the complex nature of the tumor microenvironment: 3D tumor spheroids as an evolving tool

Cancer remains a serious burden in society and while the pace in the development of novel and more effective therapeutics is increasing, testing platforms that faithfully mimic the tumor microenvironment are l...

TEM1/endosialin/CD248 promotes pathologic scarring and TGF-β activity through its receptor stability in dermal fibroblasts

Pathologic scars, including keloids and hypertrophic scars, represent a common form of exaggerated cutaneous scarring that is difficult to prevent or treat effectively. Additionally, the pathobiology of pathol...

Physiology and pharmacological targeting of phase separation

Liquid–liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and postt...

Inactivation of pentraxin 3 suppresses M2-like macrophage activity and immunosuppression in colon cancer

The tumor microenvironment is characterized by inflammation-like and immunosuppression situations. Although cancer-associated fibroblasts (CAFs) are among the major stromal cell types in various solid cancers,...

Engineered EVs with pathogen proteins: promising vaccine alternatives to LNP-mRNA vaccines

Extracellular vesicles (EVs) are tiny, lipid membrane-bound structures that are released by most cells. They play a vital role in facilitating intercellular communication by delivering bioactive cargoes to rec...

Attenuation of neurovirulence of chikungunya virus by a single amino acid mutation in viral E2 envelope protein

Chikungunya virus (CHIKV) has reemerged as a major public health concern, causing chikungunya fever with increasing cases and neurological complications.

Scaffold-based 3D cell culture models in cancer research

Three-dimensional (3D) cell cultures have emerged as valuable tools in cancer research, offering significant advantages over traditional two-dimensional (2D) cell culture systems. In 3D cell cultures, cancer c...

research paper for biological sciences

Therapeutic antibodies for the prevention and treatment of cancer

The developments of antibodies for cancer therapeutics have made remarkable success in recent years. There are multiple factors contributing to the success of the biological molecule including origin of the an...

Immune evasion in cell-based immunotherapy: unraveling challenges and novel strategies

Cell-based immunotherapies (CBIs), notably exemplified by chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapy, have emerged as groundbreaking approaches for cancer therapy. Nevertheless, akin to ...

Exploring the relationship between metabolism and immune microenvironment in osteosarcoma based on metabolic pathways

Metabolic remodeling and changes in tumor immune microenvironment (TIME) in osteosarcoma are important factors affecting prognosis and treatment. However, the relationship between metabolism and TIME needs to ...

The synergism of cytosolic acidosis and reduced NAD + /NADH ratio is responsible for lactic acidosis-induced vascular smooth muscle cell impairment in sepsis

During sepsis, serve vascular dysfunctions lead to life-threatening multiple organ failure, due to vascular smooth muscle cells (VSMC) impairments, resulting in vasoplegia, hypotension and hypoperfusion. In ad...

Localization, traffic and function of Rab34 in adipocyte lipid and endocrine functions

Excessive lipid accumulation in the adipose tissue in obesity alters the endocrine and energy storage functions of adipocytes. Adipocyte lipid droplets represent key organelles coordinating lipid storage and m...

Nano-modified viruses prime the tumor microenvironment and promote the photodynamic virotherapy in liver cancer

As of 2020, hepatocellular carcinoma (HCC), a form of liver cancer, stood as the third most prominent contributor to global cancer-related mortality. Combining immune checkpoint inhibitors (ICI) with other the...

A novel mucosal bivalent vaccine of EV-A71/EV-D68 adjuvanted with polysaccharides from Ganoderma lucidum protects mice against EV-A71 and EV-D68 lethal challenge

Human enteroviruses A71 (EV-A71) and D68 (EV-D68) are the suspected causative agents of hand-foot-and-mouth disease, aseptic meningitis, encephalitis, acute flaccid myelitis, and acute flaccid paralysis in chi...

research paper for biological sciences

A secreted form of chorismate mutase (Rv1885c) in Mycobacterium bovis BCG contributes to pathogenesis by inhibiting mitochondria-mediated apoptotic cell death of macrophages

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), and its pathogenicity is associated with its ability to evade the host defense system. The secretory form of the chorismate mutase of M. tub...

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Journal of Biomedical Science is supported by the National Science and Technology Council (NSTC) , Taiwan.

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2022 Citation Impact 11.0 - 2-year Impact Factor 10.9 - 5-year Impact Factor 2.367 - SNIP (Source Normalized Impact per Paper) 2.520 - SJR (SCImago Journal Rank)

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Biological Research

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Special series on Microbial Interactions

The nine articles of this special issue of  Biological Research  address biochemical and genetic determinants of microbial response and tolerance to stressors in different biological models and environmental contexts. Individual articles provide a broad exploration of our current knowledge of response to stressors, with a special emphasis on metal metabolism and toxic compounds.

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Special series on Antarctic Research

This special issue on Antarctic research in Biological Research comprises of recent studies, related to the discovery of several new enzymes and biotechnological applications that allow to expand the knowledge of Antarctic organisms and their potential applications.

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

Authors: Geum-Lan Hong, Kyung-Hyun Kim, Yae-Ji Kim, Hui-Ju Lee, Sung-Pil Cho, Seung-Yun Han, Seung Woo Yang, Jong-Soo Lee, Shin-Kwang Kang, Jae-Sung Lim and Ju-Young Jung

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

Authors: Binan Zhao, Haoran Peng, Yanjing Zhang, Jie Zhang, Desheng Kong, Sai Cao, Yan Li, Dan Yang, Chuanwen Sun, Xinyi Pu, Ping Zhao, Yan Xu, Kai Zhao and Liangzhi Xie

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

Authors: Sylvana I. S. Rendeiro de Noronha, Lauro Angelo Gonçalves de Moraes, James E. Hassell Jr., Christopher E. Stamper, Mathew R. Arnold, Jared D. Heinze, Christine L. Foxx, Margaret M. Lieb, Kristin E. Cler, Bree L. Karns, Sophia Jaekel, Kelsey M. Loupy, Fernanda C. S. Silva, Deoclécio Alves Chianca-Jr., Christopher A. Lowry and Rodrigo Cunha de Menezes

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

Authors: Andrea Oyarzún-Cisterna, Cristián Gidi, Fernanda Raiqueo, Roberto Amigo, Camila Rivas, Marcela Torrejón and José L. Gutiérrez

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

Authors: Simon Lange, Anna Kuntze, Neele Wüstmann, Theresa Reckers, Verena Humberg, Wilhelm G. Dirks, Sebastian Huss, Julia Vieler, Andres Jan Schrader, Martin Bögemann, Katrin Schlack and Christof Bernemann

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Awareness and current knowledge of breast cancer

Authors: Muhammad Akram, Mehwish Iqbal, Muhammad Daniyal and Asmat Ullah Khan

Stress and defense responses in plant secondary metabolites production

Authors: Tasiu Isah

Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency

Authors: Muhammad Anas, Fen Liao, Krishan K. Verma, Muhammad Aqeel Sarwar, Aamir Mahmood, Zhong-Liang Chen, Qiang Li, Xu-Peng Zeng, Yang Liu and Yang-Rui Li

Coping with drought: stress and adaptive mechanisms, and management through cultural and molecular alternatives in cotton as vital constituents for plant stress resilience and fitness

Authors: Aziz Khan, Xudong Pan, Ullah Najeeb, Daniel Kean Yuen Tan, Shah Fahad, Rizwan Zahoor and Honghai Luo

Biotechnological applications of archaeal enzymes from extreme environments

Authors: Ma. Ángeles Cabrera and Jenny M. Blamey

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Biological Research , formerly Archives of Experimental Medicine and Biology , was founded in 1964 and transferred to BioMed Central in 2014. An electronic archive of articles published between 1999 and 2013 can be found in the SciELO database.

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Manuel J Santos, Editor-in-Chief

Editor’s profile

Manuel J Santos, Editor-in-Chief

Dr Santos is an Associate Professor in the Faculty of Biological Sciences and Medicine at the Pontificia Catholic University of Chile.

Dr Santos received his MD from the University of Chile and his PhD in Cell and Molecular Biology from the Pontificia Catholic University of Chile. He majored in Medical Genetics at The John Hopkins University (USA) and The René Descartes University of Paris (France), and held a post doctorate position in Cell Biology and Genetics at the Rockefeller University (USA).

His research has focused on the biogenesis of cellular organelles, particularly peroxisomes. A pioneer in this field, his research lead him to discover a new type of human genetic disease, the peroxisomal biogenesis disorders, which include Zellweger Syndrome. More recently his research has centered on studying the role of peroxisomes in Alzheimer’s disease, and he also works in the field of bioethics.

Over the span of his career, Dr Santos has published more than 70 peer reviewed papers and been the President of the Society of Biology of Chile, the Genetics Society of Chile and the Bioethical Society of Chile.

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The Chilean Biology Society (Sociedad de Biología de Chile), previously the Biological Society of Santiago, was founded in late 1928 as a subsidiary of The Societé de Biologie of Paris, France. For several years the summaries of its communications were published in Comps Rendú of the Societé de Biologie du Paris. The Society is currently a member of the International Union of Biological Sciences (IUBS).

The Chilean Biology Society promotes theoretical and experimental studies and research leading to advancement in and dissemination of the biological sciences for the benefit of the community. To accomplish this, the Society organizes periodic scientific meetings in which scientists communicate, comment and discuss research carried out in Chilean or foreign research laboratories. In addition, relations and cooperation with similar domestic and foreign institutions are stimulated, and communication by all appropriate means of biological research carried out in Chile. 

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The Society also publishes Revista Chilena de Historia Natural ( Chilean Journal of Natural History, founded in 1897).

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Researchers develop 'founding document' on synthetic cell development

by Tara Friesen, NASA

Researchers develop 'founding document' on synthetic cell development

Cells are the fundamental units of life, forming the variety of all living things on Earth as individual cells and multicellular organisms. To better understand how cells perform the essential functions of life, scientists have begun developing synthetic cells—non-living bits of cellular biochemistry wrapped in a membrane that mimic specific biological processes.

The development of synthetic cells could one day hold the answers to developing new ways to fight disease, supporting long-duration human space flight , and better understanding the origins of life on Earth.

In a paper published recently in ACS Synthetic Biology , researchers outline the potential opportunities that synthetic cell development could unlock and the challenges that lie ahead in this groundbreaking research. They also present a roadmap to inspire and guide innovation in this intriguing field.

"The potential for this field is incredible," said Lynn Rothschild, the lead author of the paper and an astrobiologist at NASA's Ames Research Center in California's Silicon Valley. "It's a privilege to have led this group in forming what we envision will be a founding document, a resource that will spur this field on."

Synthetic cell development could have wide ranging benefits to humanity. Analyzing the intricacies that go into building a cell could guide researchers to better understand how cells first evolved or open the door to creating new forms of life more capable of withstanding harsh environments like radiation or freezing temperatures.

These innovations could also lead to advancements in food and medical sciences—creating efficiencies in food production, detecting contaminants in manufacturing, or developing novel cellular functions that act as new therapies for chronic diseases and even synthetic organ transplantation.

Building synthetic cells could also answer some of NASA's biggest questions about the possibility of life beyond Earth.

"The challenge of creating synthetic cells informs whether we're alone in the universe," said Rothschild. "We're starting to develop the skills to not just create synthetic analogs of life as it may have happened on Earth but to consider pathways to life that could form on other planets."

As research continues on synthetic cell development, Rothschild sees opportunities where it could expand our understanding of the complexities of natural life.

"Life is an amazing thing. We use the capabilities of cells all the time—we build houses with wood, we use leather in our shoes, we breathe oxygen. Life has amazing precision, and if you can harness it, it's unbelievable what we could accomplish."

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Inside every plant, animal and human cell are billions of molecular machines. They’re made up of proteins, DNA and other molecules, but no single piece works on its own. Only by seeing how they interact together, across millions of types of combinations, can we start to truly understand life’s processes.

In a paper published in Nature , we introduce AlphaFold 3, a revolutionary model that can predict the structure and interactions of all life’s molecules with unprecedented accuracy. For the interactions of proteins with other molecule types we see at least a 50% improvement compared with existing prediction methods, and for some important categories of interaction we have doubled prediction accuracy.

We hope AlphaFold 3 will help transform our understanding of the biological world and drug discovery. Scientists can access the majority of its capabilities, for free, through our newly launched AlphaFold Server , an easy-to-use research tool. To build on AlphaFold 3’s potential for drug design, Isomorphic Labs is already collaborating with pharmaceutical companies to apply it to real-world drug design challenges and, ultimately, develop new life-changing treatments for patients.

Our new model builds on the foundations of AlphaFold 2, which in 2020 made a fundamental breakthrough in protein structure prediction . So far, millions of researchers globally have used AlphaFold 2 to make discoveries in areas including malaria vaccines, cancer treatments and enzyme design. AlphaFold has been cited more than 20,000 times and its scientific impact recognized through many prizes, most recently the Breakthrough Prize in Life Sciences . AlphaFold 3 takes us beyond proteins to a broad spectrum of biomolecules. This leap could unlock more transformative science, from developing biorenewable materials and more resilient crops, to accelerating drug design and genomics research.

7PNM - Spike protein of a common cold virus (Coronavirus OC43): AlphaFold 3’s structural prediction for a spike protein (blue) of a cold virus as it interacts with antibodies (turquoise) and simple sugars (yellow), accurately matches the true structure (gray). The animation shows the protein interacting with an antibody, then a sugar. Advancing our knowledge of such immune-system processes helps better understand coronaviruses, including COVID-19, raising possibilities for improved treatments.

How AlphaFold 3 reveals life’s molecules

Given an input list of molecules, AlphaFold 3 generates their joint 3D structure, revealing how they all fit together. It models large biomolecules such as proteins, DNA and RNA, as well as small molecules, also known as ligands — a category encompassing many drugs. Furthermore, AlphaFold 3 can model chemical modifications to these molecules which control the healthy functioning of cells, that when disrupted can lead to disease.

AlphaFold 3’s capabilities come from its next-generation architecture and training that now covers all of life’s molecules. At the core of the model is an improved version of our Evoformer module — a deep learning architecture that underpinned AlphaFold 2’s incredible performance. After processing the inputs, AlphaFold 3 assembles its predictions using a diffusion network, akin to those found in AI image generators. The diffusion process starts with a cloud of atoms, and over many steps converges on its final, most accurate molecular structure.

AlphaFold 3’s predictions of molecular interactions surpass the accuracy of all existing systems. As a single model that computes entire molecular complexes in a holistic way, it’s uniquely able to unify scientific insights.

7R6R - DNA binding protein: AlphaFold 3’s prediction for a molecular complex featuring a protein (blue) bound to a double helix of DNA (pink) is a near-perfect match to the true molecular structure discovered through painstaking experiments (gray).

Leading drug discovery at Isomorphic Labs

AlphaFold 3 creates capabilities for drug design with predictions for molecules commonly used in drugs, such as ligands and antibodies, that bind to proteins to change how they interact in human health and disease.

AlphaFold 3 achieves unprecedented accuracy in predicting drug-like interactions, including the binding of proteins with ligands and antibodies with their target proteins. AlphaFold 3 is 50% more accurate than the best traditional methods on the PoseBusters benchmark without needing the input of any structural information, making AlphaFold 3 the first AI system to surpass physics-based tools for biomolecular structure prediction. The ability to predict antibody-protein binding is critical to understanding aspects of the human immune response and the design of new antibodies — a growing class of therapeutics.

Using AlphaFold 3 in combination with a complementary suite of in-house AI models, Isomorphic Labs is working on drug design for internal projects as well as with pharmaceutical partners. Isomorphic Labs is using AlphaFold 3 to accelerate and improve the success of drug design — by helping understand how to approach new disease targets, and developing novel ways to pursue existing ones that were previously out of reach.

AlphaFold Server: A free and easy-to-use research tool

8AW3 - RNA modifying protein: AlphaFold 3’s prediction for a molecular complex featuring a protein (blue), a strand of RNA (purple), and two ions (yellow) closely matches the true structure (gray). This complex is involved with the creation of other proteins — a cellular process fundamental to life and health.

Google DeepMind’s newly launched AlphaFold Server is the most accurate tool in the world for predicting how proteins interact with other molecules throughout the cell. It is a free platform that scientists around the world can use for non-commercial research. With just a few clicks, biologists can harness the power of AlphaFold 3 to model structures composed of proteins, DNA, RNA and a selection of ligands, ions and chemical modifications.

AlphaFold Server helps scientists make novel hypotheses to test in the lab, speeding up workflows and enabling further innovation. Our platform gives researchers an accessible way to generate predictions, regardless of their access to computational resources or their expertise in machine learning.

Experimental protein-structure prediction can take about the length of a PhD and cost hundreds of thousands of dollars. Our previous model, AlphaFold 2, has been used to predict hundreds of millions of structures, which would have taken hundreds of millions of researcher-years at the current rate of experimental structural biology.

Demo video showing the capabilities of the server.

Sharing the power of AlphaFold 3 responsibly

With each AlphaFold release, we’ve sought to understand the broad impact of the technology , working together with the research and safety community. We take a science-led approach and have conducted extensive assessments to mitigate potential risks and share the widespread benefits to biology and humanity.

Building on the external consultations we carried out for AlphaFold 2, we’ve now engaged with more than 50 domain experts, in addition to specialist third parties, across biosecurity, research and industry, to understand the capabilities of successive AlphaFold models and any potential risks. We also participated in community-wide forums and discussions ahead of AlphaFold 3’s launch.

AlphaFold Server reflects our ongoing commitment to share the benefits of AlphaFold, including our free database of 200 million protein structures. We’ll also be expanding our free AlphaFold education online course with EMBL-EBI and partnerships with organizations in the Global South to equip scientists with the tools they need to accelerate adoption and research, including on underfunded areas such as neglected diseases and food security. We’ll continue to work with the scientific community and policy makers to develop and deploy AI technologies responsibly.

Opening up the future of AI-powered cell biology

7BBV - Enzyme: AlphaFold 3’s prediction for a molecular complex featuring an enzyme protein (blue), an ion (yellow sphere) and simple sugars (yellow), along with the true structure (gray). This enzyme is found in a soil-borne fungus (Verticillium dahliae) that damages a wide range of plants. Insights into how this enzyme interacts with plant cells could help researchers develop healthier, more resilient crops.

AlphaFold 3 brings the biological world into high definition. It allows scientists to see cellular systems in all their complexity, across structures, interactions and modifications. This new window on the molecules of life reveals how they’re all connected and helps understand how those connections affect biological functions — such as the actions of drugs, the production of hormones and the health-preserving process of DNA repair.

The impacts of AlphaFold 3 and our free AlphaFold Server will be realized through how they empower scientists to accelerate discovery across open questions in biology and new lines of research. We’re just beginning to tap into AlphaFold 3’s potential and can’t wait to see what the future holds.

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Computer Science > Computer Vision and Pattern Recognition

Title: fast and controllable post-training sparsity: learning optimal sparsity allocation with global constraint in minutes.

Abstract: Neural network sparsity has attracted many research interests due to its similarity to biological schemes and high energy efficiency. However, existing methods depend on long-time training or fine-tuning, which prevents large-scale applications. Recently, some works focusing on post-training sparsity (PTS) have emerged. They get rid of the high training cost but usually suffer from distinct accuracy degradation due to neglect of the reasonable sparsity rate at each layer. Previous methods for finding sparsity rates mainly focus on the training-aware scenario, which usually fails to converge stably under the PTS setting with limited data and much less training cost. In this paper, we propose a fast and controllable post-training sparsity (FCPTS) framework. By incorporating a differentiable bridge function and a controllable optimization objective, our method allows for rapid and accurate sparsity allocation learning in minutes, with the added assurance of convergence to a predetermined global sparsity rate. Equipped with these techniques, we can surpass the state-of-the-art methods by a large margin, e.g., over 30\% improvement for ResNet-50 on ImageNet under the sparsity rate of 80\%. Our plug-and-play code and supplementary materials are open-sourced at this https URL .

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A scientist is looking through a microscope while backlit by a red image on a computer screen. Synthetic cell development could lead researchers to new developments in food and medical sciences and a better understanding of the origins of life on Earth.

Cells are the fundamental units of life, forming the variety of all living things on Earth as individual cells and multi-cellular organisms. To better understand how cells perform the essential functions of life, scientists have begun developing synthetic cells – non-living bits of cellular biochemistry wrapped in a membrane that mimic specific biological processes.

The development of synthetic cells could one day hold the answers to developing new ways to fight disease, supporting long-duration human spaceflight, and better understanding the origins of life on Earth.

In a paper published recently in ACS Synthetic Biology , researchers outline the potential opportunities that synthetic cell development could unlock and what challenges lie ahead in this groundbreaking research. They also present a roadmap to inspire and guide innovation in this intriguing field.

“The potential for this field is incredible,” said Lynn Rothschild, the lead author of the paper and an astrobiologist at NASA’s Ames Research Center in California’s Silicon Valley. “It’s a privilege to have led this group in forming what we envision will be a founding document, a resource that will spur this field on.”

Synthetic cell development could have wide ranging benefits to humanity. Analyzing the intricacies that go in to building a cell could guide researchers to better understand how cells first evolved or open the door to creating new forms of life more capable of withstanding harsh environments like radiation or freezing temperatures.

These innovations could also lead to advancements in food and medical sciences – creating efficiencies in food production, detecting contaminants in manufacturing, or developing novel cellular functions that act as new therapies for chronic diseases and even synthetic organ transplantation.

Building synthetic cells could also answer some of NASA’s biggest questions about the possibility of life beyond Earth.

“The challenge of creating synthetic cells informs whether we’re alone in the universe,” said Rothschild. “We’re starting to develop the skills to not just create synthetic analogs of life as it may have happened on Earth but to consider pathways to life that could form on other planets.”

As research continues on synthetic cell development, Rothschild sees opportunities where it could expand our understanding of the complexities of natural life.

“Life is an amazing thing. We use the capabilities of cells all the time – we build houses with wood, we use leather in our shoes, we breathe oxygen. Life has amazing precision, and if you can harness it, it’s unbelievable what we could accomplish.”

For news media :

Members of the news media interested in covering this topic should reach out to the  NASA Ames newsroom .

Related Terms

  • Ames Research Center
  • Cell and Molecular Biology
  • Developmental, Reproductive and Evolutionary Biology
  • Science & Research

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