January 2021

Research articles

    1. Genetics and Genomics

    DNA damage—how and why we age?

    Matt Yousefzadeh et al.
    There is now sufficient and diverse evidence to support a cogent argument that DNA damage plays a causal role in aging.
    1. Structural Biology and Molecular Biophysics

    Nanoscopic anatomy of dynamic multi-protein complexes at membranes resolved by graphene-induced energy transfer

    Nadia Füllbrunn et al.
    The axial organization and dynamics of the HOPS complex at membrane surface are resolved by graphene-induced energy transfer with subnanometer resolution.
    1. Cell Biology
    2. Stem Cells and Regenerative Medicine

    NAD+ enhances ribitol and ribose rescue of α-dystroglycan functional glycosylation in human FKRP-mutant myotubes

    Carolina Ortiz-Cordero et al.
    The combined use of NAD+ with ribitol or ribose potentiates the rescue of α-dystroglycan functional glycosylation in FKRP-mutant patient-specific iPSC-derived myotubes, representing potential novel treatments for FKRP muscular dystrophies.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Cytoplasmic chromatin fragments—from mechanisms to therapeutic potential

    Karl N Miller et al.
    Cytoplasmic chromatin fragment formation pathways in senescent cells are a potential therapeutic target for modulation of inflammation in aging, which contributes to age-associated diseases.
    1. Immunology and Inflammation

    Peripheral natural killer cells in chronic hepatitis B patients display multiple molecular features of T cell exhaustion

    Marie Marotel et al.
    Similar to T cell exhaustion, natural killer cell dysfunction in chronic hepatitis B patients results from deregulated calcium pathway.
    1. Computational and Systems Biology
    2. Medicine

    An integrative model of cardiometabolic traits identifies two types of metabolic syndrome

    Amit Frishberg et al.
    A novel type of metabolic syndrome, derived from computational modeling of phenotypic diversity in normal physiological settings, increases the risk of certain complex diseases.
    1. Immunology and Inflammation

    Induction of the IL-1RII decoy receptor by NFAT/FOXP3 blocks IL-1β-dependent response of Th17 cells

    Dong Hyun Kim et al.
    Cellular immunological and biochemical analyses reveal how decoy IL-1RII is induced by human CD4+ T cells upon TCR-stimulation and regulates the Th17-Treg balance by modulating IL-1β responsiveness in IL-1RI+ cells.
    1. Cell Biology

    Generation of stress fibers through myosin-driven reorganization of the actin cortex

    Jaakko I Lehtimäki et al.
    Live-cell microscopy studies revealed that stress fibers can be generated de novo from the actin cortex without the involvement of stress fiber precursors.
    1. Structural Biology and Molecular Biophysics

    Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

    Oliver Fleetwood et al.
    Ligands with different efficacy profiles shift the free energy landscape of the beta2 adrenergic receptor activation and stabilize diverse active-like states via the switch of microswitches lining an allosteric pathway.
    1. Stem Cells and Regenerative Medicine

    Stem cell transplantation rescued a primary open-angle glaucoma mouse model

    Siqi Xiong et al.
    Stem cell transplantation reduces intraocular pressure and preserves retinal ganglion cell function in a mouse glaucoma model, which could lead to a novel therapy for glaucoma to preserve vision.
    1. Evolutionary Biology

    The rise and fall of the ancient northern pike master sex-determining gene

    Qiaowei Pan et al.
    Tracing the evolution of an old master sex determination gene reveals a diversity of sex determination transitions, including a complete Y chromosome loss, among an old teleost order (Esociformes).
    1. Epidemiology and Global Health

    Loss of a co-twin at birth and subsequent risk of psychiatric disorders

    Huan Song et al.
    Findings of this population-based sibling-matched cohort study corroborate an association of loss of a co-twin at birth with risk of psychiatric disorders, supporting the hypothesis of twin-bond development in utero.
    1. Cell Biology
    2. Developmental Biology

    SUMO is a pervasive regulator of meiosis

    Nikhil R Bhagwat et al.
    Multi-dimensional global proteomics describes the SUMO-modified proteome during meiosis and reveals novel roles in regulating the key events of meiotic chromosome metabolism.
    1. Cell Biology

    ATP activation of peritubular cells drives testicular sperm transport

    David Fleck et al.
    Purinergic signaling controls mammalian sperm transport.
    1. Computational and Systems Biology

    Drift and termination of spiral waves in optogenetically modified cardiac tissue at sub-threshold illumination

    Sayedeh Hussaini et al.
    Excitability gradients in heart tissue, imposed by structured sub-threshold optogenetic stimulation, induce drift and termination of spiral waves, thus providing an explanation for successful optogenetic defibrillation in small animal hearts.
    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation

    Pengfei Xu et al.
    Foxc1 proteins prepare the genomes of neural crest-derived cells to facilitate their later development into the cartilages that support the embryonic face.
    1. Neuroscience

    A new model of decision processing in instrumental learning tasks

    Steven Miletić et al.
    A new model is presented to simultaneously study the latent cognitive processes underlying decision making and instrumental learning.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host–pathogen dynamics in lymphoblastoid cell lines

    Elliott D SoRelle et al.
    Single-cell RNA sequencing highlights the influence of host–pathogen interactions and stochasticity on transcriptional and phenotypic variance in lymphoblastoid cell lines derived from Epstein–Barr virus-infected primary B cells.
    1. Ecology
    2. Microbiology and Infectious Disease

    The diversity and function of sourdough starter microbiomes

    Elizabeth A Landis et al.
    In the most comprehensive survey of sourdough starter biodiversity, this work identifies processes that control the diversity and function of sourdough microbiomes at a continental scale.
    1. Neuroscience

    Deleting Mecp2 from the cerebellum rather than its neuronal subtypes causes a delay in motor learning in mice

    Nathan P Achilly et al.
    The loss of Mecp2 results in cerebellar dysfunction that contributes to the motor deficits in Rett syndrome.
    1. Evolutionary Biology
    2. Medicine

    A dietary sterol trade-off determines lifespan responses to dietary restriction in Drosophila melanogaster females

    Brooke Zanco et al.
    Micronutrients, not macronutrients, regulate lifespan.
    1. Physics of Living Systems

    Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments

    Bercem Dutagaci et al.
    Charge complementarity between RNA and proteins may be a universal principle for phase separation in biology without requiring disorder or specific multivalent interactions.
    1. Neuroscience

    Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses

    Willem AM Wybo et al.
    A flexible and accurate methodology to fit reduced compartmental models to dendritic morphologies shows that models with very few compartments can capture many dendritic computations.
    1. Microbiology and Infectious Disease

    A live attenuated-vaccine model confers cross-protective immunity against different species of the Leptospira genus

    Elsio A Wunder et al.
    A single dose of a characterized motility-deficient mutant was sufficient to induce robust anti-protein antibodies' response and cross-protective immunity against death and colonization in two different animal models of leptospirosis.
    1. Ecology
    2. Evolutionary Biology

    Thermal acclimation of tropical coral reef fishes to global heat waves

    Jacob L Johansen et al.
    The ability of animals to adjust to thermal stress is critical for survival under global warming, yet the adjustment process and scope have (until now) remained obscure in marine fishes.
    1. Biochemistry and Chemical Biology

    Curcumin promotes AApoAII amyloidosis and peroxisome proliferation in mice by activating the PPARα signaling pathway

    Jian Dai et al.
    Curcumin regulates gene expression via PPARa activation and exhibits biological activities involved in amyloidosis, peroxisome proliferation, lipid metabolism, and hepatocyte hypertrophy.
    1. Physics of Living Systems

    Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori

    Jyot D Antani et al.
    Asymmetric forward and backward swimming speeds reveal that the rotational bias, and not reversal frequencies, is an appropriate measure of chemotaxis signaling in Helicobacter pylori..
    1. Cancer Biology

    Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer

    Bahman Afsari et al.
    A supervised methodology for mutational signatures outperforms the current standard unsupervised approach revealing new tissue-dependent mutational signatures among which some for obesity.
    1. Developmental Biology
    2. Plant Biology

    Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

    Michael Borg et al.
    Epigenetic reprogramming of the distinct repressive marks H3K27me3 or H3K9me2 guides the transition between the haploid and diploid life forms that encompass the life cycle of land plants.
    1. Cell Biology

    TRIM37 prevents formation of centriolar protein assemblies by regulating Centrobin

    Fernando R Balestra et al.
    TRIM37 prevents the formation of centriolar protein assemblies through an atypical de novo assembly pathway that would otherwise threaten genome integrity.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    A novel motif of Rad51 serves as an interaction hub for recombination auxiliary factors

    Negar Afshar et al.
    Although Rad51 is the central protein involved in recombinational DNA repair, multiple auxiliary factors potentiate its activity by binding to a single, evolutionarily conserved motif.
    1. Genetics and Genomics
    2. Neuroscience

    Roles of the ClC chloride channel CLH-1 in food-associated salt chemotaxis behavior of C. elegans

    Chanhyun Park et al.
    A ClC chloride channel protein allows neurons to interpret both temporal resolution and intensity of sensory input, which thereby contributes to an experience-dependent navigation behavior.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells

    Patrick T Dolan et al.
    Distinct selective landscapes in mosquito and human cells shape dengue virus genetic diversity and highlight mechanisms of host adaptation in arboviruses.
    1. Cell Biology

    Optogenetic control of PRC1 reveals its role in chromosome alignment on the spindle by overlap length-dependent forces

    Mihaela Jagrić et al.
    Optogenetic experiments show that bridging microtubules buffer chromosome movements and promote their alignment through forces transferred to the associated kinetochore fibers, which rely on precise regulation of the overlap region.
    1. Stem Cells and Regenerative Medicine

    Scleraxis-lineage cell depletion improves tendon healing and disrupts adult tendon homeostasis

    Katherine T Best et al.
    Adult Scleraxis-lineage cells are not required for successful tendon healing but are required for maintenance of tendon homeostasis.
    1. Cell Biology

    Cross-compartment signal propagation in the mitotic exit network

    Xiaoxue Zhou et al.
    The mitotic exit network signals from spindle pole bodies to the nucleolus through the dynamic localization of its terminal kinase complex Dbf2-Mob1.
    1. Developmental Biology

    Runx2-Twist1 interaction coordinates cranial neural crest guidance of soft palate myogenesis

    Xia Han et al.
    Identification of heterogenous cranial neural crest (CNC)-derived cell populations and their roles in guiding craniofacial muscle development through cell-cell interactions.
    1. Developmental Biology

    Reciprocal interaction between mesenchymal stem cells and transit amplifying cells regulates tissue homeostasis

    Junjun Jing et al.
    The molecular regulatory mechanisms that control the interaction between mesenchymal stem cells and transit amplifying cells to maintain tissue homeostasis.
    1. Structural Biology and Molecular Biophysics

    Structural basis for transcription complex disruption by the Mfd translocase

    Jin Young Kang et al.
    Seven distinct cryo-electron microscopy structures delineate the elaborate mechanism for how E. coli Mfd, a transcription repair coupling factor, disassembles the RNA polymerase transcription elongation complex to initiate transcription-coupled repair.
    1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics

    Properdin oligomers adopt rigid extended conformations supporting function

    Dennis V Pedersen et al.
    Combining electron microscopy and solution scattering demonstrated that properdin oligomers adopt extended rigid and well-defined conformations that are integral to the biological function of this complement regulator.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Telomeric double-strand DNA-binding proteins DTN-1 and DTN-2 ensure germline immortality in Caenorhabditis elegans

    Io Yamamoto et al.
    The discovery of non-canonical telomeric dsDNA-binding proteins in Caenorhabditis elegans reveal their contribution in the maintenance of telomere length and germline immortality.
    1. Neuroscience

    Activation of MAP3K DLK and LZK in Purkinje cells causes rapid and slow degeneration depending on signaling strength

    Yunbo Li et al.
    The activity levels of two closely related MAPKKK are differentially regulated in Purkinje neuron survival.
    1. Chromosomes and Gene Expression

    The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals

    Lotte Victoria Winther Stagsted et al.
    Transcriptome and eCLIP analyses in mouse and human reveal splicing factor proline/glutamine rich (SFPQ) as a conserved and critical guardian of long-intron integrity, splicing, and circular RNA (circRNA) production.
    1. Biochemistry and Chemical Biology

    Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets

    Kelsie M Rodriguez et al.
    A combined chemical genetics, proximity labeling, and ADP-ribose site mapping approach shows that PARP-7 mono-ADP-ribosylates immune-relevant proteins on cysteine amino acids.
    1. Biochemistry and Chemical Biology
    2. Cancer Biology

    Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells

    Lavanya H Palavalli Parsons et al.
    PARP-7 is a mono(ADP-ribosyl) transferase that directs an extensive ADP-ribosylated proteome to control microtubule stability, and regulate ovarian cancer cell growth and motility.
    1. Neuroscience
    2. Stem Cells and Regenerative Medicine

    Failures of nerve regeneration caused by aging or chronic denervation are rescued by restoring Schwann cell c-Jun

    Laura J Wagstaff et al.
    In vivo experiments on transgenic mice, and cell culture studies, establish Schwann cell c-Jun as a central regulator of peripheral nerve repair, and repair failure, during aging and chronic denervation.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Collateral sensitivity associated with antibiotic resistance plasmids

    Cristina Herencias et al.
    Acquisition of antibiotic resistance plasmids induces collateral sensitivity to clinically relevant antibiotics in Escherichia coli, paving the way for targeted 'anti-plasmid' therapies able to preferentially eliminate plasmid-carrying bacteria.
    1. Developmental Biology
    2. Neuroscience

    Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes

    Maria Schörnig et al.
    Neurons mature slower in humans than in other non-human primates.
    1. Genetics and Genomics
    2. Plant Biology

    The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions

    Thierry Halter et al.
    Active DNA demethylation at some defence gene promoters is causal for DNA binding of WRKY transcription factors as well as for transcriptional activation of these genes during plant immune response.
    1. Stem Cells and Regenerative Medicine

    Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues

    Andrew W DeVilbiss et al.
    A method was developed for the metabolomic analysis of small numbers of flow cytometrically isolated cells from rare cell populations such as hematopoietic stem cells and circulating cancer cells.
    1. Ecology
    2. Microbiology and Infectious Disease

    Freshwater monitoring by nanopore sequencing

    Lara Urban et al.
    From now on, nanopore metagenomics can be used to monitor aquatic environments with high spatiotemporal resolution, by use of a benchmarked, standardised and cost-effective workflow.
    1. Evolutionary Biology

    Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

    Kathryn E Kistler, Trevor Bedford
    Phylogenetic and computational methods reveal that at least two seasonal coronaviruses are evolving adaptively in the region of the viral spike protein exposed to the human humoral immune system.
    1. Neuroscience

    Highly redundant neuropeptide volume co-transmission underlying episodic activation of the GnRH neuron dendron

    Xinhuai Liu et al.
    The arcuate nucleus kisspeptin neurons express multiple transmitters but use only the neuropeptide kisspeptin to drive the episodic secretion of gonadotropin-releasing hormone.
    1. Neuroscience

    Behavioral role of PACAP signaling reflects its selective distribution in glutamatergic and GABAergic neuronal subpopulations

    Limei Zhang et al.
    Placing the PACAP/PAC1 signaling within glutamate/GABA cell type and subregional contexts in mouse brain reveals its conspicuous role for sensorimotor circuit interaction through modulating neuronal plasticity.
    1. Ecology

    Climate-driven deoxygenation elevates fishing vulnerability for the ocean's widest ranging shark

    Marisa Vedor et al.
    Habitats of satellite-tracked blue sharks were shifted surfaceward by an oxygen minimum zone (OMZ) at depth thereby increasing their susceptibility to capture by longline fishing focused above the OMZ.
    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Atomic structures of respiratory complex III2, complex IV, and supercomplex III2-IV from vascular plants

    Maria Maldonado et al.
    The structures of plant CIII2, CIV, and SC III2+IV challenge long-standing assumptions, generate new mechanistic hypotheses and allow for the generation of more selective agricultural inhibitors.
    1. Neuroscience

    fruitless tunes functional flexibility of courtship circuitry during development

    Jie Chen et al.
    The courtship master gene fruitless tunes functional flexibility of courtship circuitry during development instead of switching on its function as conventionally viewed.
    1. Evolutionary Biology

    Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

    Milo S Johnson et al.
    Experimentally evolved yeast populations increase in fitness predictably but do not divide into coexisting lineages or dramatically increase their mutation rates after 10,000 generations.
    1. Neuroscience

    Ablation of STAT3 in Purkinje cells reorganizes cerebellar synaptic plasticity in long-term fear memory network

    Jeong-Kyu Han et al.
    Cerebellar STAT3 is indispensable for proper expression of fear memory network processing.
    1. Cancer Biology
    2. Genetics and Genomics

    Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells

    Iris E Glykofridis et al.
    Knocking out Folliculin (FLCN) in human renal epithelial cells activates STAT1/2-mediated gene expression, independent of interferon, uncovering a tissue-specific process potentially relevant in the cancer syndrome Birt-Hogg-Dubé (BHD).
    1. Computational and Systems Biology
    2. Neuroscience

    Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain

    Xuechun Wang et al.
    A dual-channel image registration pipeline combined with deep-learning inference achieves accurate-and-flexible registration/segmentation/mapping of mouse brain.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci

    Reza K Hammond et al.
    By integrating GWAS data sets with ATAC-seq and promoter-focused Capture C data, one can uncover further loci beyond those that reach genome-wide significance (p<5x10-8).
    1. Developmental Biology

    Endothelial cell-type-specific molecular requirements for angiogenesis drive fenestrated vessel development in the brain

    Sweta Parab et al.
    Identification of a developmental mechanism critical for the generation of brain vessel heterogeneity.
    1. Immunology and Inflammation

    Cytomegalovirus restricts ICOSL expression on antigen-presenting cells disabling T cell co-stimulation and contributing to immune evasion

    Guillem Angulo et al.
    ICOSL-dependent T-cell co-stimulation contributes to the host defense against herpesvirus infections, and accordingly, these pathogens have developed immune evasion mechanisms to interrupt the ICOSL:ICOS signaling pathway.
    1. Microbiology and Infectious Disease

    Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

    Philip P Adams et al.
    Multiple RNA-seq approaches globally mapped RNA 3´ ends resulting in the discovery of numerous and diverse RNA regulators.
    1. Physics of Living Systems
    2. Stem Cells and Regenerative Medicine

    Global and local tension measurements in biomimetic skeletal muscle tissues reveals early mechanical homeostasis

    Arne D Hofemeier et al.
    Combining global and local force measurements of reconstituted muscle tissue using a new chamber system that is compatible with high-resolution microscopy shows mechanical homeostasis already within a week.
    1. Developmental Biology

    Antagonism between germ cell-less and Torso receptor regulates transcriptional quiescence underlying germline/soma distinction

    Megan M Colonnetta et al.
    A molecular duel between germline and somatic determinants ensures proper establishment of transcriptional quiescence in the primordial germ cells of early Drosophila embryos.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Repeated outbreaks drive the evolution of bacteriophage communication

    Hilje M Doekes et al.
    Mathematical modelling suggests that the evolution of communication between bacterial viruses requires repeated outbreak events, and the model then predicts typical communication strategies.
    1. Developmental Biology
    2. Genetics and Genomics

    Female-biased upregulation of insulin pathway activity mediates the sex difference in Drosophila body size plasticity

    Jason W Millington et al.
    The ability to adjust body size in response to diet is greater in Drosophila females than males because of a sex difference in the nutrient-dependent regulation of the insulin pathway.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations

    Marcos H de Moraes et al.
    Interbacterial interactions can promote mutagenesis, and possibly adaptation, when intoxicated cells survive exposure to type VI secretion-delivered DNA deaminase toxins.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Modeling transfer of vaginal microbiota from mother to infant in early life

    Martin Steen Mortensen et al.
    Modeling weighted transfer ratios enable statistical analysis of maternal–infant transfer at a more general level and can indicate whether any transfer is persistent, transient, or originates from alternate sources.
    1. Developmental Biology

    Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

    Shiri Kult et al.
    The molecular identity of bi-fated tendon-to-bone attachment cells, which display a mixture of transcriptomes of two neighboring cell types, enables the formation of the unique transitional tissue of the enthesis.
    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Identification of distinct pH- and zeaxanthin-dependent quenching in LHCSR3 from Chlamydomonas reinhardtii

    Julianne M Troiano et al.
    Light-harvesting complex stress-related is a protein from photosynthetic green algae that prevents damage from sunlight via two distinct conformational processes, which protect against different timescales of solar fluctuations.
    1. Immunology and Inflammation
    2. Medicine

    The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline

    Danielle Janosevic et al.
    Single-cell RNA-sequencing identifies the precise cellular and molecular events that occur along the sepsis timeline in the kidney, pointing to potential biomarkers and therapeutic targets.
    1. Evolutionary Biology

    Evolutionary conflicts and adverse effects of antiviral factors

    Daniel Sauter, Frank Kirchhoff
    Innate antiviral factors do not always perfectly distinguish between self and foreign, and potential adverse effects of antiviral defense mechanisms for the host have been discussed.
    1. Cell Biology
    2. Evolutionary Biology

    A flagellate-to-amoeboid switch in the closest living relatives of animals

    Thibaut Brunet et al.
    The closest living relatives of animals, the choanoflagellates, switch from a flagellate to an amoeboid phenotype under confinement.
    1. Plant Biology

    Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis

    Kurataka Otsuka et al.
    Temperature-dependent fasciation mutants of Arabidopsis unexpectedly connect mitochondrial RNA processing to the control of cell proliferation during lateral root morphogenesis via electron transport chain activity and reactive oxygen species production.
    1. Neuroscience

    Brain functional networks associated with social bonding in monogamous voles

    M Fernanda López-Gutiérrez et al.
    Brain functional connectivity shows a neurobiological predisposition to social bonding, and network-wide changes occur as a result of cohabitation in the prairie vole.
    1. Computational and Systems Biology
    2. Medicine

    Reproducible analysis of disease space via principal components using the novel R package syndRomics

    Abel Torres-Espín et al.
    A tutorial and open-source software to aid in reproducible disease pattern detection using principal component analysis.
    1. Microbiology and Infectious Disease

    A mechanistic model for long-term immunological outcomes in South African HIV-infected children and adults receiving ART

    Eva Liliane Ujeneza et al.
    Long-term immune outcomes vary with age, for both adults and children in HIV-infected populations, e.g. long-term scaled carrying capacity is lower in HIV-infected younger individuals compared to older individuals.
    1. Immunology and Inflammation
    2. Medicine

    Cytokine ranking via mutual information algorithm correlates cytokine profiles with presenting disease severity in patients infected with SARS-CoV-2

    Kelsey E Huntington et al.
    A mutual information algorithm points to macrophage activation syndrome as a specific pathogenic mechanism in COVID-19, correlated with disease severity, which could be used to monitor disease and therapeutics.
    1. Cancer Biology
    2. Genetics and Genomics

    MITF reprograms the extracellular matrix and focal adhesion in melanoma

    Ramile Dilshat et al.
    Analysis of knockout and knockdown melanoma cells and TCGA melanoma data shows that the microphthalmia-associated transcription factor (MITF) is a major repressor of extracellular matrix (ECM) and focal adhesion genes.
    1. Immunology and Inflammation

    Thymic stromal lymphopoietin limits primary and recall CD8+ T-cell anti-viral responses

    Risa Ebina-Shibuya et al.
    Immunological analysis of wild-type and Crlf2-/- mice reveals a role for the cytokine thymic stromal lymphopoietin on memory CD8+ T-cell responses to viral infection, findings with potential translational implications.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    ARL3 activation requires the co-GEF BART and effector-mediated turnover

    Yasmin ElMaghloob et al.
    BART is a co-GEF for ARL3 and maintains the active ARL3-GTP until it is recycled by ARL3 effectors.
    1. Chromosomes and Gene Expression
    2. Neuroscience

    A transcriptomic taxonomy of Drosophila circadian neurons around the clock

    Dingbang Ma et al.
    Drosophila clock neurons manifest remarkable heterogeneity, which might be generally true and help explain why Drosophila has a sophisticated behavioral repertoire despite a tiny brain of about 100,000 neurons.
    1. Cell Biology

    Stable transplantation of human mitochondrial DNA by high-throughput, pressurized isolated mitochondrial delivery

    Alexander J Sercel et al.
    Applied pressure enables efficient isolated mitochondrial transfer and stable mitochondrial DNA (mtDNA) transplantation into a range of mtDNA-depleted cell types to restore respiration.
    1. Neuroscience

    Oxytocin modulates human chemosensory decoding of sex in a dose-dependent manner

    Kepu Chen et al.
    Oxytocin, but not the structurally similar vasopressin, modulates both the chemosensory decoding of femininity in straight men and that of masculinity in gay men in an inverted-U-shaped manner.
    1. Neuroscience

    Release probability increases towards distal dendrites boosting high-frequency signal transfer in the rodent hippocampus

    Thomas P Jensen et al.
    Excitatory synapses that occur further away from the postsynaptic cell soma exhibit greater neurotransmitter release probability, which appears to improve signal transfer fidelity for high-frequency afferent firing.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination

    Adam S Dingens et al.
    HIV vaccine-induced binding and neutralizing antibody epitope specificities were mapped at high resolution directly from polyclonal sera, overcoming shortcomings in traditional serum mapping approaches and enabling highly detailed vaccine design.
    1. Ecology
    2. Evolutionary Biology

    Proteomics reveals synergy between biomass degrading enzymes and inorganic Fenton chemistry in leaf-cutting ant colonies

    Morten Schiøtt, Jacobus J Boomsma
    Leaf-cutting ants use their fecal fluid to vector enzymes produced by their fungal symbiont to degrade plant biomass with a combination of degradation enzymes and Fenton chemistry.
    1. Cell Biology

    Epigenetic regulation of Wnt7b expression by the cis-acting long noncoding RNA Lnc-Rewind in muscle stem cells

    Andrea Cipriano et al.
    The epigenetic regulation of adult muscle stem cell fate by lnc-Rewind relies on the RNA-mediated recruitment of G9a methyltransferase on the Wnt7b genomic locus.
    1. Epidemiology and Global Health

    Model-based spatial-temporal mapping of opisthorchiasis in endemic countries of Southeast Asia

    Ting-Ting Zhao et al.
    High-resolution risk estimates of opisthorchiasis were produced in major endemic countries of Southeast Asia, providing valuable information for guiding disease control and serving as a baseline for future progress assessment.
    1. Immunology and Inflammation

    The clonal structure and dynamics of the human T cell response to an organic chemical hapten

    Tahel Ronel et al.
    Chronic exposure to a potent chemical contact sensitizer drives a self-limiting expansion of a polyclonal population of T cells recognizing a small number of dominant antigens.
    1. Medicine

    The gut microbiota is a transmissible determinant of skeletal maturation

    Abdul Malik Tyagi et al.
    The gut microbiota is a non-genomic, transmissible regulator of bone volume, structure, and turnover.
    1. Neuroscience
    2. Physics of Living Systems

    Random access parallel microscopy

    Mishal Ashraf et al.
    A new imaging modality is described that can simultaneously record from several dishes without using robotics, which enables researchers to perform high-throughput, continuous measurements on biological samples.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation

    E Fabian Cardozo-Ojeda et al.
    Mathematical models reveal the conditions required for long-term HIV remission using autologous transplantation of hematopoietic stem cells.
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Spatial correlations constrain cellular lifespan and pattern formation in corneal epithelium homeostasis

    Lior Strinkovsky et al.
    Rejuvenation of corneal epithelium in homeostasis is determined by the interplay between corneal cells replicative lifespan and the spatial correlation between cell replication and cell removal.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Globally defining the effects of mutations in a picornavirus capsid

    Florian Mattenberger et al.
    Comprehensive analyses of how mutations in a picornavirus capsid affect viral fitness provide novel insights into viral biology, evolution, and host interactions.
    1. Immunology and Inflammation

    Stochastic asymmetric repartition of lytic machinery in dividing CD8+ T cells generates heterogeneous killing behavior

    Fanny Lafouresse et al.
    A fraction of human CD8+ T cells unequally partitions their lytic components during division, producing cells with heterogeneous killing capacities.
    1. Neuroscience

    A rapid whisker-based decision underlying skilled locomotion in mice

    Richard A Warren et al.
    A rapid whisker-based decision underlies skilled locomotion in mice largely independent of cerebral cortex.
    1. Plant Biology

    A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme

    Katharina Eitzen et al.
    A basidiomycete yeast closely related to fungal smuts is an antagonistic microbe in the Arabidopsis leaf phyllosphere that inhibits infection by Albugo laibachii via a GH25 hydrolase with lysozyme activity.
    1. Cancer Biology

    Use of signals of positive and negative selection to distinguish cancer genes and passenger genes

    László Bányai et al.
    In contrast with earlier conclusions, negative selection has a major role in cancer evolution.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Selfing is the safest sex for Caenorhabditis tropicalis

    Luke M Noble et al.
    Out breeding depression in Caenorhabditis tropicalis is due to common maternal-offspring incompatibilities that interact with a highly heterogeneous genetic background and may provide a short-term advantage to inbreeding.
    1. Neuroscience

    Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons

    Qijing Xie et al.
    Single-cell transcriptomes of Drosophila olfactory projection neurons correspond to previously defined cell types, exhibit unique characteristics at different developmental stages, and reveal cell-type-specific gene expression programs in development and function.
    1. Neuroscience

    Microsecond interaural time difference discrimination restored by cochlear implants after neonatal deafness

    Nicole Rosskothen-Kuhl et al.
    Early deaf human CI users are often insensitive to sub-millisecond interaural time differences (ITDs); however, with synchronized CIs, early deafened rats learned to lateralize small ITDs near 50 µs.
    1. Neuroscience

    Lapses in perceptual decisions reflect exploration

    Sashank Pisupati et al.
    During perceptual decision-making, some errors on easy decisions (lapses) are not simply mistakes, but instead reflect strategic decisions to explore actions associated with uncertain rewards.
    1. Cancer Biology

    Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival

    Paul Guilhamon et al.
    Chromatin-based cancer stem cell heterogeneity typifies primary glioblastoma and includes an invasive subtype associated with a lower survival.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies

    Laura E Doepker et al.
    HIV-specific antibodies that mediate antibody-dependent cellular cytotoxicity vary in their paths to achieve function but commonly rely on mutations in multiple regions, including framework regions, to reach full potency.
    1. Genetics and Genomics
    2. Neuroscience

    A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes

    François Kroll et al.
    Zebrafish knockouts can be generated in a few hours directly from wild-type eggs and are suitable for studying continuous traits, including behaviour.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Universal and taxon-specific trends in protein sequences as a function of age

    Jennifer E James et al.
    Ancient protein domains remain shaped by amino acid availability during early life, while young animal proteins are shaped by a need for high intrinsic structural disorder.
    1. Immunology and Inflammation
    2. Medicine

    Methotrexate attenuates vascular inflammation through an adenosine-microRNA-dependent pathway

    Dafeng Yang et al.
    Investigation into methotrexate's effects in the vascular endothelium reveals it exerts anti-inflammatory effects through a unique adenosine-adenosine receptor A3-SMAD3/4-miR-181b signaling axis with implications for controlling vascular inflammation.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A Bayesian analysis of the association between Leukotriene A4 Hydrolase genotype and survival in tuberculous meningitis

    Laura Whitworth et al.
    In this ideal example of pharmacogenomics, individuals with a common variant in a gene encoding for an inflammatory lipid mediator benefit selectively from standard-of-care anti-inflammatory treatment used for tuberculous meningitis.
    1. Cancer Biology

    MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor–1

    Tessa M Popay et al.
    Interaction of oncoprotein transcription factor MYC with chromatin-associated protein host cell factor–1 controls expression of genes important for ribosome biogenesis and mitochondrial vigor, loss of which promotes tumor regression.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Immunocompetent mouse model for Crimean-Congo hemorrhagic fever virus

    David W Hawman et al.
    A mouse-adapted strain of Crimean-Congo hemorrhagic fever virus that recapitulates human disease in wild-type mice significantly improves our ability to study Crimean-Congo hemorrhagic fever virus pathogenesis.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization

    Ilaria Gori et al.
    The mechanism underlying Shprintzen–Goldberg syndrome is solved and reveals that missense mutations in the transcriptional repressor SKI abolish ligand-induced SKI degradation, which results in attenuation of TGF-β transcriptional responses.
    1. Evolutionary Biology

    Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

    Thomas Sakoparnig et al.
    For many bacterial species, recombination dominates genome evolution and phylogenetic patterns that have so far been assumed to reflect clonal relationships, in fact reflect variation in recombination rates across lineages.
    1. Structural Biology and Molecular Biophysics

    ATP and large signaling metabolites flux through caspase-activated Pannexin 1 channels

    Adishesh K Narahari et al.
    Purified Pannexin 1 channels activated by caspase cleavage in proteoliposomes reconstitute a permeation pathway for intercellular signaling molecules important in inflammation and cell clearance.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Diverse viral proteases activate the NLRP1 inflammasome

    Brian V Tsu et al.
    Proteases from diverse viruses, the first described pathogen-encoded activators of human NLRP1, cleave NLRP1 at a sequence that mimics the viral polyprotein, resulting in inflammasome activation and pro-inflammatory cytokine release.
    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins

    Xiaochuan Zhao et al.
    Combining in silico and experimental approaches to identify and understand the residue changes in the H-NS protein that allowed bacteria to adapt environment-sensing to different habitats.
    1. Developmental Biology
    2. Plant Biology

    A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

    Athul Vijayan et al.
    Deep imaging, machine-learning-based segmentation, and tissue annotation resulted in a developmental series of 3D digital ovules with cellular resolution allowing next-level analysis of the ontogenesis of this complex organ.
    1. Developmental Biology

    The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

    Aynur Kaya-Çopur et al.
    Muscle fiber growth during development is controlled by the Hippo pathway that links the assembly state of the contractile sarcomeres with the transcriptional state of the sarcomeric genes.
    1. Microbiology and Infectious Disease

    Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

    Tjorven Hinzke et al.
    Physiological differentiation during symbiosis leads to division of labor between smaller and larger cells in an uncultured bacterial tubeworm symbiont population and results in remarkable metabolic diversity and complexity.
    1. Cancer Biology
    2. Cell Biology

    Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes

    Shima Ghoroghi et al.
    A combination of animal models reveal how the molecular mechanisms of exosome secretion (RalA/B-dependent) are linked to their cargo content and their function in breast cancer pre-metastatic niche formation.
    1. Neuroscience

    Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons

    Julio D Perez et al.
    Single somata and dendrites of individual rat neurons were laser-captured and sequenced to discover and compare the subcellular transcriptomes, identifying over 4000 mRNAs in GABAergic dendrites.
    1. Cancer Biology

    The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma

    Jacob T Polaski et al.
    UPF1 mutations were reportedly present at high frequencies in a cohort of pancreatic adenosquamous carcinoma patients, but these lesions are unlikely to be functional drivers of this cancer subtype.
    1. Stem Cells and Regenerative Medicine

    Pituitary stem cells produce paracrine WNT signals to control the expansion of their descendant progenitor cells

    John P Russell et al.
    Stem cells of the pituitary gland contribute to organ growth cell non-autonomously by promoting proliferation of committed progenitors through WNT ligand secretion.
    1. Chromosomes and Gene Expression

    Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase

    Mark C Johnson et al.
    The S-phase checkpoint has roles in all phases of the cell cycle, which has implications for the majority of cancers that lack cell cycle controls.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Ca2+ signaling driving pacemaker activity in submucosal interstitial cells of Cajal in the murine colon

    Salah A Baker et al.
    An optogenetic dual-color Ca2+-imaging approach shows how submucosal pacemaker-cells, interstitial cells of Cajal, modulate smooth-muscle responses and drive colonic motility via complex Ca2+ signaling.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection

    Anastasia A Minervina et al.
    Longitudinal tracking of individual T-cell clones reveals the expansion of pre-existing T-cell memory in response to SARS-CoV-2 infection.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde

    Iman Hamid et al.
    Admixture-mediated adaptation to malaria in a human population demonstrates that detectible signatures in genomic patterns of ancestry can be leveraged to better characterize recent selection in populations with mixed ancestry.
    1. Developmental Biology

    The vascular niche controls Drosophila hematopoiesis via fibroblast growth factor signaling

    Manon Destalminil-Letourneau et al.
    Two niches contribute to the control of Drosophila blood cell homeostasis through their differential regulation of hematopoietic progenitors.
    1. Physics of Living Systems

    Epithelial colonies in vitro elongate through collective effects

    Jordi Comelles et al.
    Spontaneous elongation of epithelial colonies is related to the orientation of the mean nematic cell elongation field, as shown and tested with experiments and theory.
    1. Microbiology and Infectious Disease

    SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site

    Anna Z Mykytyn et al.
    Whereas SARS-CoV-2 utilizes cathepsins to enter most cell lines, human airway organoids revealed that entry into relevant cells is dependent on serine proteases, which can be targeted for treatment.
    1. Developmental Biology
    2. Neuroscience

    Dentate gyrus development requires a cortical hem-derived astrocytic scaffold

    Alessia Caramello et al.
    An astrocytic scaffold that depends on SOX9 guides embryonic neuronal progenitors toward the developing dentate gyrus.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies

    Manickam Gurusaran, Owen Richard Davies
    The LINC complex has a core 6:6 structure in which KASH-binding induces head-to-head interactions between SUN trimers, suggesting force transduction between cytoskeletal and nuclear components through branched LINC complex networks.
    1. Neuroscience

    A cell atlas of the chick retina based on single-cell transcriptomics

    Masahito Yamagata et al.
    A molecular atlas of the chick retina provides a comprehensive classification and characterization of 136 cell types, yielding novel insights into retinal structure, function, development, and evolution.
    1. Cancer Biology

    Visualization of stem cell activity in pancreatic cancer expansion by direct lineage tracing with live imaging

    Takahisa Maruno et al.
    Genetic lineage tracing approach combined with live imaging visualized the functional stem cell activity of Doublecortin-like kinase 1+ cells within pancreatic cancer in vivo.
    1. Neuroscience

    Human complex exploration strategies are enriched by noradrenaline-modulated heuristics

    Magda Dubois et al.
    Humans supplement complex, resource-demanding strategies with simple heuristics for solving the exploration-exploitation dilemma, and noradrenaline functioning controls their utilisation.
    1. Computational and Systems Biology
    2. Neuroscience

    Reconsidering the evidence for learning in single cells

    Samuel J Gershman et al.
    Single cells are believed to be incapable of complex forms of learning, but reconsideration of historical studies and more recent developments suggest that this orthodoxy must now be reconsidered.
    1. Cell Biology
    2. Stem Cells and Regenerative Medicine

    Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease

    Ana J Caetano et al.
    Single cell transcriptomic analysis provides a reference map for human oral muscosa in health and disease and a framework for the development of new therapeutic strategies.
    1. Cancer Biology
    2. Stem Cells and Regenerative Medicine

    Interplay of opposing fate choices stalls oncogenic growth in murine skin epithelium

    Madeline Sandoval et al.
    Skin epithelium can tolerate oncogene-expressing clones through a novel cellular mechanism of inter-clonal competition between renewing progenitors along the clone's edge and differentiating progenitors within the clone's core.
    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake

    Marc A Schureck et al.
    A high-resolution structure reveals how the RhopH complex traffics within Plasmodium-infected human erythrocytes to serve divergent, essential functions.

Magazine

    1. Cell Biology
    2. Medicine

    Research: A new era for research into aging

    Matt Kaeberlein, Jessica K Tyler
    1. Neuroscience

    Memory: A divalent boost from magnesium

    Willem J Laursen, Paul A Garrity