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Elife

2022 Nov 9

Altınışık NE.

2. Macroscopic control of cell electrophysiology through ion channel expression.

Elife

2022 Nov 9

García-Navarrete M(#), Avdovic M(#), Pérez-Garcia S(#)

3. Attention-deficit hyperactivity disorder symptoms and brain morphology: Examining confounding bias.

Elife

2022 Nov 9

Dall'Aglio L(#), Kim HH(#), Lamballais S(#)

4. Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states.

Elife

2022 Nov 9

Bergen AC(#), Kocik RA(#), Hose J

5. Convergence of two global regulators to coordinate expression of essential virulence determinants of Mycobacterium tuberculosis.

Elife

2022 Nov 9

Khan H, Paul P, Sevalkar RR

6. T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies.

Elife

2022 Nov 9

Pan M, Li B.

Elife

2022 Nov 9

Mediavilla T, Özalay Ö, Estévez-Silva HM

8. Phage resistance profiling identifies new genes required for biogenesis and modification of the corynebacterial cell envelope.

Elife

2022 Nov 9

McKitterick AC, Bernhardt TG.

9. Adapt or perish.

Elife

2022 Nov 8

Williams RBH.

10. Connecting to the long axis.

Elife

2022 Nov 8

Strange BA.

11. Sampling motion trajectories during hippocampal theta sequences.

Elife

2022 Nov 8

Ujfalussy BB, Orbán G.

12. Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila.

Elife

2022 Nov 8

Bosch JA, Ugur B, Pichardo-Casas I

13. Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex.

Elife

2022 Nov 8

McCafferty CL, Papoulas O, Jordan MA

14. Gene interaction perturbation network deciphers a high-resolution taxonomy in colorectal cancer.

Elife

2022 Nov 8

Liu Z, Weng S, Dang Q

15. Glutathione in the nucleus accumbens regulates motivation to exert reward-incentivized effort.

Elife

2022 Nov 8

Zalachoras I(#), Ramos-Fernández E(#), Hollis F

16. Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats.

Elife

2022 Nov 8

Kuchinski KS, Loos KD, Suchan DM

17. Gastrointestinal helminths increase Bordetella bronchiseptica shedding and host variation in supershedding.

Elife

2022 Nov 8

Nguyen NTD(#), Pathak AK(#), Cattadori IM.

18. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice.

Elife

2022 Nov 8

Abdel-Haq R, Schlachetzki JCM, Boktor JC

Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.

19. Alternative splicing downstream of EMT enhances phenotypic plasticity and malignant behavior in colon cancer.

Elife

2022 Nov 8

Xu T, Verhagen M, Joosten R

20. Connexin 43 hemichannels regulate mitochondrial ATP generation, mobilization, and mitochondrial homeostasis against oxidative stress.

Elife

2022 Nov 8

Zhang J, Riquelme MA, Hua R

21. Spatiotemporal properties of glutamate input support direction selectivity in the dendrites of retinal starburst amacrine cells.

Elife

2022 Nov 8

Srivastava P(#), de Rosenroll G(#), Matsumoto A

22. The molecular basis of socially induced egg-size plasticity in honey bees.

Elife

2022 Nov 8

Han B(#), Wei Q(#), Amiri E(#)

23. Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle.

Elife

2022 Nov 8

Suresh P(#), Galstyan V(#), Phillips R

24. The role of adolescent lifestyle habits in biological aging: A prospective twin study.

Elife

2022 Nov 8

Kankaanpää A, Tolvanen A, Heikkinen A

BACKGROUND: Adolescence is a stage of fast growth and development. Exposures during puberty can have long-term effects on health in later life. This study aims to investigate the role of adolescent lifestyle in biological aging. METHODS: The study participants originated from the longitudinal FinnTwin12 study (n = 5114). Adolescent lifestyle-related factors, including body mass index (BMI), leisure-time physical activity, smoking, and alcohol use, were based on self-reports and measured at ages 12, 14, and 17 years. For a subsample, blood-based DNA methylation (DNAm) was used to assess biological aging with six epigenetic aging measures in young adulthood (21-25 years, n = 824). A latent class analysis was conducted to identify patterns of lifestyle behaviors in adolescence, and differences between the subgroups in later biological aging were studied. Genetic and environmental influences on biological aging shared with lifestyle behavior patterns were estimated using quantitative genetic modeling. RESULTS: We identified five subgroups of participants with different adolescent lifestyle behavior patterns. When DNAm GrimAge, DunedinPoAm, and DunedinPACE estimators were used, the class with the unhealthiest lifestyle and the class of participants with high BMI were biologically older than the classes with healthier lifestyle habits. The differences in lifestyle-related factors were maintained into young adulthood. Most of the variation in biological aging shared with adolescent lifestyle was explained by common genetic factors. CONCLUSIONS: These findings suggest that an unhealthy lifestyle during pubertal years is associated with accelerated biological aging in young adulthood. Genetic pleiotropy may largely explain the observed associations. FUNDING: This work was supported by the Academy of Finland (213506, 265240, 263278, 312073 to J.K., 297908 to M.O. and 341750, 346509 to E.S.), EC FP5 GenomEUtwin (J.K.), National Institutes of Health/National Heart, Lung, and Blood Institute (grant HL104125), EC MC ITN Project EPITRAIN (J.K. and M.O.), the University of Helsinki Research Funds (M.O.), Sigrid Juselius Foundation (J.K. and M.O.), Yrjö Jahnsson Foundation (6868), Juho Vainio Foundation (E.S.) and Päivikki and Sakari Sohlberg foundation (E.S.).

25. New insights into anatomical connectivity along the anterior-posterior axis of the human hippocampus using in vivo quantitative fibre tracking.

Elife

2022 Nov 8

Dalton MA, D'Souza A, Lv J

26. An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteria.

Elife

2022 Nov 8

Gupta KR(#), Gwin CM(#), Rahlwes KC

27. LRG1 is an adipokine that promotes insulin sensitivity and suppresses inflammation.

Elife

2022 Nov 8

Choi CHJ, Barr W(#), Zaman S(#)

28. A connectomics-based taxonomy of mammals.

Elife

2022 Nov 7

Suarez LE, Yovel Y, van den Heuvel MP

29. The biospheric emergency calls for scientists to change tactics.

Elife

2022 Nov 7

Racimo F, Valentini E, Rijo De León G

30. Ultrafast simulation of large-scale neocortical microcircuitry with biophysically realistic neurons.

Elife

2022 Nov 7

Oláh VJ, Pedersen NP, Rowan MJM.

31. Sonic hedgehog-dependent recruitment of GABAergic interneurons into the developing visual thalamus.

Elife

2022 Nov 7

Somaiya RD, Stebbins K, Gingrich EC

32. T cell deficiency precipitates antibody evasion and emergence of neurovirulent polyomavirus.

Elife

2022 Nov 7

Lauver MD, Jin G, Ayers KN

33. Contrasting effects of Ksr2, an obesity gene, on trabecular bone volume and bone marrow adiposity.

Elife

2022 Nov 7

Gomez GA, Rundle CH, Xing W

34. Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness.

Elife

2022 Nov 7

Kowalczyk A, Chikina M, Clark N.

35. Super-resolution imaging uncovers the nanoscopic segregation of polarity proteins in epithelia.

Elife

2022 Nov 7

Mangeol P, Massey-Harroche D, Richard F

36. Whole-brain comparison of rodent and human brains using spatial transcriptomics.

Elife

2022 Nov 7

Beauchamp A, Yee Y, Darwin BC

37. DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase ii modulates catalytic function.

Elife

2022 Nov 7

Jeong J, Lee JH, Carcamo CC

38. The interpretation of computational model parameters depends on the context.

Elife

2022 Nov 4

Eckstein MK, Master SL, Xia L

39. Translational rapid ultraviolet-excited sectioning tomography for whole-organ multicolor imaging with real-time molecular staining.

Elife

2022 Nov 4

Yu W, Kang L, Tsang VTC

40. Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans.

Elife

2022 Nov 4

Kim J(#), Jimenez DS(#), Ragipani B

41. High-resolution secretory timeline from vesicle formation at the Golgi to fusion at the plasma membrane in S. cerevisiae.

Elife

2022 Nov 4

Gingras RM, Sulpizio AM, Park J

42. Optimized tight binding between the S1 segment and KCNE3 is required for the constitutively open nature of the KCNQ1-KCNE3 channel complex.

Elife

2022 Nov 4

Kasuya G, Nakajo K.

43. Spinosaurus is not an aquatic dinosaur.

Elife

2022 Nov 30

Sereno PC, Myhrvold N, Henderson DM

44. High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS.

Elife

2022 Nov 30

Wang Z, Mülleder M, Batruch I

45. Presynaptic contact and activity opposingly regulate postsynaptic dendrite outgrowth.

Elife

2022 Nov 30

Heckman EL, Doe CQ.

46. An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.

Elife

2022 Nov 30

Nguyen TT, Voeltz GK.

47. Thymic macrophages consist of two populations with distinct localization and origin.

Elife

2022 Nov 30

Zhou TA, Hsu HP, Tu YH

48. Oscillations support short latency co-firing of neurons during human episodic memory formation.

Elife

2022 Nov 30

Roux F, Parish G, Chelvarajah R

49. Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice.

Elife

2022 Nov 30

Xian F(#), Sondermann JR(#), Gomez Varela D

50. Finding abundance regulators.

Elife

2022 Nov 3

Ozguc O, Vonesch S.

51. Genome-wide base editor screen identifies regulators of protein abundance in yeast.

Elife

2022 Nov 3

Schubert OT, Bloom JS, Sadhu MJ

52. A conserved function of Human DLC3 and Drosophila Cv-c in testis development.

Elife

2022 Nov 3

Sotillos S, von der Decken I(#), Domenech Mercadé I(#)

53. Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement.

Elife

2022 Nov 3

Mitelut C, Zhang Y, Sekino Y

54. Non-coding RNAs in drug and radiation resistance of bone and soft-tissue sarcoma: a systematic review.

Elife

2022 Nov 3

Chen HH, Zhang TN, Zhang FY

BACKGROUND: Sarcomas comprise approximately 1% of all human malignancies; treatment resistance is one of the major reasons for the poor prognosis of sarcomas. Accumulating evidence suggests that non-coding RNAs (ncRNAs), including miRNAs, long ncRNAs, and circular RNAs, are important molecules involved in the crosstalk between resistance to chemotherapy, targeted therapy, and radiotherapy via various pathways. METHODS: We searched the PubMed (MEDLINE) database for articles regarding sarcoma-associated ncRNAs from inception to August 17, 2022. Studies investigating the roles of host-derived miRNAs, long ncRNAs, and circular RNAs in sarcoma were included. Data relating to the roles of ncRNAs in therapeutic regulation and their applicability as biomarkers for predicting the therapeutic response of sarcomas were extracted. Two independent researchers assessed the quality of the studies using the Würzburg Methodological Quality Score (W-MeQS). RESULTS: Observational studies revealed the ectopic expression of ncRNAs in sarcoma patients who had different responses to antitumor treatments. Experimental studies have confirmed crosstalk between cellular pathways pertinent to chemotherapy, targeted therapy, and radiotherapy resistance. Of the included studies, W-MeQS scores ranged from 3 to 10 (average score = 5.42). Of the 12 articles that investigated ncRNAs as biomarkers, none included a validation cohort. Selective reporting of the sensitivity, specificity, and receiver operating curves was common. CONCLUSIONS: Although ncRNAs appear to be good candidates as biomarkers for predicting treatment response and therapeutics for sarcoma, their differential expression across tissues complicates their application. Further research regarding their potential for inhibiting or activating these regulatory molecules to reverse treatment resistance may be useful. FUNDING: This study's literature retrieval was supported financially by the 345 Talent Project of Shengjing Hospital of China Medical University (M0949 to Tao Zhang).

55. Intracranial human recordings reveal association between neural activity and perceived intensity for the pain of others in the insula.

Elife

2022 Nov 3

Soyman E(#), Bruls R(#), Ioumpa K(#)

56. High-resolution imaging of the osteogenic and angiogenic interface at the site of murine cranial bone defect repair via multiphoton microscopy.

Elife

2022 Nov 3

Schilling K(#), Zhai Y(#), Zhou Z

57. Environmental morphing enables informed dispersal of the dandelion diaspore.

Elife

2022 Nov 29

Seale M, Zhdanov O, Soons MB

58. Functional connectivity subtypes associate robustly with ASD diagnosis.

Elife

2022 Nov 29

Urchs SGW, Tam A, Orban P

59. Conservation of oocyte development in germline cysts from Drosophila to mouse.

Elife

2022 Nov 29

Spradling AC, Niu W, Yin Q

60. Systemic racial disparities in funding rates at the National Science Foundation.

Elife

2022 Nov 29

Chen CY, Kahanamoku SS, Tripati A

61. Improving the accuracy of single-trial fMRI response estimates using GLMsingle.

Elife

2022 Nov 29

Prince JS, Charest I, Kurzawski JW

Advances in artificial intelligence have inspired a paradigm shift in human neuroscience, yielding large-scale functional magnetic resonance imaging (fMRI) datasets that provide high-resolution brain responses to thousands of naturalistic visual stimuli. Because such experiments necessarily involve brief stimulus durations and few repetitions of each stimulus, achieving sufficient signal-to-noise ratio can be a major challenge. We address this challenge by introducing GLMsingle, a scalable, user-friendly toolbox available in MATLAB and Python that enables accurate estimation of single-trial fMRI responses (glmsingle.org). Requiring only fMRI time-series data and a design matrix as inputs, GLMsingle integrates three techniques for improving the accuracy of trial-wise general linear model (GLM) beta estimates. First, for each voxel, a custom hemodynamic response function (HRF) is identified from a library of candidate functions. Second, cross-validation is used to derive a set of noise regressors from voxels unrelated to the experiment. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Comparable improvements in reliability are also observed in a smaller-scale auditory dataset from the StudyForrest experiment. These improvements translate into tangible benefits for higher-level analyses relevant to systems and cognitive neuroscience. We demonstrate that GLMsingle: (i) helps decorrelate response estimates between trials nearby in time; (ii) enhances representational similarity between subjects within and across datasets; and (iii) boosts one-versus-many decoding of visual stimuli. GLMsingle is a publicly available tool that can significantly improve the quality of past, present, and future neuroimaging datasets sampling brain activity across many experimental conditions.

62. Coordinated multiplexing of information about separate objects in visual cortex.

Elife

2022 Nov 29

Jun NY, Ruff DA, Kramer LE

63. A motor neuron disease-associated mutation produces non-glycosylated Seipin that induces ER stress and apoptosis by inactivating SERCA2b.

Elife

2022 Nov 29

Saito S, Ishikawa T, Ninagawa S

64. High spatial resolution analysis using automated indentation mapping differentiates biomechanical properties of normal vs. degenerated articular cartilage in mice.

Elife

2022 Nov 29

Masson AO, Besler B, Edwards WB

65. Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis.

Elife

2022 Nov 29

Laruelle E, Belcram K, Trubuil A

66. Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations.

Elife

2022 Nov 29

Huelsz-Prince G, Kok RNU, Goos Y

67. Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals.

Elife

2022 Nov 29

Iyer AA, Hosamani I, Nguyen JD

68. Fixation can change the appearance of phase separation in living cells.

Elife

2022 Nov 29

Irgen-Gioro S(#), Yoshida S(#), Walling V

69. Latent functional diversity may accelerate microbial community responses to temperature fluctuations.

Elife

2022 Nov 29

Smith TP, Mombrikotb S, Ransome E

70. Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks.

Elife

2022 Nov 29

Tang T(#), Zhang N(#), Bongers FJ

71. Dysregulated H19/Igf2 expression disrupts cardiac-placental axis during development of Silver-Russell syndrome-like mouse models.

Elife

2022 Nov 28

Chang S, Fulmer D, Hur SK

72. Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae.

Elife

2022 Nov 28

Miyakoshi M, Morita T, Kobayashi A

73. Cell-intrinsic ceramides determine T cell function during melanoma progression.

Elife

2022 Nov 25

Hose M(#), Günther A(#), Naser E

74. Metrics of high cofluctuation and entropy to describe control of cardiac function in the stellate ganglion.

Elife

2022 Nov 25

Gurel NZ(#), Sudarshan KB(#), Hadaya J

75. Dorsal striatum coding for the timely execution of action sequences.

Elife

2022 Nov 25

Martinez MC, Zold CL, Coletti MA

76. Kin selection spreads.

Elife

2022 Nov 24

Higham JP.

77. Retinopathy of prematurity: Metabolic risk factors.

Elife

2022 Nov 24

Fu Z, Nilsson AK, Hellstrom A

78. Nucleotide-level linkage of transcriptional elongation and polyadenylation.

Elife

2022 Nov 24

Geisberg JV(#), Moqtaderi Z(#), Fong N

79. EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling.

Elife

2022 Nov 24

Randzavola LO(#), Mortimer PM(#), Garside E

80. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes.

Elife

2022 Nov 24

Feng Y, Neme R, Beh LY

Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.

81. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

Elife

2022 Nov 24

Varier RA(#), Sideri T(#), Capitanchik C(#)

82. Dilated cardiomyopathy mutation E525K in human beta-cardiac myosin stabilizes the interacting-heads motif and super-relaxed state of myosin.

Elife

2022 Nov 24

Rasicci DV, Tiwari P, Bodt SML

83. Phenotyping single-cell motility in microfluidic confinement.

Elife

2022 Nov 23

Bentley SA(#), Laeverenz-Schlogelhofer H(#), Anagnostidis V

84. A general approach for stabilizing nanobodies for intracellular expression.

Elife

2022 Nov 23

Dingus JG, Tang JCY, Amamoto R

85. Cortex-wide response mode of VIP-expressing inhibitory neurons by reward and punishment.

Elife

2022 Nov 23

Szadai Z(#), Pi HJ(#), Chevy Q(#)

86. Centrally expressed Cav3.2 T-type calcium channel is critical for the initiation and maintenance of neuropathic pain.

Elife

2022 Nov 23

Fayad SL, Ourties G, Le Gac B

87. The RAM signaling pathway links morphology, thermotolerance, and CO(2) tolerance in the global fungal pathogen Cryptococcus neoformans.

Elife

2022 Nov 23

Chadwick BJ, Pham T, Xie X

88. Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for human bone mineral density GWAS associations.

Elife

2022 Nov 23

Al-Barghouthi BM, Rosenow WT, Du KP

89. Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction.

Elife

2022 Nov 23

Mollentze N, Keen D, Munkhbayar U

90. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein.

Elife

2022 Nov 23

Jara KA, Loening NM, Reardon PN

91. Structure of human phagocyte NADPH oxidase in the resting state.

Elife

2022 Nov 22

Liu R(#), Song K(#), Wu JX

92. The genetic risk of gestational diabetes in South Asian women.

Elife

2022 Nov 22

Lamri A, Limbachia J, Schulze KM

93. Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography.

Elife

2022 Nov 22

Borsatto A, Akkad O, Galdadas I

94. Bundling and segregation affect pheromone deposition, but not choice, in an ant.

Elife

2022 Nov 22

De Agrò M, Matschunas C, Czaczkes TJ.

95. Age acquired skewed X chromosome inactivation is associated with adverse health outcomes in humans.

Elife

2022 Nov 22

Roberts AL, Morea A, Amar A

BACKGROUND: Ageing is a heterogenous process characterised by cellular and molecular hallmarks, including changes to haematopoietic stem cells and is a primary risk factor for chronic diseases. X chromosome inactivation (XCI) randomly transcriptionally silences either the maternal or paternal X in each cell of 46, XX females to balance the gene expression with 46, XY males. Age acquired XCI-skew describes the preferential selection of cells across a tissue resulting in an imbalance of XCI, which is particularly prevalent in blood tissues of ageing females, and yet its clinical consequences are unknown. METHODS: We assayed XCI in 1575 females from the TwinsUK population cohort using DNA extracted from whole blood. We employed prospective, cross-sectional, and intra-twin study designs to characterise the relationship of XCI-skew with molecular and cellular measures of ageing, cardiovascular disease risk, and cancer diagnosis. RESULTS: We demonstrate that XCI-skew is independent of traditional markers of biological ageing and is associated with a haematopoietic bias towards the myeloid lineage. Using an atherosclerotic cardiovascular disease risk score, which captures traditional risk factors, XCI-skew is associated with an increased cardiovascular disease risk both cross-sectionally and within XCI-skew discordant twin pairs. In a prospective 10 year follow-up study, XCI-skew is predictive of future cancer incidence. CONCLUSIONS: Our study demonstrates that age acquired XCI-skew captures changes to the haematopoietic stem cell population and has clinical potential as a unique biomarker of chronic disease risk. FUNDING: KSS acknowledges funding from the Medical Research Council [MR/M004422/1 and MR/R023131/1]. JTB acknowledges funding from the ESRC [ES/N000404/1]. MM acknowledges funding from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation (CDRF), Zoe Global Ltd and the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London.

96. Global hypo-methylation in a proportion of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape.

Elife

2022 Nov 22

Boot J, Rosser G, Kancheva D

97. Whole brain correlates of individual differences in skin conductance responses during discriminative fear conditioning to social cues.

Elife

2022 Nov 22

Vinberg K, Rosén J, Kastrati G

98. Exploratory data on the clinical efficacy of monoclonal antibodies against SARS-CoV-2 Omicron variant of concern.

Elife

2022 Nov 22

Mazzaferri F, Mirandola M, Savoldi A

99. Molecular basis for the role of disulfide-linked αCTs in the activation of insulin-like growth factor 1 receptor and insulin receptor.

Elife

2022 Nov 22

Li J, Wu J, Hall C

100. The elegance of prickly sensations.

Elife

2022 Nov 21

Imambocus BN, Soba P.

101. Evolution and regulation of microbial secondary metabolism.

Elife

2022 Nov 21

Santamaria G(#), Liao C(#), Lindberg C

102. SRSF6 balances mitochondrial-driven innate immune outcomes through alternative splicing of BAX.

Elife

2022 Nov 21

Wagner AR, Weindel CG, West KO

103. SARS-CoV-2-specific CD4(+) and CD8(+) T cell responses can originate from cross-reactive CMV-specific T cells.

Elife

2022 Nov 21

Pothast CR, Dijkland RC, Thaler M

104. Genetic therapy in a mitochondrial disease model suggests a critical role for liver dysfunction in mortality.

Elife

2022 Nov 21

Sabharwal A(#), Wishman MD(#), Cervera RL(#)

105. Collateral deletion of the mitochondrial AAA+ ATPase ATAD1 sensitizes cancer cells to proteasome dysfunction.

Elife

2022 Nov 21

Winter JM, Fresenius HL, Cunningham CN

106. Measurements of damage and repair of binary health attributes in aging mice and humans reveal that robustness and resilience decrease with age, operate over broad timescales, and are affected differently by interventions.

Elife

2022 Nov 21

Farrell S, Kane AE, Bisset E

107. m(6)A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site.

Elife

2022 Nov 21

Parker MT, Soanes BK, Kusakina J

108. Altered basal ganglia output during self-restraint.

Elife

2022 Nov 2

Gu BM, Berke JD.

109. Functional interactions among neurons within single columns of macaque V1.

Elife

2022 Nov 2

Trepka EB(#), Zhu S(#), Xia R

110. Mechanisms governing target search and binding dynamics of hypoxia-inducible factors.

Elife

2022 Nov 2

Chen Y, Cattoglio C, Dailey GM

111. Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex.

Elife

2022 Nov 2

Jeon BB, Fuchs T, Chase SM

112. Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model.

Elife

2022 Nov 2

Chatterjee D, Costa CAM, Wang XF

113. Bringing cells to the edge.

Elife

2022 Nov 2

Wang T, You L.

114. Microglia shape the embryonic development of mammalian respiratory networks.

Elife

2022 Nov 2

Cabirol MJ(#), Cardoit L(#), Courtand G

115. R-spondin 3 deletion induces Erk phosphorylation to enhance Wnt signaling and promote bone formation in the appendicular skeleton.

Elife

2022 Nov 2

Nagano K, Yamana K, Saito H

116. Sugar sensation and mechanosensation in the egg-laying preference shift of Drosophila suzukii.

Elife

2022 Nov 18

Wang W, Dweck HKM, Talross GJS

117. Munc13 supports fusogenicity of non-docked vesicles at synapses with disrupted active zones.

Elife

2022 Nov 18

Tan C, de Nola G, Qiao C

118. Hedgehog regulation of epithelial cell state and morphogenesis in the larynx.

Elife

2022 Nov 18

Ramachandran J, Zhou W, Bardenhagen AE

119. A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo.

Elife

2022 Nov 18

Möller K, Brambach M(#), Villani A(#)

120. Development of visual cortex in human neonates is selectively modified by postnatal experience.

Elife

2022 Nov 18

Li M, Liu T, Xu X

121. Mettl3-mediated m(6)A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration.

Elife

2022 Nov 18

Jiang FQ(#), Liu K(#), Chen JX(#)

122. Discovery of a new class of reversible TEA domain transcription factor inhibitors with a novel binding mode.

Elife

2022 Nov 18

Hu L(#), Sun Y(#), Liu S(#)

123. In sync with the heart.

Elife

2022 Nov 17

Herman AM.

124. Three-dimensional flagella structures from animals' closest unicellular relatives, the Choanoflagellates.

Elife

2022 Nov 17

Pinskey JM, Lagisetty A, Gui L

125. Unleashing a novel function of Endonuclease G in mitochondrial genome instability.

Elife

2022 Nov 17

Dahal S, Siddiqua H, Sharma S

126. Phase separation of competing memories along the human hippocampal theta rhythm.

Elife

2022 Nov 17

Kerrén C, van Bree S, Griffiths BJ

127. Insulin sensitivity is preserved in mice made obese by feeding a high starch diet.

Elife

2022 Nov 17

Brandon AE(#), Small L(#), Nguyen TV

128. Phox2b mutation mediated by Atoh1 expression impaired respiratory rhythm and ventilatory responses to hypoxia and hypercapnia.

Elife

2022 Nov 17

Ferreira CB, Silva TM, Silva PE

129. Reevaluation of Piezo1 as a gut RNA sensor.

Elife

2022 Nov 16

Nickolls AR, O'Brien GS, Shnayder S

130. Binary and analog variation of synapses between cortical pyramidal neurons.

Elife

2022 Nov 16

Dorkenwald S(#), Turner NL(#), Macrina T(#)

131. Genetic architecture of natural variation of cardiac performance from flies to humans.

Elife

2022 Nov 16

Saha S(#), Spinelli L(#), Castro Mondragon JA

132. The CIC-ERF co-deletion underlies fusion-independent activation of ETS family member, ETV1, to drive prostate cancer progression.

Elife

2022 Nov 16

Gupta N, Song H, Wu W

133. Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections.

Elife

2022 Nov 16

Elferich J, Schiroli G, Scadden DT

134. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study.

Elife

2022 Nov 16

Hay JA(#), Kissler SM(#), Fauver JR(#)

BACKGROUND: The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. METHODS: We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of age, variant, symptom status, infection history, vaccination status and antibody titer to the founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics. The frequency of viral rebounds was quantified under multiple cycle threshold (Ct) value-based definitions. RESULTS: Among individuals detected partway through their infection, 51.0% (95% credible interval [CrI]: 48.3-53.6%) remained potentially infectious (Ct <30) 5 days post detection, with small differences across variants and vaccination status. Only seven viral rebounds (0.7%; N=999) were observed, with rebound defined as 3+days with Ct <30 following an initial clearance of 3+days with Ct ≥30. High antibody titers against the founder SARS-CoV-2 strain predicted lower peak viral loads and shorter durations of infection. Among Omicron BA.1 infections, boosted individuals had lower pre-booster antibody titers and longer clearance times than non-boosted individuals. CONCLUSIONS: SARS-CoV-2 viral kinetics are partly determined by immunity and variant but dominated by individual-level variation. Since booster vaccination protects against infection, longer clearance times for BA.1-infected, boosted individuals may reflect a less effective immune response, more common in older individuals, that increases infection risk and reduces viral RNA clearance rate. The shifting landscape of viral kinetics underscores the need for continued monitoring to optimize isolation policies and to contextualize the health impacts of therapeutics and vaccines. FUNDING: Supported in part by CDC contract #200-2016-91779, a sponsored research agreement to Yale University from the National Basketball Association contract #21-003529, and the National Basketball Players Association.

135. How vertebrates got their bite.

Elife

2022 Nov 15

Schilling TF, Le Pabic P.

136. A guide for writing anti-racist tenure and promotion letters.

Elife

2022 Nov 15

A4BL Anti-racist Tenure Letter Working Group.

137. Endocytic trafficking determines cellular tolerance of presynaptic opioid signaling.

Elife

2022 Nov 15

Jullié D, Benitez C, Knight TA

138. Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome.

Elife

2022 Nov 15

Meechan K, Guan W, Riedinger A

139. Patterns of interdivision time correlations reveal hidden cell cycle factors.

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2022 Nov 15

Hughes FA, Barr AR, Thomas P.

140. Promoter sequence and architecture determine expression variability and confer robustness to genetic variants.

Elife

2022 Nov 15

Einarsson H, Salvatore M, Vaagensø C

141. Channel-independent function of UNC-9/Innexin in spatial arrangement of GABAergic synapses in C. elegans.

Elife

2022 Nov 15

Hendi A, Niu LG, Snow AW

142. Cellular mechanisms underlying central sensitization in a mouse model of chronic muscle pain.

Elife

2022 Nov 15

Lin YL, Yang ZS, Wong WY

143. Mandrill mothers associate with infants who look like their own offspring using phenotype matching.

Elife

2022 Nov 15

Charpentier MJE(#), Poirotte C(#), Roura-Torres B

144. Contrasting parental roles shape sex differences in poison frog space use but not navigational performance.

Elife

2022 Nov 15

Pašukonis A, Serrano-Rojas SJ, Fischer MT

145. A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint.

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2022 Nov 15

Leyhr J(#), Waldmann L(#), Filipek-Górniok B

146. Taxonium, a web-based tool for exploring large phylogenetic trees.

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2022 Nov 15

Sanderson T.

147. Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognition.

Elife

2022 Nov 15

Snoeck S, Abramson BW, Garcia AGK

148. Self-configuring feedback loops for sensorimotor control.

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2022 Nov 14

Verduzco-Flores SO, De Schutter E.

149. Sublytic gasdermin-D pores captured in atomistic molecular simulations.

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2022 Nov 14

Schaefer SL, Hummer G.

150. The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers.

Elife

2022 Nov 14

Oravcová M, Nie M, Zilio N

151. Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A.

Elife

2022 Nov 14

Hoel CM(#), Zhang L(#), Brohawn SG.

152. Acetylation of a fungal effector that translocates host PR1 facilitates virulence.

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2022 Nov 14

Li J, Ma X, Wang C

153. Fast rule switching and slow rule updating in a perceptual categorization task.

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2022 Nov 14

Bouchacourt F(#), Tafazoli S(#), Mattar MG

154. High-throughput imaging and quantitative analysis uncovers the nature of plasmid positioning by ParABS.

Elife

2022 Nov 14

Köhler R, Kaganovitch E, Murray SM.

155. Molecular basis of the PIP(2)-dependent regulation of Ca(V)2.2 channel and its modulation by Ca(V) β subunits.

Elife

2022 Nov 14

Park CG, Yu W, Suh BC.

156. Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice.

Elife

2022 Nov 14

Zekri Y, Guyot R, Suñer IG

157. Structural and functional insights of the human peroxisomal ABC transporter ALDP.

Elife

2022 Nov 14

Jia Y(#), Zhang Y(#), Wang W

158. Developing a taxonomy for colorectal cancer.

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2022 Nov 11

Fang J, Wang D, Fan X.

159. Nucleus accumbens dopamine tracks aversive stimulus duration and prediction but not value or prediction error.

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2022 Nov 11

Goedhoop JN, van den Boom BJG(#), Robke R(#)

160. Robotic multi-probe single-actuator inchworm neural microdrive.

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2022 Nov 10

Smith RD, Kolb I, Tanaka S

161. Endosymbiotic selective pressure at the origin of eukaryotic cell biology.

Elife

2022 Nov 10

Raval PK, Garg SG, Gould SB.

162. Mcm2 promotes stem cell differentiation via its ability to bind H3-H4.

Elife

2022 Nov 10

Xu X(#), Hua X(#), Brown K

163. SRSF10 is essential for progenitor spermatogonia expansion by regulating alternative splicing.

Elife

2022 Nov 10

Liu W(#), Lu X(#), Zhao ZH(#)

164. An automated feeding system for the African killifish reveals the impact of diet on lifespan and allows scalable assessment of associative learning.

Elife

2022 Nov 10

McKay A(#), Costa EK(#), Chen J(#)

165. Environmental DNA from archived leaves reveals widespread temporal turnover and biotic homogenization in forest arthropod communities.

Elife

2022 Nov 10

Krehenwinkel H(#), Weber S(#), Broekmann R

166. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution.

Elife

2022 Nov 10

Castro IG(#), Shortill SP(#), Dziurdzik SK(#)

167. A low-cost, open-source evolutionary bioreactor and its educational use.

Elife

2022 Nov 1

Gopalakrishnan V(#), Crozier D(#), Card KJ(#)

168. Collective dynamics support group drumming, reduce variability, and stabilize tempo drift.

Elife

2022 Nov 1

Dotov D, Delasanta L, Cameron DJ

169. Rapid encoding of task regularities in the human hippocampus guides sensorimotor timing.

Elife

2022 Nov 1

Polti I(#), Nau M(#), Kaplan R

170. Regulated degradation of the inner nuclear membrane protein SUN2 maintains nuclear envelope architecture and function.

Elife

2022 Nov 1

Krshnan L, Siu WS, Van de Weijer M

171. Kiaa1024L/Minar2 is essential for hearing by regulating cholesterol distribution in hair bundles.

Elife

2022 Nov 1

Gao G, Guo S, Zhang Q

172. Microplankton life histories revealed by holographic microscopy and deep learning.

Elife

2022 Nov 1

Bachimanchi H, Midtvedt B, Midtvedt D

173. Instructions and experiential learning have similar impacts on pain and pain-related brain responses but produce dissociations in value-based reversal learning.

Elife

2022 Nov 1

Atlas LY, Dildine TC, Palacios-Barrios EE

Recent data suggest that interactions between systems involved in higher order knowledge and associative learning drive responses during value-based learning. However, it is unknown how these systems impact subjective responses, such as pain. We tested how instructions and reversal learning influence pain and pain-evoked brain activation. Healthy volunteers (n=40) were either instructed about contingencies between cues and aversive outcomes or learned through experience in a paradigm where contingencies reversed three times. We measured predictive cue effects on pain and heat-evoked brain responses using functional magnetic resonance imaging. Predictive cues dynamically modulated pain perception as contingencies changed, regardless of whether participants received contingency instructions. Heat-evoked responses in the insula, anterior cingulate, and other regions updated as contingencies changed, and responses in the prefrontal cortex mediated dynamic cue effects on pain, whereas responses in the brainstem's rostroventral medulla (RVM) were shaped by initial contingencies throughout the task. Quantitative modeling revealed that expected value was shaped purely by instructions in the Instructed Group, whereas expected value updated dynamically in the Uninstructed Group as a function of error-based learning. These differences were accompanied by dissociations in the neural correlates of value-based learning in the rostral anterior cingulate, thalamus, and posterior insula, among other regions. These results show how predictions dynamically impact subjective pain. Moreover, imaging data delineate three types of networks involved in pain generation and value-based learning: those that respond to initial contingencies, those that update dynamically during feedback-driven learning as contingencies change, and those that are sensitive to instruction. Together, these findings provide multiple points of entry for therapies designs to impact pain.

174. Molecular and anatomical characterization of parabrachial neurons and their axonal projections.

Elife

2022 Nov 1

Pauli JL(#), Chen JY(#), Basiri ML(#)

175. Suppressed prefrontal neuronal firing variability and impaired social representation in IRSp53-mutant mice.

Elife

2022 Nov 1

Kim W, Shin JJ, Jeong YJ

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Newmer生物