bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurable fields-to-spike causality and its dependence on cortical layer and area
Authors: Akella Shailaja , Bastos André M. , Miller Earl K. , Principe Jose C.
Published: January 2023

Distinct dynamics in different cortical layers are apparent in neuronal and local field potential (LFP) patterns, yet their associations in the context of laminar processing have been sparingly analyzed. Here, we study the laminar organization of spike-field causal flow within and across visual (V4) and frontal areas (PFC) of monkeys performing a visual task. Using an event-based quantification of LFPs and a directed information estimator, we found area and frequency specificity in the laminar organization of spike-field causal connectivity. Gamma bursts (40-80 Hz) in the superficial layers of V4 largely drove intralaminar spiking. These gamma influences also fed forward up the cortical hierarchy to modulate laminar spiking in PFC. In PFC, the direction of intralaminar information flow was from spikes → fields where these influences dually controlled top-down and bottom-up processing. Our results, enabled by innovative methodologies, emphasize the complexities of spike-field causal interactions amongst multiple brain areas and behavior.
Energetics of the Microsporidian Polar Tube Invasion Machinery
Authors: Chang Ray , Davydov Ari , Jaroenlak Pattana , Budaitis Breane , Ekiert Damian C. , Bhabha Gira , Prakash Manu
Published: January 2023

Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an unusual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive.Anncaliia algeraemicrosporidia spores (3-4µm in size) shoot out a 100-nm-wide PT at a speed of 300µm/sec, creating a shear rate of 3000 sec−1. The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ∼60-140µm (Jaroenlak et al., 2020) and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots ofA. algeraespores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT ring experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.

Statement of Signicance

Microsporidia are a group of spore-forming, intracellular parasites that infect a wide range of hosts (including humans). Once triggered, microsporidian spores (3-4µm in size) shoot out a specialized organelle called the polar tube (PT) (60-140µm long, 100 nm wide) at ultrafast speed (300µm/sec), penetrating host cells and acting as a conduit for the transport of infectious cargo. Although this process has fascinated biologists for a century, the biophysical mechanisms underlying PT extrusion are not understood. We thus take a data-driven approach to generate models for the physical basis of PT ring and cargo transport through the PT. Our approach here demonstrates the extreme limits of cellular hydraulics and the potential applications of biophysical approaches to other cellular architectures.
Discovery of highly potent small molecule pan-coronavirus fusion inhibitors
Authors: Curreli Francesca , Chau Kent , Tran Thanh-Thuy , Nicolau Isabella , Ahmed Shahad , Das Pujita , Hillyer Christopher D. , Premenko-Lanier Mary , Debnath Asim K.
Published: January 2023

The unprecedented pandemic of COVID-19, caused by a novel coronavirus, SARS-CoV-2, has led to massive human suffering, death, and economic devastation worldwide. The virus is mutating fast to more transmissible and infectious variants. The Delta variant (B.1.617.2), initially identified in India, and the omicron variant (BA.4 and BA.5) have spread worldwide. In addition, recently alarming antibody evasive SARS-CoV-2 subvariants, BQ and XBB, have been reported. These new variants may pose a substantial challenge to controlling the spread of this virus. Therefore, the continued development of novel drugs having pan-coronavirus inhibition to treat and prevent infection of COVID-19 is urgently needed. These drugs will be critically important in dealing with new pandemics that will emerge in the future. We report the discovery of several highly potent small molecule pan-coronavirus inhibitors. One of which, NBCoV63, showed low nM potency against SARS-CoV-2 (IC50: 55 nM), SARS-CoV (IC50: 59 nM), and MERS-CoV (IC50: 75 nM) in pseudovirus-based assays with excellent selectivity indices (SI: as high as > 900) demonstrating its pan-coronavirus inhibition. NBCoV63 showed equally effective antiviral potency against SARS-CoV-2 mutant (D614G) and several variants of concerns (VOCs) such as B.1.617.2 (Delta), B.1.1.529/BA.1 and BA.4/BA.5 (Omicron) and K417T/E484K/N501Y (Gamma). NBCoV63 also showed similar efficacy profiles to Remdesivir against authentic SARS-CoV-2 (Hong Kong strain) and two of its variants (Delta and Omicron) by plaque reduction in Calu3 cells. Additionally, we show that NBCoV63 inhibits virus-mediated cell-to-cell fusion in a dose-dependent manner. Furthermore, the Absorption, distribution, metabolism, and excretion (ADME) data of NBCoV63 demonstrated drug-like properties.
The STEMRI trial: magnetic resonance spectroscopy imaging can define tumor areas enriched in glioblastoma-initiating cells
Authors: Lemarié Anthony , Lubrano Vincent , Delmas Caroline , Lusque Amélie , Cerapio Juan-Pablo , Perrier Marion , Siegfried Aurore , Arnauduc Florent , Nicaise Yvan , Dahan Perrine , Filleron Thomas , Mounier Muriel , Toulas Christine , Moyal Elizabeth Cohen-Jonathan
Published: January 2023

BACKGROUND

Glioblastoma (GB) gold standard treatment combines maximally-safe surgical resection of the contrast-enhanced (CE) central tumor area, as defined by MRI, and chemo-radiotherapy. However, most patients relapse within one year in non-CE peritumoral FLAIR regions. Spectroscopy MRI (MRSI) can discriminate metabolic tumor areas with higher recurrence potential. We showed that regions with Choline/N-acetyl-aspartate index >2 (CNI+) were predictive of relapse sites post-radiotherapy in CE and FLAIR areas. As relapses are mainly imputed to a subpopulation of aggressive and resistant tumor stem-like cells, called GB-initiating cells (GIC), this suggests that CNI+ areas might be enriched in GIC.

METHODS

We conducted a prospective trial in 16 eligible GB patients subjected to preoperative MRSI/MRI and subsequent surgery/chemo-radiotherapy to investigate GIC enrichment of CNI+ versus CNI− areas, based on biopsies in CE and FLAIR. We combined in vitro/vivo biological characterization of biopsies and derived GIC lines with biopsy RNAseq analyses.

RESULTS

Biopsy characterization by FACS and RNAseq revealed that FLAIR/CNI+ areas showed an enrichment in GIC-population and in stem-related gene signature, but also in pathways related to DNA repair, adhesion/migration and mitochondrial bioenergetics. More, FLAIR/CNI+ samples gave rise to GIC-enriched neurospheres faster than CNI− counterparts. Finally, parameters assessing Biopsy GIC Content and Time to Neurosphere formation in FLAIR/CNI+ areas were associated with worse patient outcome.

CONCLUSION

Preoperative MRI/MRSI combination would certainly allow better resection and targeting of CNI+ areas in FLAIR, as their GIC-enrichment can predict worse outcome in GB patients.

TRIAL REGISTRATION

ClinicalTrials.govNCT01872221.

FUNDING

RITC (RECF1929), GRICR and Plan Cancer 2016 (HTE).
Tailoring Human Sleep: selective alteration through Brainstem Arousal Circuit Stimulation
Authors: Deli Alceste , He Shenghong , Duchet Benoit , Huang Yongzhi , Martin Sean , Sanrangmat Nagaraja , Denison Timothy , Tan Huiling , Vyazovskiy Vladyslav V. , Green Alexander
Published: January 2023

Brainstem nuclei, such as the pedunculopontine nucleus, send activating projections to cortex, modulating states of sleep, wakefulness and arousal levels. Surgical modulation of subcortical activity using deep brain stimulation (DBS) is utilised in the management of pain and movement disorders. DBS of brainstem arousal circuits in a state-dependent manner could offer an attractive alternative in severe pharmacoresistant cases of hypersomnia and in disorders of consciousness, where behavioural activation is desired.

We wanted to investigate if we can selectively induce wakefulness and/or alter sleep state through DBS of the PPN region (PPNR). To this end, we used the opportunity of implanted PPNR electrodes in stimulation-naïve patients with multiple systems atrophy. PPNR activity was recorded during both slow wave sleep (SWS) and quiet wakefulness with simultaneous cortical EEG, in order to identify differences in brainstem oscillatory patterns during different states of excitability. PPNR DBS in two gamma frequency protocols (40Hz and 100Hz) was delivered during SWS of the same sleep stage and with comparable pre-trial levels of slow wave activity.

Additionally, SHAM trials were used as a control where no stimulation was applied. We examined changes in cortical oscillatory power, changes in functional connectivity (coherence and causality) from pre- to post-stimulation and phase-locking of cortical oscillations with DBS frequencies and their sub-harmonics during stimulation. We also evaluated connectivity changes induced by DBS and corresponding differences in circuit dynamics between SWS and wakefulness.

Beta and gamma PPNR oscillatory power increased when wake was compared to sleep. We saw clear PPNR power modulation by the phase of EEG slow wave, with significant increase in gamma compared to beta power during the ‘excitable’ part of the slow-wave cycle. Gamma PPNR DBS induced transitions to wakefulness and REM, while it truncated sleep time compared to baseline. The 40Hz stimulation protocol was more efficient in reducing slow wave activity and increasing cortical beta power, compared to PPNR DBS at 100Hz. Furthermore, intrinsic cortical rhythms phase-locked with 40 Hz PPNR DBS to a significantly higher degree compared to the 100Hz protocol, with regional differences in phase-locking, suggesting a complex biological phenomenon. Finally, functional connectivity changes induced by PPNR DBS were consistent with differences in circuit dynamics between SWS and wakefulness. Overall, these results highlight the possibility of using DBS of brainstem arousal circuits to promote arousal and wakefulness, which opens new perspectives for using closed-loop approaches to modulate vigilance states in humans for therapeutic benefit.
An Exploratory Systematic Review and Meta-analysis on Period Poverty
Authors: Delanerolle Gayathri , Yang Xiaojie , Cavalini Heitor , Kurmi Om , Rostivik Camilla , Shetty Ashish , Saraswat Lucky , Taylor Julie , Sajid Sana , Rathod Shanaya , Shi Jian Qing , Phiri Peter
Published: January 2023

Background

Period povertyis a global health and social issue that needs to be addressed. The primary aim of this study was to provide a comprehensive understanding on period poverty, including outcomes associated menstruation.

Methods

All observational and randomised clinical trials reporting menstruation challenges, menstrual poverty and menstrual products were included. Our search strategy included multiple electronic databases of PubMed, Web of Science, ScienceDirect, ProQuest and EMBASE. Studies published in a peer review journal in English between the 30thof April 1980 and the 30thof April 2022 were included. The Newcastle-Ottawa Scale (NOS) was used to assess the risk of bias (RoB) of the systematic included studies. Pooled odds ratios (ORs) together with 95% confidence intervals (CIs) are reported overall and for sub-groups.

Results

A total of 80 studies were systematically selected, where 38 were included in the meta-analysis. Of the 38 studies, 28 focused on children and young girls (i.e., 10-24 years old) and 10 included participants with a wider age range of 15-49 years. The prevalence of using disposable sanitary pads was 45% (95% CI = [0.35,0.58]). The prevalence of menstrual education pre-menarche was 68% (95% CI = [0.56, 0.82]). The prevalence of good MHM was 39% (95% CI = [0.25, 0.61]). Women in rural area (OR = 0.30, 95% CI = [0.13, 0.69]) were 0.70 times less likely to have good MHM practices than those living in urban area.

Discussion

There was a lack of evidence, especially from low- and middle-income countries. Further research to better understand the scope and prevalence of period poverty should be considered. This will enable the development of improved policies to increase access to menstrual products and medical support where necessary.

Funding

Not Applicable

Registration

A systematic methodology was developed and published (CRD42022339536).
A systematic review and meta-analysis of the diagnostic accuracy of endometrial sampling tests for detecting endometrial cancer
Authors: Sakna Noha , Elgendi Marwa , Salama Mohamed , Zeinhom Ahmed , Labib Somia , Nabhan Ashraf
Published: January 2023

Objectives

to determine the diagnostic accuracy of different endometrial sampling tests for detecting endometrial carcinoma.

Design

a systematic review and meta-analysis of studies of diagnostic accuracy.

Eligibility criteria

We included published diagnostic test accuracy studies of women, of all ages, who had an endometrial sampling for preoperatively detecting endometrial cancer with verification using histopathology of hysterectomy specimens as the reference standard. We excluded case control and case series studies.

Information sources

We searched the Cochrane library, MEDLINE/PubMed, CINAHL, Web of Science, and Scopus from the date of inception of the databases to January 18, 2023. We did not apply any restrictions on language or date of publication. We searched the references of included studies and other systematic reviews.

Risk of bias

We extracted study data and assessed study quality using the revised quality assessment tool for diagnostic accuracy studies (QUADAS-2).

Synthesis of results

We used bivariate diagnostic random-effects meta-analysis and presented the results in a summary receiver operating characteristic curve. We assessed the certainty of evidence as recommended by the GRADE approach.

Results

Twelve included studies, published between 1986 and 2022, recruited 1607 participants. Seven studies were low risk of bias in all domains and all studies had low applicability concerns. The most examined index tests were Pipelle and conventional dilation and curettage. For diagnosing endometrial carcinoma, the sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio (95% confidence intervals), for Pipelle were 0.774 (0.565, 0.900), 0.985 (0.927, 0.997), 97.000 (14.000, 349.000), and 0.241 (0.101, 0.442)and for conventional dilation and curettage were 0.773 (0.333, 0.959), 0.987 (0.967, 0.995), 62.300 (18.600, 148.000), and 0.268 (0.042, 0.676); respectively.

Conclusion

High certainty evidence indicates that pre-operative endometrial sampling particularly using Pipelle or conventional curettage is accurate in diagnosing endometrial cancer. Studies assessing other endometrial sampling tests were sparse.

Systematic review registration

Center for Open Science, osf.io/h8e9z
p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs
Authors: Grit Jamie L. , McGee Lauren E. , Tovar Elizabeth A. , Essenburg Curt J. , Wolfrum Emily , Beddows Ian , Williams Kaitlin , Sheridan Rachael , Schipper Josh , Adams Marie , Arumugam Menusha , Woude Thomas Vander , Gurunathan Sharavana , Field Jeffrey M. , Wulfkuhle Julia , Petricoin Emanuel F. , Graveel Carrie R. , Steensma Matthew R.
Published: January 2023

Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity.TP53mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlyingTP53-mediated therapy responses are unclear in the context ofNF1-deficiency. We evaluated the role of two commonly altered genes,METandTP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed thatMETamplification occurs early in human MPNST progression and thatTrp53loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity.Trp53loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes inTrp53-deficient lines suggestingTrp53loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.
Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes
Authors: Jimmy John Lilly , Karn Rohit , Kumari Sweta , Sruthilaxmi Chitathoor Balasubramane , Pooja Singh , Babu Subramanian
Published: January 2023

In plants, pathogen resistance is brought about due to the binding of certain transcription factors (TF) proteins to the cis-elements of certain target genes. These cis-elements are present up-stream in the motif of the promoters of each gene. This ensures the binding of a specific transcription factor to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific transcription factor. Rice 1kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using gene ontology and gene set enrichment analysis. Gene with more than 4 TFbm in their promoter was selected. Nine genes reported to have a role in rice disease resistance were selected for further analysis.Cis-acting regulatory element analysis was carried out to find the cis-elements and to confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding nine genes were built and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies.WRKY13 was also considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped to provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected diseases resistance-related genes with WRKY13 TF protein. This study suggests the target downstream genes that are regulated by WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
Morphology as indicator of adaptive changes of model tissues in osmotically and chemically changing environments
Authors: Höllring Kevin , Vurnek Damir , Gehrer Simone , Dudziak Diana , Hubert Maxime , Smith Ana-Sunčana
Published: January 2023

We investigate the formation and maintenance of the homeostatic state in the case of 2D epithelial tissues following an induction of hyperosmotic conditions, using media enriched with 80 to 320 mOsm of mannitol, NaCl, and urea. We characterise the changes in the tissue immediately after the osmotic shock, and follow it until the new homeostatic state is formed. We characterise changes in cooperative motility and proliferation pressure in the tissue upon treatment with the help of a theoretical model based on the delayed Fisher-Kolmogorov formalism, where the delay in density evolution is induced by the the finite time of the cell division. Finally we explore the adaptation of the homeostatic tissue to highly elevated osmotic conditions by evaluating the morphology and topology of cells after 20 days in incubation. We find that hyperosmotic environments together with changes in the extracellular matrix induce different mechanical states in viable tissues, where only some remain functional. The perspective is a relation between tissue topology and function, which could be explored beyond the scope of this manuscript.

Experimental investigation of morphological effect of change of osmotic conditions on long-term tissue morphology and topology

Effect of osmotic changes on transient tissue growth behaviour

Analysis of recovery process of tissues post-osmotic-shock

Toxicity limits of osmolytes in mid- to long-term tissue evolution

Tissue adaptation to physiological changes in environment

Long-term tissue stabilisation under altered osmotic conditions.

Abstract Figure
Glycoproteome remodelling and granule-specificN-glycosylation accompany neutrophil granulopoiesis
Authors: Kawahara Rebeca , Ugonotti Julian , Chatterjee Sayantani , Tjondro Harry C. , Loke Ian , Parker Benjamin L. , Venkatakrishnan Vignesh , Dieckmann Regis , Sumer-Bayraktar Zeynep , Karlsson-Bengtsson Anna , Bylund Johan , Thaysen-Andersen Morten
Published: January 2023

Neutrophils store microbicidal glycoproteins in cytosolic granules to fight intruding pathogens, but their granule distribution and formation mechanism(s) during granulopoiesis remain unmapped. Herein, we perform comprehensive spatiotemporalN-glycoproteome profiling of isolated granule populations from blood-derived neutrophils and during their maturation from bone marrow-derived progenitors using glycomics-assisted glycoproteomics. Interestingly, the granules of resting neutrophils exhibited distinctive glycophenotypes including, most strikingly, peculiar highly truncatedN-glycosylation in the azurophilic granules. Excitingly, proteomics and transcriptomics data from discrete myeloid progenitor stages revealed that profound glycoproteome remodelling underpins the promyelocytic-to-metamyelocyte transition and that remodelling is driven primarily by changes in protein expression and less by the glycosylation machinery. Notable exceptions were the oligosaccharyltransferase subunits responsible for initiation ofN-glycoprotein biosynthesis that were strongly expressed in early myeloid progenitors correlating with high glycosylation efficiencies of the azurophilic granule proteins. Our study provides spatiotemporal insights into the complex neutrophilN-glycoproteome featuring an intriguing granule-specificN-glycosylation formed by dynamic remodelling during myeloid progenitor-to-neutrophil maturation.

Key points

Systems glycobiology reveals that profoundN-glycoproteome remodelling accompanies early neutrophil granulopoiesis

Precision glycoproteomics produces detailed cartography of neutrophils that exhibit site-, protein- and granule-specific N-glycosylation
Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression ofRUVBL1and prostate cancer progression
Authors: Tian Yijun , Dong Dandan , Wang Zixian , Wu Lang , Park Jong Y , Wei Gong-Hong , Wang Liang ,   PRACTICAL/ELLIPSE consortium
Published: January 2023

Genome-wide association studies along with expression quantitative trait loci (eQTL) mapping have identified hundreds of single nucleotide polymorphisms (SNPs) and their target genes in prostate cancer (PCa), yet functional characterization of these risk loci remains challenging. To screen for potential regulatory SNPs, we designed a CRISPRi library containing 9133 guide RNAs (gRNAs) to target 2,166 candidate SNP sites implicated in PCa and identified 117 SNPs that could regulate 90 genes for PCa cell growth advantage. Among these, rs60464856 was covered by multiple gRNAs significantly depleted in the screening (FDR<0.05). Pooled SNP association analysis in the PRACTICAL and FinnGen cohorts showed significantly higher PCa risk for the rs60464856 G allele (pvalue=1.2E-16 and 3.2E-7). Subsequent eQTL analysis revealed that the G allele is associated with increasedRUVBL1expression in multiple datasets. Further CRISPRi and xCas9 base editing proved the rs60464856 G allele leading to an elevatedRUVBL1expression. Furthermore, SILAC-based proteomic analysis demonstrated allelic binding of cohesin subunits at the rs60464856 region, where HiC dataset showed consistent chromatin interactions in prostate cell lines.RUVBL1depletion inhibited PCa cell proliferation and tumor growth in xenograft mouse model. Gene set enrichment analysis suggested an association ofRUVBL1expression with cell-cycle-related pathways. An increased expression ofRUVBL1and activations of cell-cycle pathways were correlated with poor PCa survival in TCGA datasets. Together, our CRISPRi screening prioritized about one hundred regulatory SNPs essential for prostate cell proliferation. In combination with proteomics and functional studies, we characterized the mechanistic role of rs60464856 andRUVBL1in PCa progression.
Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming
Authors: Pawar Samraat , Huxley Paul J. , Smallwood Thomas R. C. , Nesbit Miles L. , Chan Alex H. H. , Shocket Marta S. , Johnson Leah R. , Kontopoulos Dimitrios - Georgios , Cator Lauren
Published: January 2023

The capacity of arthropod populations to adapt to long-term climatic warming is uncertain. Here, we combine theory and extensive data on diverse arthropod taxa to show that their rate of thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation is predicted to be limited by the rate of shift in the temperature of peak performance of four life-history traits in a specific order: juvenile development, adult fecundity, juvenile mortality, and adult mortality. Second, thermal adaptation will be constrained due to differences in the temperature of peak performance among these four traits, which are expected to persist because of trade-offs. By compiling a new global dataset of 61 diverse arthropod species, we find strong evidence that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to climatic warming.
Amplitude modulation pattern of rat distress vocalisations during fear conditioning
Authors: Gonzalez-Palomares Eugenia , Boulanger-Bertolus Julie , Dupin Maryne , Mouly Anne-Marie , Hechavarria Julio C.
Published: January 2023

In humans, screams have strong amplitude modulations (AM) at 30 to 150 Hz. These AM correspond to the acoustic correlate of perceptual roughness. In bats, distress calls can carry AMs, which elicit heart rate increases in playback experiments. Whether amplitude modulation occurs in fearful vocalisations of other animal species beyond humans and bats remains unknown. Here we analysed the AM pattern of rats’ 22-kHz ultrasonic vocalisations emitted in a fear conditioning task. We found that the number of vocalisations decreases during the presentation of conditioned stimuli. We also observed that AMs do occur in rat 22-kHz vocalisations. AMs are stronger during the presentation of conditioned stimuli, and during escape behaviour compared to freezing. Our results suggest that the presence of AMs in vocalisations emitted could reflect the animal’s internal state of fear related to avoidance behaviour.
A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence
Authors: Kumar Nishant , Tripathi Sadhana , Sharma Neelam , Patiyal Sumeet , Devi Naorem Leimarembi , Raghava Gajendra P. S.
Published: January 2023

B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitopes in an antigen. In this study, a single method was developed for predicting both types (linear/conformational) of B-cell epitopes. The dataset used in this study contains 3875 B-cell epitopes and 3996 non-B-cell epitopes, where B-cell epitopes consist of both linear and conformational B-cell epitopes. Our primary analysis indicates that certain residues (like Asp, Glu, Lys, Asn) are more prominent in B-cell epitopes. We developed machine-learning based methods using different types of sequence composition and achieved the highest AUC of 0.80 using dipeptide composition. In addition, models were developed on selected features, but no further improvement was observed. Our similarity-based method implemented using BLAST shows a high probability of correct prediction with poor sensitivity. Finally, we came up with a hybrid model that combine alignment free (dipeptide based random forest model) and alignment-based (BLAST based similarity) model. Our hybrid model attained maximum AUC 0.83 with MCC 0.49 on the independent dataset. Our hybrid model performs better than existing methods on an independent dataset used in this study. All models trained and tested on 80% data using cross-validation technique and final model was evaluated on 20% data called independent or validation dataset. A webserver and standalone package named “CLBTope” has been developed for predicting, designing, and scanning B-cell epitopes in an antigen sequence (https://webs.iiitd.edu.in/raghava/clbtope/).
Catenin signaling controls phrenic motor neuron development and function during a narrow temporal window
Authors: Vagnozzi Alicia N. , Moore Matthew T. , de Boer Raquel López , Agarwal Aambar , Zampieri Niccolò , Landmesser Lynn T. , Philippidou Polyxeni
Published: January 2023

Phrenic Motor Column (PMC) neurons are a specialized subset of motor neurons (MNs) that provide the only motor innervation to the diaphragm muscle and are therefore essential for survival. Despite their critical role, the mechanisms that control phrenic MN development and function are not well understood. Here, we show that catenin-mediated cadherin adhesive function is required for multiple aspects of phrenic MN development. Deletion ofβ- andγ-catenin from MN progenitors results in perinatal lethality and a severe reduction in phrenic MN bursting activity. In the absence of catenin signaling, phrenic MN topography is eroded, MN clustering is lost and phrenic axons and dendrites fail to grow appropriately. Despite the essential requirement for catenins in early phrenic MN development, they appear to be dispensable for phrenic MN maintenance, as catenin deletion from postmitotic MNs does not impact phrenic MN topography or function. Our data reveal a fundamental role for catenins in PMC development and suggest that distinct mechanisms are likely to control PMC maintenance.
LRphase: an efficient method for assigning haplotype identity to long reads
Authors: Holmes Monica J. , Mahjour Babak , Castro Christopher P. , Farnum Gregory A. , Diehl Adam G. , Boyle Alan P.
Published: January 2023

Motivation

Understanding the functional effects of sequence variation is among the primary goals of contemporary genomics. Individual human genomes contain millions of variants which are thought to contribute to phenotypic variability and differential disease risks at the population level. However, because variants rarely act in isolation, we cannot accurately predict functional effects without first considering the potential effects of other interacting variants on the same chromosome. This information can be obtained by phasing the read data from sequencing experiments. However, no standalone tools are available to simply phase reads based on known haplotypes. Here we present LRphase: a user-friendly utility for simple phasing of long sequencing reads.

Availability and Implementation

LRphase is implemented in Python, and is freely available athttps://github.com/Boyle-Lab/LRphase, under the MIT license. Version 1.1.0, described in this manuscript, is available through the pip and Bioconda repositories (e.g., “pip install lrphase==1.1.0”).

Contact

apboyle@umich.edu

Supplementary Information

Supplementary methods are available as part of the online version of this publication.
Post-Ischemic Reorganization of Sensory Responses in Cerebral Cortex
Authors: Hayley P , Tuchek C , Dalla S , Borrell J , Murphy MD , Nudo RJ , Guggenmos DJ
Published: January 2023

Sensorimotor integration is critical for generating skilled, volitional movements. While stroke tends to impact motor function, there are also often associated sensory deficits that contribute to overall behavioral deficits. Because many of the cortico-cortical projections participating in the generation of volitional movement either target or pass-through primary motor cortex (in rats, caudal forelimb area; CFA), any damage to CFA can lead to a subsequent disruption in information flow. As a result, the loss of sensory feedback is thought to contribute to motor dysfunction even when sensory areas are spared from injury. Previous research has suggested that the restoration of sensorimotor integration through reorganization or de novo neuronal connections is important for restoring function. Our goal was to determine if there was crosstalk between sensorimotor cortical areas with recovery from a primary motor cortex injury. First, we investigated if peripheral sensory stimulation would evoke responses in the rostral forelimb area (RFA), a rodent homologue to premotor cortex. We then sought to identify whether intracortical microstimulation-evoked activity in RFA would reciprocally modify the sensory response. We used seven rats with an ischemic lesion of CFA. Four weeks after injury, the rats’ forepaw was mechanically stimulated under anesthesia and neural activity was recorded in the cortex. In a subset of trials, a small intracortical stimulation pulse was delivered in RFA either individually or paired with peripheral sensory stimulation. Our results point to post-ischemic connectivity between premotor and sensory cortex that may be related to functional recovery. Premotor recruitment during the sensory response was seen with a peak in spiking within RFA after the peripheral solenoid stimulation despite the damage to CFA. Furthermore, stimulation evoked activity in RFA modulated and disrupted the sensory response in sensory cortex, providing additional evidence for the transmission of premotor activity to sensory cortex and the sensitivity of sensory cortex to premotor cortex’s influence. The strength of the modulatory effect may be related to the extent of the injury and the subsequent reshaping of cortical connections in response to network disruption.
Defining the cellular complexity of the zebrafish bipotential gonad
Authors: Kossack Michelle E. , Tian Lucy , Bowie Kealyn , Plavicki Jessica S.
Published: January 2023

Zebrafish are routinely used to model reproductive development, function, and disease, yet we still lack a clear understanding of the fundamental steps that occur during early bipotential gonad development, including when endothelial cells, pericytes, and macrophage cells arrive at the bipotential gonad to support gonad growth and differentiation. Here, we use a combination of transgenic reporters and single-cell sequencing analyses to define the arrival of different critical cell types to the larval zebrafish gonad. We determined that blood initially reaches the gonad via a vessel formed from the swim bladder artery, which we have termed the gonadal artery. We find that vascular and lymphatic development occurs concurrently in the bipotential zebrafish gonad and our data suggest that similar to what has been observed in developing zebrafish embryos, lymphatic endothelial cells in the gonad may be derived from vascular endothelial cells. We mined preexisting sequencing data sets to determine whether ovarian pericytes had unique gene expression signatures. We identified 215 genes that were uniquely expressed in ovarian pericytes that were not expressed in larval pericytes. Similar to what has been shown in the mouse ovary, our data suggest thatpdgfrb+ pericytes may support the migration of endothelial tip cells during ovarian angiogenesis. Using a macrophage-driven photoconvertible protein, we found that macrophage established a nascent resident population as early as 12 dpf and can be observed removing cellular material during gonadal differentiation. This foundational information demonstrates that the early bipotential gonad contains complex cellular interactions, which likely shape the health and function of the mature, differentiated gonad.

Summary Sentence

Delineating the complex cellular interactions between vascular and lymphatic endothelial cells, pericytes, and macrophage in the bipotential gonad is essential for understanding the differentiation and functioning of the mature gonad.

Graphical Abstract
Determinants of renin cell differentiation: a single cell epi-transcriptomics approach
Authors: Martini Alexandre G , Smith Jason P. , Medrano Silvia , Sheffield Nathan C. , Sequeira-Lopez Maria Luisa S. , Gomez R. Ariel
Published: January 2023

Rationale

Renin cells are essential for survival. They control the morphogenesis of the kidney arterioles, and the composition and volume of our extracellular fluid, arterial blood pressure, tissue perfusion, and oxygen delivery. It is known that renin cells and associated arteriolar cells descend fromFoxD1+ progenitor cells, yet renin cells remain challenging to study due in no small part to their rarity within the kidney. As such, the molecular mechanisms underlying the differentiation and maintenance of these cells remain insufficiently understood.

Objective

We sought to comprehensively evaluate the chromatin states and transcription factors (TFs) that drive the differentiation ofFoxD1+ progenitor cells into those that compose the kidney vasculature with a focus on renin cells.

Methods and Results

We isolated single nuclei ofFoxD1+ progenitor cells and their descendants fromFoxD1cre/+;R26R-mTmGmice at embryonic day 12 (E12) (ncells=1234), embryonic day 18 (E18) (ncells=3696), postnatal day 5 (P5) (ncells=1986), and postnatal day 30 (P30) (ncells=1196). Using integrated scRNA-seq and scATAC-seq we established the developmental trajectory that leads to the mosaic of cells that compose the kidney arterioles, and specifically identified the factors that determine the elusive, myo-endocrine adult renin-secreting juxtaglomerular (JG) cell. We confirm the role ofNfixin JG cell development and renin expression, and identified the myocyte enhancer factor-2 (MEF2) family of TFs as putative drivers of JG cell differentiation.

Conclusions

We provide the first developmental trajectory of renin cell differentiation as they become JG cells in a single-cell atlas of kidney vascular open chromatin and highlighted novel factors important for their stage-specific differentiation. This improved understanding of the regulatory landscape of renin expressing JG cells is necessary to better learn the control and function of this rare cell population as overactivation or aberrant activity of the RAS is a key factor in cardiovascular and kidney pathologies.
Analysis of convolutional neural networks reveals the computational properties essential for subcortical processing of facial expression
Authors: Lim Chanseok , Inagaki Mikio , Shinozaki Takashi , Fujita Ichiro
Published: January 2023

Perception of facial expression is crucial in the social life of primates. This visual information is processed along the ventral cortical pathway and the subcortical pathway. Processing of face information in the subcortical pathway is inaccurate, but the architectural and physiological properties that are responsible remain unclear. We analyzed the performance of convolutional neural networks incorporating three prominent properties of this pathway: a shallow layer architecture, concentric receptive fields at the first processing stage, and a greater degree of spatial pooling. The neural networks designed in this way could be trained to classify seven facial expressions with a correct rate of 51% (chance level, 14%). This modest performance was gradually improved by replacing the three properties, one-by-one, two at a time, or all three simultaneously, with the corresponding features in the cortical pathway. Some processing units in the final layer were sensitive to spatial frequencies (SFs) in the retina-based coordinate, whereas others were sensitive to object-based SFs, similar to neurons in the amygdala. Replacement of any one of these properties affected the SF coordinate of units. All three properties constrain the accuracy of facial expression information in the subcortical pathway, and are essential for determining the coordinate of SF representation.
SUMO interacting motif (SIM) of S100A1 is critical for S100A1 post-translational protein stability
Authors: Jebessa Zegeye H. , Glaser Manuel , Zhao Jemmy , Schneider Andrea , Seenivasan Ramkumar , Busch Martin , Ritterhoff Julia , Wade Rebecca C. , Most Patrick
Published: January 2023

S100A1 is a small EF-type Ca2+sensor protein that belongs to the multigenic S100 protein family. It is abundantly expressed in cardiomyocytes (CMs) and has been described as a key regulator of CM performance due to its unique ability to interact with structural contractile proteins, regulators of cardiac Ca2+cycling, and mitochondrial proteins. However, our understanding of the molecular mechanisms regulating S100A1 protein levels is limited. We used the bioinformatics tool GPS-SUMO2.0 to identify a putative SUMO interacting motif (SIM) on S100A1. Consistently, a S100A1:SUMO interaction assay showed a Ca2+-dependent interaction of S100A1 with SUMO proteins. In neonatal rat ventricular myocytes (NRVM) and COS1 cells, S100A1 protein abundance increased in the presence of overexpressed SUMO1 without affecting the S100A1 mRNA transcript. We then generated S100A1 truncation mutants, where the SIM motif was removed by truncation or in which the core residues of the SIM motif (residues 77-79) were deleted or replaced by alanine. In COS1 cells and NRVM, overexpression of these S100A1 mutants led to elevated S100A1 mutant mRNA levels but failed to produce respective protein levels. Protein expression of these mutants could be rescued from degradation by addition of the proteasome inhibitor MG-132. By using an information-driven approach to dock the three-dimensional structures of S100A1 and SUMO, we predict a novel interaction mode between the SIM in S100A1 and SUMO. This study shows an important role of SUMO:SIM-mediated protein:protein interaction in the regulation of post-translational protein stability, and provides mechanistic insights into the indispensability of the core SIM for S100A1 post-translational stability.
Migratory patterns of two major influenza virus host species on tropical islands
Authors: Lebarbenchon Camille , Boucher Solenn , Feare Chris , Dietrich Muriel , Larose Christine , Humeau Laurence , Corre Matthieu Le , Jaeger Audrey
Published: January 2023

Animal migration is a major driver of infectious agent dispersal. Duck and seabirds migrations, for instance, play a key role in the spatial transmission dynamics and gene flows of avian influenza viruses (AIV), worldwide. On tropical islands, brown and lesser noddies (Anous stolidusandA. tenuirostris) may be important AIV hosts, but the lack of knowledge on their migratory behaviour limits our understanding of virus circulation in island networks. Here we show that high connectivity between islands generated by post-breeding behaviours could be a major driver in the spread and the maintenance of AIV among tropical islands. Tracking data highlight two types of behaviours during the non-breeding season: birds either staying in the vicinity of their breeding ground (on Bird Island, Seychelles), or moving to and roosting on other islands in the Indian Ocean. Differences in roosting places are detected between migrant birds, ranging from the Tanzanian coast to the Maldives archipelago and Tromelin Island. Epidemiological data further support that brown and lesser noddies are major hosts for AIV, although significant variation of seroprevalence between species suggest that other drivers are involved in virus infection and transmission dynamics.
Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus
Authors: López-Astacio Robert A. , Adu Oluwafemi F. , Goetschius Daniel J. , Lee Hyunwook , Weichert Wendy S. , Wasik Brian R. , Frueh Simon P. , Alford Brynn K. , Voorhees Ian E.H. , Flint Joseph F. , Saddoris Sarah , Goodman Laura B. , Holmes Edward C. , Hafenstein Susan L. , Parrish Colin R.
Published: January 2023

Canine parvovirus (CPV) is a small non-enveloped single-stranded DNA virus that causes serious diseases in dogs worldwide. The original strain of the virus (CPV-2) emerged in dogs during the late-1970s due to a host range switch of a virus similar to the feline panleukopenia virus (FPV) that infected another host. The virus that emerged in dogs had altered capsid receptor- and antibody-binding sites, with some changes affecting both functions. Further receptor and antibody binding changes arose when the virus became better adapted to dogs or to other hosts. Here, we usein vitroselection and deep sequencing to reveal how two antibodies with known interactions select for escape mutations in CPV. The antibodies bind two distinct epitopes, and one largely overlaps the host receptor binding site. We also engineered antibody variants with altered binding structures. Viruses were passaged with the wild type or mutated antibodies, and their genomes deep sequenced during the selective process. A small number of mutations were detected only within the capsid protein gene during the first few passages of selection, and most sites remained polymorphic or were slow to go to fixation. Mutations arose both within and outside the antibody binding footprints on the capsids, and all avoided the TfR-binding footprint. Many selected mutations matched those that have arisen in the natural evolution of the virus. The patterns observed reveal the mechanisms by which these variants have been selected in nature and provide a better understanding of the interactions between antibody and receptor selections.

IMPORTANCE

Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system. Here, we use anin vitromodel system and deep genome sequencing to reveal the mutations that arise in the virus genome during selection by each of two monoclonal antibodies or their engineered variants. High-resolution structures of each of the Fab: capsid complexes revealed their binding interactions. The engineered forms of the wild-type antibodies or mutant forms allowed us to examine how changes in antibody structure influence the mutational selection patterns seen in the virus. The results shed light on the processes of antibody binding, neutralization escape, and receptor binding, and likely have parallels for many other viruses.