bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptative Machine Translation between paired Single-Cell Multi-Omics Data
Authors: Martinez-de-Morentin Xabier , Khan Sumeer A. , Lehmann Robert , Qu Sisi , Maillo Alberto , Kiani Narsis A. , Prosper Felipe , Tegner Jesper , Gomez-Cabrero David
Published: January 2021

Background

Single-cell multi-omics technologies allow the profiling of different data modalities from the same cell. However, while isolated modalities only capture one view of the total information of a biological cell, an integrative analysis capturing the different modalities is challenging. In response, bioinformatics and machine learning methodologies have been developed for multi-omics single-cell analysis. Nevertheless, it is unclear if current tools can address the dual aspect of modality integration and prediction across modalities without requiring extensive parameter finetuning.

Results

We designed LIBRA, a Neural Network based framework, to learn a translation between paired multi-omics profiles such that a shared latent space is constructed. LIBRA is a state-of-the-art tool when evaluating the ability to increase cell-type (clustering) resolution in the latent space. When assessing the predictive power across data modalities, LIBRA outperforms existing tools. Finally, considering the importance of hyperparameters, we implemented anadaptative-tuningstrategy, labelled aLIBRA, in the LIBRA package. As expected, adaptive parameter optimization significantly boosts the performance of learning predictive models from paired datasets. Additionally, aLIBRA provides parameter combinations balancing the integrative and predictive tasks.

Conclusions

LIBRA is a versatile tool, uniquely targeting both integration and prediction tasks of Single-cell multi-omics data. LIBRA is a data-driven robust platform that includes an adaptive learning scheme. Furthermore, LIBRA is freely available as R and Python libraries (https://github.com/TranslationalBioinformaticsUnit/LIBRA).
Incoherent collective cell chemotaxis underlies organ dysmorphia in a model of branchio-oto-renal syndrome
Authors: Borges Augusto , Pinto Teixeira Filipe , Wibowo Indra , Hammerschmidt Matthias , Kawakami Koichi , Miranda Rodriguez Jeronimo R , Lopez-Schier Hernan
Published: January 2021

Mutations in the transcriptional co-activator Eya1 cause branchio-oto-renal syndrome (BOR) in humans and the equivalent condition in vertebrates. BOR is characterized by congenital branchial fistulas, malformations of the inner ear and kidney hypoplasia. Here we use the mechanosensory lateral line in zebrafish to better understand the role of Eya1 in organogenesis. The lateral line develops from a primordium formed by approximately 150 cells that move together from head to tail of the embryo at a constant velocity. This invariant migration occurs over a trail of Sdf1a chemokine and is controlled by the simultaneous action of two receptors. The CXCR4b is expressed in the front half of the primordium where it acts as a chemokine sensor, whereas the CXCR7b is present in the rear half, serving as a chemokine sink to ensure persistent directionality. We show that the loss of Eya1 strongly reduces the expression of CXCR7b, disrupting the coherent motion of the primordium and leading to lateral-line truncations. We also find evidence of reduced epithelial maturation in primordia lacking Eya1. These findings argue for abnormal collective cell chemotaxis as the origin of organ dysmorphia in BOR.
Microbiome-specific T follicular helper cells drive tertiary lymphoid structures and anti-tumor immunity against colorectal cancer
Authors: Overacre-Delgoffe Abigail E. , Cillo Anthony R. , Bumgarner Hannah J. , Burr Ansen H.P. , Tometich Justin T. , Bhattacharjee Amrita , Bruno Tullia C. , Vignali Dario A.A. , Hand Timothy W.
Published: January 2021

Colorectal cancer (CRC) is a common and deadly disease, and patients with metastatic tumors often fail to respond to therapy. While select members of the microbiome are associated with improved anti-tumor immunity, mechanistic understanding of how the microbiome provides a benefit is lacking. We show that modification of the CRC-associated microbiome with a single immunogenic commensal bacteria can alter T cell differentiation, inhibit tumor growth, and increase survival. Microbiome-driven control of CRC required the formation of colonic tertiary lymphoid structures (TLS) and increased infiltration of the tumor with cytotoxic immune cells. In the context of CRC, CD4+T cells specific to the newly introduced commensals differentiated into T follicular helper cells and were necessary for the formation of TLS, immune infiltration of the tumor, and control over CRC. Thus, modification of the intestinal T cell response by the microbiome can be used to augment anti-tumor immunity in colorectal cancer.
Inhibition of HSP90 reversed STAT3 mediated muscle wasting induced by cancer cachexia
Authors: Niu Mengyuan , Song Shiyu , Su Zhonglan , Wei Lulu , Li Li , Pu Wenyuan , Zhao Chen , Ding Yibing , Cao Wangsen , Gao Qian , Wang Hongwei
Published: January 2021

Cancer cachexia is one of the most common causes of death among cancer patients, no effective anti-cachectic treatment is currently available. In experimental cachectic models, aberrant activation of STAT3 in skeletal muscle has been found to contribute to muscle wasting. However, its clinical association, the factors regulating STAT3 activation, and the molecular mechanisms of STAT3-induced muscle atrophy in cancer cachexia remain incompletely understood. Here, we show that an enhanced interaction between STAT3 and HSP90, which causes the persistent STAT3 activation in the skeletal muscle of cancer cachexia patients, is the crucial event for the development of cachectic muscle wasting. Administration of HSP90 inhibitors alleviated the muscle wasting in C26 tumor-bearing cachetic mice model or C26 conditional medium induced C2C12 myotube atrophy. A mechanistic study indicated that in cachectic skeletal muscle, prolonged STAT3 activation triggered muscle wasting in a FOXO1-dependent manner, STAT3 activated FOXO1 by binding directly to its promoter. Our results provide key insights into the role of the HSP90/STAT3/FOXO1 axis in cachectic muscle wasting, which shows promising therapeutic potential as a target for the treatment of cancer cachexia.
Transcription activation is enhanced by multivalent interactions independent of phase separation
Authors: Trojanowski Jorge , Frank Lukas , Rademacher Anne , Grigaitis Pranas , Rippe Karsten
Published: January 2021

Transcription factors (TFs) consist of a DNA binding and an activation domain (AD) that are considered to be independent and exchangeable modules. However, recent studies conclude that also the physico-chemical properties of the AD can control TF assembly at chromatin by driving a phase separation into transcriptional condensates. Here, we dissected transcription activation by comparing different synthetic TFs at a reporter gene array with real-time single-cell fluorescence microscopy readouts. In these experiments, binding site occupancy, residence time and co-activator recruitment in relation to multivalent TF interactions were compared. While phase separation propensity and activation strength of the AD were correlated, the actual formation of liquid-like TF droplets had a neutral or inhibitory effect on transcription activation. Rather, we conclude that multivalent AD mediated interactions increase the transcription activation capacity of a TF by stabilizing chromatin binding and mediating the recruitment of co-activators independent of phase separation.
Development of white matter tracts between and within the dorsal and ventral streams
Authors: Vinci-Booher S. , Caron B. , Bullock D. , James K. , Pestilli F.
Published: January 2021

The degree of interaction between the ventral and dorsal visual streams has been discussed in multiple scientific domains for decades. Recently, several white matter tracts that directly connect cortical regions associated with the dorsal and ventral streams have become possible to study due to advancements in automated and reproducible methods. The developmental trajectory of this set of tracts, here referred to as the posterior vertical pathway (PVP), has yet to be described. We propose an input-driven model of white matter development and provide evidence for the model by focusing on the development of the PVP. We used reproducible, cloud-computing methods and diffusion imaging from adults and children (ages 5-8 years) to compare PVP development to that of tracts within the ventral and dorsal pathways. PVP microstructure was more adult-like than dorsal stream microstructure, but less adult-like than ventral stream microstructure. Additionally, PVP microstructure was more similar to the microstructure of the ventral than the dorsal stream and was predicted by performance on a perceptual task in children. Overall, results suggest a potential role for the PVP in the development of the dorsal visual stream that may be related to its ability to facilitate interactions between ventral and dorsal streams during learning. Our results are consistent with the proposed model, suggesting that the microstructural development of major white matter pathways is related, at least in part, to the propagation of sensory information within the visual system.

Significance Statement

Understanding white matter development is important to building predictive models that can inform interventions and targeted educational methods. We propose and provide evidence for an input-driven model of white matter development. We tested an uncharacterized aspect of human brain development. Namely, how the recently described posterior vertical white matter tracts develop. Our results suggest a developmental progression along the known, direct anatomical connections from posterior visual areas to anterior ventral and dorsal areas. Our results suggest fundamental biological mechanisms that clarify the role of white matter in predicting human learning and behavior.
Inhibition of BMP and FGF signaling prior to wound epithelium formation leads to an aberrant regenerative response in teleost fishPoecilia latipinna
Authors: Ranadive Isha , Patel Sonam , Pai Siddharth , Khaire Kashmira , Balakrishnan Suresh
Published: January 2021

The BMP and FGF pathways play a pivotal role in the successful regeneration of caudal fin of teleost fish. Individual inhibition of these pathways led to impaired caudal fin regeneration until the pharmacologic inhibitor of FGF (SU5402) and BMP (LDN193189) were metabolized off. Therefore, in the current study both these pathways were inhibited collectively wherein inhibition of BMP and FGF during the wound epithelium formation led to stalling of the process by bringing down the established levels ofshhandrunx2. In members of the treatment group, it was observed that, each blastema grows crouched rather than linear and the regrown lepidotrichia therefore remain tilted down. Amongst the other irregularities observed, the transition from epithelial to mesenchymal cells was found hindered due to down-regulation ofsnailandtwist, brought about by BMP and FGF inhibition. Compromised expression ofSnailandtwistderanged the normal levels of cadherins causing disruption in the transition of cells. Lastly, blocking BMP and FGF delayed blastema formation and proliferation due to diminished levels offgf2, fgf8, fgf10andbmp6, whilecasp3andcasp9levels remained heightened causing accelerated cell death. This study not only highlights the axial role of BMP and FGF pathways in regeneration but also accentuates the collaboration amongst the two. This ingenious coordination of signalling further reinforces the involvement of relaying messenger molecules between these crucial pathways.

Summary Statement

BMP and FGF collectively control the process of blastema formation in fish and inhibiting them prior to wound epithelium stage leads to irrevocable damage to the regenerating caudal fin.
Structural insight intoPichia pastorisfatty acid synthase
Authors: Snowden Joseph S. , Alzahrani Jehad , Sherry Lee , Stacey Martin , Rowlands David J. , Ranson Neil A. , Stonehouse Nicola J.
Published: January 2021

Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identified FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purified fromP. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure ofP. pastorisFAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identified several differences in both structural and enzymatic domains through comparison with the prototypical yeast FAS fromS. cerevisiae. Using focussed classification, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further efforts to engineer yeast FAS for synthesis of alternate products.
SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Authors: Righelli Dario , Weber Lukas M. , Crowell Helena L. , Pardo Brenda , Collado-Torres Leonardo , Ghazanfar Shila , Lun Aaron T. L. , Hicks Stephanie C. , Risso Davide
Published: January 2021

SpatialExperimentis a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations, and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms, and provide access to example datasets and visualization tools in theSTexampleData,TENxVisiumData, andggspavispackages.

Availability and Implementation

TheSpatialExperiment,STexampleData,TENxVisiumData, andggspavispackages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards.

Contact

risso.davide@gmail.com,shicks19@jhu.edu

Supplementary Information

Supplementary Tables and Figures are available online.
Maternal transfer of neutralizing antibodies to OspA after oral vaccination of the rodent reservoir
Authors: O’Connell Kathryn , Nair Nisha , Samanta Kamalika , Azevedo Jose F. , Brown Grant D. , Petersen Christine A. , Gomes-Solecki Maria
Published: January 2021

Lyme Disease presents unique challenges for public health efforts. We hypothesized that transfer of protective antibodies between mothers and offspring should occur after oral vaccination of C3H-HeN mice withE. colioverexpressing OspA. We present new evidence for maternal transfer of vaccine induced neutralizing anti-OspA IgG antibodies to mouse pups through ingestion of colostrum. Protective levels of OspA antibodies in pups were present from 2-5 weeks after birth and they persisted in some mice until 9 weeks of age. This was corroborated by detection of neutralizing antibodies in the serum of all pups at 2-3 weeks after birth and in some mice at 9 weeks of age. A clear association was found between robust antibody responses in mothers and the length of antibody persistence in the respective pups using a novel longitudinal Bayesian model. These factors are likely to impact the enzootic cycle ofB. burgdorferiwhen reservoir targeted OspA-based vaccination interventions are implemented.
MOLECULAR LANDSCAPE OF OLD AGE MELANOMA BY SURVIVAL AND IMMUNOTHERAPY RESPONSE
Authors: Smith Stephen P. , Nagore Eduardo , Budden Timothy , Kumar Rajiv , Marais Richard , Gaudy-Marqueste Caroline , Virós Amaya
Published: January 2021

Melanoma mortality particularly affects older patients, and age is a powerful independent predictor of death. The pathogenic mutations and transcriptomic changes associated with poor survival in aged patients are not known.

We analyzed 5 cohorts of metastatic (N=324, N=18, N=66) and primary melanomas (N=103, N=30) to establish the effect of age on prognosis, identify age-specific driver genes and transcriptomic changes linked to survival and immunotherapy response.

We identify the pathogenic mutations and transcriptomic changes associated with poor survival by age, and show mutations inBRAF, NRAS, CDKN2AorIDH1identify metastatic and primary melanoma aged patients with worse outcome. In contrast, activation of immune-regulatory pathways is a hallmark of long-term survival. We tested if mutations in genes linked to poor outcome are associated to immunotherapy responders, exploring combinations of agespecific mutations in metastatic immune checkpoint inhibitor aged responders. Strikingly, aged patients withBRAF, NRAS, CDKN2AorIDH1mutations and high tumor mutation burden treated with immunotherapy have an improved median survival of 12 months. These data highlight the molecular landscape of melanoma varies by age, and age stratification can refine prognosis and therapy rationales. A set of mutations identifies patients at highest risk of death who are likely immunotherapy responders.
Tau aggregates are RNA-protein assemblies that mis-localize multiple nuclear speckle components
Authors: Lester Evan , Ooi Felicia K. , Bakkar Nadine , Ayers Jacob , Woerman Amanda L. , Wheeler Joshua , Bowser Robert , Carlson George A. , Prusiner Stanley B. , Parker Roy
Published: January 2021

Tau aggregates contribute to neurodegenerative diseases including frontotemporal dementia and Alzheimer’s disease (AD). Although RNA promotes tau aggregationin vitro, whether tau aggregates in cells contain RNA is unknown. We demonstrate in cell culture and mouse brains that both cytosolic and nuclear tau aggregates contain RNA, with enrichment for snRNAs and snoRNAs. Nuclear tau aggregates colocalize with and alter the composition, dynamics, and organization of nuclear speckles, which are membraneless organelles involved in pre-mRNA splicing. Moreover, several nuclear speckle components, including SRRM2, mislocalize to cytosolic tau aggregates in cells, mouse brains, and patient brains with AD, frontotemporal dementia (FTD), and corticobasal degeneration (CBD). Consistent with these alterations we observe the presence of tau aggregates is sufficient to alter pre-mRNA splicing. This work identifies tau alteration of nuclear speckles as a feature of tau aggregation that may contribute to the pathology of tau aggregates.
UNC-2 CaV2 channel localization at presynaptic active zones depends on UNC-10/RIM and SYD-2/Liprin-α inCaenorhabditis elegans
Authors: Oh Kelly H. , Krout Mia , Richmond Janet E. , Kim Hongkyun
Published: January 2021

Presynaptic active zone proteins couple calcium influx with synaptic vesicle exocytosis. However, the control of presynaptic calcium channel clustering by active zone proteins is not completely understood. In aC. elegansforward genetic screen, we find that UNC-10/RIM (Rab3-interacting molecule) and SYD-2/Liprin-αregulate presynaptic clustering of UNC-2, the CaV2 channel ortholog. We further quantitatively analyzed live animals using endogenously GFP-tagged UNC-2 and active zone components. Consistent with the interaction between RIM and CaV2 in mammals, the intensity and number of UNC-2 channel clusters at presynaptic terminals were greatly reduced inunc-10mutant animals. To understand how SYD-2 regulates presynaptic UNC-2 channel clustering, we analyzed presynaptic localization of endogenous SYD-2, UNC-10, RIMB-1/RIM-BP (RIM binding protein), and ELKS-1. Our analysis revealed that while SYD-2 is the most critical for active zone assembly, loss of SYD-2 function does not completely abolish presynaptic localization of UNC-10, RIMB-1, and ELKS-1, suggesting an existence of SYD-2-independent active zone assembly. UNC-2 localization analysis in double and triple mutants of active zone components show that SYD-2 promotes UNC-2 clustering by partially controlling UNC-10 localization, and ELKS-1 and RIMB-1 also contribute to UNC-2 channel clustering. In addition, we find that core active zone proteins are unequal in their abundance. While the abundance of UNC-10 at the active zone is comparable to UNC-2, SYD-2 and ELKS-1 are twice more and RIMB-1 four times more abundant than UNC-2. Together our data show that UNC-10, SYD-2, RIMB-1, and ELKS-1 control presynaptic UNC-2 channel clustering in redundant yet distinct manners.

Significance Statement

Precise control of neurotransmission is dependent on the tight coupling of the calcium influx through voltage-gated calcium channels (VGCCs) to the exocytosis machinery at the presynaptic active zones. However, how these VGCCs are tethered to the active zone is incompletely understood. To understand the mechanism of presynaptic VGCC localization, we performed aC. elegansforward genetic screen and quantitatively analyzed endogenous active zones and presynaptic VGCCs. In addition to RIM (Rab3-interacting molecule), our study finds that SYD-2/Liprin-αis critical for presynaptic localization of VGCCs. Yet, the loss of SYD-2, the master active zone scaffolding protein, does not completely abolish the presynaptic localization of the VGCC, showing that the active zone is a resilient structure assembled by redundant mechanisms.
Structure and Function of an in vivo Assembled Type III-A CRISPR-Cas Complex Reveal Critical Roles of Dynamics in Activity Control
Authors: Sridhara Sagar , Rai Jay , Whyms Charlisa , Woodside Walter , Terns Michael P , Li Hong
Published: January 2021

The small RNA-mediated immunity in bacteria depends on foreign RNA-activated and self RNA-inhibited enzymatic activities. The multi-subunit Type III-A CRISPR-Cas effector complex (Csm) exemplifies this principle, but its molecular basis for regulation remains unexplained. Recognition of the foreign RNA, or cognate target RNA (CTR), triggers its single-stranded deoxyribonuclease (DNase) and cyclic oligoadenylate (cOA) synthesis activities. The same activities remain dormant in the presence of the self-RNA, or noncognate target RNA (NTR) that differs from CTR only in its 3’-protospacer flanking sequence. Here we captured four structures ofin vivoassembledLactococcus lactisCsm (LlCsm) by electron cryomicroscopy representing both the active and the inactive states. Surprisingly, in absence of bound RNA, LlCsm largely forms a minimal assembly lacking the Csm2 subunit with a stably bound catalytic subunit Csm1. Comparison of the minimal LlCsm structure and activities, both in vitro and in vivo, with those of fully assembled LlCsm reveals a molecular mechanism responsible for the viral RNA-activated and self RNA-inhibited activity of Csm1 through protein dynamics.

Graphic Art Summary
Synthetic nanobody–SARS-CoV-2 receptor-binding domain structures identify distinct epitopes
Authors: Ahmad Javeed , Jiang Jiansheng , Boyd Lisa F. , Natarajan Kannan , Margulies David H.
Published: January 2021

The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands unprecedented attention. We report four X-ray crystal structures of three synthetic nanobodies (sybodies) (Sb16, Sb45 and Sb68) bind to the receptor-binding domain (RBD) of SARS-CoV-2: binary complexes of Sb16–RBD and Sb45–RBD; a ternary complex of Sb45–RBD–Sb68; and Sb16 unliganded. Sb16 and Sb45 bind the RBD at the ACE2 interface, positioning their CDR2 and CDR3 loops diametrically. Sb16 reveals a large CDR2 shift when binding the RBD. Sb68 interacts peripherally at the ACE2 interface; steric clashes with glycans explain its mechanism of viral neutralization. Superposing these structures onto trimeric spike (S) protein models indicates these sybodies bind conformations of the mature S protein differently, which may aid therapeutic design.

One Sentence Summary

X-ray structures of synthetic nanobodies complexed with the receptor-binding domain of the spike protein of SARS-CoV-2 reveal details of CDR loop interactions in recognition of distinct epitopic sites.
MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution
Authors: Gallardo CM , Wang S , Montiel-Garcia DJ , Little SJ , Smith DM , Routh AL , Torbett BE
Published: January 2021

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolution given the read-length limitations of next-generation sequencing platforms. This has hampered the direct observation of long-range genetic interactions that code for protein-protein interfaces with relevance in both drug and vaccine development. Here we overcome these technical limitations by developing a nanopore-based long-range viral sequencing pipeline that yields accurate single molecule sequences of circulating virions from clinical samples. We demonstrate its utility in observing the evolution of individual HIV Gag-Pol genomes in response to antiviral pressure. Our pipeline, called Multi-read Hairpin Mediated Error-correction Reaction (MrHAMER), yields >1000s viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure, and enable the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit.
CNVpytor: a tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing
Authors: Suvakov Milovan , Panda Arijit , Diesh Colin , Holmes Ian , Abyzov Alexej
Published: January 2021

Detecting copy number variations (CNVs) and copy number alterations (CNAs) based on whole genome sequencing data is important for personalized genomics and treatment. CNVnator is one of the most popular tools for CNV/CNA discovery and analysis based on read depth (RD). Herein, we present an extension of CNVnator developed in Python -- CNVpytor. CNVpytor inherits the reimplemented core engine of its predecessor and extends visualization, modularization, performance, and functionality. Additionally, CNVpytor uses B-allele frequency (BAF) likelihood information from single nucleotide polymorphism and small indels data as additional evidence for CNVs/CNAs and as primary information for copy number neutral losses of heterozygosity. CNVpytor is significantly faster than CNVnator—particularly for parsing alignment files (2 to 20 times faster)—and has (20-50 times) smaller intermediate files. CNV calls can be filtered using several criteria and annotated. Modular architecture allows it to be used in shared and cloud environments such as Google Colab and Jupyter notebook. Data can be exported into JBrowse, while a lightweight plugin version of CNVpytor for JBrowse enables nearly instant and GUI-assisted analysis of CNVs by any user. CNVpytor release and the source code are available on GitHub at https://github.com/abyzovlab/CNVpytor under the MIT license.
Genomic signatures of recent convergent transitions to social life in spiders
Authors: Tong Chao , Avilés Leticia , Rayor Linda S. , Mikheyev Alexander S. , Linksvayer Timothy A.
Published: January 2021

The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
Obligate movements of an active site-linked surface domain control RNA polymerase elongation and pausing via a Phe-pocket anchor
Authors: Bao Yu , Landick Robert
Published: January 2021

The catalytic trigger loop (TL) in RNA polymerase (RNAP) alternates between unstructured and helical hairpin conformations to admit and then contact the NTP substrate during transcription. In many bacterial lineages, the TL is interrupted by insertions of 2–5 surface-exposed, sandwich-barrel hybrid motifs (SBHMs) of poorly understood function. The 188-aa, 2-SBHME. coliinsertion, called SI3, occupies different locations in halted, NTP-bound, and paused transcription complexes, but its dynamics during active transcription and pausing are undefined. Here we report design, optimization, and use of a Cys-triplet reporter to measure the positional bias of SI3 in different transcription complexes and to determine the effect of restricting SI3 movement on nucleotide addition and pausing. We describe use of H2O2as a superior oxidant for RNAP disulfide reporters. NTP binding biases SI3 toward the closed conformation whereas transcriptional pausing biases SI3 toward a swiveled position that inhibits TL folding. We find that SI3 must change location in every round of nucleotide addition and that restricting its movements inhibits both transcript elongation and pausing. These dynamics are modulated by a crucial Phe pocket formed by the junction of the two SBHM domains. This SI3 Phe pocket captures a Phe residue in the RNAP jaw when the TL unfolds, explaining the similar phenotypes of alterations in the jaw and SI3. Our findings establish that SI3 functions by modulating the TL folding to aid transcriptional regulation and to reset secondary channel trafficking in every round of nucleotide addition.

SIGNIFICANCE

RNA synthesis by cellular RNA polymerases depends on an active-site component called the trigger loop that oscillates between an unstructured loop that admits NTP substrates and a helical hairpin that positions the NTP in every round of nucleotide addition. In most bacteria, the trigger loop contains a large, surface-exposed insertion module that occupies different positions in halted transcription complexes but whose function during active transcription is unknown. By developing and using a novel disulfide reporter system, we find the insertion module also must alternate between in and out positions for every nucleotide addition, must swivel to a paused position to support regulation, and, in enterobacteria, evolved a “Phe pocket” that captures a key phenylalanine in the out and swivel positions.
DECODE: ADeep-learning Framework forCondensing Enhancers and Refining Boundaries with Large-scale Functional Assays
Authors: Chen Zhanlin , Zhang Jing , Liu Jason , Dai Yi , Lee Donghoon , Min Martin Renqiang , Xu Min , Gerstein Mark
Published: January 2021

Mapping distal regulatory elements, such as enhancers, is the cornerstone for investigating genome evolution, understanding critical biological functions, and ultimately elucidating how genetic variations may influence diseases. Previous enhancer prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have operationalized enhancer discovery as a binary classification problem without accurate enhancer boundary detection, producing low-resolution annotations with redundant regions and reducing the statistical power for downstream analyses (e.g., causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called DECODE. First, we employed direct enhancer activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network classifier for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution (∼500 bp), we implemented a weakly-supervised object detection framework for enhancer localization with precise boundary detection (at 10 bp resolution) using gradient-weighted class activation mapping.

Results

Our DECODE binary classifier outperformed thestate-of-the-artenhancer prediction methods by 24% in transgenic mouse validation. Further, DECODE object detection can condense enhancer annotations to only 12.6% of the original size, while still reporting higher conservation scores and genome-wide association study variant enrichments. Overall, DECODE improves the efficiency of regulatory element mapping with graphic processing units for deep-learning applications and is a powerful tool for enhancer prediction and boundary localization.

Availability

DEOCDE is available atdecode.gersteinlab.org

Contact

pi@gersteinlab.org
Prevention and therapy of SARS-CoV-2 and the B.1.351 variant in mice
Authors: Martinez David R. , Schaefer Alexandra , Leist Sarah R. , Li Dapeng , Gully Kendra , Yount Boyd , Feng Joy Y. , Bunyan Elaine , Porter Danielle P. , Cihlar Tomas , Montgomery Stephanie A. , Haynes Barton F. , Baric Ralph S. , Nussenzweig Michel C. , Sheahan Timothy P.
Published: January 2021

Improving the standard of clinical care for individuals infected with SARS-CoV-2 variants is a global health priority. Small molecule antivirals like remdesivir (RDV) and biologics such as human monoclonal antibodies (mAb) have demonstrated therapeutic efficacy against SARS-CoV-2, the causative agent of COVID-19. However, it is not known if combination RDV/mAb will improve outcomes over single agent therapies or whether antibody therapies will remain efficacious against variants. In kinetic studies in a mouse-adapted model of ancestral SARS-CoV-2 pathogenesis, we show that a combination of two mAbs in clinical trials, C144 and C135, have potent antiviral effects against even when initiated 48 hours after infection. The same antibody combination was also effective in prevention and therapy against the B.1.351 variant of concern (VOC). Combining RDV and antibodies provided a modest improvement in outcomes compared to single agents. These data support the continued use of RDV to treat SARS-CoV-2 infections and support the continued clinical development of the C144 and C135 antibody combination to treat patients infected with SARS-CoV-2 variants.
Games of risk and reward in carnivore communities
Authors: Ruprecht Joel , Eriksson Charlotte E. , Forrester Tavis D. , Spitz Derek B. , Clark Darren A. , Wisdom Michael J. , Bianco Marcus , Rowland Mary M. , Smith Joshua B. , Johnson Bruce K. , Levi Taal
Published: January 2021

Mesopredator release theory suggests that dominant predators suppress subordinate carnivores and ultimately shape community dynamics, but the assumption that subordinate species are only negatively affected ignores the possibility of facilitation through scavenging. We examined the interplay within a carnivore community consisting of cougars, coyotes, black bears, and bobcats using contemporaneous Global Positioning System telemetry data from 51 individuals, diet analysis from 972 DNA-metabarcoded scats, and data from 128 physical investigations of cougar kill sites, 28 of which were monitored with remote cameras. Resource provisioning from competitively-dominant cougars to coyotes through scavenging was so prolific as to be an overwhelming determinant of coyote behavior, space use, and resource acquisition. This was evident via strong attraction of coyotes to cougar kill sites, frequent scavenging of cougar-killed prey, and coyote diets that nearly matched cougars in the magnitude of ungulate consumption. Yet coyotes were often killed by cougars and used space to minimize encounters, complicating the fitness benefits gained from scavenging. We estimated that 23% (95% CI: 8–55%) of the coyote population in our study area was killed by cougars annually suggesting that coyote interactions with cougars are a complex behavioral game of risk and reward. In contrast, we found no indication that bobcat space use or diet was influenced by cougars. Black bears avoided cougars, but there was no evidence of attraction to cougar kill sites, and much lower levels of ungulate consumption and carcass visitation than for coyotes. Interspecific interactions among carnivores are multifaceted encompassing both suppression and facilitation.

Significance Statement

An incomplete understanding of the total influence competitively-dominant predators exert on subordinate species hinders our ability to anticipate the effects that changing carnivore populations will have in ecological communities. Here we show that cougars are the architects of a complex behavioral game of risk and reward, as subordinate or co-occurring carnivores are both provisioned and preyed on by the dominant predators. Each co-occurring carnivore species considered here employed a different strategy to approach the risk-reward tradeoff suggesting there are multiple viable solutions to the game. By not considering the multitude of effects dominant predators have on other carnivores, we are missing important linkages in terrestrial food webs.
Ultraviolet light-induced collagen degradation inhibits melanoma invasion
Authors: Budden Timothy , Gaudy Caroline , Porter Andrew , Kay Emily , Gurung Shilpa , Earnshaw Charles , Roeck Katharina , Craig Sarah , Traves Víctor , Krutmann Jean , Muller Patricia , Motta Luisa , Zanivan Sara , Malliri Angeliki , Furney Simon J , Nagore Eduardo , Virós Amaya
Published: January 2021

Ultraviolet radiation (UVR) increases the incidence of cutaneous melanoma1–4. The ageing, sun-exposed dermis accumulates UVR damage5, and older patients develop more melanomas at UVR-exposed sites4,6,7. As fibroblasts are functionally heterogeneous and play key roles in the stromal contribution to cancer8,9, we asked whether UVR modifies dermal fibroblast function. Here we confirmed the expression of collagen-cleaving matrix metalloprotein-1 (MMP1) by UVR-damaged fibroblasts was persistently upregulated to reduce local levels of collagen 1 (COL1A1), and found dermal COL1A1 degradation by MMP1 decreased melanoma invasion. Conversely, we show inhibiting extracellular matrix degradation and MMP1 expression restored melanoma invasion to UVR damaged dermis. We confirmedin vitrofindings in a cohort of primary cutaneous melanomas of aged humans, showing more cancer cells invade as single cells at the invasive front of melanomas expressing and depositing more collagen. We found collagen and single melanoma cell invasion are robust predictors of poor melanoma-specific survival. These data indicate melanomas arising over UVR-damaged, collagen-poor skin of the elderly are less invasive, and this reduced invasion improves survival. Consequently, although UVR increases tumour incidence, it delays primary melanoma invasion by degrading collagen. However, we show melanoma-associated fibroblasts can restore invasion in low-collagen primary tumours by increasing collagen synthesis. Finally, we demonstrate highCOL1A1gene expression is a biomarker of poor outcome across a broad range of primary cancers.
Seroprevalence ofToxoplasma gondiiamong sylvatic rodents in Poland
Authors: Grzybek Maciej , Antolová Daniela , Tołkacz Katarzyna , Alsarraf Mohammed , Behnke-Borowczyk Jolanta , Nowicka Joanna , Paleolog Jerzy , Biernat Beata , Behnke Jerzy M. , Bajer Anna
Published: January 2021

Toxoplasma gondiiis a significant pathogen affecting humans and animals. We conducted seromonitoring forT. gondiiin four sylvatic rodent species in Poland. We report an overall seroprevalence of 5.5% (3.6% forMyodes glareolusand 20% for other vole species). Seroprevalence in bank voles varied significantly between host age and sex.
Water levels primarily drive variation in photosynthesis and nutrient use of scrub Red Mangroves in the southeastern Florida Everglades
Authors: Hogan J. Aaron , Castaneda-Moya Edward , Lamb-Wotton Lukas , Troxler Tiffany , Baraloto Christopher
Published: January 2021

We investigated how differences in mangrove island micro-elevation (i.e., habitat, center vs. edge) affect tree physiology in a scrub mangrove forests of the southeastern Everglades. We measured leaf gas exchange rates of scrub Rhizophora mangle L. trees monthly during 2019, hypothesizing that CO2 assimilation (Anet) and stomatal conductance (gsw) would decline with increasing water levels and salinity, expecting more-considerable differences at mangrove-island edges than centers, where physiological stress is greatest. Water levels varied between 0 and 60 cm from the soil surface, rising during the wet season (May-October) relative to the dry season (November-April). Porewater salinity ranged from 15 to 30 ppt, being higher at mangrove-island edges than centers. Anet maximized at 15.1 μmol m-2 s-1, and gsw was typically <0.2 mol m-2 s-1, both of which were greater in the dry than the wet season and greater at island centers than edges, with seasonal variability being roughly equal to variation between habitats. After accounting for season and habitat, water level positively affected Anet in both seasons but did not affect gsw. Similarly, porewater salinity had a slightly positive marginal effect on Anet but a negligible effect on gsw. Our findings suggest that inundation stress (i.e., water level) is the primary driver of variation in leaf gas exchange rates of scrub mangroves in the Florida Everglades, while also constraining Anet more than gsw. The interaction between inundation stress due to permanent flooding and habitat varies with season as physiological stress is alleviated at higher-elevation mangrove-island center habitats during the dry season. Freshwater inflows during the wet season, increase water levels and inundation stress at higher-elevation mangrove-island centers, but also potentially alleviate salt and sulfide stress in soils. Thus, habitat heterogeneity leads to differences in nutrient and water acquisition and use between trees growing in island centers versus edges, creating distinct physiological controls on photosynthesis, which likely affect carbon flux dynamics of scrub mangroves in the Everglades.
Loss of Foxc1 and Foxc2 function in chondroprogenitor cells disrupts endochondral ossification
Authors: Almubarak Asra , Lavy Rotem , Srnic Nikola , Hu Yawen , Maripuri Devi P. , Kume Tsutomo , Berry Fred B
Published: January 2021

Endochondral ossification forms and grows the majority of the mammalian skeleton and is tightly controlled through gene regulatory networks. The forkhead box transcription factorsFoxc1andFoxc2have been demonstrated to regulate aspects of osteoblast function in the formation of the skeleton but their roles in chondrocytes to control endochondral ossification are less clear. We demonstrate that Foxc1 expression is directly regulated by SOX9 activity, one of the earliest transcription factors to specify the chondrocyte lineages. Moreover we demonstrate that elevelated expression of Foxc1 promotes chondrocyte differentiation in mouse embryonic stem cells and loss of Foxc1 function inhibits chondrogenesis in vitro. Using chondrocyte-targeted deletion of Foxc1 and Foxc2 in mice, we reveal a role for these factors in chondrocyte differentiation in vivo. Loss of both Foxc1 and Foxc2 caused a general skeletal dysplasia predominantly affecting the vertebral column. The long bones of the limb were smaller and mineralization was reduced and organization of the growth plate was disrupted. In particular, the stacked columnar organization of the proliferative chondrocyte layer was reduced in size and cell proliferation in growth plate chondrocytes was reduced. Differential gene expression analysis indicated disrupted expression patterns in chondrogenesis and ossification genes throughout the entire process of endochondral ossification inCol2-cre;Foxc1Δ/Δ;Foxc2Δ/Δembryos. Our results suggest thatFoxc1andFoxc2are required for correct chondrocyte differentiation and function. Loss of both genes results in disorganization of the growth plate, reduced chondrocyte proliferation and delays in chondrocyte hypertrophy that prevents correct ossification of the endochondral skeleton.
Pore structure controls stability and molecular flux in engineered protein cages
Authors: Adamson Lachlan S. R. , Tasneem Nuren , Andreas Michael P. , Close William , Jenner Eric N. , Szyszka Taylor N. , Young Reginald , Cheah Li Chen , Norman Alexander , MacDermott-Opeskin Hugo I. , O’Mara Megan L. , Sainsbury Frank , Giessen Tobias W. , Lau Yu Heng
Published: January 2021

Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have recently been featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern cage stability and molecular flux through their pores. In this work, we systematically designed a 24-member library of protein cage variants based on the T. maritima encapsulin, each featuring pores of different size and charge. Twelve encapsulin pore variants were successfully assembled and purified, including eight designs with exceptional and prolonged thermal stability. While pores lined with negatively charged residues resulted in more robust assemblies than their corresponding positively charged variants, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures of pore variants elucidated at resolutions between 2.5-3.6 Å. Alongside these structures, molecular dynamics simulations and stopped flow kinetics experiments reveal the importance of considering both pore size and surface charge, together with flexibility and rate determining steps, when designing protein cages for controlling molecular flux.

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Golden hamster piRNAs are necessary for early embryonic development and establishment of spermatogonia
Authors: Loubalova Zuzana , Fulka Helena , Horvat Filip , Pasulka Josef , Malik Radek , Hirose Michiko , Ogura Atsuo , Svoboda Petr
Published: January 2021

PIWI-associated RNAs (piRNAs) support the germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deletedMov10l1helicase in golden hamster, whose piRNA pathway is configured more similarly to that of other mammals.Mov10l1−/−male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and a surge in MYSERV retrotransposon expression. The rare viable spermatogenic cells showed a meiotic failure phenotype likeMov10l1−/−mice. FemaleMov10l1−/−hamsters were sterile due to post-meiotic loss of developmental competence in zygotes. Unique phenotypes ofMov10l1−/−hamsters demonstrate the adaptive nature of piRNA-mediated control of genes and retrotransposons in order to confront emerging genomic threats or acquire new physiological roles.