bluuebunny/crossref_metadata_2025 huggingface dataset:
Climatic factors and host species composition at hibernation sites drive the incidence of bat fungal disease
Authors: Blomberg AS , Lilley TM , Fritze M , Puechmaille SJ
Published: February 2023

Emerging infectious diseases pose a remarkable threat to wildlife, and their incidence will likely be further exacerbated due to climate change. Therefore, developing new, preferably minimally invasive yet effective monitoring systems is crucial for conservation. We investigated whether the occurrence of white-nose disease (WND), a fungal disease of hibernating bats, can be predicted using local climatic conditions and host community composition at hibernation sites. In addition, we used our model to predict the current worldwide potential global distribution of white-nose disease, revealing areas that may be under risk if the pathogen is introduced, and further applied our model to a climate change scenario to illuminate how the potential global distribution of the disease may shift in the future. To achieve this, we fitted a logistic regression model using open-source climate data (mean annual surface temperature (MAST), annual precipitation) and hibernation site census data from 441 hibernacula across Europe. We then applied our model to the current global climatic conditions, as well as a climate change scenario for years 2061–2080, to illuminate the current and future potential global distribution of the disease. We discovered a positive association between the occurrence of WND andMyotis emarginatus,M. myotis/blythii, andM.mystacinus/brandtii, whereasRhinolophus ferrumequinumandR. hipposideroswere negatively associated with the disease. In addition, we were able to detect several areas in the southern hemisphere, that are likely to be at risk if the pathogen is introduced, and demonstrate that climate change may cause a remarkable shift in the distribution range of the disease. We further show that MAST can be used to predict the occurrence of WND, with the highest probability in areas where MAST was 8.3 °C. Our results highlight the importance of environmental factors in controlling the manifestation of disease in localities where both the pathogen and suitable hosts are present, and the massive impact climate change could have in reshaping and expanding the geographic range where WND can occur.
Genetic features and genomic targets of human KRAB-Zinc Finger Proteins
Authors: de Tribolet-Hardy Jonas , Thorball Christian W. , Forey Romain , Planet Evarist , Duc Julien , Khubieh Bara , Offner Sandra , Fellay Jacques , Imbeault Michael , Turelli Priscilla , Trono Didier
Published: February 2023

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on more than a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
Beyond the Active Site: The addition of a remote loop reveals a new complex biological function for chitinase enzymes
Authors: Kozome Dan , Sljoka Adnan , Laurino Paola
Published: February 2023

Loops are small secondary structural elements that play a crucial role in the emergence of new enzyme functions. However, our understanding of loop functions is mainly limited to the catalytic loops. To understand the function of remote loops in enzymes, we studied Glycoside hydrolase family 19 (GH19) chitinase - an essential enzyme family for pathogen degradation in plants. By revealing the evolutionary history and loops appearance of GH19 chitinase, we discovered that one loop which is remote from the catalytic site, is necessary to acquire the new antifungal activity. We demonstrated that this remote loop directly accesses the fungal cell wall, and surprisingly, it needs to adopt a defined structure supported by long-range intramolecular interactions to perform its function. Our findings prove that Nature applies this new strategy at the molecular level to achieve a complex biological function while maintaining the original activity one in the catalytic pocket, suggesting an alternative way to design new enzyme function.
Broad-scale signatures of linked selection under divergent recombination landscapes and mating systems in natural populations of rye and barley
Authors: Waesch Christina , Dreissig Steven
Published: February 2023

Understanding the interactions between patterns of recombination, mating systems, and signatures of natural selection is a central aim in evolutionary biology. Patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Within populations, genetic shuffling is achieved through meiotic recombination, random chromosome segregation, and the frequency of outbreeding. Recombination landscapes vary between species and populations, and are further influenced by mating systems. Here, we use populations of two related grass species, rye (Secale cereale) and barley (Hordeum vulgaressp.spontaneum), that differ in their mating system, to analyse signatures of linked selection under divergent recombination landscapes. Rye (outbreeding) and barley (inbreeding) are members of the Poaceae and diverged approximately 15 M years ago. We estimated population recombination rates, analysed patterns of genetic diversity, identified signatures of linked selection, and quantified the fraction and functional class of genes affected by linked selection. In this comparison, we detected signatures of linked selection in low-recombining regions in both species. In inbreeding barley, the low-recombining fraction of the genome was more than 2-fold larger than in outbreeding rye. Furthermore, considering differences in gene density across the genome, approximately 1.5 times more genes were affected by linked selection in barley than in rye. In both species, genomic regions affected by linked selection harbour mostly genes involved in basic cellular processes. We provide empirical evidence for quantitative differences in recombination landscapes between closely related species of divergent mating systems, and discuss the consequences of linked selection and the efficacy of natural selection.

Significance statement

The ability of natural selection to disentangle beneficial from deleterious mutations across the genome is shaped by patterns of recombination, yet our understanding of the magnitude of this interaction is incomplete. In our work, we show that patterns of recombination differ between related outbreeding and inbreeding grass species, and that the efficacy of selection differs between them. We provide empirical evidence for quantitative differences in recombination landscapes and patterns of selection.
Robustness of Felsenstein’s versus Transfer Bootstrap Supports with respect to Taxon Sampling
Authors: Zaharias Paul , Lemoine Frédéric , Gascuel Olivier
Published: February 2023

The bootstrap method is based on resampling alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon-sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tends to return low supports for deep branches. The Transfer Bootstrap Expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports, without inducing falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depth, using empirical datasets. Our results show that the main critic of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.
Genome assembly of the deep-sea coralLophelia pertusa
Authors: Herrera Santiago , Cordes Erik E.
Published: February 2023

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly ofLophelia pertusafrom the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio CLR data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, andab initiogene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.
Comparative analysis ofSQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL)gene family between bryophytes and seed plants
Authors: Alisha Alisha , Szweykowska-Kulińska Zofia , Sierocka Izabela
Published: February 2023

SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE(SPL) genes encode plant-specific transcription factors which have been found to be conserved in green plants lineage. SPL proteins are important regulators of diverse plant developmental processes in bryophytes and vascular plants. In our study, we took advantage of available genome sequences of representatives of each bryophyte clade to investigate the relationships ofSPLgenes between bryophytes and model angiospermArabidopsis thaliana. We have identified fourSPLgenes in each of the two hornworts species,Anthoceros agrestisandAnthoceros punctatus, what is similar to the set ofSPLgenes present in the liverwortMarchantia polymorpha. Thus, the analyzed hornworts and liverwort genomes encode a minimal set ofSPLgenes in comparison to other land plants that may resemble an archetype ofSPLgenes present in the ancestor of land plants. The phylogenetic analysis revealed the presence of fourSPLgroups. Comparative gene structure analysis showed thatSPLsshare similar exon-intron organization within the same phylogenetic group with some exceptions in hornworts. While we have identified conserved protein motifs between bryophytes andArabidopsisin three out of four phylogenetic groups, the motif content differed explicitly in the fourth group. Since current understanding ofSPLgenes mostly arises from seed plants, the presented comparative and phylogenetic analysis will provide better understanding ofSPLgene family from the representatives of the oldest living land plants.
Label-free differential imaging of cellular components in mouse brain tissue by wide-band photoacoustic microscopy
Authors: Liu Yajing , Wong Terence T W , Shi Junhui , He Yun , Nie Liming , Wang Lihong V.
Published: February 2023

Mapping diverse cellular components with high spatial resolution is important to interrogate biological systems and study disease pathogenesis. Conventional optical imaging techniques for mapping biomolecular profiles with differential staining and labeling methods are cumbersome. Different types of cellular components exhibit distinctive characteristic absorption spectra across a wide wavelength range. By virtue of this property, a lab-made wide-band optical-resolution photoacoustic microscopy (wbOR-PAM) system, which covers wavelengths from the ultraviolet and visible to the shortwave infrared regions, was designed and developed to capture multiple cellular components in 300-μm-thick brain slices at nine different wavelengths without repetitive staining and complicated processing. This wbOR-PAM system provides abundant spectral information. A reflective objective lens with an infinite conjugate design was applied to focus laser beams with different wavelengths, avoiding chromatic aberration. The molecular components of complex brain slices were probed without labeling. The findings of the present study demonstrated a distinctive absorption of phospholipids, a major component of the cell membrane, brain, and nervous system, at 1690 nm and revealed their precise distribution with microscopic resolution in a mouse brain, for the first time. This novel imaging modality provides a new opportunity to investigate important biomolecular components without either labeling or lengthy specimen processing, thus, laying the groundwork for revealing cellular mechanisms involved in disease pathogenesis.
Investigating fine-scale breeding habitat use by amphibians in a continuous wetland using environmental DNA
Authors: Guenat Julie Morgane , Gander Antoine , Fumagalli Luca , Lavanchy Guillaume
Published: February 2023

Designing effective conservation plans to protect species from extinction requires a better understanding of their ecology. Conventional methods used to investigate habitat use are time consuming, and detectability of cryptic species is often insufficient. Environmental DNA (eDNA)-based approaches now provide an alternative for ecosystems monitoring and assessment. Nevertheless, to our knowledge, such methods have never been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchâtel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species communities as well as individual species occurrences. We showed that the main factor structuring species communities was water temperature, and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA approach is a promising tool to study species’ ecology at a small scale in continuous wetland habitats.
CD82 expression marks the endothelium to hematopoietic transition at the onset of blood specification in human
Authors: Menegatti Sara , Potts Bethany , Paredes Roberto , Garcia-Alegria Eva , Murtuza Baker Syed , Kouskoff Valerie
Published: February 2023

During embryonic development, all blood progenitors are initially generated from endothelial cells that acquire a hemogenic potential. Blood progenitors emerge through an endothelial-to-hematopoietic transition regulated by the transcription factor RUNX1. To date, we still know very little about the molecular characteristics of hemogenic endothelium and the molecular changes underlying the transition from endothelium to hematopoiesis. Here, we analysed at the single cell level a human embryonic stem cell-derived endothelial population containing hemogenic potential. RUNX1-expressing endothelial cells, which harbour enriched hemogenic potential, show very little molecular differences to their endothelial counterpart suggesting priming toward hemogenic potential rather than commitment. Additionally, we identify CD82 as a marker of the endothelium-to-hematopoietic transition. CD82 expression is rapidly upregulated in newly specified blood progenitors then rapidly downregulated as further differentiation occurs. Together our data suggest that endothelial cells are first primed toward hematopoietic fate, then rapidly undergo the transition from endothelium to blood.
Integrative single-cell transcriptomics clarifies adult neurogenesis and macroglia evolution
Authors: Morizet David , Foucher Isabelle , Alunni Alessandro , Bally-Cuif Laure
Published: February 2023

Macroglia fulfill essential functions in the adult vertebrate brain, producing and maintaining neurons and regulating neuronal communication. However, we still know little about their emergence and diversification. We used the zebrafishD. rerioas a distant vertebrate model with moderate glial diversity as anchor to reanalyze datasets covering over 600 million years of evolution. We identify core features of adult neurogenesis and innovations in the mammalian lineage with a potential link to the rarity of radial glia-like cells in adult humans. Our results also suggest that functions associated with astrocytes originated in a multifunctional cell type fulfilling both neural stem cell and astrocytic functions before these diverged. Finally, we identify conserved elements of macroglial cell identity and function and their time of emergence during evolution.

One-Sentence Summary

Radial glia of the adult zebrafish forebrain associate transcriptomic features of adult neural stem cells and astrocytes
Singular superlet transform achieves markedly improved time-frequency super-resolution for separating complex neural signals
Authors: Kesgin Kaan , Jörntell Henrik
Published: February 2023

Time-frequency decomposition is a well-established method to unmix signals generated by multiple sources with unique characteristics. However, there are cases of high signal complexity where existing time-frequency decomposition tools are insufficient for localizing and representing short-bursting signals. One example is the currently highly popular extracellular low-impedance recordings from multi-electrode arrays in the brainin vivowhere each neuron repeatedly generates a specific signal ‘fingerprint’ (characteristic spike waveform) that can be mixed with the signals of 100s of other sources, including the spikes of nearby neurons. Here we derive the singular superlet transform (SST) method, which enables highly localized representations of fast and short bursts compared to other super-resolution spectral estimators, while also requiring orders of magnitude fewer operations. We demonstrate a substantial edge of SST over current methods in isolating specific neuronal spikes with high-fidelity in challenging, complex recording signals from neocortexin vivo. We also exemplify SST’s generic signal processing capability by achieving outstanding resolution in the decomposition of complex acoustic data.
Continuous, long-term crawling behavior characterized by a robotic transport system
Authors: Yu James , Dancausse Stephanie , Paz Maria , Faderin Tolu , Gaviria Melissa , Shomar Joseph , Zucker Dave , Venkatachalam Vivek , Klein Mason
Published: February 2023

Detailed descriptions of behavior provide critical insight into the structure and function of nervous systems. InDrosophilalarvae and many other systems, short behavioral experiments have been successful in characterizing rapid responses to a range of stimuli at the population level. However, the lack of long-term continuous observation makes it difficult to dissect comprehensive behavioral dynamics of individual animals and how behavior (and therefore the nervous system) develops over time. To allow for long-term continuous observations in individual fly larvae, we have engineered a robotic instrument that automatically tracks and transports larvae throughout an arena. The flexibility and reliability of its design enables controlled stimulus delivery and continuous measurement over developmental time scales, yielding an unprecedented level of detailed locomotion data. We utilize the new system’s capabilities to perform continuous observation of exploratory behavior over a duration of six hours with and without a thermal gradient present, and in a single larva for over 30 hours. Long-term free-roaming behavior and analogous short-term experiments show similar dynamics that take place at the beginning of each experiment. Finally, characterization of larval thermotaxis in individuals reveals a bimodal distribution in navigation efficiency, identifying distinct phenotypes that are obfuscated when only analyzing population averages.
From Policy to Practice: Tracking an Open Science Funding Initiative
Authors: Ratan Kristen , McIntosh Souad , Shah Hetal V. , Lewis Matt , Dumanis Sonya B. , Vines Timothy H. , Schekman Randy , Riley Ekemini A
Published: February 2023

This is a critical moment in the open science landscape. Over the past few years there has been growing momentum to improve open research policies and require grantees to share all research outputs, from datasets to code to protocols, inFAIR (findable, accessible, interoperable and reusable [FAIR]) repositorieswith persistent identifiers attached. The Aligning Science Across Parkinson’s (ASAP) initiative has made substantial investments in improving open science compliance monitoring for its grantees, requiring grantees to update their manuscripts if not all research outputs have been linked in the initial manuscript version. Here, we evaluate ASAP’s effectiveness in improving research output sharing for all articles processed through the ASAP compliance workflow between March 1, 2022, and October 1, 2022. Our ultimate goal in sharing our findings is to assist other funders and institutions as they consider open science implementation. By normalizing the open science and compliance process across funding bodies, we hope to simplify and streamline researcher, institutional, and funder workflows, allowing researchers to focus on science by easily leveraging resources and building upon the work of others.
Three rules for epigenetic inheritance of human Polycomb silencing
Authors: Shafiq Tiasha A. , Moazed Danesh
Published: February 2023

Heritable expression of developmental genes is mediated by autoregulating transcription factor networks (TFNs) and Polycomb repressive chromatin silencing complexes (PRCs). Whether the mammalian Polycomb pathway mediates DNA sequence-independent epigenetic memory at genes being activated by TFNs remains unknown. Here, we show that, in human cells, newly induced Polycomb silencing at initially active developmental genes can be inherited for many cell divisions. However, when Polycomb silencing is similarly induced near ubiquitously expressed housekeeping genes, it is not heritable. Inheritance requires the recognition of CG-rich DNA by a Polycomb accessory protein, MTF2/PCL2, the histone H3 lysine 27 trimethylation (H3K27me3) and histone H2A lysine 119 mono-ubiquitination (H2AK119ub1) activities of PRC1 and PRC2, and their associated positive feedback (read-write). In the absence of H3K27me3, H2AK119ub1 can mediate inheritance of silencing by a mechanism that requires the recognition of H2AK119ub1 by the variant Polycomb Repressive Complex 1. These findings indicate that inheritance of Polycomb silencing in human cells (1) depends on sequence features of developmental gene loci (2) requires PRC1 and H2AK119ub1, and (3) can be mediated by PRC1-H2AK119ub1 independently of H3K27me3.
SMCHD1 loss triggers DUX4 expression by disrupting splicing in FSHD2
Authors: Engal Eden , Sharma Aveksha , Taqatqa Nadeen , Bentata Mercedes , Jaffe-Herman Shiri , Geminder Ophir , Lewis Reyut , Gotkine Marc , Salton Maayan , Drier Yotam
Published: February 2023

Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1) is a non-canonical member of the structural maintenance of chromosomes (SMC) protein family involved in the regulation of chromatin structure, epigenetic regulation, and transcription. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy type 2 (FSHD2), a rare genetic disorder characterized by progressive muscle weakness and wasting, believed to be caused by aberrant expression of DUX4 in muscle cells. Here we suggest a new role for SMCHD1 as a regulator of alternative splicing in various cell types. We demonstrate how SMCHD1 mutations cause splicing alterations of DNA Methyltransferase 3 Beta DNMT3B which can lead to hypomethylation, DUX4 expression, and FSHD pathogenesis. Analyzing RNA-seq data from muscle biopsies of FSHD2 patients and Smchd1 knocked out cells, we found that hundreds of genes were mis-spliced upon loss of SMCHD1. At least 20% of mis-spliced genes were associated with abnormalities of the musculature. Moreover, we show that mis-spliced exons tend to be bound by SMCHD1, and these exons demonstrate a slower elongation rate, suggesting SMCHD1 binding promotes exon exclusion by slowing RNA polymerase II (RNAPII). Specifically, we discovered that SMCHD1 mutations promote the splicing of the DNMT3B1 isoform of DNMT3B by perturbing RNAPII elongation rate and recruitment of the splicing factor RBM5. The mis-splicing of DNMT3B leads to hypomethylation of the D4Z4 region and DUX4 overexpression. These results suggest that mis-splicing by SMCHD1 may play a major role in FSHD2 pathogenesis by promoting the mis-splicing of different targets including DNMT3B, and highlight the potential for targeting splicing as a therapeutic strategy for this disorder.

Significance statement

Our study sheds light on how the loss of SMCHD1 drives the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD), a rare genetic disorder characterized by muscle weakness and wasting. We found that SMCHD1 mutations led to changes in splicing of hundreds of genes, 20% of which were related to muscle abnormalities. We found that SMCHD1 tends to bind mis-spliced exons and that its binding slows down the elongation rate of RNA polymerase II often leading to the exclusion of the exon. One of these targets is DNA Methyltransferase 3 Beta (DNMT3B), and we show that the isoform promoted by SMCHD1 mutations leads to hypomethylation of a repeat region near DUX4 and to DUX4 overexpression, a known cause for FSHD. Our results provide insight into the molecular mechanisms underlying this disorder, and suggest splicing modulation as a therapeutic strategy for FSHD.
Ultrasensitive response explains the benefit of combination chemotherapy despite drug antagonism
Authors: Patterson Sarah C. , Pomeroy Amy E. , Palmer Adam C.
Published: February 2023

Most aggressive lymphomas are treated with combination chemotherapy, commonly as multiple cycles of concurrent drug administration. Concurrent administration is in theory optimal when combination therapies have synergistic (more than additive) drug interactions. We investigated pharmacodynamic interactions in the standard 4-drug ‘CHOP’ regimen in Peripheral T-Cell Lymphoma (PTCL) cell lines, and found that CHOP consistently exhibits antagonism and not synergy. We tested whether staggered treatment schedules could improve tumor cell kill by avoiding antagonism, using month-longin vitromodels of concurrent or staggered treatments. Surprisingly, we observed that tumor cell kill is maximized by concurrent drug administration despite antagonistic drug-drug interactions. We propose that an ultrasensitive dose response, as described in radiology by the linear-quadratic (LQ) model, can reconcile these seemingly contradictory experimental observations. The LQ model describes the relationship between cell survival and dose, and in radiology has identified scenarios favoring hypofractionated radiation – the administration of fewer large doses rather than multiple smaller doses. Specifically, hypofractionated treatment can be favored when cells require an accumulation of DNA damage, rather than a ‘single hit’, in order to die. By adapting the LQ model to combination chemotherapy and accounting for tumor heterogeneity, we find that tumor cell kill is maximized by concurrent administration of multiple drugs, even when chemotherapies have antagonistic interactions. Thus, our study identifies a new mechanism by which combination chemotherapy can be clinically beneficial that is not reliant on positive drug-drug interactions.
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing
Authors: Salavati M. , Clark R. , Becker D. , Kühn C. , Plastow G. , Dupont S. , Moreira G.C.M. , Charlier C. , Clark E.L.
Published: February 2023

Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programmes. The fine mapping of promoters (transcription start sites [TSS]) and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific phenotypes. To this aim we used Cap Analysis Gene Expression (CAGE) sequencing to define TSS and their co-expressed short-range enhancers (<1kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9) and analysed tissue- and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the three populations (Holstein, Charolais x Holstein and Kinsella beef composite [KC]). In addition, we performed a comparative analysis of our cattle dataset with available data for seven other species to identify TSS and TSS-Enhancers that are specific to cattle. The CAGE dataset will be combined with other transcriptomic information for the same tissues generated in the BovReg project to create a new high-resolution map of transcript diversity across tissues and populations in cattle. Here we provide the CAGE dataset and annotation tracks for TSS and TSS Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programmes.
SalmonellaTyphimurium effector SseI regulates host peroxisomal dynamics to acquire lysosomal cholesterol for better intracellular growth
Authors: Raj Desh , Nair Abhilash Vijay , Sharma Jyotsna , Prakash Shakti , Kaushik Aman , Basu Swarnali , Sahu Shikha , Singh Shriya , Bhosale Vivek , Chandra Tulika , Ghoshal Uday C , Dasgupta Arunava , Siddiqi Mohammad Imran , Gupta Shashi Kumar , Chakravortty Dipshikha , Ammanathan Veena , Lahiri Amit
Published: February 2023

IntracellularSalmonellaresides and multiplies in cholesterol-rich specialized compartment calledSalmonella-containing vacuoles (SCVs) and avoids fusion with acidic lysosomes. Given, lysosomes are primary organelle that redistributes LDL derived cholesterol to other organelles; we questioned how lysosomal cholesterol can be transported to SCV. We demonstrate here that peroxisomes are recruited to SCVs in human primary macrophages, epithelial cells and functions as pro-bacterial organelles. Further, this interaction is assisted by SseI, aSalmonellaeffector protein containing mammalian peroxisome targeting sequence. SseI localizes to peroxisome, interacts and activates a host Ras GTPase, ARF-1 on the peroxisome membrane. Activation of ARF-1 leads to recruitment of phosphatidylinsolitol-5- phosphate-4 kinase to generate phosphatidylinsolitol-4-5-bisphosphate on peroxisomes. Accordingly, theΔsseIstrain showed reduced virulence in cell lines and during mice infection. Taken together, our work identified a fascinating mechanism by which a pathogen targets host organelles via its secretory effectors and exploits host metabolic intermediates for its intracellular proliferation.
Comparative Features of Calretinin, Calbindin and Parvalbumin Expressing Interneurons in Mouse and Monkey Primary Visual and Frontal Cortices
Authors: Medalla Maria , Mo Bingxin , Nasar Rakin , Zhou Yuxin , Park Junwoo , Luebke Jennifer I
Published: February 2023

Much is known about differences in pyramidal cells across cortical areas and species, but studies of interneurons have focused on comparisons within single cortical areas and/or species. Here we quantified the distribution and somato-dendritic morphology of interneurons expressing one or more of the calcium binding proteins (CaBPs) calretinin (CR), calbindin (CB) and/or parvalbumin (PV) in mouse (Mus musculus) versus rhesus monkey (Macaca mulatta) in two functionally and cytoarchitectonically distinct regions- the primary visual and frontal cortical areas. The density, laminar distribution and morphology of interneurons were assessed in serial brain sections using immunofluorescent multi-labeling, stereological counting and 3D reconstructions. There were significantly higher densities of CB+ and PV+ neurons in visual compared to frontal areas in both species. The main species difference was the significantly greater density and proportion of CR+ interneurons and lower extent of CaBP co-expression in monkey compared to mouse cortices. Cluster analyses revealed that the somato-dendritic morphology of layer 2-3 inhibitory interneurons is more dependent on CaBP expression than on species and area. Only modest effects of species were observed for CB+ and PV+ interneuron morphologies, while CR+ neurons showed no difference. By contrast to pyramidal cells which show highly distinctive area- and species-specific features, here we found more subtle differences in the distribution and features of interneurons across areas and species. These data yield insight into how nuanced differences in the population organization and properties of neurons may underlie specializations in cortical regions to confer species and area-specific functional capacities.

Key Points:

Somato-dendritic morphology of distinct interneurons did not substantially scale and vary across areas and species- differences were mainly dependent on CaBP expression.

Cortical diversity in inhibitory function across areas and species is thus likely to be derived from differential laminar distribution and densities of distinct interneuron subclasses.

In contrast to pyramidal cells which differ widely in distribution and morphology across areas and species, the features of interneurons appears to be relatively more conserved across areas and species.
Forest cover is more important than habitat integrity or landscape configuration in determining habitat use by mammals in a human-modified landscape in Colombia
Authors: Pardo Lain E. , Gómez-Valencia Bibiana , Deere Nicolas J. , Varón Yenifer Herrera , Soto Carolina , Noguera-Urbano Elkin A. , Sánchez-Clavijo Lina M. , Romero Luis , Díaz-Pulido Angélica , Quintero José Manuel Ochoa
Published: February 2023

Human activities shape the structure of landscapes in different ways and hence modify animal communities depending on the type and intensity of these activities. The Montes de Maria subregion of Colombia has experienced a heavy transformation of most areas despite covering one of the last remnants of dry forest, a critically endangered ecosystem. However, the effects of this transformation have been little explored. Here, we used a multispecies occupancy model (MSOM) to understand the relative influence of three components of land-use change – deforestation (remaining habitat amount), degradation of habitat quality (habitat quality) and fragmentation (landscape configuration) on mammalian habitat use across a mosaic of tropical dry forest in Colombia. Our data suggest that the percentage of forest cover was substantially important for herbivores, and consistently showed a moderate effect on the entire community and some individual species. High variability in species-specific responses to the examined variables hindered broad taxonomic generalizations, nevertheless, we detected a moderate positive effect of forest cover in both diet specialists and generalists species, as well as in species with small home ranges. Although omnivores responses, tended to use less complex landscapes (mosaics of land uses), there was high uncertainty in this response. The lack of substantial effects on most species, and the absence of threatened species across this anthropogenic landscape, suggests that the current community is composed of species tolerant to habitat modifications, but not only diet generalist species. This is most likely the result of a long filtering process caused by land use transformation and hunting which could have caused non-sensitive species to distribute relatively homogenously across this landscape. Our results suggest that conservation strategies in the study area should focus on conserving and expanding as much forest as possible rather than only improving the quality of already existing forest patches.
PrePPI: A structure informed proteome-wide database of protein-protein interactions
Authors: Petrey Donald , Zhao Haiqing , Trudeau Stephen , Murray Diana , Honig Barry
Published: February 2023

We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural clues within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) clue is derived from templatebased modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing onE. coliand human protein-protein interaction (PPI) databases. A PrePPI database of ~1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features (https://honiglab.c2b2.columbia.edu/PrePPI). PrePPI is a state-of- the-art resource that offers an unprecedented structure-informed view of the human interactome.

Graphic Abstract
Integrated Stress Response signaling acts as a metabolic sensor in fat tissues to regulate oocyte maturation and ovulation
Authors: Grmai Lydia , Michaca Manuel , Lackner Emily , Nampoothiri V.P. Narayanan , Vasudevan Deepika
Published: February 2023

Reproduction is an energy-intensive process requiring systemic coordination. However, the inter-organ signaling mechanisms that relay nutrient status to modulate reproductive output are poorly understood. Here, we useDrosophila melanogasteras a model to establish the Integrated Stress response (ISR) transcription factor, Atf4, as a fat tissue metabolic sensor which instructs oogenesis. We demonstrate that Atf4 regulates the lipase Brummer to mediate yolk lipoprotein synthesis in the fat body. Depletion ofAtf4in the fat body also blunts oogenesis recovery after amino acid deprivation and re-feeding, suggestive of a nutrient sensing role for Atf4. We also discovered that Atf4 promotes secretion of a fat body-derived neuropeptide, CNMamide, which modulates neural circuits that promote egg-laying behavior (ovulation). Thus, we posit that ISR signaling in fat tissue acts as a “metabolic sensor” that instructs female reproduction: directly, by impacting yolk lipoprotein production and follicle maturation, and systemically, by regulating ovulation.
The non-deterministic genotype-phenotype map of RNA secondary structure
Authors: García-Galindo Paula , Ahnert Sebastian E. , Martin Nora S.
Published: February 2023

Selection and variation are both key aspects in the evolutionary process. Previous research on the mapping between molecular sequence (genotype) and molecular fold (phenotype) has shown the presence of several structural properties in different biological contexts, implying that these might be universal in evolutionary spaces. The deterministic genotype-phenotype (GP) map that links short RNA sequences to minimum free energy secondary structures has been studied extensively because of its computational tractability and biologically realistic nature. However, this mapping ignores the phenotypic plasticity of RNA. We define a GP map that incorporates non-deterministic phenotypes, and take RNA as a case study; we use the Boltzmann probability distribution of folded structures and examine the structural properties of non-deterministic (ND) GP maps for RNA sequences of length 12 and coarse-grained RNA structures of length 30 (RNAshapes30). A framework is presented to study robustness, evolvability and neutral spaces in the non-deterministic map. This framework is validated by demonstrating close correspondence between the non-deterministic quantities and sample averages of their deterministic counterparts. When using the non-deterministic framework we observe the same structural properties as in the deterministic GP map, such as bias, negative correlation between genotypic robustness and evolvability, and positive correlation between phenotypic robustness and evolvability.
luxAgene fromEnhygromyxa salinaencodes a functional homodimeric luciferase
Authors: Yudenko Anna , Bazhenov Sergey V. , Aleksenko Vladimir A. , Goncharov Ivan M. , Semenov Oleg , Remeeva Alina , Nazarenko Vera V. , Kuznetsova Elizaveta , Fomin Vadim V. , Konopleva Maria N. , Al Ebrahim Rahaf , Sluchanko Nikolai N. , Ryzhykau Yury , Semenov Yury S. , Kuklin Alexander , Manukhov Ilya V. , Gushchin Ivan
Published: February 2023

Several clades of luminescent bacteria are known currently. They all contain similarluxoperons, which include the genesluxAandluxBencoding a heterodimeric luciferase. The aldehyde oxygenation reaction is catalyzed by the subunit LuxA, while LuxB is inactive. Recently, genomic analysis identified a subset of bacterial species with rearrangedluxoperons lackingluxB. Here, we show that the product of theluxAgene from the reducedluxACDEoperon ofEnhygromyxa salinais luminescent upon addition of aldehydes bothin vivoinEscherichia coliandin vitro. Overall,EsLuxA is less bright compared with luciferases fromAliivibrio fischeri(AfLuxAB) andPhotorhabdus luminescens(PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure ofEsLuxA determined at the resolution of 2.71 Å reveals a classical monooxygenase fold, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil inVibrio harveyiLuxA, form α-helices inEsLuxA. Phylogenetic analysis showsEsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of theluxAgene and its speciation toluxAandluxBin the previously described luminescent bacteria. Our work paves the way for discovery of new luciferases that have an advantage of being encoded by a single gene.
Syndapin Regulates the RAP-1 GTPase to Control Endocytic Recycling via RHO-1 and Non-Muscle Myosin II
Authors: Rodriguez-Polanco Wilmer R. , Norris Anne , Velasco Agustin B. , Gleason Adenrele M. , Grant Barth D.
Published: February 2023

After endocytosis, many plasma membrane components are recycled via narrow-diameter membrane tubules that emerge from early endosomes to form recycling endosomes, eventually leading to their return to the plasma membrane. We previously showed that the F-BAR and SH3 domain Syndapin/PACSIN-family protein SDPN-1 is requiredin vivofor basolateral endocytic recycling in theC. elegansintestine. Here we sought to determine the significance of a predicted interaction between the SDPN-1 SH3 domain and a target sequence in PXF-1/PDZ-GEF1/RAPGEF2, a known exchange factor for Rap-GTPases. We found that endogenous mutations we engineered into the SDPN-1 SH3 domain, or its binding site in the PXF-1 protein, interfere with recyclingin vivo, as does loss of the PXF-1 target RAP-1. Rap-GTPases have been shown in several contexts to negatively regulate RhoA activity. Our results show that RHO-1/RhoA is enriched on SDPN-1 and RAP-1 positive endosomes in theC. elegansintestine, and loss of SDPN-1 or RAP-1 elevates RHO-1(GTP) levels on intestinal endosomes. Furthermore, we found that depletion of RHO-1 suppressedsdpn-1mutant recycling defects, indicating that control of RHO-1 activity is a key mechanism by which SDPN-1 acts to promote endocytic recycling. RHO-1/RhoA is well-known for controlling actomyosin contraction cycles, although little is known of non-muscle myosin II on endosomes. Our analysis found that non-muscle myosin II is enriched on SDPN-1 positive endosomes, with two non-muscle myosin II heavy chain isoforms acting in apparent opposition. Depletion ofnmy-2inhibited recycling likesdpn-1mutants, while depletion ofnmy-1suppressedsdpn-1mutant recycling defects, indicating actomyosin contractility in controlling recycling endosome function.
CRISPR/Cas9-Based Edition of Frataxin Gene inDictyostelium discoideumfor Friedreich’s Ataxia Disease Modeling
Authors: Gentili Hernan G. , Pignataro María Florencia , Olmos Justo , Pavan Florencia , Ibáñez Itati , Santos Javier , Velázquez Duarte Francisco
Published: February 2023

In this paper we describe the development of a new model system for Friedreich’s Atax- ia (FA) usingDictyostelium discoideum. We investigated the conservation of function between humans andD. discoideumand showed that DdFXN can substitute the human version in the interaction and activation of the Fe-S assembly supercomplex. We edited thefxnlocus and isolated a defective mutant, clone 8, which presents landmarks of frataxin deficiency, such as a decrease in Fe-S cluster-dependent enzymatic functions, growth rate reduction, and increased sensitivity to oxidative stress. In addition multicellular development is affected as well as grow on bacterial lawn.

We also assessed the rescuing capacity of DdFXN-G122V, a version that mimics a human variant present in some FA patients. While the expression of DdFXN-G122V rescues growth and enzymatic activity defects, as DdFXN does, multicellular development defects were only partially rescued

The results of the study suggest that this new model system offers a wide range of pos- sibilities to easily explore diverse phenotypes in FA and develop drug or treatment screenings for designing and evaluating therapeutic strategies.