bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus
Authors: Etherington GJ , Nash W , Ciezarek A , Mehta TK , Barria A , Peñaloza C , Khan MGQ , Durrant A , Forrester N , Fraser F , Irish N , Kaithakottil GG , Lipscombe J , Trong T , Watkins C , Swarbreck D , Angiolini E , Cnaani A , Gharbi K , Houston RD , Benzie JAH , Haerty W 
Published: May 2022

BackgroundThe Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.FindingsUsing a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.ConclusionBecause of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.
Transposable elements are associated with the variable response to influenza infection
Authors: Chen Xun , Pacis Alain Sarabia , Aracena Katherine A , Gona Saideep , Kwan Tony , Groza Cristian , Lin Yen Lung , Sindeaux Renata Helena Monteiro , Yotova Vania , Pramatarova Albena , Simon Marie-Michelle , Pastinen Tomi M. , Barreiro Luis , Bourque Guillaume 
Published: May 2022

SUMMARYInfluenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Given that transposable elements (TEs) contribute to the activation of innate immunity, we wanted to explore their potential role in this variability. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using ATAC-seq we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators in stably enriched TE families and with other factors in variable families, including KRAB-ZNFs. We also observed a strong association between basal TE transcripts and viral load post infection. Finally, we built a predictive model suggesting that TEs, and host factors regulating TEs, contribute to the variable response to infection.
Multiple omic investigations of freeze tolerance adaptation in the aquatic ectothermic vertebrate, the Amur sleeper
Authors: Lv Wenqi , Jiang Haifeng , Qian Yuting , Meng Minghui , Wang Cheng , Sun Ning , Lu Yongrui , Bing Houhua , Fang Chengchi , Irwin David M. , He Shunping , Yang Liandong 
Published: May 2022

AbstractFreeze tolerance is an amazing overwintering strategy that enables ectotherms to occupy new niches and survive in cold climates. However, the genetic basis underpinning this ecologically relevant adaptation is largely unknown. Amur sleeper is the only known freeze-tolerant fish species that can overwinter with its entire body frozen in ice. Here, we sequenced the chromosome-level genome of the Amur sleeper and performed comparative genomic, transcriptomic, and metabolomic analyses to investigate this remarkable adaptation. Phylogenetic analyses showed that the Amur sleeper diverged from its close relative with no cold hardiness about 15.07 million years ago and revealed two unusual population expansions during the glacial epochs. Integrative omics data identified a synchronous regulation of genes and metabolites involved in hypometabolism and cellular stress response, and several related genes showed strong evidence of accelerated evolution and positive selection. Potential evolutionary innovations that might aid in freezing survival were found to be associated with the dynamic rearrangement of the cytoskeleton to maintain cell viability, redistribution of water and cryoprotectants to limit cell volume reduction, and inhibition in nerve activity to facilitate dormancy, demonstrating a coordinated evolution for this complex adaptation. Overall, our work provides valuable resources and opportunities to unveil the genetic basis of freeze tolerance adaptation in ectothermic vertebrates.
Bi-Phasic Quasistatic Brain Communication for Fully Untethered Connected Brain Implants
Authors: Chatterjee Baibhab , Nath Mayukh , Gaurav Kumar K , Xiao Shulan , Jayant Krishna , Sen Shreyas 
Published: May 2022

ABSTRACTWireless communication using electro-magnetic (EM) fields acts as the backbone for information exchange among wearable devices around the human body. However, for Implanted devices, EM fields incur high amount of absorption in the tissue, while alternative modes of transmission including ultrasound, optical and magnetoelectric methods result in large amount of transduction losses due to conversion of one form of energy to another, thereby increasing the overall end-to-end energy loss. To solve the challenge of wirelesspowering and communication in a brain implant with low end-end channel loss, we present Bi-Phasic Quasistatic Brain Communication (BP-QBC), achieving < 60dB worst-case end-to-end channel loss at a channel length of ~55mm, by using Electro-quasistatic (EQS) Signaling thatavoids transduction losses due to no field-modality conversion. BP-QBC utilizes dipole coupling based signal transmission within the brain tissue using differential excitation in the transmitter (TX) and differential signal pick-up at the receiver (RX), while offering ~41X lower power w.r.t. traditional Galvanic Human Body Communication (G-HBC) at a carrier frequency of 1MHz, by blocking any DC current paths through the brain tissue. Since the electrical signal transfer through the human tissue is electro-quasistatic up to several 10’s of MHz range, BP-QBC allows a scalable (bps-10Mbps) duty-cycled uplink (UL) from the implant to an external wearable. The power consumption in the BP-QBC TX is only 0.52 μW at 1Mbps (with 1% duty cycling), which is within the range of harvested power in the downlink (DL) from a wearable hub to an implant through the EQS brain channel, with externally applied electric currents < 1/5th of ICNIRP safety limits. Furthermore, BP-QBCeliminates the need for sub-cranial interrogators/repeaters, as it offers better signal strength due to no field transduction. Such low end-to-end channel loss with high data rates enabled by a completely new modality of brain communication and powering has deep societal and scientific impact in the fields of neurobiological research, brain-machine interfaces, electroceuticals and connected healthcare.
A detailed behavioral, videographic, and neural dataset on object recognition in mice
Authors: Rodgers Chris C. 
Published: May 2022

AbstractMice adeptly use their whiskers to touch, recognize, and learn about objects in their environment. This ability is enabled by computations performed by populations of neurons in the somatosensory cortex. To understand these computations, we trained mice to use their whiskers to recognize different shapes while we recorded activity in the barrel cortex, which processes whisker input. Here, we present a large dataset of high-speed video of the whiskers, along with rigorous tracking of the entire extent of multiple whiskers and every contact they made on the shape. We used spike sorting to identify individual neurons, which responded with precise timing to whisker contacts and motion. These data will be useful for understanding the behavioral strategies mice use to identify objects by touch, as well as the neuronal responses that mediate those strategies. More generally, our carefully curated labeled data could be used to develop new computer vision algorithms for tracking body posture, or for extracting responses of individual neurons from large-scale neural recordings.
Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase Lck
Authors: Prakaash Dheeraj , Cook Graham P. , Acuto Oreste , Kalli Antreas C. 
Published: May 2022

ABSTRACTThe membrane-bound lymphocyte-specific protein-tyrosine kinase (Lck) triggers T cell antigen receptor signalling to initiate adaptive immune responses. Despite many structure-function studies, the mode of action of Lck and the potential role of plasma membrane lipids in regulating Lck’s activity remains elusive. Advances in molecular dynamics simulations of membrane proteins in complex lipid bilayers have opened a new perspective in gathering such information. Here, we have modelled the full-length Lck open and closed conformations available from crystallographic studies and simulated its interaction with the inner leaflet of the T cell plasma membrane. In both conformations, we found that the unstructured unique domain and the structured domains including the kinase interacted with the membrane with a preference for PIP lipids. Interestingly, our simulations suggest that the Lck-SH2 domain interacts with lipids differently in the open and closed Lck conformations, demonstrating that lipid interaction can potentially regulate Lck’s conformation and in turn modulate T cell signalling. Additionally, the Lck-SH2 and kinase domain residues that significantly contacted PIP lipids are found to be conserved among the Src family of kinases, thereby potentially representing similar PIP interactions within the family.
KaicoTracker: a robust and automated locomotory analysis for baculovirus-infected silkworm larvae
Authors: Hikida Hiroyuki , Katsuma Susumu 
Published: May 2022

AbstractBombyx mori nucleopolyhedrovirus (BmNPV) is a pathogen of the domestic silkworm, Bombyx mori, whose infection drastically alters larval locomotory patterns and activity. As B. mori is the only insect that has been completely domesticated, its larvae are typically inactive. In contrast, BmNPV-infected larvae exhibit vigorous movement. Recently, we developed a method for locomotory analysis of BmNPV-infected B. mori larvae, which yielded high-resolution data on BmNPV-induced host locomotory alteration. However, this method had a disadvantage when analyzing the behavior of uninfected larvae, as they were typically inactive and difficult to distinguish from the background. In addition, the analysis processes involve many manual steps, which reduces analysis throughput. We have developed KaicoTracker, a new tool for automated locomotory analysis of BmNPV-infected B. mori larvae, using Python and OpenCV. This tool is an all-inclusive package that tracks and quantifies larval locomotion and verifies the accuracy of the tracking. Larval locomotion is tracked by motion tracking function based on k-Nearest Neighbor implemented in OpenCV. Based on the tracking results, the positions of the larvae are determined, and locomotory distance, speed, duration, and frequency are calculated. The larval positions are marked on the original video, allowing tracking precision to be examined. By analyzing previously obtained data, we confirmed that this tool provides a robust analysis of inactive larvae with fewer manual steps.
The neighboring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes
Authors: Talbi Nacera , Fokkens Like , Audran Corinne , Petit-Houdenot Yohann , Pouzet Cécile , Blaise Françoise , Gay Elise , Rouxel Thierry , Balesdent Marie-Hélène , Rep Martijn , Fudal Isabelle 
Published: May 2022

AbstractWith only a few exceptions, fungal effectors (small secreted proteins) have long been considered as species- or even isolate-specific. With the increasing availability of high-quality fungal genomes and annotations, trans-species or trans-genera families of effectors are being uncovered. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus responsible for stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighboring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome show that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes in a pair always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and / or petioles and stems. Of the two protein pairs further investigated Lmb_jn3_08094/Lmb_jn3_08095 and Lmb_jn3_09745 / Lmb_jn3_09746, one (Lmb_jn3_09745 / Lmb_jn3_09746) had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair. AvrLm10A homologues are present in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi whereas fewer AvrLm10B homologues were identified. One of the AvrLm10A homologues, SIX5, is an effector from Fusarium oxysporum f.sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A homologues were associated with at least eight distinct putative effector families, suggesting an ability of AvrLm10A/SIX5 to cooperate with diverse effectors. These results point to a general role of the AvrLm10A/SIX5 protein as a ‘cooperator protein’, able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighboring AvrLm10A homologue.
Non-cell-autonomous HSC70.1 chaperone displays homeostatic feed-back regulation by binding its own mRNA
Authors: Yang Lei , Zhou Yuan , Wang Shuangfeng , Xu Ying , Ostendorp Steffen , Tomkins Melissa , Kehr Julia , Morris Richard J. , Kragler Friedrich 
Published: May 2022

SummaryHeat shock proteins of the HSC70/HSP70 family are evolutionarily conserved chaperones that are involved in protein folding, protein transport and RNA binding. Arabidopsis HSC70 chaperones are thought to act as housekeeping chaperones and as such are involved in many growth-related pathways. Whether Arabidopsis HSC70 binds RNA and its function has remained an open question. Here, we show that the HSC70.1 chaperone binds its own mRNA via its C-terminal Short Variable Region (SVR) and inhibits its own translation. We propose that this negative protein-transcript feedback loop may establish an on-demand chaperone pool that allows for a rapid response to stress. Furthermore, we show that the SVR encoding RNA region is necessary for HSC70.1 transcript mobility to distant tissues and that HSC70.1 transcript and not protein mobility is required to rescue root growth and flowering time of hsc70 mutants. In summary, it seems that the Arabidopsis HSC70.1 chaperone can form a complex with its own transcript to regulate its translation and that both protein and transcript can act in a non-cell-autonomous manner maintaining chaperone homestasis between tissues.
E-SNPs&GO: Embedding of protein sequence and function improves the annotation of human pathogenic variants
Authors: Manfredi Matteo , Savojardo Castrense , Martelli Pier Luigi , Casadio Rita 
Published: May 2022

AbstractMotivationThe advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing protein sequences. Discriminating harmful protein variations from neutral ones is one of the crucial challenges in precision medicine. Computational tools based on artificial intelligence provide models for protein sequence encoding, bypassing database searches for evolutionary information. We leverage the new encoding schemes for an efficient annotation of protein variants.ResultsE-SNPs&GO is a novel method that, given an input protein sequence and a single residue variation, can predict whether the variation is related to diseases or not. The proposed method, for the first time, adopts an input encoding completely based on protein language models and embedding techniques, specifically devised to encode protein sequences and GO functional annotations. We trained our model on a newly generated dataset of 65,888 human protein single residue variants derived from public resources. When tested on a blind set comprising 6,541 variants, our method outperforms recent approaches released in literature for the same task, reaching a MCC score of 0.71. We propose E-SNPs&GO as a suitable, efficient and accurate large-scale annotator of protein variant datasets.Contactpierluigi.martelli@unibo.it
The gastric mucosa of Atlantic salmon (Salmo salar) is abundant in highly active chitinases
Authors: Holen Matilde Mengkrog , Tuveng Tina Rise , Kent Matthew Peter , Vaaje-Kolstad Gustav 
Published: May 2022

ABSTRACTThe Atlantic salmon (Salmo salar) genome contains 10 chitinase encoding genes, but little is known about the function of these chitinases. We show that the protein products of three genes, the family 18 glycoside hydrolase (GH18) chitinases Chia.3, Chia.4, and Chia.7 are secreted in the stomach mucosa and are amongst the most abundant proteins in this matrix. Chia.3 and Chia.4, sharing 95% sequence identity, were not possible to separate by standard chromatographic methods and were thus purified as a chitinase pair. Biochemical analysis revealed chitinolytic activity towards β-chitin for up to 24 hours at pH 2-6. Furtherin vitroanalysis showed that this chitinase pair efficiently degraded various chitin-containing substrates to chitobiose (GlcNAc2) suggesting that Atlantic salmon has the potential to utilize novel chitin-containing feed sources.
Roles and interactions of the specialized initiation factors EIF4E2, EIF4E5 and EIF4E6 inTrypanosoma brucei: EIF4E2 maintains the abundances of S-phase mRNAs
Authors: Falk Franziska , Melo Palhares Rafael , Waithaka Albina , Clayton Christine 
Published: May 2022

SummaryTrypanosoma bruceihas six versions of the cap-binding translation initiation factor EIF4E. We investigated the functions of EIF4E2, EIF4E3, EIF4E5 and EIF4E6 in bloodstream forms. We confirmed the protein associations previously found in procyclic forms, and detected specific co-purification of some RNA-binding proteins. Bloodstream forms lacking EIF4E5 grew normally and differentiated to replication-incompetent procyclic forms. Depletion of EIF4E6 inhibited bloodstream-form trypanosome growth and translation. EIF4E2 co-purified only the putative RNA binding protein SLBP2. Bloodstream forms lacking EIF4E2 multiplied slowly, had a low maximal cell density, and expressed the stumpy-form marker PAD1, but showed no evidence for enhanced stumpy-form signalling. EIF4E2 knock-out cells differentiated readily to replication-competent procyclic forms. EIF4E2 was strongly associated with mRNAs that are maximally abundant in S-phase, three of which are bound and stabilized by the Pumilio domain protein PUF9. The same mRNAs had decreased abundances in EIF4E2 knock-out cells. Yeast 2-hybrid results suggested that PUF9 interacts directly with SLBP2, but PUF9 was not detected in EIF4E2 pull-downs. We suggest that the EIF4E2-SLBP2 complex might interact with PUF9, and its bound RNAs, only early during G1/S, stabilizing the mRNAs in preparation for translation later in S-phase or in early G2.
CAMML with the Integration of Marker Proteins (ChIMP)
Authors: Schiebout Courtney , Frost H. Robert 
Published: May 2022

AbstractMotivationCell typing is a critical task in the analysis of single cell data, particularly when studying diseased tissues that contain a complex mixture of normal tissue and infiltrating immune cells. Unfortunately, the sparsity and noise of single cell data make accurate cell typing at the level of individual cells extremely difficult. To address these challenges, we previously developed the CAMML method for multi-label cell typing of single cell RNA-sequencing (scRNA-seq) data. CAMML uses weighted gene sets to score each profiled cell for multiple potential cell types. While CAMML outperforms other scRNA-seq cell typing techniques, it only leverages transcriptomic data so cannot take advantage of newer multi-omic single cell assays that jointly profile gene expression and protein abundance (e.g., joint scRNA-seq/CITE-seq).ResultWe developed the ChIMP (CAMML with the Integration of Marker Proteins) method to support multi-label cell typing of individual cells jointly profiled via scRNA-seq and CITE-seq. ChIMP combines cell type scores computed on scRNA-seq data via the CAMML approach with discretized CITE-seq measurements for cell type marker proteins. The multi-omic cell type scores generated by ChIMP allow researchers to more precisely and conservatively cell type joint scRNA-seq/CITE-seq data.
Lifelong regeneration of cerebellar Purkinje neurons after induced cell ablation in zebrafish
Authors: Pose-Méndez Sol , Schramm Paul , Winter Barbara , Meier Jochen C. , Ampatzis Konstantinos , Köster Reinhard W. 
Published: May 2022

AbstractZebrafish have an impressive capacity to regenerate neurons in the central nervous system. However, regeneration of the principal neuron of the evolutionary conserved cerebellum, the Purkinje cell (PC), is believed to be limited to developmental stages based on invasive lesions. In contrast, non-invasive cell type specific ablation by induced apoptosis closer represents processes of neurodegeneration. We demonstrate that the ablated larval PC population entirely recovers in number, quickly reestablishes electrophysiological properties and properly integrates into circuits to regulate cerebellum-controlled behavior. PC progenitors are present in larvae and adults, and PC ablation in adult cerebelli results in an impressive PC regeneration of different PC subtypes able to restore behavioral impairments. Interestingly, caudal PCs are more resistant to ablation and regenerate more efficiently, suggesting a rostro-caudal pattern of de- and regeneration properties. These findings demonstrate that the zebrafish cerebellum is able to regenerate functional PCs during all stages of the animal’s life.
Phase Separation and Correlated Motions in Motorized Genome
Authors: Jiang Zhongling , Qi Yifeng , Kamat Kartik , Zhang Bin 
Published: May 2022

AbstractThe human genome is arranged in the cell nucleus non-randomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of non-equilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parameterized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that non-equilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.