bluuebunny/crossref_metadata_2025_split huggingface dataset:
An evolutionarily conserved cis-regulatory element of Nkx3.2 contributes to early jaw joint morphology in zebrafish
Authors: Leyhr Jake , Waldmann Laura , Filipek-Górniok Beata , Zhang Hanqing , Allalou Amin , Haitina Tatjana 
Published: November 2021

AbstractThe acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in gnathostomes but undetectable in the jawless hagfish. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.
easier: interpretable predictions of antitumor immune response from bulk RNA-seq data
Authors: Lapuente-Santana Óscar , Marini Federico , Ustjanzew Arsenij , Finotello Francesca , Eduati Federica 
Published: November 2021

AbstractImmunotherapy with immune checkpoint blockers (ICB) is associated with striking clinical success, but only in a small fraction of patients. Thus, we need computational biomarker-based methods that can anticipate which patients will respond to treatment. Current established biomarkers are imperfect due to their incomplete view of the tumor and its microenvironment. We have recently presented a novel approach that integrates transcriptomics data with biological knowledge to study tumors at a more holistic level. Validated in four different solid cancers, our approach outperformed the state-of-the-art methods to predict response to ICB. Here, we introduce estimate systems immune response (easier), an R/Bioconductor package that applies our approach to quantify biomarkers and assess patients’ likelihood to respond to immunotherapy, providing just the patients’ baseline bulk-tumor RNA-sequencing (RNA-seq) data as input.
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
Authors: Madissoon Elo , Oliver Amanda J. , Kleshchevnikov Vitalii , Wilbrey-Clark Anna , Polanski Krzysztof , Orsi Ana Ribeiro , Mamanova Lira , Bolt Liam , Richoz Nathan , Elmentaite Rasa , Pett J. Patrick , Huang Ni , He Peng , Dabrowska Monika , Pritchard Sophie , Tuck Liz , Prigmore Elena , Knights Andrew , Oszlanczi Agnes , Hunter Adam , Vieira Sara F. , Patel Minal , Georgakopoulos Nikitas , Mahbubani Krishnaa , Saeb-Parsy Kourosh , Clatworthy Menna , Bayraktar Omer Ali , Stegle Oliver , Kumasaka Natsuhiko , Teichmann Sarah A. , Meyer Kerstin B. 
Published: November 2021

SummaryMultiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).
AlphaFill: enriching the AlphaFold models with ligands and co-factors
Authors: Hekkelman Maarten L. , de Vries Ida , Joosten Robbie P. , Perrakis Anastassis 
Published: November 2021

AbstractArtificial intelligence (AI) methods for constructing structural models of proteins on the basis of their sequence are having a transformative effect in biomolecular sciences. The AlphaFold protein structure database makes available hundreds of thousands of protein structures. However, all these structures lack cofactors essential for their structural integrity and molecular function (e.g. hemoglobin lacks a bound heme), key ions essential for structural integrity (e.g. zinc-finger motifs) or catalysis (e.g. Ca2+or Zn2+in metalloproteases), and ligands that are important for biological function (e.g. kinase structures lack ADP or ATP). Here, we present AlphaFill, an algorithm based on sequence and structure similarity, to “transplant” such “missing” small molecules and ions from experimentally determined structures to predicted protein models. These publicly available structural annotations are mapped to predicted protein models, to help scientists interpret biological function and design experiments.
The role of four cholesterol-recognition motifs localized between amino acid residues 400-550 in regulating translocation and lytic activity of Adenylate Cyclase Toxin
Authors: Amuategi Jone , Alonso Rocío , Ostolaza Helena 
Published: November 2021

ABSTRACTAdenylate Cyclase Toxin (ACT or CyaA) is an important virulence factor secreted by Bordetella pertussis, the bacterium causative of whooping cough, playing an essential role in the establishment of infection in the respiratory tract. ACT is a pore-forming cytolysin belonging to the RTX (Repeats in ToXin) family of leukotoxins, capable of permeabilizing several cell types and pure lipid vesicles. Besides, the toxin delivers its N-terminal adenylate cyclase domain into the target cytosol, where catalyzes the conversion of ATP into cAMP, which affects cell signalling. In this study we have made two major observations. First, we show that ACT binds free cholesterol, and identify in its sequence 38 potential cholesterol-recognition motifs. Second, we reveal that four of those motifs are real, functional cholesterol-binding sites. Mutations of the central phenylalanine residues in said motifs have an important impact on the ACT lytic and translocation activities, suggesting their direct intervention in cholesterol recognition and toxin functionality. From our data a likely transmembrane topology can be inferred for the ACT helices constituting the translocation and the hydrophobic regions. From this topology a simple and plausible mechanism emerges by which ACT could translocate its AC domain into target cells, challenging previous views in the field. Blocking the ACT-cholesterol interactions might thus be an effective approach for inhibiting ACT toxicity on cells, and this could help in mitigating the severity of pertussis disease in humans.
Recurrent evolution of cross-resistance in response to selection for improved post-infection survival in Drosophila melanogaster
Authors: Singh Aparajita , Basu Aabeer , Shit Biswajit , Hegde Tejashwini , Bansal Nitin , Prasad Nagaraj Guru 
Published: November 2021

AbstractThe host susceptibility to one pathogen can decrease, increase, or remain unaffected by virtue of the host evolving resistance towards a second pathogen. Negative correlations between a host susceptibility to different pathogens is an often-cited explanation for maintenance of genetic variation in immune function determining traits in a host population. In this study, we investigated the change in susceptibility of Drosophila melanogaster flies to various novel bacterial pathogens after being experimentally selected for increased resistance to one particular bacterial pathogen. We independently selected flies to become more resistant towards Enterococcus faecalis and Pseudomonas entomophila, and baring a few exceptions the evolved populations exhibited cross-resistance against the range of pathogens tested in the study. Neither the identity of the native pathogen nor the host sex was major determining factors in predicting the pattern of cross-resistance exhibited by the selected populations. We therefore report that a generalized cross-resistance to novel pathogens can repeatedly evolve in response to selection for resistance against a single pathogen.
Effect of landscape structure on genetic structure of the Lesser horseshoe bat (Rhinolophus hipposideros) in Britanny colonies
Authors: Rodriguez Alexandra , Petit Eric 
Published: November 2021

AbstractSome species are difficult to observe and others, need to be not disturbed because of their vulnerability. In response to the difficulty of studying the dispersal behaviors of these species, some areas of biology have been combined in order to access the information despite practical limitations. Here we present the combination of several methodologies from landscape ecology to non- invasive population genetics that allow us to obtain important information onRinolophus hipposideros, a vulnerable European bat. We genotyped 18 georeferrenced colonies in Brittany (France) from droppings collected in their refuges. We used 6 microsatellite markers in order to obtain the genetic distances between them. On the other hand we calculated Euclidian distances between the refuges occupied by these colonies and some ecological distances with the Pathmatrix module of ArcGis 3.2. We tested hypothesis about the difficulty of dispersal of the species in areas without forest cover or with a low density of hedges. Thanks to the Monmonier algorithm we could infer possible genetic barriers between the colonies and we could compare their location to the presence of landscape barriers (areas with little tree cover). We detected a pattern of isolation by distance that reveals limited dispersal capacities in the species but no pattern linked to ecological distances. We found that some of the neighboring colonies with greater genetic distances between them were located in areas with low density of hedges which could suggest an impact of this landscape element in their movements. Finer studies should allow us to conclude on the need or not of forest cover in the dispersal of this species.Abstract Figure
DLL4 and VCAM1 enhance the emergence of T cell-competent hematopoietic progenitors from human pluripotent stem cells
Authors: Michaels Yale S. , Edgar John M. , Major Matthew C. , Castle Elizabeth L. , Zimmerman Carla , Yin Ting , Hagner Andrew , Lau Charles , Ibañez-Rios M. Iliana , Knapp David J.H.F. , Zandstra Peter W. 
Published: November 2021

ABSTRACTT cells are key mediators of the adaptive immune response and show tremendous efficacy as cellular therapeutics. However, obtaining primary T cells from human donors is expensive and variable. Pluripotent stem cells (PSCs) have the potential to serve as a consistent and renewable source of T cells, but differentiating PSCs into hematopoietic progenitors with T cell potential remains a significant challenge. Here, we developed an efficient serum- and feeder-free protocol for differentiating human PSCs into hematopoietic progenitors and T cells. This defined method allowed us to study the impact of individual recombinant proteins on blood emergence and lineage potential. We demonstrate that the presence of DLL4 and VCAM1 during the endothelial-to-hematopoietic transition (EHT) enhances downstream progenitor T cell output by >80-fold. Using single cell transcriptomics, we showed that these two proteins synergise to drive strong notch signalling in nascent hematopoietic stem and progenitor cells and that VCAM1 additionally drives a pro-inflammatory transcriptional program. Finally, we applied this differentiation method to study the impact of cytokine concentration dynamics on T cell maturation. We established optimised media formulations that enabled efficient and chemically defined differentiation of CD8αβ+, CD4-, CD3+, TCRαβ+ T cells from PSCs.
Diverse digital and fuzzy composite transcriptional elements are prevalent features of mammalian cis-regulomes
Authors: Chaudhri Virendra K. , Singh Harinder 
Published: November 2021

AbstractMammalian transcriptional regulatory sequences are comprised of complex combinations of simple transcription factor (TF) motifs. Stereospecific juxta-positioning of simple TF motifs generates composite elements (CEs), that increase combinatorial and regulatory specificity of TF-DNA interactions. Although a small number of CEs and their cooperative or anti-cooperative modes of TF binding have been thoroughly characterized, a systematic analysis of CE diversity, prevalence and properties in cis-regulomes has not been undertaken. We developed a computational pipeline termed CEseek to discover >20,000 CEs in open chromatin regions of diverse immune cells and validated many using CAP-SELEX, ChIP-Seq and STARR-seq datasets. Strikingly, the CEs manifested a bimodal distribution of configurations, termed digital and fuzzy, based on their stringent or relaxed stereospecific constraints, respectively. Digital CEs mediate cooperative as well as anti-cooperative binding of structurally diverse TFs that likely reflect AND/OR genomic logic gates. In contrast, fuzzy CEs encompass a less diverse set of TF motif pairs that are selectively enriched in p300 associated, multi-genic enhancers. The annotated CEs greatly expand the regulatory DNA motif lexicon and the universe of TF-TF interactions that underlie combinatorial logic of gene regulation.
The structure of the Physcomitrium Patens Photosystem I Reveals a Unique Lhca2 Paralogue replacing Lhca4
Authors: Gorski C , Riddle R , Toporik H , Da Z , Dobson Z , Williams D , Mazor Y 
Published: November 2021

AbstractThe moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red shifted Lhca4 antennae are present in the photosystem I light harvesting complex of many green lineage plants but absent from P. patens. The Cryo-EM structure of the P. patens photosystem I light harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in cyanobacteria and several algal species but lost in higher plants, and the PsaO subunit responsible for binding light harvesting complex II. The blue shifted Lhca2 paralogue and chlorophyll b enrichment relative to higher plants make the P. patens PSI-LHCI spectroscopically unique among other green lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent shaped LHCI common in higher plants and contains a unique Lhca2 paralogue which facilitates the mosses adaptation to low light niches.
Deep Learning Applications in Single-Cell Omics Data Analysis
Authors: Erfanian Nafiseh , Heydari A. Ali , Iañez Pablo , Derakhshani Afshin , Ghasemigol Mohammad , Farahpour Mohsen , Nasseri Saeed , Safarpour Hossein , Sahebkar Amirhossein 
Published: November 2021

AbstractTraditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic diseases. However, the single-cell technologies generate massive amounts of data that are often high-dimensional, sparse, and complex, thus making analysis with traditional computational approaches difficult and unfeasible. To tackle these challenges, many are turning to deep learning (DL) methods as potential alternatives to the conventional machine learning (ML) algorithms for single-cell studies. DL is a branch of ML capable of extracting high-level features from raw inputs in multiple stages. Compared to traditional ML, DL models have provided significant improvements across many domains and applications. In this work, we examine DL applications in genomics, transcriptomics, spatial transcriptomics, and multi-omics integration, and address whether DL techniques will prove to be advantageous or if the single-cell omics domain poses unique challenges. Through a systematic literature review, we find that DL has not yet revolutionized or addressed the most pressing challenges of the single-cell omics field. However, using DL models for single-cell omics has shown promising results (in many cases outperforming the previous state-of-the-art models) in data preprocessing and downstream analysis, but many DL models still lack the needed biological interpretability. Although developments of DL algorithms for single-cell omics have generally been gradual, recent advances reveal that DL can offer valuable resources in fast-tracking and advancing research in single-cell.Abstract Figure
Dispersal of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: Combining population genetics and tracking data
Authors: Chua Michelle , Ho Simon Y. W. , McMahon Clive R. , Jonsen Ian , de Bruyn Mark 
Published: November 2021

AbstractMarine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the genetic diversity and natal source populations of these seals has not been characterized. Determining the genetic diversity of moulting populations like this one provides essential information on seal dispersal, inter-population mixing, and foraging behaviours. In this study, we combined genetic and animal tracking data on these moulting seals to identify levels of genetic diversity, natal source population, and movement behaviours during foraging and haul-out periods. Using mitochondrial sequence data, we identified two major breeding lineages of seals at Davis Base. We found that the majority of the seals originated from breeding stocks within the South Atlantic Ocean and South Indian Ocean. One seal was grouped with the Macquarie Island breeding stock (South Pacific Ocean). The Macquarie Island population, unlike the other two stocks, is decreasing in size. Tracking data revealed long-distance foraging activity of the Macquarie Island seal around Crozet Islands. We speculate that changes to the Antarctic marine environment have resulted in a shift in foraging and dispersal strategies, which subsequently affects seal population growth rates. These findings have implications for conservation management plans aimed at improving the population status of the southern elephant seal.
In Vitro Proliferation and Long-Term Preservation of Functional Primary Rat Hepatocytes in Cell Fibers
Authors: Mazari-Arrighi Elsa , Okitsu Teru , Teramae Hiroki , Aoyagi Hoshimi , Kiyosawa Mahiro , Yano Mariko , Takeuchi Shoji 
Published: November 2021

AbstractPrimary hepatocytes are essential cellular resource for drug screening and medical transplantation. Since culture systems for them have already succeeded in reconstituting the biomimetic microenvironment, acquiring additional capabilities both to expand primary hepatocytes and to handle them easily would be expected as progress to the next stage. This paper describes a culture system for primary rat hepatocytes that is equipped with scalability and handleability relying on cell fiber technology. Cell fibers are cell-laden core-shell hydrogel microfibers; in the core regions, cells are embedded in extracellular matrix proteins, cultured three-dimensionally, and exposed to soluble growth factors in the culture medium through the hydrogel shells. By encapsulating primary rat hepatocytes within cell fibers, we first demonstrated they increase in number while keeping their viability and their hepatic specific functions for up to thirty days of subsequent culture. Then, we demonstrated the potency of the primary rat hepatocytes that proliferate in cell fibers not only as cell-based sensors to detect drugs that damage hepatic functions and hepatocellular processes but also as transplants to improve the plasma albumin concentrations of congenital analbuminemia. Therefore, our culture system could serve for innovating strategies and promising developments in applying primary hepatocytes to both pharmaceutical and medical fields.
Rapid detection of φx-174 virus based on synchronous fluorescence of Tryptophan
Authors: Farber Yair , Shlosberg Yaniv , Schechter Israel , Armon Robert 
Published: November 2021

AbstractDevelopment of rapid methods for detection of virus particles based on their intrinsic fluorescence is challenging. Pure viruses may be detected in filtered solutions, based on the strong fluorescence of the amino acid Tryptophan (Trp) in their proteins. Nevertheless, Trp also exists in high quantities in the hosts and host cultivation media. In this work, we show that a separation of the bacteriophage φx-174 from its E. coli host (grown on the standard cultivation medium “Nutrient Agar”) by simple extraction and filtration is not sufficient for its detection based on the intrinsic fluorescence since ~70 % of the Trp fluorescence is derived from impurities. We formulate a new cultivation medium with very low Trp concentration. We apply synchronous fluorescence measurements to show that no Trp fluorescence is detected in the extract solution upon incubation of this medium substrate with ammonium acetate extraction buffer. Finally, we detect φx-174 based on the spectral fingerprint of its intrinsic Trp content by synchronous fluorescence measurements. The concept of coupling intrinsic fluorescence-based methods to impurities reduction in the source, may pave the way towards future development of simple, cheap, and rapid methods for detection of viral pathogens.