bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct gene-selective roles for a network of core promoter factors inDrosophilaneural stem cell identity
Authors: Neves Alexandre , Eisenman Robert N. 
Published: October 2018

AbstractThe transcriptional mechanisms that allow neural stem cells (NSC) to balance self-renewal with differentiation are not well understood. Employing an in vivo RNAi screen we identify here NSC-TAFs, a subset of nine TATA-binding protein associated factors (TAFs), as NSC identity genes inDrosophila. We found that depletion of NSC-TAFs results in decreased NSC clone size, reduced proliferation, defective cell polarity and increased hypersensitivity to cell cycle perturbation, without affecting NSC survival. Integrated gene expression and genomic binding analyses revealed that NSC-TAFs function with both TBP and TRF2, and that NSC-TAF-TBP and NSC-TAF-TRF2 shared target genes encode different subsets of transcription factors and RNA-binding proteins with established or emerging roles in NSC identity and brain development. Taken together, our results demonstrate that core promoter factors are selectively required for NSC identityin vivoby promoting cell cycle progression and NSC cell polarity as well as by restraining premature differentiation. Because pathogenic variants in a subset of TAFs have all been linked to human neurological disorders, this work may stimulate and inform future animal models of TAF-linked neurological disorders.Author summaryThe brains of many animal species are built with brain stem cells. Having too many brain stem cells can lead to brain tumors whereas too few can lead to birth defects such as microcephaly. A number of next generation sequencing studies have implicated proteins referred to as TATA-box-binding protein associated factors (TAFs) in human neurological disorders including microcephaly, but prior to this study, their function in brain development was unknown. Here we use brain stem cells, known as neural stem cells (NSCs), from the fruit flyDrosophila melanogasteras a model system to decipher how TAFs control brain stem cell identity. By combining genetics and low-input genomics, we show that TAFs directly control NSC cell division and cell polarity but do not appear to be required for NSC survival. We further show that TAFs accomplish these functions by associating either with their canonical partner TBP (TATA-binding protein) or the related protein TRF2. In summary, our study reveals unexpected and gene-selective functions of a unique subset of TAFs and their binding partners, which could inform future studies that seek to model human neurological disorders associated with TAFs.
Epithelial WNT2B and Desert Hedgehog are necessary for human colonoid regeneration after bacterial cytotoxin injury
Authors: In Julie G. , Yin Jianyi , Doucet Michele , Cole Robert N. , DeVine Lauren , Donowitz Mark , Zachos Nicholas C. , Blutt Sarah E. , Estes Mary K. , Kovbasnjuk Olga 
Published: October 2018

SUMMARYIntestinal regeneration and crypt hyperplasia after radiation or pathogen injury relies on Wnt signaling to stimulate stem cell proliferation. Mesenchymal Wnts are essential for homeostasis and regeneration in mice, but the role of epithelial Wnts remains largely uncharacterized. Using the enterohemorrhagicE. colisecreted cytotoxin, EspP to induce injury to human colonoids, we evaluated a simplified, epithelial regeneration model that lacks mesenchymal Wnts. Here, we demonstrate that epithelial-produced WNT2B is upregulated following injury and essential for regeneration. Hedgehog signaling, specifically activation via the ligand Desert Hedgehog (DHH), but not Indian or Sonic Hedgehog, is another driver of regeneration and modulates WNT2B expression. These findings highlight the importance of epithelial WNT2B and DHH in regulating human colonic regeneration after injury.
Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates, and humans
Authors: Jüttner Josephine , Szabo Arnold , Gross-Scherf Brigitte , Morikawa Rei K. , Rompani Santiago B. , Teixeira Miguel , Hantz Peter , Szikra Tamas , Esposti Federico , Cowan Cameron S. , Bharioke Arjun , Patino-Alvarez Claudia P. , Keles Özkan , Roth Chiara N. , Kusnyerik Akos , Gerber-Hollbach Nadin , Azoulay Thierry , Hartl Dominik , Krebs Arnaud , Schübeler Dirk , Hajdu Rozina , Lukats Akos , Nemeth Janos , Nagy Zoltan Z. , Wu Kun-Chao , Wu Rong-Han , Xiang Lue , Fang Xiao-Long , Jin Zi-Bing , Goldblum David , Hasler Pascal W. , Scholl Hendrik , Krol Jacek , Roska Botond 
Published: October 2018

SummaryTargeting genes to specific neuronal or glial cell types is valuable both for understanding and for repairing brain circuits. Adeno-associated viral vectors (AAVs) are frequently used for gene delivery, but targeting expression to specific cell types is a challenge. We created a library of 230 AAVs, each with a different synthetic promoter designed using four independent strategies. We show that ~11% of these AAVs specifically target expression to neuronal and glial cell types in the mouse retina, mouse brain, non-human primate retinain vivo, and in the human retinain vitro. We demonstrate applications for recording, stimulation, and molecular characterization, as well as the intersectional and combinatorial labeling of cell types. These resources and approaches allow economic, fast, and efficient cell-type targeting in a variety of species, both for fundamental science and for gene therapy.
Biphasic unbinding of Zur from DNA for transcription (de)repression in Live Bacteria
Authors: Jung Won , Chen Peng 
Published: October 2018

AbstractTranscription regulator on-off binding to DNA constitutes a mechanistic paradigm in gene regulation, in which the repressors/activators bind to operator sites tightly while the corresponding non-repressors/non-activators do not. Another paradigm regards regulator unbinding from DNA to be a unimolecular process whose kinetics is independent of regulator concentration. Using single-molecule single-cell measurements, we find that the behaviors of the zinc-responsive uptake regulator Zur challenges these paradigms. Apo-Zur, a non-repressor and presumed non-DNA binder, can bind to chromosome tightly in live E. coli cells, likely at non-consensus sequence sites. Moreover, the unbinding from DNA of its apo-non-repressor and holo-repressor forms both show a biphasic, repressed-followed-by-facilitated kinetics with increasing cellular protein concentrations. The facilitated unbinding likely occurs via a ternary complex formation mechanism; the repressed unbinding is first-of-its-kind and likely results from protein oligomerization on chromosome, in which an inter-protein salt-bridge plays a key role. This biphasic unbinding could provide functional advantages in Zur's facile switching between repression and derepression.
Structural insight into TRPV5 channel function and modulation
Authors: Dang Shangyu , van Goor Mark K. , Wang YongQiang , Julius David , Cheng Yifan , van der Wijst Jenny 
Published: October 2018

AbstractTRPV5 (transient receptor potential vanilloid) is a unique calcium-selective TRP channel that is essential for calcium homeostasis. TRPV5 and its close homologue TRPV6 do not exhibit thermosensitivity or ligand-dependent activation, unlike other TRPV channels, but are constitutively opened at physiological membrane potentials. Here, we report high resolution electron cryo-microscopy (cryo-EM) structures of truncated and full length TRPV5 in lipid nanodisc, as well as a TRPV5 W583A mutant structure and a complex structure of TRPV5 with calmodulin (CaM). These structures highlight and explain functional differences between the thermosensitive and calcium-selective TRPV channels. An extended S1-S2 linker folds on top of the channel that might shield it from modulation by extracellular factors. Resident lipid densities in the homologous vanilloid pocket are different from those previously found in TRPV1, supporting a comparatively more rigid architecture of TRPV5. A ring of tryptophan residues (W583) at the bottom of the pore coordinates a density and mutation of W583 resultes in opening of the lower gate. Moreover, we provide structural insight into the calcium-dependent channel inactivation and propose a flexible stoichiometry for TRPV5 and CaM binding.
Enhancing acute kidney injury regeneration by promoting cellular dedifferentiation in zebrafish
Authors: Skvarca Lauren Brilli , Han Hwa In , Espiritu Eugenel B. , Missinato Maria A. , Rochon Elizabeth R. , McDaniels Michael D. , Roman Beth L. , Waxman Joshua S. , Watkins Simon C. , Davidson Alan J. , Tsang Michael , Hukriede Neil A. 
Published: October 2018

ABSTRACTAcute kidney injury (AKI) is a serious disorder for which there is no approved pharmaceutical treatment. Following injury, native nephrons display limited regenerative capabilities, relying on the dedifferentiation and proliferation of renal tubular epithelial cells (RTECs) that survive the insult. Previously, we identified 4-(phenylthio)butanoic acid (PTBA), a histone deacetylase inhibitor (HDI) that enhances renal recovery and showed that PTBA treatment increased RTEC proliferation and reduced renal fibrosis. Here, we investigated the regenerative mechanisms of PTBA in zebrafish models of larval renal injury and adult cardiac injury. With respect to renal injury, we showed that delivery of PTBA using an esterified prodrug (UPHD25) increases the reactivation of the renal progenitor gene Pax2a, enhances dedifferentiation of RTECs, reduces Kidney injury molecule-1 expression, and lowers the number of infiltrating macrophages. Further, we find that the effects of PTBA on RTEC proliferation depend upon retinoic acid signaling and demonstrate the therapeutic properties of PTBA are not restricted to the kidney but also increase cardiomyocyte proliferation and decrease fibrosis following cardiac injury in adult zebrafish. These studies provide key mechanistic insights into how PTBA enhances tissue repair in models of acute injury and lay the groundwork for translating this novel HDI into the clinic.SUMMARY STATEMENTMortality associated with acute kidney injury (AKI) is in part due to limited treatments available to ameliorate kidney injury. We identified a compound that enhances AKI recovery by promoting cellular dedifferentiation.
Co-regulation of hormone receptors, neuropeptides, and steroidogenic enzymes across the vertebrate social behavior network
Authors: Horton Brent M. , Ryder T. Brandt , Moore Ignacio T. , Balakrishnan Christopher N. 
Published: October 2018

AbstractThe vertebrate basal forebrain and midbrain contain a set of interconnected nuclei that control social behavior. Conserved anatomical structures and functions of these nuclei have now been documented among fish, amphibians, reptiles, birds and mammals, and these brain regions have come to be known as the vertebrate social behavior network (SBN). While it is known that nuclei (nodes) of the SBN are rich in steroid and neuropeptide activity linked to behavior, simultaneous variation in the expression of neuroendocrine genes among several SBN nuclei has not yet been described in detail. In this study, we use RNA-seq to profile gene expression across seven brain regions representing five nodes of the vertebrate SBN in a passerine bird, the wire-tailed manakin Pipra filicauda. Using weighted gene co-expression network analysis (WGCNA), we reconstructed sets of coregulated genes, revealing striking patterns of variation in neuroendocrine gene expression across the SBN. We describe regional expression variation networks comprising a broad set of hormone receptors, neuropeptides, steroidogenic enzymes, catecholamines, and other neuroendocrine signaling molecules. Our findings highlight how heterogeneity of brain gene expression across the SBN can provide functional insights into the neuroendocrine and genetic mechanisms that underlie vertebrate social behavior.
RefSoil+: A reference for antimicrobial resistance genes on soil plasmids
Authors: Dunivin TK , Choi J , Howe AC , Shade A 
Published: October 2018

AbstractPlasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were relatively larger than other described plasmids, which is a trait associated with plasmid mobility. There was no relationship between chromosome size and plasmid size or number, suggesting that these genomic traits are independent in soil. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a baseline for the diversity, composition, and host-associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.ImportanceSoil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate knowledge of soil plasmid characteristics so that the content, host-associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource for investigating clinic-environment dynamics of important plasmid-associated genes, including antibiotic resistance genes.
Structural basis of HEAT-kleisin interactions in the human condensin I subcomplex
Authors: Hara Kodai , Kinoshita Kazuhisa , Migita Tomoko , Murakami Kei , Shimizu Kenichiro , Takeuchi Kozo , Hirano Tatsuya , Hashimoto Hiroshi 
Published: October 2018

ABSTRUCTCondensin I is a multi-protein complex that plays an essential role in mitotic chromosome assembly and segregation in eukaryotes. It is composed of five subunits: two SMC (SMC2 and SMC4), a kleisin (CAP-H) and two HEAT-repeat (CAP-D2 and -G) subunits. Although it has been shown that balancing acts of the two HEAT-repeat subunits enable this complex to support dynamic assembly of chromosomal axes in vertebrate cells, its underlying mechanisms remain poorly understood. Here, we report the crystal structure of a human condensin I subcomplex comprising hCAP-G and hCAP-H. hCAP-H binds to the concave surfaces of a harp-shaped HEAT repeat domain of hCAP-G. A physical interaction between hCAP-G and hCAP-H is indeed essential for mitotic chromosome assembly recapitulated in Xenopus egg cell-free extracts. Furthermore, this study reveals that the human CAP-G-H subcomplex has the ability to interact with not only a double-stranded DNA, but also a single-stranded DNA, implicating potential, functional divergence of the vertebrate condensin I complex in mitotic chromosome assembly.
The ATR kinase of Trypanosoma brucei links DNA damage signalling and monoallelic control of surface antigen gene expression during antigenic variation
Authors: Black Jennifer Ann , Crouch Kathryn , Lemgruber Leandro , Lapsley Craig , Dickens Nicholas , Mottram Jeremy C. , McCulloch Richard 
Published: October 2018

AbstractTo evade mammalian immunity, Trypanosoma brucei switches the variant surface glycoprotein (VSG) expressed on its surface. Key to this reaction are controls exerted to ensure only one of many subtelomeric multigene VSG expression sites are transcribed at a time. DNA repair activities have to date been implicated only in catalysis of VSG switching by recombination, not transcriptional control. However, how VSG switching is signalled to guide the appropriate reaction, or to integrate switching into parasite growth, is unknown. Here we show that loss of ATR, a DNA damage signalling protein kinase, is lethal and causes increased nuclear genome lesions. ATR depletion also causes expression of mixed VSGs on the cell surface, increased transcription of genes from silent expression sites, and altered localisation of RNA Polymerase I and VEX1, factors involved in VSG transcription. The work therefore reveals that VSG expression control is mediated by a nuclear DNA damage signalling factor.
Evolution of influenza genome diversity during infection in immunocompetent patients
Authors: Pichon Maxime , Simon Bruno , Valette Martine , Bal Antonin , Picard Caroline , Escuret Vanessa , Ottmann Michèle , Gillet Yves , Ader Florence , Lina Bruno , Josset Laurence 
Published: October 2018

AbstractIntroductionMinor frequency viruses play many important roles during viral infection that cannot be explained by the consensus sequence alone. In influenza, immunosuppressed individuals appear to generate numerous viral variants, leading to subpopulations with important role in infection. The objective of the present study was to describe viral diversification over time in immunocompetent patients during influenza virus infection.MethodsAll clinical records of patients admitted to the Lyon university hospital (Lyon, France) during the influenza infection epidemics of the 2010-2015 period and sampled at least twice during their clinical management were retrospectively analyzed. To estimate performance of the sequencing procedures, well-characterized plasmids containing each of the 8 segments of influenza viruses were used as quality controls. Diversity, i.e. the number of validated single nucleotide variants, was analyzed to compare characteristics over time and according to clinical severity (mild, severe with neurological complications, severe with respiratory complications).ResultsAfter validation on quality controls (n=51), and verification of possible confusion bias, a 5%-threshold of detection was applied to clinical viral sequences (n=29). At this threshold, amino-acid coordinates (n=183/4,246, 4.31%) were identified as having at least one mutation during clinical course, independently of the clinical severity. Considering a threshold of 4 days of symptoms, as a limit for early and late sampling, diversity was significantly higher in late samples for the mild group, compared to both early mild and severe groups (p<0.05). At a single-segment scale, for PB2-coding segment, diversity was significantly higher in early samples of the neurological group than in both early and late samples in the respiratory group and for late samples in the mild group (p<0.05). For the NS1-coding segment, significant differences were observed between initial diversity of mild and severe patients, as for early and late samples in mild patients (p<0.01). Discussion. This study is the first describing diversity through time, associating biological and clinical information during viral diversification, during the infection of an immunocompetent human host. This latter opens a large field of investigation in infectious disease management using next-generation sequencing and suggest development of new therapies, focusing on non-antigenic viral properties, in non-vaccine fields of research
Combined strategy of siRNA and osteoclast actin cytoskeleton automated imaging to identify novel regulators of bone resorption shows a non-mitotic function for anillin
Authors: Maurin Justine , Morel Anne , Hassen-Khodja Cedric , Vives Virginie , Jurdic Pierre , Machuca-Gayet Irma , Blangy Anne 
Published: October 2018

AbstractOsteoclasts are the main cells responsible for the resorption of mineralized extracellular matrices. They are the major targets for anti-resorptive therapies to manage osteoporosis, a major public health problem. Osteoclasts are giant multinucleated cells that can organize their a unique adhesion structure based on a belt of podosomes, which is the keystone of the bone resorption apparatus. We combined differential transcriptomics and siRNA screening approaches to get a broader view of cytoskeletal regulators that participate in the control of osteoclast cytoskeleton and identify novel regulators of bone resorption by osteoclasts. We identified 20 new candidate regulators of osteoclasts cytoskeleton including Fkbp15, Spire1, Tacc2 and RalA, for which we confirmed they are necessary for proper organization of the podosome belt. We also showed that Anillin, well known for its role during cytokinesis, is essential in osteoclasts for correct podosome patterning and efficient bone resorption. In particular, Anillin controls the levels of the GTPase RhoA, a known regulator of osteoclast cytoskeleton and resorption activity. Finally, we set up and validated an automated imaging strategy based on open-source software for automatic and objective measurement of actin cytoskeleton organization in osteoclasts. We provide these pipelines that are useful to automatically assess the effect of collections of siRNAs or chemical compounds on osteoclast cytoskeleton or differentiation.
Posterior axis formation requiresDlx5/Dlx6expression at the neural plate border
Authors: Narboux-Neme Nicolas , Ekker Marc , Levi Giovanni , Heude Églantine 
Published: October 2018

ABSTRACTNeural tube defects (NTDs), one of the most common birth defects in human, present a multifactorial etiology with a poorly defined genetic component. TheDlx5andDlx6bigenic cluster encodes two evolutionary conserved homeodomain transcription factors, which are necessary for proper vertebrate development. It has been shown thatDlx5/6genes are essential for anterior neural tube closure, however their role in the formation of the posterior structures has never been described. Here, we show thatDlx5/6expression is required during vertebrate posterior axis formation.Dlx5presents a similar expression pattern in neural plate border cells during posterior neurulation of zebrafish and mouse.Dlx5/6-inactivation in the mouse results in a phenotype reminiscent of NTDs characterized by open thoracic and lumbar vertebral arches and failure of epaxial muscle formation at the dorsal midline. Thedlx5a/6azebrafish morphants present posterior NTDs associated with abnormal delamination of neural crest cells showing altered expression of cell adhesion molecules and defects of motoneuronal development. Our findings provide new molecular leads to decipher the mechanisms of vertebrate posterior neurulation and might help to gather a better understanding of human congenital NTDs etiology.