Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 48,092 bioRxiv papers from 215,637 authors.
Most tweeted bioRxiv papers, last 24 hours
390 results found. For more information, click each entry to expand.
15 tweets microbiology
The viral RNA (vRNA) genome of influenza viruses is replicated by the RNA-dependent RNA polymerase (RNAP) via a complementary RNA (cRNA) intermediate. The vRNA promoter can adopt multiple conformations when bound by the RNAP. However, the dynamics, determinants, and biological role of these conformations are unknown; further, little is known about cRNA promoter conformations. To probe the RNA conformations adopted during initial replication, we monitored single, surface-immobilised vRNA and cRNA initiation complexes in real-time. Our results show that, while the 3′ terminus of the vRNA promoter exists in dynamic equilibrium between pre-initiation and initiation conformations, the cRNA promoter exhibited very limited dynamics. Two residues in the proximal 3′ region of the cRNA promoter (residues absent in the vRNA promoter) allowed the cRNA template strand to reach further into the active site, limiting promoter dynamics. Our results highlight promoter-dependent differences in influenza initiation mechanisms, and advance our understanding of virus replication.
14 tweets neuroscience
Animals generate diverse motor behaviors, yet how the same motor neurons generate distinct behaviors remains an open question. Drosophila larvae have multiple behaviors, e.g. forward crawling, backward crawling, self-righting and escape, and all of the body wall motor neurons (MNs) driving these behaviors have been identified. Despite impressive progress in mapping larval motor circuits, the role of most motor neurons in locomotion remains untested, the majority of premotor neurons (PMNs) remain to be identified, and a full understanding of proprioceptor-PMN-MN connectivity is missing. Here we report a comprehensive larval proprioceptor-PMN-MN connectome; describe individual muscle/MN phase activity during both forward and backward locomotor behaviors; identify PMN-MN connectivity motifs that could generate muscle activity phase relationships, plus selected experimental validation; identify proprioceptor-PMN connectivity that provides an anatomical explanation for the role of proprioception in promoting locomotor velocity; and identify a new candidate escape motor circuit. Finally, we generate a recurrent network model that produces the observed sequence of motor activity, showing that the identified pool of premotor neurons is sufficient to generate two distinct larval behaviors. We conclude that different locomotor behaviors can be generated by a specific group of premotor neurons generating behavior-specific motor rhythms.
14 tweets developmental biology
Topologically Associating Domains (TADs) have been proposed to both guide and constrain enhancer activity. Shh is located within a TAD known to contain all its enhancers. To investigate the importance of chromatin conformation and TAD integrity on developmental gene regulation, we have manipulated the Shh TAD, creating internal deletions, deleting CTCF sites including those at TAD boundaries, as well as larger deletions and inversions of TAD boundaries. Chromosome conformation capture and fluorescence in situ hybridisation assays were used the investigate changes in chromatin conformation that result from these manipulations. Our data suggest that the substantial alteration of TAD structure has no readily detectable effect on Shh expression patterns during development, except where enhancers are deleted, and results in no detectable phenotypes. Only in the case of a larger deletion of one TAD boundary could some ectopic influence of the Shh limb enhancer be detected on a gene, Mnx1 in the neighbouring TAD. Our data suggests that, contrary to expectations, the developmental regulation of Shh expression is remarkably robust to TAD perturbations.
14 tweets scientific communication and education
Researchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage. Here, we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find preprints are being downloaded more than ever before (1.1 million tallied in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of 2,100 per month. We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between journal impact factor and preprint downloads. Lastly, we developed Rxivist.org, a web application providing multiple ways of interacting with preprint metadata.
14 tweets neuroscience
Memories of positive experiences require the brain to link places, events, and reward outcomes. Neural processing underlying the association of spatial experiences with reward is thought to depend on interactions between the hippocampus and the nucleus accumbens (NAc)1-9. Hippocampal projections to the NAc arise from both the ventral hippocampus (vH) and the dorsal hippocampus (dH)6-12, and studies using optogenetic interventions have demonstrated that either vH5,6 or dH7 input to the NAc can support behaviors dependent on spatial-reward associations. It remains unclear, however, whether dH, vH, or both coordinate memory processing of spatial-reward information in the hippocampal-NAc circuit under normal conditions. Times of memory reactivation within and outside the hippocampus are marked by hippocampal sharp-wave ripples (SWRs)13-19, discrete events which facilitate investigation of inter-regional information processing. It is unknown whether dH and vH SWRs act in concert or separately to engage NAc neuronal networks, and whether either dH or vH SWRs are preferentially linked to spatial-reward representations. Here we show that dH and vH SWRs occur asynchronously in the awake state and that NAc spatial-reward representations are selectively activated during dH SWRs. We performed simultaneous extracellular recordings in the dH, vH, and NAc of rats learning and performing an appetitive spatial task and during sleep. We found that individual NAc neurons activated during SWRs from one subdivision of the hippocampus were typically suppressed or unmodulated during SWRs from the other. NAc neurons activated during dH versus vH SWRs showed markedly different task-related firing patterns. Only dH SWR-activated neurons were tuned to similarities across spatial paths and past reward, indicating a specialization for the dH-NAc, but not vH-NAc, network in linking reward to discrete spatial paths. These temporally and anatomically separable hippocampal-NAc interactions suggest that dH and vH coordinate opposing channels of mnemonic processing in the NAc.
13 tweets plant biology
MADS-box transcription factors (TFs) are ubiquitous among eukaryotes, and classified into two groups: type I or SRF (Serum Response Factor)-like, and type II or MEF2 (Myocyte Enhancing Factor2)-like. In flowering plants, type I MADS-box TFs are associated with reproductive development and many are active in the endosperm, a nutritive tissue supporting the embryo. Deregulation of these genes has been frequently linked to failure of endosperm development and seed inviability, both in the Brassicaceae, and in crop species like tomato and rice. Nevertheless, a mechanistic explanation for these observations, clarifying the role of MADS-box TFs in endosperm development, remains to be established. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) has a central role in endosperm development as a master regulator of imprinted gene expression, especially of paternally expressed genes (PEGs), which have been previously implicated in endosperm development. Control of imprinted gene expression by PHE1 is mediated by parental asymmetry of epigenetic modifications in PHE1 DNA-binding sites, conferring different accessibilities to maternal and paternal alleles. Importantly, we show that the CArG-box-like DNA-binding motifs used by PHE1 to access gene promoters are carried by RC/Helitron transposable elements (TEs), providing an example of molecular domestication of these elements. Hence, this work shows that TEs are intrinsically linked to imprinting: not only by enforcing specific epigenetic landscapes, but also by serving as important sources of cis-regulatory elements. Moreover, it provides an example of how TEs can widely distribute TF binding sites in a plant genome, allowing to recruit crucial endosperm regulators into a single transcriptional network.
13 tweets genomics
This paper compares genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulation. Breeding programs have to maximize genetic gain but also ensure sustainability by maintaining genetic variation. Numerous studies showed that genomic selection increases genetic gain. Although genomic selection is a well-established method, small populations still struggle with choosing the most sustainable strategy to adopt this type of selection. We developed a simulator of a dairy population and simulated a model after the Slovenian Brown Swiss population with ~10,500 cows. We compared different truncation selection scenarios by varying i) the method of sire selection and their use on cows or bull-dams, and ii) selection intensity and the number of years a sire is in use. Furthermore, we compared different optimum contribution selection scenarios with optimization of sire selection and their usage. We compared the scenarios in terms of genetic gain, selection accuracy, generation interval, genetic and genic variance, the rate of coancestry, effective population size, and the efficiency of converting genetic variation into genetic gain. The results show that early use of genomically tested sires increased genetic gain compared to progeny testing as expected from changes in selection accuracy and generation interval. A faster turnover of sires from year to year and higher intensity increased the genetic gain even further, but increased the loss of genetic variation per year. While maximizing intensity gave the lowest conversion efficiency, a faster turn-over of sires gave an intermediate conversion efficiency. The largest conversion efficiency was achieved with the simultaneous use of genomically and progeny tested sires that were used over several years. Compared to truncation selection optimizing sire selection and their usage increased the conversion efficiency by either achieving comparable genetic gain for a smaller loss of genetic variation or achieving higher genetic gain for a comparable loss of genetic variation. Our results will help breeding organizations to implement sustainable genomic selection.
13 tweets genetics
Background: Minimal phenotyping refers to the reliance on self-reported responses to one or two questions for disease case identification instead of full diagnostic criteria. This strategy has been applied in genome-wide association studies (GWAS) on major depressive disorder (MDD), leading to lowering of phenotyping costs, increasing sample sizes, and more GWAS hits. It assumes that any increase in diagnostic noise, and its impact on the nature of GWAS loci thus identified, can be mitigated by the large increase in sample size. Methods: We assess the impact of using different definitions of MDD in 337,198 White-British, unrelated samples in the UKBiobank with GWAS, analyses of heritability and genetic correlation, and comparison with previously published statistics on MDD and other psychiatric conditions. Definitions of MDD include seeking medical help for anxiety or depression, reporting MDD or its cardinal symptoms, and meeting full DSM criteria for MDD. Findings: Heritability of depression defined by minimal phenotyping (<15%) is lower than DSM-based MDD (26%), and the former shares as much genetic liability with DSM-MDD (0.81) as it does a non-MDD help-seeking condition (0.84). While minimal phenotyping-based depression and DSM-based MDD show similar shared genetic liability with other conditions like neuroticism, a greater proportion of the genome contribute to the former (77%) than the latter (64%). Enrichment of heritability in CNS specific genes is found in both minimal phenotyping definitions of depression and other psychiatric conditions, but not DSM-MDD. GWAS loci identified in the minimal phenotyping definitions of depression, even when found in DSM-based MDD, show similar effects in other psychiatric conditions. Interpretation: Using minimal phenotyping strategy for GWAS, when applied to MDD, carries significant potential risks. It primarily identifies non-specific genetic factors shared between MDD and other psychiatric conditions, biases our view of genetic architecture of MDD, and limits our ability to identify pathways specific to MDD.
12 tweets neuroscience
Electro-encephalography (EEG) source connectivity is an emerging approach to estimate brain networks with high time/space resolution. Here, we aim to evaluate the effect of different functional connectivity (FC) methods on the EEG-source space networks at rest. The two main families of FC methods tested are: i) the FC methods that do not remove the zero-lag connectivity including the Phase Locking Value (PLV) and the Amplitude Envelope Correlation (AEC) and ii) the FC methods that remove the zero-lag connections such as the Phase Lag Index (PLI) and orthogonalisation approach combined with PLV (PLVorth) and AEC (AECorth). Methods are evaluated on resting state dense-EEG signals recorded from 20 healthy participants. Networks obtained by each FC method are compared with fMRI networks at rest (from the Human Connectome Project -HCP-, N=487). Results show low correlations for all the FC methods, however PLV and AEC networks are significantly correlated with fMRI networks (ro = 0.12, p = 1.93x10-8 and ro = 0.06, p = 0.007, respectively), while other methods are not. These observations are consistent for each EEG frequency bands and for different FC matrices threshold. Furthermore, the effect of electrode density was also tested using four EEG montages (dense-EEG 256 electrodes, 128, 64 and 32 electrodes). Results show no significant differences between the four EEG montages in terms of correlations with the fMRI networks. Our main message here is to be careful when selecting the FC methods and mainly those that remove the zero-lag connections as they can affect the network characteristics. More comparative studies (based on simulation and real data) are still needed in order to make EEG source connectivity a mature technique to address questions in cognitive and clinical neuroscience.
12 tweets cell biology
Long arrays of simple, tandemly repeated DNA sequences (known as satellites) are enriched in centromeres and pericentromeric regions, and contribute to chromosome segregation and other heterochromatin functions. Surprisingly, satellite DNAs are expressed in many multicellular eukaryotes, and their aberrant transcription may contribute to carcinogenesis and cellular toxicity. Satellite transcription and/or RNAs may also promote centromere and heterochromatin activities. However, we lack direct evidence that satellite DNA transcripts are required for normal cell or organismal functions. Here, we show that satellite RNAs derived from AAGAG tandem repeats are transcribed in many cell types throughout Drosophila melanogaster development, enriched in neuronal tissues and testes, localized within heterochromatic regions, and important for viability. Strikingly, we find that AAGAG transcripts are necessary for male fertility and are specifically required for normal histone-protamine exchange and sperm chromatin organization. Since AAGAG RNA-dependent events happen late in spermatogenesis when the transcripts are not detected, we speculate that AAGAG RNA functions in primary spermatocytes to prime post-meiosis steps in sperm maturation. In addition to demonstrating specific essential functions for AAGAG RNAs, comparisons between closely related Drosophila species suggest that satellite repeats and their transcription evolve quickly to generate new functions.
12 tweets synthetic biology
Therapeutic antibody optimization is time and resource intensive, largely because it requires low-throughput screening (10^3 variants) of full-length IgG in mammalian cells, typically resulting in only a few optimized leads. Here, we use deep learning to interrogate and predict antigen-specificity from a massive diversity of antibody sequence space. Using a mammalian display platform and the therapeutic antibody trastuzumab, rationally designed site-directed mutagenesis libraries are introduced by CRISPR/Cas9-mediated homology-directed repair (HDR). Screening and deep sequencing of relatively small libraries (10^4) produced high quality data capable of training deep neural networks that accurately predict antigen-binding based on antibody sequence (~85% precision). Deep learning is then used to predict millions of antigen binders from an in silico library of ~10^8 variants. Finally, these variants are subjected to multiple developability filters, resulting in tens of thousands of optimized lead candidates, which when a small subset of 30 are expressed, all 30 are antigen-specific. With its scalability and capacity to interrogate a vast protein sequence space, deep learning offers great potential for antibody engineering and optimization.
11 tweets genomics
Background & Aims: The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or 'adapt'; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses to characterize molecular changes underpinning adaptation to SGS. Methods: Single-cell RNA-sequencing was performed on epithelial cells isolated from distal SI of mice following 50% proximal small bowel resection (SBR) vs. sham surgery. Single-cell profiles were clustered based on transcriptional similarity, reconstructing differentiation events from intestinal stem cells (ISCs) through to mature enterocytes. An unsupervised computational approach to score cell identity was used to quantify changes in regional (proximal vs distal) SI identity, validated using immunofluorescence, immunohistochemistry, qPCR, western blotting, and RNA-FISH. Results: Uniform Manifold Approximation and Projection-based clustering and visualization revealed differentiation trajectories from ISCs to mature enterocytes in sham and SBR. Cell identity scoring demonstrated segregation of enterocytes by regional SI identity: SBR enterocytes assumed more mature proximal identities. This was associated with significant upregulation of lipid metabolism and oxidative stress gene expression, which was validated via orthogonal analyses. Observed upstream transcriptional changes suggest retinoid metabolism and proximal transcription factor Creb3l3 drive proximalization of cell identity in response to SBR. Conclusions: Adaptation to proximal SBR involves regional reprogramming of ileal enterocytes toward a proximal identity. Interventions bolstering the endogenous reprogramming capacity of SI enterocytes, conceivably by engaging the retinoid metabolism pathway, merit further investigation, as they may increase enteral feeding tolerance, and obviate intestinal failure, in SGS.
11 tweets neuroscience
Tissue clearing methods enable imaging of intact biological specimens without sectioning. However, reliable and scalable analysis of such large imaging data in 3D remains a challenge. Towards this goal, we developed a deep learning-based framework to quantify and analyze the brain vasculature, named Vessel Segmentation & Analysis Pipeline (VesSAP). Our pipeline uses a fully convolutional network with a transfer learning approach for segmentation. We systematically analyzed vascular features of the whole brains including their length, bifurcation points and radius at the micrometer scale by registering them to the Allen mouse brain atlas. We reported the first evidence of secondary intracranial collateral vascularization in CD1-Elite mice and found reduced vascularization in the brainstem as compared to the cerebrum. VesSAP thus enables unbiased and scalable quantifications for the angioarchitecture of the cleared intact mouse brain and yields new biological insights related to the vascular brain function.
11 tweets genetics
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting the domesticated cotton fiber phenotype. We used 465 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 68 QTL associated with phenotypic changes under domestication. These QTL average approximately 46 Mbp in size, and together represent 29% (647 Mbp) of the 2,260 Mbp genome. Although over 70% of QTL were recovered from the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environmentally labile, with only 41% shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and discussed in the context of the phenotype. We found some support for the previously noted biased recruitment under domestication of factors from one of the two co-resident genomes of allopolyploid cotton. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.
10 tweets molecular biology
CHoP-In (CRISPR/Cas9-mediated, Homology-independent, PCR-product Integration) is a fast and cloning-free strategy for genomic editing of mammalian cells. The desired integration fragment is produced as a PCR product, flanked by the Cas9 recognition sequences of the target locus. When co-transfected with the cognate Cas9/guide RNA, double strand breaks are introduced at the target genomic locus and at both ends of the PCR product. This allows incorporation into the genomic locus via hon-homologous end joining. The approach is versatile, allowing N-terminal, C-terminal or internal tag integration and gives predictable genomic integrations, as demonstrated for a selection of key membrane trafficking proteins. The lack of any donor vectors offers advantages over existing methods in terms of both speed and hands-on time. As such this approach will be a useful addition to the genome editing toolkit of those working in mammalian cell systems.
10 tweets microbiology
Molecular motors convert chemical energy directly into mechanical work and are found in all domains of life. These motors are critical to intracellular transport, motility, macromolecular protein assembly, and many essential processes. A wide-spread class of related bacterial motors drive the dynamic activity of extracellular fibers, such as type IV pili (T4P), that are extended and retracted using so-called secretion motor ATPases. Among these, the tight adherence (tad) pili are critical for surface sensing, surface attachment, and biofilm formation. How tad pili undergo dynamic cycles of extension and retraction despite lacking a dedicated retraction motor ATPase has remained a mystery. Here we find that a bifunctional pilus motor ATPase, CpaF, drives both activities through ATP hydrolysis. Specifically, we show that mutations within the ATP hydrolysis active site of Caulobacter crescentus CpaF result in a correlated reduction in the rates of extension and retraction. Moreover, a decrease in the rate of ATP hydrolysis directly scales with a decrease in the force of retraction and reduced dynamics in these CpaF mutants. This mechanism of motor protein bifunctionality extends to another genus of tad-bearing bacteria. In contrast, the T4aP subclass of pili possess dedicated extension and retraction motor ATPase paralogs. We show that these processes are uncoupled using a slow ATP hydrolysis mutation in the extension ATPase of competence T4aP of Vibrio cholerae that decreases the rate of extension but has no effect on the rate of retraction. Thus, a single motor ATPase is able to drive the bidirectional processes of pilus fiber extension and retraction.
10 tweets systems biology
The mechanisms of organ size control remain poorly understood. A key question is how cells collectively sense the overall status of a tissue. We addressed this problem focusing on mouse liver regeneration, which is controlled by Hippo signalling. Using digital tissue reconstruction and quantitative image analysis, we found that the apical surface of hepatocytes forming the bile canalicular network expands concomitant with an increase of F-actin and phospho-Myosin, to compensate an overload of bile acids. Interestingly, these changes are sensed by the Hippo transcriptional co-activator YAP, which localizes to the apical F-actin-rich region and translocates to the nucleus in dependence of the acto-myosin system. This mechanism tolerates moderate bile acid fluctuations under tissue homeostasis, but activates YAP in response to sustained bile acid overload. Using an integrated biophysical-biochemical model of bile pressure and Hippo signalling, we explained this behaviour by the existence of a mechano-sensory mechanism that activates YAP in a switch-like manner. We propose that the apical surface of hepatocytes acts as a self-regulatory mechano-sensory system that responds to critical levels of bile acids as readout of tissue status.
10 tweets genomics
Simone Maestri, Emanuela Cosentino, Marta Paterno, Hendrik Freitag, Jhoana M. Garces, Luca Marcolungo, Massimiliano Alfano, Iva Njunjić, Menno Schilthuizen, Ferry Slik, Michele Menegon, Marzia Rossato, Massimo Delledonne
Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION platform. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure reliable and robust performance under suboptimal field conditions without increasing costs. Here we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard molecular biology protocols and reagents that tolerate adverse environmental conditions. Barcodes are sequenced using MinION technology and analyzed with ONTrack, an original de novo assembly pipeline that requires as few as 500 reads per sample. ONTrack-derived consensus barcodes have high accuracy, ranging from 99,8% to 100%, despite the presence of homopolymer runs. The ONTrack pipeline has a user-friendly interface and returns consensus sequences in minutes. The remarkable accuracy and low computational demand of the ONTrack pipeline, together with the inexpensive equipment and simple protocols, make the proposed workflow particularly suitable for tracking species under field conditions.
9 tweets synthetic biology
Genetic programs operating in an history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed an automated workflow that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare.
9 tweets neuroscience
The stability of neural dynamics arises through a tight coupling of excitatory (E) and inhibitory (I) signals. Genetically encoded voltage indicators (GEVIs) can report both spikes and subthreshold dynamics in vivo, but voltage alone only reveals the combined effects of E and I synaptic inputs, not their separate contributions individually. Here we combine optical recording of membrane voltage with simultaneous optogenetic manipulation to probe E and I individually in barrel cortex Layer 1 (L1) neurons in awake mice. Our studies show that L1 neurons integrate thalamocortical excitation and lateral inhibition to produce precisely timed responses to whisker stimuli. Top-down neuromodulatory inputs drive additional excitation in L1. Together, these results suggest a model for computation in L1 consistent with its hypothesized role in attentional gating of the underlying cortex.
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