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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,572 bioRxiv papers from 308,082 authors.

Most tweeted bioRxiv papers, last 24 hours

487 results found. For more information, click each entry to expand.

81: Glacier ice archives fifteen-thousand-year-old viruses
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Posted to bioRxiv 07 Jan 2020

Glacier ice archives fifteen-thousand-year-old viruses
7 tweets ecology

Zhi-Ping Zhong, Natalie E. Solonenko, Yueh-Fen Li, Maria C. Gazitúa, Simon Roux, Mary E. Davis, James L Van Etten, Ellen Mosley-Thompson, Virginia I Rich, Matthew B. Sullivan, Lonnie G. Thompson

While glacier ice cores provide climate information over tens to hundreds of thousands of years, study of microbes is challenged by ultra-low-biomass conditions, and virtually nothing is known about co-occurring viruses. Here we establish ultra-clean microbial and viral sampling procedures and apply them to two ice cores from the Guliya ice cap (northwestern Tibetan Plateau, China) to study these archived communities. This method reduced intentionally contaminating bacterial, viral, and free DNA to background levels in artificial-ice-core control experiments, and was then applied to two authentic ice cores to profile their microbes and viruses. The microbes differed significantly across the two ice cores, presumably representing the very different climate conditions at the time of deposition that is similar to findings in other cores. Separately, viral particle enrichment and ultra-low-input quantitative viral metagenomic sequencing from ~520 and ~15,000 years old ice revealed 33 viral populations (i.e., species-level designations) that represented four known genera and likely 28 novel viral genera (assessed by gene-sharing networks). In silico host predictions linked 18 of the 33 viral populations to co-occurring abundant bacteria, including Methylobacterium, Sphingomonas, and Janthinobacterium, indicating that viruses infected several abundant microbial groups. Depth-specific viral communities were observed, presumably reflecting differences in the environmental conditions among the ice samples at the time of deposition. Together, these experiments establish a clean procedure for studying microbial and viral communities in low-biomass glacier ice and provide baseline information for glacier viruses, some of which appear to be associated with the dominant microbes in these ecosystems.

82: A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
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Posted to bioRxiv 21 Jan 2020

A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
7 tweets bioinformatics

Dimitrios V Vavoulis, Anthony Cutts, Jenny C Taylor, Anna Schuh

Tumours are composed of genotypically and phenotypically distinct cancer cell populations (clones), which are subject to a process of Darwinian evolution in response to changes in their local micro-environment, such as drug treatment. In a cancer patient, this process of continuous adaptation can be studied through next-generation sequencing of multiple tumour samples combined with appropriate bioinformatics and statistical methodologies. One family of statistical methods for clonal deconvolution seeks to identify groups of mutations and estimate the prevalence of each group in the tumour, while taking into account its purity and copy number profile. These methods have been used in the analysis of cross-sectional data, as well as for longitudinal data by discarding information on the timing of sample collection. Two key questions are how (in the case of longitudinal data) can we incorporate such information in our analyses and if there is any benefit in doing so. Regarding the first question, we incorporated information on the temporal spacing of longitudinally collected samples into standard non-parametric approaches for clonal deconvolution by modelling the time dependence of the prevalence of each clone as a Gaussian process. This permitted reconstruction of the temporal profile of the abundance of each clone continuously from several sparsely collected samples and without any strong prior assumptions on the functional form of this profile. Regarding the second question, we tested various model configurations on a range of whole genome, whole exome and targeted sequencing data from patients with chronic lymphocytic leukaemia, on liquid biopsy data from a patient with melanoma and on synthetic data. We demonstrate that incorporating temporal information in our analysis improves model performance, as long as data of sufficient volume and complexity are available for estimating free model parameters. We expect that our approach will be useful in cases where collecting a relatively long sequence of tumour samples is feasible, as in the case of liquid cancers (e.g. leukaemia) and liquid biopsies. The statistical methodology presented in this paper is freely available at github.com/dvav/clonosGP.

83: High Capacity poly(2-oxazoline) formulation of TLR 7/8 agonist extends survival in a chemo-insensitive, metastatic model of Lung Adenocarcinoma
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Posted to bioRxiv 12 Dec 2019

High Capacity poly(2-oxazoline) formulation of TLR 7/8 agonist extends survival in a chemo-insensitive, metastatic model of Lung Adenocarcinoma
7 tweets pharmacology and toxicology

Natasha Vinod, Duhyeong Hwang, Salma H. Azam, Amanda E. D. Van Swearingen, Elizabeth Wayne, Sloane C. Fussell, Marina Sokolsky-Papkov, Chad V. Pecot, Alexander V Kabanov

About 40% of the NSCLC patients have Stage IV cancer at the time of diagnosis. The only viable treatment options for metastatic disease are systemic chemotherapy and immunotherapy. Nonetheless, chemoresistance remains a major cause of chemotherapy failure. New immunotherapeutic modalities such as anti-PD1 checkpoint blockade have shown promise; however, response to such strategies is highly variable across patients. Here, we show that our novel poly(2-oxazoline) (POx) based nanomicellar formulation of Resiquimod, an imidazoquinoline TLR 7/8 agonist, had a superior tumor inhibitory effect in a metastatic model of lung adenocarcinoma, relative to anti-PD1 immune checkpoint blockade therapy as well as platinum-based chemotherapy, which is the mainstay of treatment for NSCLC. Investigation of the in vivo immune status following Resiquimod PM (POx micellar formulation of Resiquimod) treatment showed that Resiquimod-based stimulation of antigen-presenting cells in the tumor microenvironment resulted in the mobilization of anti-tumor CD8+ immune response. Our study demonstrates the promise of optimally delivered and nano-formulated Resiquimod as a new immunomodulating therapeutic strategy for the treatment of metastatic NSCLC.

84: Sample size evolution in neuroimaging research: an evaluation of highly-cited studies (1990-2012) and of latest practices (2017-2018) in high-impact journals
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Posted to bioRxiv 17 Oct 2019

Sample size evolution in neuroimaging research: an evaluation of highly-cited studies (1990-2012) and of latest practices (2017-2018) in high-impact journals
7 tweets neuroscience

Denes Szucs, John PA Ioannidis

We evaluated 1038 of the most cited structural and functional (fMRI) magnetic resonance brain imaging papers (1161 studies) published during 1990-2012 and 273 papers (302 studies) published in top neuroimaging journals in 2017 and 2018. 96% of highly cited experimental fMRI studies had a single group of participants and these studies had median sample size of 12, highly cited clinical fMRI studies (with patient participants) had median sample size of 14.5, and clinical structural MRI studies had median sample size of 50. The sample size of highly cited experimental fMRI studies increased at a rate of 0.74 participant/year and this rate of increase was commensurate with the median sample sizes of neuroimaging studies published in top neuroimaging journals in 2017 (23 participants) and 2018 (24 participants). Only 4 of 131 papers in 2017 and 5 of 142 papers in 2018 had pre-study power calculations, most for single t-tests and correlations. Only 14% of highly cited papers reported the number of excluded participants whereas about 45% of papers in 2017 and 2018 reported excluded participants. Targeted interventions from publishers and funders could facilitate increase in sample sizes and adherence to better standards.

85: Accurate And Versatile 3D Segmentation Of Plant Tissues At Cellular Resolution
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Posted to bioRxiv 18 Jan 2020

Accurate And Versatile 3D Segmentation Of Plant Tissues At Cellular Resolution
6 tweets plant biology

Adrian Wolny, Lorenzo Cerrone, Athul Vijayan, Rachele Tofanelli, Amaya Vilches Barro, Marion Louveaux, Christian Wenzl, Susanne Steigleder, Constantin Pape, Alberto Bailoni, Salva Duran-Nebreda, George Bassel, Jan U. Lohmann, Fred A. Hamprecht, Kay Schneitz, Alexis Maizel, Anna Kreshuk

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on fixed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, and acquisition settings. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface.

86: The optoretinogram reveals how human photoreceptors deform in response to light
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Posted to bioRxiv 18 Jan 2020

The optoretinogram reveals how human photoreceptors deform in response to light
6 tweets neuroscience

Vimal Prabhu Pandiyan, Aiden Maloney Bertelli, James Kuchenbecker, Kevin C Boyle, Tong Ling, B. Hyle Park, Austin Roorda, Daniel Palanker, Ramkumar Sabesan

Limited accessibility of retinal neurons to electrophysiology on a cellular scale in-vivo has restricted studies of their signaling to in-vitro preparations and animal models. Physiological changes underlying neural activity are mediated by variations in electrical potential that alter the surface tension of the cell membrane. In addition, physiological processes affect concentration of the cell's constituents that results in variation of osmotic pressure. Both these phenomena affect the neuron's shape which can be detected using interferometric imaging, thereby enabling non-invasive label-free imaging of physiological activity in-vivo with cellular resolution. Here, we apply high-speed phase-resolved optical coherence tomography in line-field configuration to image the biophysical phenomena associated with phototransduction in human cone photoreceptors in vivo. We demonstrate that individual cones exhibit a biphasic response to light: an early ms-scale fast contraction of the outer segment immediately after the onset of the flash stimulus followed by a gradual (hundreds of ms) expansion. We demonstrate that the contraction can be explained by rapid charge movement accompanying the isomerization of cone opsins, consistent with the early receptor potential observed in the electroretinogram and classical electrophysiology in-vitro. We demonstrate the fidelity of such all-optical recording of light-induced activity in the human retina, namely the optoretinogram, across a range of spatiotemporal scales. This approach incorporates functional evaluation into a routine clinical examination of retinal structure and thus holds enormous potential to serve as a biomarker for early disease diagnosis and monitoring therapeutic efficacy.

87: Production location of the gelling agent Phytagel has a significant impact on Arabidopsis thaliana seedling phenotypic analysis
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Posted to bioRxiv 20 Jan 2020

Production location of the gelling agent Phytagel has a significant impact on Arabidopsis thaliana seedling phenotypic analysis
6 tweets plant biology

Caitlin N. Jacques, Anna K. Hulbert, Shelby Westenskow, Michael M. Neff

Background:  Recently, it was found that 1% Phytagel plates used to conduct  Arabidopsis thaliana  seedling phenotypic analysis no longer reproduced previously published results. This Phytagel, which is produced in China (Phytagel C), has replace American-made Phytagel (Phytagel), which is no longer commercially available. In this study, we present the impact of Phytagel produced in the United States vs. China on seedling phenotypic analysis. As a part of this study, an alternative gelling agent has been identified that is capable of reproducing previously published seedling morphometrics.  Results:  Phytagel and Phytagel C were investigated based on their ability to reproduce the subtle phenotype of the  sob3-4 esc-8  double mutant. Fluence-rate-response analysis of seedlings grown on 1% Phytagel C plates failed to replicate the  sob3-4 esc-8  subtle phenotype seen on 1% Phytagel. Furthermore, root penetrance analysis showed a significant difference between  sob3-4 esc-8  seedlings grown on 1% Phytagel and 1% Phytagel C. It was also found that 1% Phytagel C was significantly harder than 1% Phytagel. As a replacement for Phytagel C, Gellan was tested. 1% Gellan was able to reproduce the subtle phenotype of  sob3-4 esc-8 . Furthermore, there was no significant difference in root penetration of the wild type or  sob3-4 esc-8  seedlings between 1% Phytagel and 1% Gellan. This may be due to the significant reduction in hardness in 1% Gellan plates compared to 1% Phytagel plates. Finally, we tested additional concentrations of Gellan and found that seedlings on 0.6% Gellan looked more uniform while also being able to reproduce previously published results. Conclusions:  Phytagel has been the standard gelling agent for several studies involving the characterization of subtle seedling phenotypes. After production was moved to China, Phytagel C was no longer capable of reproducing these previously published results. An alternative gelling agent, Gellan, was able to reproduce previously published seedling phenotypes at both 1% and 0.6% concentrations. The information provided in this manuscript is beneficial to the scientific community as whole, specifically phenomics labs, as it details key problematic differences between gelling agents that should be performing identically (Phytagel and Phytagel C).

88: Vps13D is required for mitochondrial fission and mitophagy triggered by fission defects in Drosophila neurons
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Posted to bioRxiv 22 Jan 2020

Vps13D is required for mitochondrial fission and mitophagy triggered by fission defects in Drosophila neurons
6 tweets cell biology

Ryan Insolera, Péter Lorincz, Alec J Wishnie, Gábor Juhász, Catherine A Collins

Members of the Vps13 family of proteins have recently been suggested to function in lipid exchange at inter-organelle contact sites. While all family members (VPS13A-D) have been implicated in neurodevelopmental and neurodegenerative diseases, the biological functions of these proteins in neurons are not known. Here we report two cellular functions for the essential gene Vps13D in Drosophila motoneurons: the first is in the initiation of mitochondrial fission; the second is in the progression of selective mitophagy, which becomes induced in neurons as a consequence of the fission defect. Loss of Vps13D in neurons leads to unique mitophagy intermediates that also appear when fission is disrupted simultaneously with impairment to autophagy machinery. This novel identification of intermediates trapped in late stages of mitophagy enables new insight into mechanisms of mitochondrial quality control in neurons in vivo.

89: The Linker Domain of SNAP25 Acts as a Flexible Molecular Spacer to Ensure Efficient S-Acylation
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Posted to bioRxiv 22 Jan 2020

The Linker Domain of SNAP25 Acts as a Flexible Molecular Spacer to Ensure Efficient S-Acylation
6 tweets cell biology

Christine Salaun, Jennifer Greaves, Nicholas C.O. Tomkinson, Luke H. Chamberlain

S-Acylation of the SNARE protein SNAP25 is mediated by a subset of Golgi zDHHC enzymes, in particular zDHHC17. The ankyrin repeat (ANK) domain of this enzyme interacts with a short linear motif known as the zDHHC ANK binding motif (zDABM) in SNAP25 (112-VVASQP-117), which is downstream of the S-acylated cysteine-rich domain (85-CGLCVCPC-92). In this study, we have investigated the importance of the flexible linker (amino acids 93-111; referred to as the mini-linker region) that separates the zDABM and S-acylated cysteines. Shortening the mini-linker had no effect of zDHHC17 interaction but blocked S-acylation. Insertion of additional flexible glycine-serine repeats had no effect on S-acylation, whereas extended and rigid alanine-proline repeats perturbed this process. Indeed, a SNAP25 mutant in which the mini-linker region was substituted with a flexible glycine-serine linker of the same length underwent efficient S-acylation. Furthermore, this mutant displayed the same intracellular localisation as wild-type SNAP25, showing that the sequence of the mini-linker is not important in this context. By using the results of previous peptide array experiments, we generated a SNAP25 mutant predicted to have a higher affinity zDABM, and this mutant showed enhanced interaction with zDHHC17 in cells. Interestingly, this mutant was S-acylated with reduced efficiency, implying that a lower affinity interaction of the SNAP25 zDABM with zDHHC17 is optimal for S-acylation efficiency. Overall, the results of this study show that amino acids 93-111 in SNAP25 act as a flexible molecular spacer to ensure efficient coupling of enzyme-substrate interaction and S-acylation.

90: Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex
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Posted to bioRxiv 21 Jan 2020

Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex
6 tweets biochemistry

João Leandro, Susmita Khamrui, Hui Wang, Chalada Suebsuwong, Natalia S Nemeria, Khoi Huynh, Moses Moustakim, Cody Secor, May Wang, Tetyana Dodatko, Brandon Stauffer, Christopher G Wilson, Chunli Yu, Michelle R. Arkin, Frank Jordan, Roberto Sanchez, Robert J. DeVita, Michael B Lazarus, Sander M Houten

DHTKD1 is the E1 component of the 2-oxoadipic acid dehydrogenase complex (OADHc), which functions in the L-lysine degradation pathway. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q (CMT2Q) and eosinophilic esophagitis (EoE). A crystal structure and inhibitors of DHTKD1 could improve the understanding of these clinically distinct disorders, but are currently not available. Here we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.1 Å. The protein assembles as a dimer with residues from both monomers contributing to cofactor binding. We also report the impact of ten DHTKD1 missense mutations on the encoded proteins by enzyme kinetics, thermal stability and structural modeling. Some DHTKD1 variants displayed impaired folding (S777P and S862I), whereas other substitutions rendered the enzyme inactive (L234G, R715C and R455Q) or affected the thermal stability and catalytic efficiency (V360A and P773L). Three variants (R163Q, Q305H and G729R) surprisingly showed wild type like properties. Our work provides a structural basis for further understanding of the function of DHTKD1 and a starting point for selective small molecule inhibitors of the enzyme, which could help tease apart the role of this enzyme in several human pathologies.

91: Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism
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Posted to bioRxiv 20 Jan 2020

Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism
6 tweets biochemistry

Gustavo A. Bezerra, William R. Foster, Henry J Bailey, Kevin G. Hicks, Sven W. Sauer, Bianca Dimitrov, Juergen G. Okun, Jared Rutter, Stefan Koelker, Wyatt W. Yue

DHTKD1 is a lesser-studied E1 enzyme belonging to the family of 2-oxoacid dehydrogenases. DHTKD1, in complex with the E2 (dihydrolipoamide succinyltransferase, DLST) and E3 (lipoamide dehydrogenase, DLD) components, is implicated in lysine and tryptophan catabolism by catalysing the oxidative decarboxylation of 2-oxoadipate (2OA) in the mitochondria. Here, we solved the crystal structure of human DHTKD1 at 1.9 Å resolution in binary complex with the thiamine diphosphate (ThDP) cofactor. Our structure explains the evolutionary divergence of DHTKD1 from the well-characterized homologue 2-oxoglutarate (2OG) dehydrogenase, in its preference for the larger 2OA substrate than 2OG. Inherited DHTKD1 missense mutations cause the lysine metabolic condition 2-aminoadipic and 2-oxoadipic aciduria. Reconstruction of the missense variant proteins reveal their underlying molecular defects, which include protein destabilisation, disruption of protein-protein interactions, and alterations in the protein surface. We further generated a 5.0 Å reconstruction of the human DLST inner core by single-particle electron microscopy, revealing a 24-mer cubic architecture that serves as a scaffold for assembly of DHTKD1 and DLD. This structural study provides a starting point to develop small molecule DHTKD1 inhibitors for probing mitochondrial energy metabolism.

92: Creating supported plasma membrane bilayers using acoustic pressure
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Posted to bioRxiv 20 Jan 2020

Creating supported plasma membrane bilayers using acoustic pressure
6 tweets biophysics

Erdinc Sezgin, Dario Carugo, Ilya Levental, Eleanor Stride, Christian Eggeling

Model membrane systems are essential tools for biology, enabling study of biological processes in a simplified setting to reveal the underlying physicochemical principles. As cell-derived membrane systems, giant plasma membrane vesicles (GPMVs) constitute an intermediate model between native cellular plasma and artificial membranes. Certain applications, however, require planar membrane surfaces. Here, we report a novel approach for creating supported plasma membrane bilayers (SPMBs) by bursting cell-derived GPMVs using an ultrasonic pressure field generated within an acoustofluidic device. We show that the mobility of outer leaflet molecules is preserved in SPMBs, suggesting that they are accessible on the surface of the bilayers. Such model membrane systems will be useful for many applications requiring detailed characterization of plasma membrane dynamics.

93: DrawAlignR: An interactive tool for across run chromatogram alignment visualization
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Posted to bioRxiv 17 Jan 2020

DrawAlignR: An interactive tool for across run chromatogram alignment visualization
6 tweets bioinformatics

Shubham Gupta, Justin Sing, Arshia Mahmoodi, Hannes Rost

Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

94: Age dependent changes in synaptic NMDA receptor composition in adult human cortical neurons
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Posted to bioRxiv 21 Jan 2020

Age dependent changes in synaptic NMDA receptor composition in adult human cortical neurons
6 tweets neuroscience

Chrysia Maria Pegasiou, Ardalan Zolnourian, DIego Gomez-Nicola, Katrin Deinhardt, James Nicoll, Aminul Ahmed, Girish Vajramani, Paul Grundy, Matthijs Verhoog, Huib Mansvelder, V. Hugh Perry, Diederik Bulters, Mariana Vargas-Caballero

The molecular processes underlying the ageing-related decline in cognitive performance and memory observed in humans are poorly understood. Studies in rodents have shown that N-methyl-D-aspartate receptors (NMDARs) containing GluN2B subunits can enhance the ability of synapses to undergo long term potentiation. In ageing rodents, the contribution of GluN2B to synaptic function is reduced compared to younger animals and the decline in GluN2B subunit expression is correlated with impaired memory functions. However, the contribution of GluN2B containing receptors to synaptic transmission in cortical synapses has not been previously studied. We investigated the synaptic contribution of GluN2A and GluN2B containing NMDARs in adult human neurons using fresh non-pathological temporal cortical tissue resected during neurosurgical procedures. The tissue we obtained fulfilled quality criteria by the absence of inflammation markers and proteomic degradation. We show an age-dependent decline in the NMDA/AMPA receptor ratio in adult human temporal cortical synapses. We demonstrate that GluN2B containing NMDA receptors contribute to synaptic responses in the adult human brain with a reduced contribution in older individuals. With previous evidence demonstrating the critical role of synaptic GluN2B in regulating synaptic strength and memory storage in mice, this progressive reduction of GluN2B in the human brain during aging may underlie a molecular mechanism in the age-related decline in cognitive abilities and memory observed in humans.

95: Insulin-stimulated glucose uptake partly relies on p21-activated kinase (PAK)-2, but not PAK1, in mouse skeletal muscle
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Posted to bioRxiv 07 Feb 2019

Insulin-stimulated glucose uptake partly relies on p21-activated kinase (PAK)-2, but not PAK1, in mouse skeletal muscle
6 tweets cell biology

Lisbeth L. V. Møller, Merna Jaurji, Rasmus Kjøbsted, Giselle A. Joseph, Agnete B. Madsen, Jonas R. Knudsen, Annemarie Lundsgaard, Nicoline R. Andersen, Peter Schjerling, Pia Jensen, Robert S. Krauss, Erik A. Richter, L. Sylow

Objective: Skeletal muscle glucose uptake is essential for maintaining whole-body glucose homeostasis and accounts for the majority of glucose disposal in response to insulin. The group I p21-activated kinase (PAK) isoforms PAK1 and PAK2 are activated in response to insulin in skeletal muscle. Interestingly, PAK1/2 signalling is impaired in insulin-resistant mouse and human skeletal muscle and PAK1 has been suggested to be required for insulin-stimulated GLUT4 translocation. However, the relative contribution of PAK1 and PAK2 to insulin-stimulated glucose uptake in mature skeletal muscle is unresolved. The aim of the present investigation was to determine the requirement for PAK1 and PAK2 in whole-body glucose homeostasis and insulin-stimulated glucose uptake in skeletal muscle. Methods: Glucose uptake was measured in isolated skeletal muscle incubated with a pharmacological inhibitor (IPA-3) of group I PAKs and in muscle from whole-body PAK1 knockout (KO), muscle-specific PAK2 (m)KO and double whole-body PAK1 and muscle-specific PAK2 knockout mice. Results: The whole-body respiratory exchange ratio was largely unaffected by lack of PAK1 and/or PAK2. Whole-body glucose tolerance was mildly impaired in PAK2 mKO, but not PAK1 KO mice. IPA-3 partially reduced (-20%) insulin-stimulated glucose uptake in mouse soleus muscle. In contrast to a previous study of GLUT4 translocation in PAK1 KO mice, PAK1 KO muscles displayed normal insulin-stimulated glucose uptake in vivo and in isolated muscle. On the contrary, glucose uptake was slightly reduced in response to insulin in glycolytic extensor digitorum longus muscle lacking PAK2, alone (-18%) or in combination with PAK1 KO (-12%). Conclusions: Insulin-stimulated glucose uptake partly relies on PAK2, but not PAK1, in mouse skeletal muscle. Thus, the present study challenges that group I PAKs, and especially PAK1, are major regulators of whole-body glucose homeostasis and insulin-stimulated glucose uptake in skeletal muscle.

96: Temperature change has the same effect as genetic variation on a morphological trait involved in reproductive isolation between Drosophila sister species
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Posted to bioRxiv 20 Jan 2020

Temperature change has the same effect as genetic variation on a morphological trait involved in reproductive isolation between Drosophila sister species
6 tweets evolutionary biology

Alexandre E Peluffo, Mehdi Hamdani, Alejandra Vargas-Valderrama, Jean R. David, Mallard François, Francois Graner, Virginie Courtier-Orgogozo

Phenotypic plasticity, the capacity of one genotype to generate distinct phenotypes in different environments, is usually thought to facilitate species divergence by opening novel ecological niches to plastic individuals. Here we reveal a case of speciation where this "plasticity first" scenario might not hold. Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Under the lock-and-key hypothesis, rapid morphological evolution is associated with a high match between male and female genitalia of the same species and a low match between male and females of closely related species. Previous studies have suggested plasticity of genitalia to be a proof against the lock-and-key hypothesis since the environmentally triggered phenotypic change could modify the "key". Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and D. yakuba. We designed a semi-automatic measurement pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that ventral branches are not plastic in D. yakuba but that in D. santomea temperature change phenocopies interspecific genetic variation between both species for ventral branches shape. Our results suggest that speciation of D. santomea and D. yakuba was associated with a gain of plasticity and that genitalia plasticity can be compatible with the lock-and-key hypothesis.

97: Species-specific oscillation periods of human and mouse segmentation clocks are due to cell autonomous differences in biochemical reaction parameters
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Posted to bioRxiv 26 May 2019

Species-specific oscillation periods of human and mouse segmentation clocks are due to cell autonomous differences in biochemical reaction parameters
5 tweets developmental biology

Mitsuhiro Matsuda, Hanako Hayashi, Jordi Garcia-Ojalvo, Kumiko Yoshioka-Kobayashi, Ryoichiro Kageyama, Yoshihiro Yamanaka, Makoto Ikeya, Junya Toguchida, Cantas Alev, Miki Ebisuya

While the mechanisms of embryonic development are similar between mouse and human, the tempo is in general slower in human. The cause of interspecies differences in developmental time remains a mystery partly due to lack of an appropriate model system. Since murine and human embryos differ in their sizes, geometries, and nutrients, we use in vitro differentiation of pluripotent stem cells (PSCs) to compare the same type of cells between the species in similar culture conditions. As an example of well-defined developmental time, we focus on the segmentation clock, oscillatory gene expression that regulates the timing of sequential formation of body segments. In this way we recapitulate the murine and human segmentation clocks in vitro, showing that the species-specific oscillation periods are derived from cell autonomous differences in the speeds of biochemical reactions. Presomitic mesoderm (PSM)-like cells induced from murine and human PSCs displayed the oscillatory expression of HES7, the core gene of the segmentation clock, with oscillation periods of 2-3 hours (mouse PSM) and 5-6 hours (human PSM). Swapping HES7 loci between murine and human genomes did not change the oscillation periods dramatically, denying the possibility that interspecies differences in the sequences of HES7 loci might be the cause of the observed period difference. Instead, we found that the biochemical reactions that determine the oscillation period, such as the degradation of HES7 and delays in its expression, are slower in human PSM compared with those in mouse PSM. With the measured biochemical parameters, our mathematical model successfully accounted for the 2-3-fold period difference between mouse and human. We further demonstrate that the concept of slower biochemical reactions in human cells is generalizable to several other genes, as well as to another cell type. These results collectively indicate that differences in the speeds of biochemical reactions between murine and human cells give rise to the interspecies period difference of the segmentation clock and may contribute to other interspecies differences in developmental time.

98: Benchmarking joint multi-omics dimensionality reduction approaches for cancer study
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Posted to bioRxiv 14 Jan 2020

Benchmarking joint multi-omics dimensionality reduction approaches for cancer study
5 tweets bioinformatics

L Cantini, Pooya Zakeri, Celine Hernandez, Aurelien Naldi, Denis Thieffry, Elisabeth Remy, Anais Baudot

High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve this multi-omics data integration, Joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehensive benchmark with practical guidelines. We performed a systematic evaluation of nine representative jDR methods using three complementary benchmarks. First, we evaluated their performances in retrieving ground-truth sample clustering from simulated multi-omics datasets. Second, we used TCGA cancer data to assess their strengths in predicting survival, clinical annotations and known pathways/biological processes. Finally, we assessed their classification of multi-omics single-cell data. From these in-depth comparisons, we observed that intNMF performs best in clustering, while MCIA offers a consistent and effective behavior across many contexts. The full code of this benchmark is implemented in a Jupyter notebook - multi-omics mix (momix) - to foster reproducibility, and support data producers, users and future developers.

99: CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing in Botrytis cinerea
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Posted to bioRxiv 20 Jan 2020

CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing in Botrytis cinerea
5 tweets genetics

Matthias Hahn, Thomas Leisen, Fabian Bietz, Janina Werner, Alex Wegner, Ulrich Schaffrath, David Scheuring, Felix Willmund, Andreas Mosbach, Gabriel Scalliet

CRISPR/Cas has become the state-of-the-art technology for genetic manipulation in diverse organisms, enabling targeted genetic changes to be performed with unprecedented efficiency. Here we report on the first establishment of robust CRISPR/Cas editing in the important necrotrophic plant pathogen Botrytis cinerea based on the introduction of optimized Cas9-sgRNA ribonucleoprotein complexes (RNPs) into protoplasts. Editing yields were further improved by development of a novel strategy that combines RNP delivery with transiently stable telomeres containing vectors, which allowed temporary selection and convenient screening of marker-free editing. We demonstrate that this approach provides vastly superior editing rates compared to existing CRISPR/Cas-based methods in filamentous fungi, including the model plant pathogen Magnaporthe oryzae. The high performance of telomere vector-mediated coediting was demonstrated by random mutagenesis of codon 272 of the sdhB gene, a major determinant of resistance to succinate dehydrogenase inhibitor (SDHI) fungicides by in bulk replacement of the codon 272 with codons encoding all 20 amino acids. All exchanges were found at similar frequencies in the absence of selection but SDHI selection allowed the identification of novel amino acid substitutions which conferred differential resistance levels towards different SDHI fungicides. The increased efficiency and easy handling of RNP-based cotransformation is expected to greatly facilitate molecular research in B. cinerea and other fungi.

100: Quantification of amyloid fibril polymorphism by nano-morphometry reveals the individuality of filament assembly
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Posted to bioRxiv 15 Jan 2020

Quantification of amyloid fibril polymorphism by nano-morphometry reveals the individuality of filament assembly
5 tweets biophysics

Liam D Aubrey, Ben J. F. Blakeman, Liisa Lutter, Christopher Serpell, Mick F. Tuite, Louise C Serpell, Wei-Feng Xue

Amyloid fibrils are highly polymorphic structures formed by many different proteins. They provide biological function but also abnormally accumulate in numerous human diseases. The physicochemical principles of amyloid polymorphism are not understood due to lack of structural insights at the single-fibril level. To identify and classify different fibril polymorphs and to quantify the level of heterogeneity is essential to decipher the precise links between amyloid structures and their functional and disease associated properties such as toxicity, strains, propagation and spreading. Employing gentle, force-curve based AFM, we produce detailed images, from which the 3D reconstruction of individual filaments in heterogeneous amyloid samples is achieved. Distinctive fibril polymorphs are then classified by hierarchical clustering, and sample heterogeneity is objectively quantified. These data demonstrate the polymorphic nature of fibril populations, provide important information regarding the energy landscape of amyloid self-assembly, and offer quantitative insights into the structural basis of polymorphism in amyloid populations.

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