bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite
Authors: Séité Sarah , Harrison Mark C. , Sillam-Dussès David , Lupoli Roland , Van Dooren Tom J. M. , Robert Alain , Poissonnier Laure-Anne , Lemainque Arnaud , Renault David , Acket Sébastien , Andrieu Muriel , Viscarra José , Sul Hei Sook , de Beer Z. Wilhelm , Bornberg-Bauer Erich , Vasseur-Cognet Mireille 
Published: May 2021

ABSTRACTKings and queens of eusocial termites can live for decades, while queens sustain a nearly maximal fertility. To investigate the molecular mechanisms underlying their long lifespan, we carried out transcriptomics, lipidomics and metabolomics inMacrotermes natalensison sterile short-lived workers, long-lived kings and five stages spanning twenty years of adult queen maturation. Reproductives share gene expression differences from workers in agreement with a reduction of several aging-related processes, involving upregulation of DNA damage repair and mitochondrial functions. Anti-oxidant gene expression is downregulated, while peroxidability of membranes in queens decreases. Against expectations, we observed an upregulated gene expression in fat bodies of reproductives of several components of the IIS pathway, including an insulin-like peptide,Ilp9.This pattern does not lead to deleterious fat storage in physogastric queens, while simple sugars dominate in their hemolymph and large amounts of resources are allocated towards oogenesis. Our findings support the notion that all processes causing aging need to be addressed simultaneously in order to prevent it.
Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer
Authors: Li Hongjia , Zhang Hui , Wan Xiaohua , Yang Zhidong , Li Chengmin , Li Jintao , Han Renmin , Zhu Ping , Zhang Fa 
Published: May 2021

ABSTRACTMotivationCryo-electron microscopy (cryo-EM) is a widely-used technology for ultrastructure determination, which constructs the three-dimensional (3D) structures of protein and macromolecular complex from a set of two-dimensional (2D) micrographs. However, limited by the electron beam dose, the micrographs in cryo-EM generally suffer from extremely low signal-to-noise ratio (SNR), which hampers the efficiency and effectiveness of downstream analysis. Especially, the noise in cryo-EM is not simple additive or multiplicative noise whose statistical characteristics are quite different from the ones in natural image, extremely shackling the performance of conventional denoising methods.ResultsHere, we introduce the Noise-Transfer2Clean (NT2C), a denoising deep neural network (DNN) for cryo-EM to enhance image contrast and restore specimen signal, whose main idea is to improve the denoising performance by correctly discovering the noise model of cryo-EM images and transferring the statistical nature of noise into the denoiser. Especially, to cope with the complex noise model in cryo-EM, we design a contrast-guided noise and signal re-weighted algorithm to achieve clean-noisy data synthesis and data augmentation, making our method authentically achieve signal restoration based on noise’s true properties. To our knowledge, NT2C is the first denoising method that resolves the complex noise model in cryo-EM images. Comprehensive experimental results on simulated datasets and real datasets show that NT2C achieved a notable improvement in image denoising and specimen signal restoration, comparing with the state-of-art methods. A real-world case study shows that NT2C can improve the recognition rate on hard-to-identify particles by 19% in the particle picking task.
Concerns regarding vaccination as a management strategy against koala retrovirus
Authors: Joyce Briony A. , Watterson Daniel , Isaacs Ariel , Chappell Keith J. 
Published: May 2021

AbstractKoalas are of great cultural, ecological and economic significance to Australia. However, they are in steep decline throughout much of their geographic range, with the recently endogenized koala retrovirus (KoRV) presumed to be a contributing factor. Olagoke, et al. 1 have proposed vaccination against KoRV as a suitable control mechanism to reduce the severity of KoRV infections and suggest that their recombinant vaccine is effective at invoking a neutralising immune response and significantly reducing viral loads. Here, we report the findings of our own attempts to detect antibodies specific to the KoRV envelope protein (Env) in infected animals. Antibodies against Env were undetectable in all animals, as would be expected in the case of an endogenous virus antigen which should proceed towards a pathway of self-tolerance. This finding calls into question the results of Olagoke, et al. 1, and prior work by this team 2,3. Following a critical review of this work 1–3, we have identified a number of assay inaccuracies and possible over interpretations of the data and conclude that further work to develop and test a vaccine against KoRV in koalas is not supported by evidence.
A Keller-Segel model for C elegans L1 aggregation
Authors: Avery Leon , Ingalls Brian , Dumur Catherine , Artyukhin Alexander 
Published: May 2021

AbstractWe describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh–2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh–2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type.Author summaryAmong the most complex of animal behaviors are collective behaviors, in which animals interact with each other so as to produce large-scale organization. Starved first-stage larvae of the nematode Caenorhabditis elegans exhibit such a behavior: they come together to form aggregates of several hundred worms. How and why they do this are unknown. To address these questions, we developed a mathematical model of starved L1 aggregation. This model reproduced the main features of the behavior.
Orc6 at replication fork enables efficient mismatch repair
Authors: Lin Yo-Chuen , Chakraborty Arindam , Liu Dazhen , Mitra Jaba , Kadyrova Lyudmila Y , Hsu Rosaline Y.C. , Arif Mariam K. , Adusumilli Sneha , Ha Taekjip , Kadyrov Farid A , Prasanth Kannanganattu V. , Prasanth Supriya G. 
Published: May 2021

AbstractIn eukaryotes, the Origin Recognition Complex (ORC) is required for the initiation of DNA replication. The smallest subunit of ORC, Orc6, is essential for pre-replication complex (pre-RC) assembly and cell viability in yeast and for cytokinesis in metazoans. However, unlike other ORC components, the role of human Orc6 in replication remains to be resolved. Here, we identify an unexpected role for hOrc6, which is to promote S-phase progression post pre-RC assembly and DNA damage response. Orc6 localizes at the replication fork and is an accessory factor of the mismatch repair (MMR) complex. In response to oxidative damage during S-phase, often repaired by MMR, Orc6 facilitates MMR complex assembly and activity, without which the checkpoint signaling is abrogated. Mechanistically, Orc6 directly binds to MutSα and enhances the chromatin-association of MutLα, thus enabling efficient mismatch repair. Based on this, we conclude that hOrc6 plays a fundamental role in genome surveillance during S-phase.Abstract FigureHighlightsHuman Orc6 is dispensable for G1 licensing, but required for S-phase progressionHuman Orc6 at the replication fork is an accessory factor for MMR complexDepletion of hOrc6 sensitizes cells to DNA damage and impairs ATR activationHuman Orc6 regulates MMR complex assembly and activity
Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1
Authors: Tocco Chiara , Øvsthus Martin , Bjaalie Jan G. , Leergaard Trygve B. , Studer Michèle 
Published: May 2021

AbstractAxonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. Combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines, and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei.Summary statementCortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.
Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function
Authors: Si Yunda , Yan Chengfei 
Published: May 2021

AbstractDeep residual learning has shown great success in protein contact prediction. In this study, a new deep residual learning-based protein contact prediction model was developed. Comparing with previous models, a new type of residual block hybridizing 1D and 2D convolutions was designed to increase the effective receptive field of the residual network, and a new loss function emphasizing the easily misclassified residue pairs was proposed to enhance the model training. The developed protein contact prediction model referred to as DRN-1D2D was first evaluated on 105 CASP11 targets, 76 CAMEO hard targets and 398 membrane proteins together with two in house-developed reference models based on either the standard 2D residual block or the traditional BCE loss function, from which we confirmed that both the dimensional hybrid residual block and the singularity enhanced loss function can be employed to improve the model performance for protein contact prediction. DRN-1D2D was further evaluated on 39 CASP13 and CASP14 free modeling targets together with the two reference models and six state-of-the-art protein contact prediction models including DeepCov, DeepCon, DeepConPred2, SPOT-Contact, RaptorX-Contact and TripleRes. The result shows that DRN-1D2D consistently achieved the best performance among all these models.
Rapid inactivation of SARS-CoV-2 variants by continuous and intermittent irradiation with a deep-ultraviolet light-emitting diode (DUV-LED) device
Authors: Inagaki Hiroko , Saito Akatsuki , Kaneko Chiho , Sugiyama Hironobu , Okabayashi Tamaki , Fujimoto Shouichi 
Published: May 2021

AbstractMore than 1 year has passed since social activities have been restricted due to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More recently, novel SARS-CoV-2 variants have been spreading around the world, and there is growing concern of higher transmissibility of the variants and weaker protective efficacy of vaccine against the variants. Immediate measures are needed to reduce human exposure to the virus. In this study, the antiviral efficacy of deep-ultraviolet light-emitting diode (DUV-LED) irradiation (280 ± 5 nm, 3.75 mW/cm2) against three SARS-CoV-2 variants was evaluated. For the B.1.1.7, B.1.351, and P.1 strains, the infectious titer reduction rates of 96.3%, 94.6%, and 91.9%, respectively, were already recognized with the irradiation of virus stocks for 1 s, and the rates increased to 99.9%, 99.9%, and 99.8%, respectively, with irradiation for 5 s. We also tested the effect of pulsed DUV-LED irradiation (7.5 mW/cm2, duty rate: 50%, frequency: 1 KHz) under the same output conditions as continuous irradiation, and found that the antiviral efficacy of pulsed and continuous irradiation was the same. These findings suggest that SARS-CoV-2 may be instantly inactivated by DUV-LED irradiation if the DUV-LED device is further developed and optimized to increase its output.
Increased abundance of Cbl E3 ligases alters PDGFR signaling in recessive dystrophic epidermolysis bullosa
Authors: Martínez-Martínez Esther , Tölle Regine , Donauer Julia , Gretzmeier Christine , Bruckner-Tuderman Leena , Dengjel Jörn 
Published: May 2021

ABSTRACTIn recessive dystrophic epidermolysis bullosa (RDEB), loss of collagen VII, the main component of anchoring fibrils critical for epidermal-dermal cohesion, affects several intracellular signaling pathways and leads to impaired wound healing and fibrosis. In skin fibroblasts, wound healing is also affected by platelet-derived growth factor receptor (PDGFR) signaling. To study a potential effect of loss of collagen VII on PDGFR signaling we performed unbiased disease phosphoproteomics. Whereas RDEB fibroblasts exhibited an overall weaker response to PDGF, Cbl E3 ubiquitin ligases, negative regulators of growth factor signaling, were stronger phosphorylated. This increase in phosphorylation was linked to higher Cbl protein levels due to increased TGFβ signaling in RDEB. In turn, increased Cbl levels led to increased PDGFR ubiquitination, internalization, and degradation negatively affecting MAPK and AKT downstream signaling pathways. Thus, our results indicate that elevated TGFβ signaling leads to an attenuated response to growth factors, which contribute to impaired dermal wound healing in RDEB.
The sum of two halves may be different from the whole. Effects of splitting sequencing samples across lanes
Authors: Williams Eleanor C. , Chazarra-Gil Ruben , Shahsavari Arash , Mohorianu Irina 
Published: May 2021

AbstractThe advances in high throughput sequencing (HTS) enabled the characterisation of biological processes at an unprecedented level of detail; the majority of hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains one of the main challenges. Although variability in results may be introduced at various stages, e.g. alignment, summarisation or detection of differences in expression, one source of variability was systematically omitted: the sequencing design which propagates through analyses and may introduce an additional layer of technical variation.We illustrate qualitative and quantitative differences arising from splitting samples across lanes, on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling, and peaks’ properties. At single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10x data are presented.The observed reduction in the number of unique sequenced fragments reduces the level of detail on which the different prediction approaches depend. Further, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias.
The type 2 diabetes factor methylglyoxal mediates axon initial segment shortening and neuronal network activity changes
Authors: Griggs Ryan B. , Nguyen Duc V.M. , Yermakov Leonid M. , Jaber Jeneane M. , Shelby Jennae N. , Steinbrunner Josef K. , Miller John A. , Gonzalez-Islas Carlos , Wenner Peter , Susuki Keiichiro 
Published: May 2021

AbstractRecent evidence suggests that alteration of axon initial segment (AIS) geometry (i.e., length or position along the axon) contributes to CNS dysfunction in neurological diseases. For example, AIS length is shorter in the prefrontal cortex of type 2 diabetic mice with cognitive impairment. The key type 2 diabetes-related factor that alters AIS geometry is unknown. Here, we tested whether modifying the levels of insulin, glucose, or methylglyoxal, a reactive carbonyl species that is a metabolite of glucose, changes AIS geometry in mature cultures of dissociated postnatal mouse cortex using immunofluorescent imaging of the AIS proteins AnkyrinG and βIV spectrin. Neither insulin nor glucose modification appreciably altered AIS length. Elevation of methylglyoxal produced reversible AIS shortening without cell death. Multi-electrode array recordings revealed a biphasic effect of methylglyoxal on neuronal network activity: an immediate, transient ∼300% increase in spiking and bursting rates was followed by a ∼20% reduction from baseline at 3 h. AIS length was unchanged at 0.5 h or 3 h after adding methylglyoxal, whereas development of AIS shortening at 24 h was associated with restoration of spiking to baseline levels. Immunostaining for the excitatory neuron marker Ca2+/calmodulin-dependent protein kinase II alpha revealed AIS shortening in both excitatory and inhibitory neuron populations. This suggests that complex mechanisms maintain neuronal network operation after acute exposure to the disease metabolite methylglyoxal. Importantly, our results indicate that methylglyoxal could be a key mediator of AIS shortening during type 2 diabetes.Significance StatementSmall changes in the structure of the axon initial segment affect neuronal function and may be a key mediator of neurological complications in various disease states. However, the specific disease factors that mediate structural changes at the axon initial segment are relatively unknown. This is the first study to show that increase of methylglyoxal is sufficient to reduce axon initial segment length and modulate neuronal network function. Methylglyoxal is a disease factor implicated in a wide variety of conditions including type 2 diabetes, Alzheimer’s disease, and aging. Thus, these findings could significantly impact the understanding of neurological complications in several disease states and are of broad pathophysiological relevance.
The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis
Authors: Federico Antonio , Pavel Alisa , Moebus Lena , McKean David , del Giudice Giusy , Fortino Vittorio , Smith Catherine , Weidinger Stephan , de Rinaldis Emanuele , Greco Dario 
Published: May 2021

AbstractIn recent years, a growing interest in the characterization of the molecular basis of psoriasis has been observed. However, despite the availability of a large amount of molecular data, many pathogenic mechanisms of psoriasis are still poorly understood. In this study, we performed an integrated analysis of 23 public transcriptomic datasets encompassing both lesional and uninvolved skin samples from psoriasis patients. We defined comprehensive gene co-expression network models of psoriatic lesions and uninvolved skin. Moreover, we collected, curated and exploited a wide range of functional information from multiple public sources in order to systematically annotate the inferred networks.The integrated transcriptomics analysis of public datasets shed light on a number of genes which are frequently deregulated in the psoriatic lesion compared with the unaffected skin in a large number of studies. In particular, CRABP2, LCN2, S100A12 and PDZK1IP1 were found to be deregulated in all of the datasets analyzed.Furthermore, the analysis of co-expression networks highlights genes showing aberrant patterns of connectivity in the lesional network as compared to the network inferred from unaffected skin samples. For instance, we identified co-expression patterns of SERPINB4, KYNU and S100A12 as being the most affected by the disease. Network analysis allowed us to identify YPEL1 and HUS1 as plausible, previously unknown, actors in the expression of the psoriasis phenotype. In addition, by exploiting topological properties of the network models, we highlighted a set of 250 non-deregulated genes, 223 of which have never been associated with the disease before, including CACNA1A, HADH, ATP5MC1 and CBARP among others.Finally, we characterized specific communities of co-expressed genes sustaining relevant molecular functions and specific immune cell types expression signatures playing a role in the psoriasis lesion. Overall, integrating experimental driven results with curated functional information from public repositories represents an efficient approach to empower knowledge generation about psoriasis and may be applicable to other complex diseases.
Mycobacterium abscessus HelR interacts with RNA Polymerase to confer intrinsic rifamycin resistance
Authors: Hurst-Hess Kelley R. , Saxena Aavrati , Ghosh Pallavi 
Published: May 2021

AbstractRifampicin (RIF) constitutes the frontline therapy against M. tuberculosis as well as most slow-growing non-tuberculous mycobacteria (NTM). However, RIF is completely ineffective against M. abscessus despite the absence of mutations in the rifampicin resistance determining region of Mab_rpoB. This has been attributed to the presence of an ADP-ribosyltransferase (Arr) activity that inactivates RIF. Rifabutin (RBT), a close analogue of RIF, has recently been shown to be effective against M. abscessus in vitro and in a mouse model and comprises a promising therapeutic against M. abscessus infections. Using RNA sequencing we show that exposure of M. abscessus to sublethal doses of RIF and RBT results in ∼25-fold upregulation of Mab_helR in laboratory and clinical isolates; an isogenic deletion of Mab_helR is hypersensitive to RIF and RBT, and over-expression of Mab_helR confers RIF tolerance in M. tuberculosis implying that helR constitutes a significant determinant of inducible RIF and RBT resistance. We demonstrate a preferential association of MabHelR with RNA polymerase in vivo in bacteria exposed to RIF and showed that purified MabHelR can rescue transcription inhibition in the presence of RIF in in vitro transcription assays. Furthermore, MabHelR can dissociate RNAP from RIF-stalled initiation complexes in vitro, a species we envisage accumulates upon RIF exposure. Lastly, we show that the tip of the PCh-loop of Mab_helR, in particular residues E496 and D497 that are in proximity to RIF, is critical for conferring RIF resistance without being required for RNAP dissociation from stalled complexes. This suggests that HelR may be additionally involved in displacing RIF bound to RNAP and function as an RNAP protection protein.Significance StatementBacterial RNA polymerase is a target for the potent and broad-spectrum rifamycin group of antibiotics. Mutations within rpoB and inactivation by a diverse group of enzymes constitute the most widespread mechanisms of resistance. Herein we report an unprecedented mechanism of rifamycin resistance in M. abscessus mediated by MabHelR, a putative SF1 like helicase, that involves disassembly of RIF-stalled initiation complexes, likely followed by displacement of the antibiotic, leading to RNAP recycling. The mechanism is reminiscent of the role of HflX and ribosome protection proteins in resistance to ribosome targeting antibiotics and suggests that removal of stalled macromolecular complexes and their recycling comprises a widespread but underappreciated mechanism of antibiotic resistance. Rifampicin (RIF) is pivotal in the control of M. tuberculosis infections but ineffective against M. abscessus. Identification of inducible rifamycin resistance determinants in M. abscessus is therefore particularly crucial for informing treatment strategies and development of novel therapeutic approaches.