bluuebunny/crossref_metadata_2025 huggingface dataset:
Oncological Outcomes After Anastomotic Leakage After Surgery for Colon or Rectal Cancer
Authors: Koedam Thomas W. A. , Bootsma Boukje T. , Deijen Charlotte L. , van de Brug Tim , Kazemier Geert , Cuesta Miguel A. , Fürst Alois , Lacy Antonio M. , Haglind Eva , Tuynman Jurriaan B. , Daams Freek , Bonjer Hendrik J.
Published: March 2020

Objective:

The aim of this study was to evaluate oncological outcome for patients with and without anastomotic leakage after colon or rectal cancer surgery.

Summary of Background Data:

The role of anastomotic leakage in oncological outcome after colorectal cancer surgery is still topic of debate and impact on follow-up and consideration for further treatment remains unclear.

Methods:

Patients included in the international, multicenter, non-inferior, open label, randomized, controlled trials COLOR and COLOR II, comparing laparoscopic surgery for curable colon (COLOR) and rectal (COLOR II) cancer with open surgery, were analyzed. Patients operated by abdominoperineal excision were excluded. Both univariate and multivariate analyses were performed to investigate the impact of leakage on overall survival, disease-free survival, local and distant recurrences, adjusted for possible confounders. Primary endpoints in the COLOR and COLOR II trial were disease-free survival and local recurrence at 3-year follow-up, respectively, and secondary endpoints included anastomotic leakage rate.

Results:

For colon cancer, anastomotic leakage was not associated with increased percentage of local recurrence or decreased disease-free-survival. For rectal cancer, an increase of local recurrences (13.3% vs 4.6%; hazard ratio 2.96; 95% confidence interval 1.38–6.34; P = 0.005) and a decrease of disease-free survival (53.6% vs 70.9%; hazard ratio 1.67; 95% confidence interval 1.16–2.41; P = 0.006) at 5-year follow-up were found in patients with anastomotic leakage.

Conclusion:

Short-term morbidity, mortality, and long-term oncological outcomes are negatively influenced by the occurrence of anastomotic leakage after rectal cancer surgery. For colon cancer, no significant effect was observed; however, due to low power, no conclusions on the influence of anastomotic leakage on outcomes after colon surgery could be reached. Clinical awareness of increased risk of local recurrence after anastomotic leakage throughout the follow-up is mandatory.

Trial Registration: Registered with ClinicalTrials.gov, number NCT00387842 and NCT00297791.
COVID-19 Outbreak and Surgical Practice
Authors: Aminian Ali , Safari Saeed , Razeghian-Jahromi Abdolali , Ghorbani Mohammad , Delaney Conor P.
Published: March 2020

Little is known about surgical practice in the initial phase of coronavirus disease 2019 (COVID-19) global crisis. This is a retrospective case series of 4 surgical patients (cholecystectomy, hernia repair, gastric bypass, and hysterectomy) who developed perioperative complications in the first few weeks of COVID-19 outbreak in Tehran, Iran in the month of February 2020. COVID-19 can complicate the perioperative course with diagnostic challenge and a high potential fatality rate. In locations with widespread infections and limited resources, the risk of elective surgical procedures for index patient and community may outweigh the benefit.
Musical mirror-symmetrical movement tasks: comparison of rhythm versus melody-playing
Authors: Tokgoz Serhat , Aydogdu Demet , Ilhan Barkin , Sahin Yusuf , Bariseri Nurtug , Ozturkler Batu Mehmet , Çukur Tolga
Published: March 2020

Bimanual mirror-symmetrical movement (MSM) is relatively easy to control movement. Different MSM tasks may have different activations and interhemispheric interactions. The purpose of this study is to compare anatomo-physiological features such as hemispheric activations and dominance of two different MSMs, namely melody-playing and rhythm. We examined functional MRI (fMRI) recordings in a group of fifteen right-handed pianists performing two separate tasks: bimanual rhythm and bimanual melody-playing on two different keyboards with standard key order for right hand and reversed for left hand, which allows homolog fingers’ movements. Activations and laterality indices on fMRI were examined. The results show that significant cerebellar activations (especially in anterior cerebellum) in both groups. Significant primary sensorimotor cortical activations are observed in the melody-playing group. While there are also bilaterally symmetric activations, and laterality indices suggest overall lateralization towards the left hemisphere in both groups. Activations in the left fronto-parietal cortex, left putamen and left thalamus in conjunction with right cerebellar activations suggest that the left cortico-thalamo-cerebellar loop may be a dominant loop. Dynamic causal modeling (DCM) indicates the presence of causal influences from the left to the right cerebral cortex. In conclusion, melody-playing with bimanual MSM is a complex in-phase task and may help activate the bilateral cortical areas, and left hemisphere is dominant according to laterality indices and DCM results. On the other hand, bimanual rhythm is a simpler in-phase task and may help activate subcortical areas, which might be independent of the voluntary cortical task.
Correlation between universal BCG vaccination policy and reduced mortality for COVID-19
Authors: Miller Aaron , Reandelar Mac Josh , Fasciglione Kimberly , Roumenova Violeta , Li Yan , Otazu Gonzalo H.
Published: March 2020

COVID-19 has spread to most countries in the world. Puzzlingly, the impact of the disease varies in different countries. This variation is attributed to differences in cultural norms, mitigation efforts, and health infrastructure. Here, we propose that national differences in COVID-19 impact could be partially explained by different national policies with respect to Bacillus Calmette-Guérin (BCG) vaccination. BCG vaccination has been reported to offer broad protection from other respiratory infections besides tuberculosis. We compared BCG vaccination policies with the morbidity and mortality for COVID-19 for middle-high and high-income countries. We found that countries without universal policies of BCG vaccination (Italy, the Netherlands, USA) have been more severely affected compared to countries with universal and long-standing BCG policies. The difference cannot be accounted for by differences in disease onset, adoption of early social distancing policies, state of health services, nor income level. Reduced mortality suggests BCG vaccination could be a potential new tool in the fight against COVID-19.
Codon usage and evolutionary rates of the 2019-nCoV genes
Authors: Dilucca Maddalena , Forcelloni Sergio , Pavlopoulou Athanasia , Georgakilas Alexandros G. , Giansanti Andrea
Published: March 2020

Severe acute respiratory syndrome coronavirus 2 (2019-nCoV), which first broke out in Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a mortality ranging from 3% to 6%. To better understand the evolution of the newly emerging 2019-nCoV, in this paper, we analyze the codon usage pattern of 2019-nCoV. For this purpose, we compare the codon usage of 2019-nCoV with that of other 30 viruses belonging to the subfamily of orthocoronavirinae. We found that 2019-nCoV shows a rich composition of AT nucleotides that strongly influences its codon usage, which appears to be not optimized to human host. Then, we study the evolutionary pressures influencing the codon usage and evolutionary rates of the sequences of five conserved genes that encode the corresponding proteins (viral replicase, spike, envelope, membrane and nucleocapsid) characteristic of coronaviruses. We found different patterns of both mutational bias and nature selection that affect the codon usage of these genes at different extents. Moreover, we show that the two integral membrane proteins proteins (matrix and envelope) tend to evolve slowly by accumulating nucleotide mutations on their genes. Conversely, genes encoding nucleocapsid (N), viral replicase and spike proteins are important targets for the development of vaccines and antiviral drugs, tend to evolve faster as compared to other ones. Taken together, our results suggest that the higher evolutionary rate observed for these two genes could represent a major barrier in the development of antiviral therapeutics 2019-nCoV.
Negative selection may cause grossly altered but broadly stable karyotypes in metastatic colorectal cancer
Authors: Cross William , Nowinski Salpie , Cresswell George D , Mossner Maximilian , Banerjee Abhirup , Lu Bingxin , Williams Marc , Vlachogiannis Georgios , Gay Laura , Baker Ann-Marie , Kimberley Christopher , Whiting Freddie , Belnoue-Davis Hayley , Martinez Pierre , Traki Maria , Walther Viola , Smith Kane , Fernandez-Mateos Javier , Yara Erika , Oliveira Erica , Milite Salvatore , Caravagna Giulio , James Chela , Elia George , Berner Alison , Choi Ryan Changho , Ramagiri Pradeep , Chauhan Ritika , Matthews Nik , Murphy Jamie , Antoniou Anthony , Clark Susan , Mitchison Miriam , Aleong Jo-Anne Chin , Domingo Enric , Spiteri Inmaculada , McDonald Stuart AC , Shibata Darryl , Lacle Miangela M , Wang Lai Mun , Moorghen Morgan , Tomlinson Ian PM , Novelli Marco , Jansen Marnix , Watson Alan , Wright Nicholas A , Bridgewater John , Rodriguez-Justo Manuel , Barnes Chris P , Kocher Hemant , Leedham Simon J , Sottoriva Andrea , Graham Trevor A
Published: March 2020

Aneuploidy, the loss and gain of whole and part chromosomes, is near-ubiquitous in cancer genomes and likely defines cancer cell biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterised. Here we perform longitudinal genomic analysis of 755 samples from a total of 167 patients with colorectal-derived neoplastic lesions that represent distinct stages of tumour evolution through metastasis and treatment. Adenomas typically had few copy number alterations (CNAs) and most were subclonal, whereas cancers had many clonal CNAs, suggesting that progression goes through a CNA bottleneck. Individual CRC glands from the same tumour typically had very similar karyotypes, despite evidence of ongoing instability at the cell level in patient tumours, cell lines and organoids. CNAs in metastatic lesions sampled from liver and other organs, after chemotherapy or targeted therapies, and in late recurrences were typically similar to the primary tumour. Mathematical modelling and statistical inference indicated that these data are consistent with the action of negative selection on CNAs that ‘traps’ cancer cell genomes on a fitness peak defined by the specific pattern of chromosomal aberrations. These data suggest that the initial progression of colorectal cancer requires the traversal of a rugged fitness landscape and subsequent CNA evolution, including metastatic dissemination and therapeutic resistance, is constrained by negative selection.
Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins
Authors: Saha Piyali , Shumate Justin L. , Caldwell Jenna G. , Elghobashi-Meinhardt Nadia , Lu Albert , Zhang Lichao , Olsson Niclas E. , Elias Joshua E. , Pfeffer Suzanne R.
Published: March 2020

Transport of LDL-derived cholesterol from lysosomes into the cytoplasm requires NPC1 protein; NPC1L1 mediates uptake of dietary cholesterol. We introduced single disulfide bonds into NPC1 and NPC1L1 to explore the importance of inter-domain dynamics in cholesterol transport. Using a sensitive method to monitor lysosomal cholesterol efflux, we find that NPC1’s N-terminal domain need not release from the rest of the protein for efficient cholesterol export. Either introducing single disulfide bonds to constrain lumenal/extracellular domains or shortening a cytoplasmic loop abolishes transport activity by both NPC1 and NPC1L1. The widely prescribed cholesterol uptake inhibitor, Ezetimibe, blocks NPC1L1; we show that interface residues that lie at the interface between NPC1L1’s three extracellular domains comprise the drug’s binding site. These data support a model in which cholesterol passes through the cores of NPC1/NPC1L1 proteins; concerted movement of various domains is needed for transfer and Ezetimibe blocks transport by binding to multiple domains simultaneously.
HamHeat: A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization
Authors: Rakov Alexey V. , Schifferli Dieter M. , Liu Shu-Lin , Mastriani Emilio
Published: March 2020

The problem of fast calculation of Hamming distance inferred from many sequence datasets is still not a trivial task. Here, we present HamHeat, as a new software package to efficiently calculate Hamming distance for hundreds of aligned protein or DNA sequences of a large number of residues or nucleotides, respectively. HamHeat uses a unique algorithm with many advantages, including its ease of use and the execution of fast runs for large amounts of data. The package consists of three consecutive modules. In the first module, the software ranks the sequences from the most to the least frequent variant. The second module uses the most common variant as the reference sequence to calculate the Hamming distance of each additional sequence based on the number of residue or nucleotide changes. A final module formats all the results in a comprehensive table that displays the sequence ranks and Hamming distances.

Availability and implementation

HamHeat is based on Python 3 and AWK, runs on Linux system and is available under the MIT License at:https://github.com/alexeyrakov/HamHeat.

Contact

rakovalexey@gmail.com
DAISM-DNNXMBD: Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks
Authors: Lin Yating , Li Haojun , Xiao Xu , Zhang Lei , Wang Kejia , Yang Wenxian , Yu Rongshan , Han Jiahuai
Published: March 2020

Understanding the immune cell abundance of cancer and other disease-related tissues has an important role in guiding disease treatments. Computational cell type proportion estimation methods have been previously developed to derive such information from bulk RNA sequencing (RNA-seq) data. Unfortunately, our results show that the performance of these methods can be seriously plagued by the mismatch between training data and real-world data. To tackle this issue, we propose the DAISM-DNNXMBD1 pipeline that trains a deep neural network (DNN) with dataset-specific training data populated from a small number of calibrated samples using DAISM, a novel Data Augmentation method with an In Silico Mixing strategy. The evaluation results demonstrate that the DAISM-DNN pipeline outperforms other existing methods consistently and substantially for all the cell types under evaluation on real-world datasets.
Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system inLigustrum vulgare(Oleaceae)
Authors: De Cauwer Isabelle , Vernet Philippe , Billiard Sylvain , Godé Cécile , Bourceaux Angélique , Ponitzki Chloé , Saumitou-Laprade Pierre
Published: March 2020

The breakdown of self-incompatibility (SI) in angiosperms is one of the most commonly observed evolutionary transitions. While multiple examples of SI breakdown have been documented in natural populations, there is strikingly little evidence of stable within-population polymorphism with both inbreeding (self-compatible) and outcrossing (self-incompatible) individuals. This absence of mating system polymorphism corroborates theoretical expectations that predict that in/outbreeding polymorphism is possible only under very restricted conditions. However, theory also predicts that a diallelic sporophytic SI system facilitates the maintenance of such polymorphism. We tested this prediction by studying the mating system ofLigustrum vulgareL., an entomophilous hermaphroditic species of the Oleaceae family. Using stigma tests with controlled pollination and paternity assignment of open-pollinated progenies, we confirmed the existence of two self-incompatibility groups in this species. We also demonstrated the existence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the expression of the pollen component of SI. We then estimated the selfing rate in a garden experiment. Our results finally show that the observed low frequency of self-compatible individuals in natural populations is compatible with theoretical predictions only if inbreeding depression is very high.
Ergothioneine, a metabolite of the gut bacteriumLactobacillus reuteri, protects against stress-induced sleep disturbances
Authors: Matsuda Yoshiki , Ozawa Nobuyuki , Shinozaki Takiko , Wakabayashi Ken-ichi , Suzuki Kosuke , Kawano Yusuke , Ohtsu Iwao , Tatebayashi Yoshitaka
Published: March 2020

The relationships between depression and gut microbiota, particularly those involving the immune system, have become a major focus of recent research. Here, we analyzed changes in gut microbiota and their sulfur metabolites in the feces of a depression rat model using the modified 14-day social defeat stress (SDS) paradigm. Our results showed that SDS increased fecalLactobacillus reuteriin correlation with ergothioneine levels at around day 11, which continued for at least one month following SDS administration. In vitro study further revealed thatL. reuteriis capable of producing ergothioneine. Although the known anti-inflammatory and anti-oxidative actions of ergothioneine suggested that the increased fecal ergothioneine levels may be related to intestinal anti-inflammatory defense mechanisms, no change was observed in the plasma ergothioneine levels during the same observation period, indicating that the defense mechanisms may not be sufficiently reflected in the body. As ergothioneine is a natural ingredient that is absorbed mainly from the upper gastrointestinal tract, we hypothesized that oral ergothioneine may exert antidepressant effects. As expected, oral administration of ergothioneine prior to and during the SDS paradigm had a preventative effect on SDS-induced depressive behaviors, such as social avoidance and depression-like sleep abnormalities, particularly those of rapid eye movement sleep. These findings indicate that ergothioneine, a metabolite ofL. reuteri, may be a common substance in the microbiota-gut-brain axis that prevents stress-induced sleep disturbances, especially those associated with depression.
Systematics of a radiation of Neotropical suboscines (Aves: Thamnophilidae:Epinecrophylla)
Authors: Johnson Oscar , Howard Jeffrey T. , Brumfield Robb T.
Published: March 2020

The stipple-throated antwrens of the genusEpinecrophylla(Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny ofEpinecrophyllaantwrens and the first population-level genetic analyses for most species in the genus. Most of our analyses are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to confidently place the western Amazonian taxonpyrrhonota. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in theornatagroup currently regarded as species, and in thehaematonotaandleucophthalmagroups we found paraphyly at the species and subspecies levels, respectively. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group, discuss the biogeographic patterns that we uncover, and suggest areas for further study.
Tissue interactions govern pattern formation in the posterior lateral line of medaka
Authors: Seleit Ali , Gross Karen , Onistschenko Jasmin , Hoang Oi Pui , Theelke Jonas , Centanin Lázaro
Published: March 2020

Vertebrate organs are arranged in a stereotypic, species-specific position along the animal body plan. Substantial morphological variation exists between related species, especially so in the vastly diversified teleost clade. It is still unclear how tissues, organs and systems can accommodate such diverse scaffolds. Here, we use the sequential formation of neuromasts in the posterior lateral line (pLL) system of medaka fish to address tissue-interactions defining a pattern. We show that the pLL pattern is established independently of its neuronal wiring, and demonstrate that the neuromast precursors that constitute the pLL behave as autonomous units during pattern construction. We uncover the necessity of epithelial integrity for correct pLL patterning by disruptingkeratin 15(krt15) and creating epithelial lesions that lead to novel neuromast positioning. By usingkrt15/wtchimeras, we determined that the new pLL pattern depends exclusively on the mutant epithelium, which instructswtneuromast to locate ectopically. Inducing epithelial lesions by 2-photon laser ablation during pLL morphogenesis phenocopieskrt15genetic mutants and reveals that epithelial integrity defines the final position of the embryonic pLL neuromasts. Our results show that a fine-balance between primordium intrinsic properties and instructive interactions with the surrounding tissues is necessary to achieve proper organ morphogenesis and patterning. We speculate that this logic likely facilitates the accommodation of sensory modules to changing and diverse body plans.
Purine metabolism regulates DNA repair and therapy resistance in glioblastoma
Authors: Zhou Weihua , Yao Yangyang , Scott Andrew J. , Wilder-Romans Kari , Dresser Joseph J. , Werner Christian K. , Sun Hanshi , Pratt Drew , Sajjakulnukit Peter , Zhao Shuang G. , Davis Mary , Morgan Meredith A. , Rehemtualla Alnawaz , Nelson Barbara S. , Halbrook Christopher J. , Zhang Li , Gatto Francesco , Xiong Jianping , Castro Maria G. , Lowenstein Pedro , Chandrasekaran Sriram , Lawrence Theodore S. , Lyssiotis Costas A. , Wahl Daniel R.
Published: March 2020

Intratumoral genomic heterogeneity in glioblastoma (GBM) is a barrier to overcoming therapy resistance, and new strategies that are effective independent of genotype are urgently needed. By correlating intracellular metabolite levels with radiation resistance across dozens of genomically-distinct models of GBM, we found that purine metabolites strongly correlated with radiation resistance. Inhibiting purine, but not pyrimidine, synthesis radiosensitized GBM cells and patient-derived neurospheres by impairing DNA repair in a nucleoside-dependent fashion. Likewise, administration of exogenous purine nucleosides protected sensitive GBM models from radiation by promoting DNA repair. Combining an FDA-approved inhibitor ofde novopurine synthesis with radiation arrested growth in GBM xenograft models and depleted intratumoral guanylates. High expression of the rate-limiting enzyme ofde novoGTP synthesis was associated with shorter survival in GBM patients. Together, these findings indicate that inhibitingde novopurine synthesis may be a promising strategy to overcome therapy resistance in this genomically heterogeneous disease.
North American Breeding Bird Survey status and trend estimates to inform a wide-range of conservation needs, using a flexible Bayesian hierarchical generalized additive model
Authors: Smith Adam C. , Edwards Brandon P.M.
Published: March 2020

The status and trend estimates derived from the North American Breeding Bird Survey (BBS), are critical sources of information for bird conservation. However, the estimates are partly dependent on the statistical model used. Therefore, multiple models are useful because not all of the varied uses of these estimates (e.g. inferences about long-term change, annual fluctuations, population cycles, recovery of once declining populations) are supported equally well by a single statistical model. Here we describe Bayesian hierarchical generalized additive models (GAM) for the BBS, which share information on the pattern of population change across a species’ range. We demonstrate the models and their benefits using data a selection of species; and we run a full cross-validation of the GAMs against two other models to compare predictive fit. The GAMs have better predictive fit than the standard model for all species studied here, and comparable predictive fit to an alternative first difference model. In addition, one version of the GAM described here (GAMYE) estimates a population trajectory that can be decomposed into a smooth component and the annual fluctuations around that smooth. This decomposition allows trend estimates based only on the smooth component, which are more stable between years and are therefore particularly useful for trend-based status assessments, such as those by the IUCN. It also allows for the easy customization of the model to incorporate covariates that influence the smooth component separately from those that influence annual fluctuations (e.g., climate cycles vs annual precipitation). For these reasons and more, this GAMYE model is a particularly useful model for the BBS-based status and trend estimates.

LAY SUMMARY

The status and trend estimates derived from the North American Breeding Bird Survey are critical sources of information for bird conservation, but they are partly dependent on the statistical model used.

We describe a model to estimate population status and trends from the North American Breeding Bird Survey data, using a Bayesian hierarchical generalized additive mixed-model that allows for flexible population trajectories and shares information on population change across a species’ range.

The model generates estimates that are broadly useful for a wide range of common conservation applications, such as IUCN status assessments based on trends or changes in the rates of decline for species of concern; and the estimates have better or similar predictive accuracy to other models., and
Homeostatic Plasticity Requires Remodeling of the Homer-Shank Interactome
Authors: Heavner Whitney E. , Speed Haley , Lautz Jonathan D. , Gniffke Edward P. , Immendorf Karen B. , Welsh John P. , Smith Stephen E.P.
Published: March 2020

Neurons maintain constant levels of excitability using homeostatic scaling, which adjusts relative synaptic strength in response to large changes in overall activity. It is still unknown how homeostatic scaling affects network-level protein interactions in the synapse despite extensive reporting of individual scaling-associated transcriptomic and proteomic changes. Here, we assessed a glutamatergic synapse protein interaction network (PIN) composed of 380 binary interactions among 21 protein members to identify protein complexes altered by synaptic scaling in vitro and in vivo. In cultured cortical neurons, we observed widespread bidirectional PIN alterations during up- and downscaling that reflected rapid glutamate receptor shuttling via synaptic scaffold remodeling. Sensory deprivation of the barrel cortex caused a PIN response that reflected changes in mGluR tone and NMDAR-dependent metaplasticity, consistent with emerging models of homeostatic plasticity in the barrel cortex that restore excitatory/inhibitory balance. Mice lackingHomer1orShank3Bdid not undergo normal PIN rearrangements, suggesting that these Autism Spectrum Disorder (ASD)-linked proteins serve as structural hubs for synaptic homeostasis. Our approach demonstrates how changes in the protein content of synapses during homeostatic plasticity translate into functional PIN alterations that mediate changes in neuron excitability.
Zika virus replicates in skeletal muscle contributing to peripheral viral amplification prior to reach neural tissue
Authors: Gavino-Leopoldino Daniel , Figueiredo Camila Menezes , Barcellos Letícia Gonçalves , da Silva Mariana Oliveira Lopes , Bernardino Araújo Suzana Maria , da Silva Neris Rômulo Leão , Miranda Laryssa Daniele , Ladislau Leandro , Benjamim Claudia Farias , Da Poain Andrea Thompson , Clarke Julia Rosauro , Figueiredo Claudia Pinto , Assunção-Miranda Iranaia
Published: March 2020

Zika virus (ZIKV) infections are still a worldwide concern due to the severity of neurological outcomes. ZIKV neurotropism is well characterized, but peripheral tissue could be sites of viral amplification, contributing to endothelial-barrier crossing and access to peripheral nerves. During acute and late phases of infection, ZIKV can be detected in several body fluids, eyes, testis and vagina. However, the importance of initial replication sites for the establishment of infection and viral spread remain unknown. Here we demonstrated that ZIKV replicates primarily in human muscle precursor cells, resulting in cell death and inhibition of myogenesis. ZIKV also replicates in fetal muscle after maternal transmission and in infected neonate mice, inducing lesions and inflammation. Muscle was an important site of viral amplification, sustaining higher peripheral viral loads than liver and spleen. In addition, ZIKV showed rapid and sustained replication kinetics in muscle even before replication in the neural tissues, persisting until 16 days post infection. Our results highlight the importance of muscle in ZIKV pathogenesis as a peripheral site of viral amplification which may contribute to ZIKV reaching neural structures.

Author Summary

Zika Virus (ZIKV) neurotropism and its deleterious effects on central nervous system have been well characterized. But, investigations of the initial replication sites for the establishment of infection and viral spread to neural tissues remain under explored. Here we demonstrated that ZIKV replicates primarily in human skeletal muscle precursor cells, resulting in cell death and disrupted myogenesis. ZIKV also replicates in muscle of fetus and neonate mice inducing muscle damage and inflammation. Muscle replication occurs before amplification in peripheral nerves and brain, contributing to the increase of peripheral ZIKV load and dissemination. In addition, ZIKV RNA still been detected in skeletal muscle at late stages of infection. Overall, our findings showed that skeletal muscle is involved in ZIKV pathogenesis, contributing to a broader understanding of ZIKV infection. Thus, opens new aspects in the investigation of the long-term consequence of early infection.
Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich’s ataxia patient cells
Authors: Vilema-Enríquez G , Quinlan R , Kilfeather P , Mazzone R , Saqlain S , del Molino del Barrio I , Donato A , Corda G , Li F , Vedadi M , Németh AH , Brennan PE , Wade-Martins R
Published: March 2020

The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich’s ataxia (FRDA) are linked to epigenetic modification of theFXNlocus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation ofFXNexpression and represent a novel therapeutic target. Using a humanFXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression ofFXNby approximately 1.5-fold in the reporter cell line and in several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4–7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogues were synthesized and shown to give a 20-fold increase in potency for increasingFXNexpression. Overall, our results suggest that histone methylation is important in the regulation ofFXNexpression, and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.
One leaf for all: Chemical traits of single leaves measured at the leaf surface using Near infrared-reflectance spectroscopy (NIRS)
Authors: Bon Matteo Petit , Böhner Hanna , Kaino Sissel , Moe Torunn , Bråthen Kari Anne
Published: March 2020

The leaf is an essential unit for measures of plant ecological traits. Yet, measures of plant chemical traits are often achieved by merging several leaves, masking potential foliar variation within and among plant individuals. This is also the case with cost-effective measures derived using Near-infrared reflectance spectroscopy (NIRS). The calibration models developed for converting NIRS spectral information to chemical traits are typically based on spectra from merged and milled leaves. In this study we ask if such calibration models can be applied to spectra derived from whole leaves, providing measures of chemical traits of single leaves.

We sampled cohorts of single leaves from different biogeographic regions, growth forms, species and phenological stages in order to include variation in leaf and chemical traits. For each cohort we first sampled NIRS-spectra from each whole, single leaf, including leaf sizes down to Ø 4 mm (the minimum area of our NIRS application). Next, we merged, milled and tableted the leaves and sampled spectra from the cohort as a tablet. We applied arctic-alpine calibration models to all spectra and derived chemical traits. Finally, we evaluated the performance of the models in predicting chemical traits of whole, single leaves by comparing the traits derived at the level of leaves to that of the tablets.

We found that the arctic-alpine calibration models can successfully be applied to single, whole leaves for measures of Nitrogen (R2=0.88, RMSE=0.824), Phosphorus (R2=0.65, RMSE=0.081), and Carbon (R2=0.78, RMSE=2.199) content. For Silicon content we found the method acceptable when applied to Silicon-rich growth forms (R2=0.67, RMSE=0.677). We found a considerable variation in chemical trait values among leaves within the cohorts.

This time- and cost-efficient NIRS-application provides non-destructive measures of a set of chemical traits in single, whole leaves, including leaves of small sizes. The application can facilitate research into the scales of variability of chemical traits and include intraindividual variation. Potential trade-offs among chemical traits and other traits within the leaf unit can be identified and be related to ecological processes. In sum this NIRS-application can facilitate further ecological understanding of the role of leaf chemical traits.
A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1
Authors: González de Cózar Jose M. , Carretero-Junquera Maria , Ciesielski Grzegorz L. , Miettinen Sini M. , Varjosalo Markku , Kaguni Laurie S. , Dufour Eric , Jacobs Howard T.
Published: March 2020

In eukaryotes, ribonuclease H1 (RNase H1) is involved in the processing and removal of RNA/DNA hybrids in both nuclear and mitochondrial DNA. The enzyme comprises a C-terminal catalytic domain and an N-terminal hybrid-binding domain (HBD), separated by a linker of variable length, which in Drosophila melanogaster (Dm) is exceptionally long, 115 amino acids. Molecular modeling predicted this extended linker to fold into a structure similar to the conserved HBD. We measured catalytic activity and substrate binding by EMSA and biolayer interferometry, using a deletion series of protein variants. Both the catalytic domain and the conserved HBD were required for high-affinity binding to heteroduplex substrates, whilst loss of the novel HBD led to a ∼90% drop in K[cat] with a decreased K[M], and a large increase in the stability of the RNA/DNA hybrid-enzyme complex. The findings support a bipartite binding model for the enzyme, whereby the second HBD facilitates dissociation of the active site from the product, allowing for processivity. We used shotgun proteomics to identify protein partners of the enzyme involved in mediating these effects. Single-stranded DNA-binding proteins from both the nuclear and mitochondrial compartments, respectively RpA-70 and mtSSB, were prominently detected by this method. However, we were not able to document direct interactions between mtSSB and Dm RNase H1 when co-overexpressed in S2 cells, or functional interactions in vitro. Further studies are needed to determine the exact reaction mechanism of Dm RNase H1, the nature of its interaction with mtSSB and the role of the second HBD in both.
Changes within neural population codes can be inferred from psychophysical threshold studies
Authors: Hays Jason , Soto Fabian A.
Published: March 2020

The use of population encoding models has come to dominate the study of human visual neuroscience, serving as a primary tool for making inferences about neural code changes based on indirect measurements. A popular approach in computational neuroimaging is to use such models to obtain estimates of neural population responses via inverted encoding modeling. Recent research suggests that this approach may be prone to identifiability problems, with multiple mechanisms of encoding change producing similar changes in the estimated population responses. Psychophysical data might be able to provide additional constraints to infer the encoding change mechanism underlying some behavior of interest. However, computational work aimed at determining to what extent different mechanisms can be differentiated using psychophysics is lacking. Here, we used simulation to explore exactly which of a number of changes in neural population codes could be differentiated from observed changes in psychophysical thresholds. Eight mechanisms of encoding change were under study, chosen because they have been proposed in the previous literature as mechanisms for improved task performance (e.g., due to attention or learning): specific and nonspecific gain, specific and nonspecific tuning, specific suppression, specific suppression plus gain, and inward and outward tuning shifts. We simulated psychophysical thresholds as a function of both external noise (TvN curves) or stimulus value (TvS curves) for a number of variations of each one of the models. With the exception of specific gain and specific tuning, all studied mechanisms produced qualitatively different patterns of change in the TvN and TvS curves, suggesting that psychophysical studies can be used as a complement to inverted encoding modeling, and provide strong constraints on inferences based on the latter. We use our results to provide recommendations for interested researchers and to re-interpret previous psychophysical data in terms of mechanisms of encoding change.
Global COVID-19 fatality analysis reveals Hubei-like countries potentially with severe outbreaks
Authors: Lv Boyan , Li Zhongyan , Chen Yajuan , Long Cheng , Fu Xinmiao
Published: March 2020

1. CFR in Iran in the early stage of the outbreak is the highest among all the countries 2. CFRs in the USA and Italy are similar to that in Hubei Province in the early stage of the outbreak. 3. CFRs in South Korea are similar to that outside Hubei (in China), indicating less severe outbreaks therein. 4. Our findings highlight the potential severity of outbreaks globally, particular in the USA.
CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks
Authors: Zhong Ellen D. , Bepler Tristan , Berger Bonnie , Davis Joseph H.
Published: March 2020

Cryo-EM single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many protein complexes are flexible and can change conformation and composition as a result of functionally-associated dynamics. Such dynamics are poorly captured by current analysis methods. Here, we present cryoDRGN, an algorithm that for the first time leverages the representation power of deep neural networks to efficiently reconstruct highly heterogeneous complexes and continuous trajectories of protein motion. We apply this tool to two synthetic and three publicly available cryo-EM datasets, and we show that cryoDRGN provides an interpretable representation of structural heterogeneity that can be used to identify discrete states as well as continuous conformational changes. This ability enables cryoDRGN to discover previously overlooked structural states and to visualize molecules in motion.
Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence
Authors: Bakshi Somenath , Leoncini Emanuele , Baker Charles , Cañas-Duarte Silvia J. , Okumus Burak , Paulsson Johan
Published: March 2020

As bacteria transition from exponential to stationary phase they change greatly in size, morphology, growth and expression-profiles. These responses also vary between individual cells, but it has proven difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. We developed a platform for tracking >105parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations. Initial applications show that for bothEscherichia coliandBacillus subtilis, growth changes from an ‘adder’ mode in exponential phase to mixed ‘adders-timers’ entering stationary phase, and then a near-perfect ‘sizer’ upon exit – creating broadly distributed cell sizes in stationary phase but rapidly returning to narrowly distributed sizes upon exit. Furthermore, cells that undergo more divisions entering stationary phase suffer reduced survival after long periods of dormancy but are the only cells observed that persist against antibiotics.
SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
Authors: Karamitros Timokratis , Papadopoulou Gethsimani , Bousali Maria , Mexias Anastasios , Tsiodras Sotiris , Mentis Andreas
Published: March 2020

In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 - COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, but also in the design of accurate diagnostics.

We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher-frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host but also strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene.

Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.
Hierarchical progressive learning of cell identities in single-cell data
Authors: Michielsen Lieke , Reinders Marcel J.T. , Mahfouz Ahmed
Published: March 2020

Supervised methods are increasingly used to identify cell populations in single-cell data. Yet, current methods are limited in their ability to learn from multiple datasets simultaneously, are hampered by the annotation of datasets at different resolutions, and do not preserve annotations when retrained on new datasets. The latter point is especially important as researchers cannot rely on downstream analysis performed using earlier versions of the dataset. Here, we presentscHPL, a hierarchical progressive learning method which allows continuous learning from single-cell data by leveraging the different resolutions of annotations across multiple datasets to learn and continuously update a classification tree. We evaluate the classification and tree learning performance using simulated as well as real datasets and show thatscHPLcan successfully learn known cellular hierarchies from multiple datasets while preserving the original annotations.scHPLis available athttps://github.com/lcmmichielsen/hierarchicalprogressivelearning.
Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling inC. elegans
Authors: Cermak Nathan , Yu Stephanie K. , Clark Rebekah , Huang Yung-Chi , Flavell Steven W.
Published: March 2020

Animal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these diverse motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematodeC. elegansare coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the mainC. elegansmotor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner.
A New High-throughput Screening (HiTS) Method for Phages – Enabling Crude Isolation and Fast Identification of Diverse Phages with Therapeutic Potential
Authors: Olsen Nikoline S. , Hendriksen Niels Bohse , Hansen Lars H. , Kot Witold
Published: March 2020

Bacteriophage therapy and application of phages as biocontrol in plant production and food processing, all necessitates acquisition of suitable phages. Depending on purpose, the selection criteria of phage characteristics include lifestyle (lytic/lysogenic), host range, physical stability and absence of unwanted genetic traits such as integrases, antibiotic resistance or bacterial virulence factors. The exclusivity of antibiotic resistant clinical infections and possible development of phage-resistance instigates a need to continually build sizeable phage libraries and also be able to rapidly isolate and characterise novel phages of specified bacterial hosts. Current methods for phage isolation are both laborious and time consuming, suitable only for the isolation of a limited number of phages. Thus, we developed theHigh-ThroughputScreening(HITS) method for phages for fast isolation and identification of potentially hundreds of distinct phages against single hosts. This scalable method enables screening of hundreds of samples, in multiple simultaneous setups with varying parameters increasing the likelihood of isolating multiple distinct phages specific for the given conditions. The efficiency of the method is emphasised by our screening of 200 environmental samples, resulting in the identification of an abundance of unique phage species lytic toEscherichia coli, Salmonella Enterica, Enterococcus faecalisandPseudomonas aeruginosa.