bluuebunny/crossref_metadata_2025 huggingface dataset:
Connectome-based predictive modeling of individual anxiety
Authors: Wang Zhihao , Goerlich Katharina S. , Ai Hui , Aleman André , Luo Yuejia , Xu Pengfei
Published: February 2020

Anxiety-related illnesses are highly prevalent in human society. Being able to identify neurobiological markers signaling high trait anxiety could aid the assessment of individuals with high risk for mental illness. Here, we applied connectome-based predictive modeling (CPM) to whole-brain resting-state functional connectivity (rsFC) data to predict the degree of anxiety in 76 healthy participants. Using a computational “lesion” method in CPM, we then examined the weights of the identified main brain areas as well as their connectivity. Results showed that the CPM could predict individual anxiety from whole-brain rsFC, especially from limbic areas-whole brain and prefrontal cortex-whole brain. The prediction power of the model significantly decreased from (simulated) lesions of limbic areas, lesions of the connectivity within the limbic system, and lesions of the connectivity between limbic regions and the prefrontal cortex.

Although the same model also predicted depression, anxiety-specific networks could be identified independently, centered at the prefrontal cortex. These findings highlight the important role of the limbic system and the prefrontal cortex in the prediction of anxiety. Our work provides evidence for the usefulness of connectome-based modeling of rsFC in predicting individual personality differences and indicates its potential for identifying personality structures at risk of developing psychopathology.
Interpreting pathogen genetic diversity during measles epidemics
Authors: Worby CJ , Bozick BA , Gastañaduy PA , Yang Luojun , Rota PA , Grenfell BT
Published: February 2020

While measles remains endemic in parts of the world, efforts to eliminate measles transmission continue, and viral sequence data may shed light on progress towards these goals. Genetic diversity has been used as a proxy for disease prevalence; however, seasonally-driven disease dynamics are typically characterized by deep population bottlenecks between epidemics, which severely disrupt the genetic signal. Here, we simulate measles metapopulation dynamics, and show that it is the population bottleneck, rather than epidemic size, which plays the largest role in observed pathogen diversity. While high levels of vaccination greatly reduces measles diversity, paradoxically, diversity increases with intermediate levels of vaccination, despite reducing incidence. We examined diversity and incidence using published data to compare our simulated outcomes with real observations, finding a significant relationship between harmonic mean incidence and genetic diversity. Our study demonstrates that caution should be taken when interpreting pathogen diversity, particularly for short-term, local dynamics.
Efficient Exact Inference for Dynamical Systems with Noisy Measurements using Sequential Approximate Bayesian Computation
Authors: Schälte Yannik , Hasenauer Jan
Published: February 2020

Motivation

Approximate Bayesian Computation (ABC) is an increasingly popular method for likelihood-free parameter inference in systems biology and other fields of research, since it allows analysing complex stochastic models. However, the introduced approximation error is often not clear. It has been shown that ABC actually gives exact inference under the implicit assumption of a measurement noise model. Noise being common in biological systems, it is intriguing to exploit this insight. But this is difficult in practice, since ABC is in general highly computationally demanding. Thus, the question we want to answer here is how to efficiently account for measurement noise in ABC.

Results

We illustrate exemplarily how ABC yields erroneous parameter estimates when neglecting measurement noise. Then, we discuss practical ways of correctly including the measurement noise in the analysis. We present an efficient adaptive sequential importance sampling based algorithm applicable to various model types and noise models. We test and compare it on several models, including ordinary and stochastic differential equations, Markov jump processes, and stochastically interacting agents, and noise models including normal, Laplace, and Poisson noise. We conclude that the proposed algorithm could improve the accuracy of parameter estimates for a broad spectrum of applications.

Availability

The developed algorithms are made publicly available as part of the open-source python toolbox pyABC (https://github.com/icb-dcm/pyabc).

Contact

jan.hasenauer@uni-bonn.de

Supplementary information

Supplementary information is available atbioRxivonline. Supplementary code and data are available online athttp://doi.org/10.5281/zenodo.3631120.
The challenge of distinguishing cell-cell complexes from singlet cells in non-imaging flow cytometry and single-cell sorting
Authors: Burel Julie G , Pomaznoy Mikhail , Arlehamn Cecilia S Lindestam , Seumois Gregory , Vijayanand Pandurangan , Sette Alessandro , Peters Bjoern
Published: February 2020

Our recent work has highlighted that care needs to be taken when interpreting single cell data originating from flow cytometry acquisition or cell sorting: We found that doublets of T cells bound to other immune cells are often present in the live singlet gate of human peripheral blood samples acquired by flow cytometry. This hidden ‘contamination’ generates atypical gene signatures of mixed cell lineage in what is assumed to be single cells, which can lead to data misinterpretation, such as the description of novel immune cell types. Here, based on the example of T cell-monocyte complexes, we identify experimental and data analysis strategies to help distinguishing between singlets and cell-cell complexes in non-imaging flow cytometry and single-cell sorting. We found robust molecular signatures in both T cell-monocyte and T cell-B cell complexes that can distinguish them from singlets at both protein and mRNA levels. Imaging flow cytometry with appropriate gating strategy (matching the one used in cell sorting) and direct microscopy imaging after cell sorting were the two methods of choice to detect the presence of cell-cell complexes in suspicious dual-expressing cells. We finally applied this knowledge to highlight the likely presence of T cell-B cell complexes in a recently published dataset describing a novel cell population with mixed T cell and B cell lineage properties.
Reducing shock imminence eliminates poor avoidance in rats
Authors: Laughlin Lindsay C. , Moloney Danielle M. , Samels Shanna B. , Sears Robert M. , Cain Christopher K.
Published: February 2020

In signaled active avoidance (SigAA), rats learn to suppress Pavlovian freezing and emit actions to escape threats and prevent footshocks. SigAA is critical for understanding aversively-motivated instrumental behavior and anxiety-related active coping. However, with standard protocols ∼25% of rats exhibit high freezing and poor avoidance. This has dampened enthusiasm for the paradigm and stalled progress. We demonstrate that reducing shock imminence with long-duration warning signals leads to greater freezing suppression and perfect avoidance in all subjects. This suggests that instrumental SigAA mechanisms evolved to cope with distant harm and protocols that promote inflexible Pavlovian reactions are poorly-designed to study avoidance.
Understanding population structure in an evolutionary context: population-specificFSTand pairwiseFST
Authors: Kitada Shuichi , Nakamichi Reiichiro , Kishino Hirohisa
Published: February 2020

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. PairwiseFSTmeasures population structure, whereas population-specificFSTmeasures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specificFSTestimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwiseFSTdistance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specificFSTvalues identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwiseFSTvalues represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specificFSTindicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to seashores with abundant rainfall, and to the south with dry summers. Genomic data highlight the power of the bias-corrected moment estimators ofFST, whether global, pairwise, or population-specific, that provide unbiased estimates ofFST. AllFSTmoment estimators described in this paper have reasonable process times and are useful in population genomics studies. The R codes for our method and simulations are available in the Supplemental Material.
Neurothreads: Cryogel carrier-based differentiation and delivery of mature neurons in the treatment of Parkinson’s disease
Authors: Filippova Aleksandra , Bonini Fabien , Efremova Liudmila , Preynat-Seauve Olivier , Béduer Amélie , Krause Karl-Heinz , Braschler Thomas
Published: February 2020

We presentin-vivotransplantation of mature dopaminergic neurons by means of macroporous, injectable carriers, to enhance cell therapy in Parkinson’s disease. The carriers are synthesized by crosslinking carboxymethylcellulose at subzero temperatures, resulting in cylindrical, highly resilient porous cryogels, which we term Neurothreads. We develop efficient covalent immobilization of the neural adhesion proteins laminin 111, collagen IV and fibronectin, as well as of the extracellular matrix extract Matrigel to the Neurothreads. We observe the highest neural spreading on laminin 111 and Matrigel. We show compatibility with established dopaminergic differentiation of both HS420 human embryonic stem cells and the LUHMES midbrain model cell line. The porous Neurothread carriers withstand compression during minimally invasive stereotactic injection, and ensure viability of mature neurons including extended neurites. Implanted into the striatum in mice, the Neurothreads enable survival of transplanted mature neurons obtained by directed differentiation of the HS420 human embryonic stem cells, as a dense tissuein situ, including dopaminergic cells. With the successfulin-vivotransfer of intact, mature and fully open 3D neural networks, we provide a powerful tool to extend established differentiation protocols to higher maturity and to enhance preconfigured neural network transplantation.
Biotic and abiotic drivers of soil microbial functions across tree diversity experiments
Authors: Cesarz Simone , Craven Dylan , Auge Harald , Bruelheide Helge , Castagneyrol Bastien , Hector Andy , Jactel Hervé , Koricheva Julia , Messier Christian , Muys Bart , O’Brien Michael J. , Paquette Alain , Ponette Quentin , Potvin Catherine , Reich Peter B. , Scherer-Lorenzen Michael , Smith Andrew R , Verheyen Kris , Eisenhauer Nico
Published: February 2020

Aim

Soil microorganisms are essential for the functioning of terrestrial ecosystems. Although soil microbial communities and functions may be linked to the tree species composition and diversity of forests, there has been no comprehensive study of how general potential relationships are and if these are context-dependent. A global network of tree diversity experiments (TreeDivNet) allows for a first examination of tree diversity-soil microbial function relationships across environmental gradients.

Location

Global

Major Taxa Studied

Soil microorganisms

Methods

Soil samples collected from eleven tree diversity experiments in four biomes across four continents were used to measure soil basal respiration, microbial biomass, and carbon use efficiency using the substrate-induced respiration method. All samples were measured using the same analytical device in the same laboratory to prevent measurement bias. We used linear mixed-effects models to examine the effects of tree species diversity, environmental conditions, and their interactions on soil microbial functions.

Results

Across biodiversity experiments, abiotic drivers, mainly soil water content, significantly increased soil microbial functions. Potential evapotranspiration (PET) increased, whereas soil C-to-N ratio (CN) decreased soil microbial functions under dry soil conditions, but high soil water content reduced the importance of other abiotic drivers. Tree species richness and phylogenetic diversity had overall similar, but weak and context-dependent (climate, soil abiotic variables) effects on soil microbial respiration. Positive tree diversity effects on soil microbial respiration were most pronounced at low PET, low soil CN, and high tree density. Soil microbial functions increased with the age of the experiment.

Main conclusions

Our results point at the importance of soil water content for maintaining high levels of soil microbial functions and modulating effects of other environmental drivers. Moreover, overall tree diversity effects on soil microbial functions seem to be negligible in the short term (experiments were 1-18 years old). However, context-dependent tree diversity effects (climate, soil abiotic variables) have greater importance at high tree density, and significant effects of experimental age call for longer-term studies. Such systematic insights are key to better integrate soil carbon dynamics into the management of afforestation projects across environmental contexts, as today’s reforestation efforts remain focused largely on aboveground carbon storage and are still dominated by less diverse forests stands of commercial species.
Highly efficient cardiac differentiation and maintenance by thrombin-coagulated fibrin hydrogels enriched with decellularized porcine heart extracellular matrix
Authors: Navaee Fatemeh , Renaud Philippe , Braschler Thomas
Published: February 2020

We provide a blend of cardiac decellularized extracellular matrix (dECM) from porcine ventricular tissue and fibrinogen for the formation of anin-vitro3D cardiac cell culture model. Rapid and specific coagulation with thrombin allows gentle inclusion of cells while avoiding sedimentation during formation of the dECM-fibrin composite. We use the system in co-culture with Nor-10 fibroblasts to enhance cardiogenic differentiation of the H9c2 myoblast cell line. The combination of co-culture and appropriate substrate allows to abrogate the use of retinoids, classically considered necessary for cardiogenic H9c2 differentiation. Further enhancement of differentiation efficiency is obtained by 3D embedding. We then proceed with culture of rat neonatal cardiomyocytes in the 3D system. While for H9c2 cells, the collagen content of the dECM was the key factor required for efficient differentiation, the use of dECM-fibrin has specific advantages regarding the culture of neonatal cardiomyocytes. Calcium imaging and analysis of beating motion both indicate that the dECM-fibrin composite significantly enhances recovery, frequency, synchrony and maintenance of spontaneous beating, as compared to various controls including matrigel, pure fibrin and collagen I, but also a fibrin-collagen I blend.
Discovery of an evolutionarily conserved smooth muscle cell-specific lncRNACARMN
Authors: Dong Kunzhe , Shen Jian , He Xiangqin , Wang Liang , Hu Guoqing , Bunting Kirstopher M. , Dixon-Melvin Rachael , Zheng Zeqi , Xin Hongbo , Xiang Meixiang , Vazdarjanova Almira , Zhou Jiliang
Published: February 2020

Differentiated vascular smooth muscle cells (VSMCs) are critical in maintaining vascular homeostasis by expressing a unique repertoire of contractile genes. Despite the well-defined coding transcriptome in differentiated VSMCs, little is known about the non-coding gene expression signature. Herein, by de novo analyzing publicly available RNA-seq and single cell RNA-seq datasets generated from different tissues and cell types, we unambiguously identifiedCARMN(CARdiac Mesoderm Enhancer-associated Non-coding RNA) as an evolutionarily conserved, SMC-specific lncRNA.CARMNwas initially annotated as the host gene ofMIR143/145cluster and recently reported to play roles in cardiac differentiation. Here, we generated aCarmnGFP knock-in reporter mouse model and confirmed its specific expression in SMCsin vivo. In addition, we foundCarmnis transcribed independently fromMir143/145and only expressed transiently in embryonic cardiomyocytes and thereafter becomes restricted to adult SMCs in both human and mouse. Furthermore, we demonstrated thatCARMNexpression is not only dramatically decreased in human vascular diseases but functionally critical in maintaining VSMC contractile phenotypein vitro. In conclusion, we provided the first evidence showing thatCARMNis an evolutionarily conserved SMC-specific lncRNA, down-regulated in different human vascular diseases, and a key lncRNA for maintaining SMC contractile phenotype.
Alteration of perivascular spaces in early cognitive decline
Authors: Sepehrband Farshid , Barisano Giuseppe , Sheikh-Bahaei Nasim , Choupan Jeiran , Cabeen Ryan P , Crawford Malcolm S , Mack Wendy J , Chui Helena C , Ringman John M , Toga Arthur W ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2020

Vascular contributions to early cognitive decline are increasingly recognized, prompting further investigation into the nature of related changes in perivascular space. Using magnetic resonance imaging, we show that, compared to a cognitively normal sample, individuals with early cognitive dysfunction have altered perivascular space presence and distribution, irrespective of Amyloid-β. Surprisingly, we noted decreased perivascular space presence in the anterosuperior medial temporal lobe, which was associated with neurofibrillary tau tangle deposition in the entorhinal cortex, one of the hallmarks of early Alzheimer’s disease pathology. Our results suggest that anatomically-specific alteration of the perivascular spaces may provide an early biomarker of cognitive impairment in aging adults.
Targeting Reactive Aldehyde Detoxification by Aldehyde Dehydrogenase 2 (ALDH2) as a Treatment Strategy for Endometriosis
Authors: McAllister Stacy L. , Sinharoy Pritam , Vasu Megana
Published: February 2020

Endometriosis affects ∼176 million women worldwide, yet on average, women experience pain ∼10 years from symptom onset before being properly diagnosed. Standard treatments (drugs or surgery) often fail to provide long-term pain relief. Elevated levels of reactive aldehydes such as 4-hydroxynonenal (4-HNE) have been implicated in the peritoneal fluid of women with endometriosis and upon accumulation, reactive aldehydes can form protein-adducts and/or generate pain. A key enzyme in detoxifying reactive aldehydes to less reactive forms, is the mitochondrial enzyme aldehyde dehydrogenase-2 (ALDH2). Here, we tested the hypothesis that aberrant reactive aldehyde detoxification by ALDH2, underlies endometriosis and its associated pain. We determined, in the eutopic and ectopic endometrium of women with severe (stage IV) peritoneal endometriosis, that ALDH2 enzyme activity was decreased, which was associated with decreased ALDH2 expression and increased 4-HNE adduct formation compared to the eutopic endometrium of controls in the proliferative phase. Using a rodent model of endometriosis and an ALDH2*2 knock-in mouse with decreased ALDH2 activity, we determined that increasing ALDH2 activity with the enzyme activator Alda-1 could prevent endometriosis lesion development as well as alleviate pain-associated behaviors in proestrus. Overall, our findings suggest that targeting the ALDH2 enzyme in endometriosis may lead to better treatment strategies and in the proliferative phase, that increased 4-HNE adduct formation within the endometrium may serve as a less invasive diagnostic biomarker to reduce years of suffering in women.

One Sentence Summary

ALDH2 activity influences endometriosis and its associated pain.
Novel software for automated morphometric analysis of stented arteries
Authors: Resnick Aviel , Hooshdaran Bahman , Pressly Benjamin B. , Guerrero David T. , Alferiev Ivan S. , Chorny Michael , Levy Robert J. , Fishbein Ilia
Published: February 2020

Morphometric analysis of explanted arteries remains the gold standard in assessing pathological mechanisms of arterial disease, and the efficacy of therapeutic interventions. Software currently used for morphometric analysis (ImageJ, ImagePro, etc.) requires manual tracing of each region of interest by the user to obtain direct and derived data needed for analysis. Manual segmentation of borders between differently stained arterial compartments is time-consuming and prone to bias, even when the operator is blind to the treatment type. Here, we report newly designed morphometric software, floodSeg, which greatly aids analysis through semiautomated segmentation, followed by automated computation and data entry. The program includes tools for both rapid component selection, and precision user-controlled contour correction. In practice, segmentation occurs following the selection of seed points and corresponding threshold values, for each desired component. The flood fill algorithm is used to map out components, followed by Sklansky’s convex-hull algorithm to obtain the outer contours. If necessary, convexity defects can be overcome through manual point placement on top of existing points, and regeneration of the contour. floodSeg was tested using a set of non-uniformly stained stented rat arteries, and compared against manually obtained results. The accuracy of the resulting measurements was within the expected limit based on repeated manual measurements by the same operator, and did not exceed 3%. Most notably, the duration for data acquisition using floodSeg was less than 20% of the time required for manual measurements by an experienced operator. Thus, our contribution is an improvement on widely used software, with significant potential for application in a multitude of areas of pathology practice.
Characterization and Mitigation of Fragmentation Enzyme-Induced Dual Stranded Artifacts
Authors: Gregory C. Thomas , Ngankeu Apollinaire , Orwick Shelley , Kautto Esko , Woyach Jennifer A. , Byrd John C. , Blachly James S.
Published: February 2020

High-throughput short-read sequencing relies on fragmented DNA for optimal sampling of input nucleic acid. Several vendors now offer proprietary enzyme cocktails as a cheaper and more streamlined method of fragmentation when compared to acoustic shearing. We have discovered that these enzymes induce the formation of library molecules containing regions of nearby DNA from opposite strands. Sequencing reads derived from these molecules can lead to artifact-derived variant calls appearing at variant allele frequencies less than 5%. We present Fragmentation Artifact Detection and Elimination (FADE), software to remove these artifacts from mapped reads and mitigate artifact-related effects on downstream analysis. We find that the artifacts principally affect downstream analyses that are sensitive to a 1-3% artifact bias in the sequencing reads, such as targeted resequencing and rare variant discovery.

Availability

Data are deposited at SRA under accession No. PRJNA602687 Software described in this manuscript is freely available athttps://github.com/blachlylab/fade
Pial surface CSF-contacting texture, subpial and funicular plexus in the thoracic spinal cord in monkey: NADPH diaphorase histological configuration
Authors: Li Yinhua , Hou Wei , Jia Yunge , Wen Xiaoxin , Rao Chenxu , Xu Ximeng , Wei Zichun , Bai Lu , Tan Huibing
Published: February 2020

In spinal cord, white matter is distinguished from grey matter in that it contains ascending and descending axonal tracts. While grey matter gets concentrated with neuronal cell bodies. Notable cell bodies and sensory modality of cerebral spinal fluid (CSF) in white matter are still elusive in certain segment of the spinal cord. Monkey Spinal cord was examined by NADPH diaphorase (NADPH-d) histochemistry. We found that NADPH-d positive neurons clustered and featured flat plane in mediolateral funiculus in caudal thoracic and rostral lumber spinal cord, especially evident in the horizontal sections. Majority of NADPH-d funicular neurons were relatively large size and moderately-or lightly-stained neurons. In horizontal section, the multipolar processes of the neurons were thicker than that of regular other neurons. The processes oriented laterally or obliquely in the lateral funiculus. Some of neuronal cell bodies and proximal processes attached NADPH-d positive buttons or puncta. The neuronal processes interlaced network medially linked to lateral horn (intermediolateral nucleus, IML) and laterally to subpial region, in which formed subpial plexus with subpial NADPH-d neurons. Subpial plexus appeared to contacting externally with CSF. The subpial plexus patterned like round brackets located in lateromarginal pial surface. Compared with sympathetic IML in rostral thoracic segments and sacral parasympathetic IML, the funicular plexus configurated a specialized neuro-texture in caudal thoracic segments. The dendritic arbor of funicular neuron featured variety geometric plane shapes. The funicular plexus oriented exclusive layered flat-plane organization between lateral horn and subpial region in caudal thoracic and rostral lumber spinal cord. The subpial plexus may work as CSF sensor outside of spinal cord. The cluster of funicular neurons may function as locomotion sensor, besides visceral regulation. Different to periventricular CSF contacting or pericentral canal structures, NADPH-d funicular neurons and subpial plexus that located in the pial surface. With advantage of NADPH-d, we found funicular neurons which termed academically as funicular plexus and specialized localization for subpial structure we termed subpial plexus. The funicular texture was regarded as neuronal bridge between the interior CSF in the central canal and external CSF out of the pial surface.
Characterization of an ECF56-family sigma factor fromStreptomyces venezuelaereveals a highly conserved regulome
Authors: Thompson Mitchell G. , Zargar Amin , Cruz-Morales Pablo , De Rond Tristan , Chang Samantha , Pearson Allison N. , Goyal Garima , Barajas Jesus F. , Blake-Hedges Jacquelyn M. , Phelan Ryan M. , Reyes-Umana Victor , Hernández Amanda C. , Hillson Nathan J. , Shih Patrick M. , Keasling Jay D.
Published: February 2020

Bacteria often possess alternative sigma factors that initiate the transcription of specific genes under environmental stresses, the largest and most diverse group being the extracytoplasmic function (ECF) sigma factors. The regulation of ECF activity is crucial for ensuring the distinct transcription of stress responsive genes only occurs under the appropriate conditions. While most ECFs are comprised of only the core σ2and σ4regions, a unique form of ECF sigma factor regulation also contains a C-terminal extension bearing homology to the NTF2 superfamily of protein domains. While previous work has shown that this NTF2 domain can affect transcriptional activityin vivoin ECF41 and ECF42, its role in the newly classified ECF56 subgroup is unknown. In this work, we show that truncation of the C-terminus of the ECF56 sigma factor SVEN_4562 ofStreptomyces venezuelaeupregulates its activity in a hybrid assay. Through transcriptomics inS. venezuelae, we found that this truncated ECF56 sigma factor has a highly conserved promoter sequencein vivo. Bioinformatic assays illustrated that deep branches of theActinobacteriaphylum contained putative ECF56 promoter motifs identical to those found in theS. venezuelaeECF56 regulon. We validated these findings throughex situhybrid assays illustrating that truncated ECF56 sigma factors from phylogenetically diverseActinobacteriaactivate transcription from these promoters. Importantly, our work shows that the genetic infrastructure of the ECF56 family of sigma factors is highly conserved and performs important functions yet to be understood inActinobacteria.

Importance

Most ECF sigma-factors rely on anti-sigma factor regulation; in contrast, the unique classes of ECF sigma-factors that contain a C-terminal extension are thought to respond directly to an environmental signal. Here we show that thecis-acting regulatory element of the ECF56 regulon is likely highly conserved in manyActinobacteria, with exact nucleotide level conservation over ~2 billion years of evolution. The high conservation of this genetic architecture, as well as a conserved gene content within the regulon, strongly point to a specialized and important role inActinobacteriabiology.
The bacterial quorum sensing signal DSF hijacksArabidopsis thalianasterol biosynthesis to suppress plant innate immunity
Authors: Tran Tuan Minh , Ma Zhiming , Triebl Alexander , Nath Sangeeta , Cheng Yingying , Gong Ben-Qiang , Han Xiao , Wang Junqi , Li Jian-Feng , Wenk Markus R. , Torta Federico , Mayor Satyajit , Yang Liang , Miao Yansong
Published: February 2020

Quorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely under-studied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced byXanthomonas campestrispv.campestriscan suppress pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) inArabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of oligomerization states and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile ofArabidopsis, with a particular increase of the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate PAMP-triggered host immunity.

SIGNIFICANCE STATEMENT

Bacteria rely on small signalling molecules called quorum sensing (QS) signals to communicate and coordinate their behaviors. QS is known to regulate gene expression, production of virulence factors, and biofilm formation for pathogenic bacteria to effectively colonize their hosts and cause diseases. In this work, we found a class of QS molecule called diffusible-signal factor (DSF), produced by devastating phytopathogenic bacteria such asXanthomonasspp. andXylella fastidiosa, could communicate directly with plant host and subvert plant innate immunity by inducing plant sterol production and thereby, attenuating receptor signalling through hindering the receptor clustering and plant endocytosis. The results significantly enrich our understanding of the mechanisms in the tug-of-war between bacterial pathogenesis and host immunity.
Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning
Authors: Song Zhigang , Zou Shuangmei , Zhou Weixun , Huang Yong , Shao Liwei , Yuan Jing , Gou Xiangnan , Jin Wei , Wang Zhanbo , Chen Xin , Ding Xiaohui , Liu Jinhong , Yu Chunkai , Ku Calvin , Liu Cancheng , Sun Zhuo , Xu Gang , Wang Yuefeng , Zhang Xiaoqing , Wang Dandan , Wang Shuhao , Xu Wei , Davis Richard C. , Shi Huaiyin
Published: February 2020

Gastric cancer is among the most malignant tumours with the highest incidence and mortality rates. The early detection and accurate histopathological diagnosis of gastric cancer are essential factors that can help increase the chances of successful treatment. While the worldwide shortage of pathologists has imposed burdens on current histopathology services, it also offers a unique opportunity for the use of artificial intelligence assistance systems to alleviate the workload and increase diagnostic accuracy. To the best of our knowledge, there has not been a clinically applicable histopathological assistance system with high accuracy that can generalize to whole slide images created with diverse digital scanner models from different hospitals. Here, we report a clinically applicable artificial intelligence assistance system developed at the Chinese PLA General Hospital, China, using a deep convolutional neural network trained with 2,123 pixel-level annotated H&E-stained whole slide images. The model achieved a sensitivity near 100% and an average specificity of 80.6% on a real-world test dataset, which included 3,212 whole slide images digitalized with three scanner models. We showed that the system could aid pathologists in improving diagnostic accuracy and preventing misdiagnoses. Moreover, we demonstrated that our system could perform robustly with 1,582 whole slide images from two other medical centres. Our study suggests the feasibility and benefits of using histopathological artificial intelligence assistance systems in routine practice scenarios.
Primary Human Hepatocytes Maintain Long-term Functions in Porous Silk Scaffolds Containing Extracellular Matrix Proteins
Authors: Kukla David A. , Stoppel Whitney L. , Kaplan David L. , Khetani Salman R.
Published: February 2020

The shortage of donor organs for transplantation has prompted the development of alternative implantable human liver tissues; however, the need for a clinically viable liver tissue that can be fabricated using physiologically-relevant primary human hepatocytes (PHHs) is unmet. Purified silk proteins provide desirable features for generating implantable tissues, such as sustainable sourcing from insects/arachnids, biocompatibility, tunable mechanical properties and degradation rates, and low immunogenicity upon implantation; however, the utility of such scaffolds to generate human liver tissues using PHHs remains unclear. Here, we show that the incorporation of type I collagen during the fabrication and/or autoclaving of silk scaffolds was necessary to enable robust PHH attachment/function. Scaffolds with small pores (73 +/- 25 µm) promoted higher PHH functions than large pores (235 +/- 84 µm). Further incorporation of growth-arrested 3T3-J2 fibroblasts into scaffolds enhanced PHH functions up to 5-fold for 5 months in culture, an unprecedented longevity, and functions were better retained than 2D configurations. Lastly, encapsulating PHHs within Matrigel™ while housed in the silk/collagen scaffold led to higher functions than Matrigel or silk/collagen alone. In conclusion, porous silk scaffolds are useful for generating long-term PHH +/- fibroblast tissues which may ultimately find applications in regenerative medicine and drug development.
JNK signaling controls branching, nucleokinesis, and positioning of centrosomes and primary cilia in migrating cortical interneurons
Authors: Smith Skye E. , Coker Nicholas K. , Tucker Eric S.
Published: February 2020

Aberrant migration of inhibitory interneurons can alter the formation of cortical circuitry and lead to severe neurological disorders including epilepsy, autism, and schizophrenia. However, mechanisms involved in directing the migration of these cells remain incompletely understood. In the current study, we used live-cell confocal microscopy to explore the mechanisms by which the c-Jun NH2-terminal kinase (JNK) pathway coordinates leading process branching and nucleokinesis, two cell biological processes that are essential for the guided migration of cortical interneurons. Pharmacological inhibition of JNK signaling disrupts the kinetics of leading process branching, rate and amplitude of nucleokinesis, and leads to the rearward mislocalization of the centrosome and primary cilium to the trailing process. Genetic loss ofJnkfrom interneurons corroborates our pharmacological observations and suggests that important mechanics of interneuron migration depend on the intrinsic activity of JNK. These findings suggest that JNK signaling regulates leading process branching, nucleokinesis, and the trafficking of centrosomes and cilia during interneuron migration, and further implicates JNK signaling as an important mediator of cortical development.

Summary Statement

Loss of JNK signaling reduces growth cone branching frequency, limits interstitial side branch duration, alters rate and amplitude of nucleokinesis, and mislocalizes centrosomes and primary cilia in migrating cortical interneurons.
A preliminary ecological profile of Kyasanur Forest disease virus hosts among the mammalian wildlife of the Western Ghats, India
Authors: Walsh Michael G. , Mor Siobhan M. , Maity Hindol , Hossain Shah
Published: February 2020

Kyasanur Forest disease (KFD) is one of India’s severe arboviruses capable of causing prolonged debilitating disease. It has been expanding beyond its historical endemic locus at an alarming rate over the last two decades. The natural nidus of this zoonosis is located in the monsoon rainforest of the Western Ghats, India, which is one of the world’s most important biodiversity hotspots. Definitive reservoir hosts for KFD virus (KFDV) have yet to be delineated, and thus much of the infection ecology of this virus, and its consequent transmission dynamics, remains uncertain. Given its unique biogeographical context, identifying ecological parameters of KFDV relevant to the virus’ epidemiology has been complex and challenging. The challenge has been exacerbated by diminished research efforts in wildlife surveillance over the last two decades, coinciding with the expansion of the range of KFD across the region. The current investigation sought to define a preliminary ecological profile of KFDV hosts based on their life history and feeding traits to aid in re-establishing targeted wildlife surveillance and to discern those ecological traits of wildlife hosts that may improve our understanding of KFD epidemiology. The importance of fast-living among KFDV hosts was of special interest with respect to the latter aim. We compared mammalian traits between host and non-host species using general additive models and phylogenetic generalised linear models. This study found that both body mass and forest forage were strongly associated with mammalian host infection status, but that reproductive life history traits were not. These findings will help in structuring ecologically based wildlife surveillance and field investigations, while also helping to parameterise novel epidemiological models of zoonotic infection risk that incorporate species functional traits in a region where biogeography, landscape ecology, and community ecology manifest extraordinary complexity, particularly under growing anthropogenic pressure.
Prebiotics and community composition influence gas production of the human gut microbiota
Authors: Yu Xiaoqian , Gurry Thomas , Tu Nguyen Le Thanh , Richardson Hunter S. , Alm Eric J.
Published: February 2020

Prebiotics confer benefits to human health often by promoting the growth of gut bacteria that produce metabolites valuable to the human body, such as short chain fatty acids (SCFAs). While prebiotic selection has strongly focused on maximizing the production of SCFAs, less attention has been paid to gases, a byproduct of SCFA production that also has physiological effects on the human body. Here, we investigate how the content and volume of gas production by human gut microbiota is affected by the chemical composition of the prebiotic and by the composition of the microbiota. We first constructed a linear systems model based on mass and electron balance and compared the theoretical product range of two prebiotics, inulin and pectin. Modeling shows that pectin is more restricted in product space, with less potential for H2 but more potential for CO2 production. An ex vivo experimental system showed pectin degradation produced significantly less H2 than inulin, but CO2 production fell outside the theoretical product range, suggesting fermentation of fecal debris. Microbial community composition also impacted results: methane production was dependent on the presence of Methanobacteria, while inter-individual differences in H2 production during inulin degradation was driven by a Lachnospiraceae taxon. Overall, these results suggest that both the chemistry of the prebiotic and the composition of the microbiota are relevant to gas production. Metabolic processes that are relatively prevalent in the microbiome, such as H2 production will depend more on substrate, while rare metabolisms like methanogenesis depend more strongly on microbiome composition.

Importance

Prebiotic fermentation in the gut often leads to the co-production of short chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely taken into account during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic and the community composition of the human gut microbiota can affect the volume and content of gas production during prebiotic fermentation. Specifically, more prevalent metabolic processes such as hydrogen production was strongly affected by the oxidation state of the probiotic, while rare metabolisms such as methane production was less affected by the chemical nature of the substrate and entirely dependent on the presence of Methanobacteria in the microbiota.
Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability
Authors: Tsai Kevin , Vasudevan Ananda Ayyappan Jaguva , Martinez Campos Cecilia , Emery Ann , Swanstrom Ronald , Cullen Bryan R.
Published: February 2020

Covalent modifications added to individual nucleotides on mRNAs, called epitranscriptomic modifications, have recently emerged as key regulators of both cellular and viral mRNA function1,2and RNA methylation has now been shown to enhance the replication of human immunodeficiency virus 1 (HIV-1) and several other viruses3–11. Recently, acetylation of the N4position of cytidine (ac4C) was reported to boost cellular mRNA function by increasing mRNA translation and stability12. We therefore hypothesized that ac4C and N-acetyltransferase 10 (NAT10), the cellular enzyme that adds ac4C to RNAs, might also have been subverted by HIV-1 to increase viral gene expression. We now confirm that HIV-1 transcripts are indeed modified by addition of ac4C at multiple discreet sites and demonstrate that silent mutagenesis of a subset of these ac4C addition sites inhibits HIV-1 gene expression incis. Moreover, reduced expression of NAT10, and the concomitant decrease in the level of ac4C on viral RNAs, inhibits HIV-1 replication by reducing HIV-1 RNA stability. Interestingly Remodelin, a previously reported inhibitor of NAT10 function13,14, also inhibits HIV-1 replication without affecting cell viability, thus raising the possibility that the addition of ac4C to viral mRNAs might emerge as a novel cellular target for antiviral drug development.
Homeostatic Plasticity Commonly Fails at the Intersection of Autism-Gene Mutations and a Novel Class of Common Phenotypic Modifier
Authors: Genç Özgür , An Joon Y. , Fetter Richard D. , Kulik Yelena , Zunino Giulia , Sanders Stephan J. , Davis Graeme W.
Published: February 2020

We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1,CHD8,CHD2,WDFY3,ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP). Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, we find that PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen,PDPK1andPPP2R5D,are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation ofCREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.
Global reference mapping and dynamics of human transcription factor footprints
Authors: Vierstra Jeff , Lazar John , Sandstrom Richard , Halow Jessica , Lee Kristen , Bates Daniel , Diegel Morgan , Dunn Douglas , Neri Fidencio , Haugen Eric , Rynes Eric , Reynolds Alex , Nelson Jemma , Johnson Audra , Frerker Mark , Buckley Michael , Kaul Rajinder , Meuleman Wouter , Stamatoyannopoulos John A.
Published: February 2020

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits1, yet it remains challenging to distinguish variants that impact regulatory function2. Genomic DNase I footprinting enables quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin3–5. However, to date only a small fraction of such sites have been precisely resolved on the human genome sequence5. To enable comprehensive mapping of transcription factor footprints, we produced high-density DNase I cleavage maps from 243 human cell and tissue types and states and integrated these data to delineate at nucleotide resolution ~4.5 million compact genomic elements encoding transcription factor occupancy. We map the fine-scale structure of ~1.6 million DHS and show that the overwhelming majority is populated by well-spaced sites of single transcription factor:DNA interaction. Cell context-dependent cis-regulation is chiefly executed by wholesale actuation of accessibility at regulatory DNA versus by differential transcription factor occupancy within accessible elements. We show further that the well-described enrichment of disease- and phenotypic trait-associated genetic variants in regulatory regions1,6is almost entirely attributable to variants localizing within footprints, and that functional variants impacting transcription factor occupancy are nearly evenly partitioned between loss- and gain-of-function alleles. Unexpectedly, we find that the global density of human genetic variation is markedly increased within transcription factor footprints, revealing an unappreciated driver of cis-regulatory evolution. Our results provide a new framework for both global and nucleotide-precision analyses of gene regulatory mechanisms and functional genetic variation.