bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate
Authors: Hofmann Katharina , Huptas Christopher , Doll Etienne V. , Scherer Siegfried , Wenning Mareike
Published: February 2020

Two strains, WS 5063T and WS 5067, isolated from raw cow’s milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown,

Pseudomonas

species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel

Pseudomonas

species. It was most closely related to

Pseudomonas synxantha

DSM 18928T with an ANIm of 91.4 %. The DNA G+C content of WS 5063T was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4–34 °C and at pH values of pH 5.5–8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for

Pseudomonas

species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063T (=DSM 108987T=LMG 31232T) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).
Endogenous SIRT3 activity is dispensable for normal hearing recovery after noise exposure in young adult mice
Authors: Patel Sally , Shah Lisa , Dang Natalie , Tan Xiaodong , Almudevar Anthony , White Patricia M.
Published: February 2020

Occupational noise-induced hearing loss (NIHL) affects millions of people worldwide and presents a large social and personal burden. Some genetic variants in the mitochondrial oxidative stress response correlate strongly with susceptibility to NIHL in both humans and mice. Here we test the hypothesis that SIRT3, a regulator of the mitochondrial oxidative stress response, is required in mice for endogenous recovery of auditory thresholds after a sub-traumatic noise exposure. We expose homozygousSirt3-KOmice and their wild-type littermates to a noise dose that confers a temporary threshold shift, but is not sufficient to permanently reduce cochlear function, compromise cell survival, or damage synaptic structures. We find no difference in hearing function after recovery from noise exposure between the two genotypes, when measured by either auditory brainstem response (ABR) or distortion product otoacoustic emissions (DPOAE). We show that SIRT3-specific immunoreactivity is present in outer hair cells, around the post-synaptic regions of inner hair cells, and faintly within inner hair cells. Nonetheless, outer hair cells and auditory synapses show no increase in loss after noise exposure in the homozygousSirt3-KOmouse. These data show that SIRT3-dependent processes are not necessary for endogenous hearing recovery after a single, sub-traumatic noise exposure. They demonstrate the existence of cellular mechanisms of cochlear homeostasis in addition to the mitochondrial oxidative stress response. We also present a novel statistical analysis for identifying differences between peak 1 amplitude progressions in ABR waveforms.
Tracking the spread of novel coronavirus (2019-nCoV) based on big data
Authors: Zhao Xumao , Liu Xiang , Li Xinhai
Published: February 2020

The novel coronavirus (2019-nCoV) appeared in Wuhan in late 2019 have infected 34,598 people, and killed 723 among them until 8th February 2020. The new virus has spread to at least 316 cities (until 1st February 2020) in China. We used the traffic flow data from Baidu Map, and number of air passengers who left Wuhan from 1st January to 26th January, to quantify the potential infectious people. We developed multiple linear models with local population and air passengers as predicted variables to explain the variance of confirmed cases in every city across China. We found the contribution of air passengers from Wuhan was decreasing gradually, but the effect of local population was increasing, indicating the trend of local transmission. However, the increase of local transmission is slow during the early stage of novel coronavirus, due to the super strict control measures carried out by government agents and communities.
The Ph.D. Panic: Examining the relationships among teaching anxiety, teaching self-efficacy, and coping in Biology graduate teaching assistants (GTAs)
Authors: Chen Musgrove Miranda M. , Schussler Elisabeth E.
Published: February 2020

Anxiety among graduate students in the United States has increased over the last several decades, affecting not only their overall mental health but also reducing retention in graduate programs. Teachers with high teaching anxiety can negatively impact student learning, yet the impacts of teaching anxiety on graduate teaching assistants (GTAs) is not well studied. Biology GTAs teach most introductory Biology labs and discussions nationally, thus broadly influencing the quality of undergraduate education. In Fall 2016, we investigated Biology GTA teaching anxiety at a large research-intensive southeastern university by (1) measuring teaching anxiety of Biology GTAs, and (2) exploring the relationships among teaching anxiety, self-efficacy, and coping. Using multiple linear regressions, we found that greater teaching self-efficacy is related to lower teaching anxiety in Biology GTAs (R2adi=0.65,p<0.001). Coping strategies and frequencies did not significantly contribute to teaching anxiety in our models. We found similar levels of teaching anxiety across genders, ethnicities, student citizenship status (domestic vs. international) and teaching experience level. However, there were significant differences among student subgroups in teaching self-efficacy and coping strategies. Effective coping may contribute to the lack of anxiety differences among some of the student subgroups. These results can inform teaching professional development for GTAs, and encourage greater awareness and dialogue about the impacts of mental health issues in academia.
Potential G-quadruplex forming sequences andN6-methyladenosine colocalize at human pre-mRNA intron splice sites
Authors: Jara-Espejo Manuel , Fleming Aaron M. , Burrows Cynthia J.
Published: February 2020

Using bioinformatic analysis of published data, we identify in human mRNA that potential G-quadruplex forming sequences (PQSs) colocalize with the epitranscriptomic modificationsN6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). A deeper analysis of the colocalized m6A and PQSs found them intronic in pre-mRNA near 5′ and 3′ splice sites. The loop lengths and sequence context of the m6A-bearing PQSs found short loops most commonly comprised of A nucleotides. This observation is consistent with literature reports of intronic m6A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m6A and PQSs in pre-mRNA at intron splice junctions suggests that these features could be involved in alternative mRNA splicing. A similar analysis for PQSs around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m6A.

TOC Graphic
Exploring the coronavirus epidemic using the new WashU Virus Genome Browser
Authors: Flynn Jennifer A. , Purushotham Deepak , Choudhary Mayank NK , Zhuo Xiaoyu , Fan Changxu , Matt Gavriel , Li Daofeng , Wang Ting
Published: February 2020

Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have been sequenced and uploaded to NCBI’s GenBank [1], providing insight into the virus’s evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing virus genomic data. The browser is home to 16 complete 2019-nCoV genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and Ebola virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU Epigenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed athttps://virusgateway.wustl.edu, and documentation is available athttps://virusgateway.readthedocs.io/.
The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit
Authors: Kraushar Matthew L. , Krupp Ferdinand , Turko Paul , Ambrozkiewicz Mateusz C. , Sprink Thiemo , Imami Koshi , Vieira-Vieira Carlos H. , Schaub Theres , Harnett Dermot , Münster-Wandowski Agnieszka , Bürger Jörg , Zinnall Ulrike , Borisova Ekaterina , Yamamoto Hiroshi , Rasin Mladen-Roko , Beule Dieter , Landthaler Markus , Mielke Thorsten , Tarabykin Victor , Vida Imre , Selbach Matthias , Spahn Christian M.T.
Published: February 2020

Protein synthesis must be finely tuned in the nervous system, as it represents an essential feature of neurodevelopmental gene expression, and dominant pathology in neurological disease. However, the architecture of ribosomal complexes in the developing mammalian brain has not been analyzed at high resolution. This study investigates the architecture of ribosomesex vivofrom the embryonic and perinatal mouse neocortex, revealing Ebp1 as a 60S peptide tunnel exit binding factor at near-atomic resolution by multiparticle cryo-electron microscopy. The impact of Ebp1 on the neuronal proteome was analyzed by pSILAC and BONCAT coupled mass spectrometry, implicating Ebp1 in neurite outgrowth proteostasis, within vivoembryonic Ebp1 knockdown resulting in dysregulation of neurite outgrowth. Our findings reveal Ebp1 as a central component of neocortical protein synthesis, and the 60S peptide tunnel exit as a focal point of gene expression control in the molecular specification of neuronal morphology.

Graphical abstract
Anodal transcranial direct-current stimulation over the left dorsolateral prefrontal cortex and perception of emotional faces
Authors: Brasil-Neto Joaquim , Bernardes Tamiris , Silva Camila Rosa da , Iannone Aline , Garcia Ana , Tavares Maria Clotilde Henriques
Published: February 2020

The prefrontal cortices have been shown to be engaged in the perception of emotional faces, and imaging studies correlate activation of the left dorsolateral prefrontal cortex (l-DLPFC) with correct identification of emotional expressions. Transcranial direct current stimulation (tDCS)has been shown to modulate cortical function and might influence the perception of emotional faces. Our aim was to evaluate the possible effects of tDCS on a task that required correct identification of emotions represented by human faces presented on a screen. Ten volunteers (ages 18-30; mean = 23.2; SD = 4.3) were evaluated. The experiments were carried out in two 20 minutes stimulation sessions (real and sham tDCS) 4 days apart, at least, to avoid carryover effects, and session orders were randomized. The anode was placed over the l-DLPFC (F3 of the international 10-20 EEG electrode positioning system) and the cathode over the contralateral supraorbital region. Emotional stimuli were 120 consecutive human faces to be verbally classified as “happy”, “surprised”, “neutral”, “angry” or “sad”. Real anodal tDCS over the l-DLPFC resulted in significantly longer response times with a trend towards increased error rates, compared to the sham condition.
Administration of fusion cytokines induces tumor regression and systemic antitumor immunity
Authors: Zhang Jinyu , Zhao Xuan
Published: February 2020

The curative effects of cancer immunotherapy are hard to be improved in solid tumors. Cytokines, as powerful immune regulators, show potential in awaking host antitumor immunity. We have previously found that administration of certain cytokine combinations induced complete tumor clearance. Here we constructed the cognate fusion cytokines and evaluated their antitumor effects in various mouse tumor models.In situinduced expression of the fusion cytokine IL12IL2GMCSF led to tumor eradication, even those in high advanced stage. An immune memory against other irrelated syngeneic tumors was elicited. Flow cytometry analysis revealed that tumor infiltrating CD3+ cells greatly increased, accompanied with an elevation of CD8+/CD4+ ratio. The fusion protein exhibited superior immune activating capability to cytokine mixtures in vitro, and induced tumor regression in various immune competent tumor models by intratumoral injection. To improve translational potential, an immunocytokine IL12IL2DiaNFGMCSF for systemic administration was constructed by inserting tumor targeting diabody. The protein also displayed good activities in vitro. Intravenous infusion of IL12IL2DiaNFGMCSF induced a tumor infiltrating immune cell alteration like IL12IL2GMCSF, with moderate serum IFNγ increment. Therapeutic effects were observed in various tumor models after systemic administration of IL12IL2DiaNFGMCSF, with slight toxicity. These results provide the feasibility of developing a versatile cancer immunotherapy remedy.
A cryptic pocket in Ebola VP35 allosterically controls RNA binding
Authors: Cruz Matthew A. , Frederick Thomas E. , Mallimadugula Upasana , Singh Sukrit , Vithani Neha , Zimmerman Maxwell I. , Porter Justin R. , Moeder Katelyn E. , Amarasinghe Gaya K. , Bowman Gregory R.
Published: February 2020

Protein-protein and protein-nucleic acid interactions are often considered difficult drug targets because the surfaces involved lack obvious druggable pockets. Cryptic pockets could present opportunities for targeting these interactions, but identifying and exploiting these pockets remains challenging. Here, we apply a general pipeline for identifying cryptic pockets to the interferon inhibitory domain (IID) of Ebola viral protein 35 (VP35). VP35 plays multiple essential roles in Ebola’s replication cycle but lacks pockets that present obvious utility for drug design. Using adaptive sampling simulations and machine learning algorithms, we predict VP35 harbors a cryptic pocket that is allosterically coupled to a key dsRNA-binding interface. Thiol labeling experiments corroborate the predicted pocket and mutating the predicted allosteric network supports our model of allostery. Finally, covalent modifications that mimic drug binding allosterically disrupt dsRNA binding that is essential for immune evasion. Based on these successes, we expect our pipeline is equally applicable to other proteins.
Real-time suppression and amplification of frequency-specific neural activity using stimulation evoked oscillations
Authors: Sanabria David Escobar , Johnson Luke A. , Yu Ying , Busby Zachary , Nebeck Shane , Zhang Jianyu , Harel Noam , Johnson Matthew D. , Molnar Gregory F. , Vitek Jerrold L.
Published: February 2020

Background

Approaches to predictably control neural oscillations are needed to understand their causal role in brain function in healthy or diseased states and to advance the development of neuromodulation therapies. In this study, we present a closed-loop neural control and optimization framework to actively suppress or amplify low-frequency neural oscillations observed in local field potentials in real-time by using electrical stimulation.

Objective/Hypothesis

The rationale behind this control approach and our working hypothesis is that neural oscillatory activity evoked by electrical pulses can suppress or amplify spontaneous oscillations via destructive or constructive interference when stimulation pulses are continuously delivered with appropriate amplitudes and at precise phases of these oscillations in a closed-loop scheme.

Methods

We tested our hypothesis in two nonhuman primates that exhibited a robust increase in low-frequency (8-30 Hz) oscillatory power in the subthalamic nucleus (STN) following administration of the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). To test our neural control approach, we targeted 8-17 Hz oscillations and used electrode arrays and electrical stimulation waveforms similar to those used in humans chronically implanted with brain stimulation systems. Stimulation parameters that maximize the suppression or amplification of neural oscillations were predicted using mathematical models of the stimulation evoked oscillations.

Results

Our neural control and optimization approach was capable of actively and robustly suppressing or amplifying oscillations in the targeted frequency band (8-17 Hz) in real-time in the studied subjects.

Conclusions

The results from this study support our hypothesis and suggest that the proposed neural control framework allows one to characterize in controlled experiments the functional role of frequency-specific neural oscillations by using electrodes and stimulation waveforms currently being employed in humans.
Stochastic synchronization of dynamics on the human connectome
Authors: Pang James C. , Gollo Leonardo L. , Roberts James A.
Published: February 2020

Synchronization is a collective mechanism by which oscillatory networks achieve their functions. Factors driving synchronization include the network’s topological and dynamical properties. However, how these factors drive the emergence of synchronization in the presence of potentially disruptive external inputs like stochastic perturbations is not well understood, particularly for real-world systems such as the human brain. Here, we aim to systematically address this problem using a large-scale model of the human brain network (i.e., the human connectome). The results show that the model can produce complex synchronization patterns transitioning between incoherent and coherent states. When nodes in the network are coupled at some critical strength, a counterintuitive phenomenon emerges where the addition of noise increases the synchronization of global and local dynamics, with structural hub nodes benefiting the most. This stochastic synchronization effect is found to be driven by the intrinsic hierarchy of neural timescales of the brain and the heterogeneous complex topology of the connectome. Moreover, the effect coincides with clustering of node phases and node frequencies and strengthening of the functional connectivity of some of the connectome’s subnetworks. Overall, the work provides broad theoretical insights into the emergence and mechanisms of stochastic synchronization, highlighting its putative contribution in achieving network integration underpinning brain function.
Cross-sectional and longitudinal associations of threat and deprivation on cognition, emotional processing and psychopathology in children and adolescents
Authors: Schäfer Julia Luiza , McLaughlin Katie A. , Manfro Gisele Gus , Pan Pedro , Rohde Luis Augusto , Miguel Eurípedes Constantino , Salum Giovanni Abrahão
Published: February 2020

Background

Exposure to childhood adversity has been consistently associated with poor developmental outcomes, but it is unclear whether these associations vary across different forms of adversity. We examined cross-sectional and longitudinal associations between two types of adversity—threat and deprivation—with cognition, emotional processing, and psychopathology in a middle-income country.

Methods

The sample consisted of 2,511 children and adolescents (6-17 years old) from the Brazilian High-Risk Cohort for Psychiatric Disorders. Parent reports on childhood adversity were used to construct threat and deprivation latent constructs. Psychopathology was measured by the CBCL which generated a measure of general psychopathology (the “p” factor). Executive function (EF) and attention orienting toward angry faces were assessed using cognitive tasks. All measures were acquired at two time-points 3-years apart. Cross-lagged panel models were estimated to evaluate longitudinal associations.

Results

Psychopathology was associated with threat and deprivation cross-sectionally, and higher levels of threat and deprivation predicted increases in general psychopathology at follow-up. For EF, worse performance was more strongly associated with deprivation than threat at baseline, and only with deprivation at follow-up. Deprivation was associated with attention orienting away from angry faces cross-sectionally, but neither form of adversity was associated with changes over time in attention bias.

Conclusion

Both types of adversity are associated with current and future psychopathology and with current, but not future, EF. Threat was more strongly linked to higher psychopathology, whereas deprivation was more strongly linked to lower EF. Lack of longitudinal associations between deprivation and EF mean reverse causality cannot be excluded.
Interfruit : Deep Learning Network for Classifying Fruit Images
Authors: Liu Wenzhong
Published: February 2020

Fruit classification is conductive to improving the self-checkout and packaging systems. The convolutional neural networks automatically extract features through the direct processing of original images, which has attracted extensive attention from researchers in fruit classification. However, due to the similarity of fruit color, it is difficult to recognize at a higher accuracy. In the present study, a deep learning network, Interfruit, was built to classify various types of fruit images. A fruit dataset involving 40 categories was also constructed to train the network model and to assess its performance. According to the evaluation results, the overall accuracy of Interfruit reached 93.17% in the test set, which was superior to that of several advanced methods. According to the findings, the classification system, Interfruit, recognizes fruits with high accuracy, which has a broad application prospect.
Delta Oscillations Are a Robust Biomarker of Dopamine Depletion Severity and Motor Dysfunction in Awake Mice
Authors: Whalen Timothy C. , Willard Amanda M. , Rubin Jonathan E. , Gittis Aryn H.
Published: February 2020

Delta oscillations (0.5–4 Hz) are a robust but often overlooked feature of basal ganglia pathophysiology in Parkinson’s disease and their relationship to parkinsonian akinesia has not been investigated. Here, we establish a novel approach to detect spike oscillations embedded in noise to provide the first study of delta oscillations in awake, dopamine depleted mice. We find that approximately half of neurons in the substantia nigra reticulata exhibit delta oscillations in dopamine depletion and that these oscillations are a strong indicator of dopamine loss and akinesia, outperforming measures such as changes in firing rate, irregularity, bursting and synchrony. We further establish that these oscillations are caused by the loss of D2 receptor activation and do not require motor cortex, contrary to previous findings in anesthetized animals. These results give insight into how dopamine loss leads to dysfunction and suggest a reappraisal of delta oscillations as a biomarker in Parkinson’s disease.
Axonal mechanisms mediating GABA-A receptor inhibition of striatal dopamine release
Authors: Kramer Paul F. , Twedell Emily L. , Shin Jung Hoon , Zhang Renshu , Khaliq Zayd M.
Published: February 2020

Axons of midbrain dopaminergic neurons innervate the striatum where they contribute to movement and reinforcement learning. Past work has shown that striatal GABA tonically inhibits dopamine release, but whether GABA-A receptors directly modulate transmission or act indirectly through circuit elements is unresolved. Here, we use whole-cell and perforated-patch recordings to test for GABA-A receptors on the main dopaminergic neuron axons and branching processes within striatum. Application of GABA depolarized axons, but also decreased the amplitude of axonal spikes, limited propagation and reduced striatal dopamine release. The mechanism of inhibition involved sodium channel inactivation and shunting. Lastly, we show that the positive allosteric modulator diazepam enhanced GABA-A currents on dopaminergic neuron axons and directly inhibited release, but also likely acts by reducing excitatory drive from cholinergic interneurons. Thus, we reveal the mechanisms of GABA-A receptor modulation of dopamine release and provide new insight into the actions of benzodiazepines within the striatum.
The Omics Discovery REST interface
Authors: Dass Gaurhari , Vu Manh-Tu , Xu Pan , Audain Enrique , Hitz Marc-Phillip , Hermjakob Henning , Perez-Riverol Yasset
Published: February 2020

The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.
Association of gut microbiota with metabolism in juvenile Atlantic Salmon
Authors: Dvergedal H. , Sandve S.R. , Angell I.L. , Klemetsdal G. , Rudi K.
Published: February 2020

The gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links between gut microbes and fish genetics and production phenotypes are not well understood.

In this study, we investigate the associations between gut microbial communities, fish feed conversion, and fish genetics in the domestic Atlantic salmon. Microbial community composition was determined for 230 juvenile fish from 23 full-sib families and was then regressed on growth, carbon and nitrogen metabolism, and feed efficiency. We only found weak associations between host genetics and microbial composition. However, we did identify significant (p< 0.05) associations between the abundance of three microbial operational taxonomical units (OTUs) and fish metabolism phenotypes. Two OTUs were associated with both carbon metabolism in adipose tissue and feed efficiency, while a third OTU was associated with weight gain.

In conclusion, this study demonstrates an intriguing association between host lipid metabolism and the gut microbiota composition in Atlantic salmon.
Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration
Authors: Costa Emanuel Cura , Otsuki Leo , Albors Aida Rodrigo , Tanaka Elly M. , Chara Osvaldo
Published: February 2020

Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Alborset al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rostet al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modelling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during 85 hours after amputation within~830□m of the injury. We adapted FUCCI technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding bona fide spinal cord regeneration.
Unfolded protein response and scaffold independent pheromone MAP kinase signalling controlVerticillium dahliaegrowth, development and plant pathogenesis
Authors: Starke Jessica , Harting Rebekka , Maurus Isabel , Bremenkamp Rica , Kronstad James W. , Braus Gerhard H.
Published: February 2020

Development and virulence of the vascular plant pathogenVerticillium dahliaeare connected and depend on a complex interplay between the unfolded protein response, a Ham5 independent pheromone MAP kinase module and formation of precursors for oxylipin signal molecules.

Genes coding for the unfolded protein response regulator Hac1, the Ham5 MAPK scaffold protein, and the oleate Δ12-fatty acid desaturase Ode1 were deleted and their functions in growth, differentiation, and virulence on plants were studied using genetic, cell biology, and plant infection experiments.

The unfolded protein response transcription factor Hac1 is required for initial root colonization, fungal conidiation and propagation inside the host and is essential for resting structure formation. Microsclerotia development, growth and virulence require the pheromone response MAPK pathway, but without the Ham5 scaffold function. Single ER-associated enzymes for linoleic acid production make important contributions to fungal growth but have only a minor impact on the pathogenicity ofV. dahliae.

Fungal growth, sporulation, dormant structure formation and plant infection require a network of the Hac1-regulated unfolded protein response, a scaffold-independent pheromone response MAPK pathway and formation of precursors for signalling. This network includes interesting targets for disease management of the vascular pathogenV. dahliae.
An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue
Authors: Hartmann Jonas , Wong Mie , Gallo Elisa , Gilmour Darren
Published: February 2020

Quantitative microscopy is becoming increasingly crucial in efforts to disentangle the complexity of organogenesis, yet adoption of the potent and ever-growing toolbox provided by modern data science has been slow, primarily because data-driven tools focus on “big data” whereas microscopy produces “rich data”. We tackle this issue using a newly developed algorithm for point cloud-based morphometry to unpack the rich information encoded in high-resolution 3D image data into a straightforward numerical representation. This allowed us to employ machine learning for multi-modal data integration of cell morphology, intracellular organization, gene expression and annotated contextual knowledge that facilitates data exploration. We apply these techniques to construct and explore a quantitative atlas of cellular architecture for the zebrafish posterior lateral line primordium, an experimentally tractable model of complex self-organized organogenesis. In doing so, we are able to retrieve both previously established and novel biologically relevant patterns, demonstrating the potential of our data-driven approach.
DYRK3-Controlled Phase Separation Organizes the Early Secretory Pathway
Authors: Gallo Raffaella , Rai Arpan , Pelkmans Lucas
Published: February 2020

The dual-specificity kinase DYRK3 controls formation and dissolution of several intracellular condensates thereby regulating various cell physiological processes. Here we report that DYRK3 establishes a dynamic equilibrium between condensation and dissolution of proteins associated with membranous structures of the early secretory pathway to organize membrane traffic between the ER and the Golgi complex in mammalian cells. This depends on the peripheral membrane protein Sec16A, whose N-terminal disordered region forms DYRK3-controlled liquid-like condensates on the surface of the ER and co-phase separates with multiple ER exit site components and a subset of matrix proteins specifically associated with ERGIC and cis-Golgi. Our findings support a mechanism whereby multiple interacting and differentially regulated intracellular condensates create favorable environments for directional membrane traffic in eukaryotic cells.
Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma
Authors: Rogerson Connor , Ogden Samuel , Britton Edward ,   the OCCAMS consortium, Ang Yeng , Sharrocks Andrew D.
Published: February 2020

Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths and yet compared to other common cancers, we know relatively little about the underlying molecular mechanisms. Barrett’s oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the specific events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies of BO and OAC and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin in OAC cells to directly regulate cell cycle genes specifically in OAC. Our findings have potential prognostic significance as the survival of patients with high expression of KLF5 target genes is significantly lower. We have provided new insights into the gene expression networks in OAC and the mechanisms behind progression to OAC, chiefly the repurposing of KLF5 for novel regulatory activity in OAC.
Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries
Authors: Auguet Olga Tosas , Niehus Rene , Gweon Hyun Soon , Berkley James A. , Waichungo Joseph , Njim Tsi , Edgeworth Jonathan D. , Batra Rahul , Chau Kevin , Swann Jeremy , Walker Sarah A. , Peto Tim E. A. , Crook Derrick W. , Lamble Sarah , Turner Paul , Cooper Ben S. , Stoesser Nicole
Published: February 2020

Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are amongst the most important causes of drug-resistant bacterial infections. We developed a novel AMR surveillance approach for Enterobacterales by profiling pooled human faecal metagenomes from three sites (n=563 individuals; Cambodia, Kenya, UK) to derive a taxonomy-adjusted AMR metric (“resistance potential”) which could be used to predict the aggregate percentage of resistant invasive Enterobacterales infections within each setting. Samples were sequenced (Illumina); taxonomic and resistance gene profiling was performed using ResPipe. Data on organisms causing bacteraemia and meningitis and antibiotic susceptibility test results from 2010-2017 were collated for each site. Bayesian generalised linear models with a binomial likelihood were fitted to determine the capacity of the resistance potential to predict AMR in Enterobacterales infections in each setting. The most informative model accurately predicted the numbers of resistant infections in the target populations for 14/14 of antibiotics in the UK, 12/12 in Kenya, and 9/12 in Cambodia. Intermittent metagenomics of pooled human samples could represent a powerful pragmatic and economical approach for determining and monitoring AMR in clinical infections, especially in resource-limited settings.
Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice
Authors: Wan Sizhe , Huang Chenkai
Published: February 2020

Liver fibrosis often appears in chronic liver disease, with extracellular matrix (ECM) deposition as the main feature. Due to the presence of the liver-gut axis, the destruction of intestinal homeostasis is often accompanied by the development of liver fibrosis. The inconsistent ecological environment of different intestinal sites may lead to differences in the microbiota. The traditional Chinese medicine Ursolic acid (UA) has been proven to protect the liver from fibrosis. We investigated the changes in the microbiota of different parts of the intestine during liver fibrosis and the effect of UA on these changes based on high-throughput sequencing technology. Sequencing results suggest that the diversity and abundance of intestinal microbiota decline and the composition of the microbiota is disordered, the potentially beneficial Firmicutes bacteria are reduced, and the pathways for functional prediction are changed in the ilea and anal faeces of liver fibrosis mice compared with normal mice. However, in UA-treated liver fibrosis mice, these disorders improved. It is worth noting that the bacterial changes in the ilea and anal faeces are not consistent. In conclusion, in liver fibrosis, the microbiota of different parts of the intestines have different degrees of disorder, and UA can improve this disorder. This may be a potential mechanism for UA to achieve anti-fibrosis. This study provides theoretical guidance for the UA targeting of intestinal microbiota for the treatment of liver fibrosis.
Astroglial FMRP modulates synaptic signaling and behavior phenotypes in FXS mouse model
Authors: Jin Shan-Xue , Higashimori Haruki , Schin Christina , Tamashiro Alessandra , Men Yuqin , Chiang Ming Sum R , Jarvis Rachel , Cox Dan , Feig Larry , Yang Yongjie
Published: February 2020

Fragile X syndrome (FXS) is one of the most common inherited intellectual disability (ID) disorders, in which the loss of FMRP protein induces a range of cellular signaling changes primarily through excess protein synthesis. Although neuron-centered molecular and cellular events underlying FXS have been characterized, how different CNS cell types are involved in typical FXS synaptic signaling changes and behavioral phenotypes is largely unknown. Recent evidence suggests that selective loss of astroglial FMRP is able to dysregulate glutamate uptake, increase spine density, and impair motor-skill learning. Here we investigated the effect of astroglial FMRP on synaptic signaling and FXS-related behavioral and learning phenotypes in astroglial Fmr1 cKO and cON mice in which FMRP expression is selectively diminished or restored in astroglia. We found that selective loss of astroglial FMRP contributes to cortical hyperexcitability by enhancing NMDAR-mediated evoked but not spontaneous miniEPSCs and elongating cortical UP state duration. Selective loss of astroglial FMRP is also sufficient to increase locomotor hyperactivity, significantly diminish social novelty preference, and induce memory acquisition and extinction deficits in astroglial Fmr1 cKO mice. Importantly, re-expression of astroglial FMRP is able to significantly rescue the hyperactivity (evoked NMDAR response, UP state duration, and open field test) and social novelty preference in astroglial Fmr1 cON mice. These results demonstrate a profound role of astroglial FMRP in the evoked synaptic signaling, spontaneously occurring cortical UP states, and FXS-related behavioral and learning phenotypes and provide important new insights in the cell type consideration for the FMRP reactivation strategy.
Protein-protein interactions in neurodegenerative diseases: a conspiracy theory
Authors: Thompson Travis B. , Chaggar Pavanjit , Kuhl Ellen , Goriely Alain ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2020

Neurodegenerative diseases such as Alzheimer’s or Parkinson’s are associated with the prion-like propagation and aggregation of toxic proteins. A long standing hypothesis that amyloid-beta drives Alzheimer’s disease has proven the subject of contemporary controversy; leading to new research in both the role of tau protein and its interaction with amyloid-beta. Conversely, recent work in mathematical modeling has demonstrated the relevance of nonlinear reaction-diffusion type equations to capture essential features of the disease. Such approaches have been further simplified, to network-based models, and offer researchers a powerful set of computationally tractable tools with which to investigate neurodegenerative disease dynamics.

Here, we propose a novel, coupled network-based model for a two-protein system that includes an enzymatic interaction term alongside a simple model of aggregate transneuronal damage. We apply this theoretical model to test the possible interactions between tau proteins and amyloid-beta and study the resulting coupled behavior between toxic protein clearance and proteopathic phenomenology. Our analysis reveals ways in which amyloid-beta and tau proteins may conspire with each other to enhance the nucleation and propagation of different diseases, thus shedding new light on the importance of protein clearance and protein interaction mechanisms in prion-like models of neurodegenerative disease.

Author Summary

In 1906 Dr. Alois Alzheimer delivered a lecture to the Society of Southwest German Psychiatrists. Dr. Alzheimer presented the case of Ms. Auguste Deter; her symptoms would help to define Alzheimer’s disease (AD). Over a century later, with an aging world population, AD is at the fore of global neurodegenerative disease research. Previously, toxic amyloid-beta protein (Aβ) was thought to be theprimarydriver of AD development. Recent research suggests that another protein, tau, plays a fundamental role. Toxic tau protein contributes to cognitive decline and appears to interact with toxic Aβ; research suggests that toxic Aβmay further increase the effects of toxic tau.

Theoretical mathematical models are an important part of neurodegenerative disease research. Such models: enable extensible computational exploration; illuminate emergent behavior; and reduce research costs. We have developed a novel, theoretical mathematical model of two interacting species of proteins within the brain. We analyze the mathematical model and demonstrate a computational implementation in the context of Aβ-tau interaction in the brain. Our model clearly suggests that: the removal rate of toxic protein plays a critical role in AD; and the Aβ-tau ‘conspiracy theory’ is a nuanced, and exciting path forward for Alzheimer’s disease research.
Phosphorylation controls RNA binding and transcription by the influenza virus polymerase
Authors: Dawson Anthony R. , Wilson Gary M. , Freiberger Elyse C. , Mondal Arindam , Coon Joshua J. , Mehle Andrew
Published: February 2020

The influenza virus polymerase transcribes and replicates the viral genome. The proper timing and balance of polymerase activity is important for successful replication. We previously showed that phosphorylation regulates genome replication by controlling assembly of the replication machinery (Mondal, et al. 2017). However, it remained unclear whether phosphorylation directly regulated polymerase activity. Here we identified polymerase phosphosites that control its function. Mutating phosphosites in the catalytic subunit PB1 altered polymerase activity and virus replication. Biochemical analyses revealed phosphorylation events that disrupted global polymerase function by blocking the NTP entry channel or preventing RNA binding. We also identified a regulatory site that split polymerase function by specifically suppressing transcription. These experiments show that host kinases phospho-regulate viral RNA synthesis directly by modulating polymerase activity and indirectly by controlling assembly of replication machinery. Further, they suggest polymerase phosphorylation may bias replication versus transcription at discrete times or locations during the infectious cycle.
An essential membrane protein modulates the proteolysis of LpxC to control lipopolysaccharide synthesis inEscherichia coli
Authors: Fivenson Elayne M. , Bernhardt Thomas G.
Published: February 2020

Gram-negative bacteria are surrounded by a complex cell envelope that includes two membranes. The outer membrane prevents many drugs from entering these cells and is thus a major determinant of their intrinsic antibiotic resistance. This barrier function is imparted by the asymmetric architecture of the membrane with lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The LPS and phospholipid synthesis pathways share a common intermediate. Proper membrane biogenesis therefore requires that the flux through each pathway be balanced. InEscherichia coli, a major control point in establishing this balance is the committed step of LPS synthesis mediated by LpxC. Levels of this enzyme are controlled through its degradation by the inner membrane protease FtsH and its presumed adaptor protein LapB(YciM). How turnover of LpxC is controlled has remained unclear for many years. Here, we demonstrate that the essential protein of unknown function YejM(PbgA), which we have renamed ClxD (control ofLpxCdegradation), participates in this regulatory pathway. Suppressors of ClxD essentiality were identified inlpxCandlapB, and LpxC overproduction was shown to be sufficient to allow survival of ΔclxDmutants. Furthermore, the half-life of LpxC was shown to be reduced in cells lacking ClxD, and genetic and physical interactions between LapB and ClxD were detected. Taken together, our results are consistent with a model in which ClxD directly modulates LpxC turnover by FtsH-LapB to regulate LPS synthesis and maintain membrane homeostasis.

SIGNIFICANCE

The outer membrane is a major determinant of the intrinsic antibiotic resistance of Gram-negative bacteria. It is composed of both lipopolysaccharide (LPS) and phospholipid, and the synthesis of these lipid species must be balanced for the membrane to maintain its barrier function in blocking drug entry. In this report, we identify an essential protein of unknown function as a key new factor in maintaining LPS/phospholipid balance in the model bacteriumEscherichia coli. Our results provide novel insight into how this organism and most likely other Gram-negative bacteria maintain membrane homeostasis and their intrinsic resistance to antibiotics.
ΦX174 Attenuation by Whole Genome Codon Deoptimization
Authors: Van Leuven James T. , Ederer Martina M. , Burleigh Katelyn , Scott LuAnn , Hughes Randall A. , Codrea Vlad , Ellington Andrew D. , Wichman Holly , Miller Craig
Published: February 2020

Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion. We systematically recoded all non-overlapping genes of the bacteriophage ΦX174 with codons rarely used in itsE. colihost. The fitness of recombinant viruses decreases as additional deoptimizing mutations are made to the genome, although not always linearly, and not consistently across genes. Combining deoptimizing mutations may reduce viral fitness more or less than expected from the effect size of the constituent mutations and we point out difficulties in untangling correlated compositional features. We test our model by optimizing the same genes and find that the relationship between codon usage and fitness does not hold for optimization, suggesting that wild-type ΦX174 is at a fitness optimum. This work highlights the need to better understand how selection acts on patterns of synonymous codon usage across the genome and provides a convenient system to investigate the genetic determinants of virulence.