bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genomics of a bioluminescent symbiosis sheds light on symbiont transmission and specificity
Authors: Gould A.L. , Dunlap P.V.
Published: August 2019

All organisms depend on symbiotic associations with bacteria for their success, yet the processes by which specific symbioses are established and persist remain largely undescribed. To examine the ecological mechanisms involved in maintaining symbiont specificity over host generations, we examined the population genomics of a binary symbiosis involving the coral reef cardinalfishSiphamia tubiferand the luminous bacteriumPhotobacterium mandapamensis. Using restriction site-associated sequencing (RAD-Seq) methods we demonstrate that the facultative symbiont ofS. tubiferexhibits genetic structure at spatial scales of tens of kilometers in Okinawa, Japan in the absence of physical dispersal barriers and in contrast to the host fish. These results suggest the host’s behavioral ecology help structure symbiont populations at a reef site by symbiont enrichment, consequently fostering symbiont specificity. This approach also revealed several symbiont genes that were divergent between host populations including genes known to play a role in other host-bacteria associations.
Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy
Authors: Grier Alex , Laniewski Nathan , Gill Ann L. , Kessler Haeja A. , Huyck Heidie , Carbonell Elizabeth , Holden-Wiltse Jeanne , Bandyopadhyay Sanjukta , Carnahan Jennifer , Dylag Andrew M. , Topham David J. , Falsey Ann R. , Caserta Mary T. , Pryhuber Gloria S. , Gill Steven R. , McDavid Andrew , Scheible Kristin M.
Published: August 2019

Neonatal immune-microbiota co-development is poorly understood, yet appropriate recognition of – and response to – pathogens and commensal microbiota is critical to health. In this longitudinal study of 148 pre- and 119 full-term infants from birth through one year of age we found that postmenstrual age, or weeks from conception, not post-natal age, is the dominant factor influencing T cell and mucosal microbiota development. Numerous features of the T cell and microbiota functional development remain unexplained, however, by either age metric and are instead shaped by discrete peri- and post-natal events. Most strikingly, we establish that prenatal antibiotics or infection disrupt the normal T cell population developmental trajectory, influencing subsequent respiratory microbial colonization and predicting respiratory morbidity. In this way, early exposures imprint the postnatal immune-microbiota axis and place an infant at significant risk for respiratory morbidity in early childhood.

One Sentence Summary

T cells and microbiota follow predictable, coordinated trajectories in newborns, and their coordination is an important determinant of illness in the first year.

Graphical Abstract

Nasal and rectal microbiome was assessed weekly in the NICU, monthly post-discharge, and when respiratory illness symptoms occurred. T cells were characterized at birth (cord blood), 36-42 weeks postmenstrual age, and at 12 months. Quarterly respiratory morbidity surveys determined the 12-month outcome of persistent respiratory disease. More frequent illnesses and chronic disease outcomes occurred by one year of age if development of these systems was discordant or disrupted.
BET proteins are required for transcriptional activation of the senescent beta cell secretome in Type 1 Diabetes
Authors: Thompson Peter J. , Shah Ajit , Apostolopolou Charalampia-Christina , Bhushan Anil
Published: August 2019

OBJECTIVE

Type 1 Diabetes (T1D) results from progressive loss of pancreatic beta cells due to autoimmune destruction. We recently reported that during the natural history of T1D in humans and the female nonobese diabetic (NOD) mouse model, beta cells acquire a senescence-associated secretory phenotype (SASP) that is a major driver of disease onset and progression, but the mechanisms that activate SASP in beta cells were not explored. The objective of this study was to identify transcriptional mechanisms of SASP activation in beta cells.

METHODS

We used the female NOD mouse model of spontaneous autoimmune T1D and ex vivo experiments on NOD mouse and human islets to test the hypothesis that Bromodomain Extra-Terminal domain (BET) proteins activate the beta cell SASP transcriptional program.

RESULTS

Here we show that beta cell SASP is transcriptionally controlled by BET proteins, including BRD4. Chromatin analysis of key beta cell SASP genes in NOD islets revealed binding of BRD4 at active regulatory regions. BET protein inhibition in NOD islets diminished not only the transcriptional activation and secretion of SASP factors but also the non-cell autonomous activity. BET protein inhibition also decreased the extent of SASP induction in human islets exposed to DNA damage. The BET protein inhibitor iBET-762 prevented diabetes in NOD mice and also attenuated SASP in beta cells in vivo.

CONCLUSIONS

Taken together, our findings support a crucial role for BET proteins in the activation of the beta cell SASP transcriptional program. These studies suggest avenues for preventing T1D by transcriptional inhibition of SASP.
Size and mass prediction of almond kernels using machine learning image processing
Authors: Vidyarthi Sriram K , Tiwari Rakhee , Singh Samrendra K
Published: August 2019

After harvesting almond crop, accurate measurement of almond kernel sizes is a significant specification to plan, develop and enhance almond processing operations. The size and mass of the individual almond kernels are vital parameters usually associated with almond quality, particularly head almond yield. In this study, we propose a novel methodology that combines image processing and machine-learning ensemble that accurately measures the size and mass of whole raw almond kernels (classification - Nonpareil) simultaneously. We have developed an image-processing algorithm using recursive method to identify the individual almond kernels from an image and estimate the size of the kernels based on the occupied pixels by a kernel. The number of pixels representing an almond kernel was used as its digital fingerprint to predict its size and mass. Various popular machine learning (ML) models were implemented to build a stacked ensemble model (SEM), predicting the mass of the individual almond kernels based on the features derived from the pixels of the individual kernels in the image. The prediction accuracy and robustness of image processing and SEM were analyzed using uncertainty quantification. The mean error in estimating the average length of 1000 almond kernel was 3.12%. Similarly, mean errors associated with predicting the 1000 kernel mass were 0.63%. The developed algorithm in almond imaging in this study can be used to facilitate a rapid almond yield and quality appraisals.
M-GWAS for the gut microbiome in Chinese adults illuminates on complex diseases
Authors: Liu Xiaomin , Tang Shanmei , Zhong Huanzi , Tong Xin , Jie Zhuye , Ding Qiuxia , Wang Dan , Guo Ruidong , Xiao Liang , Xu Xun , Yang Huanming , Wang Jian , Zong Yang , Liu Xiao , Zhang Yong , Brix Susanne , Kristiansen Karsten , Hou Yong , Jia Huijue , Zhang Tao
Published: August 2019

The gut microbiome has been established as a key environmental factor to health. Genetic influences on the gut microbiome have been reported, yet, doubts remain as to the significance of genetic associations. Here, we provide shotgun data for whole genome and whole metagenome from a Chinese cohort, identifying no less than 20% genetic contribution to the gut microbiota. Using common variants-, rare variants- and copy number variations (CNVs)-based association analyses, we identified abundant signals associated with the gut microbiome especially in metabolic, neurological and immunological functions. The controversial concept of enterotypes may have a genetic attribute, with the top 2 loci explaining 11% of the Prevotella-Bacteroides variances. Stratification according to gender led to the identification of differential associations in males and females. Genetically encoded responses to ectopic presence of oral bacteria in the gut appear to be a common theme in a number of diseases investigated by MWAS (Metagenome-wide association studies). Our two-stage M-GWAS (Microbiome genome-wide association studies) on a total of 1295 individuals unequivocally illustrates that neither microbiome nor GWAS studies could overlook one another in our quest for a better understanding of human health and diseases.

Highlights

M-GWAS using high-depth whole genome identifies contributions from rare variants and CNVs.

Gut microbial modules such as butyrate, amino acids, mucin degradation show genetic associations.

Gender differential M-GWAS underscores differences in metabolic and psychological predispositions.

Some of the MWAS markers for colorectal cancer and cardiometabolic diseases show genetic associations.
N-terminal autoprocessing and acetylation of MARTX Makes-Caterpillars Floppy-like effector is stimulated by ADP-Ribosylation Factor 1 in advance of Golgi fragmentation
Authors: Herrera Alfa , Muroski John , Sengupta Ranjan , Nguyen Hong Hanh , Agarwal Shivangi , Ogorzalek Loo Rachel R. , Mattoo Seema , Loo Joseph A. , Satchell Karla J. F.
Published: August 2019

Studies have successfully elucidated the mechanism of action of several effector domains that comprise the MARTX toxins ofVibrio vulnificus. However, the biochemical linkage between the cysteine proteolytic activity of Makes Caterpillars Floppy-like (MCF) effector and its cellular effects remains unknown. In this study, we identify the host cell factors that activatein vivoandin vitroMCF autoprocessing as ADP-Ribosylation Factor 1 (ARF1) and ADP-ribosylation Factor 3 (ARF3). Autoprocessing activity is enhanced when ARF1 is in its active (GTP-bound) form compared to the inactive (GDP-bound) form. Subsequent to auto-cleavage, MCF is acetylated on its exposed N-terminal glycine residue. Acetylation apparently does not dictate subcellular localization, as MCF is found localized throughout the cell. However, the cleaved form of MCF gains the ability to bind to the specialized lipid phosphatidylinositol 5-phosphate enriched in Golgi and other membranes necessary for endocytic trafficking, suggesting a fraction of MCF may be subcellular localized. Traditional thin-section electron microscopy, high-resolution cryoAPEX localization, and fluorescent microscopy show that MCF causes Golgi dispersal resulting in extensive vesiculation. In addition, host mitochondria are disrupted and fragmented. Surprisingly, ARF1 is not itself processed or post-translationally modified by MCF. Further, only catalytically inactive MCF stably associates with ARF1, thus serving as a substrate trap. Our data indicate that ARF1 is a cross-kingdom activator of MCF, but reveal that MCF mediates cytotoxicity likely by directly targeting another yet to be identified protein. This study begins to elucidate the biochemical activity of this important domain and gives insight into how it may promote disease progression.
Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa
Authors: Waters Joshua C. , Jhaveri Deval , Biffinger Justin C. , Lee Kwangwon
Published: August 2019

Bioethanol production from lignocellulosic biomass has received increasing attention over the past decade. Many attempts have been made to reduce the cost of bioethanol production by combining the separate steps of the process into a single-step process known as consolidated bioprocessing. This requires identification of organisms that can efficiently decompose lignocellulose to simple sugars and ferment the pentose and hexose sugars liberated to ethanol. There have been many attempts in engineering laboratory strains by adding new genes or modifying genes to expand the capacity of an industrial microorganism. There has been less attention in improving bioethanol-related processes utilizing natural variation existing in the natural ecotypes. In this study, we sought to identify genomic loci contributing to variation in saccharification of cellulose and fermentation of glucose in the fermenting cellulolytic fungus Neurospora crassa through quantitative trait loci (QTL) analysis. We identified one major QTL contributing to fermentation of glucose and multiple putative QTL’s underlying saccharification. Understanding the natural variation of the major QTL gene would provide new insights in developing industrial microbes for bioethanol production.
State of pedestrian road safety in Uganda: are interventions failing or absent?
Authors: Osuret Jimmy , Namatovu Stella , Biribawa Claire , Balugaba Bonny E , Zziwa Esther Bayiga , Muni Kennedy , Ningwa Albert , Oporia Frederick , Mutto Milton , Kyamanywa Patrick , Guwatudde David , Kobusingye Olive
Published: August 2019

Introduction

In Uganda, pedestrians are the most frequently injured category of road users, accounting for 40% of road traffic fatalities and 25% of serious injuries every year. There is paucity of information on existing pedestrian interventions and challenges that affect their implementation in Uganda. In this paper, we ascertain the state of pedestrian road safety interventions in Uganda and explore the challenges in the process of design, implementation, monitoring and evaluation of existing interventions.

Methods

We conducted a qualitative study that started with a desk review of existing policy documents, police statistics, media reports, non-governmental organization reports, and published research. We supplemented the review with 14 key informant interviews and 4 focus group discussions. Participants were drawn from various agencies and stakeholders responsible for road safety. In total, we collected and synthesized data on the design, implementation, and evaluation of pedestrian safety interventions from 25 documents. Data were analyzed using qualitative thematic content analysis.

Results

The National Road Safety Council within the Ministry of Works and Transport is the lead agency tasked with coordinating all road safety efforts, while the Uganda Police is largely engaged in enforcing pedestrian safety. We identified several existing policies and regulations for pedestrian safety like the Non-Motorized Transport policy whose implementation has been inadequate. Implementation is constrained by weak institutional capacity and limited resources. Moreover, road safety stakeholders operated in silos and this hindered efforts to coordinate pedestrian safety activities. Interventions like road designs were implemented with limited reference to any supporting data and therefore did not cater for pedestrian needs.

Conclusion

There are interventions targeting pedestrian safety in Uganda, but effective implementation is lacking or failing due to constraints related to weak institutional capacity. This necessitates strategies to mobilize resources to strengthen the capacity of the lead agency to effectively coordinate road safety interventions.
Evaluating and improving heritability models using summary statistics
Authors: Speed Doug , Holmes John , Balding David J
Published: August 2019

There is currently much debate regarding the best way to model how heritability varies across the genome. The authors of GCTA recommend the GCTA-LDMS-I Model, the authors of LD Score Regression recommend the Baseline LD Model, while we have instead recommended the LDAK Model. Here we provide a statistical framework for assessing heritability models using summary statistics from genome-wide association studies. Using data from studies of 31 complex human traits (average sample size 136,000), we show that the Baseline LD Model is the most realistic of the existing heritability models, but that it can be improved by incorporating features from the LDAK Model. Our framework also provides a method for estimating the selection-related parameter α from summary statistics. We find strong evidence (P<1e-6) of negative genome-wide selection for traits including height, systolic blood pressure and college education, and that the impact of selection is stronger inside functional categories such as coding SNPs and promoter regions.
Mutation accumulation in chromosomal inversions maintains wing pattern polymorphism in a butterfly
Authors: Jay Paul , Chouteau Mathieu , Whibley Annabel , Bastide Héloïse , Llaurens Violaine , Parrinello Hugues , Joron Mathieu
Published: August 2019

While natural selection favours the fittest genotype, polymorphisms are maintained over evolutionary timescales in numerous species. Why these long-lived polymorphisms are often associated with chromosomal rearrangements remains obscure. Combining genome assemblies, population genomic analyses, and fitness assays, we studied the factors maintaining multiple mimetic morphs in the butterfly Heliconius numata. We show that the polymorphism is maintained because three chromosomal inversions controlling wing patterns express a recessive mutational load, which prevents their fixation despite their ecological advantage. Since inversions suppress recombination and hamper genetic purging, their formation fostered the capture and accumulation of deleterious variants. This suggests that many complex polymorphisms, instead of representing adaptations to the existence of alternative ecological optima, could be maintained primarily because chromosomal rearrangements are prone to carrying recessive harmful mutations.
Prediction of a cell-type specific mouse mesoconnectome using gene expression data
Authors: Timonidis Nestor , Bakker Rembrandt , Tiesinga Paul
Published: August 2019

Reconstructing brain connectivity at sufficient resolution for computational models designed to study the biophysical mechanisms underlying cognitive processes is extremely challenging. For such a purpose, a mesoconnectome that includes laminar and cell-type specificity would be a major step forward. We analysed the ability of gene expression patterns to predict cell-type and laminar specific projection patterns and analyzed the biological context of the most predictive groups of genes. To achieve our goal, we used publicly available volumetric gene expression and connectivity data and pre-processed it for prediction by averaging across brain regions, imputing missing values and rescaling. Afterwards, we predicted the strength of axonal projections and their binary form using expression patterns of individual genes and co-expression patterns of spatial gene modules.

For predicting projection strength, we found that ridge (L2-regularized) regression had the highest cross-validated accuracy with a median r2 score of 0.54 which corresponded for binarized predictions to a median area under the ROC value of 0.89. Next, we identified 200 spatial gene modules using the dictionary learning and sparse coding approach. We found that these modules yielded predictions of comparable accuracy, with a median r2 score of 0.51. Finally, a gene ontology enrichment analysis of the most predictive gene groups resulted in significant annotations related to postsynaptic function.

Taken together, we have demonstrated a prediction pipeline that can be used to perform multimodal data integration to improve the accuracy of the predicted mesoconnectome and support other neuroscience use cases.
Implicit perceptual memory can increase or decrease with ageing
Authors: Zhivago KA , Shashidhara Sneha , Garani Ranjini , Purokayastha Simran , Rao Naren P. , Murthy Aditya , Arun SP
Published: August 2019

A decline in declarative or explicit memory has been extensively characterized in cognitive ageing and is a hallmark of cognitive impairments. However, whether and how implicit perceptual memory varies with ageing or cognitive impairment is unclear. Here, we compared implicit perceptual memory and explicit memory measures in three groups of subjects: (1) 59 healthy young volunteers (20-30 years); (2) 238 healthy old volunteers (50-90 years) and (3) 21 patients with mild cognitive impairment MCI (50-90 years). To measure explicit memory, subjects were tested on standard recognition and recall tasks. To measure implicit perceptual memory, we used a classic perceptual priming paradigm. Subjects had to report the shape of a visual search pop-out target. Implicit priming was measured as the speedup in response time for targets with the same vs different color/position on consecutive trials.

Our main findings are as follows: (1) Explicit memory was weaker in old compared to young subjects, and in MCI compared to age-matched controls; (2) Surprisingly, implicit perceptual memory did not always decline with age: color priming was smaller in older subjects but position priming was larger; (3) Position priming was less frequent in the MCI group compared to age-matched controls; (4) Implicit and explicit memory measures were uncorrelated in all three groups. Thus, implicit memory can increase or decrease with age or cognitive impairment, but this decline does not covary with explicit memory. We propose that incorporating explicit and implicit measures can yield a richer characterization of memory.
Fish larvae tackle the complex fluid-structure interactions of undulatory swimming with simple actuation
Authors: Voesenek Cees J. , Li Gen , Muijres Florian T. , van Leeuwen Johan L.
Published: August 2019

Most fish swim with body undulations that result from fluid-structure interactions between the fish’s internal tissues and the surrounding water. As just-hatched larvae can swim effectively without a fully-developed brain, we hypothesise that fish larvae tackle the underlying complex physics with simple actuation patterns. To address this hypothesis, we developed a dedicated experimental-numerical approach to calculate the lateral bending moment distributions, which represent the system’s net actuation. The bending moment varies over time and along the fish’s central axis due to muscle actions, passive tissues, inertia, and fluid dynamics. Our 3D analysis of a large dataset of swimming events of larvae from 3 to 12 days after fertilisation shows that these bending moment patterns are not only relatively simple but also strikingly similar throughout early development, and from fast starts to periodic swimming. This suggests also similar muscle activation patterns, allowing fish larvae to produce swimming movements relatively simply, yet effectively, while restructuring their neuromuscular control system.
Regulation of amino acid and nucleotide metabolism by crustacean hyperglycemic hormone in the muscle and hepatopancreas of the crayfishProcambarus clarkii
Authors: Li Wenfeng , Chiu Kuo-Hsun , Lee Chi-Ying
Published: August 2019

To comprehensively characterize the metabolic roles of crustacean hyperglycemic hormone (CHH), metabolites in two CHH target tissues of the crayfishProcambarus clarkii, whose levels were significantly different between CHH-silenced and saline-treated control animals, were analyzed using bioinformatics tools provided by an on-line analysis suite (MetaboAnalyst). Analysis with Metabolic Pathway Analysis (MetPA) indicated that in the muscle Glyoxylate and dicarboxylate metabolism, Nicotinate and nicotinamide metabolism, Alanine, aspartate and glutamate metabolism, Pyruvate metabolism, and Nitrogen metabolism were significantly affected by silencing of CHH gene expression at 24 hours post injection (hpi), while only Nicotinate and nicotinamide metabolism remained significantly affected at 48 hpi. In the hepatopancreas, silencing of CHH gene expression significantly impacted, at 24 hpi, Pyruvate metabolism and Glycolysis or gluconeogenesis, and at 48 hpi, Glycine, serine and threonine metabolism. Moreover, analysis using Metabolite Set Enrichment Analysis (MSEA) showed that many metabolite sets were significantly affected in the muscle at 24hpi, including Ammonia recycling, Nicotinate and nicotinamide metabolism, Pyruvate metabolism, Purine metabolism, Warburg effect, Citric acid cycle, and metabolism of several amino acids, and at 48 hpi only Nicotinate and nicotinamide metabolism, Glycine and serine metabolism, and Ammonia recycling remained significantly affected. In the hepatopancreas, MSEA analysis showed that Fatty acid biosynthesis was significantly impacted at 24 hpi. Finally, in the muscle, levels of several amino acids decreased significantly, while those of 5 other amino acids or related compounds significantly increased in response to CHH gene silencing. Levels of metabolites related to nucleotide metabolism significantly decreased across the board at both time points. In the hepatopancreas, the effects were comparatively minor with only levels of thymine and urea being significantly decreased at 24 hpi. The combined results showed that the metabolic effects of silencing CHH gene expression were far more diverse than suggested by previous studies that emphasized on carbohydrate and energy metabolism. Based on the results, metabolic roles of CHH on the muscle and hepatopancreas were summarized and discussed.
Tritrophic interactions involving a dioecious fig tree, its fig pollinating wasp and fig nematodes
Authors: Jauharlina J. , Oktarina Hartati , Sriwati Rina , Kanzaki Natsumi , Quinnell Rupert J. , Compton Stephen G.
Published: August 2019

Many species of fig trees (Ficus spp., Moraceae) have nematodes that develop inside their inflorescences (figs). Nematodes are carried into young figs by females of the trees’ host-specific pollinating fig wasps (Agaonidae) that enter the figs to lay their eggs. The majority of Asian fig trees are functionally dioecious. Pollinators that enter figs on female trees cannot reproduce and offspring of any nematodes they carry will also be trapped inside. The biology of the nematodes is diverse, but poorly understood. We contrasted the development of nematodes carried by the pollinating fig wasp Ceratosolen solmsi marchali into figs on male and female trees of Ficus hispida in Sumatra, Indonesia. Figs were sampled from both male and female trees over a six-month period, with the nematodes extracted to record their development of their populations inside the figs. Populations of three species of nematodes developed routinely inside figs of both sexes: Caenorhabditis sp. (Rhabditidae), Ficophagus cf. centerae and Martininema baculum (both Aphelenchoididae). This is the first record of a Caenorhabditis sp. associated with F. hispida. Mean numbers of nematodes reached around 120-140 in both male and female figs. These peak population sizes coincided with the emergence of the new generation of adult fig wasps in male fig trees. We conclude that figs on female trees can support development and reproduction of some nematode species, but the absence of vectors means that their populations cannot persist beyond the lifetime of a single fig. Just like their fig wasp vectors, the nematodes cannot avoid this routine source of mortality.
Post-translational epigenetics: PRMT7 regulates RNA-binding capacity and protein stability to controlLeishmaniaparasite virulence
Authors: Ferreira Tiago R. , Dowle Adam A. , Parry Ewan , Alves-Ferreira Eliza V. C. , Kolokousi Foteini , Larson Tony R. , Plevin Michael J. , Cruz Angela K. , Walrad Pegine B.
Published: August 2019

RNA binding proteins (RBPs) are the primary gene regulators in kinetoplastids as transcriptional control is nearly absent, makingLeishmaniaan exceptional model for investigating methylation of non-histone substrates. Arginine methylation is an evolutionarily conserved protein modification catalyzed by Protein aRginine MethylTransferases (PRMTs). The chromatin modifier PRMT7 is the only Type III PRMT found in higher eukaryotes and a restricted number of unicellular eukaryotes. InLeishmania major, PRMT7 is a cytoplasmic protein implicit in pathogenesis with unknown substrates. Using comparative methyl-SILAC proteomics for the first time in protozoa, we identified 40 putative targets, including 17 RBPs hypomethylated upon PRMT7 knockout. PRMT7 can modify Alba3 and RBP16trans-regulators (mammalian RPP25 and YBX2 homologs, respectively) as direct substratesin vitro. The absence of PRMT7 levelsin vivoselectively reduces Alba3 mRNA-binding capacity to specific target transcripts and can impact the relative stability of RBP16 in the cytoplasm. RNA immunoprecipitation analyses demonstrate PRMT7-dependent methylation promotes Alba3 association with select target transcripts and stability ofδ-amastinsurface antigen. These results highlight a novel role for PRMT7-mediated arginine methylation upon RBP substrates, suggesting a regulatory pathway controlling gene expression and virulence inLeishmania. This work introducesLeishmaniaPRMTs as epigenetic regulators of mRNA metabolism with mechanistic insight into the functional manipulation of RBPs by methylation.
Evaluation of 20 enset (Ensete ventricosum) landraces for response to Xanthomonas vasicola pv. musacearum infection
Authors: Muzemil Sadik , Chala Alemayehu , Tesfaye Bezuayehu , Studholme David J. , Grant Murray , Yemataw Zerihun , Olango Temesgen Magule
Published: August 2019

Bacterial wilt, caused by Xanthomonas vasicola pv. musacearum (Xvm), formerly X. campestris pv. musacearum, is the most threatening and economically important disease of enset (Ensete ventricosum), the multipurpose food security crop orphan to south and southwestern Ethiopia. Xvm has also had a major impact on banana and plantain production in East Africa following its detection in Uganda in 2001 and subsequent spread. Effective control of this disease currently relies on integrated disease management (IDM) strategies including minimization of field pathogen inoculum and deployment of wilt resistant enset landraces. Identifying landraces with stable and durable Xvm resistance will greatly accelerate breeding of varieties that can be included as a component of IDM. In this study, 20 enset landraces previously reported to exhibit lower susceptibility to Xvm were grown in pots under open field conditions and inoculated with an aggressive Xvm inoculum isolated from a disease hotspot area. Longitudinal and survival analyses were applied to each landrace, based on disease units representing a combination of area-under-disease progress stairs, disease index and apparent infection rate. Considerable variation was observed among the 20 landraces; however, none exhibited full immunity to Xvm infection. Three landraces, viz. Hae’la, Mazia and Lemat (HML), showed lowest susceptibility to Xvm as evidenced by lower disease units and higher survival rates. Landraces Kuro, Gezewet, Bededet, and Alagena showed similar levels of Xvm infection as did HML, but with lower survival rates. By contrast, landrace Arkia showed the highest infection level and lowest survival rate, suggesting a high degree of susceptibility to Xvm. This study identifies new material that can be used in future breeding programmes to develop Xvm-resistant enset varieties.
Flotillin mediated membrane fluidity controls peptidoglycan synthesis and MreB movement
Authors: Zielińska Aleksandra , Savietto Abigail , de Sousa Borges Anabela , Martinez Denis , Berbon Melanie , Roelofsen Joël R. , Hartman Alwin M. , de Boer Rinse , van der Klei Ida J. , Hirsch Anna K. H. , Habenstein Birgit , Bramkamp Marc , Scheffers Dirk-Jan
Published: August 2019

The bacterial plasma membrane is an important cellular compartment. In recent years it has become obvious that protein complexes and lipids are not uniformly distributed within membranes. Current hypotheses suggest that flotillin proteins are required for the formation of complexes of membrane proteins including cell-wall synthetic proteins. We show here that bacterial flotillins are important factors for membrane fluidity homeostasis. Loss of flotillins leads to a decrease in membrane fluidity that in turn leads to alterations in MreB dynamics and, as a consequence, in peptidoglycan synthesis. These alterations are reverted when membrane fluidity is restored by a chemical fluidizer. In vitro, the addition of a flotillin increases membrane fluidity of liposomes. Our data support a model in which flotillins are required for direct control of membrane fluidity rather than for the formation of protein complexes via direct protein-protein interactions.
Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation
Authors: Rennison Diana J. , Rudman Seth M. , Schluter Dolph
Published: August 2019

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.
Investigating dual Ca2+modulation of the ryanodine receptor 1 by molecular dynamics simulation
Authors: Zheng Wenjun , Wen Han
Published: August 2019

The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+-activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (e.g., with Ca2+bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+binding site for activation. Toward elucidating the Ca2+-modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of bound and solvent Ca2+(total simulation time is > 5 microseconds). In the presence of solvent Ca2+, Ca2+binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+binding. The rich structural and dynamic information gained from this study will guide future mutational and functional studies of RyR1 activation and inhibition by Ca2+.

Statement of Significance

The ryanodine receptors (RyR) are key players in calcium signaling, and make prominent targets for drug design owning to their association with many diseases of cardiac and skeletal muscles. However, the molecular mechanism of their activation and inhibition by Ca2+remains elusive for the lack of high-resolution structural and dynamic information. Recent solutions of RyR1 structures by cryo-EM have paved the way for structure-based investigation of this important receptor by atomistic molecular simulation. This study presented, to our knowledge, the most extensive MD simulation of RyR1 core structure. Our simulation has offered new insights to the dual modulation mechanism of Ca2+, in which Ca2+binding to the activating site primes RyR1 activation by elevating its dynamics while solvent Ca2+inhibits RyR1 by reducing its dynamics. Additionally, our simulation has yielded a new wiring diagram of the allosterically coupled RyR1 domains informed by disease mutations.
PuMA: a papillomavirus genome annotation tool
Authors: Pace J. , Youens-Clark K. , Freeman C. , Hurwitz B. , Van Doorslaer K.
Published: August 2019

High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of ‘viral metagenomics’ has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on the genomic organization of that virus. There is a need to develop analytical approaches to reconstruct, annotate, and classify viral genomes. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate novel papillomaviruses. PuMA provides an accessible method for automated papillomavirus genome annotation. PuMA currently has a 98% accuracy when benchmarked against the 481 reference genomes in the papillomavirus episteme (PaVE). Finally, PuMA was used to annotate 168 newly isolated papillomaviruses, and successfully annotated 1424 viral features. To demonstrate its general applicability, we developed a version of PuMA that can annotate polyomaviruses.

PuMA is available on GitHub (https://github.com/KVD-lab/puma) and through the iMicrobe online environment (https://www.imicrobe.us/#/apps/puma)
DNA unwinding mechanism of a eukaryotic replicative CMG helicase
Authors: Yuan Zuanning , Georgescu Roxana , Bai Lin , Zhang Dan , Li Huilin , O’Donnell Mike
Published: August 2019

High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understand the unwinding mechanism. The eukaryotic replicative CMG helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the OB fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 Å, revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a separation pin, unwinding is achieved via a “dam-and-diversion tunnel” for steric exclusion unwinding. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation.
A Maxent modelling with a geospatial approach for the Habitat suitability of Flamingos in an Evanescing Ramsar site (Sambhar Lake, India) over the changing climatic scenarios
Authors: Kshitij Divyansh Laxmikant Sharma , Raj Alok
Published: August 2019

Wetlands play a crucial role in the biosphere and provide numerous services. They performed multiple functions such as groundwater recharge, water purification, conservation of biological resources, act as a carbon sink and habitat of amphibians and birds. A Ramsar site-the Sambhar Lake is one of the largest inland saline wetland present in the arid region of Rajasthan, India has unique habitat suitability for the winter avifauna migrants like flamingoes and falcons. The occurrence of suitable climatic conditions and food availability like brine shrimps (Artemia salina) attracts flocks of migratory birds. From the last three decades, Sambhar Lake has been continuously facing degradation due to anthropogenic activities, which disturb Lake’s natural ecology and existence. These cause disturbances in habitat suitability of migratory birds in the Sambhar Lake, which leads to a reduction of population density of migratory birds. Therefore, this study aimed to assess the degradation and vulnerability of Sambhar Lake and the habitat suitability of migratory birds using Maxent Habitat Suitability model. This model provides a platform to integrate the bird’s occurrence data with the bioclimatic variables using remote sensing and Geographical Information System, and provides bird’s habitat suitability as well as predicts future bird’s occurrence scenarios. Landsat-5 and Sentinel-2 imagery for the year 1996 and 2019 respectively were used in this study. Four indicators such as LULC NDWI, MSI and SABI depicts the environmental condition of the Sambhar Lake. Output form Maxent model reveals that the Sambhar lake area with increasing anthropogenic activities has become unsuitable for flamingos. A remarkable loss of breeding sites of animal, particularly avian fauna (flamingos) is seen in the recent years due to different types of threats posed on the Ramsar site. Increase in Salt crust and Vegetation area from 36.8055 to 123.837 Sq. Km. and 26.5347 to 36.857 Sq. Km. respectively have taken place. While a decrease in saline water area from 88.8309 to 19.3256 Sq. Km has been observed, within the vicinity of Sambhar Lake as clearly shown through LULC map. The future prediction of the distribution of species in the region for the year 2050 shows that the most suitable regions will be near to Jhapok and nearby waters of Salt Lake City as the drains from the city opens in the lake where the flamingoes get Algae in the form of food. Active steps are needed for the lake conservation to reduce the risks of migratory bird’s population.
Catecholaminergic axons in the neocortex of adult mice regrow following brain injury
Authors: Dougherty Sarah E. , Kajstura Tymoteusz J. , Jin Yunju , Chan-Cortés Michelle H. , Kota Akhil , Linden David J.
Published: August 2019

Serotonin axons in the adult rodent brain can regrow and recover their function following several forms of injury including controlled cortical impact (CCI), a neocortical stab wound, or systemic amphetamine toxicity. To assess whether this capacity for regrowth is unique to serotonergic fibers, we used CCI and stab injury models to assess whether fibers from other neuromodulatory systems can also regrow following injury. Using tyrosine-hydoxylase (TH) immunohistochemistry we measured the density of catecholaminergic axons before and at various time points after injury. One week after CCI injury we observed a pronounced loss, across cortical layers, of TH+ axons posterior to the site of injury. One month after CCI injury the same was true of TH+ axons both anterior and posterior to the site of injury. This loss was followed by significant recovery of TH+ fiber density across cortical layers, both anterior and posterior to the site of injury, measured three months after injury. TH+ axon loss and recovery over weeks to months was also observed throughout cortical layers using the stab injury model. Double label immunohistochemistry revealed that nearly all TH+ axons in neocortical layer 1/2 are also dopamine-beta-hyroxylase+ (DBH+; presumed norepinephrine), while TH+ axons in layer 5 are a mixture of DBH+ and dopamine transporter+ types. This suggests that noradrenergic axons can regrow following CCI or stab injury in the adult mouse neocortex and leaves open the question of whether dopaminergic axons can do the same.

Highlights

We measured catecholaminergic axon density using tyrosine hydroxylase immunohistochemistry following two forms of brain injury.

Both controlled cortical impact and cortical stab injuries caused extensive damage to catecholaminergic axons in the neocortex of adult mice.

Following both types of injury, axon density slowly returned to control values over many weeks, including, in the case of stab injury, regrowth across the stab rift.

Together with previous results showing serotonin axon regrowth, these findings suggest that monaminergic axons have an unusual capacity for regrowth following injury in the adult mammalian brain
Targeting MEK5 impairs non-homologous end-joining repair and sensitizes prostate cancer to DNA damaging agents
Authors: Broustas Constantinos G. , Duval Axel J. , Chaudhary Kunal R. , Friedman Richard A. , Virk Renu K. , Lieberman Howard B.
Published: August 2019

Radiotherapy is commonly used to treat a variety of solid human tumors, including localized prostate cancer. However, treatment failure often ensues due to tumor intrinsic or acquired radioresistance. Here we find that the MEK5/ERK5 signaling pathway is associated with resistance to genotoxic stress in aggressive prostate cancer cells. MEK5 knockdown by RNA interference sensitizes prostate cancer cells to ionizing radiation (IR) and etoposide treatment, as assessed by clonogenic survival and short-term proliferation assays. Mechanistically, MEK5 downregulation impairs phosphorylation of the catalytic subunit of DNA-PK at serine 2056 in response to IR or etoposide treatment. Although MEK5 knockdown does not influence the initial appearance of radiation- and etoposide-induced γH2AX and 53BP1 foci, it markedly delays their resolution, indicating a DNA repair defect. A cell-based assay shows that non-homologous end joining (NHEJ) is compromised in cells with ablated MEK5 protein expression. Finally, MEK5 silencing combined with focal irradiation causes strong inhibition of tumor growth in mouse xenografts, compared with MEK5 depletion or radiation alone. These findings reveal a convergence between MEK5 signaling and DNA repair by NHEJ in conferring resistance to genotoxic stress in advanced prostate cancer and suggest targeting MEK5 as an effective therapeutic intervention in the management of this disease.
Simulations of proposed mechanisms of FtsZ-driven cell constriction
Authors: Nguyen Lam T. , Oikonomou Catherine M. , Jensen Grant J.
Published: August 2019

To divide, bacteria must constrict their membranes against significant force from turgor pressure. A tubulin homo-log, FtsZ, is thought to drive constriction, but how FtsZ filaments might generate constrictive force in the absence of motor proteins is not well understood. There are two predominant models in the field. In one, filaments overlap to form complete rings around the circumference of the cell; as filaments slide against each other to maximize lateral contact, the rings constrict. In the other, filaments exert force on the membrane by a GTP-hydrolysis-induced switch in conformation from straight to bent. Here we developed software, ZCONSTRICT, for quantitative 3D simulations of Gram-negative bacterial cell division to test these two models and identify critical conditions required for them to work. We find that the avidity of lateral interactions quickly halts the sliding of filaments, so a mechanism such as depolymerization or treadmilling is required to sustain constriction by filament sliding. For filament bending, we find that a mechanism such as the presence of a rigid linker is required to constrain bending within the division plane and maintain the distance observed in vivo between the filaments and the membrane. We also explored the recent observation of constriction associated with a single FtsZ filament and found that it can be explained by the filament bending model if there is a rigid connection between the filament and the cell wall. Together, our work sheds light on the physical principles underlying bacterial cell division and informs future experiments to elucidate the mechanism of FtsZ.
Therapeutically exploring persister metabolism in bacteria
Authors: Mohiuddin Sayed G. , Hoang Thuy , Saba Adesola , Karki Prashant , Orman Mehmet A.
Published: August 2019

Bacterial persisters are rare phenotypic variants that are temporarily tolerant to high concentrations of antibiotics. We have previously discovered that persisters are mostly derived from stationary-phase cells with high redox activities that are maintained by endogenous protein and RNA degradation. This intracellular degradation resulted in self-inflicted damage that transiently repressed the cellular functions targeted by antibiotics. Leveraging this knowledge, we developed an assay integrating a degradable fluorescent protein system and a small library, containing FDA-approved drugs and antibiotics, to detect chemicals that target persister metabolism. We identified several metabolic inhibitors, including anti-psychotic drugs, that can reduce Escherichia coli persistence. These chemical inhibitors also reduce Pseudomonas aeruginosa persistence, potentially verifying the existence of similar mechanisms in a medically relevant organism.