bluuebunny/crossref_metadata_2025 huggingface dataset:
Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae:
Theodoxus
)
Authors: Sands Arthur F. , Neubauer Thomas A. , Nasibi Saeid , Harandi Majid Fasihi , Anistratenko Vitaliy V. , Wilke Thomas , Albrecht Christian
Published: October 2019

The Caspian Sea has been a highly dynamic environment throughout the Quaternary and witnessed major oscillations in lake level, which were associated with changes in salinity and habitat availability. Such environmental pressures are considered to drive strong phylogeographic structures in species by forcing populations into suitable refugia. However, little is actually known on the effect of lake-level fluctuations in the Caspian Sea on its aquatic biota. We compared the phylogeographic patterns of the aquatic Neritidae snail genus
Theodoxus
across the Pontocaspian region with refugial populations in southern Iran. Three gene fragments were used to determine relationships and divergence times between the sampled populations in both groups. A dated phylogeny and statistical haplotype networks were generated in conjunction with the analyses of molecular variance and calculations of isolation by distance using distance-based redundancy analyses. Extended Bayesian skyline plots were constructed to assess demographic history. Compared with the southern Iranian populations, we found little phylogeographic structure for the Pontocaspian
Theodoxus
group, with more recent diversification, homogeneity of haplotypes across the Pontocaspian region and a relatively stable demographic history since the Middle Pleistocene. Our results argue against a strong influence of Caspian Sea low stands on the population structure post the early Pleistocene, whereas high stands may have increased the dispersal possibilities and homogenization of haplotypes across the Pontocaspian region during this time. However, during the early Pleistocene, a more dramatic low stand in the Caspian Sea, around a million years ago, may have caused the reduction in
Theodoxus
diversity to a single lineage in the region. In addition, our results provide new insights into
Theodoxus
taxonomy and outlooks for regional conservation.
Cellular morphology of leg musculature in the water bearHypsibius exemplaris(Tardigrada) unravels serial homologies
Authors: Gross Vladimir , Mayer Georg
Published: October 2019

Tardigrades (water bears) are microscopic, segmented ecdysozoans with four pairs of legs. Lobopodous limbs that are similar to those seen in tardigrades are hypothesized to represent the ancestral state of Panarthropoda (Tardigrada + Onychophora + Arthropoda), and their evolutionary history is important to our understanding of ecdysozoan evolution. Equally important is our understanding of the functional morphology of these legs, which requires knowledge of their musculature. Tardigrade musculature is well documented but open questions remain. For example, while the muscular organization of each trunk segment and its legs is unique, three of the four trunk segments are nevertheless relatively homonomous. To what extent, then, do leg muscles show segmental patterns? Specifically, which leg muscles are serially repeated and which are unique? The present study addresses these questions using a combination of techniques intended to visualize both the overall layout and fine structure of leg muscles in the eutardigradeHypsibius exemplaris. In doing so, we propose serial homologies for all leg muscles in each of the four legs and reveal new details of their cellular structure and attachment sites. We compare our results to those of previous studies and address the functional implications of specialized muscle cell morphologies.
Functional morphology of a lobopod: case study of an onychophoran leg
Authors: Oliveira Ivo de Sena , Kumerics Andreas , Jahn Henry , Müller Mark , Pfeiffer Franz , Mayer Georg
Published: October 2019

Segmental, paired locomotory appendages are a characteristic feature of Panarthropoda—a diversified clade of moulting animals that includes onychophorans (velvet worms), tardigrades (water bears) and arthropods. While arthropods acquired a sclerotized exoskeleton and articulated limbs, onychophorans and tardigrades possess a soft body and unjointed limbs called lobopods, which they inherited from Cambrian lobopodians. To date, the origin and ancestral structure of the lobopods and their transformation into the jointed appendages are all poorly understood. We therefore combined high-resolution computed tomography with high-speed camera recordings to characterize the functional anatomy of a trunk lobopod from the onychophoran
Euperipatoides rowelli
. Three-dimensional reconstruction of the complete set of muscles and muscle fibres as well as non-muscular structures revealed the spatial relationship and relative volumes of the muscular, excretory, circulatory and nervous systems within the leg. Locomotory movements of individual lobopods of
E. rowelli
proved far more diverse than previously thought and might be governed by a complex interplay of 15 muscles, including one promotor, one remotor, one levator, one retractor, two depressors, two rotators, one flexor and two constrictors as well as muscles for stabilization and haemolymph control. We discuss the implications of our findings for understanding the evolution of locomotion in panarthropods.
Dive behaviour and foraging effort of female Cape fur sealsArctocephalus pusillus pusillus
Authors: Kirkman S. P. , Costa D. P. , Harrison A.-L. , Kotze P. G. H. , Oosthuizen W. H. , Weise M. , Botha J. A. , Arnould J. P. Y.
Published: October 2019

While marine top predators can play a critical role in ecosystem structure and dynamics through their effects on prey populations, how the predators function in this role is often not well understood. In the Benguela region of southern Africa, the Cape fur seal (Arctocephalus pusillus pusillus) population constitutes the largest marine top predator biomass, but little is known of its foraging ecology other than its diet and some preliminary dive records. Dive information was obtained from 32 adult females instrumented with dive recorders at the Kleinsee colony (29°34.17′ S, 16°59.80′ E) in South Africa during 2006–2008. Most dives were in the depth range of epipelagic prey species (less than 50 m deep) and at night, reflecting the reliance of Cape fur seals on small, vertically migrating, schooling prey. However, most females also performed benthic dives, and benthic diving was prevalent in some individuals. Benthic diving was significantly associated with the frequency with which females exceeded their aerobic dive limit. The greater putative costs of benthic diving highlight the potential detrimental effects to Cape fur seals of well-documented changes in the availability of epipelagic prey species in the Benguela.
Dynamical stability of water distribution networks
Authors: Masuda Naoki , Meng Fanlin
Published: October 2019

Water distribution networks are hydraulic infrastructures that aim to meet water demands at their various nodes. Water flows through pipes in the network create nonlinear dynamics on networks. A desirable feature of water distribution networks is high resistance to failures and other shocks to the system. Such threats would at least transiently change the flow rate in various pipes, potentially undermining the functionality of the whole water distribution system. Here we carry out a linear stability analysis for a nonlinear dynamical system representing the flow rate through pipes that are interconnected through an arbitrary pipe network with reservoirs and consumer nodes. We show that the steady state is always locally stable and develop a method to calculate the eigenvalue that corresponds to the mode that decays the most slowly towards the equilibrium, which we use as an index for resilience of the system. We show that the proposed index is positively correlated with the recovery rate of the pipe network, which was derived from a realistic and industrially popular simulator. The present analytical framework is expected to be useful for deploying tools from nonlinear dynamics and network analysis in the design, resilience management and scenario testing of water distribution networks.
Sensory gaze stabilization in echolocating bats
Authors: Eitan O. , Kosa G. , Yovel Y.
Published: October 2019

Sensing from a moving platform is challenging for both man-made machines and animals. Animals' heads jitter during movement, so if the sensors they carry are not stabilized, any spatial estimation might be biased. Flying animals, like bats, seriously suffer from this problem because flapping flight induces rapid changes in acceleration which moves the body up and down. For echolocating bats, the problem is crucial. Because they emit a sound to sense the world, an unstable head means sound energy pointed in the wrong direction. It is unknown how bats mitigate this problem. By tracking the head and body of flying fruit bats, we show that they stabilize their heads, accurately maintaining a fixed acoustic-gaze relative to a target. Bats can solve the stabilization task even in complete darkness using only echo-based information. Moreover, the bats point their echolocation beam below the target and not towards it, a strategy that should result in better estimations of target elevation.
Measuring chromosome conformation by fluorescence microscopy
Authors: Ross Brian C. , Anaclerio Fabio , Lorusso Nicola , Ventura Mario , Costello Jim
Published: October 2019

Measurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by ‘connecting the dots’. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.
Flow-cytometric microglial sorting coupled with quantitative proteomics identifies moesin as a highly-abundant microglial protein with relevance to Alzheimer’s disease
Authors: Rayaprolu Sruti , Gao Tianwen , Xiao Hailian , Ramesha Supriya , Weinstock Laura D. , Shah Jheel , Duong Duc M. , Dammer Eric B. , Webster James A. , Lah James J. , Wood Levi B. , Betarbet Ranjita , Levey Allan I. , Seyfried Nicholas T. , Rangaraju Srikant
Published: October 2019

Background

Proteomic characterization of microglia provides the most proximate assessment of functionally relevant molecular mechanisms of neuroinflammation. However, microglial proteomics studies have been limited by low cellular yield and contamination by non-microglial proteins using existing enrichment strategies.

Methods

We coupled magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) of microglia with tandem mass tag-mass spectrometry (TMT-MS) to obtain a highly-pure microglial proteome and identified a core set of highly-abundant microglial proteins in adult mouse brain. We interrogated existing human proteomic data for Alzheimer’s disease (AD) relevance of highly-abundant microglial proteins and performed immuno-histochemical andin-vitrovalidation studies.

Results

Quantitative multiplexed proteomics by TMT-MS of CD11b+ MACS-enriched (N= 5 mice) and FACS-isolated (N= 5 mice), from adult wild-type mice, identified 1,791 proteins. A total of 203 proteins were highly abundant in both datasets, representing a core-set of highly abundant microglial proteins. In addition, we found 953 differentially enriched proteins comparing MACS and FACS-based approaches, indicating significant differences between both strategies. The FACS-isolated microglia proteome was enriched with cytosolic, endoplasmic reticulum, and ribosomal proteins involved in protein metabolism and immune system functions, as well as an abundance of canonical microglial proteins. Conversely, the MACS-enriched microglia proteome was enriched with mitochondrial and synaptic proteins and higher abundance of neuronal, oligodendrocytic and astrocytic proteins. From the 203 consensus microglial proteins with high abundance in both datasets, we confirmed microglial expression of moesin (Msn) in wild-type and 5xFAD mouse brains as well as in human AD brains. Msn expression is nearly exclusively found in microglia that surround Aβ plaques in 5xFAD brains. Inin-vitroprimary microglial studies, Msn silencing by siRNA decreased Aβ phagocytosis and increased lipopolysaccharide-induced production of the pro-inflammatory cytokine, tumor necrosis factor (TNF). In network analysis of human brain proteomic data, Msn was a hub protein of an inflammatory co-expression module positively associated with AD neuropathological features and cognitive dysfunction.

Conclusions

Using FACS coupled with TMT-MS as the method of choice for microglial proteomics, we define a core set of highly-abundant adult microglial proteins. Among these, we validate Msn as highly-abundant in plaque-associated microglia with relevance to human AD.
Energy-based and energy-free food-consumption are correlated in captive non-human-primates: A novel dispenser for feeding and behavioral enrichment
Authors: Shohat Yosef , Paz Rony , Pryluk Raviv , Taub Aryeh H.
Published: October 2019

Non-human primates (NHP) provide an important model for studying biological mechanisms that underlie behavior and cognition, and are crucial for supplying translational knowledge that can aid the development of new clinical approaches. At the same time, the importance of the 3Rs to minimize suffering during experiments encouraged the development of environmental enrichment programs. Among them, tools for feeding and foraging are central. However, it remains unclear whether the behavioral enrichment tools are used by the animals only for feeding and to satisfy hunger (and hence for survival), or whether these feeding tools serve also as behavioral enrichment in itself (namely, the animals enjoy it per-se). To answer this, we designed a novel dispenser method – that requires significant yet reasonable energetic effort to obtain food - and tested food consumption via the dispenser compared to free-access, namely that did not require any effort on the animal side. We found that primates consumed food from both the dispenser and when presented in free-access, and importantly, that the consumption via the dispenser was in correlation with the consumption in free-access. This was similar across different subjects, different times during the day, and different types of food. We suggest that monkeys can benefit from using the dispenser for food consumption, but also benefit from it for play (i.e. as behavioral enrichment in itself). Such an approach allows non-human-primates to preserve their natural food procurement activities.
Differences in signalling, trafficking and glucoregulatory properties of glucagon-like peptide-1 receptor agonists exendin-4 and lixisenatide
Authors: Pickford Philip , Lucey Maria , Fang Zijian , Bitsi Stavroula , Broichhagen Johannes , Hodson David J. , Minnion James , Rutter Guy A , Bloom Stephen R , Tomas Alejandra , Jones Ben
Published: October 2019

Background and purpose

Amino acid substitutions at the N-termini of glucagon-like peptide-1 receptor agonist (GLP-1RA) peptides result in distinct patterns of intracellular signalling, sub-cellular trafficking and efficacyin vivo. Here we aimed to determine whether sequence differences at the ligand C-termini of clinically approved GLP-1RAs exendin-4 and lixisenatide lead to similar phenomena. We also sought to establish the impact of the C-terminus on signal bias resulting from modifications elsewhere in the molecule.

Experimental approach

Exendin-4, lixisenatide, and N-terminally substituted analogues with biased signalling characteristics were compared across a range ofin vitrotrafficking and signalling assays in different cell types. Fluorescent ligands and new time-resolved FRET approaches were developed to study agonist behaviours at the cellular and sub-cellular level. Anti-hyperglycaemic and anorectic effects of each parent ligand, and their biased derivatives, were assessed in mice.

Key results

Lixisenatide and exendin-4 showed equal binding affinity, but lixisenatide was 5-fold less potent for cAMP signalling. Both peptides were rapidly endocytosed, but the GLP-1R recycled more slowly to the plasma membrane after lixisenatide treatment. These combined deficits resulted in reduced maximal sustained insulin secretion and reduced anti-hyperglycaemic and anorectic effects in mice. N-terminal substitutions to both ligands had favourable effects on their pharmacology, resulting in improved insulin release and lowering of blood glucose.

Conclusion and implications

Changes to the C-terminus of exendin-4 affect signalling potency and GLP-1R trafficking via mechanisms unrelated to GLP-1R occupancy. These differences were associated with changes in their ability to control blood glucose and therefore may be therapeutically relevant.
Expression and purification of Protease Activated Receptor 4 (PAR4) and analysis with histidine hydrogen deuterium exchange
Authors: de la Fuente Maria , Han Xu , Miyagi Masaru , Nieman Marvin T.
Published: October 2019

Protease activated receptors (PARs) are G-protein coupled receptors (GPCRs) that are activated by proteolyis of the N-terminus, which exposes a tethered ligand that interacts with the receptor. Numerous studies have focused on the signaling pathways mediated by PARs. However, the structural basis for initiation of these pathways is unknown. Here, we describe a strategy for the expression and purification of PAR4. This is the first PAR family member to be isolated without stabilizing modifications for biophysical studies. We monitored PAR4 activation with histidine-hydrogen deuterium exchange (His-HDX). PAR4 has 9 histidines that are spaced throughout the protein allowing a global view of solvent accessible and non-accessible regions. Peptides containing each of the 9 His residues were used to determine the t1/2 for each His residue in apo or thrombin activated PAR4. The thrombin cleaved PAR4 had a 2-fold increase (p > 0.01) in t1/2 values observed for four histidine residues (His180, His229, His240, and His380) demonstrating that these regions have decreased solvent accessibility upon thrombin treatment. In agreement, thrombin cleaved PAR4 also was resistant to thermolysin digestion. In contrast, activation with the PAR4 agonist peptide was digested at the same rate as apo PAR4. Further analysis showed the C-terminus is protected in thrombin activated PAR4 compared to uncleaved or agonist peptide treated PAR4. The studies described here are the first to examine the tethered ligand activation mechanism for a PAR family member using biophysically and shed light on the overall conformational changes that follow activation of PARs by a protease.
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement
Authors: Patel Avinash B. , Moore Camille M. , Greber Basil J. , Luo Jie , Ranish Jeff , Nogales Eva
Published: October 2019

Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility1,2. The Saccharomyces cerevisiae RSC (Remodeling the Structure of Chromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair2–4. Here we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored through the interactions between the N-terminus of Sth1 and the core. Our cryo-EM analysis also shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of Rsc8 SWRIM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.
Integrative genomic, transcriptomic, and epigenomic analyses of benign prostatic hyperplasia reveal new options for therapy
Authors: Liu Deli , Shoag Jonathan , Poliak Daniel , Goueli Ramy S. , Ravikumar Vaishali , Redmond David , Vosoughi Aram , Fontugne Jacqueline , Pan Heng , Lee Daniel , Thomas Domonique , Salari Keyan , Wang Zongwei , Romanel Alessandro , Te Alexis , Lee Richard , Chughtai Bilal , Olumi Aria F. , Mosquera Juan Miguel , Demichelis Francesca , Elemento Olivier , Rubin Mark A. , Sboner Andrea , Barbieri Christopher E.
Published: October 2019

Benign prostatic hyperplasia (BPH), a nonmalignant enlargement of the prostate, is one of the most common diseases affecting aging men, but the underlying molecular features of BPH remain poorly understood, and therapeutic options are limited. Here we employed a comprehensive molecular investigation of BPH, including genomic, transcriptomic and epigenetic profiling of 18 BPH cases. At the molecular level, we found no evidence of neoplastic features in BPH: no evidence of driver genomic alterations, including low coding mutation rates, mutational signatures consistent with aging tissues, minimal copy number alterations, and no genomic rearrangements. Similarly at the epigenetic level, we found global hypermethylation was the dominant process (unlike most neoplastic processes). By integrating transcriptional and methylation signatures, we identified two BPH subgroups with distinct clinical features and associated signaling pathways, which were validated in two independent cohorts. Finally, our analyses nominatedmTORinhibitors as a potential subtype-specific therapeutic option. Supporting this, a cohort of men exposed tomTORinhibitors showed a significant decrease in prostate size. Our results demonstrate that BPH consists of distinct molecular subgroups, with potential for subtype-specific precision therapy viamTORinhibition.
Low dose Cold Atmospheric Plasma induces membrane oxidation, stimulates endocytosis and enhances uptake of nanomaterials in Glioblastoma multiforme cells
Authors: He Zhonglei , Liu Kangze , Scally Laurence , Manaloto Eline , Gunes Sebnem , Ng Sing Wei , Maher Marcus , Tiwari Brijesh , Byrne Hugh J , Bourke Paula , Tian Furong , Cullen Patrick J , Curtin James F
Published: October 2019

Cold atmospheric plasma (CAP) has demonstrated synergistic cytotoxic effects with nanoparticles, especially promoting the uptake and accumulation of nanoparticles inside cells. However, the mechanisms driving the effects need to be explored. In this study, we investigate the enhanced uptake of theranostic nanomaterials by CAP. Numerical modelling of the uptake of gold nanoparticle into U373MG Glioblastoma multiforme (GBM) cells predicts that CAP may introduce a new uptake route. We demonstrate that cell membrane repair pathways play the main role in this stimulated new uptake route, following non-toxic doses of dielectric barrier discharge CAP (30 s, 75 kV). CAP treatment induces cellular membrane damage, mainly via lipid peroxidation as a result of reactive oxygen species (ROS) generation. Membranes rich in peroxidated lipids are then trafficked into cells via membrane repairing endocytosis. We confirm that the enhanced uptake of nanomaterials is clathrin-dependent using chemical inhibitors and silencing of gene expression. Therefore, CAP-stimulated membrane repair increases endocytosis and accelerates the uptake of gold nanoparticles into U373MG cells after CAP treatment. Our data demonstrate the utility of CAP to model membrane oxidative damage in cells and characterise a previously unreported mechanism of membrane repair to trigger nanomaterial uptake which will be useful for developing more efficient deliveries of nanoparticles and pharmaceuticals into cancer cells for tumour therapy and diagnosis. This mechanism of RONS-induced endocytosis will also be of relevance to other cancer therapies that induce an increase in extracellular RONS.
Perceptual Invariance of Words and Other Learned Sounds in Non-human Primates
Authors: Melchor Jonathan , Morán Isaac , Figueroa Tonatiuh , Lemus Luis
Published: October 2019

The ability to invariably identify spoken words and other naturalistic sounds in different temporal modulations and timbres requires perceptual tolerance to numerous acoustic variations. However, the mechanisms by which auditory information is perceived to be invariant are poorly understood, and no study has explicitly tested the perceptual constancy skills of nonhuman primates. We investigated the ability of two trained rhesus monkeys to learn and then recognize multiple sounds that included multisyllabic words. Importantly, we tested their ability to group unexperienced sounds into corresponding categories. We found that the monkeys adequately categorized sounds whose formants were at close Euclidean distance to the learned sounds. Our results indicate that macaques can attend and memorize complex sounds such as words. This ability was not studied or reported before and can be used to study the neuronal mechanisms underlying auditory perception.
Modulating Sphingosine-1-Phosphate receptors to improve chemotherapy delivery to Ewing sarcoma
Authors: Marmonti Enrica , Savage Hannah , Zhang Aiqian , Alvarez Claudia , Morrell Miriam , Schadler Keri
Published: October 2019

Tumor vasculature is innately dysfunctional. Poorly functional tumor vessels inefficiently deliver chemotherapy to tumor cells; vessel hyper-permeability promotes chemotherapy delivery primarily to a tumor’s periphery. Here we identify a method for enhancing chemotherapy delivery and efficacy in Ewing sarcoma (ES) in mice by modulating tumor vessel permeability. Vessel permeability is partially controlled by the G protein-coupled Sphinosine-1-phosphate receptors 1 and 2 (S1PR1 and S1PR2) on endothelial cells. S1PR1 promotes endothelial cell junction integrity while S1PR2 destabilizes it. We hypothesize that an imbalance of S1PR1:S1PR2 is partially responsible for the dysfunctional vascular phenotype characteristic of ES and that by altering the balance in favor of S1PR1, ES vessel hyper-permeability can be reversed. In this study, we demonstrate that pharmacologic activation of S1PR1 by SEW2871 or inhibition of S1PR2 by JTE-013 caused more organized, mature, and functional tumor vessels. Importantly, S1PR1 activation or S1PR2 inhibition improved chemotherapy delivery to the tumor and anti-tumor efficacy. Our data suggests that pharmacologic targeting of S1PR1 and S1PR2 may be a useful adjuvant to standard chemotherapy for ES patients.

NOVELTY AND IMPACT

This study demonstrates that Sphingosine-1-Phosphate (S1P) receptors are potential novel targets for tumor vasculature remodeling and adjuvant therapy for the treatment of Ewing Sarcoma. Unlike receptor tyrosine kinases that have already been extensively evaluated for use as vascular normalizing agents in oncology, S1P receptors are G protein-coupled receptors, which have not been well studied in tumor endothelium. Pharmacologic activators and inhibitors of S1P receptors are currently in clinical trials for treatment of auto-immune and cardiovascular diseases, indicating potential for clinical translation of this work.
New genome assemblies reveal patterns of domestication and adaptation acrossBrettanomyces(Dekkera) species
Authors: Roach Michael J. , Borneman Anthony R.
Published: October 2019

Background

Yeast of the genusBrettanomycesare of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species ofBrettanomyces. For instance,Brettanomyces bruxellensishas been heavily studied and many resources are available for this species, whereasBrettanomyces nanusis rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus.

Results

Strains for each of the five widely accepted species ofBrettanomyces(Brettanomyces anomalus,B. bruxellensis,Brettanomyces custersianus,Brettanomyces naardenensis, andB. nanus) were sequenced using a combination of long- and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Sweeping and extensive structural variation between the species’ genomes were observed and gene expansions in fermentation-relevant genes (particularly inB. bruxellensisandB. nanus) were identified. Numerous horizontal gene transfer (HGT) events in allBrettanomycesspecies’, including an HGT event that is probably responsible for allowingB. bruxellensisandB. anomalusto utilize sucrose were also observed.

Conclusions

Genomic adaptations and some evidence of domestication that have taken place inBrettanomycesare outlined. These new genome assemblies form a valuable resource for future research inBrettanomyces.
A HypomorphicCystathionine ß-SynthaseGene Contributes to Cavefish Eye Loss by Disrupting Optic Vasculature
Authors: Ma Li , Gore Aniket V. , Castranova Daniel , Shi Janet , Ng Mandy , Tomins Kelly A. , van der Weele Corine M. , Weinstein Brant M. , Jeffery William R.
Published: October 2019

Vestigial structures are key indicators of evolutionary descent but the mechanisms underlying their development are poorly understood. This study examines vestigial eye formation in the teleostAstyanax mexicanus, which consists of a sighted surface-dwelling morph and different populations of blind cave morphs. Cavefish embryos initially develop optic primordia but vestigial eyes are formed during larval development. Multiple genetic factors are involved in cavefish eye loss but none of the mutated genes have been identified. Here we identifycystathionine ß-synthase(cbsa), which encodes the key enzyme of the transsulfuration pathway, as a mutated gene responsible for eye degeneration in multiple cavefish populations. The inactivation ofcbsaaffects eye development by inducing accumulation of the transsulfuration intermediate homocysteine and defects in optic vasculature, including aneurysms and eye hemorrhages, leading to oxygen deficiency. Our findings suggest that localized modifications in the circulatory system and hypoxia had important roles in the evolution of vestigial eyes in blind cavefish.
Identification of Fis1 interactors inToxoplasma gondiireveals a novel protein required for peripheral distribution of the mitochondrion
Authors: Jacobs Kylie , Charvat Robert , Arrizabalaga Gustavo
Published: October 2019

Toxoplasma gondii’s singular mitochondrion is very dynamic and undergoes morphological changes throughout the parasite’s life cycle. During parasite division, the mitochondrion elongates, enters the daughter cells just prior to cytokinesis and undergoes fission. Extensive morphological changes also occur as the parasite transitions from the intracellular to the extracellular environment. We show that treatment with the ionophore monensin causes reversible constriction of the mitochondrial outer membrane, and that this effect depends on the function of the fission related protein Fis1. We also observed that mislocalization of the endogenous Fis1 causes a dominant negative effect that affects the morphology of the mitochondrion. As this suggests Fis1 interacts with proteins critical for maintenance of mitochondrial structure, we performed various protein interaction trap screens. In this manner we identified a novel outer mitochondrial membrane protein, LMF1, which is essential for positioning of the mitochondrion in intracellular parasites. Normally, while inside a host cell, the parasite mitochondrion is maintained in a lasso shape that stretches around the parasite periphery where it has regions of coupling with the parasite pellicle, suggesting the presence of membrane contact sites. In intracellular parasites lacking LMF1 the mitochondrion is retracted away from the pellicle and instead is collapsed, as only normally seen in extracellular parasites. We show that this phenotype is associated with defects in parasite fitness and mitochondrial segregation. Thus, LMF1 is necessary for mitochondrial association with the parasite pellicle during intracellular growth and proper mitochondrial morphology is a prerequisite for mitochondrial division.

IMPORTANCE

Toxoplasma gondiiis an opportunistic pathogen that can cause devastating tissue damage in the immunocompromised and the congenitally infected. Current therapies are not effective against all life stages of the parasite and many cause toxic effects. The single mitochondrion of this parasite is a validated drug target and it changes its shape throughout its life cycle. When the parasite is inside of a cell, the mitochondrion adopts a lasso shape that lies in close proximity to the pellicle. The functional significance of this morphology is not understood nor are the proteins involved currently known. We have identified a protein that is required for proper mitochondrial positioning at the periphery and that likely plays a role in tethering this organelle. Loss of this protein results in dramatic changes to the mitochondrial morphology and significant parasite division and propagation defects. Our results give important insight into the molecular mechanisms regulating mitochondrial morphology.
Specific decreasing of Na+ channel expression on the lateral membrane of cardiomyocytes causes fatal arrhythmias in Brugada syndrome
Authors: Tsumoto Kunichika , Ashihara Takashi , Naito Narumi , Shimamoto Takao , Amano Akira , Kurata Yasutaka , Kurachi Yoshihisa
Published: October 2019

One phenotypic feature of Brugada syndrome (BrS) is slowed conduction due to the reduction (loss-of-function) of Na+ channels. In contrast, recent clinical observations in BrS patients highlighted the poor correlation between the phenotype (typical ECG change or lethal arrhythmia) and the genotype (SCN5A mutation). Inspired by our previous theoretical study which showed that reduced Na+ channels in the lateral membrane (LM) of ventricular myocytes caused the slowing of conduction under myocardial ischemia, we hypothesized that a loss-of-function of Na+ channels caused by the decreases in Na+ channel expression within myocytes leads to phase-2 reentry (P2R), the major triggering mechanism of lethal arrhythmias in BrS. We constructed an in silico human ventricular myocardial strand and ring models, and investigated the relationship between the subcellular Na+ channel distribution and P2R. Reducing Na+ channel expression in the LM of each myocyte caused not only the notch-and-dome but also loss-of-dome type action potentials and slowed conduction, both of which are typically observed in BrS patients. Furthermore, we showed that both the reduction in Na+ channels on the LM of each myocyte and tissue-level heterogeneity of Na+ channel expression were essential for P2R as well as P2R-mediated reentrant excitation. Our data suggest that the alteration in subcellular Na+ channel distribution together with a tissue-level heterogeneity of Na+ channels can cause arrhythmogenesis in BrS.
Cell type specific genetic regulation of gene expression across human tissues
Authors: Kim-Hellmuth Sarah , Aguet François , Oliva Meritxell , Muñoz-Aguirre Manuel , Wucher Valentin , Kasela Silva , Castel Stephane E. , Hamel Andrew R. , Viñuela Ana , Roberts Amy L. , Mangul Serghei , Wen Xiaoquan , Wang Gao , Barbeira Alvaro N. , Garrido-Martín Diego , Nadel Brian , Zou Yuxin , Bonazzola Rodrigo , Quan Jie , Brown Andrew , Martinez-Perez Angel , Soria José Manuel ,   GTEx Consortium, Getz Gad , Dermitzakis Emmanouil T. , Small Kerrin S. , Stephens Matthew , Xi Hualin S. , Im Hae Kyung , Guigó Roderic , Segrè Ayellet V. , Stranger Barbara E. , Ardlie Kristin G. , Lappalainen Tuuli
Published: October 2019

The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci (cis-QTLs) for the majority of genes across a wide range of human tissues. However, the interpretation of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. Here, we map interactions between computational estimates of cell type abundance and genotype to identify cell type interaction QTLs for seven cell types and show that cell type interaction eQTLs provide finer resolution to tissue specificity than bulk tissuecis-eQTLs. Analyses of genetic associations to 87 complex traits show a contribution from cell type interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.

One Sentence Summary

Estimated cell type abundances from bulk RNA-seq across tissues reveal the cellular specificity of quantitative trait loci.
Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes
Authors: Wagner Susan , Herrmannová Anna , Hronová Vladislava , Sen Neelam , Hannan Ross D. , Hinnebusch Alan G. , Shirokikh Nikolay E. , Preiss Thomas , Valášek Leoš Shivaya
Published: October 2019

Translational control targeting mainly the initiation phase is central to the regulation of gene expression. Understanding all of its aspects requires substantial technological advancements. Here we modified yeast Translational Complex Profile sequencing (TCP-seq), related to ribosome profiling, and adopted it for mammalian cells. Human TCP-seq, capable of capturing footprints of 40S subunits (40Ses) in addition to 80S ribosomes (80Ses), revealed that mammalian and yeast 40Ses distribute similarly across 5’UTRs indicating considerable evolutionary conservation. We further developed a variation called Selective TCP-seq (Sel-TCP-seq) enabling selection for 40Ses and 80Ses associated with an immuno-targeted factor in yeast and human. Sel-TCP-seq demonstrated that eIF2 and eIF3 travel along 5’UTRs with scanning 40Ses to successively dissociate upon start codon recognition. Manifesting the Sel-TCP-seq versatility for gene expression studies, we also identified four initiating 48S conformational intermediates, provided novel insights into ATF4 and GCN4 mRNA translational control, and demonstrated co-translational assembly of initiation factor complexes.
Unconventional kinetochore kinases KKT10/19 promote the metaphase to anaphase transition in Trypanosoma brucei
Authors: Ishii Midori , Akiyoshi Bungo
Published: October 2019

The kinetochore is a macromolecular protein complex that drives chromosome segregation in eukaryotes. Unlike most eukaryotes that have canonical kinetochore proteins, evolutionarily divergent kinetoplastids such as Trypanosoma brucei have unconventional kinetochore proteins. T. brucei also lacks a canonical spindle checkpoint system and it therefore remains unknown how mitotic progression is regulated in this organism. Here we characterized two paralogous kinetochore proteins with a CLK-like kinase domain, KKT10 and KKT19, which localize at kinetochores in metaphase but disappear at the onset of anaphase. We found that these proteins are functionally redundant. Double knockdown of KKT10/19 led to a significant delay in the metaphase to anaphase transition. A kinase-dead mutant of KKT10 failed to rescue the KKT10/19 depletion phenotype, suggesting that its kinase activity is essential. We also found that phosphorylation of two kinetochore proteins KKT4 and KKT7 depends on KKT10/19 in vivo. Finally, we showed that the N-terminal part of KKT7 directly interacts with KKT10 and that kinetochore localization of KKT10 depends not only on KKT7 but also on the KKT8 complex. Our results reveal that kinetochore localization of KKT10/19 is tightly controlled to regulate the metaphase to anaphase transition in T. brucei.

Trypanosoma brucei has unique kinetochore proteins and lacks a canonical spindle checkpoint system. How mitotic progression is regulated in this organism remains unclear. Here we show that two redundant protein kinases KKT10/19 promote the metaphase to anaphase transition.
A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila
Authors: Zappia Maria Paula , de Castro Lucia , Ariss Majd M. , Islam Abul B.M.M.K. , Frolov Maxim V
Published: October 2019

InDrosophila, the wing disc-associated adult muscle precursors (AMPs) give rise to the fibrillar indirect flight muscles (IFM) and the tubular direct flight muscles (DFM). To understand early transcriptional events underlying this muscle diversification, we performed single cell RNA-sequencing experiments and built a cell atlas of AMPs associated with third instar larval wing disc. Our analysis identified distinct transcriptional signatures for IFM and DFM precursors that underlie the molecular basis of their divergence. The atlas further revealed various states of differentiation of AMPs, thus illustrating previously unappreciated spatial and temporal heterogeneity among them. We identified and validated novel markers for both IFM and DFM precursors at various states of differentiation by immunofluorescence and genetic tracing experiments. Finally, we performed a systematic genetic screen using a panel of markers from the reference cell atlas as an entry point and found a novel gene,Ama, which is functionally important in muscle development. Thus, our work provides a framework of leveraging scRNA-seq for gene discovery and therefore, this strategy can be applied to other scRNA-seq datasets.
Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring required for female reproductive behaviors inDrosophila
Authors: Nallasivan Mohanakarthik P. , Haussmann Irmgard U. , Civetta Alberto , Soller Matthias
Published: October 2019

The post-mating response induced by male-derived sex-peptide inDrosophilafemales is a well-established model to elucidate how complex innate behaviors are hard-wired into the brain. Here, we found that the channel nuclear pore proteinNup54gene is essential for the sex-peptide response as viable mutant alleles do not lay eggs and reduce receptivity upon sex-peptide exposure. Nup54 directs correct wiring of few adult brain neurons that expresspickpocketand are required for egg laying, but channel Nups also mediate sexual differentiation and male X-chromosome dosage compensation. Consistent with links of Nups to speciation, the Nup54 promoter is a hot spot for rapid evolution and promoter variants alter expression in transgenes. These results implicate altered expression of Nup54 to the onset of speciation processes leading to changes in neuronal wiring and sexual differentiation as a response to sexual conflict arising from male-derived SP to direct the female post-mating response.
Polyglutamine-related aggregates serve as a potent antigen source for cross presentation by dendritic cells
Authors: Tabachnick-Cherny Shira , Berko Dikla , Pinto Sivan , Curato Caterina , Wolf Yochai , Porat Ziv , Karmona Rotem , Tirosh Boaz , Jung Steffen , Navon Ami
Published: October 2019

Protective MHC-I dependent immune responses require an overlap between repertoires of proteins directly presented on target cells and cross-presented by professional antigen presenting cells (APC), specifically dendritic cells (DCs). How stable proteins that rely on DRiPs for direct presentation are captured for cell-to-cell transfer remains enigmatic. Here we address this issue using a combination ofin vitroandin vivoapproaches involving stable and unstable versions of ovalbumin model antigens displaying DRiP-dependent and -independent antigen presentation, respectively. Apoptosis, but not necrosis of donor cells was found associated with robust p62-dependent global protein aggregate formation and captured stable proteins permissive for DC cross-presentation. Potency of aggregates to serve as antigen source was directly demonstrated using polyglutamine-equipped model substrates. Collectively, our data implicate global protein aggregation in apoptotic cells as a mechanism that ensures the overlap between MHC-I epitopes presented directly or cross-presented by APC and demonstrate the unusual ability of DC to process stable protein aggregates.

Protective T cell immunity relies on the overlap of the antigen repertoire expressed by cells and the repertoire presented by dendritic cells that are required to trigger naïve T cells. We suggest a mechanism that contributes to ensure this antigenic overlap. Our findings demonstrate that upon apoptosis stable proteins are aggregated in p62-dependent pathway and that dendritic cells are capable to efficiently process these aggregates to retrieve antigens for T cell stimulation.
Transcriptional analysis of wheat seedlings inoculated with Fusarium culmorum under continual exposure to disease defence inductors
Authors: Antalová Zuzana , Bleša Dominik , Martinek Petr , Matušinsky Pavel
Published: October 2019

A facultative parasite of cereals, Fusarium culmorum is a soil-, air- and seed-borne fungus causing foot and root rot, fusarium seedling blight, and especially Fusarium head blight, a spike disease leading to decreased yield and mycotoxin contamination of grain. In the present study, we tested changes in expression of wheat genes (B2H2, ICS, PAL, and PR2) involved in defence against diseases. We first compared expression of the analysed genes in seedlings of non-inoculated and artificially inoculated wheat (variety Bohemia). The second part of the experiment compared expression of these genes in seedlings grown under various treatment conditions. These treatments were chosen to determine the effects of prochloraz, sodium bicarbonate, ergosterol, aescin and potassium iodide on expression of the analysed defence genes. In addition to the inoculated and non-inoculated cultivar Bohemia, we examined two other varieties of wheat with contrasting resistance to Fusarium sp. infection. These were the blue aleurone layer variety Scorpion that is susceptible to Fusarium sp. infection and variety V2-49-17 with yellow endosperm and partial resistance to Fusarium sp. infection. In this manner, we were able to compare potential effects of inductors upon defence gene expression among three varieties with different susceptibility to infection but also between inoculated and non-inoculated seedlings of a single variety. The lowest infection levels were detected in the sodium bicarbonate treatment. Sodium bicarbonate had not only negative influence on Fusarium growth but also positively affected expression of plant defence genes. Expression of the four marker genes shown to be important in plant defence was significantly affected by the treatments. The greatest upregulation in comparison to the water control was identified under all treatments for the B2H2 gene. Only expression of PAL under the ergosterol and prochloraz treatments were not statistically significant.