bluuebunny/crossref_metadata_2025 huggingface dataset:
A comprehensive proteomic SWATH-MS workflow for profiling blood extracellular vesicles: a new avenue for glioma tumour surveillance
Authors: Hallal Susannah , Azimi Ali , Wei Heng , Ho Nicholas , Lee Maggie , Sim Hao-Wen , Sy Joanne , Shivalingam Brindha , Buckland Michael E. , Kaufman Kimberley L.
Published: March 2020

There is a real need for biomarkers that can indicate glioma disease burden and inform clinical management, particularly in the recurrent glioblastoma (GBM; grade IV glioma) setting where treatment-associated brain changes can confound current and expensive tumour surveillance methods. In this regard, extracellular vesicles (EVs; 30-1000 nm membranous particles) hold major promise as robust tumour biomarkers. GBM-EVs encapsulate molecules that reflect the identity and molecular state of their cell-of-origin and cross the blood-brain-barrier into the periphery where they are readily accessible. Despite the suitability of circulating-EVs for GBM biomarker discovery, sample complexity has hindered comprehensive quantitative proteomic studies. Here, sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) was used in conjunction with a targeted data extraction strategy to comprehensively profile circulating-EVs isolated from plasma. Plasma-EVs sourced from pre-operative glioma II-IV patients (n=41) and controls (n=11) were sequenced by SWATH-MS, and the identities and absolute quantities of the proteins were extracted by aligning the SWATH-MS data against a custom glioma spectral library comprised of 8662 high confidence protein species. Overall, 4054 plasma-EV proteins were quantified across the cohorts, and putative circulating-EV biomarker proteins identified (adjustedp-value<0.05) included previously reported GBM-EV proteins identifiedin vitroand in neurosurgical aspirates. Principle component analyses showed that plasma-EV protein profiles clustered according to glioma subtype and WHO-grade, and plasma-EV proteins reflected the extent of glioma aggression. Using SWATH-MS, we describe the most comprehensive proteomic plasma-EV profiles for glioma and highlight the promise of this approach as an accurate and sensitive tumour monitoring method. Objective blood-based measurements of glioma tumour activity will support the implementation of next-generation, patient-centred therapies and are ideal surrogate endpoints for recurrent progression that would allow clinical trial protocols to be more dynamic and adapt to the individual patient and their cancer.
RPG: A low-cost, open-source, high-performance solution for displaying visual stimuli
Authors: Imbriotis Vivian , Ranson Adam , Connelly William M
Published: March 2020

The development of new high throughput approaches for neuroscience such as high-density silicon probes and 2-photon imaging have led to a renaissance in visual neuroscience. However, generating the stimuli needed to evoke activity in the visual system still represents a non-negligible difficulty for experimentalists. While several widely used software toolkits exist to deliver such stimuli, they all suffer from some shortcomings. Primarily, the hardware needed to effectively display such stimuli comes at a significant financial cost, and secondly, triggering and/or timing the stimuli such that it can be accurately synchronized with other devices requires the use of legacy hardware, further hardware, or bespoke solutions.

Here we present RPG, a Python package written for the Raspberry Pi, which overcomes these issues. Specifically, the Raspberry Pi is a low-cost, credit card sized computer with general purpose input/output pins, allowing RPG to be triggered to deliver stimuli and to provide real-time feedback on stimulus timing. RPG delivers stimuli at >60 frames per second and the feedback of frame timings is accurate to 10s of microseconds.

We provide a simple to use Python interface that is capable of generating drifting sine wave gratings, Gabor patches and displaying raw images/video.
Axial Elongation of Caudalized Human Organoids Mimics Neural Tube Development
Authors: Libby ARG , Joy DA , Elder NH , Bulger EA , Krakora MZ , Gaylord EA , Mendoza-Camacho F , Butts JC , McDevitt TC
Published: March 2020

Axial elongation of the neural tube is critical during mammalian embryogenesis to establish the anterior-posterior body axis1, but this process is difficult to interrogate directly because it occurs post-implantation2,3. Here we report an organoid model of neural tube extension by caudalized human pluripotent stem cell (hPSC) aggregates that recapitulates the morphologic and temporal gene expression patterns of neural tube development. Axially extending organoids consisting largely of longitudinally elongated neuroepithelial compartments also contained TBXT(+)SOX2(+) neuromesodermal progenitors, PAX6(+)nestin(+) neural progenitor populations, and MEOX1(+) paraxial mesoderm populations. Wnt agonism stimulated singular axial extensions in a dose-dependent manner, and elongated organoids displayed regionalized rostral-caudal HOX gene expression, with spatially distinct hindbrain (HOXB1) expression from brachial (HOXC6) and thoracic (HOXB9) regions. CRISPR-interference-mediated silencing of the TBXT, a downstream Wnt target, increased neuroepithelial compartmentalization and resulted in multiple extensions per aggregate. Further, knock-down of BMP inhibitors, Noggin and Chordin, induced elongation phenotypes that mimicked murine knockout models. These results indicate the potent morphogenic capacity of caudalized hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early nervous system development in humans.
Hedgehog produced by the Drosophila wing imaginal disc induces distinct expression responses in three target tissues
Authors: Hatori Ryo , Kornberg Thomas B.
Published: March 2020

Hedgehog (Hh) is an evolutionarily conserved signaling protein that has essential roles in animal development and homeostasis. We investigated Hh signaling in the region of the Drosophila wing imaginal disc that produces Hh and is near the tracheal air sac primordium (ASP) and myoblasts. Hh distributes in concentration gradients in the wing disc anterior compartment, ASP, and myoblasts and activates different sets of genes in each tissue. Some transcriptional targets of Hh signal transduction are common to the disc, ASP, and myoblasts, whereas others are tissue-specific. Signaling in the three tissues is cytoneme-mediated and cytoneme-dependent. We conclude that a single source of Hh in the wing disc regulates cell type-specific responses in three discreet target tissues.

Hedgehog produced by the wing imaginal disc signals to wing disc, myoblast and tracheal cells
The combination of mitogenic stimulation and cell cycle arrest induces senescence in equine and human cartilage explants
Authors: Copp Michaela E. , Flanders Margaret C. , Gagliardi Rachel , Gilbertie Jessica M. , Sessions Garrett A. , Chubinskaya Susanna , Loeser Richard F. , Schnabel Lauren V. , Diekman Brian O.
Published: March 2020

Objective

Cellular senescence is a phenotypic state characterized by stable cell-cycle arrest, enhanced lysosomal activity, and the secretion of inflammatory molecules and matrix degrading enzymes. Senescence has been implicated in osteoarthritis (OA) pathophysiology; however, the mechanisms that drive senescence induction in cartilage and other joint tissues are unknown. While numerous physiological signals are capable of initiating the senescence phenotype, one emerging theme is that growth-arrested cells convert to senescence in response to sustained mitogenic stimulation. The goal of this study was to develop anin vitroarticular cartilage explant model to investigate the mechanisms of senescence induction.

Design

This study utilized healthy articular cartilage derived from cadaveric equine stifles and human ankles. Explants were irradiated or treated with palbociclib to initiate cell cycle arrest, and mitogenic stimulation was provided by serum-containing medium (horse) and the inclusion of growth factors (human). The primary readout of senescence was a quantitative flow cytometry assay to detect senescence-associated β galactosidase activity (SA-β-gal).

Results

Irradiation of equine explants caused 25.39% of cells to express high levels of SA-β-gal, as compared to 3.82% in control explants (p=0.0031). For human cartilage, explants that received both mitogenic stimulation and cell cycle arrest showed increased rates of senescence induction as compared to baseline control (7.16% vs. 2.34% SA-β-gal high, p=0.0007).

Conclusions

Treatment of cartilage explants with mitogenic stimuli in the context of cell-cycle arrest reliably induces high levels of SA-β gal activity, which provides a physiologically relevant model system to investigate the mechanisms of senescence induction.
CROP: A CRISPR/Cas9 guide selection program based on mapping guide variants
Authors: Aprilyanto Victor , Aditama Redi , Tanjung Zulfikar Achmad , Utomo Condro , Liwang Tony
Published: March 2020

The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target propensity of guide RNAs and thereby allowing the user to select the optimum guides. The approach used by CROP involves generating substitution, deletion and insertion combinations which are then mapped into the reference genome. Based on these mapped variants, scoring and alignment are conducted and then reported as a table comprising the off-target propensity of all guide RNAs from a given gene sequence. The Python script for this program is freely available from:https://github.com/vaprilyanto/crop.
GTP-dependent formation of straight oligomers leads to nucleation of microtubules
Authors: Ayukawa Rie , Iwata Seigo , Imai Hiroshi , Kamimura Shinji , Hayashi Masahito , Ngo Kien Xuan , Minoura Itsushi , Uchimura Seiichi , Makino Tsukasa , Shirouzu Mikako , Shigematsu Hideki , Sekimoto Ken , Gigant Benoît , Muto Etsuko
Published: March 2020

Microtubule (MT) nucleation is essential for cellular activities, but its mechanism is not known because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. In cells, MTs are nucleated at tubulin concentrations significantly lower than those required for spontaneous nucleation in vitro. The high efficiency of nucleation is due to the synergistic effects of various cellular factors, but the underlying mechanism has not been clarified yet. Here, combining negative stain electron microscopy and kinetic analysis, we demonstrate that the formation of single-stranded straight oligomers with critical size is essential for nucleation in vitro. While the single-stranded oligomers of GTP-tubulin that form prior to MT nucleation show variable curvatures including a few straight oligomers, only curved oligomers are observed among the GDP-bound counterparts. The Y222F mutation in β-tubulin increases the proportion of straight oligomers and drastically accelerates MT nucleation. Our results support a model in which GTP binding causes a small shift in the distribution of oligomer curvature, generating a minor population of straight oligomers compatible with lateral association and further growth to MTs. Our study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.
Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques
Authors: Theis Kevin R. , Romero Roberto , Winters Andrew D. , Jobe Alan H. , Gomez-Lopez Nardhy
Published: March 2020

The prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony ofCutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.

IMPORTANCE

Microbial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of thein uterocolonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.
Model-based ordination of pin-point cover data: effect of management on dry heathland
Authors: Damgaard Christian , Hansen Rikke Reisner , Hui Francis K. C.
Published: March 2020

Recently, there has been an increasing interest in model-based approaches for the statistical modelling of the joint distribution of multi-species abundances. The Dirichlet-multinomial distribution has been proposed as a suitable candidate distribution for the joint species distribution of pin-point plant cover data and is here applied in a model-based ordination framework. Unlike most model-based ordination methods, both fixed and random effects are in our proposed model structured asp-dimensional vectors and added to the latent variables before the inner product with the species-specific coefficients. This changes the interpretation of the parameters, so that the fixed and random effects now measure the relative displacement of the vegetation by the fixed and random factors in thep-dimensional latent variable space. This parameterization allows statistical inference of the effect of fixed and random factors in vector space, and makes it easier for practitioners to perform inferences on species composition in a multivariate setting. The method was applied on plant pin-point cover data from dry heathlands that had received different management treatments (burned, grazed, harvested, unmanaged), and it was found that treatment have a significant effect on heathland vegetation both when considering plant functional groups or when the taxonomic resolution was at the species level.
Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods
Authors: Nasheri Neda , Harlow Jennifer , Chen Angela , Dussault Forest , Corneau Nathalie , Bidawid Sabah
Published: March 2020

Enteric viruses, such as human norovirus (NoV) and hepatitis A virus (HAV), are the major causes of foodborne illnesses worldwide. These viruses are shed in high numbers, have low infectious dose, and may remain infectious for weeks in the environment and food. While numerous viral survival studies have been conducted in fresh fruits and produce, limited information is available regarding viral survival and transmission in low moisture foods (LMF). LMFs are generally considered as ready-to-eat products, which undergo no or minimal pathogen reduction steps. However, numerous foodborne outbreaks associated with LMFs have been reported in recent years. The objective of this study was to examine the survival of foodborne viruses in LMFs during long-term storage at ambient temperature and to evaluate the efficacy of advanced oxidative process (AOP) treatment in the inactivation of these viruses. For this purpose, select LMFs such as pistachios, chocolate, and cereal were inoculated with HAV and the norovirus surrogates, murine norovirus (MNV) and feline calicivirus (FCV), then viral survival on these food matrices was measured over a four-week incubation at ambient temperature, by both plaque assay and droplet-digital RT-PCR (ddRT-PCR). We observed an approximately 0.5 log reduction in viral genome copies, and 1 log reduction in viral infectivity for all three tested viruses following storage of select inoculated LMFs for 4 weeks. Therefore, the present study shows that foodborne viruses can persist for long-time in LMFs. Next, we examined the inactivation efficacy of AOP treatment, which combines UV-C, ozone, and hydrogen peroxide vapor, and observed that while approximately 100% inactivation can be achieved for FCV, MNV, and HAV in chocolate, the inactivation efficiency diminishes to approximately 90% in pistachios and 70% in cereal. AOP treatment could therefore be a good candidate for the elimination of foodborne viruses from certain LMFs depending on the food matrix and surface of treatment.

Importance

Low moisture foods have been increasingly recognized as important vehicles of foodborne pathogens. In the present study, we demonstrated that foodborne viruses remain infectious during long-term storage on select low moisture foods. In addition, we evaluated the efficacy of an advanced oxidative process in the inactivation of foodborne viruses in low moisture foods. This research will help increase the safety of low moisture foods and reduce the number of foodborne illnesses due to contaminated products.
A bivariate zero-inflated negative binomial model and its applications to biomedical settings
Authors: Cho Hunyong , Liu Chuwen , Preisser John S. , Wu Di
Published: March 2020

Summary

The zero-inflated negative binomial (ZINB) distribution has been widely used for count data analyses in various biomedical settings due to its capacity of modeling excess zeros and overdispersion. When there are correlated count variables, a bivariate model is essential for understanding their full distributional features. For this purpose, we develop a Bivariate Zero-Inflated Negative Binomial (BZINB) model that has a simple latent variable framework and parameters with intuitive interpretations. Using this model, we examine two biomedical data examples where the counts are zero-inflated—single cell RNA sequencing (scRNA-seq) data and dental caries count indices. In scRNA-seq data example, a correlation between a pair of genes is estimated after adjusting for the effects of dropout events represented by excess zeros. In the dental caries data, we analyze how the treatment with Xylitol mints affects the marginal mean and other patterns of response manifested in the two dental caries traits. AnRpackage ‘bzinb’ is available on CRAN.
Circ_0005962 functions as an oncogene to aggravate non-small cell lung cancer progression via circ_0005962/miR-382-5p/PDK4 regulatory network
Authors: Zhang Zhihong , Shan Zhenxiu , Chen Rubin , Peng Xiaorong , Xu Bin , Xiao Liang , Zhang Guofei
Published: March 2020

Non-small cell lung cancer (NSCLC) is a leading threat to human lives with high incidence and mortality. Circular RNAs (circRNAs) were reported to play important roles in human cancers. The purpose of this study was to investigate the role of circ_0005962 and explore the underlying functional mechanisms. The expression of circ_0005962, miR-382-5p and pyruvate dehydrogenase kinase 4 (PDK4) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation and cell apoptosis were assessed by cell counting kit-8 (CCK-8) assay and flow cytometry assay, respectively. The protein levels of Beclin 1, light chain3 (LC3-II/LC3-I), PDK4, Cleaved Caspase 3 (C-caspase 3) and proliferating cell nuclear antigen (PCNA) were examined using western blot analysis. Glycolysis was determined according to the levels of glucose consumption and lactate production. The interaction between miR-382-5p and circ_0005962 or PDK4 was predicted by the online tool CircInteractome or starbase and verified by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Xenograft model was constructed to investigate the role of circ_0005962in vivo. circ_0005962 expressed with a high level in NSCLC tissues and cells. Circ_0005962 knockdown inhibited proliferation, autophagy, and glycolysis but promoted apoptosis in NSCLC cells. MiR-382-5p was targeted by circ_0005962, and its inhibition reversed the role of circ_0005962 knockdown. Besides, PDK4, a target of miR-382-5p, was regulated by circ_0005962 through miR-382-5p, and its overexpression abolished the effects of miR-382-5p reintroduction. Circ_0005962 knockdown suppressed tumor growthin vivo. Circ_0005962 knockdown restrained cell proliferation, autophagy, and glycolysis but stimulated apoptosis through modulating the circ_0005962/miR-382-5p/PDK4 axis. Our study broadened the insights into understanding the mechanism of NSCLC progression.
Identification and characterization of long noncoding RNAs and their association with acquisition of blood meal inCulex quinquefasciatus
Authors: Azlan Azali , Halim Mardani Abdul , Mohamad Faisal , Azzam Ghows
Published: March 2020

The Southern house mosquito,Culex quinquefasciatus(Cx. quinquefasciatus) is an important vector that transmit multiple diseases including West Nile encephalitis, Japanese encephalitis, St. Louis encephalitis and lymphatic filariasis. Long noncoding RNAs (lncRNAs) involve in many biological processes such development, infection, and virus-host interaction. However, there is no systematic identification and characterization of lncRNAs inCx. quinquefasciatus. Here, we report the first ever lncRNA identification inCx. quinquefasciatus. By using 31 public RNA-seq datasets, a total of 4,763 novel lncRNA transcripts were identified, of which 3,591, 569, and 603 were intergenic, intronic, and antisense respectively. Examination of genomic features revealed thatCx. quinquefasciatusshared similar characteristics with other species such as short in length, low GC content, low sequence conservation, and low coding potential. Furthermore, compared to protein-coding genes,Cx. quinquefasciatuslncRNAs had lower expression values, and tended to be expressed in temporally-specific fashion. In addition, weighted correlation network and functional annotation analyses showed that lncRNAs may have roles in blood meal acquisition of adult femaleCx. quinquefasciatusmosquitoes. This study presents the first systematic identification and analysis ofCx. quinquefasciatuslncRNAs and their association with blood feeding. Results generated from this study will facilitate future investigation on the function ofCx. quinquefasciatuslncRNAs.
A bHLH transcription factor (VfTT8) underlieszt2, the locus determining zero tannin content in faba bean (Vicia faba L.)
Authors: Gutierrez Natalia , Avila Carmen M. , Torres Ana M.
Published: March 2020

Faba bean (Vicia fabaL.) is an important protein-rich fodder crop widely cultivated in temperate areas. However, antinutritional compounds such as condensed tannins, limit the use of this protein source in monogastric feed formulations. Previous studies demonstrated that two recessive and complementary genes,zt1andzt2, control the absence of tannin and the white flower colour in faba bean. An ortholog of theMedicagoWD40 transcription factor, (TTG1) was reported to encode the zt1 phenotypes but the responsible gene for zt2 is still unknown. A candidate gene approach combined with linkage mapping, comparative genomics and gene expression has been used in this study to fine map thezt2genomic region and to identify the regulatory gene controlling both traits. Seventy-two genes, including 23 regulatory genes (MYB and bHLH) predicted to be associated with anthocyanin expression together with WRKY proteins were screened and genotyped in three mapping populations. The linkage groups constructed identified the regulatory gene,TRANSPARENT TESTA8(TT8), encoding a basic helix-loop-helix transcription factor (bHLH), as the best candidate forzt2. This finding was supported by qPCR analyses and further validated in different genetic backgrounds. Accordingly, VfTT8 was down-regulated in white flowered types, in contrast to the levels of expression in wild genotypes. Our results provide new insights on the regulatory mechanisms for tannin biosynthesis in faba bean and will favour the development of an ultimate zt2 diagnostic marker for the fast generation of new value-added cultivars free of tannins and improved nutritional value.
Reactive oxygen species as important regulators of cell division
Authors: Qi Weiliang , Ma Li , Wang Fei , Wang Ping , Wu Junyan , Jin Jiaojiao , Liu Songqing , Sun Wancang
Published: March 2020

Currently, the role of reactive oxygen species (ROS) in plant growth is a topic of interest. In this study, we discuss the role of ROS in cell division. We analyzed ROS’ impact on the stiffness of plant cell walls and whether ROS play an important role inBrassica napus’ ability to adapt to cold stress. Cultivated sterile seedlings and calli of cold-tolerant cultivar 16NTS309 were subjected to cold stress at 25°C and 4°C, respectively. Under normal conditions, O2.−mainly accumulated in the leaf edges, shoot apical meristem, leaf primordia, root tips, lateral root primordia, calli of meristematic nodular tissues, cambia, vascular bundles and root primordia, which are characterized by high division rates. After exposure to cold stress, the malondialdehyde and ROS (O2.−) contents in roots, stems and leaves of cultivar 16NTS309 were significantly higher than under non-cold conditions (P< 0.05). ROS (O2.−) were not only distributed in these zones, but also in other cells, at higher levels than under normal conditions. A strong ROS-based staining appeared in the cell wall. The results support a dual role for apoplastic ROS, in which they have direct effects on the stiffness of the cell wall, because ROS cleave cell-wall, and act as wall loosening agents, thereby either promoting or restricting cellular division. This promotes the appearance of new shoots and a strong root system, allowing plants to adapt to cold stress.
Are dogs with congenital hearing and/or vision impairments so different from sensory normal dogs? A survey of demographics, morphology, health, behaviour, communication, and activities
Authors: Savel Sophie , Sombé Patty
Published: March 2020

The births of domestic dogs with pigment deletion and associated congenital hearing and/or vision impairments are increasing, as a result of mutations of certain genes expressing popular coat colour patterns (Merle, piebald, Irish spotting). The future of these dogs is often pessimistic (early euthanasia or placement in rescues/fosters, lack of interactions and activities for adults). These pessimistic scenarios result from popular assumptions predicting that dogs with congenital hearing/vision impairments exhibit severe Merle-related health troubles (cardiac, skeletal, neurological), impairment-related behavioural troubles (aggressiveness, anxiety), and poor capacities to communicate, to be trained, and to be engaged in leisure or work activities. However, there is no direct scientific testing, and hence no evidence or refutation, of these assumptions. We therefore addressed an online questionnaire to owners of 223 congenitally sensory impaired (23 vision impaired, 63 hearing impaired, 137 hearing and vision impaired) and 217 sensory normal dogs from various countries. The sensory normal cohort was matched in age, lifetime with owner, breed and sex with the sensory impaired cohort, and was used as a baseline. The questionnaire assessed demographics, morphology, sensory impairments, health and behavioural troubles, activities, and dog-owner communication. Most hearing and vision impaired dogs exhibited abnormal pigment deletion in their coat and irises. Vision impaired dogs additionally exhibited ophthalmic abnormalities related to Merle. The results refute all above-listed assumptions, except for neurological troubles. We however suggest that reports of neurological troubles could be partially accounted for by lacks of diagnosis of breed-related drug sensitivity and impairment-related compulsive behaviours. Results about communication and activities are particularly optimistic. The need for future studies of numerous dogs from various breeds tested for Merle, piebald and medical-drug-resistance genes, and the beneficial effects that present and future research may have on the future of sensory impaired dogs, are discussed.
Specialised functions of two common plasmid mediated toxin-antitoxin systems,ccdABandpemIK, inEnterobacteriaceae
Authors: Wu Alma Y. , Kamruzzaman Muhammad , Iredell Jonathan R.
Published: March 2020

Toxin-antitoxin systems (TAS) are commonly found on bacterial plasmids and are involved in plasmid maintenance. Even though the same TAS are present in a variety of plasmid types and bacterial species, differences in their sequences, expression and functions are not well defined. Here, we aimed to identify commonly occurring plasmid TAS inEscherichia coliandKlebsiella pneumoniaeand compare the sequence, expression and plasmid stability function of their variants. 27 putative type II TAS were identified from 1063 plasmids ofKlebsiella pneumoniaein GenBank. Among these,ccdABandpemIKwere found to be most common, also occurring in plasmids ofE. coli. Comparisons ofccdABvariants, taken fromE. coliandK. pneumoniae, revealed sequence differences, whilepemIKvariants from IncF and IncL/M plasmids were almost identical. Similarly, the expression and plasmid stability functions ofccdABvariants varied according to the host strain and species, whereas the expression and functions ofpemIKvariants were consistent among host strains. The specialised functions of some TAS may determine the host specificity and epidemiology of major antibiotic resistance plasmids.
The Role of Potassium and Host Calcium Signaling inToxoplasma gondiiegress
Authors: Vella Stephen A. , Moore Christina A. , Li Zhu-Hong , Hortua Triana Miryam A. , Potapenko Evgeniy , Moreno Silvia N J
Published: March 2020

Toxoplasma gondii, an obligate intracellular parasite, is capable of invading virtually any nucleated cell. Ca2+signaling is universal and bothT. gondiiand its mammalian host cell will utilize Ca2+signaling to stimulate diverse cellular functions. Egress ofT. gondiifrom the host cell is an essential step for the infection cycle ofT. gondiiand a cytosolic Ca2+increase initiates the Ca2+signaling cascade that culminates in stimulation of motility and egress. In this work we demonstrate that intracellularT. gondiiis capable of taking up Ca2+from the host cytoplasm when this concentration is increased during host signaling events. Both intracellular and extracellular Ca2+sources are important to reach a threshold of cytosolic Ca2+needed for a successful egress. Two peaks of Ca2+were observed in single parasites that egressed with the second peak resulting from Ca2+influx. We patched infected host cells to allow a precise delivery of exact concentrations of Ca2+for stimulating motility and egress. Using this approach, we found that low potassium concentration modulates but do not trigger host cell egress. This is the first study using whole-cell patches to study the role of ions such as K+and Ca2+inT. gondiiegress.
Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize
Authors: Aguirre-Liguori Jonás A. , Luna-Sánchez Javier A. , Gasca-Pineda Jaime , Eguiarte Luis E.
Published: March 2020

Massive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS,FIS,FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics.FISwas particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.
TagSeqTools: a flexible and comprehensive analysis pipeline for NAD tagSeq data
Authors: Zhong Huan , Cai Zongwei , Yang Zhu , Xia Yiji
Published: March 2020

NAD tagSeq has recently been developed for the identification and characterization of NAD+-capped RNAs (NAD-RNAs). This method adopts a strategy of chemo-enzymatic reactions to label the NAD-RNAs with a synthetic RNA tag before subjecting to the Oxford Nanopore direct RNA sequencing. A computational tool designed for analyzing the sequencing data of tagged RNA will facilitate the broader application of this method. Hence, we introduce TagSeqTools as a flexible, general pipeline for the identification and quantification of tagged RNAs (i.e., NAD+-capped RNAs) using long-read transcriptome sequencing data generated by NAD tagSeq method. TagSeqTools comprises two major modules,TagSeekfor differentiating tagged and untagged reads, andTagSeqQuantfor the quantitative and further characterization analysis of genes and isoforms. Besides, the pipeline also integrates some advanced functions to identify antisense or splicing, and supports the data reformation for visualization. Therefore, TagSeqTools provides a convenient and comprehensive workflow for researchers to analyze the data produced by the NAD tagSeq method or other tagging-based experiments using Oxford nanopore direct RNA sequencing. The pipeline is available athttps://github.com/dorothyzh/TagSeqTools, under Apache License 2.0.
Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability
Authors: Chang Roger L. , Stanley Julian A. , Robinson Matthew C. , Sher Joel W. , Li Zhanwen , Chan Yujia A. , Omdahl Ashton R. , Wattiez Ruddy , Godzik Adam , Matallana-Surget Sabine
Published: March 2020

Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS-susceptibility essential. The radiation-resistant bacteriumDeinococcus radioduransaccumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ-irradiation inEscherichia coliandD. radioduransat multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS-susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS-resistance of theD. radioduransproteome. Our model predicts proteome maintenance machinery and proteins protecting against ROS are more resistant inD. radiodurans. Our findings substantiate that protein-intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.

One Sentence Summary

Proteins differ in intrinsic susceptibility to oxidation, a mode of evolutionary adaptation for stress tolerance in bacteria.
The evolutionary history of Neandertal and Denisovan Y chromosomes
Authors: Petr Martin , Hajdinjak Mateja , Fu Qiaomei , Essel Elena , Rougier Hélène , Crevecoeur Isabelle , Semal Patrick , Golovanova Liubov V. , Doronichev Vladimir B. , Lalueza-Fox Carles , de la Rasilla Marco , Rosas Antonio , Shunkov Michael V. , Kozlikin Maxim B. , Derevianko Anatoli P. , Vernot Benjamin , Meyer Matthias , Kelso Janet
Published: March 2020

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4andDenisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a,Mezmaiskaya 2andEl Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.
Complete sequences ofSchizosaccharomyces pombesubtelomeres reveal multiple patterns of genome variation
Authors: Kaji Takuto , Oizumi Yusuke , Tashiro Sanki , Takeshita Yumiko , Kanoh Junko
Published: March 2020

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeastSchizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess singleSHregions. Whole sequences ofSHregions revealed that eachSHregion consists of two distinct parts: the telomere-proximal part with mosaics of multiple common segments showing high variation among subtelomeres and strains, and the telomere-distal part showing high sequence similarity among subtelomeres with some insertions and deletions. The newly sequencedSHregions showed differences in nucleotide sequences and common segment composition compared to those in theS. pombegenome database (PomBase), which is in striking contrast to the regions outside ofSH, where mutations are rarely detected. Furthermore, we identified new subtelomeric RecQ-type helicase genes,tlh3andtlh4, which add to the already knowntlh1andtlh2, and found that thetlh1–4genes show high sequence variation. Our results indicate thatSHsequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins
Authors: Panda Arup , Tuller Tamir
Published: March 2020

Intrinsically disordered proteins (IDPs) were recognized as an important class of proteins in all domains of life for their functional importance. However, how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly known. Randomly generated sequences are free of any selective constraints thus these sequences are commonly used as null models. Considering different types of random protein models here we seek to understand how disorder potential of natural eukaryotic and prokaryotic proteins differs from random sequences. Comparing proteome-wide disorder content between real and random sequences of 12 model organisms we noticed that while in eukaryotes natural sequences tend to be more disordered than random sequences prokaryotes follow an opposite trend. By analyzing position-wise disorder profile, here we showed that there is a general trend of higher disorder near the N and C-terminal regions of eukaryotic proteins as compared to the random models; however, either no or a weak such trend was found in prokaryotic proteins. Moreover here we showed that this preference is not due to the biases either in the amino acid or nucleotide composition or other factors at the respective sites. Instead, these regions were found to be endowed with a higher fraction of protein-protein binding sites suggesting their functional importance. Here, we proposed various explanations for this pattern such as improving the efficiency of protein-protein interaction, ribosome movement, and post-translational modification,etc.However, further studies are needed to clearly understand the biophysical mechanisms causing the trend.
A redetermination of the crystal structure of the mannitol complex NH4[Mo2O5(C6H11O6)]·H2O: hydrogen-bonding scheme and Hirshfeld surface analysis
Authors: Mirzaei Masoud , Tahmasebi Morteza , Mague Joel T.
Published: March 2020

The redetermined structure [for the previous study, see: Godfrey & Waters (1975). Cryst. Struct. Commun.
4, 5–8] of ammonium μ-oxido-μ-[1,5,6-trihydroxyhexane-2,3,4-tris(olato)]bis[dioxidomolybdenum(V)] monohydrate, NH4[Mo2(C6H11O6)O5]·H2O, was obtained from an attempt to prepare a glutamic acid complex from the [Co2Mo10H4O38]6− anion. Subsequent study indicated the complex arose from a substantial impurity of mannitol in the glutamic acid sample used. All hydrogen atoms have been located in the present study and the packing displays N—H...O, O—H...O and C—H...O hydrogen bonds. A Hirshfeld surface analysis was also performed.
Crystal structure of 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane bis[chloridochromate(VI)] dichloride from synchrotron X-ray data
Authors: Moon Dohyun , Choi Jong-Ha
Published: March 2020

The crystal structure of title compound, (C14H36N4)[CrO3Cl]2Cl2, has been determined by synchrotron radiation X-ray crystallography at 220 K. The macrocyclic cation lies across a crystallographic inversion center and hence the asymmetric unit contains one half of the organic cation, one chlorochromate anion and one chloride anion. Both the Cl− anion and chlorochromate Cl atom are involved in hydrogen bonding. In the crystal, hydrogen bonds involving the 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane (TMC) N—H groups and C—H groups as donor groups and three O atoms of the chlorochromate and the chloride anion as acceptor groups link the components, giving rise to a three-dimensional network.
GYY4137 exhibits anti‐atherosclerosis effect in apolipoprotein E (−/−) mice via PI3K/Akt and TLR4 signalling
Authors: Zheng Yaofu , Lv Ping , Huang Jun , Ke Junsong , Yan Jumei
Published: March 2020

Hydrogen sulphide (H2S) had been suggested to be involved in the pathogenesis of atherosclerosis, but the underlying molecular mechanisms are poorly understood. In this study, we aimed to investigate the anti‐atherosclerosis effect of morpholin‐4‐ium‐methoxyphenyl‐morpholino‐phosphinodithioate (GYY4137) in RAW264.7 cell‐derived foam cells formation and in the atherosclerotic plaque of ApoE−/− mice fed with a high‐fat diet, and study the underlying mechanisms of phosphatidylinositol 3‐kinase (PI3K), serine/ threonine kinase (Akt) and Toll‐like receptor 4 (TLR4) signalling pathway. In the ApoE−/− mice fed with a high‐fat diet, daily GYY4137 administration for 8 weeks effectively decreased carotid atherosclerotic plaque area and the volume of foam cells, regulated the lipid metabolism, down‐regulated the pro‐inflammatory cytokine levels and up‐regulated the anti‐inflammatory cytokines levels. Consistent with these findings, in the RAW264.7 cell‐derived foam cells, GYY4137 ameliorated foam cell formation in vitro, and decreased the expression of pro‐inflammatory cytokines. Furthermore, our studies showed that GYY4137 could activate the PI3K/Akt signalling pathway and consequently reduce the expression of TLR4 to be critical for foam cell formation, preventing atherosclerotic plaque formation and destabilization. LY294002, a PI3K inhibitor, could inhibit the phosphorylation of Akt and reduce the expression of TLR4, thus reduce the foam cell source and lipid volume in the unstable plaque tissue. Our results suggest that GYY4137 is an attractive novel therapeutic reagent for atherosclerosis diseases. This mechanism may be partially attributed to regulating the PI3K/Akt/TLR4 signalling pathway.
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
Authors: Lood Cédric , Danis‐Wlodarczyk Katarzyna , Blasdel Bob G. , Jang Ho Bin , Vandenheuvel Dieter , Briers Yves , Noben Jean‐Paul , van Noort Vera , Drulis‐Kawa Zuzanna , Lavigne Rob
Published: March 2020

Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage‐bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA‐Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non‐coding RNAs (ncRNAs) and 93 virion‐associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA‐Seq revealed a gradual take‐over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA‐pncB1‐nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene‐sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage‐encoded hijacking mechanisms.