bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Portrait of North-West Indian Population based on X ChromosomeAluInsertion Markers
Authors: Singh Gagandeep , Srinivas Yellapu 
Published: September 2019

AbstractAluinsertion elements represent the largest family of Short Interspersed Nuclear Elements (SINEs) in the human genome. PolymorphicAluelements are stable and conservative markers that can potentially be applied in studying human origin and relationships as they are identical by descent and known for lack of insertion in ancestral state. In this study, 10Aluinsertions of X chromosome were utilized to tabulate allele frequency distributions and compute parameters of forensic relevance in the 379 unrelated healthy individuals belonging to four different ethnic groups (Brahmin, Khatri, Jat Sikh and Scheduled Caste) of North-West India. Furthermore, theDAandFSTvalues of pairwise interpopulation differentiations, multidimensional scaling and Bayesian structure clustering analysis were also computed to probe the genetic relationships between present studied populations and with other 21 reference populations. Six X-Aluinsertions were observed to be polymorphic in all the populations, whereas the others appeared as monomorphic in at least one studied population. The insertion allele frequencies were in the range of 0.15 at Ya5DP3 to 0.9888 at Ya5DP77. Most polymorphicAluelements showed moderate to low genetic diversity. The maximum value of power of exclusion (PE) was 0.1645 at Ya5NBC37 marker, whereas the minimum was 0.0001 at Ya5DP4 locus, implying the significance of X chromosomeAluelements in forensic genetic investigations. Genetic relationships agree with a geographical pattern of differentiation among populations. The results of present study establish that X chromosomeAluelements comprise a reliable set of genetic markers useful to describe human population relationships and structure.
Urban birdsongs: higher minimum song frequency of an urban colonist persists in a common garden experiment
Authors: Reichard Dustin G. , Atwell Jonathan W. , Pandit Meelyn M. , Cardoso Gonçalo C. , Price Trevor D. , Ketterson Ellen D. 
Published: September 2019

AbstractEnvironmental changes caused by urbanization and noise pollution can have profound effects on acoustic communication. Many organisms use higher sound frequencies in urban environments with low-frequency noise, but the developmental and evolutionary mechanisms underlying these shifts are less clear. We used a common garden experiment to ask whether changes in minimum song frequency observed 30 years after a songbird colonized an urban environment are a consequence of behavioral flexibility or canalized changes that occur early in development. We captured male juvenile dark-eyed juncos (Junco hyemalis thurberi) from two recently diverged populations (urban and mountain) soon after they reached independence (aged 25-40 days), raised them in identical indoor aviaries, and studied their songs at an age of three years. We found that the large population difference in minimum frequency observed in the field persisted undiminished in the common garden despite the absence of noise. We also found some song sharing between the common garden and natal field populations, indicating that early song memorization before capture could contribute to the persistent song differences in adulthood. These results are the first to show that frequency shifts in urban birdsong are maintained in the absence of noise by genetic evolution and/or early life experiences.
Endogenous esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose
Authors: Seo Hyeongmin , Nicely Preston N. , Trinh Cong T. 
Published: September 2019

ABSTRACTMedium chain esters are potential drop-in biofuels and versatile chemicals. Currently, these esters are largely produced by the conventional chemical process that uses harsh operating conditions and requires high energy input. Alternatively, the microbial conversion route has recently emerged as a promising platform for sustainable and renewable ester production. The ester biosynthesis pathways can utilize either esterases/lipases or alcohol acyltransferase (AAT), but the AAT-dependent pathway is more thermodynamically favorable in aqueous fermentation environment. Even though cellulolytic thermophiles such as Clostridium thermocellum harboring the engineered AAT-dependent pathway can directly convert lignocellulosic biomass into esters, the production is currently not efficient and requires optimization. One potential bottleneck is the ester degradation caused by the endogenous carbohydrate esterases (CEs) whose functional roles are poorly understood. In this study, we developed a simple, high-throughput colorimetric assay to screen the endogenous esterases of C. thermocellum responsible for ester hydrolysis. We identified, characterized, and disrupted two critical endogenous esterases that significantly contributes to isobutyl acetate degradation in C. thermocellum. We demonstrated that not only did the engineered esterase-deficient strain alleviate ester hydrolysis but also helped improve isobutyl acetate production while not affecting its robust metabolism for effective cellulose assimilation.IMPORTANCECarbohydrate esterases (CEs) are important enzymes in the deconstruction of lignocellulosic biomass by the cellulolytic thermophile C. thermocellum, yet some are potential ester degraders in a microbial ester production system. Currently, the functional roles of CEs for hydrolyzing medium chain esters and negatively affecting the ester microbial biosynthesis are not well understood. This study discovered novel CEs responsible for isobutyl acetate degradation in C. thermocellum and hence identified one of the critical bottlenecks for direct conversion of lignocellulosic biomass into esters.
An exploration of ambigrammatic sequences in narnaviruses
Authors: DeRisi Joseph L. , Huber Greg , Kistler Amy , Retallack Hanna , Wilkinson Michael , Yllanes David 
Published: September 2019

ABSTRACTNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.
Evolutionary route of resistant genes in Staphylococcus aureus
Authors: John Jiffy , George Sinumol , Nori Sai Ravi Chandra , Nelson-Sathi Shijulal 
Published: September 2019

AbstractMulti-drug resistant S. aureus is a leading concern worldwide. Coagulase-Negative Staphylococci (CoNS) are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-S. aureus reference bacterial genomes. Our results reveals that S. aureus has a large open pan-genome where 97 (55%) of its known resistant related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides and aminoglycosides. However, the physically linked mec-box genes (MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec resistant gene phylogenies reveals that genes such as blaZ, ble, kmA and tetK that are responsible for beta-lactam, bleomycin, kanamycin and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec encoded resistant genes in S. aureus, mostly present in plasmid are laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.
Improving Social Interactive Learning through Dual Brain Stimulation
Authors: Pan Yafeng , Novembre Giacomo , Song Bei , Zhu Yi , Hu Yi 
Published: September 2019

AbstractSocial interactive learning denotes the ability to acquire new information from a conspecific – a prerequisite for cultural evolution and survival. As inspired by recent neurophysiological research, here we tested whether social interactive learning can be augmented by exogenously synchronizing oscillatory brain activity across an instructor and a learner engaged in a naturalistic song-learning task. We used a dual brain stimulation protocol entailing the trans-cranial delivery of synchronized electric currents in two individuals simultaneously. When we stimulated inferior frontal brain regions, with 6 Hz alternating currents being in-phase between the instructor and the learner, the dyad exhibited spontaneous and synchronized body movement. Remarkably, this stimulation also led to enhanced learning performance. A mediation analysis further disclosed that interpersonal movement synchrony acted as a partial mediator of the effect of dual brain stimulation on learning performance, i.e. possibly facilitating the effect of dual brain stimulation on learning. Our results provide a causal demonstration that inter-brain synchrony is a sufficient condition to improve real-time information transfer between pairs of individuals.SignificanceThe study of social behavior, including but not limited to social learning, is undergoing a paradigm shift moving from single- to multi-person brain research. Yet, nearly all evidence in this area is purely correlational: inter-dependencies between brains’ signals are used to predict success in social behavior. For instance, inter-brain synchrony has been shown to be associated with successful communication, cooperation, and joint attention. Here we took a radically different approach. We stimulated two brains simultaneously, hence manipulating inter-brain synchrony, and measured the resulting effect upon behavior in the context of a social learning task. We report that frequency- and phase-specific dual brain stimulation can lead to the emergence of spontaneous synchronized body movement between an instructor and a learner. Remarkably, this can also augment learning performance.
MicroRNA-210 Knockout Alters Dendritic Density and Behavioural Flexibility
Authors: Watts Michelle , Williams Gabrielle , Lu Jing , Nithianantharajah Jess , Claudianos Charles 
Published: September 2019

AbstractMicroRNAs exert post-transcriptional control over eukaryotic genomes and are integral for regulating complex functions in neurodevelopment, neuroplasticity and cognitive processing. The microRNA-210 (miR-210) is a highly-conserved, hypoxia-regulated miRNA that has been shown to be dysregulated in Alzheimer’s Disease. We have recently also identified a significant enrichment of neurodegenerative diseases among miR-210 targets within the human transcriptome. To further elucidate the role of miR-210 in neuronal function and cognitive behaviour, we utilised conditional miR-210 knockout mice to characterise miR-210 regulation and function in primary hippocampal neurons and measured visual discrimination and reversal learning using rodent touchscreen assays. We found that miR-210 expression was induced by neuronal activation and loss of neuronal miR-210 increased oxidative metabolism and ROS production as well as dendritic density and branchingin vitro. We also found that loss of miR-210 in knockout mice increased behavioural flexibility and reduced perseverative responding during reversal learning which required updating of information and feedback. These data support a conserved, activity-dependent role for miR-210 in cognitive function through modulation of neuronal metabolism.
Two distinct trophectoderm lineage stem cells from human pluripotent stem cells
Authors: Mischler Adam , Karakis Victoria , Mahinthakumar Jessica , Carberry Celeste , San Miguel Adriana , Rager Julia , Fry Rebecca , Rao Balaji M. 
Published: September 2019

SummaryTrophoblasts are the principal cell type of the placenta. The use of human trophoblast stem cells (hTSCs) as a model for studies of early placental development is hampered by limited genetic diversity of existing hTSC lines, and constraints on using human fetal tissue or embryos needed to generate additional cell lines. Here we report the derivation of two distinct stem cells of the trophectoderm lineage from human pluripotent stem cells. The first is a CDX2- stem cell equivalent to primary hTSCs – they both exhibit identical expression of key markers, are maintained in culture and differentiate under similar conditions, and share high transcriptome similarity. The second is a CDX2+ putative human trophectoderm stem cell (hTESC) with distinct cell culture requirements and differences in gene expression and differentiation relative to hTSCs. Derivation of hTSCs and hTESCs from pluripotent stem cells significantly enables construction of models for normal and pathological placental development.
High content analysis of granuloma histology and neutrophilic inflammation in adult zebrafish infected with Mycobacterium marinum
Authors: Cheng Tina , Kam Julia Y , Johansen Matt D , Oehlers Stefan H 
Published: September 2019

AbstractInfection of zebrafish with natural pathogen Mycobacterium marinum is a useful surrogate for studying the human granulomatous inflammatory response to infection by Mycobacterium tuberculosis. The adaptive immune system of the adult stage zebrafish offers an advance on the commonly used embryo infection model as adult zebrafish form granulomas with striking similarities to human-M. tuberculosis granulomas. Here, we present workflows to perform high content analyses of granulomas in adult zebrafish infected with M. marinum by cryosectioning to take advantage of strong endogenous transgenic fluorescence adapted from common zebrafish embryo infection tools. Specific guides to classifying granuloma necrosis and organisation, quantifying bacterial burden and leukocyte infiltration of granulomas, and visualizing extracellular matrix remodelling and foam cell formation are also provided. We use these methods to characterize neutrophil recruitment to M. marinum granulomas across time and find an inverse relation to granuloma necrosis suggesting granuloma necrosis is not a marker of immunopathology in the natural infection system of the adult zebrafish-M. marinum pairing. The methods can be easily translated to studying the zebrafish adaptive immune response to other chronic and granuloma-forming pathogens.
Embryonic expression patterns of panarthropod Teneurin-m/odd Oz genes suggest a possible function in segmentation
Authors: Janssen Ralf 
Published: September 2019

AbstractBackgroundA hallmark of arthropods is their segmented body, and the so-called Drosophila segmentation gene cascade that controls this process serves as one of the best-studied gene regulatory networks. An important group of segmentation genes is represented by the pair-rule genes (PRGs). One of these genes was thought to be the type-II transmembrane protein encoding gene Tenascin-m (Ten-m (aka odd Oz)). Ten-m, however, does not have a pair-rule function in Drosophila, despite its characteristic PRG-like expression pattern. A recent study in the beetle Tribolium castaneum showed that its Ten-m gene is not expressed like a segmentation gene, and hence is very unlikely to have a function in segmentation.ResultsIn this study, I present data from a range of arthropods covering the arthropod tree of life, and an onychophoran, representing a closely related group of segmented animals. At least one ortholog of Ten-m/odz in each of these species is expressed in the form of transverse segmental stripes in the ectoderm of forming and newly formed segments – a characteristic of genes involved in segmentation.ConclusionsThe new expression data support the idea that Ten-m orthologs after all may be involved in panarthropod segmentation.
The impact of the Greek economic recession on workplace learning
Authors: Papakonstantinidis Stavros 
Published: September 2019

Purpose
The paper aims to examine the impact of the Greek economic recession on workplace learning. Specifically, it surveys the views of Greek business professionals regarding whether workplace learning could be used as a competitive advantage in achieving business success.

Design/methodology/approach
The paper follows a qualitative research method and discusses the findings of semi-structured interviews with professionals in various industries in Greece.

Findings
This study provides evidence of an overall reluctance to adopt formal learning strategies. Although hiring and retaining the best talent at work is seen as a competitive advantage, Greek professionals do not attribute success to formal workplace learning. Instead, digitalization of informal learning becomes essential for acquiring new knowledge.

Social implications
In the first few years of Greece’s economic recovery, companies aim to keep their budgets low in anything that seems luxurious and ultimately unnecessary. The paper discusses some implications of the implementation of digitalized informal learning in business.

Originality/value
This study is the first to explore how Greek professionals from various business sectors and managerial levels view workplace learning during the initial years of the country’s economic recovery.
Effect of Carcass Chilling on the Palatability Traits and Safety of Fresh Red Meat
Authors: Zhang Yimin , Mao Yanwei , Li Ke , Luo Xin , Hopkins David L. 
Published: September 2019

AbstractChilling procedures have been widely used in livestock abattoirs since the development of refrigeration systems. The major criteria when applying chilling regimes is not only complying with regulations, but economic concerns, and also meat safety and quality assurance requirements. Given recent developments, an updated review is required to guide the industry to choose the best chilling method and to inspire the development of new approaches to chilling. Thus in this paper, the quality and microbial safety of beef, lamb, pork, venison, and bison resulting from different chilling treatments has been reviewed, as well as the underlying mechanism(s) for the different impacts on meat quality traits as a result of different chilling regimes. The effect of fast chilling on the tenderness of beef and lamb is a focus, as some new findings, have recently been reported, while multistep chilling is highlighted as it incorporates the advantages of fast chilling to reduce carcass weight loss, resulting in similar quality improvements as found with slow chilling. It is, suggested, that if spray chilling can be combined with the second phase of multi‐step chilling, it will benefit the meat industry in terms of both meat quality and safety. Future studies should focus on combinations of chilling methods with new technologies, such as medium voltage electrical stimulation, muscle stretching, or ultrasound and so on, to move meat quality and safety to a new level.
Using Regulatory Sandboxes to Support Responsible Innovation in the Humanitarian Sector
Authors: Martin Aaron , Balestra Giulia 
Published: September 2019

AbstractThe global regulatory community continues to explore new approaches to supervising innovation. Among these, so‐called ‘regulatory sandboxes’ are proving to be particularly appealing to the financial sector as it seeks to promote technological and data‐driven innovation. These ‘playgrounds’ for innovation are also spreading to other regulated sectors such as telecommunications, data protection, energy, and environmental protection, allowing participants to test new business models and technologies under the supervision of regulators while the applicable rules are temporarily relaxed. Regulators can provide targeted guidance to sandbox participants, including help with understanding how an innovation fits within the existing regulatory framework. As of July 2019, at least 50 sandboxes were either in operation or under consideration globally. Significantly, many of these are based in countries that host large numbers of displaced persons. This commentary explores the potential role for sandboxes in promoting responsible humanitarian innovation. Through a review of the literature, we discuss the stated benefits of the sandbox approach while also acknowledging notable risks and challenges to their sustained deployment. We then reflect on how the humanitarian sector might engage regulators and other stakeholders through sandboxes to develop and catalyze innovations that better serve those affected by humanitarian crises, including the displaced.