bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity in natural transformation frequencies and regulation acrossVibriospecies
Authors: Simpson Chelsea A. , Podicheti Ram , Rusch Douglas B. , Dalia Ankur B. , van Kessel Julia C. 
Published: June 2019

AbstractIn marineVibriospecies, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in severalVibriospecies. Here, we show that TfoX expression in twoVibrio campbelliistrains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strainV. campbelliiBB120 (previously classified asVibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation inV. campbelliiDS40M4. This result is in contrast toVibrio choleraethat requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar toV. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studiedV. choleraecompetence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies amongVibriospecies indicates a wide disparity among even closely related strains, withVibrio vulnificushaving the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency inVibrio vulnificus.SignificanceNaturally transformable or competent bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows thatVibriospecies that inhabit marine environments exhibit a wide diversity in natural transformation capability ranging from non-transformable to high transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) is conserved among closely related species but differs throughout the genus. Expression of two key transcription factors, TfoX and QstR, are necessary and sufficient to stimulate high levels of transformation inVibrio campbelliiand recover low rates of transformation inVibrio vulnificus.
Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish
Authors: Fang Wei , Wen Yi , Wei Xiangyun 
Published: June 2019

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.
Vesicular stomatitis virus transcription is inhibited by TRIM69 in the interferon-induced antiviral state
Authors: Kueck Tonya , Bloyet Louis-Marie , Cassella Elena , Zang Trinity , Schmidt Fabian , Brusic Vesna , Tekes Gergely , Pornillos Owen , Whelan Sean P. J. , Bieniasz Paul D. 
Published: June 2019

ABSTRACTInterferons (IFNs) induce the expression of many interferon stimulated genes (ISGs), many of which are responsible for the cellular ‘antiviral state’ in which the replication of numerous viruses is blocked. How the majority of individual ISGs inhibit the replication of particular viruses is unknown. We conducted a loss-of-function screen to identify genes required for the activity of IFNαagainst vesicular stomatitis virus, Indiana serotype (VSVIND), a prototype negative strand RNA virus. Our screen revealed that TRIM69, a member of tripartite motif family of proteins, is a VSVINDinhibitor. TRIM69 potently inhibited VSVINDreplication through a previously undescribed transcriptional inhibition mechanism. Specifically, TRIM69 physically associates with the VSVINDphosphoprotein (P), requiring a specific peptide target sequence encoded therein. P is a cofactor for the viral polymerase, and is required for viral RNA synthesis as well as the assembly of replication compartments. By targeting P, TRIM69 inhibits pioneer transcription of the incoming virion-associated minus strand RNA, thereby preventing the synthesis of viral mRNAs, and consequently impedes all downstream events in the VSVINDreplication cycle. Unlike some TRIM proteins, TRIM69 does not inhibit viral replication by inducing degradation of target viral proteins. Rather, higher-order TRIM69 multimerization is required for its antiviral activity, suggesting that TRIM69 functions by sequestration or anatomical disruption of the viral machinery required for VSVINDRNA synthesis.SIGNIFICANCE STATEMENTInterferons are important antiviral cytokines that work by inducing hundreds of host genes whose products inhibit replication of many viruses. While the antiviral activity of interferon has long been known, the identities and mechanisms of action of most interferon-induced antiviral proteins remain to be discovered. We identified gene products that are important for the antiviral activity of interferon against vesicular stomatitis virus (VSV) a model virus that whose genome consists a single RNA molecule with negative sense polarity. We found that a particular antiviral protein, TRIM69, functions by a previously undescribed molecular mechanism. Specifically, TRIM69 interacts with, and inhibits the function, of a particular phosphoprotein (P) component the viral transcription machinery, preventing the synthesis of viral messenger RNAs.
Human pluripotent stem cell modeling of tuberous sclerosis complex reveals lineage-specific therapeutic vulnerabilities
Authors: Delaney Sean P. , Julian Lisa M. , Pietrobon Adam , Yockell-Lelièvre Julien , Doré Carole , Wang Ting T. , Doyon Valerie C. , Raymond Angela , Patten David A. , Kristof Arnold S. , Harper Mary-Ellen , Sun Hongyu , Stanford William L. 
Published: June 2019

SUMMARYmTORC1 hyperactivation resulting from inactivating TSC2 mutations underlie the multi-system tumor disorder tuberous sclerosis complex (TSC) and the rare pulmonary neoplasm lymphangioleiomyomatosis (LAM). Mutation-bearing neural precursor cells (NPCs) lead to the formation of TSC brain tumors during development, while the cell of origin of TSC mesenchymal tumors such as LAM is unknown. We report the first model of multi-system TSC cell types, characterized by NPCs and neural crest cells (NCCs) differentiated in parallel from multiple engineered TSC2−/− human pluripotent stem cell (hPSC) lines. These cells successfully model defining phenotypes of neural and mesenchymal TSC, with transcriptomic signatures reflecting those observed in patient tumors, thus establishing TSC2−/− NCCs as a powerful model of LAM. Employing this rich cellular and transcriptomic resource, we identified lineage-specific catabolic signaling mechanisms that drive divergent cell behavior and therapeutic sensitivities that, in turn, demonstrate the power of employing lineage-specific stem cell models to dissect multi-system diseases.
Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation
Authors: Wasik Brian R. , Voorhees Ian E.H. , Barnard Karen N. , Lawrence Brynn K. , Weichert Wendy S. , Hood Grace , Nogales Aitor , Martínez-Sobrido Luis , Holmes Edward C. , Parrish Colin R. 
Published: June 2019

ABSTRACTInfluenza A viruses have regularly jumped to new hosts to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus, but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here we examine the processes of influenza A virus infection and evolution in mice by comparing deep sequence variation of a human H1N1 pandemic virus, a seasonal H3N2 virus, and a H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with that seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc.SIGNIFICANCEMice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals, but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not effect influenza evolution in this model. Overall this shows that mice provide a useful animal model for influenza, but that host passage evolution will vary depending on the virus being tested.
Prevalence of antimicrobial resistance genes and integrons in commensal Gram-negative bacteria in a college community
Authors: Rubin Julia , Mussio Kaitlyn , Xu Yuqi , Suh Joy , Riley Lee W. 
Published: June 2019

AbstractAlthough the human intestinal microbiome has been shown to harbor antimicrobial drug-resistance genes (ARG), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California university, and compared these genes to those found in uropathogenic Escherichia coli isolated from patients with community-acquired urinary tract infection (CA-UTI). We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction (PCR) for ARG encoding resistance against ampicillin (AMP), trimethoprim-sulfamethoxazole (TMP-SMX), gentamicin (GENT), and colistin (COL). We found antimicrobial resistant GNB from 85 (83%) of 102 non-redundant rectal swab samples. Sixty-seven (66%) of these samples contained ß-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA,blaOXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A15, and dhfr-B3), and aminoglycoside resistance genes (aadA5, aadA1, and aadB). Integron sequences were found in 37 fecal samples. These genes were found in 11 different GNB species isolated from the fecal samples. The same ARG were found in E. coli strains isolated from patients with CA-UTI examined at the college outpatient health clinic. The high prevalence of clinically-common ARG and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARG that appear in E. coli strains causing extraintestinal infections in the same community.ImportanceIncreasing frequency of antimicrobial resistance (AMR) in human pathogenic bacteria has compromised our ability to treat infections. Since mobile antibiotic resistance genes (ARG) are readily exchanged between different species of bacteria through horizontal gene transfer, there is interest in investigating sources of these genes. The normal intestinal flora has been shown to contain a wide variety of ARG, which may have been introduced via food-containing AMR bacteria. We sought to assess the prevalence of ARG carriage in the intestines of a healthy population and determine if these ARG are found in E. coli strains that cause community-acquired urinary tract infection (CA-UTI) in the same community. Our findings indicate that the human intestine may serve as an important reservoir as well as a site in which ARG are transferred into E. coli that cause UTI. Further research is needed to reduce ARG carriage and devise new strategies to prevent AMR infections.
Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits
Authors: Oláh Viktor János , Lukacsovich David , Winterer Jochen , Lőrincz Andrea , Nusser Zoltan , Földy Csaba , Szabadics János 
Published: June 2019

AbstractCCK-expressing interneurons (CCK+INs) are crucial for controlling hippocampal activity. We found two firing phenotypes of CCK+INs in rat CA3 area; either possessing a previously undetected membrane potential-dependent firing or regular firing phenotype, due to different low-voltage-activated potassium currents. These different excitability properties destine the two types for distinct functions, because the former is essentially silenced during realistic 8-15 Hz oscillations. The general excitability, morphology and gene-profiles of the two types were surprisingly similar. Even the expression of Kv4.3 channels were comparable, despite evidences showing that Kv4.3-mediated currents underlie the distinct firing properties. Instead, the firing phenotypes were correlated with the presence of distinct isoforms of Kv4 auxiliary subunits (KChIP1 vs. KChIP4e and DPP6S). Our results reveal the underlying mechanisms of two previously unknown types of CCK+INs and demonstrate that alternative splicing of few genes, which may be viewed as a minor event in the cells’ whole transcriptome, can underlie distinct cell-type identity.
Polarized Entamoeba: A model for stable bleb driven motility
Authors: Krishnan Deepak , Ghosh Sudip Kumar 
Published: June 2019

AbstractProtozoan parasites Entamoeba histolytica and Entamoeba invadens formed a polarized phenotype, an elongated shape with a single leading edge and a trailing edge when treated with pentoxifylline. The leading edge of the polarized morphology was a spherical protrusion devoid of F-actin but with occasional F-actin scars, indicating the presence of bleb. The polarized form was stable bleb driven since the blebbing was limited to the leading edge. Pentoxifylline induced chemokinesis in Entamoeba as it switched the motility pattern from slow and random to fast and directionally persistent. Pentoxifylline speeded up the cell aggregation in E. invadens during growth and encystation due to enhanced chemotaxis of the polarized form. The transformation of non-polarized adherent trophozoites to nonadherent stable bleb driven form occurred via lamellipodial and bleb driven adherent intermediate phenotypes. The nonadherent polarized phenotype was highly motile under confinement and moved by rearward plasma membrane flow. In contrast to pentoxifylline, adenosine, the adenosine receptor agonist, stimulated the formation of multiple protrusions leading to random motility. Thus pentoxifylline might prevent lateral protrusions by inhibiting adenosine receptor, producing the monopodial polarized morphology.Summary statementPentoxifylline, the adenosine receptor antagonist induced a stable bleb driven polarized morphology in Entamoeba characterized by fast, directionally persistent and highly chemotactic motility.
Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field
Authors: Li Hongquan , Soto-Montoya Hazel , Voisin Maxime , Valenzuela Lucas Fuentes , Prakash Manu 
Published: June 2019

AbstractAccess to quantitative, robust, yet affordable diagnostic tools is necessary to reduce global infectious disease burden. Manual microscopy has served as a bedrock for diagnostics with wide adaptability, although at a cost of tedious labor and human errors. Automated robotic microscopes are poised to enable a new era of smart field microscopy but current platforms remain cost prohibitive and largely inflexible, especially for resource poor and field settings. Here we present Octopi, a low-cost ($250-$500) and reconfigurable autonomous microscopy platform capable of automated slide scanning and correlated bright-field and fluorescence imaging. Being highly modular, it also provides a framework for new disease-specific modules to be developed. We demonstrate the power of the platform by applying it to automated detection of malaria parasites in blood smears. Specifically, we discovered a spectral shift on the order of 10 nm for DAPI-stained Plasmodium falciparum malaria parasites. This shift allowed us to detect the parasites with a low magnification (equivalent to 10x) large field of view (2.56 mm2) module. Combined with automated slide scanning, real time computer vision and machine learning-based classification, Octopi is able to screen more than 1.5 million red blood cells per minute for parasitemia quantification, with estimated diagnostic sensitivity and specificity exceeding 90% at parasitemia of 50/ul and 100% for parasitemia higher than 150/l. With different modules, we further showed imaging of tissue slice and sputum sample on the platform. With roughly two orders of magnitude in cost reduction, Octopi opens up the possibility of a large robotic microscope network for improved disease diagnosis while providing an avenue for collective efforts for development of modular instruments.One sentence summaryWe developed a low-cost ($250-$500) automated imaging platform that can quantify malaria parasitemia by scanning 1.5 million red blood cells per minute.
Multiplexed code of navigation variables in anterior limbic areas
Authors: Laurens Jean , Abrego Amada , Cham Henry , Popeney Briana , Yu Yan , Rotem Naama , Aarse Janna , Asprodini Eftihia K. , Dickman J. David , Angelaki Dora E. 
Published: June 2019

AbstractThe brain’s navigation system integrates multimodal cues to create a sense of position and orientation. Here we used a multimodal model to systematically assess how neurons in the anterior thalamic nuclei, retrosplenial cortex and anterior hippocampus of mice, as well as in the cingulum fiber bundle and the white matter regions surrounding the hippocampus, encode an array of navigational variables when animals forage in a circular arena. In addition to coding head direction, we found that some thalamic cells encode the animal’s allocentric position, similar to place cells. We also found that a large fraction of retrosplenial neurons, as well as some hippocampal neurons, encode the egocentric position of the arena’s boundary. We compared the multimodal model to traditional methods of head direction tuning and place field analysis, and found that the latter were inapplicable to multimodal regions such as the anterior thalamus and retrosplenial cortex. Our results draw a new picture of the signals carried and outputted by the anterior thalamus and retrosplenial cortex, offer new insights on navigational variables represented in the hippocampus and its vicinity, and emphasize the importance of using multimodal models to investigate neural coding throughout the navigation system.
Adult third culture kids: adjustment and personal development
Authors: Lauring Jakob , Guttormsen David S. A. , McNulty Yvonne Maria 
Published: June 2019

Purpose
The purpose of this paper is to explore how interaction adjustment influences personal development for expatriates and to examine whether the effect differs between adults that have, and have not, lived abroad during their adolescence.

Design/methodology/approach
The authors use survey responses from 424 business expatriates in Asia distinguishing between adult third culture kids (ATCKs) that have lived abroad during their adolescence and adult mono-culture kids (AMCKs) who have not.

Findings
The results show that while interaction adjustment generally improves the experience of personal development, this effect is stronger for ATCKs. AMCKs will experience personal development almost independently of their interaction adjustment with host nationals solely due to the novelty of the international experience. For ATCKs, just being in the new country is not enough for them to feel they have developed personally; they need to engage more deeply with the local population to achieve this.

Originality/value
The authors still know very little about ATCKs and about how expatriation during their adulthood develops them personally, given they have already had international experiences at a young age.
Risk assessment of construction projects in China under traditional and industrial production modes
Authors: Gao Jingxin , Ren Hong , Cai Weiguang 
Published: June 2019

Purpose
High risk is one of the most prominent characteristics of the Chinese construction industry, and it poses a significant threat to construction projects. Owing to initiatives aimed at achieving high efficiency, low carbon emissions, etc., industrialization of the construction industry has become an inevitable trend in China. However, it remains to be discussed whether industrialization of construction can reduce the risks entailed in construction projects compared with traditional construction. The paper aims to discuss these issues.

Design/methodology/approach
Based on the theory of risk life cycle, this paper proposes a practical risk assessment technique to assess the risk life cycle, including the risk occurrence time and potential financial losses. This technique is then applied to assess the differences between the risks involved in an engineering, procurement and construction (EPC) project executed via traditional and industrial production modes.

Findings
The results show that the total duration of risks in the industrial construction project is half of that in the traditional project. In addition, the expected financial loss entailed in the industrial construction project is 29 percent lower than that in the traditional construction project. Therefore, industrial construction has the potential to optimize risk performance.

Originality/value
There is no significant difference between the traditional and industrial construction models in terms of probability of risk. The maximum total loss might occur in the procurement stage in the case of industrial production, and in the construction stage in the case of traditional production. Moreover, the total expected loss from risk in the EPC project in the industrial production mode is only half of that in the traditional production route. This study is expected to provide a new risk evaluation technique and promote an understanding of the life cycle of risk management in the construction industry.