bluuebunny/crossref_metadata_2025 huggingface dataset:
Current Management of Self-Inflicted Wounds in Surgery
Authors: David Joshua A. , Rifkin William J. , Chiu Ernest S.
Published: November 2018

Objective

Despite the presence of self-inflicted wounds (SIWs) across all of medicine, our current understanding of SIWs in surgery is limited. Here, we detail the pertinent aspects of the history, diagnosis, decision making, and management of SIWs as they relate to the field of surgery. In addition, we present the first comprehensive review of SIWs across the surgical literature.

Summary Background Data

Self-inflicted wounds have been recognized for much of recorded human history and span a wide spectrum of patient behaviors, motivations, and underlying psychiatric illnesses.

Methods

We performed a comprehensive literature review of SIWs in the surgical literature. In total, 189 articles were identified.

Results

The most common site of primary SIW was the upper extremity (36.2%), and the most common presenting injuries were lacerations (22.7%). Forty-two percent of patients had received prior surgical procedures for their SIWs, and the average length of time preceding treatment or diagnosis of an injury as an SIW was 2.29 years. Self-inflicted wounds resulting from foreign body insertions were most common (25.9%). Psychiatric factors accounted for most SIW production (35%), of which factitious disorder was the most common (12.7%). Other motivations for SIW production included autoeroticism (8.6%), substance related (6.6%), organic brain disease (5.0%), and self-therapy/surgery by patients (1.7%). Surgical management was ultimately required for nearly 75% of SIWs and was successful in most cases.

Conclusions

Self-inflicted wounds are frequently encountered in all surgical specialties and encompass many anatomic locations, presentations, and patient-motivating factors. Surgical intervention is common, and successful outcomes are often achieved.
Plasma miR-181a-5p Downregulation Predicts Response and Improved Survival After FOLFIRINOX in Pancreatic Ductal Adenocarcinoma
Authors: Meijer Laura L. , Garajová Ingrid , Caparello Chiara , Le Large Tessa Y. S. , Frampton Adam E. , Vasile Enrico , Funel Niccola , Kazemier Geert , Giovannetti Elisa
Published: November 2018

Objective:

The aim of the study was to identify plasma microRNA (miRNA) biomarkers for stratifying and monitoring patients with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC) treated with FOLFIRINOX, and to investigate their functional roles.

Summary Background Data:

FOLFIRINOX has become a standard therapy for patients with advanced PDAC and can be used to potentially downstage disease. However, only a subset of patients respond, and biomarkers to guide decision-making are urgently needed.

Methods:

We used microarray-based profiling to discover deregulated miRNAs in pre- and postchemotherapy plasma samples from patients based on their progression-free survival (PFS) after FOLFIRINOX. Nine candidate plasma miRNAs were validated in an independent cohort (n = 43). The most discriminative plasma miRNA was correlated with clinicopathological factors and survival, and also investigated in an additional cohort treated with gemcitabine plus nab-paclitaxel. Expression patterns were further evaluated in matched tumor tissues. In vitro studies explored its function, key downstream gene-targets, and interaction with 5-fluorouracil, irinotecan, and oxaliplatin.

Results:

Plasma miR-181a-5p was significantly downregulated in non-progressive patients after FOLFIRINOX. In multivariate analysis, this decline correlated with improved PFS and overall survival, especially when combined with CA19-9 decline [hazard ratio (HR) = 0.153, 95% confidence interval (CI), 0.067–0.347 and HR = 0.201, 95% CI, 0.070–0.576, respectively]. This combination did not correlate with survival in patients treated with gemcitabine plus nab-paclitaxel. Tissue expression of miR-181a-5p reflected plasma levels. Inhibition of miR-181a-5p coupled with oxaliplatin exposure in pancreatic cell lines decreased cell viability.

Conclusions:

Plasma miR-181a-5p is a specific biomarker for monitoring FOLFIRINOX response. Decline in plasma miR-181a-5p and CA19-9 levels is associated with better prognosis after FOLFIRINOX and may be useful for guiding therapeutic choices and surgical exploration.
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Authors: Arredondo-Alonso Sergio , Rogers Malbert R. C. , Braat Johanna C. , Verschuuren Tess D. , Top Janetta , Corander Jukka , Willems Rob J. L. , Schürch Anita C.
Published: November 2018

Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E. faecium=0.92, F1-score K. pneumoniae=0.90, F1-score E. coli=0.76), which outperformed other existing plasmid prediction tools using a benchmarking set of isolates. We demonstrated the scalability of our models by accurately predicting the plasmidome of a large collection of 1644 E. faecium isolates and illustrate its applicability by predicting the location of antibiotic-resistance genes in all three species. The SVM classifiers are publicly available as an R package and graphical-user interface called ‘mlplasmids’. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.
High-throughput determination of the antigen specificities of T cell receptors in single cells
Authors: Zhang Shu-Qi , Ma Ke-Yue , Schonnesen Alexandra A. , Zhang Mingliang , He Chenfeng , Sun Eric , Williams Chad M. , Jia Weiping , Jiang Ning
Published: November 2018

We present tetramer-associated T-cell receptor sequencing (TetTCR-Seq), a method to link T cell receptor (TCR) sequences to their cognate antigens in single cells at high throughput. Binding is determined using a library of DNA-barcoded antigen tetramers that is rapidly generated by in vitro transcription and translation. We applied TetTCR-Seq to identify patterns in TCR cross-reactivity with cancer neo-antigens and to rapidly isolate neo-antigen-specific TCRs with no cross-reactivity to the wild-type antigen.
Novel 3,6-Dihydroxypicolinic Acid Decarboxylase Mediated Picolinic Acid Catabolism inAlcaligenes faecalisJQ135
Authors: Jiguo Qiu , Yanting Zhang , Shigang Yao , Hao Ren , Meng Qian , Qing Hong , Zhenmei Lu , Jian He
Published: November 2018

Alcaligenesfaecalisstrain JQ135 utilizes picolinic acid (PA) as sole carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA) with no further degradation. A novel decarboxylase PicC was identified that was found to be responsible for the decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. Although, PicC belonged to amidohydrolase_2 family, it shows low similarity (<45%) when compared to other reported amidohydrolase_2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated thatpicCwas essential for PA degradation. The PicC was Zn2+-dependent non-oxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. TheKmandkcattowards 3,6DHPA were observed to be 13.44 μM and 4.77 s-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity.

Importance

Picolinic acid is a natural toxic pyridine derived from L-tryptophan metabolism and some aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus, a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6DHPA was an intermediate in PA catabolism process and further identified and characterized a novel amidohydrolase_2 family decarboxylase PicC. It was also shown that PicC could catalyze the decarboxylation process of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding PA degradation pathway and the underlying molecular mechanism.
The complete plastid genomes of four species from Brassicales
Authors: Mu Weixue , Yang Ting , Liu Xin
Published: November 2018

Brassicales is a diverse angiosperm order with about 4,700 recognized species. Here, we assembled and described the complete plastid genomes from four species of Brassicales: Capparis urophylla F.Chun (Capparaceae), Carica papaya L. (Caricaceae), Cleome rutidosperma DC. (Cleomaceae), and Moringa oleifera Lam. (Moringaceae), including two plastid genomes newly assembled for two families (Capparaceae and Moringaceae). The four plastid genomes are 159,680 base pairs on average in length and encode 78 protein-coding genes. The genomes each contains a typical structure of a Large Single-Copy (LSC) region and a Small Single-Copy (SSC) region separated by two Inverted Repeat (IR) regions. We performed the maximum-likelihood (ML) phylogenetic analysis using three different data sets of 66 protein-coding genes (ntAll, ntNo3rd and AA). Our phylogenetic results from different dataset are congruent, and are consistent with previous phylogenetic studies of Brassiales.
Cities of the future, visualizing climate change to inspire actions
Authors: Bastin Jean-Francois , Clark Emily , Elliott Thomas , Hart Simon , den Hoogen Johan van , Hordijk Iris , Ma Haozhi , Majumder Sabiha , Manoli Gabriele , Maschler Julia , Mo Lidong , Routh Devin , Yu Kailiang , Zohner Constantin , Crowther Thomas, W.
Published: November 2018

Combating against climate change requires unified action across all sectors of society. However, this collective action is precluded by the ‘consensus gap’ between scientific knowledge and public opinion. A growing body of evidence suggests that facts do not persuade people to act. Instead, it is visualization - the ability to simulate relatable scenarios - is the most effective approach for motivating behavior change. Here, we exemplify this approach, using current climate projections to enable people to visualize cities of the future, rather than describing intangible climate variables. Analyzing city pairs for 520 major cities of the world, we characterize which cities will most closely resemble the climate conditions of which other major cities by 2050. On average, most cities will resemble cities that are over 1000km south, and 22% of cities will experience climate conditions that are not currently experienced by any existing major cities. We predict that London’s climate in 2050 will resemble Barcelona’s climate today, Madrid will resemble to Marrakesh, Moscow to Sofia, Seattle to San Francisco, Stockholm to Budapest, Tokyo to Changsha, etc. Our approach illustrates how complex climate data can be packaged to provide tangible information. By allowing people to visualize their own climate futures, we hope to empower citizens, policy makers and scientists to visualize expected climate impacts and adapt decision making accordingly.
Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: similarities and differences in cell behaviour
Authors: Kotini Maria Paraskevi , Andaloussi Mäe Maarja , Belting Heinz-Georg , Betsholtz Christer , Affolter Markus
Published: November 2018

Branching morphogenesis is a fascinating process whereby a simple network of biological tubes increases its complexity by adding new branches to existing ones, generating an enlarged structure of interconnected tubes. Branching morphogenesis has been studied extensively in animals and much has been learned about the regulation of branching at the cellular and molecular level. Here, we discuss studies of the Drosophila trachea and of the vertebrate vasculature, which have revealed how new branches are formed and connect (anastomose), leading to the establishment of complex tubular networks. We briefly describe the cell behaviour underlying tracheal and vascular branching. Although similar at many levels, the branching and anastomosis processes characterized thus far show a number of differences in cell behaviour, resulting in somewhat different tube architectures in these two organs. We describe the similarities and the differences and discuss them in the context of their possible developmental significance. We finish by highlighting some old and new data, which suggest that live imaging of the development of capillary beds in adult animals might reveal yet unexplored endothelial behaviour of endothelial cells.
Multicolor fluorescent imaging by space-constrained computational hyperspectral imaging
Authors: Wang Yina , Yang Bin , Feng Siyu , Pessino Veronica , Huang Bo
Published: November 2018

Hyperspectral imaging is a powerful technique to simultaneously study multiple fluorophore labels with overlapping emissions. Here we present a computational hyperspectral imaging method, which uses the sample spatial fluorescence information as a reconstruction constraint. Our method addresses both the under-sampling issue of compressive hyperspectral imaging and the low throughput issue of scanning hyperspectral imaging. With simulated and experimental data, we have demonstrated the superior reconstruction precision of our method in two and three-color imaging. We have experimentally validated this method in differentiating cellular structures labeled with two red-colored fluorescent proteins, tdTomato and mCherry, which have highly overlapping emission spectra. Our method has the advantage of totally free wavelength choice and can also be combined with conventional filter-based sequential multi-color imaging to further expand the choices of probes.
Efficient reverse breeding by VIGS-mediated transient crossover reduction
Authors: Calvo-Baltanas Vanesa , Wijnen Cris L. , Lukhovitskaya Nina , de Snoo C. Bastiaan , Hohenwarter Linus , de jong Hans , Schnittger Arp , Wijnker Erik
Published: November 2018

F1 heterozygotes are traditionally generated by crossing homozygous parental lines. The opposite is achieved through reverse breeding, in which parental lines are generated from a heterozygote. Reverse breeding can be used to develop new F1 hybrid varieties without having prior access to homozygous breeding lines. For successful reverse breeding, the heterozygotes’ homologous chromosomes must be divided over two haploid complements, which is achieved by suppression of meiotic crossover (CO) recombination. We here show two innovations that facilitate efficient reverse breeding. Firstly, we demonstrate that downregulation of CO rates can be accomplished using virus-induced gene silencing (VIGS). We obtain transgene-free parental lines for a heterozygote in just two generations. Secondly, we show that incomplete CO suppression opens up several alternative strategies for the preservation of hybrid phenotypes through reverse breeding.
Adenosine Deaminase Acting on RNA 1 Associates with Orf Virus OV20.0 and Enhances Viral Replication
Authors: Liao Guan-Ru , Tseng Yeu-Yang , Tseng Jing-Yu , Lin Fong-Yuan , Yamada Yumiko , Liu Hao-Ping , Kuan Chih-Ying , Hsu Wei-Li
Published: November 2018

Orf virus (ORFV) infects sheep and goats and is also an important zoonotic pathogen. The viral protein OV20.0 has been shown to suppress innate immunity by targeting the double-stranded RNA (dsRNA)-activated protein kinase (PKR) by multiple mechanisms. These mechanisms include a direct interaction with PKR and binding with two PKR activators, dsRNA and the cellular PKR activator (PACT), which ultimately leads to the inhibition of PKR activation. In the present study, we identified a novel association between OV20.0 and adenosine deaminase acting on RNA 1 (ADAR1). OV20.0 bound directly to the dsRNA binding domains (RBDs) of ADAR1 in the absence of dsRNA. Additionally, OV20.0 preferentially interacted with RBD1 of ADAR1, which was essential for its dsRNA binding ability and for the homodimerization that is critical for intact adenosine (A)-to-inosine (I) editing activity. Finally, the association with OV20.0 suppressed the A-to-I editing ability of ADAR1, while ADAR1 played a proviral role during ORFV infection by inhibiting PKR phosphorylation. These observations revealed a new strategy used by OV20.0 to evade antiviral responses via PKR.

Importance

Viruses evolve specific strategies to counteract host innate immunity. ORFV, an important zoonotic pathogen, encodes OV20.0 to suppress PKR activation via multiple mechanisms, including interactions with PKR and two PKR activators. In this study, we demonstrated that OV20.0 interacts with ADAR1, a cellular enzyme responsible for converting adenosine (A) to inosine (I) in RNA. The RNA binding domains, but not the catalytic domain, of ADAR1 are required for this interaction. The OV20.0-ADAR1 association affects the functions of both proteins; OV20.0 suppressed the A-to-I editing of ADAR1, while ADAR1 elevated OV20.0 expression. The proviral role of ADAR1 is likely due to the inhibition of PKR phosphorylation. As RNA editing by ADAR1 contributes to the stability of the genetic code and the structure of RNA, these observations suggest that in addition to serving as a PKR inhibitor, OV20.0 might modulate ADAR1-dependent gene expression to combat antiviral responses or achieve efficient viral infection.
Common spatiotemporal processing of visual features shapes object representation
Authors: Papale Paolo , Betta Monica , Handjaras Giacomo , Malfatti Giulia , Cecchetti Luca , Rampinini Alessandra , Pietrini Pietro , Ricciardi Emiliano , Turella Luca , Leo Andrea
Published: November 2018

Biological vision relies on representations of the physical world at different levels of complexity. Relevant features span from simple low-level properties, as contrast and spatial frequencies, to object-based attributes, as shape and category. However, how these features are integrated into coherent percepts is still debated. Moreover, these dimensions often share common biases: for instance, stimuli from the same category (e.g., tools) may have similar shapes. Here, using magnetoencephalography, we revealed the temporal dynamics of feature processing in human subjects attending to pictures of items pertaining to different semantic categories. By employing Relative Weights Analysis, we mitigated collinearity between model-based descriptions of stimuli and showed that low-level properties (contrast and spatial frequencies), shape (medial-axis) and category are represented within the same spatial locations early in time: 100-150ms after stimulus onset. This fast and overlapping processing may result from independent parallel computations, with categorical representation emerging later than the onset of low-level feature processing, yet before shape coding. Categorical information is represented both before and after shape also suggesting a role for this feature in the refinement of categorical matching.
Discovering human transcription factor interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
Authors: Shrestha Shaleen , Sewell Jared Allan , Santoso Clarissa Stephanie , Forchielli Elena , Pro Sebastian Carrasco , Martinez Melissa , Fuxman Bass Juan Ignacio
Published: November 2018

Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false positive and negative predictions. To address these limitations, we developed two approaches based on enhanced yeast one-hybrid assays. The first approach interrogates the binding of >1,000 human TFs to repetitive DNA elements, while the second evaluates TF binding to single nucleotide variants, short insertions and deletions (indels), and novel DNA motifs. Using the first approach, we detected the binding of 75 TFs, including several nuclear hormone receptors and ETS factors, to the highly repetitive Alu elements. Using the second approach, we identified cancer-associated changes in TF binding, including gain of interactions involving ETS TFs and loss of interactions involving KLF TFs to different mutations in the TERT promoter, and gain of a MYB interaction with an 18 bp indel in the TAL1 super-enhancer. Additionally, we identified the TFs that bind to three uncharacterized DNA motifs identified in DNase footprinting assays. We anticipate that these approaches will expand our capabilities to study genetic variation and under-characterized genomic regions.
Studying Human Behaviour with Virtual Reality: The Unity Experiment Framework
Authors: Brookes Jack , Warburton Matthew , Alghadier Mshari , Mon-Williams Mark , Mushtaq Faisal
Published: November 2018

Virtual Reality systems offer a powerful tool for human behaviour research. The ability to create three-dimensional visual scenes and measure responses to the visual stimuli enables the behavioural researcher to test hypotheses in a manner and scale that were previously unfeasible. For example, a researcher wanting to understand interceptive timing behaviour might wish to violate Newtonian mechanics, so objects move in novel 3D trajectories. The same researcher may wish to collect such data with hundreds of participants outside the laboratory, and the use of a VR headset makes this a realistic proposition. The difficulty facing the researcher is that sophisticated 3D graphics engines (e.g. Unity) have been created for game designers rather than behavioural scientists. In order to overcome this barrier, we have created a set of tools and programming syntaxes that allow logical encoding of the common experimental features required by the behavioural scientist. The Unity Experiment Framework (UXF) allows the researcher to readily implement several forms of data collection, and provides researchers with the ability to easily modify independent variables. UXF does not offer any stimulus presentation features, so the full power of the Unity game engine can be exploited. We use a case study experiment, measuring postural sway in response to an oscillating virtual room, to show how UXF can replicate and advance upon behavioural research paradigms. We show that UXF can simplify and speed up development of VR experiments created in commercial gaming software and facilitate the efficient acquisition of large quantities of behavioural research data.
EFCAB9 is a pH-Dependent Ca2+Sensor that Regulates CatSper Channel Activity and Sperm Motility
Authors: Hwang Jae Yeon , Nadja Mannowetz , Zhang Yongdeng , Everley Robert A. , Gygi Steven P. , Bewersdorf Joerg , Lishko Polina V. , Chung Jean-Ju
Published: November 2018

Varying pH of luminal fluid along the female reproductive tract is a physiological cue that modulates sperm motility. CatSper is a sperm-specific, pH-sensitive calcium channel essential for hyperactivated motility and male fertility. Multi-subunit CatSper channel complexes organize linear Ca2+signaling nanodomains along the sperm tail. Here, we identify EF-hand calciumbinding domain-containing protein 9 (EFCAB9) as a dual function, cytoplasmic machine modulating the channel activity and the domain organization of CatSper. Knockout mice studies demonstrate that EFCAB9, in complex with the CatSper subunit, CAT SPERζ, is essential for pH-dependent and Ca2+sensitive activation of the CatSper channel. In the absence of EFCAB9, sperm motility and fertility is compromised and the linear arrangement of the Ca2+signaling domains is disrupted. EFCAB9 interacts directly with CATSPERζ in a Ca2+dependent manner and dissociates at elevated pH.These observations suggest that EFCAB9 is a long-sought, intracellular, pH-dependent Ca2+sensor that triggers changes in sperm motility.

Highlights

Efcab9encodes an evolutionarily conserved, sperm-specific EF-hand domain protein

Efcab9-deficient mice have sperm motility defects and reduced male fertility

EFCAB9 is a pH-tuned Ca2+sensor for flagellar CatSper Ca2+channel

EFCAB9 is a dual function machine in gatekeeping and domain organization of CatSper
Experimental Human Challenge Reveals Distinct Mechanisms of Acquisition or Protection Against Pneumococcal Colonization
Authors: Nikolaou Elissavet , Jochems Simon P. , Mitsi Elena , Pojar Sherin , Negera Edessa , Reiné Jesús , Carniel Beatriz , Soares-Schanoski Alessandra , Connor Victoria , Adler Hugh , Zaidi Seher Raza , Hales Caz , Hill Helen , Hyder-Wright Angela , Gordon Stephen B. , Rylance Jamie , Ferreira Daniela M.
Published: November 2018

Colonization of the upper respiratory tract with Streptococcus pneumoniae is the precursor of pneumococcal pneumonia and invasive disease. Following exposure, however, it is unclear which human immune mechanisms determine whether a pathogen will colonize. We used a human challenge model to investigate host-pathogen interactions in the first hours and days following intranasal exposure to Streptococcus pneumoniae. Using a novel home sampling method, we measured early immune responses and bacterial density dynamics in the nose and saliva after pneumococcal exposure. We found that nasal colonization can take up to 24 hours to become established. Also, two distinct bacterial clearance profiles were associated with protection: nasal clearers with immediate clearance of bacteria in the nose by the activity of pre-existent mucosal neutrophils and saliva clearers with detectable pneumococcus in saliva at one-hour post challenge and delayed clearance mediated by an inflammatory response and increased neutrophil activity 24 hours post bacterial encounter.
Functional Interrogation of Lynch Syndrome Associated MSH2 Missense Variants Using CRISPR-Cas9 Gene Editing in Human Embryonic Stem Cells
Authors: Rath Abhijit , Mishra Akriti , Ferreira Victoria Duque , Hu Chaoran , Grady James P. , Heinen Christopher D.
Published: November 2018

Lynch syndrome (LS) is a hereditary cancer predisposition condition caused by inactivating germline mutations in one of the DNA mismatch repair (MMR) genes. Identifying a deleterious germline mutation by DNA sequencing is important for confirming an LS diagnosis. Frameshift and nonsense mutations significantly alter the protein product and likely impair MMR function. However, the implication of a missense mutation is often difficult to interpret. Referred to as variants of uncertain significance (VUS), their discovery hampers the definitive LS diagnosis. To determine the pathogenic significance of a VUS it is helpful to know its impact on protein function. Functional studies in the test tube and in cellular models have been performed for some VUS, however, these studies have been limited by the artificial nature of the assays. We report here an improved functional assay in which we engineered site-specific MSH2 VUS using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene editing in human embryonic stem cells. This approach introduces the variant into the endogenous MSH2 loci, while simultaneously eliminating the wild-type gene. We then characterized the impact of the variants on cellular MMR functions including DNA damage response signaling upon challenge with a DNA alkylating agent and the repair of DNA microsatellites. We classified the MMR functional capability of 8 of 10 VUS under study providing valuable information for determining their likelihood of being bona fide LS mutations. This improved human cell-based assay system for functionally testing MMR gene VUS will facilitate the identification of high risk LS patients.

Significance Statement

Understanding how cancer-associated missense variants in MMR genes affect function helps determine whether they truly contribute to disease. Laboratory assays previously utilized are limited by their artificial nature. To improve this, we introduced variants directly into the endogenous MMR loci in hESCs using CRISPR-Cas9 gene editing. This approach allows us to assess each variant while being expressed by its normal regulatory elements in a cellular environment. Our results will help guide the management of patients world-wide who carry these variants. At the same time, this study provides a technical road map for assessing the functional effects of all LS-associated variants, as well as variants linked to other genetic diseases where a cell-based functional assay is available.
Cysteine dioxygenase 1 is a metabolic liability for non-small cell lung cancer
Authors: Kang Yun Pyo , Torrente Laura , Liu Min , Asara John M. , Dibble Christian C. , DeNicola Gina M.
Published: November 2018

NRF2 is emerging as a major regulator of cellular metabolism. However, most studies have been performed in cancer cells, where co-occurring mutations and tumor selective pressures complicate the influence of NRF2 on metabolism. Here we use genetically engineered, non-transformed primary cells to isolate the most immediate effects of NRF2 on cellular metabolism. We find that NRF2 promotes the accumulation of intracellular cysteine and engages the cysteine homeostatic control mechanism mediated by cysteine dioxygenase 1 (CDO1), which catalyzes the irreversible metabolism of cysteine to cysteine sulfinic acid (CSA). Notably,CDO1is preferentially silenced by promoter methylation in non-small cell lung cancers (NSCLC) harboring mutations in KEAP1, the negative regulator of NRF2. CDO1 silencing promotes proliferation of NSCLC by limiting the futile metabolism of cysteine to the wasteful and toxic byproducts CSA and sulfite, and depletion of cellular NADPH. Thus, CDO1 is a metabolic liability for NSCLC cells with high intracellular cysteine, particularly NRF2/KEAP1 mutant cells.
A pilot study of the effects ofMycoplasma ovipneumoniaeexposure on domestic lamb growth and performance
Authors: Besser Thomas E. , Levy Jessica , Ackerman Melissa , Nelson Danielle , Manlove Kezia , Potter Kathleen A. , Busboom Jan , Benson Margaret
Published: November 2018

Mycoplasma ovipneumoniaeis a globally distributed pathogen that has been associated with pneumonia in both domestic and wild Caprinae. It is closely related toM. hyopneumoniae, a respiratory pathogen of swine that is associated with decreased growth rates of pigs as well as clinical respiratory disease. In order to assess the effects ofM. ovipneumoniaeon lamb performance, we generated a cohort of lambs free ofM. ovipneumoniaeby segregation of test negative ewes after lambing, then compared the growth and carcass quality traits ofM. ovipneumoniae-freeand -colonized lambs from weaning to harvest. Some signs of respiratory disease were observed during the feeding trial in both lamb groups, but theM. ovipneumoniae-exposedgroup included more affected lambs and higher average disease scores. At harvest, lungs of lambs in both groups showed few grossly visible lesions, although theM. ovipneumoniae-exposedgroup did exhibit increased microscopic lung lesions (P<0.05). In addition,M. ovipneumoniaeexposed lambs produced lower average daily gains (P<0.05), and lower yield grade carcasses (P<0.05) compared to those of non-exposed lambs. The results demonstrated the feasibility of test and segregation for elimination ofM. ovipneumoniaefrom groups of sheep and suggested that this pathogen may impair lamb growth and productivity even in the absence of overt respiratory disease.
The effect of heavy metal contamination on human and animal health in the vicinity of a zinc smelter
Authors: Shen Xiaoyun , Chi Yongkuan , Xiong Kangning
Published: November 2018

A diagnosis of heavy metal poisoning in sheep living on pasture in the vicinity of a zinc smelter was made based on laboratory tests and clinical signs in livestock in the Wumeng mountain area of China. Heavy metal contamination has generated serious harm to the health of local farmers after passing through the food chain. The levels of copper, zinc, cadmium, and lead in irrigation water, soil, forages, and animal tissues were measured in samples taken from within the vicinity of a zinc smelter and control samples. Heavy metal concentrations in foods (corn, rice, and wheat) and human tissues (blood and hair) from local farmers living in affected areas and controls were also determined. Hematological values were determined in human and animal samples. The copper, zinc, cadmium, and lead concentrations in irrigation water, soils, and forages were markedly higher than the levels in healthy pastures. Cadmium and lead concentrations were 177.82 and 16.61 times greater in forages than controls, respectively, and 68.71 and 15.66 times greater in soils than controls, respectively. Heavy metal concentrations in food (corn, rice, and wheat) in affected areas were markedly higher than in the control samples. Cadmium and lead concentrations in the tissues of affected sheep were markedly higher than in control animals (P< 0.01). Cadmium and lead concentrations in blood and hair samples from affected farmers were markedly higher than the control samples (P < 0.01). The occurrence of anemia in affected persons and animals followed a hypochromic and microcytic pattern. The intake of cadmium and lead was estimated according to herbage ingestion rates. It was found that the levels of cadmium and lead accumulated in sheep through the ingestion of vegetation growing in the sites closest to the zinc smelter were approximately 3.36 mg Cd/kg body wt./day and 38.47 mg Pb/kg body wt./day. This surpassed the fatal dosages for sheep of 1.13 mg Cd/kg body wt/day and 4.42 mg Pb/kg body wt./day. Serum total antioxidant capacity in affected humans and animals was significantly lower than in the controls (P < 0.01). The serum protein parameters in affected humans and animals were significantly reduced (P < 0.01). It was therefore concluded that heavy metal contamination has caused serious harm to sheep in this area. The heavy metal concentrations in food and grain also pose a significant risk to human health in the Chinese Wumeng mountain area.
Inferring novel lncRNA associated with Ventricular septal defect by DNA methylation interaction network
Authors: Zhang Min , Gu Yue , Su Mu , Zhang Shumei , Chen Chuangeng , Lv Wenhua , Zhang Yan
Published: November 2018

Ventricular septal defect (VSD) is one of the most common types of congenital heart disease. To find more and more molecular alteration is conducive to explore the mechanism and biomarker in VSD. Herein we devised a predictive strategy to uncover novel lncRNA of VSD integrating DNA methylation, gene expression and lncRNA expression of early embryo and VSD by profiles from GEO database. In totally, 175 lncRNAs, 7290 genes and 3002 DNA methylation genes were obtained by logistic regression analysis associated with embryonic development. Moreover, 7304 DMGs were significant differential methylated by Wilcoxon rank test and Student’s test in VSD. We constructed the lncRNA-mRNA co-expression network in embryo (LMCNe). Then, a reconstructed co-expression weighted network (RCWN) was built integrated LMCNe and the DNA methylation associated network (DMAN) based on the correlation of the DNA methylation level and protein interaction network between embryonic development and VSD. We extracted top 10 lncRNAs with higher score performing DRaWR from the weight network, which as potential VSD related lncRNAs. Six lncRNAs showed a high level of expression in the heart tissue recorded in the NONOCOND database. Furthermore, associated lncRNA genes DCAF8L1, NIT1, SH2D7 and DOCK9-AS2 in validated samples showed a prominently association with VSD. These outcomes provide a reference for lncRNA involved in VSD initialization and a new insight for studies of VSD-associated lncRNAs.

Author Summary

Ventricular septal defect (VSD) is one of the most common types of congenital heart disease and has a high mortality rate in infants. Many molecular markers have proved effective as biomarker in VSD like DNA methylation and lncRNA. lncRNA is a type of non-coding RNA which has important effect in regulation gene expression and disease occurrence. VSD is an embryonic stage developmental disease. Therefore we hypothesized that lncRNA which was associated with DNA methylation and mRNA in early embryonic development may also affect the occurrence of VSD. So in this work, from the perspective of embryonic development, we devised a predictive strategy to uncovering novel lncRNA of VSD. In our result, four lncRNA associated genes were found differential expressed in VSD and normal samples by qPCR validation. The identification of lncRNA associated with ventricular septal defect is beneficial to further study the mechanism of VSD from the molecular level and also provides a good molecular marker for clinical therapeutic and diagnosis. At the same time, it also provides a new insight for the researches of lncRNA associated with VSD.
Aneuvis: Web-based exploration of numerical chromosomal variation in single cells
Authors: Piqué Daniel G , Andriani Grasiella A , Maggi Elaine , Zimmerman Samuel E , Greally John M , Montagna Cristina , Mar Jessica C.
Published: November 2018

Motivation

Aberrations in chromosomal copy number are one of the most common molecular features observed in cancer. Quantifying the degree of numerical chromosomal variation in single cells across a population of cells is of interest to researchers studying whole chromosomal instability (W-CIN). W-CIN, a state of high numerical chromosomal variation, contributes to treatment resistance in cancer.

Results

Here, we introduce aneuvis, a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation.

Availability and Implementation

Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/. Website implemented using Shiny version 1.0.5 with all major browsers supported. All source code for the application is available at https://github.com/dpique/aneuvis.
Inhalation of marijuana affects Drosophila heart function
Authors: Gómez IM , Rodríguez MA , Santalla M , Kassis G , Colman Lerner JE , Aranda O , Sedán D , Andrinolo D , Valverde CA , Ferrero P
Published: November 2018

Medical uses of marijuana have been recently approved in many countries, and after a long ban on research, there is despicable scientific evidence regarding its action and side effects. We investigated the effect of inhalation of vaporized marijuana on cardiac function in Drosophila melanogaster, a suitable genetic model for assessing cardiovascular function. Chronic exposure of adult flies to vaporized marijuana reduces heart rate, increments contractility and prolongs relaxation. These changes are manifested in the cardiomyocytes with no effect in calcium handling, and in the absence of the canonical cannabinoids receptors identified in mammals. Our results are the first evidence of the in vivo impact of phytocannabinoids in D. melanogaster and open new paths for genetic screenings using vaporized compounds, providing a simple and affordable platform prior to mammalian models.
The landscape of antigen-specific T cells in human cancers
Authors: Li Bo , Liu Longchao , Zhang Jian , Chen Jiahui , Ye Jianfeng , Filatenkov Alexander , Shukla Sachet , Qiao Jian , Zhan Xiaowei , Wu Catherine , Fu Yang-Xin
Published: November 2018

Antigen-specific T cells can be orchestrated to kill cancer cells in immunotherapies but the utilities of the TCR information have not been fully explored. Here, we leveraged previous efforts on tumor TCR repertoire, and developed a novel algorithm to characterize antigen-specific TCR clusters. Joint analysis with gene expression revealed novel regulators for T cell activation. Investigation of single-cell sequencing data revealed a novel subset of tissue-resident memory T cell population with elevated metabolic status. Integrative analysis of TCR clusters with HLA alleles and cancer genomics data identified candidate antigens derived from missense mutations, frameshift indels, and tumor-associated gene overexpression. Predicted antigenHSFX1was further validated using vaccinated humanized HLA-A*02:01 mice. Finally, high abundant cancer-associated TCRs were observed in the blood repertoire of early breast cancer patients, suggesting new avenues for noninvasive early detection. Thus, our analysis identified cancer-associated T cells with broad utilities in immune monitoring and cancer immunotherapies.
Chiral twisting in cytoskeletal polymers regulates filament size and orientation
Authors: Shi Handuo , Quint David , Gopinathan Ajay , Huang Kerwyn Casey
Published: November 2018

While cytoskeletal proteins in the actin family are structurally similar, as filaments they act as critical components of diverse cellular processes across all kingdoms of life. In many rod-shaped bacteria, the actin homolog MreB directs cell-wall insertion and maintains cell shape, but it remains unclear how structural changes to MreB affect its physiological function. To bridge this gap, we performed molecular dynamics simulations forCaulobacter crescentusMreB and then utilized a coarse-grained biophysical model to successfully predict MreB filament propertiesin vivo.We discovered that MreB double protofilaments exhibit left-handed twisting that is dependent on the bound nucleotide and membrane binding; the degree of twisting determines the limit length and orientation of MreB filamentsin vivo.Membrane binding of MreB also induces a stable membrane curvature that is physiologically relevant. Together, our data empower the prediction of cytoskeletal filament size from molecular dynamics simulations, providing a paradigm for connecting protein filament structure and mechanics to cellular functions.
Embryonic In Situ Hybridization for the Tardigrade Hypsibius exemplaris
Authors: Smith Frank W.
Published: November 2018

In situ hybridization is a method for visualizing embryonic gene expression that is amenable to nonmodel systems. Here, an in situ hybridization protocol is presented for the tardigrade Hypsibius exemplaris This method allows gene expression to be visualized directly and with fluorescence microscopy.
Microinjection of dsRNA in Tardigrades
Authors: Tenlen Jennifer R.
Published: November 2018

Classical genetic analysis in the tardigrade Hypsibius exemplaris is a challenge because these animals are parthenogens. The publication of the H. exemplaris genome has facilitated the study of targeted genes by RNA interference (RNAi), a robust mechanism to disrupt gene function. This protocol describes microinjection of double-stranded RNA (dsRNA) in tardigrades using techniques adapted from protocols originally developed in Caenorhabditis elegans. A DNA template (either genomic or cDNA) is used to prepare dsRNA, to which T7 polymerase binding sites are added at the 5′ end of each strand. The dsRNA is injected into adult tardigrades, preferably targeting the gonad or intestine. Injected adults are allowed to recover in spring water and then transferred to culture dishes or individual wells of a 96-well plate.
Introducing the recovery inspiration group: promoting hope for recovery with inspirational recovery stories
Authors: Elsegood Kelly J. , Anderson Lucinda , Newton Rachel
Published: November 2018

Purpose

The purpose of this paper is to undertake a preliminary evaluation of a novel intervention – Recovery Inspiration Group, which uses recovery stories to promote hope and inspiration for recovery among people with complex mental health difficulties.

Design/methodology/approach

The Recovery Inspiration Group was delivered to women on a specialist personality disorder inpatient unit, who were concurrently participating in a dialectical behaviour therapy (DBT) Programme. In total, 12 service users participated in the RIG and as part of the intervention, wrote down key reflections after hearing each recovery story. A thematic analysis of these reflections formed the primary basis of the evaluation. Descriptive statistics derived from a service user feedback survey (n=6) supplemented the qualitative findings.

Findings

Three themes were identified in the qualitative data, suggesting that participants had engaged with recovery-oriented reflections and experiences: recovery stories as validating and inspiring; Generalisation of DBT skills; shifting perspectives of recovery: doing better rather than being better. The survey results unanimously endorsed the RIG as a worthwhile and validating experience, which participants would recommend to other service users.

Practical implications

Recovery Inspiration Group appears to be a low-cost and easily replicable intervention with the potential to promote hope and inspiration for recovery among people with complex mental health difficulties.

Originality/value

Recovery Inspiration Group is a novel approach to harnessing the wisdom of people with lived experience of mental health difficulties, to foster hope among users of mental health inpatient services.
China’s role in the new round of restructuring of regional division of labor in East Asia
Authors: Liu Hongzhong , Shi Daqian
Published: November 2018

Purpose

The purpose of this paper is to explain the reasons and development trend of the new round of restructuring of regional division of labor in East Asia after the global financial crisis and the role of China in the process.

Design/methodology/approach

The paper probes into four factors leading to the adjustment of regional division of labor in East Asia before analyzing its development trend trough comparing the change of roles of China and ASEAN in the process.

Findings

After the flying-geese division and regional production network, East Asia’s regional division of labor is getting a new round of structural adjustment. The analysis of this paper shows that this adjustment is mainly due to global financial crisis, post-crisis de-globalization, the rebalancing of East Asian economies and China’s economic transformation. From the adjustment direction, the main trend is ASEAN gradually replacing China to become the new assembly plant area, while China becomes a new manufacturing power by its rising status in the global value chain.

Originality/value

The paper describes the development trend of the new round of restructuring of regional division of labor in East Asia in the future and gives the policy implications for the East Asian countries.