bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumor Budding and Other Risk Factors of Lymph Node Metastasis in Submucosal Early Gastric Carcinoma
Authors: Du Mingzhan , Chen Ling , Cheng Yuqing , Wang Yaohui , Fan Xiangshan , Zhang Yifen , Zhou Xiaoli , Guo Lingchuan , Xu Guifang , Zou Xiaoping , Huang Qin
Published: May 2019

Compared with early gastric intramucosal carcinoma, submucosal carcinoma is known to have a higher risk for lymph node metastasis (LMN), but risk factors in submucosal carcinoma remain elusive. In this multicenter study with 621 radical gastrectomies for submucosal early gastric carcinoma, we investigated tumor budding and other risk factors of LMN that were identified in 172 cases (27.7%). Overall, independent high-risk factors for LMN included lymphovascular invasion (odds ratio, 3.9; 95% confidence interval, 2.5-6.1), tumor budding (odds ratio, 3.3; 95% confidence interval, 1.9-5.9), mixed tubular/papillary adenocarcinoma with poorly cohesive carcinoma (odds ratio, 2.1; 95% confidence interval, 1.0-4.3), and female sex (odds ratio, 1.6; 95% confidence interval, 1.0-2.6), whereas gastric cardiac submucosal carcinomas had a significantly lower risk for LMN (odds ratio, 0.5; 95% confidence interval, 0.3-0.9). In 276 well/moderately differentiated tubular or papillary submucosal early gastric carcinomas, independent risk factors were tumor budding (odds ratio, 3.7; 95% confidence interval, 1.6-8.7), deep submucosal (SM2) invasion (odds ratio, 3.1; 95% confidence interval, 1.3-7.6), and lymphovascular invasion (odds ratio, 2.7; 95% confidence interval, 1.3-5.6). In 174 cases without tumor budding and lymphovascular invasion, no LMN was identified in 47 cardiac tumors, and 15 tumors <1.0 cm in size. In conclusion, tumor budding, lymphovascular invasion, mixed tubular/papillary adenocarcinoma with poorly cohesive carcinoma, and female gender were found to be significant high-risk factors for LMN in submucosal early gastric carcinoma, while submucosal gastric cardiac carcinoma had a significantly lower risk for nodal metastasis.
Metastasizing Pleomorphic Adenoma
Authors: Wasserman Jason K. , Dickson Brendan C. , Smith Adam , Swanson David , Purgina Bibianna M. , Weinreb Ilan
Published: May 2019

Pleomorphic adenoma (PA) is the most common salivary gland neoplasm. On a molecular level PA is characterized by a translocation involvingPLAG1orHMGA2. PA is considered to be a benign tumor although it can undergo malignant transformation. Alternatively, cases of histologically benign PA “metastasizing” to lymph nodes or distant body sites are well documented. Several theories have been proposed to explain this behavior. However, there is a lack of molecular data available to assess the relationship of metastasizing PA (MPA) and their benign counterparts. In this study we describe 4 cases of MPAs and perform the first molecular study linking them to conventional PA. The index case was identified in the course of routine clinical practice, while the other cases were retrieved from the archives of the authors. Slides were reviewed to confirm the diagnosis of both the primary/recurrent tumor and the metastasis. Fluorescence in situ hybridization (FISH) was performed in all cases and RNA sequencing was performed on the index case. In all cases there was a history of recurrent PA involving the parotid. Lymph node metastases were identified in 2 cases; non–lymph node metastases were identified in 3 cases. All the metastases were histologically benign. RNA sequencing performed on the index case demonstrated a novelHMGA2-TMTC2translocation, which was confirmed by separate FISH break-apart assays for both genes. FISH performed on the remaining cases demonstrated rearrangement ofPLAG1in all 3 cases. This study demonstrates that MPA harbors the same disease-defining molecular hallmark as their benign counterparts.
Use of Immunohistochemical Markers (HNF-1β, Napsin A, ER, CTH, and ASS1) to Distinguish Endometrial Clear Cell Carcinoma From Its Morphologic Mimics Including Arias-Stella Reaction
Authors: Ji Jennifer X. , Cochrane Dawn R. , Tessier-Cloutier Basile , Leung Samuel , Cheng Angela S. , Chow Christine , Gilks Blake , Huntsman David G. , Hoang Lynn N.
Published: May 2019

The diagnosis of clear cell (CC) carcinoma of the endometrium can be challenging, especially when endometrioid (EC) and serous (SC) endometrial cancers exhibit nonspecific clear cell changes, in carcinomas with mixed histology and in the setting of Arias-Stella reaction (ASR). In this study, classic CC immunohistochemical markers (Napsin A, HNF-1β, and ER) and 2 recent novel markers, cystathionine gamma-lyase (CTH) and arginosuccinate synthase (ASS1), are assessed for their utility in distinguishing CC from its morphologic mimics. Tissue microarrays containing 64 CC, 128 EC, 5 EC with clear cell change, 16 SC, 5 mixed carcinomas, and 11 whole ASR sections were stained, with 12 additional examples of ASR stained subsequently. A cutoff of 70% and moderate intensity were used for HNF-1β, 80% of cells and strong intensity were used for CTH, and any staining was considered positive for the remaining markers. For differentiating CC from pure EC and SC, HNF-1β, Napsin A, and CTH all performed well. HNF-1β had higher specificity (99.3% vs. 95.1%) but lower sensitivity (55.8% vs. 73.1%) compared with Napsin A. CTH did not substantially outperform HNF- 1β or Napsin A (sensitivity 51.9%, specificity 99.3%). ASS1 and ER were not helpful (specificities of 60.1% and 22.6%). For differentiating CC from ASR, HNF-1β, Napsin A, and CTH stained a large proportion of ASR and were not useful. However, ER positivity and ASS1 negativity were helpful for identifying ASR (specificity 88.2% and 95.1%, respectively). EC with clear cell changes exhibited immunohistochemical patterns similar to pure EC (HNF-1β−, ER+, and CTH−). No markers were useful in confirming the CC components in mixed carcinomas.
Imaging Features of Hepatocellular Carcinoma
Authors: Son Jinwoo , Hwang Shin Hye , Park Sumi , Han Kyunghwa , Chung Yong Eun , Choi Jin-young , Kim Myeong-jin , Park Mi-Suk
Published: May 2019

Objectives

The aim of this study was to compare the major imaging features of hepatocellular carcinoma (HCC) on magnetic resonance imaging (MRI) scans with Gd-EOB-DTPA (EOB) and extracellular agent (ECA; Gd-DTPA) contrast media.

Materials and Methods

Among 184 surgically proven HCCs in 169 patients who underwent a liver MRI with either EOB (n = 120) or ECA (n = 49), 55 HCCs were matched according to tumor size, Edmonson grade (major and worst), and gross type for each of the 2 contrast media. For the qualitative analysis, 2 board-certified radiologists independently reviewed arterial phase hyperenhancement, hypointensity on portal venous phase, hypointensity on delayed or transitional phase (DP/TP, 120–150 seconds), and capsule appearance. For the quantitative analysis, a third radiologist measured the signal intensity at each phase by placing the region of interest for tumor and normal liver parenchyma. The lesion-to-liver contrast (LLC) and lesion-to-liver contrast enhancement ratio (LLCER) were calculated.

Results

On qualitative analysis, hypointensity on DP/TP was seen more frequently with EOB (91% in reader 1, 89% in reader 2) than with ECA (73% in reader 1, 75% in reader 2; P = 0.026). Capsule appearance was seen less frequently with EOB (31% in reader 1, 44% in reader 2) than with ECA (73% in reader 1, 78% in reader 2; P < 0.001). On quantitative analysis, the LLC on arterial phase (AP) was better with ECA (P = 0.003), whereas LLC on DP was better with EOB (P < 0.001). The LLCER from precontrast to AP was higher with ECA (P = 0.022), whereas the LLCER from portal venous phase to DP was higher with EOB (P < 0.001).

Conclusions

ECA-MRI revealed better LLC on AP and detection rate of capsule appearance than EOB-MRI. EOB-MRI showed superior LLC on TP.
Efficacy and Safety of Electroconvulsive Therapy in Adolescents
Authors: Karayağmurlu Ali , Coşkun Murat , Elboğa Gülçin , Ghaziuddin Neera , Karayağmurlu Elif , Gökçen Cem , Altindağ Abdurrahman
Published: May 2019

Objective

The aim of this study was to report the efficacy and safety of electroconvulsive therapy (ECT) in manic, depressed, psychotic, and catatonic adolescent patients.

Methods

Medical records of 78 adolescents who had received ECT in Department of Psychiatry, Gaziantep University Medical Faculty, during 2011 to 2017 were reviewed. Sixty-two subjects in this sample were identified to have complete records and met the study inclusion criteria.

Results

The mean ± SD age of subjects was 17.11 ± 1.04 years and female sex was 53.2% (n = 33). Primary the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision or the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition diagnoses were bipolar mood disorders (n = 33, 53.2%), major depressive disorder (n = 16, 25.8%), schizophrenia (n = 8, 12.9%), and schizoaffective disorders (n = 5, 8.1%). Electroconvulsive therapy was significantly effective in treating manic, depressive, psychotic, and catatonia symptoms as evidenced by significant differences in pretreatment and posttreatment scores in outcome measures including Hamilton Depression Rating Scale, Young Mania Rating Scale, Positive and Negative Syndrome Scale, and Clinical Global Impression-Severity Scale (P < 0.001). Presence of comorbidity adversely affected treatment response (P = 0.001). However, ECT was also effective in those with comorbid diagnoses (P < 0.001). Depressive symptoms in patients with bipolar depression responded better than those with unipolar depression (P = 0.012). Electroconvulsive therapy was generally safe with subjective memory complaints (85%), headache (69%), and prolonged seizure (8%) as the reported adverse effects possibly related to ECT. Four subjects (6%) developed a manic switch during ECT.

Conclusions

Electroconvulsive therapy is an effective and a safe treatment option in adolescent patients with severe and resistant psychopathology. Although comorbidity may decrease treatment response, ECT seems to be effective even in the presence of multiple psychiatric diagnoses.
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
Authors: Wang Wenxi , Wang Zihao , Li Xintong , Ni Zhongfu , Hu Zhaorong , Xin Mingming , Peng Huiru , Yao Yingyin , Sun Qixin , Guo Weilong
Published: May 2019

Background

The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate genomic variations across hundreds or even thousands of samples in the post-genomic era. The management and exploration of these large-scale genomic variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new genomic variation data in diverse species.

Results

Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale genomic variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs.

Conclusions

SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.
Temporal Gut Microbial Changes Predict RecurrentClostridium difficilein Patients with and without Ulcerative Colitis
Authors: Lee Allen A. , Rao Krishna , Limsrivilai Julajak , Gillilland Merritt , Malamet Benjamin , Briggs Emily , Young Vincent B. , Higgins Peter DR
Published: May 2019

Background

Ulcerative colitis (UC) carries an increased risk of primary and recurrentClostridium difficileinfection (rCDI) and CDI is associated with UC flares. We hypothesized that specific fecal microbial changes associate with UC flare and rCDI.

Methods

We conducted a prospective observational cohort study of 57 patients with UC and CDI, CDI only, and UC flare only. Stool samples were collected at baseline, at the end of antibiotic therapy, and after reconstitution for 16S rRNA sequencing. The primary outcomes were recurrent UC flare and rCDI. Logistic regression and Lasso models were constructed for analysis.

Results

There were 21 (45.7%) patients with rCDI, while 11 (34.4%) developed UC flare. Patients with rCDI demonstrated significant inter-individual (P=.008) and intra-individual differences (P=.004 relative to baseline samples) in community structure by Jensen-Shannon distance (JSD) compared with non-rCDI. Two cross-validated models identified by Lasso regression predicted risk of rCDI: a baseline model with female gender, hospitalization for UC in the past year, increased Ruminococcaceae and Verrucomicrobia, and decreased Eubacteriaceae, Enterobacteriaceae, Lachnospiraceae, and Veillonellaceae (AuROC=0.94); and a model 14 days after completion of antibiotics with female gender, increased Shannon diversity, Ruminococcaceae and Enterobacteriaceae, and decreased community richness and Faecalibacterium (AuROC=0.9). Adding JSD between baseline and post-treatment samples to the latter model improved fit (AuROC=0.94). A baseline model including UC hospitalization in the past year and increased Bacteroidetes showed good fit characteristics for predicting increased risk of UC flare (AuROC=0.88).

Conclusion

Fecal microbial features at baseline and following therapy predict rCDI risk in patients with and without UC. These results may help risk stratify patients to guide management.
Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans
Authors: Knaus Brian J. , Tabima Javier F. , Shakya Shankar K. , Judelson Howard S. , Grünwald Niklaus J.
Published: May 2019

The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3x). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of super-fit clone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby higher copy number provides fitness leading to replacement of prior clonal lineages.
Community-level signatures of ecological succession in natural bacterial communities
Authors: Pascual-García Alberto , Bell Thomas
Published: May 2019

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We present an integrative top-down analysis of over 700 bacterial communities sampled from water-filled beech tree-holes in the United Kingdom at distances between <5m to >100km, combining an analyses of community composition (16S rRNA sequencing) with assays of community functional capacity (exo-enzymatic activities, ATP production, CO2 dissipation and yield). The communities were grown in laboratory conditions in a complex growth medium, what allowed us to investigate the relationship between composition and function, excluding confounding environmental factors. We found a distance-decay trend in the similarity of the communities, and simulated data allowed us to reject the hypothesis that stochastic processes dominated the assembly of the communities, suggesting that niche effects prevailed. Consistent with this idea, clustering of communities lead us to identify six distinct community classes encompassing samples collected at often distant locations. Using structural equation modelling, we explored how functions were interrelated, demonstrating that a representative functional signature can be associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions with PiCRUST. Notably, this approach allowed us to show that these classes contain distinct genetic repertoires reflecting community-level ecological strategies. We finally formulated an over-arching ecological hypothesis about how local conditions drive succession in these habitats. The ecological strategies resemble the classical distinction between r- and K-strategists and could be extrapolated to other systems, suggesting that a coarse grained picture of microbial ecological succession may be explained by relatively simple ecological mechanisms.
De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits
Authors: Ng Simon , Juang Yu-Chi , Chandramohan Arun , Kristal Kaan Hung Yi , Sadruddin Ahmad , Yuen Tsz Ying , Ferrer Fernando J. , Lee Xue’Er Cheryl , Xi Liew , Johannes Charles W. , Brown Christopher J. , Kannan Srinivasaraghavan , Aronica Pietro G. , Berglund Nils , Verma Chandra S. , Liu Lijuan , Stoeck Alexander , Sawyer Tomi K. , Partridge Anthony W. , Lane David P.
Published: May 2019

Discovery of false-positive target binding, due to assay interference or aggregation, presents a significant problem for drug discovery programs. These issues may often be unrealized and could lead researchers astray if not subject to independent verification of reproducibility and/or on-target mechanism of action. Although well-documented for small molecules, this issue has not been widely explored for peptide modality. As a case study, we demonstrate that two purported KRas inhibitors, stapled peptide SAH-SOS1A and macrocyclic peptide cyclorasin 9A5, exemplify false-positive molecules – both in terms of their sub-micromolar KRas binding affinities and their on-target cellular activities. We observed that the apparent binding of fluorescein-labeled SAH-SOS1A given by a fluorescence polarization assay is sensitive to detergent. False-positive readouts can arise from peptide adsorption to the surface of microplates. Hence, we used surface plasmon resonance and isothermal titration calorimetry to unambiguously show that both SAH-SOS1A and cyclorasin 9A5 are non-binders for KRas. Thermal shift assay and hydrogen-deuterium exchange mass spectrometry further demonstrate that both peptides destabilize KRas and induce unfolding of the protein. Furthermore, both peptides caused significant release of intracellular lactate dehydrogenase, suggesting that membrane rupture rather than on-target activity is accountable for their reported cytotoxicity. Finally, both peptides exhibited off-target activities by inhibiting the proliferation of U-2 OS and A549 cells, despite their independency of the KRas signaling pathway. Our findings demonstrate the critical need to employ orthogonal binding assays and cellular counter-screens to de-risk false-positive molecules. More rigorous workflows should lead to improved data and help obviate inadvertent scientific conclusions.

Significance statement

False positive molecule hits occur frequently in high-throughput screens and can contaminate the scientific literature. This has become an increasingly serious issue in small molecule drug discovery and chemical probe development and it is not surprising that peptides may be similarly prone to assay interference. Using KRas as a target and two known macrocyclic peptide inhibitors as a case study, we clearly show that reporter-free biophysical assays and cellular counter-screens offer the solution to detect and de-risk the potential of false-positive compounds. We further discuss the advantages, limitations and overall strategic importance of such methods.
Clinical manifestations and phenotypic analysis of new ANK1 gene mutations in 12 Chinese children with hereditary spherocytosis
Authors: Xie Fei , Lei Lei , Cai Bin , Gan Lu , Gao Yu , Liu Xiaoying , Zhou Lin , Jiang Jinjin
Published: May 2019

Objective

To summarize the clinical features and laboratory examination of ANK1 gene in 12 children with hereditary spherocytosis in China, and to determine the genetic mutations in those children.

Methods

The clinical data of children and their parents were collected and analyzed. The sequence of related genes was analyzed by second-generation sequencing technology. The suspected pathogenic mutations were detected by Sanger sequencing

Results

New mutations in the coding region of ANK1 was detected in 12 patients, which caused amino acid changes in the gene encoding, causing structural changes or loss of function.

Conclusion

ANK1 (c.1914_c.1918delTTTG), ANK1 (c.399T>G), ANK1 (c.1564delC), ANK1 (c.4439dupA
), ANK1 (c.4510_4513del), ANK1 (c.2961delC), ANK1 (c.2142dupT), ANK1 (c.2858+1G>C), ANK1 (c.3235delG), ANK1 (c.4739A>G), ANK1 (c.2638-2 A>G), ANK1 (c. 4739A>G) mutations in the coding region of the gene are the cause of suspicious disease in these 12 Chinese children. At the same time, second-generation gene sequencing technology is an effective means of confirming HS. Different types of mutations (P=0.388)and different mutation areas (P=0.660)had no significant effect on the severity of anemia. The 12 gene mutation sites in this study have not been included in the human genome database, dbSNP (v138) and ExAC databases. The new ANK1 gene mutations found in HS children can provide further exploration of the genetic etiology of HS in Chinese population.
Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan
Authors: Matsuoka Shunsuke , Sugiyama Yoriko , Sato Hirotoshi , Katano Izumi , Harada Ken , Doi Hideyuki
Published: May 2019

Growing evidence has revealed high diversity and spatial heterogeneity of fungal communities including in local habitats in terrestrial ecosystems. These findings highlight the considerable sampling effort, analysis time, and costs required for the investigation of fungal diversity over large spatial scales. Recently, the analysis of environmental DNA in river water has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. However, previous studies have not investigated the spatial structure of fungal DNA assemblages in river water. In the present study, we investigate fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding in water across different branches of river over forest landscapes. The river water was found to contain both phylogenetically and functionally diverse fungal DNA, including aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, branches. In addition, the assemblages were more similar between spatially closer branches. These results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure can be obtained by investigating the fungal DNA assemblages in river water.
Modality-specific circuits for skylight orientation in the fly visual system
Authors: Sancer Gizem , Kind Emil , Plazaola Haritz , Balke Jana , Pham Tuyen , Hasan Amr , Münch Lucas , Mathejczyk Thomas F. , Wernet Mathias F.
Published: May 2019

In the fly optic lobe ∼800 highly stereotypical columnar microcircuits are arranged retinotopically to process visual information. Differences in cellular composition and synaptic connectivity within functionally specialized columns remains largely unknown. Here we describe the cellular and synaptic architecture in medulla columns located downstream of photoreceptors in the ‘dorsal rim area’ (DRA), where linearly polarized skylight is detected for guiding orientation responses. We show that only in DRA medulla columns, both R7 and R8 photoreceptors target to the bona fide R7 target layer where they form connections with previously uncharacterized, modality-specific Dm neurons: Two morphologically distinct DRA-specific cell types (termed Dm-DRA1 and Dm-DRA2) stratify in separate sublayers and exclusively contact polarization-sensitive DRA inputs, while avoiding overlaps with color-sensitive Dm8 cells. Using the activity-dependent GRASP and trans-Tango techniques, we confirm that DRA R7 cells are synaptically connected to Dm-DRA1, whereas DRA R8 form synapses with Dm-DRA2. Finally, using live imaging of ingrowing pupal photoreceptor axons, we show that DRA R7 and R8 termini reach layer M6 sequentially, thus separating the establishment of different synaptic connectivity in time. We propose that a duplication of R7→Dm circuitry in DRA ommatidia serves as an ideal adaptation for detecting linearly polarized skylight using orthogonal e-vector analyzers.
A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system
Authors: Gillingham Mark A.F. , Montero B. Karina , Wihelm Kerstin , Grudzus Kara , Sommer Simone , Santos Pablo S.C.
Published: May 2019

ABSTRACT

Genotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most next-generation sequencing genotyping pipelines have been validated in non-model systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and copy number variation (CNV) within a PCR remains poorly described. Here we investigate the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well defined “optimal” primers, we simulated a non-model species situation by designing “naive” primers, with sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA) to the data, and compared its performance with another, previously published, pipeline. ACACIA yielded very high allele calling accuracy (>98%). Non-chimeric artefacts increased linearly with increasing CNV but chimeric artefacts leveled when amplifying more than 4-6 alleles. As expected, we found heterogeneous amplification efficiency of allelic variants when co-amplifying multiple loci. Using our validated ACACIA pipeline and the example data of this study, we discuss in detail the pitfalls researchers should avoid in order to reliably genotype complex multigene systems. ACACIA and the datasets used in this study are publicly available at GitLab and FigShare (https://gitlab.com/psc_santos/ACACIAandhttps://figshare.com/projects/ACACIA/66485).
Programmed Switch in The Mitochondrial Degradation Pathways During Human Retinal Ganglion Cell Differentiation from Stem Cells is Critical for RGC Survival
Authors: Das Arupratan , Bell Claire M. , Berlinicke Cynthia A. , Marsh-Armstrong Nicholas , Zack Donald J.
Published: May 2019

Retinal ganglion cell (RGC) degeneration is the root cause for vision loss in glaucoma as well as in other forms of optic neuropathies. Genetic analysis indicated abnormal mitochondrial quality control (MQC) as a major risk factor for optic neuropathies. However, nothing is known on how MQC regulates human retinal ganglion cell (hRGC) health and survival. Human pluripotent stem cells (hPSCs) provide opportunity to differentiate hRGCs and understand the abnormal MQC associated hRGC degeneration in great detail. Degradation of damaged mitochondria is a very critical step of MQC, here we have used stem cell derived hRGCs to understand the damaged mitochondrial degradation pathways for hRGC survival. Using pharmacological methods, we have investigated the role of the proteasomal and endo-lysosomal pathways in degrading damaged mitochondria in hRGCs and their precursor stem cells. We find that upon mitochondrial damage with the proton uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP), hRGCs more efficiently degraded mitochondria than their precursor stem cells. We further identified that for degrading damaged mitochondria, stem cells predominantly use the ubiquitine-proteasome system (UPS) while hRGCs use the endo-lysosomal pathway. UPS inhibition causes apoptosis in stem cells, while hRGC viability is dependent on the endo-lysosomal pathway but not on the UPS pathway. This suggests manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma. Endo-lysosome dependent cell survival is also conserved for other human neurons as differentiated human cerebral cortical neurons also degenerated upon endo-lysosomal inhibition but not for the proteasome inhibition.

SIGNIFICANCE STATEMENT

Using human stem cells we have shown a switch in the mitochondrial degradation pathway during hRGC differentiation where endo-lysosomal pathway becomes the predominant pathway for cellular homeostasis and hRGC survival which is also true for human cortical neurons. These findings suggest manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma as well as for other neurodegenerative diseases.
The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex
Authors: Bouvrais H. , Chesneau L. , Cunff Y. Le , Fairbrass D. , Soler N. , Pastezeur S. , Pécot T. , Kervrann C. , Pécréaux J.
Published: May 2019

In theCaenorhabditis eleganszygote, astral microtubules generate forces, pushing against and pulling from the cell periphery. They are essential to position the mitotic spindle. By measuring the dynamics of astral microtubules at the cortex, we revealed the presence of two populations, residing there for 0.4 s and 1.8 s, which correspond to the pulling and pushing events, respectively. Such an experiment offers a unique opportunity to monitor both forces that position the spindle under physiological conditions and study their variations along the anteroposterior axis (space) and the mitotic progression (time). By investigating pulling-force-generating events at the microscopic level, we showed that an anteroposterior asymmetry in dynein on-rate – encoding pulling-force imbalance – is sufficient to cause posterior spindle displacement. The regulation by spindle position – reflecting the number of microtubule contacts in the posterior-most region – reinforces this imbalance only in late-anaphase. Furthermore, we exhibited the first direct proof that the force-generator increasing persistence to pull (processivity) accounts for the temporal control of pulling force throughout mitosis. We thus propose a three-fold control of pulling force, by the polarity, spindle position and mitotic progression. Focusing on pushing force, we discovered a correlation between its density and the stability of the spindle position during metaphase, which strongly suggests that the pushing force contributes to maintaining the spindle at the cell centre. This force remains constant and symmetric along the anteroposterior axis during the division. The pulling one increases in intensity and becomes dominant at anaphase. In conclusion, the two-population study enabled us to decipher the complex regulation of the spindle positioning during cell division.
Novel differential linear B-cell epitopes to identify Zika and dengue virus infections in patients
Authors: Amrun Siti Naqiah , Yee Wearn-Xin , Bakar Farhana Abu , Lee Bernett , Kam Yiu-Wing , Lum Fok-Moon , Tan Jeslin J.L. , Lim Vanessa W.X. , Watthanaworawit Wanitda , Ling Clare , Nosten Francois , Renia Laurent , Leo Yee-Sin , Ng Lisa F.P.
Published: May 2019

Background

Recent Zika virus (ZIKV) outbreaks challenged existing laboratory diagnostic standards, especially for serology-based methods. Due to the genetic and structural similarity of ZIKV with other flaviviruses, this results in cross-reactive antibodies which confounds serological interpretations.

Methods

Plasma from Singapore ZIKV patients was screened longitudinally for antibody responses and neutralizing capacities against ZIKV. Samples from healthy controls, ZIKV and DENV patients were further assessed using ZIKV and DENV peptides of precursor membrane (prM), envelope (E) or non-structural 1 (NS1) viral proteins in a peptide-based ELISA for epitope identification. Identified epitopes were re-validated and diagnostically evaluated using sera of patients with DENV, bacteria or unknown infections from Thailand.

Results

Long-lasting ZIKV-neutralizing antibodies were elicited during ZIKV infection. Thirteen potential linear B-cell epitopes were identified and of these, four common flavivirus, three ZIKV-specific, and one DENV-specific differential epitopes had more than 50% sensitivities and specificities. Notably, ZIKV-specific peptide 26 on domain I/II of E protein (amino acid residues 271-288) presented 80% sensitivity and 85.7% specificity. Importantly, the differential epitopes also showed significance in differentiating non-flavivirus patient samples.

Conclusions

Linear B-cell epitope candidates to differentiate ZIKV and DENV infections were identified, providing the first step towards the design of a much-needed serology-based assay.
Myeloid Lineage Enhancers Drive Oncogene Synergy in CEBPA/CSF3R Mutant Acute Myeloid Leukemia
Authors: Braun Theodore P. , Okhovat Mariam , Coblentz Cody , Carratt Sarah A. , Foley Amy , Schonrock Zachary , Nevonen Kimberly , Davis Brett , Garcia Brianna , LaTocha Dorian , Weeder Benjamin R. , Grzadkowski Michal R. , Estabrook Joey C. , Manning Hannah G. , Watanabe-Smith Kevin , Smith Jenny L. , Leonti Amanda R. , Ries Rhonda E. , Jeng Sophia , McWeeney Shannon , Genua Cristina Di , Drissen Roy , Nerlov Claus , Meshinchi Soheil , Carbone Lucia , Druker Brian J. , Maxson Julia E.
Published: May 2019

Acute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. This finding of mutation-synergy is broadly applicable other mutations that activate the JAK/STAT pathway or disrupt CEBPA function (i.e. activating mutations in JAK3 and Core Binding Factor translocations). The interaction between these distinct classes of mutations occurs at the level of myeloid lineage enhancers where mutant CEBPA prevents activation of subset of differentiation associated enhancers. To confirm this enhancer-dependent mechanism, we demonstrate that CEBPA mutations must occur as the initial event in AML initiation, confirming predictions from clinical sequencing data. This improved mechanistic understanding will facilitate therapeutic development targeting the intersection of oncogene cooperativity.
NMDA receptor activation induces long-term potentiation of glycine synapses
Authors: Kloc Michelle L. , Pradier Bruno , Chirila Anda M. , Kauer Julie A.
Published: May 2019

Of the fast ionotropic synapses, glycinergic synapses are the least well understood, but are vital for the maintenance of inhibitory signaling in the brain and spinal cord. Glycinergic signaling comprises half of the inhibitory signaling in the spinal cord, and glycinergic synapses are likely to regulate local nociceptive processing as well as the transmission to the brain of peripheral nociceptive information. Here we have investigated the rapid and prolonged potentiation of glycinergic synapses in the superficial dorsal horn of young male and female mice after brief activation of NMDA receptors (NMDARs). Glycinergic inhibitory postsynaptic currents (IPSCs) evoked with lamina II-III stimulation in identified GABAergic neurons in lamina II were potentiated by bath-applied Zn2+ and were depressed by the prostaglandin PGE2, consistent with the presence of both GlyRα1- and GlyRα3-containing receptors. NMDA application rapidly potentiated synaptic glycinergic currents. Whole-cell currents evoked by exogenous glycine were also rapidly potentiated by NMDA, indicating that the potentiation results from altered numbers or conductance of postsynaptic glycine receptors. Repetitive depolarization alone of the postsynaptic GABAergic neuron also potentiated glycinergic synapses, and intracellular EGTA prevented both NMDA-induced and depolarization-induced potentiation of glycinergic IPSCs. Driving trpv1 lineage afferents optogenetically also triggered NMDAR-dependent potentiation of glycinergic synapses. Our results suggest that during peripheral injury or inflammation, nociceptor firing during injury is likely to potentiate glycinergic synapses on GABAergic neurons. This disinhibition mechanism may be engaged rapidly, altering dorsal horn circuitry to promote the transmission of nociceptive information to the brain.

Significance

Of the fast ionotropic synapses, glycinergic synapses are the least well understood, yet glycinergic synapses comprise half of the inhibition in the spinal cord, and are likely to regulate local nociceptive processing as well as the transmission to the brain of peripheral nociceptive information. Here we report that bath applied NMDA, repetitive postsynaptic depolarization, or optogenetic activation of primary nociceptor afferents all produce LTP at superficial dorsal horn synapses. During peripheral injury or inflammation, nociceptor firing is likely to engage this mechanism in inhibitory neurons, rapidly altering dorsal horn circuitry to promote the transmission of nociceptive information to the brain.
CELF1 is an EIF4E binding protein that promotes translation of epithelial-mesenchymal transition effector mRNAs
Authors: Chaudhury Arindam , Pal Rituraj , Kongchan Natee , Zhao Na , Zhu Yingmin , Olokpa Emuejevoke , Cheema Shebna A. , del Rincon Sonia , Reineke Lucas C. , Mao Sufeng , Lloyd Richard E. , Sardiello Marco , Rosen Jeffrey M. , Neilson Joel R.
Published: May 2019

Mounting evidence is revealing a granularity within gene regulation that occurs at the level of mRNA translation. Within mammalian cells, canonical cap-dependent mRNA translation is dependent upon the interaction between the m7G cap-binding protein eukaryotic initiation factor 4E (eIF4E) and the scaffolding protein eukaryotic initiation factor 4G (eIF4G), the latter of which facilitates pre-translation initiation complex assembly, mRNA circularization, and ultimately ribosomal scanning. In breast epithelial cells, we previously demonstrated that the CELF1 RNA-binding protein promotes the translation of epithelial to mesenchymal transition (EMT) effector mRNAs containing GU-rich elements (GREs) within their 3’ untranslated regions (UTRs). Here we show that within this context, CELF1 directly binds to both the eIF4E cap-binding protein and Poly(A) binding protein (PABP), promoting translation of GRE-containing mRNAs in mesenchymal cells. Disruption of this CELF1/eIF4E interaction inhibits both EMT induction and experimental metastasis. Our findings illustrate a novel way in which non-canonical mechanisms of translation initiation underlie transitional cellular states within the context of development or human disease.
Alteration of Gut Microbiome in Lung Cancer Patients
Authors: Ming Li , Fang Yu , Xiaohui Chen , Huan Zhou , Xiaoqing Wei , Yinhui Liu , Yuanyu Liu , Li Tang , Jieli Yuan , Shu Wen , Jun Chen
Published: May 2019

Lung cancer is the leading cause of cancer death. Better understanding of factors and pathways involved in lung cancer is needed to improve diagnose and treatment strategies. Recent studies have provided insights into the possible correlation between intestinal dysbiosis and cancer development. Although the immunological relationship between gut and lung had been suggested by many researches, however, to date, no study had investigated the characterization of gut microbiome in treatment naïve lung cancer patients, whether it is distinct from that of health individuals and contribute to the onset and development of lung cancer remain unclear. In this study, we investigated whether gut microbiome of lung cancer patients (LC, n=28) is altered compare with that of matched healthy individuals (HC, n=19) by high throughout sequencing of the V3-V4 regions of 16S rDNA in their fecal samples. We also identified microbiota signatures specific for different histological types of lung cancer, including SSC, ADC, and SCLC. The gut microbiome of lung cancer patients is characterized by decreased relative abundance of Prevotella, and increased bacteria groups such as Actinomyces, and Streptococcus, etc. We also detected a mild structural shift in gut microbiome between ADC and SCLC patients. Our results showed that the gut microbiome of lung cancer patients altered significantly compared with healthy individuals. However, the association between microbial dysbiosis and lung cancer is not clearly understood, future studies involving larger cohorts and metagenomics, or metabolomics, may elucidate the correlations between gut microbiota and lung cancer development.

IMPORTANCE

This is the first report to show the alteration of gut microbiome in lung cancer patients. Our results showed that the gut microbiome of lung cancer patients altered significantly compared with healthy individuals.
Transgenerational inheritance of betaine-induced epigenetic alterations in estrogen-responsive IGF-2/IGFBP2 genes in rat hippocampus
Authors: Yang Yang , Yang Shu , Jiang Wenduo , Qi Fulei , Zhao Ruqian
Published: May 2019

Betaine as a methyl donor participates in DNA methylation. Here, we sought to investigate the effects of betaine on hippocampal expression of neurogenesis genes and their DNA methylation status across three generations. Pregnant rats (F0) were fed control and betaine-supplemented diets throughout gestation and lactation; and female F1 and F2 offspring at weaning, together with the F0 dams, were used in the study. Hippocampal expression of aromatase, estrogen receptor α and estrogen related receptor β was down-regulated in F1, together with the estrogen-responsive IGF-2/IGFBP2 genes. However, all these genes were up-regulated in F2, which follows the same pattern of F0. In agreement with changes in mRNA expression, the imprinting control region (ICR) of IGF-2 gene was hypomethylated in F1 but hypermethylated in F2 and F0. In contrast, the promoter DNA methylation status of all the affected genes was hypermethylated in F1 but hypomethylated in F2 and F0. Betaine homocysteine methyltransferase followed same pattern of transgenerational inheritance. These results indicate that betaine exerts a transgenerational effect on hippocampal expression of estrogen-responsive genes in rat offspring, which is associated with corresponding alterations in DNA methylation on ICR of IGF-2 gene and the promoter of affected genes.

Author Summary

Epigenetic transgenerational inheritance is defined as the phenotypic change across generations and germline transmission of epigenetic information without direct genetic manipulation or environmental exposure. Maternal and paternal diet has been shown to have transgenerational behavioral and physiological effects. Maternal intake of methyl donors, including folate, betaine, and choline during different gestation period alters epigenetic modifications of many imprinted genes in the genomic DNA isolated from cord blood. Betaine as a methyl donor nutrition plays an important role in brain development. However, the effect of maternal betaine supplementation on transgenerational inheritance of imprinted gene IGF-2 in offspring hippocampus is still unknown. Here, we sought to investigate the effects of betaine on rat hippocampal expression of neurogenesis genes and their DNA methylation status across three generations. We found that betaine significantly decreased estrogen-responsive genes IGF-2/IGFBP2 expression in rat F1 offspring, yet increased in F2 offspring, which is associated with corresponding alterations in DNA methylation on ICR of IGF-2 gene and the promoter of affected genes. Our results suggesting that maternal methyl donor nutrition supplementation may be exert an epigenetic transgenerational effect on female offspring.
Exploring the food tourism landscape and sustainable economic development goals in Dhofar Governorate, Oman
Authors: Enzenbacher Debra J.
Published: May 2019

Purpose

This exploratory research opens a new avenue of tourism destination enquiry for Dhofar Governorate, Oman. It examines the relationship between the food tourism landscape in the country’s southernmost region and the Government’s stated economic development goals. Tourism is a new industry here and in need of sustainable development. The purpose of this paper is to identify how the natural and human resources of the region may be harnessed to expand food tourism pathways and achieve sustainable economic development e.g. maximising stakeholder benefits.

Design/methodology/approach

The literature review highlights many new developments in food tourism for this baseline study. Qualitative and quantitative (i.e. mixed) methods are used including a case study, a pilot survey of key Government stakeholders in Oman’s Ministry of Tourism, food factory tours and interviews with their executives in Dhofar, direct and participant observation at food establishments and events, visits to popular roadside and market food stalls in Salalah and tourism trend analysis.

Findings

Some recent trends in food tourism elsewhere may be adapted in Salalah and spark interest in the food culture and heritage of Dhofar. This, in turn, may bring multiple benefits to the destination’s stakeholders. The governorate’s environment yields a rich variety of agricultural and other food products that may be used to provide new forms of food tourism and increase the region’s appeal to tourists beyond the Khareef season. Further possible benefits include safeguarding local food knowledge, production, culture and heritage, developing SMEs, creating new jobs and increasing visitor stay and spend.

Research limitations/implications

The study is conducted solely in English, whereas Arabic is the mother tongue in Oman. Dhofar is the country’s largest governorate occupying a vast area, not all of which is covered by the study. More data are needed to inform tourism development, policymaking and planning in Dhofar.

Practical implications

Improving tourism’s sustainability profile, creating successful food tourism products and services and achieving Dhofar’s economic development goals require concerted effort. All are in the best interest of the tourism stakeholders concerned.

Social implications

This paper provides a foundation for future research on this topic. It highlights the importance of placing food tourism development on a sustainable footing to protect and preserve Dhofar’s unique food culture, heritage, traditions and environment, extend the main tourism season and maximise benefits to stakeholders.

Originality/value

Recent trends in food tourism are investigated to gauge their applicability in this dynamic region of Oman. Ideas are presented demonstrating possible food tourism pathways to sustainable economic development that benefit a wide range of stakeholders e.g. food tours, food factory tours and shops, food festivals and cookery-school holidays and/or classes.