bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of the regulation of stalk development in flowering Chinese cabbage (Brassica campestris) by RNA sequencing
Authors: Huang Xinmin , Lei Yuling , Guan Hongling , Hao Yanwei , Liu Houcheng , Sun Guangwen , Chen Riyuan , Song Shiwei 
Published: November 2017

AbstractFlowering Chinese cabbage is a stalk vegetable whose quality and yield are directly related to stalk development. However, no comprehensive investigations on stalk development have been performed. To address this issue, the present study used RNA sequencing to investigate transcriptional regulation at three key stages (seedling, bolting, and flowering) of stalk development in flowering Chinese cabbage. Anatomical analysis revealed that cell division was the main mode of stalk thickening and elongation at all key stages. Among the 35,327 genes expressed in shoot apices, 34,448 were annotated and 879 were identified as novel transcripts. We identified 11,514 differentially expressed genes (DEGs) among the three stages of stalk development. Functional analysis revealed that these DEGs were significantly enriched in ‘ribosome’ and ‘plant hormone signal transduction’ pathways and were involved in hormone signal transduction, cell cycle progression, and the regulation of flowering time. The roles of these genes in stalk development were explored, and a putative gene-regulation network for the stalk flowering time was established. These findings provide insight into the molecular mechanisms of stalk development in flowering Chinese cabbage that provides a new theoretical basis for stalk vegetable breeding.
Visualizing the GPCR Network: Classification and Evolution
Authors: Hu Geng-Ming , Mai Te-Lun , Chen Chi-Ming 
Published: November 2017

AbstractIn this study, we delineate an unsupervised clustering algorithm, minimum span clustering (MSC), and apply it to detect G-protein coupled receptor (GPCR) sequences and to study the GPCR network using a base dataset of 2770 GPCR and 652 non-GPCR sequences. High detection accuracy can be achieved with a proper dataset. The clustering results of GPCRs derived from MSC show a strong correlation between their sequences and functions. By comparing our level 1 MSC results with the GPCRdb classification, the consistency is 87.9% for the fourth level of GPCRdb, 89.2% for the third level, 98.4% for the second level, and 100% for the top level (the lowest resolution level of GPCRdb). The MSC results of GPCRs can be well explained by estimating the selective pressure of GPCRs, as exemplified by investigating the largest two subfamilies, peptide receptors (PRs) and olfactory receptors (ORs), in class A GPCRs. PRs are decomposed into three groups due to a positive selective pressure, whilst ORs remain as a single group due to a negative selective pressure. Finally, we construct and compare phylogenetic trees using distance-based and character-based methods, a combination of which could convey more comprehensive information about the evolution of GPCRs.
Excessive fuel availability amplifies the FTO-mediated obesity risk: results from the TUEF and Whitehall II studies
Authors: Wagner Róbert , Tabák Ádám G. , Fehlert Ellen , Fritsche Louise , Jaghutriz Benjamin A. , Bánhegyi Róbert J. , Schmid Sebastian M. , Staiger Harald , Machicao Fausto , Peter Andreas , Häring Hans-Ulrich , Fritsche Andreas , Heni Martin 
Published: November 2017

AbstractVariation in FTO is the most important common genetic determinant of body weight. Altered energy metabolism could underlie this association. We hypothesized that higher circulating glucose or triglycerides can amplify the FTO impact on BMI. In 2671 subjects of the TUEF study, we investigated the interaction effect of fasting glucose and triglyceride levels with rs9939609 in FTO on BMI. We analysed the same interaction effect by longitudinally utilizing mixed effect models in the prospective Whitehall II study. In TUEF, we detected an interaction effect between fasting glucose and fasting triglycerides with rs9939609 on BMI (p = 0.0005 and p = 5 × 10−7, respectively). The effect size of one risk allele was 1.4 ± 0.3 vs. 2.2 ± 0.44 kg/m² in persons with fasting glucose levels below and above the median, respectively. Fasting triglycerides above the median increased the per-allele effect from 1.4 ± 0.3 to 1.7 ± 0.4 kg/m2. In the Whitehall II study, body weight increased by 2.96 ± 6.5 kg during a follow-up of 13.5 ± 4.6 yrs. Baseline fasting glucose and rs9939609 interacted on weight change (p = 0.009). Higher fasting glucose levels may amplify obesity-risk in FTO carriers and lead to an exaggerated weight gain over time. Since weight gain perpetuates metabolic alterations, this interplay may trigger a vicious circle that leads to obesity and diabetes.
The prognostic value of AGR2 expression in solid tumours: a systematic review and meta-analysis
Authors: Tian Shao-bo , Tao Kai-xiong , Hu Jia , Liu Zhi-bo , Ding Xue-liang , Chu Ya-nan , Cui Jin-yuan , Shuai Xiao-ming , Gao Jin-bo , Cai Kai-lin , Wang Ji-liang , Wang Guo-bin , Wang Lin , Wang Zheng 
Published: November 2017

AbstractThe prognostic value of anterior gradient-2 (AGR2) in tumours remains inconclusive. Here, we systematically reviewed the literature evidence and assessed the association between AGR2 expression and prognosis in solid tumours. The primary outcomes were overall survival (OS), disease-specific survival (DSS), and disease-free survival (DFS)/recurrence-free survival (RFS)/progression-free survival (PFS). All analyses were performed by STATA 12.0, with the hazard ratio (HR) or odds ratios (OR), and 95% confidence interval (CI) as the effect size estimate. A total of 20 studies containing 3285 cases were included. Pooled analyses revealed that AGR2 overexpression had an unfavourable impact on OS (HR 1.93, 95% CI 1.32–2.81) and time to tumour progression (TTP) (DFS/RFS/PFS) (HR 1.60 95% CI 1.06–2.40) in solid tumour patients. Subgroup analyses indicated that AGR2 overexpression in breast cancer patients was significantly associated with poor OS (HR 3.02, 95% CI 1.03–8.81) and TTP (HR 1.93, 95% CI 1.17–3.20). Excluding breast cancer, AGR2 overexpression was also found to have a significant correlation with poor OS in the remaining solid tumour patients (HR 1.51, 95% CI 1.04–2.19). Overall, AGR2 might be a potential biomarker to predict prognosis in solid tumour patients.
The M25 gene products are critical for the cytopathic effect of mouse cytomegalovirus
Authors: Kutle Ivana , Sengstake Sarah , Templin Corinna , Glaß Mandy , Kubsch Tobias , Keyser Kirsten A. , Binz Anne , Bauerfeind Rudolf , Sodeik Beate , Čičin-Šain Luka , Dezeljin Martina , Messerle Martin 
Published: November 2017

AbstractCell rounding is a hallmark of the cytopathic effect induced by cytomegaloviruses. By screening a panel of deletion mutants of mouse cytomegalovirus (MCMV) a mutant was identified that did not elicit cell rounding and lacked the ability to form typical plaques. Altered cell morphology was assigned to the viral M25 gene. We detected an early 2.8 kb M25 mRNA directing the synthesis of a 105 kDa M25 protein, and confirmed that a late 3.1 kb mRNA encodes a 130 kDa M25 tegument protein. Virions lacking the M25 tegument protein were of smaller size because the tegument layer between capsid and viral envelope was reduced. The ΔM25 mutant did not provoke the rearrangement of the actin cytoskeleton observed after wild-type MCMV infection, and isolated expression of the M25 proteins led to cell size reduction, confirming that they contribute to the morphological changes. Yields of progeny virus and cell-to-cell spread of the ΔM25 mutant in vitro were diminished and replication in vivo was impaired. The identification of an MCMV gene involved in cell rounding provides the basis for investigating the role of this cytopathic effect in CMV pathogenesis.
Adoptive Transfer of Ceramide Synthase 6 Deficient Splenocytes Reduces the Development of Colitis
Authors: Scheffel Matthew J. , Helke Kristi , Lu Ping , Bowers Jacob S. , Ogretmen Besim , Garrett-Mayer Elizabeth , Paulos Chrystal M. , Voelkel-Johnson Christina 
Published: November 2017

AbstractSphingolipids regulate critical cellular processes including inflammation. Ceramide, which serves a central role in sphingolipid metabolism, is generated by six ceramide synthases (CerS) that differ in substrate specificity. CerS6 preferentially generates C16-ceramide and its mRNA is highly expressed in immune tissues. In this study we analyzed how deficiency of CerS6 impacts on the development of colitis using an adoptive transfer model. Adoptive transfer of CerS6-deficient splenocytes, which have significantly decreased levels of C16-ceramide, showed that CerS6-deficiency protected against the development of colitis. However, adoptively transferred cells isolated from the lamina propria of the large intestine from wild type or CerS6-deficient groups showed no differences in the percentages of immune-suppressive regulatory T cells, pro-inflammatory Th17 cells, or their ability to express IL-17. In vitro polarization of wild type or CerS6-deficient splenocytes also revealed no defects in the development of T cell subsets. Our data suggest that protection from colitis following adoptive transfer of CerS6-deficient splenocytes maybe related to their ability to migrate and proliferate in vivo rather than subset development or cytokine expression.
Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis
Authors: Blom Sami , Paavolainen Lassi , Bychkov Dmitrii , Turkki Riku , Mäki-Teeri Petra , Hemmes Annabrita , Välimäki Katja , Lundin Johan , Kallioniemi Olli , Pellinen Teijo 
Published: November 2017

AbstractThe paradigm of molecular histopathology is shifting from a single-marker immunohistochemistry towards multiplexed detection of markers to better understand the complex pathological processes. However, there are no systems allowing multiplexed IHC (mIHC) with high-resolution whole-slide tissue imaging and analysis, yet providing feasible throughput for routine use. We present an mIHC platform combining fluorescent and chromogenic staining with automated whole-slide imaging and integrated whole-slide image analysis, enabling simultaneous detection of six protein markers and nuclei, and automatic quantification and classification of hundreds of thousands of cells in situ in formalin-fixed paraffin-embedded tissues. In the first proof-of-concept, we detected immune cells at cell-level resolution (n = 128,894 cells) in human prostate cancer, and analysed T cell subpopulations in different tumour compartments (epithelium vs. stroma). In the second proof-of-concept, we demonstrated an automatic classification of epithelial cell populations (n = 83,558) and glands (benign vs. cancer) in prostate cancer with simultaneous analysis of androgen receptor (AR) and alpha-methylacyl-CoA (AMACR) expression at cell-level resolution. We conclude that the open-source combination of 8-plex mIHC detection, whole-slide image acquisition and analysis provides a robust tool allowing quantitative, spatially resolved whole-slide tissue cytometry directly in formalin-fixed human tumour tissues for improved characterization of histology and the tumour microenvironment.
Phagocytosis of environmental or metabolic crystalline particles induces cytotoxicity by triggering necroptosis across a broad range of particle size and shape
Authors: Honarpisheh Mohsen , Foresto-Neto Orestes , Desai Jyaysi , Steiger Stefanie , Gómez Lidia Anguiano , Popper Bastian , Boor Peter , Anders Hans-Joachim , Mulay Shrikant R. 
Published: November 2017

AbstractIn crystallopathies, crystals or crystalline particles of environmental and metabolic origin deposit within tissues, induce inflammation, injury and cell death and eventually lead to organ-failure. The NLRP3-inflammasome is involved in mediating crystalline particles-induced inflammation, but pathways leading to cell death are still unknown. Here, we have used broad range of intrinsic and extrinsic crystal- or crystalline particle-sizes and shapes, e.g. calcium phosphate, silica, titanium dioxide, cholesterol, calcium oxalate, and monosodium urate. As kidney is commonly affected by crystallopathies, we used human and murine renal tubular cells as a model system. We showed that all of the analysed crystalline particles induce caspase-independent cell death. Deficiency of MLKL, siRNA knockdown of RIPK3, or inhibitors of necroptosis signaling e.g. RIPK-1 inhibitor necrostatin-1s, RIPK3 inhibitor dabrafenib, and MLKL inhibitor necrosulfonamide, partially protected tubular cells from crystalline particles cytotoxicity. Furthermore, we identify phagocytosis of crystalline particles as an upstream event in their cytotoxicity since a phagocytosis inhibitor, cytochalasin D, prevented their cytotoxicity. Taken together, our data confirmed the involvement of necroptosis as one of the pathways leading to cell death in crystallopathies. Our data identified RIPK-1, RIPK3, and MLKL as molecular targets to limit tissue injury and organ failure in crystallopathies.
Bacillus Classification Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry—Effects of Culture Conditions
Authors: Shu Lin-Jie , Yang Yu-Liang 
Published: November 2017

AbstractMatrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a reliable and rapid technique applied widely in the identification and classification of microbes. MALDI-TOF MS has been used to identify many endospore-forming Bacillus species; however, endospores affect the identification accuracy when using MALDI-TOF MS because they change the protein composition of samples. Since culture conditions directly influence endospore formation and Bacillus growth, in this study we clarified how culture conditions influence the classification of Bacillus species by using MALDI-TOF MS. We analyzed members of the Bacillus subtilis group and Bacillus cereus group using different incubation periods, temperatures and media. Incubation period was found to affect mass spectra due to endospores which were observed mixing with vegetative cells after 24 hours. Culture temperature also resulted in different mass spectra profiles depending on the temperature best suited growth and sporulation. Conversely, the four common media for Bacillus incubation, Luria-Bertani agar, nutrient agar, plate count agar and brain-heart infusion agar did not result in any significant differences in mass spectra profiles. Profiles in the range m/z 1000–3000 were found to provide additional data to the standard ribosomal peptide/protein region m/z 3000–15000 profiles to enable easier differentiation of some highly similar species and the identification of new strains under fresh culture conditions. In summary, control of culture conditions is vital for Bacillus identification and classification by MALDI-TOF MS.
Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease
Authors: Ren Chao , Liu Feng , Ouyang Zhangyi , An Gaole , Zhao Chenghui , Shuai Jun , Cai Shuhong , Bo Xiaochen , Shu Wenjie 
Published: November 2017

AbstractEnhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures. Gene Ontology (GO) analysis revealed that eRNAs play key roles in human cell identity. Furthermore, we detected numerous known and novel functional RNA structures within eRNA regions. To better characterize the cis-regulatory effects of non-coding variation in these structural ncRNAs, we performed a comprehensive analysis of the genetic variants of structural ncRNAs in eRNA regions that are associated with inflammatory autoimmune diseases. Disease-associated variants of the structural ncRNAs were disproportionately enriched in immune-specific cell types. We also identified riboSNitches in lymphoid eRNAs and investigated the potential pathogenic mechanisms by which eRNAs might function in autoimmune diseases. Collectively, our findings offer valuable insights into the function of eRNAs and suggest that eRNAs might be effective diagnostic and therapeutic targets for human diseases.
FOXA2 alleviates CCl4-induced liver fibrosis by protecting hepatocytes in mice
Authors: Wang Wei , Yao Li-Jia , Shen Weifeng , Ding Kai , Shi Pei-Mei , Chen Fei , He Jin , Ding Jin , Zhang Xin , Xie Wei-Fen 
Published: November 2017

AbstractThe liver-enriched transcription factor Forkhead Box A2 (FOXA2) has been reported to be involved in bile acid homeostasis and bile duct development. However, the role of FOXA2 in liver fibrogenesis remains undefined. In this study, we found that the abundance of FOXA2 was significantly lower in fibrotic livers of patients and mice treated with CCl4 than in controls. Interestingly, the expression level of FOXA2 decreased in hepatocytes, whereas FOXA2 was elevated in hepatic stellate cells (HSCs) of mouse fibrotic livers. Hepatocyte-specific ablation of FOXA2 in adult mice exacerbated liver fibrosis induced by CCl4. Either lentivirus LV-CMV-FOXA2 mediated FOXA2 overexpression in the liver or adeno-associated virus AAV8-TBG-FOXA2-mediated hepatocyte-specific upregulation of FOXA2 alleviated hepatic fibrosis. Overexpression of FOXA2 in HSCs did not obviously affect hepatic fibrogenesis. Additionally, FOXA2 knockout in hepatocytes resulted in aberrant transcription of metabolic genes. Furthermore, hepatocyte-specific knockout of FOXA2 enhanced endoplasmic reticulum stress (ER stress) and the apoptosis of hepatocytes, whereas FOXA2 overexpression in hepatocytes suppressed ER stress and hepatocyte apoptosis in mouse fibrotic livers. In conclusion, our findings suggested that FOXA2-mediated hepatocyte protection has a therapeutic role in hepatic fibrosis, and thus may be a new, promising anti-fibrotic option for treating chronic liver diseases.
Targeting a non-oncogene addiction to the ATR/CHK1 axis for the treatment of small cell lung cancer
Authors: Doerr Fabian , George Julie , Schmitt Anna , Beleggia Filippo , Rehkämper Tim , Hermann Sarah , Walter Vonn , Weber Jean-Philip , Thomas Roman K. , Wittersheim Maike , Büttner Reinhard , Persigehl Thorsten , Reinhardt H. Christian 
Published: November 2017

AbstractSmall cell lung cancer (SCLC) is a difficult to treat subtype of lung cancer. One of the hallmarks of SCLC is its almost uniform chemotherapy sensitivity. However, chemotherapy response is typically transient and patients frequently succumb to SCLC within a year following diagnosis. We performed a transcriptome analysis of the major human lung cancer entities. We show a significant overexpression of genes involved in the DNA damage response, specifically in SCLC. Particularly CHEK1, which encodes for the cell cycle checkpoint kinase CHK1, is significantly overexpressed in SCLC, compared to lung adenocarcinoma. In line with uncontrolled cell cycle progression in SCLC, we find that CDC25A, B and C mRNAs are expressed at significantly higher levels in SCLC, compared to lung adenocarcinoma. We next profiled the efficacy of compounds targeting CHK1 and ATR. Both, ATR- and CHK1 inhibitors induce genotoxic damage and apoptosis in human and murine SCLC cell lines, but not in lung adenocarcinoma cells. We further demonstrate that murine SCLC tumors were highly sensitive to ATR- and CHK1 inhibitors, while Kras
G12D
-driven murine lung adenocarcinomas were resistant against these compounds and displayed continued growth under therapy. Altogether, our data indicate that SCLC displays an actionable dependence on ATR/CHK1-mediated cell cycle checkpoints.
Proteome-wide identification of lysine 2-hydroxyisobutyrylation reveals conserved and novel histone modifications in Physcomitrella patens
Authors: Yu Zhiming , Ni Jun , Sheng Wei , Wang Zhikun , Wu Yuhuan 
Published: November 2017

AbstractProtein lysine 2-hydroxyisobutyrylation (Khib) is a newly identified post-translational modification found in animal and yeast cells. Previous research suggested that histone Khib is involved in male cell differentiation and plays a critical role in the regulation of chromatin functions in animals. However, information regarding protein Khib in plants is still limited. In this study, using a specific antibody and LC-MS/MS methods, we identified 11,976 Khib sites in 3,001 proteins in Physcomitrella patens. The bioinformatics analysis indicated that these Khib-modified proteins were involved in a wide range of molecular functions and cellular processes, and showed diverse subcellular localizations. Furthermore, an comparism of Khib sites in histone proteins among human, mouse and P. patens found conserved sites in the H3 and H4 histone proteins and novel sites in H1, H2A and H2B histone proteins in P. patens. This is the first report on Khib post-translational modifications in plants, and the study provides a comprehensive profile of Khib sites in histone and non-histone proteins in Physcomitrella patens.
Intrinsic and extrinsic factors drive ontogeny of early-life at-sea behaviour in a marine top predator
Authors: Carter Matt I. D. , Russell Deborah J. F. , Embling Clare B. , Blight Clint J. , Thompson David , Hosegood Philip J. , Bennett Kimberley A. 
Published: November 2017

AbstractYoung animals must learn to forage effectively to survive the transition from parental provisioning to independent feeding. Rapid development of successful foraging strategies is particularly important for capital breeders that do not receive parental guidance after weaning. The intrinsic and extrinsic drivers of variation in ontogeny of foraging are poorly understood for many species. Grey seals (Halichoerus grypus) are typical capital breeders; pups are abandoned on the natal site after a brief suckling phase, and must develop foraging skills without external input. We collected location and dive data from recently-weaned grey seal pups from two regions of the United Kingdom (the North Sea and the Celtic and Irish Seas) using animal-borne telemetry devices during their first months of independence at sea. Dive duration, depth, bottom time, and benthic diving increased over the first 40 days. The shape and magnitude of changes differed between regions. Females consistently had longer bottom times, and in the Celtic and Irish Seas they used shallower water than males. Regional sex differences suggest that extrinsic factors, such as water depth, contribute to behavioural sexual segregation. We recommend that conservation strategies consider movements of young naïve animals in addition to those of adults to account for developmental behavioural changes.
Nitric oxide contributes to high-salt perception in a blood-sucking insect model
Authors: Cano Agustina , Pontes Gina , Sfara Valeria , Anfossi Diego , Barrozo Romina B. 
Published: November 2017

AbstractIn all organisms, salts produce either appetitive or aversive responses depending on the concentration. While low-salt concentration in food elicits positive responses to ingest, high-salt triggers aversion. Still the mechanisms involved in this dual behavior have just started to be uncovered in some organisms. In Rhodnius prolixus, using pharmacological and behavioral assays, we demonstrated that upon high-salt detection in food a nitric oxide (NO) dependent cascade is activated. This activation involves a soluble guanylate cyclase (sGC) and the production of cyclic guanosine monophosphate (cGMP). Thus, appetitive responses to low-salt diets turn to aversion whenever this cascade is activated. Conversely, insects feed over aversive high-salt solutions when it is blocked by reducing NO levels or by affecting the sGC activity. The activation of NO/sGC/cGMP cascade commands the avoidance feeding behavior in R. prolixus. Investigations in other insect species should examine the possibility that high-salt aversion is mediated by NO/sSG/cGMP signaling.