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Molecular classification

Pavan K Bhatraju, Leila R Zelnick, Jerald Herting, Ronit Katz, Carmen Mikacenic, Susanna Kosamo, Eric D Morrell, Cassianne Robinson-Cohen, Carolyn S Calfee, Jason D Christie, Kathleen D Liu, Michael A Matthay, William O Hahn, Victoria Dmyterko, Natalie S J Slivinski, Jim A Russell, Keith R Walley, David C Christiani, W Conrad Liles, Jonathan Himmelfarb, Mark M Wurfel
OBJECTIVE: The aim of this study was to identify and test whether AKI sub-phenotypes have prognostic and therapeutic implications. METHODS: First, latent class analysis methodology was applied independently in two critically ill populations (Discovery: n=794 and Replication: n=425) with AKI. Second, a parsimonious classification model was developed to identify AKI sub-phenotypes. Third, the classification model was applied to patients with AKI in the Vasopressin in Septic Shock (VASST: n=271) clinical trial and differences in treatment response were determined...
October 18, 2018: American Journal of Respiratory and Critical Care Medicine
Sneeha Veerakumar, Ramesh Pathy Manian
Agarases (agarose 4-glycanohydrolase; EC are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, β-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of β-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant β-agarases...
October 2018: 3 Biotech
Beatriz Navarro, Stefania Zicca, Maria Minutolo, Maria Saponari, Daniela Alioto, Francesco Di Serio
A new RNA virus has been identified from a sweet orange tree in southern Italy. This virus, tentatively named citrus virus A (CiVA), has a bipartite genome composed of (i) a negative-stranded (ns) RNA1, encoding the viral RNA-dependent RNA polymerase (RdRp), and (ii) an ambisense RNA2, coding for the putative movement protein (MP) and nucleocapsid protein (NP), with the two open reading frames separated by a long AU-rich intergenic region (IR) adopting a hairpin conformation. CiVA genomic RNAs and the encoded proteins resemble those of the recently discovered citrus concave gum-associated virus (CCGaV)...
2018: Frontiers in Microbiology
Jean-Marie Tan, Lisa N Tom, H Peter Soyer, Mitchell S Stark
Melanocytic naevi are common melanocytic proliferations that may simulate the appearance of cutaneous melanoma. Naevi commonly harbour somatic mutations implicated in melanomagenesis but in most cases lack the necessary genomic alterations required for melanoma development. While the mitogen-activated protein kinase pathway and ultraviolet radiation strongly contribute to naevogenesis, the somatic mutational landscape of dermoscopic naevus subsets distinguishes some of the molecular hallmarks of naevi in relation to melanoma...
October 17, 2018: Dermatology: International Journal for Clinical and Investigative Dermatology
Marion Classe, Hui Yao, Roger Mouawad, Chad J Creighton, Alice Burgess, Frederick Allanic, Michel Wassef, Xavier Leroy, Benjamin Verillaud, Geoffrey Mortuaire, Franck Bielle, Christophe Le Tourneau, Jean-Emmanuel Kurtz, David Khayat, Xiaoping Su, Gabriel G Malouf
Esthesioneuroblastoma (ENB) is a rare cancer of the olfactory mucosa, with no established molecular stratification to date. We report similarities of ENB with tumors arising in the neural crest and perform integrative analysis of these tumors. We propose a molecular-based subtype classification of ENB as basal or neural, both of which have distinct pathological, transcriptomic, proteomic, and immune features. Among the basal subtype, we uncovered an IDH2 R172 mutant-enriched subgroup (∼35%) harboring a CpG island methylator phenotype reminiscent of IDH2 mutant gliomas...
October 16, 2018: Cell Reports
Daphne W Bell, Lora Hedrick Ellenson
Endometrial cancer is the most commonly diagnosed gynecologic malignancy in the United States. Endometrioid endometrial carcinomas constitute approximately 85% of newly diagnosed cases; serous carcinomas represent approximately 3-10% of diagnoses; clear cell carcinoma accounts for <5% of diagnoses; and uterine carcinosarcomas are rare, biphasic tumors. Longstanding molecular observations implicate PTEN inactivation as a major driver of endometrioid carcinomas; TP53 inactivation as a major driver of most serous carcinomas, some high-grade endometrioid carcinomas, and many uterine carcinosarcomas; and inactivation of either gene as drivers of some clear cell carcinomas...
October 17, 2018: Annual Review of Pathology
Eugene I Hwang, Marcel Kool, Peter C Burger, David Capper, Lukas Chavez, Sebastian Brabetz, Chris Williams-Hughes, Catherine Billups, Linda Heier, Alok Jaju, Jeff Michalski, Yimei Li, Sarah Leary, Tianni Zhou, Andreas von Deimling, David T W Jones, Maryam Fouladi, Ian F Pollack, Amar Gajjar, Roger J Packer, Stefan M Pfister, James M Olson
PURPOSE: Children with histologically diagnosed high-risk medulloblastoma, supratentorial primitive neuroectodermal tumor of the CNS (CNS-PNET), and pineoblastoma (PBL) have had poor survival despite intensive treatment. We included these patients in this Children's Oncology Group trial. Molecular profiling later revealed tumor heterogeneity that was not detectable at protocol inception. Enrollment of patients with CNS-PNET/PBL was subsequently discontinued, and outcomes for this part of the study are reported here...
October 17, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
Manuel Scimeca, Nicoletta Urbano, Rita Bonfiglio, Orazio Schillaci, Elena Bonanno
BACKGROUND: In this study, we investigated the relationship between the expression of the main in situ markers of breast cancer and the presence of breast osteoblast-like cells (BOLCs). METHODS: We collected 100 breast biopsies. Serial paraffin sections were obtained from each biopsy to perform histological classifications and immunohistochemical analyses (RUNX2, RANKL, vimentin, TGFβ, Ki67, CD44, ER, PR and HER2). RESULTS: Linear regression analysis showed a positive and significant correlation between the number of BOLCs and the expression of EMT-related markers (vimentin and TGFβ), Ki67 and ER...
October 17, 2018: British Journal of Cancer
P Zhang, R K Ran, A Y Abdullahi, X L Shi, Y Huang, Y X Sun, Y Q Liu, X X Yan, J X Hang, Y Q Fu, M W Wang, W Chen, G Q Li
Dipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region...
October 17, 2018: Journal of Helminthology
Silas Bossert, Elizabeth A Murray, Eduardo A B Almeida, Seán G Brady, Bonnie B Blaimer, Bryan N Danforth
Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineages is now a standard method, it is still not clear if UCE data can be readily combined with published transcriptomes. In this study, we evaluate the combination of UCEs and transcriptomes in a single analysis using genome-, transcriptome-, and UCE data for 79 bees in the largest and most biologically diverse bee family, Apidae...
October 13, 2018: Molecular Phylogenetics and Evolution
Cíntia Luíza Silva-Luz, José Rubens Pirani, John Daniel Mitchell, Douglas Daly, Natalie do Valle Capelli, Diego Demarco, Susan K Pell, Gregory M Plunkett
Schinus, best known by its few cultivated and invasive species, is the largest genus of Anacardiaceae in southern South America. It is remarkably diverse compared to closely related genera, with approximately 42 species, most of which occur in several arid vegetation types and extend into Andean and Atlantic moist forests. The most comprehensive taxonomic revision of the genus dates to 1957, recognizing S. subg. Schinus and S. subg. Duvaua, the latter of which were further divided into two sections. Subsequent studies have highlighted morphological inconsistencies in this infrageneric classification, and species delimitation remains a challenge...
October 13, 2018: Molecular Phylogenetics and Evolution
Ingmar Blümcke, Roland Coras, Annika K Wefers, David Capper, Eleonora Aronica, Albert Becker, Mrinalini Honavar, Thomas J Stone, Thomas S Jacques, Hajime Miyata, Angelika Mühlebner, Jose Pimentel, Figen Söylemezoğlu, Maria Thom
Low-grade epilepsy-associated brain tumours (LEAT) are the second most common cause for drug-resistant, focal epilepsy, i.e. ganglioglioma (GG) and dysembryoplastic neuroepithelial tumours (DNT). However, molecular pathogenesis, risk factors for malignant progression, and their frequent association with drug-resistant focal seizures remain poorly understood. This contrasts recent progress in understanding the molecular-genetic basis and targeted treatment options in diffuse gliomas. The Neuropathology Task Force of the International League against Epilepsy examined available literature to identify common obstacles in diagnosis and research of LEAT...
October 16, 2018: Neuropathology and Applied Neurobiology
Xiaogang Guo, Tao Han, Pingping Hu, Xiaojun Guo, Changming Zhu, Youbao Wang, Shaoyan Chang
BACKGROUND: Prostate cancer (PCa) is a common malignant human tumor and one of the main causes of cancer-related deaths in men. At present, prostate-specific antigen levels are widely used to diagnose PCa in the clinic, but they are not sufficient for an accurate early diagnosis or prognosis. METHODS: To identify potential molecular markers for PCa, we used real-time PCR to measure the expression levels of various microRNAs, including miR-1825, miR-484, miR-205, miR-141, and let-7b, in the serum of 72 PCa patients and 34 healthy controls...
October 15, 2018: International Urology and Nephrology
Yan-Chao Yin, Xiao-Dong Zhang, Zhi-Qiang Gao, Ting Hu, Ying Liu
Chalcone isomerase (CHI) is the second rate-limiting and the first reported enzyme involved in the biosynthetic pathway of flavonoids. It catalyzes the intramolecular cyclization reaction, converting the bicyclic chalcone into tricyclic (2S)-flavanone. In this paper, we obtained and analyzed 916 DNA sequences, 1310 mRNA sequences, and 2403 amino acid sequences of CHI registered in NCBI by Jan 2018. The full length of CHI DNA sequences ranges from 218 to 3758 bp, CHI mRNA sequences ranges from 265 to 1436 bp, and CHI amino acid sequences ranges from 35 to 465 amino acid residues...
October 15, 2018: Molecular Biotechnology
Jean-Marc Chavatte, Grégory Karadjian, Irène Landau
Here, we report new insights on the erythrocytic murine parasite Anthemosoma garnhami, which was first described from Ethiopia in 1969. Its classification has been debated for years, as this parasite presents some intermediate characters between the Haemosporidia and the Piroplasmida. Based on electron-microscopy, immunological, biochemical and drug sensitivity studies, it was finally assigned to the piroplasms, in the family Anthemosomatidae. In 1985, Anthemosoma sp. was reported from Namibia, and since then, no investigation has involved this parasite...
October 15, 2018: Parasitology Research
Joana Ferreira, Ana Félix, Jochen K Lennerz, Esther Oliva
This review addresses known features and recent developments in the histological, immunohistochemical, and molecular characterization of endometrial stromal neoplasms. We discuss the spectrum of these tumors, from the benign endometrial stromal nodule to low-grade endometrial stromal sarcoma to uterine undifferentiated sarcomas with a special emphasis on the expanding group of high-grade stromal sarcomas, recently added to the 2014 WHO classification, not only discussing the well-established YWHAE-FAM22 tumors but also two new groups, presenting with BCOR alterations including those with BCOR tandem internal duplications or NTRK fusions...
October 15, 2018: Virchows Archiv: An International Journal of Pathology
Guojun Liu, Zihao Chen, Irina G Danilova, Mikhail A Bolkov, Irina A Tuzankina, Guoqing Liu
Basal and luminal subtypes of muscle-invasive bladder cancer (MIBC) have distinct molecular profiles and heterogeneous clinical behaviors. The interactions between mRNAs and lncRNAs, which might be regulated by miRNAs, have crucial roles in many cancers. However, the miRNA-dependent crosstalk between lncRNA and mRNA in specific MIBC subtypes still remains unclear. In this study, we first classified MIBC into two conservative subtypes using miRNA, mRNA and lncRNA expression data derived from The Cancer Genome Atlas...
2018: Frontiers in Genetics
Yuanping Wang, Lipeng Hao, Lifeng Pan, Caoyi Xue, Qing Liu, Xuetao Zhao, Weiping Zhu
Sixty norovirus outbreaks that occurred in Pudong District, Shanghai in 2017 and affected 959 people were summarised. Of the outbreaks, 29 (48.3%), 27 (45.0%), and 4 (6.7%) occurred in kindergartens, primary schools, and middle schools, respectively. Although the total number of outbreaks peaked in March (13/60, 21.7%), outbreaks in kindergartens and primary schools peaked in April (6/29, 20.7%) and March (8/27, 29.6%), respectively. Primary schools had the highest median number of cases per outbreak (19) and the highest proportion of cases (54...
October 15, 2018: Scientific Reports
T K Shameera Ahamed, Vijisha K Rajan, K Sabira, K Muraleedharan
Developments of novel inhibitors to prevent the function of 5-lipoxygenase (5-LOX) proteins that are responsible for a variety of inflammatory and allergic disease are a major challenge in the scientific community. In this study, robust QSAR classification models for predicting 5-LOX activity were developed using machine learning algorithms. The Support Vector Machines (SVM), Logistic Regression, k-Nearest Neighbour (NN) and Decision Trees were adopted to improve the prediction ability of the classification models...
October 5, 2018: Computational Biology and Chemistry
Jennifer G Andrews, Molly Lamb, Kristin Conway, Natalie Street, Christina Westfield, Emma Ciafaloni, Dennis Matthews, Christopher Cunniff, Shree Pandya, Deborah J Fox, M D STARnet
Dystrophinopathies are caused by mutations in DMD resulting in progressive muscle weakness. They are historically divided into the more severe Duchenne (DMD) and milder Becker (BMD) muscular dystrophy phenotypes. Classification is important for research and clinical care. The purpose of this study was to describe a multi-variable approach to classifying cases from the Muscular Dystrophy Surveillance, Tracking, and Research Network (MD STARnet) and to assess the accuracy of the diagnostic classification scheme...
October 3, 2018: Journal of Neuromuscular Diseases
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