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https://www.readbyqxmd.com/read/28817638/the-transcriptional-profiling-of-human-in-vivo-generated-plasma-cells-identifies-selective-imbalances-in-monoclonal-gammopathies
#1
Luis M Valor, Beatriz Rodríguez-Bayona, Ana B Ramos-Amaya, José A Brieva, Antonio Campos-Caro
Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment...
2017: PloS One
https://www.readbyqxmd.com/read/28814718/adaptive-and-non-adaptive-divergence-in-a-common-landscape
#2
Joost A M Raeymaekers, Anurag Chaturvedi, Pascal I Hablützel, Io Verdonck, Bart Hellemans, Gregory E Maes, Luc De Meester, Filip A M Volckaert
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes-three-spined and nine-spined stickleback-differ in the strength and nature of neutral and adaptive divergence along a salinity gradient...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814516/baculovirus-molecular-evolution-via-gene-turnover-and-recurrent-positive-selection-of-key-genes
#3
Tom Hill, Robert L Unckless
Hosts and viruses are locked in an evolutionary arms race. Hosts are constantly evolving to suppress virulence and replication, while viruses, reliant on host machinery for survival and reproduction, develop counter-strategies to escape this immune defense. Viruses must also adapt to novel conditions when establishing themselves in a host species. Both processes provide strong selection for viral adaptation. Understanding adaptive evolution in insect viruses can help us better understand adaptive evolution in general, and is important due to their use as biocontrol agents, and for protecting ecologically or economically important species from outbreaks...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28813638/impact-of-70-gene-signature-use-on-adjuvant-chemotherapy-decisions-in-patients-with-estrogen-receptor-positive-early-breast-cancer-results-of-a-prospective-cohort-study
#4
Anne Kuijer, Marieke Straver, Bianca den Dekker, Annelotte C M van Bommel, Sjoerd G Elias, Carolien H Smorenburg, Jelle Wesseling, Sabine C Linn, Emiel J Th Rutgers, Sabine Siesling, Thijs van Dalen
Purpose Gene-expression profiles increasingly are used in addition to conventional prognostic factors to guide adjuvant chemotherapy (CT) decisions. The Dutch guideline suggests use of validated gene-expression profiles in patients with estrogen receptor (ER) -positive, early-stage breast cancer without overt lymph node metastases. We aimed to assess the impact of a 70-gene signature (70-GS) test on CT decisions in patients with ER-positive, early-stage breast cancer. Patients and Methods In a prospective, observational, multicenter study in patients younger than 70 years old who had undergone surgery for ER-positive, early-stage breast cancer, physicians were asked whether they intended to administer adjuvant CT before deployment of the 70-GS test and after the test result was available...
August 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28812922/a-circulating-micro-rna-signature-serves-as-a-diagnostic-and-prognostic-indicator-in-sarcoidosis
#5
Christian Ascoli, Yue Huang, Cody Schott, Benjamin A Turturice, Ahmed Metwally, David L Perkins, Patricia W Finn
Micro-RNAs (miRNAs) act as post-transcriptional regulators of gene expression. In sarcoidosis, aberrant miRNA expression may enhance immune responses mounted against an unknown antigenic agent. We tested whether a distinct miRNA signature functions as a diagnostic biomarker and explored its role as an immune modulator in sarcoidosis. Expression of miRNAs from peripheral blood mononuclear cells from subjects that met clinical and histopathologic criteria for sarcoidosis were compared to those from matched controls in the ACCESS study...
August 16, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28809135/detecting-signatures-of-past-pathogen-selection-on-human-hla-loci-are-there-needles-in-the-haystack
#6
Bridget S Penman, Sunetra Gupta
Human leucocyte antigens (HLAs) are responsible for the display of peptide fragments for recognition by T-cell receptors. The gene family encoding them is thus integral to human adaptive immunity, and likely to be under strong pathogen selection. Despite this, it has proved difficult to demonstrate specific examples of pathogen-HLA coevolution. Selection from multiple pathogens simultaneously could explain why the evolutionary signatures of particular pathogens on HLAs have proved elusive. Here, we present an individual-based model of HLA evolution in the presence of two mortality-causing pathogens...
August 15, 2017: Parasitology
https://www.readbyqxmd.com/read/28809126/comprehensive-epigenetic-analysis-of-the-signature-genes-in-lung-adenocarcinoma
#7
Yunfeng Zhang, Weidong Zhao, Jia Zhang
AIM: This study aimed to explore the epigenetic modifications of signature genes in lung adenocarcinoma. MATERIALS & METHODS: The data of miRNA expression, mRNA expression and DNA methylation were downloaded from The Cancer Genome Atlas. Differential analysis was performed, followed by correlation analysis of miRNA-mRNA and DNA methylation-mRNA. RESULTS: A total of 14 significant inverse correlations between gene expression and DNA methylation were identified, the expressions of which were selected for further validation via GSE27262, displaying similar pattern with that of the integrated analysis...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28808023/prefrontal-cortex-modulates-posterior-alpha-oscillations-during-top-down-guided-visual-perception
#8
Randolph F Helfrich, Melody Huang, Guy Wilson, Robert T Knight
Conscious visual perception is proposed to arise from the selective synchronization of functionally specialized but widely distributed cortical areas. It has been suggested that different frequency bands index distinct canonical computations. Here, we probed visual perception on a fine-grained temporal scale to study the oscillatory dynamics supporting prefrontal-dependent sensory processing. We tested whether a predictive context that was embedded in a rapid visual stream modulated the perception of a subsequent near-threshold target...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28806983/profiling-of-metalloprotease-activities-in-cerebrospinal-fluids-of-patients-with-neoplastic-meningitis
#9
Catharina Conrad, Kristina Dorzweiler, Miles A Miller, Douglas A Lauffenburger, Herwig Strik, Jörg W Bartsch
BACKGROUND: Neoplastic invasion into leptomeninges and subarachnoid space, resulting in neoplastic meningitis (NM) is a fatal complication of advanced solid and hematological neoplasms. Identification of malignant involvement of the cerebrospinal fluid (CSF) early in the disease course has crucial prognostic and therapeutic implications, but remains challenging. As indicators of extracellular matrix (ECM) degradation and breakdown of the blood-brain-barrier, Matrix Metalloproteases (MMPs) and A Disintegrin and Metalloproteases (ADAMs) are potential analytes for cerebral pathophysiology and metastatic dissemination of tumor cells into the CSF...
August 14, 2017: Fluids and Barriers of the CNS
https://www.readbyqxmd.com/read/28806759/peculiar-genes-selection-a-new-features-selection-method-to-improve-classification-performances-in-imbalanced-data-sets
#10
Federica Martina, Marco Beccuti, Gianfranco Balbo, Francesca Cordero
High-Throughput technologies provide genomic and trascriptomic data that are suitable for biomarker detection for classification purposes. However, the high dimension of the output of such technologies and the characteristics of the data sets analysed represent an issue for the classification task. Here we present a new feature selection method based on three steps to detect class-specific biomarkers in case of high-dimensional data sets. The first step detects the differentially expressed genes according to the experimental conditions tested in the experimental design, the second step filters out the features with low discriminative power and the third step detects the class-specific features and defines the final biomarker as the union of the class-specific features...
2017: PloS One
https://www.readbyqxmd.com/read/28806597/a-nested-multivariate-chemometrics-based-calibration-strategy-for-direct-trace-biometal-analysis-in-soft-tissue-utilizing-energy-dispersive-x-ray-fluorescence-edxrf-and-scattering-spectrometry
#11
REVIEW
J J Okonda, K H Angeyo, J M Mangala, S M Kisia
Compton scatter-modulated fluorescence and multivariate chemometric (artificial neural network (ANN) and principal component regression (PCR)) calibration strategy was explored for direct rapid trace biometals (Mn, Fe, Cu, Zn, Se) analysis in "complex" matrices (model soft tissues). This involved spectral feature selection (multiple fluorescence signatures) normalized to or in conjunction with Compton scatter. ANN model resulted in more accurate trace biometal determination (R(2)>0.9) compared to PCR. Hybrid nested (ANN and PCR) approach led to optimized accurate biometals' concentrations in Oyster tissue (≤ ± 10%)...
August 8, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28805995/germline-pms2-and-somatic-poleexo-mutations-cause-hypermutability-of-the-leading-dna-strand-in-biallelic-mismatch-repair-deficiency-syndrome-brain-tumors
#12
Andrianova Maria, Ghati Kasturirangan Chetan, Madathan Kandi Sibin, Thomas Mckee, Doron Merkler, Rao Kvl Narasinga, Pascale Ribaux, Jean-Louis Blouin, Periklis Makrythanasis, Vladimir B Seplyarskiy, Stylianos E Antonarakis, Sergey I Nikolaev
Biallelic Mismatch Repair Deficiency (bMMRD) in tumors is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1 and results to a characteristic mutational profile. In this study we describe the genetic basis of ultramutated high grade brain tumors in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant R802X in the PMS2 gene...
August 14, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28804485/transcriptional-profiling-of-midguts-prepared-from-trypanosoma-t-congolense-positive-glossina-palpalis-palpalis-collected-from-two-distinct-cameroonian-foci-coordinated-signatures-of-the-midguts-remodeling-as-t-congolense-supportive-niches
#13
Jean M Tsagmo Ngoune, Flobert Njiokou, Béatrice Loriod, Ginette Kame-Ngasse, Nicolas Fernandez-Nunez, Claire Rioualen, Jacques van Helden, Anne Geiger
Our previous transcriptomic analysis of Glossina palpalis gambiensis experimentally infected or not with Trypanosoma brucei gambiense aimed to detect differentially expressed genes (DEGs) associated with infection. Specifically, we selected candidate genes governing tsetse fly vector competence that could be used in the context of an anti-vector strategy, to control human and/or animal trypanosomiasis. The present study aimed to verify whether gene expression in field tsetse flies (G. p. palpalis) is modified in response to natural infection by trypanosomes (T...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28803874/range-expansion-compromises-adaptive-evolution-in-an-outcrossing-plant
#14
Santiago C González-Martínez, Kate Ridout, John R Pannell
Neutral genetic diversity gradients have long been used to infer the colonization history of species [1, 2], but range expansion may also influence the efficacy of natural selection and patterns of non-synonymous polymorphism in different parts of a species' range [3]. Recent theory predicts both an accumulation of deleterious mutations and a reduction in the efficacy of positive selection as a result of range expansion [4-8]. These signatures have been sought in a number of studies of the human range expansion out of Africa, but with contradictory results [9-14]...
August 4, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28803255/panel-of-serum-metabolites-discriminates-cancer-patients-and-healthy-participants-of-lung-cancer-screening-a-pilot-study
#15
Małgorzata Roś-Mazurczyk, Anna Wojakowska, Łukasz Marczak, Krzysztof Polański, Monika Pietrowska, Joanna Polanska, Rafał Dziadziuszko, Jacek Jassem, Witold Rzyman, Piotr Widlak
INTRODUCTION: Blood biomarkers may support early diagnosis of lung cancer by enabling pre-selection of candidates for computed tomography screening or discrimination between benign and malignant screening-detected nodules. We aimed to identify features of serum metabolome distinguishing individuals with early-detected lung cancer from healthy participants of the lung cancer screening program. METHODS: Blood samples were collected in the course of a low-dose computed tomography screening program performed in the Gdansk district (Northern Poland)...
August 12, 2017: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/28799347/ultrafast-%C3%AE-cc-bond-cleavage-of-acetone-upon-excitation-to-3p-and-3d-rydberg-states-by-femtosecond-time-resolved-photoelectron-imaging
#16
O Hüter, F Temps
The radiationless electronic relaxation and α -CC bond fission dynamics of jet-cooled acetone in the S1 (nπ(*)) state and in high-lying 3p and 3d Rydberg states have been investigated by femtosecond time-resolved mass spectrometry and photoelectron imaging. The S1 state was accessed by absorption of a UV pump photon at selected wavelengths between λ = 320 and 250 nm. The observed acetone mass signals and the S1 photoelectron band decayed on sub-picosecond time scales, consistent with a recently proposed ultrafast structural relaxation of the molecules in the S1 state away from the Franck-Condon probe window...
December 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28797549/predicting-thyroid-nodule-malignancy-at-several-prevalence-values-with-a-combined-bethesda-molecular-test
#17
Hélène Lasolle, Benjamin Riche, Myriam Decaussin-Petrucci, Emmanuelle Dantony, Véronique Lapras, Catherine Cornu, Joël Lachuer, Jean-Louis Peix, Jean-Christophe Lifante, Oana-Maria Capraru, Samia Selmi-Ruby, Bernard Rousset, Françoise Borson-Chazot, Pascal Roy
OBJECTIVE: Investigation of thyroid nodules using fine-needle aspiration cytology (FNAC) gives indeterminate results in up to 30% of samples using the Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). We present a combined Bethesda-molecular predictor of nodule malignancy to improve the accuracy of the preoperative diagnosis of thyroid nodules. DESIGN: The study sought to detect a molecular signature of thyroid nodule malignancy. METHODS: A molecular test was performed on FNACs from 128 thyroid nodules from prospectively included patients, collected in a tertiary center...
July 22, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28797473/biomarker-research-to-improve-clinical-outcomes-of-peritoneal-dialysis-consensus-of-the-european-training-and-research-in-peritoneal-dialysis-eutripd-network
#18
REVIEW
Christoph Aufricht, Robert Beelen, Matthias Eberl, Michel Fischbach, Donald Fraser, Achim Jörres, Klaus Kratochwill, Manuel LópezCabrera, Peter Rutherford, Claus-Peter Schmitt, Nicholas Topley, Janusz Witowski
Peritoneal dialysis (PD) therapy substantially requires biomarkers as tools to identify patients who are at the highest risk for PD-related complications and to guide personalized interventions that may improve clinical outcome in the individual patient. In this consensus article, members of the European Training and Research in Peritoneal Dialysis Network (EuTRiPD) review the current status of biomarker research in PD and suggest a selection of biomarkers that can be relevant to the care of PD patients and that are directly accessible in PD effluents...
August 8, 2017: Kidney International
https://www.readbyqxmd.com/read/28796930/recurrence-associated-gene-signature-optimizes-recurrence-free-survival-prediction-of-colorectal-cancer
#19
Xianglong Tian, Xiaoqiang Zhu, Tingting Yan, Chenyang Yu, Chaoqin Shen, Ye Hu, Jie Hong, Haoyan Chen, Jing-Yuan Fang
High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis-related mRNAs may potentially enrich genes with the ability to predict cancer recurrence,therefore we attempted to build a recurrence-associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model was employed...
August 10, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28796803/adaptive-introgression-from-distant-caribbean-islands-contributed-to-the-diversification-of-a-microendemic-adaptive-radiation-of-trophic-specialist-pupfishes
#20
Emilie J Richards, Christopher H Martin
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon...
August 2017: PLoS Genetics
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