Functional analysis of structural variants in single cells using Strand-seq

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations

Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution

The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia

Functional analysis of structural variants in single cells using Strand-seq

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations

The effects of Enterococcus faecium Cernelle 68 (SF 68) on output properties and some haematological parameters in broilers

To investigate the effects of Enterococcus faecium Cernelle 68 on output properties and some haematological and biochemical properties in broiler chicks. 130,male Ross-308 broiler chick's were, used. The animals were divided into two groups as control and experimental 35 mg/kg Enterococcus faecium Cernelle 68 was supplemented to diet of the experimental group. Body weight gain. food consumption and feed efficiency ratio were determined on day 14, 28, 42 and 49. Also on the same days, red blood cell (RBC), white blood, cell (WBC), thrombocyte counts, packed cell,volume (PCV), haemoglobin (Hb) amount and serum creatine,kinase (CK), lactate dehydrogenase (LDH), aspartate aminotransferase (AST), alanine aminotransferase (ALT), total protein, albumin, triglyceride, cholesterol, and glucose levels were determined from the blood samples of randomly selected 15 animals from both control and experimental groups. After blood samples were taken, carcass weight, small intestine weight and ileum pH of the animals were determined during autopsy. It has been determined that, food consumption was less in probiotic group than in control, and feed efficiency ratio of the probiotic group was higher than that of the control group, but these differences were not statistically significant. The carcass weight of the probiotic group was higher on day 49 (P < 0,05). It has been determined that, the probiotic had no effect on small intestine weight and ileum pH.,No statistically significant change was observed in RBC, WBC, thrombocyte, PCV, and Hb values. AST and ALT levels of the probiotic group decreased statistically on day 49 (P < 0,05). The cholesterol level of the probiotic group was statistically lower than that of the control group on day 14 (P < 0,05). These results show that Enterococcus faecium Cernelle 68 will bring economic advantage to the breeders by improving feed efficiency ratio and carcass weight, and it is safe for the host animal and it is well tolerated by the organism

Tensile fracture strength of Brisbane tuff by static and cyclic loading tests

This research presents the results of laboratory experiments during the investigation of tensile strength-strain characteristics of Brisbane tuff disc specimens under static and diametral cyclic loading. Three different cyclic loading methods were used; namely, sinusoidal cyclic loading, type I and II increasing cyclic loading with various amplitude values. The first method applied the stress amplitude-cycle number (s-n) curve approach to the measurement of the indirect tensile strength (ITS) and fracture toughness (K ) values of rocks for the first time in the literature. The type I and II methods investigated the effect of increasing cyclic loading on the ITS and K of rocks. For Brisbane tuff, the reduction in ITS was found to be 30 % under sinusoidal loading, whereas type I and II increasing cyclic loading caused a maximum reduction in ITS of 36 %. The maximum reduction of the static K of 46 % was obtained for the highest amplitude type I cyclic loading tested. For sinusoidal cyclic loading, a maximum reduction of the static K of 30 % was obtained. A continuous irreversible accumulation of damage was observed in dynamic cyclic tests conducted at different amplitudes and mean stress levels. Scanning electron microscope images showed that fatigue damage in Brisbane tuff is strongly influenced by the failure of the matrix because of both inter-granular fracturing and trans-granular fracturing. The main characteristic was grain breakage under cyclic loading, which probably starts at points of contact between grains and is accompanied by the production of very small fragments, probably due to frictional sliding within the weak matrix

Mean platelet volume could be possible biomarker in early diagnosis and monitoring of gastric cancer

Gastric cancer is the fourth most frequent cancer and the second cause of cancer-related deaths worldwide. The early diagnosis of gastric cancer is fundamental in decreasing the mortality rates. It has been shown that MPV level is a sign of inflammation in hepatocellular carcinoma and pancreatic adenocarcinoma. The aim of this study is to examine whether MPV would be a useful inflammatory marker for differentiating gastric cancer patients from healthy controls. Thirty-one gastric cancer patients and 31 age-sexes matched healthy subjects included into the study. Patients with hypertension, hematological and renal disease, heart failure, chronic infection, hepatic disorder and other cancer were excluded from the study. MPV level was significantly higher in pre-operative gastric cancer patients compared to healthy subjects (8.31 fL vs. 7.85; p: 0.007). ROC analysis suggested 8.25 fL as the cut-off value for MPV (AUC: 0.717, sensitivity: 61%, specificity: 81%). Surgical tumor resection resulted in a significant decrease in MPV level (8.31 fL vs. 7.55 fL; p: 0.001). No significant difference was found in MPV level between the post-operative group and control subjects. We did not find statistically significant difference between MPV and TNM stages. In conclusion, changes in MPV values may be used as an easily available biomarker for monitoring the healthy patients for GC risk and may prompt physicians to make an early diagnosis of GC. © 2014 Informa UK Ltd