DNA Dynamics during Early Double-Strand Break Processing Revealed by Non-Intrusive Imaging of Living Cells

Chromosome breakage is a major threat to genome integrity. The most accurate way to repair DNA double strand breaks (DSB) is homologous recombination (HR) with an intact copy of the broken locus. Mobility of the broken DNA has been seen to increase during the search for a donor copy. Observing chromosome dynamics during the earlier steps of HR, mainly the resection from DSB ends that generates recombinogenic single strands, requires a visualization system that does not interfere with the process, and is small relative to the few kilobases of DNA that undergo processing. Current visualization tools, based on binding of fluorescent repressor proteins to arrays of specific binding sites, have the major drawback that highly-repeated DNA and lengthy stretches of strongly bound protein can obstruct chromatin function. We have developed a new, non-intrusive method which uses protein oligomerization rather than operator multiplicity to form visible foci. By applying it to HO cleavage of the MAT locus on Saccharomyces cerevisiae chromosome III, we provide the first real-time analysis of resection in single living cells. Monitoring the dynamics of a chromatin locus next to a DSB revealed transient confinement of the damaged chromatin region during the very early steps of resection, consistent with the need to keep DNA ends in contact. Resection in a yku70 mutant began ∼10 min earlier than in wild type, defining this as the period of commitment to homology-dependent repair. Beyond the insights into the dynamics and mechanism of resection, our new DNA-labelling and -targeting method will be widely applicable to fine-scale analysis of genome organization, dynamics and function in normal and pathological contexts.     

Joint wireless power transfer and task offloading in mobile edge computing: a survey

Cluster Computing - The promising technique of Wireless Power Transfer (WPT) to end devices and sensors has gained the attention of researchers recently. Mobile edge computing (MEC) is also...     

Structure and histochemical organization of the spleen of Agama stellio (Sauria: Agamidae) and Chalcides ocellatus (Sauria: Scincidae)

The spleen of Agama stellio is composed mainly of red pulp; the white pulp is poorly developed, and its clusters are scattered throughout the organ and contain lymphocytes, reticular cells, and some plasma cells. The red pulp consists of clear reticular cells intermingled with blood cells, sinusoids, and pigment cells. The spleen of Chalcides ocellatus is encapsulated by connective tissue and is composed of white and red pulp. The white pulp consists of lymphoid tissue that surrounds the central arterioles, forming the periarteriolar lymphocyte sheath (PALS). The red pulp is composed of a system of venous sinuses and cords. The results of various histochemical procedures designed to demonstrate mucosubstances, proteins, and nucleic acids indicate that the spleen in these species resembles the mammalian spleen. © 1993 Wiley-Liss, Inc.     

Cytokine physiognomies of MSCs from varied sources confirm the regenerative commitment post-coculture with activated neutrophils

The interaction of mesenchymal stromal cells (MSCs) with paracrine signals and immunological cells, and their responses and regenerative commitment thereafter, is understudied. In the current investigation, we compared MSCs from the umbilical cord blood (UCB), dental pulp (DP), and liposuction material (LS) on their ability to respond to activated neutrophils. Cytokine profiling (interleukin-1α [IL-1α], IL-2, IL-4, IL-6, IL-8, tumor necrosis factor-α [TNF-α], interferon-γ [IFN-γ], transforming growth factor-β [TGF-β]), cellular proliferation and osteogenic differentiation patterns were assessed. The results showed largely comparable cytokine profiles with higher TNF-α and IFN-γ levels in LSMSCs owing to their mature cellular phenotype. The viability and proliferation between LS/DP/UCB MSCs were comparable in the coculture group, while direct activation of MSCs with lipopolysaccharide (LPS) showed comparable proliferation with significant cell death in UCB MSCs and slightly higher cell death in the other two types of MSC. Furthermore, when MSCs post-neutrophil exposure were induced for osteogenic differentiation, though all the MSCs devoid of the sources differentiated, we observed rapid and significant turnover of DPMSCs positive of osteogenic markers rather than LS and UCB MSCs. We further observed a significant turnover of IL-1α and TGF-β at mRNA and cytokine levels, indicating the commitment of MSCs to differentiate through interacting with immunological cells or bacterial products like neutrophils or LPS, respectively. Taken together, these results suggest that MSCs have more or less similar cytokine responses devoid of their anatomical niche. They readily switch over from the cytokine responsive cell phenotype at the immunological microenvironment to differentiate and regenerate tissue in response to cellular signals.     

Brain Systems for Probabilistic and Dynamic Prediction: Computational Specificity and Integration

A computational approach to functional specialization suggests that brain systems can be characterized in terms of the types of computations they perform, rather than their sensory or behavioral domains. We contrasted the neural systems associated with two computationally distinct forms of predictive model: a reinforcement-learning model of the environment obtained through experience with discrete events, and continuous dynamic forward modeling. By manipulating the precision with which each type of prediction could be used, we caused participants to shift computational strategies within a single spatial prediction task. Hence (using fMRI) we showed that activity in two brain systems (typically associated with reward learning and motor control) could be dissociated in terms of the forms of computations that were performed there, even when both systems were used to make parallel predictions of the same event. A region in parietal cortex, which was sensitive to the divergence between the predictions of the models and anatomically connected to both computational networks, is proposed to mediate integration of the two predictive modes to produce a single behavioral output.     

A combination of urinary biomarker panel and PancRISK score for earlier detection of pancreatic cancer: A case–control study

BackgroundPancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, with around 9% of patients surviving >5 years. Asymptomatic in its initial stages, PDAC is mostly diagnosed late, when already a locally advanced or metastatic disease, as there are no useful biomarkers for detection in its early stages, when surgery can be curative. We have previously described a promising biomarker panel (LYVE1, REG1A, and TFF1) for earlier detection of PDAC in urine. Here, we aimed to establish the accuracy of an improved panel, including REG1B instead of REG1A, and an algorithm for data interpretation, the PancRISK score, in additional retrospectively collected urine specimens. We also assessed the complementarity of this panel with CA19-9 and explored the daily variation and stability of the biomarkers and their performance in common urinary tract cancers.Methods and findingsClinical specimens were obtained from multiple centres: Barts Pancreas Tissue Bank, University College London, University of Liverpool, Spanish National Cancer Research Center, Cambridge University Hospital, and University of Belgrade. The biomarker panel was assayed on 590 urine specimens: 183 control samples, 208 benign hepatobiliary disease samples (of which 119 were chronic pancreatitis), and 199 PDAC samples (102 stage I–II and 97 stage III–IV); 50.7% were from female individuals. PDAC samples were collected from patients before treatment. The samples were assayed using commercially available ELISAs. Statistical analyses were performed using non-parametric Kruskal–Wallis tests adjusted for multiple comparisons, and multiple logistic regression. Training and validation datasets for controls and PDAC samples were obtained after random division of the whole available dataset in a 1:1 ratio. The substitution of REG1A with REG1B enhanced the performance of the panel to detect resectable PDAC. In a comparison of controls and PDAC stage I–II samples, the areas under the receiver operating characteristic curve (AUCs) increased from 0.900 (95% CI 0.843–0.957) and 0.926 (95% CI 0.843–1.000) in the training (50% of the dataset) and validation sets, respectively, to 0.936 in both the training (95% CI 0.903–0.969) and the validation (95% CI 0.888–0.984) datasets for the new panel including REG1B. This improved panel showed both sensitivity (SN) and specificity (SP) to be >85%. Plasma CA19-9 enhanced the performance of this panel in discriminating PDAC I–II patients from controls, with AUC = 0.992 (95% CI 0.983–1.000), SN = 0.963 (95% CI 0.913–1.000), and SP = 0.967 (95% CI 0.924–1.000). We demonstrate that the biomarkers do not show significant daily variation, and that they are stable for up to 5 days at room temperature. The main limitation of our study is the low number of stage I–IIA PDAC samples (n = 27) and lack of samples from individuals with hereditary predisposition to PDAC, for which specimens collected from control individuals were used as a proxy.ConclusionsWe have successfully validated our urinary biomarker panel, which was improved by substituting REG1A with REG1B. At a pre-selected cutoff of >80% SN and SP for the affiliated PancRISK score, we demonstrate a clinically applicable risk stratification tool with a binary output for risk of developing PDAC (‘elevated’ or ‘normal’). PancRISK provides a step towards precision surveillance for PDAC patients, which we will test in a prospective clinical study, UroPanc.

Silvana Debernardi and colleagues establish a clinical risk score and a biomarker panel for early detection of pancreatic cancer.     

Purification of β-xylosidase from Aspergillus tamarii using ground oats and a possible application on the fermented hydrolysate by Pichia stipitis

In this study we determined that Aspergillus tamarii Kita is able to utilize Avena sativa L. (oats) for the production of β-xylosidase under static or shaking conditions in submerged liquid-state (LSF), solid-state (SSF) and slurry-state (SlSF) cultures. The produced enzyme was purified and characterized. Maximum yield occurred under shaking conditions in SSF cultures (33.7 U/ml), with 24.9 and 5.5 U/ml produced in SISF and LSF cultures, respectively. Peptone was found to be the best nitrogen additive and enhanced enzyme production (41.5 U/ml). The produced enzyme was precipitated by ammonium sulfate (60 %) and further purified by gel filtration through a Sephadex G-100 and ion exchange column of diethylaminoethyl cellulose, with a yield of 40.57 % and 35.73-fold purification. Enzyme activity was optimal at pH 5.5 and 55 °C. The purified enzyme retained full activity even at the end of a 1-h incubation at this optimal condition. Midpoint of thermal inactivation (Tm) was recorded at 60 °C after 90 min of exposure. The Michaelis–Menten constant, maximal reaction velocity, turnover number and specificity constant of the purified enzyme were calculated to be 0.075 mg/ml, 71.42 U/mg of protein, 7.14/S and 95.2 mg/ml/s, respectively. The inability of the purified enzyme to hydrolyze celluloses indicated that the enzyme was a free cellulase. The most efficient enzyme activators were Mg2+, followed by Mn2+ and Zn2+ in that order. The molecular mass of the purified enzyme was 91 kDa as determined by SDS-PAGE. The possibility of using the fermentation of ground oat hydrolysate for the production of ethanol and xylitol in the presence of Pichia stipitis Pignal was assessed. The maximum production of ethanol and xylitol were obtained after 72 h of fermentation, resulting in 11.06 and 21.51 g/l respectively.     

Extracellular enzymatic activity of aquatic and aero-aquatic conidial fungi

Nineteen species of aquatic and areo-aquatic conidial fungi were tested for their ability to produce extracellular enzymes which degrade cellulose, starch, lipids, proteins and tannic acid. The cellulolytic activity was determined by using both solid and liquid media. The activity of other enzymes was examined using solid media. Two-thirds of the species were able to hydrolyze soluble cellulose (CMC) incorporated in solid and liquid media with varying degrees of activity. Extracellular culture filtrates ofAegerita candida, Helicodendron giganteum andH. tubulosum contained a Cl-Cx enzyme complex that could degrade both soluble cellulose (CMC) and crystalline cellulose (filter paper). Lipase activity was demonstrated by 11 species. Fourteen of the species showed activity for amylase and protease, but only 11 of the 16 were capable of degrading tannic acid.