PPCAS: Implementation of a Probabilistic Pairwise Model for Consistency-Based Multiple Alignment in Apache Spark

Large-scale data processing techniques, currently known as Big-Data, are used to manage the huge amount of data that are generated by sequencers. Although these techniques have significant advantages, few biological applications have adopted them. In the Bioinformatic scientific area, Multiple Sequence Alignment (MSA) tools are widely applied for evolution and phylogenetic analysis, homology and domain structure prediction. Highly-rated MSA tools, such as MAFFT, ProbCons and T-Coffee (TC), use the probabilistic consistency as a prior step to the progressive alignment stage in order to improve the final accuracy. In this paper, a novel approach named PPCAS (Probabilistic Pairwise model for Consistency-based multiple alignment in Apache Spark) is presented. PPCAS is based on the MapReduce processing paradigm in order to enable large datasets to be processed with the aim of improving the performance and scalability of the original algorithm.This work was supported by the MEyC-Spain [contract TIN2014-53234-C2-2-R]

Zika virus impairs the development of blood vessels in a mouse model of congenital infection

Zika virus (ZIKV) is associated with brain development abnormalities such as primary microcephaly, a severe reduction in brain growth. Here we demonstrated in vivo the impact of congenital ZIKV infection in blood vessel development, a crucial step in organogenesis. ZIKV was injected intravenously in the pregnant type 2 interferon (IFN)-deficient mouse at embryonic day (E) 12.5. The embryos were collected at E15.5 and postnatal day (P)2. Immunohistochemistry for cortical progenitors and neuronal markers at E15.5 showed the reduction of both populations as a result of ZIKV infection. Using confocal 3D imaging, we found that ZIKV infected brain sections displayed a reduction in the vasculature density and vessel branching compared to mocks at E15.5; altogether, cortical vessels presented a comparatively immature pattern in the infected tissue. These impaired vascular patterns were also apparent in the placenta and retina. Moreover, proteomic analysis has shown that angiogenesis proteins are deregulated in the infected brains compared to controls. At P2, the cortical size and brain weight were reduced in comparison to mock-infected animals. In sum, our results indicate that ZIKV impairs angiogenesis in addition to neurogenesis during development. The vasculature defects represent a limitation for general brain growth but also could regulate neurogenesis directly

Recording Lifetime Behavior and Movement in an Invertebrate Model

Characterization of lifetime behavioral changes is essential for understanding aging and aging-related diseases. However, such studies are scarce partly due to the lack of efficient tools. Here we describe and provide proof of concept for a stereo vision system that classifies and sequentially records at an extremely fine scale six different behaviors (resting, micro-movement, walking, flying, feeding and drinking) and the within-cage (3D) location of individual tephritid fruit flies by time-of-day throughout their lives. Using flies fed on two different diets, full sugar-yeast and sugar-only diets, we report for the first time their behavioral changes throughout their lives at a high resolution. We have found that the daily activity peaks at the age of 15–20 days and then gradually declines with age for flies on both diets. However, the overall daily activity is higher for flies on sugar-only diet than those on the full diet. Flies on sugar-only diet show a stronger diurnal localization pattern with higher preference to staying on the top of the cage during the period of light-off when compared to flies on the full diet. Clustering analyses of age-specific behavior patterns reveal three distinct young, middle-aged and old clusters for flies on each of the two diets. The middle-aged groups for flies on sugar-only diet consist of much younger age groups when compared to flies on full diet. This technology provides research opportunities for using a behavioral informatics approach for understanding different ways in which behavior, movement, and aging in model organisms are mutually affecting

Noninjection Synthesis of CdS and Alloyed CdSxSe1−xNanocrystals Without Nucleation Initiators

CdS and alloyed CdSxSe1−x nanocrystals were prepared by a simple noninjection method without nucleation initiators. Oleic acid (OA) was used to stabilize the growth of the CdS nanocrystals. The size of the CdS nanocrystals can be tuned by changing the OA/Cd molar ratios. On the basis of the successful synthesis of CdS nanocrystals, alloyed CdSxSe1−x nanocrystals can also be prepared by simply replacing certain amount of S precursor with equal amount of Se precursor, verified by TEM, XRD, EDX as well as UV–Vis absorption analysis. The optical properties of the alloyed CdSxSe1−x nanocrystals can be tuned by adjusting the S/Se feed molar ratios. This synthetic approach developed is highly reproducible and can be readily scaled up for potential industrial production

Modelling overdispersion with integer-valued moving average processes

A new first-order integer-valued moving average, INMA(1), model based on the negative binomial thinning operation defined by Risti´c et al. [21] is proposed and characterized. It is shown that this model has negative binomial (NB) marginal distribution when the innovations follow a NB distribution and therefore it can be used in situations where the data present overdispersion. Additionally, this model is extended to the bivariate context. The Generalized Method of Moments (GMM) is used to estimate the unknown parameters of the proposed models and the results of a simulation study that intends to investigate the performance of the method show that, in general, the estimates are consistent and symmetric. Finally, the proposed model is fitted to a real dataset and the quality of the adjustment is evaluated.publishe

Formation of PbSe/CdSe Core/Shell Nanocrystals for Stable Near-Infrared High Photoluminescence Emission

PbSe/CdSe core/shell nanocrystals with quantum yield of 70% were obtained by the “successive ion layer adsorption and reaction” technology in solution. The thickness of the CdSe shell was exactly controlled. A series of spectral red shifts with the CdSe shell growth were observed, which was attributed to the combined effect of the surface polarization and the expansion of carriers’ wavefunctions. The stability of PbSe nanocrystals was tremendously improved with CdSe shells

Behavior and Impact of Zirconium in the Soil–Plant System: Plant Uptake and Phytotoxicity

Because of the large number of sites they pollute, toxic metals that contaminate terrestrial ecosystems are increasingly of environmental and sanitary concern (Uzu et al. 2010, 2011; Shahid et al. 2011a, b, 2012a). Among such metals is zirconium (Zr), which has the atomic number 40 and is a transition metal that resembles titanium in physical and chemical properties (Zaccone et al. 2008). Zr is widely used in many chemical industry processes and in nuclear reactors (Sandoval et al. 2011; Kamal et al. 2011), owing to its useful properties like hardness, corrosion-resistance and permeable to neutrons (Mushtaq 2012). Hence, the recent increased use of Zr by industry, and the occurrence of the Chernobyl and Fukashima catastrophe have enhanced environmental levels in soil and waters (Yirchenko and Agapkina 1993; Mosulishvili et al. 1994 ; Kruglov et al. 1996)

Hepatitis C Virus Reveals a Novel Early Control in Acute Immune Response

Recognition of viral RNA structures by the intracytosolic RNA helicase RIG-I triggers induction of innate immunity. Efficient induction requires RIG-I ubiquitination by the E3 ligase TRIM25, its interaction with the mitochondria-bound MAVS protein, recruitment of TRAF3, IRF3- and NF-κB-kinases and transcription of Interferon (IFN). In addition, IRF3 alone induces some of the Interferon-Stimulated Genes (ISGs), referred to as early ISGs. Infection of hepatocytes with Hepatitis C virus (HCV) results in poor production of IFN despite recognition of the viral RNA by RIG-I but can lead to induction of early ISGs. HCV was shown to inhibit IFN production by cleaving MAVS through its NS3/4A protease and by controlling cellular translation through activation of PKR, an eIF2α-kinase containing dsRNA-binding domains (DRBD). Here, we have identified a third mode of control of IFN induction by HCV. Using HCVcc and the Huh7.25.CD81 cells, we found that HCV controls RIG-I ubiquitination through the di-ubiquitine-like protein ISG15, one of the early ISGs. A transcriptome analysis performed on Huh7.25.CD81 cells silenced or not for PKR and infected with JFH1 revealed that HCV infection leads to induction of 49 PKR-dependent genes, including ISG15 and several early ISGs. Silencing experiments revealed that this novel PKR-dependent pathway involves MAVS, TRAF3 and IRF3 but not RIG-I, and that it does not induce IFN. Use of PKR inhibitors showed that this pathway requires the DRBD but not the kinase activity of PKR. We then demonstrated that PKR interacts with HCV RNA and MAVS prior to RIG-I. In conclusion, HCV recruits PKR early in infection as a sensor to trigger induction of several IRF3-dependent genes. Among those, ISG15 acts to negatively control the RIG-I/MAVS pathway, at the level of RIG-I ubiquitination.These data give novel insights in the machinery involved in the early events of innate immune response

Mitotic Spindle Orients Perpendicular to the Forces Imposed by Dynamic Shear

Orientation of the division axis can determine cell fate in the presence of morphogenetic gradients. Understanding how mitotic cells integrate directional cues is therefore an important question in embryogenesis. Here, we investigate the effect of dynamic shear forces on confined mitotic cells. We found that human epithelial cells (hTERT-RPE1) as well as MC3T3 osteoblasts align their mitotic spindle perpendicular to the external force. Spindle orientation appears to be a consequence of cell elongation along the zero-force direction in response to the dynamic shear. This process is a nonlinear response to the strain amplitude, requires actomyosin activity and correlates with redistribution of myosin II. Mechanosteered cells divide normally, suggesting that this mechanism is compatible with biological functions