A Java Program for LRE-Based Real-Time qPCR that Enables Large-Scale Absolute Quantification

Background: Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Findings: Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. Conclusions: The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples

Forecasting the combined effects of climate and land use change on Mexican bats

Aim: Climate and land use change are among the most important threatening processes driving biodiversity loss, especially in the tropics. Although the potential impacts of each threat have been widely studied in isolation, few studies have assessed the impacts of climate and land cover change in combination. Here, we evaluate the exposure of a large mammalian clade, bats, to multiple scenarios of environmental change and dispersal to understand potential consequences for biodiversity conservation. / Location: Mexico. / Methods: We used ensemble species distribution models to forecast changes in environmental suitability for 130 bat species that occur in Mexico by 2050s under four dispersal assumptions and four combined climate and land use change scenarios. We identified regions with the strongest projected impacts for each scenario and assessed the overlap across scenarios. / Results: The combined effects of climate and land use change will cause an average reduction in environmental suitability for 51% of the species across their range, regardless of scenario. Overall, species show a mean decrease in environmental suitability in at least 46% of their current range in all scenarios of change and dispersal. Climate scenarios had a higher impact on species environmental suitability than land use scenarios. There was a spatial overlap of 43% across the four environmental change scenarios for the regions projected to have the strongest impacts. / Main conclusions: Combined effects of future environmental change may result in substantial declines in environmental suitability for Mexican bats even under optimistic scenarios. This study highlights the vulnerability of megadiverse regions and an indicator taxon to human disturbance. The consideration of combined threats can make an important difference in how we react to changes to conserve our biodiversity as they pose different challenges

Non-singlet Baryons in Less Supersymmetric Backgrounds

We analyze the holographic description of non-singlet baryons in various backgrounds with reduced supersymmetries and/or confinement. We show that they exist in all AdS_5xY_5 backgrounds with Y_5 an Einstein manifold bearing five form flux, for a number of quarks 5N/8< k< N, independently on the supersymmetries preserved. This result still holds for gamma_i deformations. In the confining Maldacena-Nunez background non-singlet baryons also exist, although in this case the interval for the number of quarks is reduced as compared to the conformal case. We generalize these configurations to include a non-vanishing magnetic flux such that a complementary microscopical description can be given in terms of lower dimensional branes expanding into fuzzy baryons. This description is a first step towards exploring the finite 't Hooft coupling region.Comment: 36 Pages, 1 figure, Latex, v2: few minor changes, JHEP versio

Lessons from building an automated pre-departure sequencer for airports

Commercial airports are under increasing pressure to comply with the Eurocontrol collaborative decision making (CDM) initiative, to ensure that information is passed between stakeholders, integrate automated decision support or make predictions. These systems can also aid effective operations beyond the airport by communicating scheduling decisions to other relevant parties, such as Eurocontrol, for passing on to downstream airports and enabling overall airspace improvements. One of the major CDM components is aimed at producing the target take-off times and target startup-approval times, i.e. scheduling when the aircraft should push back from the gates and start their engines and when they will take off. For medium-sized airports, a common choice for this is a “pre-departure sequencer” (PDS). In this paper, we describe the design and requirements challenges which arose during our development of a PDS system for medium sized international airports. Firstly, the scheduling problem is highly dynamic and event driven. Secondly, it is important to end-users that the system be predictable and, as far as possible, transparent in its operation, with decisions that can be explained. Thirdly, users can override decisions, and this information has to be taken into account. Finally, it is important that the system is as fair as possible for all users of the airport, and the interpretation of this is considered here. Together, these factors have influenced the design of the PDS system which has been built to work within an existing large system which is being used at many airport

Sexually dimorphic gene expression in bovine conceptuses at the initiation of implantation

In cattle, maternal recognition of pregnancy occurs on Day 16 via secretion of interferon tau (IFNT) by the conceptus. The endometrium can distinguish between embryos with different developmental competencies. In eutherian mammals, X-chromosome inactivation (XCI) is required to ensure an equal transcriptional level of most X-linked genes for both male and female embryos in adult tissues, but this process is markedly different in cattle than mice. We examined how sexual dimorphism affected conceptus transcript abundance and amino acid composition as well as the endometrial transcriptome during the peri-implantation period of pregnancy. Of the 5132 genes that were differentially expressed on Day 19 in male compared to female conceptuses, 2.7% were located on the X-chromosome. Concentrations of specific amino acids were higher in the uterine luminal fluid with male compared to female conceptuses, while female conceptuses had higher transcript abundance of specific amino acid transporters (SLC6A19 and SLC1A35). Of note, the endometrial transcriptome was not different in cattle gestating a male or a female conceptus. These data support the hypothesis that, far from being a blastocyst specific phenomenon, XCI is incomplete before and during implantation in cattle. Despite differences in transcript abundance and amino acid utilization in male versus female conceptuses, the sex of the conceptus itself does not elicit a different transcriptomic response in the endometrium

Role of mitochondrial raft-like microdomains in the regulation of cell apoptosis

Lipid rafts are envisaged as lateral assemblies of specific lipids and proteins that dissociate and associate rapidly and form functional clusters in cell membranes. These structural platforms are not confined to the plasma membrane; indeed lipid microdomains are similarly formed at subcellular organelles, which include endoplasmic reticulum, Golgi and mitochondria, named raft-like microdomains. In addition, some components of raft-like microdomains are present within ER-mitochondria associated membranes. This review is focused on the role of mitochondrial raft-like microdomains in the regulation of cell apoptosis, since these microdomains may represent preferential sites where key reactions take place, regulating mitochondria hyperpolarization, fission-associated changes, megapore formation and release of apoptogenic factors. These structural platforms appear to modulate cytoplasmic pathways switching cell fate towards cell survival or death. Main insights on this issue derive from some pathological conditions in which alterations of microdomains structure or function can lead to severe alterations of cell activity and life span. In the light of the role played by raft-like microdomains to integrate apoptotic signals and in regulating mitochondrial dynamics, it is conceivable that these membrane structures may play a role in the mitochondrial alterations observed in some of the most common human neurodegenerative diseases, such as Amyotrophic lateral sclerosis, Huntington's chorea and prion-related diseases. These findings introduce an additional task for identifying new molecular target(s) of pharmacological agents in these pathologies

Bone Biomarkers Help Grading Severity of Coronary Calcifications in Non Dialysis Chronic Kidney Disease Patients

BACKGROUND: Osteoprotegerin (OPG) and fibroblast growth factor-23 (FGF23) are recognized as strong risk factors of vascular calcifications in non dialysis chronic kidney disease (ND-CKD) patients. The aim of this study was to investigate the relationships between FGF23, OPG, and coronary artery calcifications (CAC) in this population and to attempt identification of the most powerful biomarker of CAC: FGF23? OPG? METHODOLOGY/PRINCIPAL FINDINGS: 195 ND-CKD patients (112 males/83 females, 70.8 [27.4-94.6] years) were enrolled in this cross-sectional study. All underwent chest multidetector computed tomography for CAC scoring. Vascular risk markers including FGF23 and OPG were measured. Logistic regression analyses were used to study the potential relationships between CAC and these markers. The fully adjusted-univariate analysis clearly showed high OPG (≥10.71 pmol/L) as the only variable significantly associated with moderate CAC ([100-400[) (OR = 2.73 [1.03;7.26]; p = 0.04). Such association failed to persist for CAC scoring higher than 400. Indeed, severe CAC was only associated with high phosphate fractional excretion (FEPO(4)) (≥38.71%) (OR = 5.47 [1.76;17.0]; p = 0.003) and high FGF23 (≥173.30 RU/mL) (OR = 5.40 [1.91;15.3]; p = 0.002). In addition, the risk to present severe CAC when FGF23 level was high was not significantly different when OPG was normal or high. Conversely, the risk to present moderate CAC when OPG level was high was not significantly different when FGF23 was normal or high. CONCLUSIONS: Our results strongly suggest that OPG is associated to moderate CAC while FGF23 rather represents a biomarker of severe CAC in ND-CKD patients

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation