Loop-mediated isothermal amplification (LAMP) method for rapid detection of Trypanosoma brucei rhodesiense

Loop-mediated isothermal amplification (LAMP) of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions. In the present study, a LAMP test was designed from the serum resistance-associated (SRA) gene of Trypanosoma brucei rhodesiense, the cause of the acute form of African sleeping sickness, and used to detect parasite DNA from processed and heat-treated infected blood samples. The SRA gene is specific to T. b. rhodesiense and has been shown to confer resistance to lysis by normal human serum. The assay was performed at 62°C for 1 h, using six primers that recognised eight targets. The template was varying concentrations of trypanosome DNA and supernatant from heat-treated infected blood samples. The resulting amplicons were detected using SYTO-9 fluorescence dye in a real-time thermocycler, visual observation after the addition of SYBR Green I, and gel electrophoresis. DNA amplification was detected within 35 min. The SRA LAMP test had an unequivocal detection limit of one pg of purified DNA (equivalent to 10 trypanosomes/ml) and 0.1 pg (1 trypanosome/ml) using heat-treated buffy coat, while the detection limit for conventional SRA PCR was ∼1,000 trypanosomes/ml. The expected LAMP amplicon was confirmed through restriction enzyme RsaI digestion, identical melt curves, and sequence analysis. The reproducibility of the SRA LAMP assay using water bath and heat-processed template, and the ease in results readout show great potential for the diagnosis of T. b. rhodesiense in endemic regions

Origin of 1015−101610^{15}-10^{16}G Magnetic Fields in the Central Engine of Gamma Ray Bursts

Various authors have suggested that the gamma-ray burst (GRB) central engine is a rapidly rotating, strongly magnetized, $(\sim 10^{15}-10^{16}$ G) compact object. The strong magnetic field can accelerate and collimate the relativistic flow and the rotation of the compact object can be the energy source of the GRB. The major problem in this scenario is the difficulty of finding an astrophysical mechanism for obtaining such intense fields. Whereas, in principle, a neutron star could maintain such strong fields, it is difficult to justify a scenario for their creation. If the compact object is a black hole, the problem is more difficult since, according to general relativity it has "no hair" (i.e., no magnetic field). Schuster, Blackett, Pauli, and others have suggested that a rotating neutral body can create a magnetic field by non-minimal gravitational-electromagnetic coupling (NMGEC). The Schuster-Blackett form of NMGEC was obtained from the Mikhail and Wanas's tetrad theory of gravitation (MW). We call the general theory NMGEC-MW. We investigate here the possible origin of the intense magnetic fields $\sim 10^{15}-10^{16}$ G in GRBs by NMGEC-MW. Whereas these fields are difficult to explain astrophysically, we find that they are easily explained by NMGEC-MW. It not only explains the origin of the $\sim 10^{15}-10^{16}$G fields when the compact object is a neutron star, but also when it is a black hole.Comment: 9 pages, accepted for publication in JCA

Substance P regulates puberty onset and fertility in the female mouse

Puberty is a tightly regulated process that leads to reproductive capacity. Kiss1 neurons are crucial in this process by stimulating GnRH, yet how Kiss1 neurons are regulated remains unknown. Substance P (SP), an important neuropeptide in pain perception, induces gonadotropin release in adult mice in a kisspeptin-dependent manner. Here, we assessed whether SP, through binding to its receptor NK1R (neurokinin 1 receptor), participates in the timing of puberty onset and fertility in the mouse. We observed that 1) selective NK1R agonists induce gonadotropin release in prepubertal females; 2) the expression of Tac1 (encoding SP) and Tacr1 (NK1R) in the arcuate nucleus is maximal before puberty, suggesting increased SP tone; 3) repeated exposure to NK1R agonists prepubertally advances puberty onset; and 4) female Tac1-/- mice display delayed puberty; moreover, 5) SP deficiency leads to subfertility in females, showing fewer corpora lutea and antral follicles and leading to decreased litter size. Thus, our findings support a role for SP in the stimulation of gonadotropins before puberty, acting via Kiss1 neurons to stimulate GnRH release, and its involvement in the attainment of full reproductive capabilities in female mice. Copyright © 2015 by the Endocrine Society

Relationships Between Sulcal Asymmetries and Corpus Callosum Size: Gender and Handedness Effects

Magnetic resonance imaging was used to establish the presence and nature of relationships between sulcal asymmetries and mid-sagittal callosal size in neurologically intact subjects, and to determine the influences of sex and handedness. Against a background of long-standing disputes, effects of gender and handedness on callosal size, shape, and variability were additionally examined. Both positive and negative correlations between sulcal asymmetry and callosal size were observed, with effects influenced by sex and handedness. The direction of relationships, however, were dependent on the regional asymmetry measured and on whether real or absolute values were used to quantify sulcal asymmetries. Callosal measurements showed no significant effects of sex or handedness, although subtle differences in callosal shape were observed in anterior and posterior regions between males and females and surface variability was increased in males. Individual variations in callosal size appear to outrange any detectable divergences in size between groups. Relationships between sulcal asymmetries and callosal size, however, are influenced by both sex and handedness. Whether magnitudes of asymmetry are related to increases or decreases in callosal size appears dependent on the chosen indicators of asymmetry. It is an oversimplification, therefore, to assume a single relationship exists between cerebral asymmetries and callosal connection

Vortex dynamics and states of artificially layered superconducting films with correlated defects

Linear resistances and $IV$-characteristics have been measured over a wide range in the parameter space of the mixed phase of multilayered a-TaGe/Ge films. Three films with varying interlayer coupling and correlated defects oriented at an angle $\approx 25$ from the film normal were investigated. Experimental data were analyzed within vortex glass models and a second order phase transition from a resistive vortex liquid to a pinned glass phase. Various vortex phases including changes from three to two dimensional behavior depending on anisotropy have been identified. Careful analysis of $IV$-characteristics in the glass phases revealed a distinctive $T$ and $H$-dependence of the glass exponent $\mu$. The vortex dynamics in the Bose-glass phase does not follow the predicted behavior for excitations of vortex kinks or loops.Comment: 16 pages, 10 figures, 3 table

The JCMT Gould Belt survey: Dense core clusters in Orion B

The James Clerk Maxwell Telescope Gould Belt Legacy Survey obtained SCUBA-2 observations of dense cores within three sub-regions of OrionB: LDN1622, NGC2023/2024, and NGC2068/2071, all of which contain clusters of cores. We present an analysis of the clustering properties of these cores, including the two-point correlation function and Cartwright’s Q parameter. We identify individual clusters of dense cores across all three regions using a minimal spanning tree technique, and find that in each cluster, the most massive cores tend to be centrally located. We also apply the independent M–Σ technique and find a strong correlation between core mass and the local surface density of cores. These two lines of evidence jointly suggest that some amount of mass segregation in clusters has happened already at the dense core stage

Regional Conformational Flexibility Couples Substrate Specificity and Scissile Phosphate Diester Selectivity in Human Flap Endonuclease 1

Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5′-terminus/flap through the arch and recognition of a single nucleotide 3′-flap by the α2–α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2–α3 loop are disordered without substrate. Disorder within the arch explains how 5′-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1–DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1–DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble

Using GIS to integrate old and new archaeological data from Stone Age deposits in Karonga, Malawi

The Karonga District of northern Malawi has an extensive Stone Age archaeological record, primarily represented by stone artefacts that occur in both superficial and buried contexts. Work conducted in the 1960s provided initial documentation of this record. Some of this was presented in summary form in a small number of publications. However, most data were restricted to unpublished field notes, maps, and other static or largely inaccessible formats. GIS has been an essential tool for bringing together these diverse datasets in a digital format to facilitate integration of new research and promote reinvestigation of old sites. Examples from both the regional and site scale demonstrate how old data have been combined with recent survey and excavation data to document, analyse, interpret, and archive current knowledge about the rich Stone Age record of northern Malawi. A significant result from this approach has been the suggested reinterpretation of the Mwanganda’s Village Site

A methodology to compile multi-hazard interrelationships in a data-scarce setting: an application to Kathmandu Valley, Nepal

This paper introduces a multifaceted methodology to identify and compile single natural hazards and multi-hazard interrelationships within the context of data-scarce urban settings, exemplified by Kathmandu Valley, Nepal. This approach integrates (i) five blended types of evidence to support a more nuanced and holistic understanding of a hazardscape where data are scarce and (ii) a 2-hour stakeholder workshop with seven participants to provide greater context to the hazards, consider their impacts through the co-production of multi-hazard interrelationship scenarios, and how this methodology could support more people-centred disaster risk reduction (DRR) strategies. We use blended evidence types, including academic literature, grey literature, media, databases, and social media, to systematically search for exemplars of single hazards and multi-hazard interrelationships that have influenced or could potentially influence Kathmandu Valley. We collated 58 sources of evidence for single hazards and 21 sources of evidence for multi-hazard interrelationships. Using these sources, our study identified 21 single hazard types across six hazard groups (geophysical, hydrological, shallow Earth processes, atmospheric, biophysical, and space/celestial hazards) and 83 multi-hazard interrelationships (12 that have direct case study evidence of previous influence in Kathmandu Valley) that might influence Kathmandu Valley. These exemplars are collated into two databases that accompany this paper. We supplement these exemplars with multi-hazard interrelationship scenarios and multi-hazard impacts developed by stakeholders engaged in DRR research and practice in Kathmandu Valley. The results illustrate the complexity of the hazard landscape, with many single hazards and multi-hazard interrelationships potentially influencing Kathmandu Valley. The research emphasises the importance of inclusive DRR strategies that recognise disaggregated impacts experienced by different social groups. This knowledge can inform the development of dynamic risk scenarios in planning and civil protection, thus strengthening multi-hazard approaches to DRR in “Global South” urban areas such as Kathmandu Valley