Photostabilized titanium dioxide and a fluorescent brightener as adjuvants for a nucleopolyhedrovirus

Titanium dioxide (TiO₂)reflects ultraviolet light, and so could beexpected to protect the occlusion bodies (OBs)of nucleopolyhedroviruses (NPVs) fromdegradation by sunlight. However, in thepresence of sunlight and water, TiO₂catalyzes the formation of hydrogen peroxide,which can degrade OBs. We tested microfineTiO₂ that had been photostabilized(particles were coated to prevent catalyticactivity), as a UV protectant for the OBs ofthe NPV of Helicoverpa zea (Boddie). Inthe absence of UV, activity of the OBs wasreduced by nonphotostabilized TiO₂ but wasunaffected by photostabilized TiO₂ or byzinc oxide (ZnO). None of these materialsinfluenced larval feeding rates. Undersimulated sunlight, photostabilizedTiO₂ protected the OBs to a greater degreethan did ZnO. Photostabilized TiO₂ wascompatible with a viral enhancer, thefluorescent brightener Blankophor HRS. Undersimulated sunlight, both materials increasedactivity of the OBs, relative to OBs withneither material, in a largely additive manner. In bioassays of foliage collected from fieldplots of lima bean plants sprayed with OBs withor without one or both of these materials,TiO₂ increased persistence of the OBs, butBlankophor HRS had no significant effect.     

Protein intake and stress levels in nurses and housewives of Pakistan

Stress has many biological effects on human daily life. In the present study, dietary protein intake was correlated with the investigated stress levels of nurses and housewives of the targeted urban population. Age group ranged from 30 to 45 years and both the groups belonged to middle socioeconomic status. After calculations of environmental, psychological and physiological stresses, it was observed that the levels of stress in housewives were significantly higher than those of nurses. Recommended dietary allowances, RDA and actual protein intakes, API were also compared in both the groups. The found protein intake was less in housewives as compared to that of nurses.     

A bioenergetic model of a mixed production fermentation

A bioenergetic model has been developed for the fermentation of glucose by Bacillus polymyxa. This model uses energy balances to determine which pathways are utilized by the substrate. The model can predict substrate consumption, biomass formation, and the product distribution for this fermentation. The products are carbon dioxide, water, 2,3-butanediol, and ethanol, where ethanol represents lumped anaerobic products.     

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Background

Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far been difficult to accelerate effectively on GPUs.

Results

We first analyze the characteristics of the semi-global alignment with traceback in GATK HC and then propose a new algorithm that allows for retrieving the optimal alignment efficiently on GPUs. For the first stage, we choose intra-task parallelization model to calculate the position of the optimal alignment score and the backtracking matrix. Moreover, in the first stage, our GPU implementation also records the length of consecutive matches/mismatches in addition to lengths of consecutive insertions and deletions as in the CPU-based implementation. This helps efficiently retrieve the backtracking matrix to obtain the optimal alignment in the second stage.

Conclusions

Experimental results show that our alignment kernel with traceback is up to 80x and 14.14x faster than its CPU counterpart with synthetic datasets and real datasets, respectively. When integrated into GATK HC (alongside a GPU accelerated pair-HMMs forward kernel), the overall acceleration is 2.3x faster than the baseline GATK HC implementation, and 1.34x faster than the GATK HC implementation with the integrated GPU-based pair-HMMs forward algorithm. Although the methods proposed in this paper is to improve the performance of GATK HC, they can also be used in other pairwise alignments and applications.

     

Theoretical and electrophysiological evidence for axial loading about aortic baroreceptor nerve terminals in rats

Arterial baroreceptors are essential for neurocirculatory control, providing rapid hemodynamic feedback to the central nervous system. The pressure-dependent discharge of carotid and aortic baroreceptor afferents has been extensively studied. A common assumption has been that circumferential deformation of the arterial wall is the predominant mechanical force affecting baroreceptor discharge. However, in vivo the arterial tree is under significant longitudinal tension, leading to the hypothesis that axially directed forces may contribute to baroreceptor function. To test this hypothesis, we utilized a combination of finite element modeling methods and an in vitro rat aortic arch preparation. Model formulation utilized traditional analytic constructs available in the literature followed by refinement of model material parameters through direct comparison of computationally and experimentally generated pressure-diameter curves. The numerical simulations strongly indicated a functional role for axial loading within the region of the baroreceptive nerve terminal. This prediction was confirmed through single-fiber recording of baroreceptor nerve discharge under conditions with and without longitudinal tension in the vessel preparation. The recordings (n = 5) demonstrated that longitudinal tension significantly (P < 0.02) lowered both the pressure threshold (P(th), mmHg) for baroreceptor discharge and sensitivity (S(th), Hz/mmHg). The effect was nearly instantaneous and sustained; i.e., under longitudinal tension average P(th) was 84 +/- 3 mmHg and S(th) was 0.71 +/- 0.15 Hz/mmHg, which immediately increased to a P(th) of 94 +/- 4 mmHg and a S(th) of 1.20 +/- 0.32 Hz/mmHg with loss of axial tension. Possible explanations of how an abrupt change in axial loading could result in a synchronized increase in afferent drive of the baroreceptor reflex, and the potentiating effect this could have on neurogenically mediated orthostatic intolerance are discussed.     

Identification and comparative analysis of <Emphasis Type="Italic">Brassica juncea</Emphasis> pathogenesis-related genes in response to hormonal,biotic and abiotic stresses

Pathogenesis-related proteins (PRs) are the antimicrobial proteins which are commonly used as signatures of defense signaling pathways and systemic acquired resistance. However, in Brassica juncea most of the PR proteins have not been fully characterized and remains largely enigmatic. In this study, full-length cDNA sequences of SA (PR1, PR2, PR5) and JA (PR3, PR12 and PR13) marker genes were isolated from B. juncea and were named as BjPR proteins. BjPR proteins showed maximum identity with known PR proteins of Brassica species. Further, expression profiling of BjPR genes were investigated after hormonal, biotic and abiotic stresses. Pre-treatment with SA and JA stimulators downregulates each other signature genes suggesting an antagonistic relationship between SA and JA in B. juncea. After abscisic acid (ABA) treatment, SA signatures were downregulated while as JA signature genes were upregulated. During Erysiphe cruciferarum infection, SA- and JA-dependent BjPR genes showed distinct expression pattern both locally and systemically, thus suggesting the activation of SA- and JA-dependent signaling pathways. Further, expression of SA marker genes decreases while as JA-responsive genes increases during drought stress. Interestingly, both SA and JA signature genes were induced after salt stress. We also found that BjPR genes displayed ABA-independent gene expression pattern during abiotic stresses thus providing the evidence of SA/JA cross talk. Further, in silico analysis of the upstream regions (1.5 kb) of both SA and JA marker genes showed important cis-regulatory elements related to biotic, abiotic and hormonal stresses.