Life at the extreme: Lessons from the genome

© 2012 BioMed Central Ltd. Extremophile plants thrive in places where most plant species cannot survive. Recent developments in high-throughput technologies and comparative genomics are shedding light on the evolutionary mechanisms leading to their adaptation

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

© 2018 Shrestha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis-and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell

Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae

© 2014 Wang et al. Background: Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. These properties have been designated as \u27extra-transcriptional\u27 effects of the Pol III complex. Previous coding sequence microarray studies using Pol III factor mutants to determine global effects of Pol III complex assembly on Pol II promoter activity revealed only modest effects that did not correlate with the proximity of Pol III complex binding sites. Results: Given our recent results demonstrating that tDNAs block progression of intergenic Pol II transcription, we hypothesized that extra-transcriptional effects within intergenic regions were not identified in the microarray study. To reconsider global impacts of Pol III complex binding, we used RNA sequencing to compare transcriptomes of wild type versus Pol III transcription factor TFIIIC depleted mutants. The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5\u27- and 3\u27-extended transcripts, and de-repression of adjacent genes and intergenic regions. Conclusions: The results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. The results may also be relevant to synthetic biology efforts to design a minimal yeast genome

Comparative study of hybrid artificial intelligence approaches for predicting peak shear strength along soil-Geocomposite drainage layer interfaces

Peak shear strength of soil-Geocomposite Drain Layer (GDL) interfaces is an important parameter in the designing and operating related engineering structures. In this paper, a database compiled from 316 large direct shear tests on soil-GDL interfaces has been established. Based on this database, five different machine learning models: Back Propagation Artificial Neural Network (BPANN) and Support Vector Machine (SVM), with hyperparameters optimised by Particle Swarm Optimisation Algorithm (PSO) and Genetic Algorithm (GA), respectively, and Extreme Learning Machine (ELM) optimised by Exhaustive Method, were adopt to assess the peak shear strength of soil-GDL interfaces. Then, a comprehensive investigation and comparison of the predictive performance for the models was conducted. Also, based on the selected optimal machine learning model, sensitivity analysis was conducted, and an empirical equation developed based on it. The research indicated that GA and PSO could significantly increase forecasting precision in a small number of iterations. The BPANN model optimised by PSO has the highest forecasting precision based on the statistics criteria: Root-Mean-Square Error, Correlation Coefficient, Coefficient of Determination, Wilmot’s Index of Agreement, and Mean Absolute Percentage Error. The normal stress has the biggest impact on the peak shear strength, followed by drainage core type, moisture saturation of the soil layer, shearing surface, soil type, consolidation condition, geotextile specification, soil density and drainage core thickness, and the ranking is affected partly by the data distribution of input parameters in the database based on mechanism analysis. An empirical equation developed from the optimal model was proposed to estimate the peak shear strength, which provides convenience for geotechnical engineering personnel with limited knowledge of machine learning technique

The cytoplasmic carbonic anhydrases βCA2 and βCA4 are required for optimal plant growth at low CO\u3csub\u3e2\u3c/sub\u3e

© 2016 American Society of Plant Biologists. All Rights Reserved. Carbonic anhydrases (CAs) are zinc metalloenzymes that interconvert CO2 and HCO3-. In plants, both α-and β-type CAs are present. We hypothesize that cytoplasmic bCAs are required to modulate inorganic carbon forms needed in leaf cells for carbonrequiring reactions such as photosynthesis and amino acid biosynthesis. In this report, we present evidence that βCA2 and βCA4 are the two most abundant cytoplasmic CAs in Arabidopsis (Arabidopsis thaliana) leaves. Previously, βCA4 was reported to be localized to the plasma membrane, but here, we show that two forms of βCA4 are expressed in a tissue-specific manner and that the two proteins encoded by βCA4 localize to two different regions of the cell. Comparing transfer DNA knockout lines with wild-type plants, there was no reduction in the growth rates of the single mutants, βca2 and βca4. However, the growth rate of the double mutant, βca2βca4, was reduced significantly when grown at 200μL L-1 CO2. The reduction in growth of the double mutant was not linked to a reduction in photosynthetic rate. The amino acid content of leaves from the double mutant showed marked reduction in aspartate when compared with the wild type and the single mutants. This suggests the cytoplasmic CAs play an important but not previously appreciated role in amino acid biosynthesis

Impacts of HIV/AIDS on food consumption and wild food use in rural South Africa

HIV/AIDS can affect household food consumption in many ways, including through reductions in availability and quality of labour, reductions in earned income, and increased expenditure on medications. In rural South Africa, these negative effects can be buffered by social safety net programs provided by government and collection of wild foods. Despite some acknowledgement of the potential safety net role of wild foods, however, their contribution relative to other food sources in the context of HIV/AIDS remains underexplored. Here we report empirical findings from two rural communities in the Eastern Cape province of South Africa. Qualitative and quantitative methods were used to characterise food sources, intake and calories from 68 HIV/AIDS afflicted households and 87 non-afflicted households every quarter over 12 months. Results show that diets were moderately well-balanced though limited in variety, with cereal items contributing 52 % to total calorie intake. The bulk of food consumed by households was purchased, with supplementation from own production, collected wild vegetables and collected wild fruits. Up to 20 % of respondents from both HIV/ AIDS afflicted and non-afflicted households had insufficient daily caloric intake. Multivariate analyses show that, all else equal, individuals living in households afflicted by HIV/AIDS consumed fewer calories, had less diverse diets, and were more dependent on wild foods than those living in non-afflicted households. Given the detrimental effects of HIV/AIDS on income and home production, wild foods represent a free and readily available food source for vulnerable households

Multivariate analysis reveals that BVDV field isolates do not show a close VN-based antigenic relationship to US vaccine strains

Objective Evaluate bovine viral diarrhea virus (BVDV) antigenicity by using virus neutralization titers (VNT) analyzed using the principal component analysis (PCA) from antisera generated against US-based vaccine strains against both US-origin field isolates and non-US-origin field isolates. Results Data from both independent analyses demonstrated that several US-origin and non-US-origin BVDV field isolates appear to be antigenically divergent from the US-based vaccine strains. Results from the combined analysis provided greater insight into the antigenic diversity observed among BVDV isolates. Data from this study further support genetic assignment into BVDV subgenotypes, as well as strains within subgenotypes is not representative of antigenic relatedness. PCA highlights isolates that are antigenically divergent from members of the same species and subgenotype and conversely isolates that belong to different subgenotypes have similar antigenic characteristics when using antisera from US-based vaccine isolates

In vitro method to evaluate virus competition between BVDV-1 and BVDV-2 strains using the PrimeFlow RNA assay

Bovine viral diarrhea viruses (BVDV), segregated in BVDV-1 and BVDV-2 species, lead to substantial economic losses to the cattle industry worldwide. It has been hypothesized that there could be differences in level of replication, pathogenesis and tissue tropism between BVDV-1 and BVDV-2 strains. Thus, this study developed an in vitro method to evaluate virus competition between BVDV-1 and BVDV-2 strains. To this end the competitive dynamics of BVDV-1a, BVDV-1b, and BVDV-2a strains in cell cultures was evaluated by a PrimeFlow RNA assay. Similar results were observed in this study, as was observed in an earlier in vivo transmission study. Competitive exclusion was observed as the BVDV-2a strains dominated and excluded the BVDV-1a and BVDV-1b strains. The in vitro model developed can be used to identify viral variations that result in differences in frequency of subgenotypes detected in the field, vaccine failure, pathogenesis, and strain dependent variation in immune responses

ECONOMIC FEASIBILITY OF GROWING GURICIDIA UNDER COCONUTS AS AN ENERGY SOURCE FOR DEN ORO THERMAL POWER PLANTS; AN EX-ANTE APPRAISASL

Growth of the demand for electricity intimately follows the growth of theeconomy of Sri Lanka. Since the hydro resources. the major source of electricityare insufficient to meet the growing demand for electricity, alternative powersources have to be employed. Gliricidia proves to be a promising source ofbiomass energy. Firms generating dendro-thermal power express theirwillingness to establish dendro-thermal power plants at the Coconut ResearchInstitute of Sri Lanka on build-operate and transfer (BOT) basis, and to purchaseGliricidia dry wood delivered at the power plant at Rs. 1250/MT. This studyexamines whether the farmers can supply Gliricidia at the above price with areasonable margin for them. The break-even price of a MT of dry wood deliveredat the power plant located 10 km from the coconut estate was computedemploying discounted cash now method. This was Rs.977, implying a margin ofsome 28(10 for growers. The analysis further demonstrated that the break-evenprice was more sensiti ve to variations in wood yield than the variations intransporting distances. The ex-ante appraisal concludes that the raising ofGliricidia under coconuts as an energy source for dendro-therrnal power plants isan economically viable proposition. However, other socio-economic factorsinlluencing the adoption of new technologies may be worth investigating.