Decolorization of Textile Effluents Applying Sequential Operation of Prepared Activated Carbons

Three activated carbons were prepared from bio-waste material and their adsorption efficiency in removal of textile effluents was tested. During sequential operation of these carbons, textile effluents were decolorized with better results like 7, 5 and 3 m-1 absorbance at wavelengths of 436, 525 and 620 nm respectively. 2 g of each adsorbent and at optimum contact time of 40 min removed 93% of color form collected textile effluents

Effect of Feeding Differently Processed Sweet Sorghum (Sorghum bicolor L. Moench) Bagasse Based complete Diet on Nutrient Utilization and Microbial N Supply in Growing Ram Lambs

This study was carried out to identify appropriate processing method for efficient utilization of sweet sorghum bagasse (SSB), an agro-industrial by product of ethanol industry after blending with concentrate. SSB based complete diet with roughage to concentrate ratio of 50:50 was processed into mash (SSBM), expander extruded pellet (SSBP), chop form (SSBC) and evaluated in comparison to sorghum stover based complete diet in mash form (SSM). Twenty four Nellore X Deccani ram lambs (9 month age; 21.1 ± 0.57 kg body weight) were randomly divided into four groups of six animals each and the experimental complete diets were allotted at random to each group and evaluated for their intake, nutrient utilization and microbial N supply. Among all the groups, the average dry matter (DM) intake (g/kg w0.75), digested DM, organic matter and crude protein were higher (P < 0.01) in lambs fed SSBP diet. The cellulose digestibility was higher (P < 0.05) in lambs fed SSBP diet than those fed SSM and SSBC diets. Intake of digestible crude protein (DCP, g/d) and metabolizable energy (MJ/d) were higher (P < 0.01) in lambs fed SSBP diet. The SSBP diet had higher (P < 0.01) DCP and N (P < 0.05) balance compared to other three diets. Increased (P < 0.01) purine derivatives and microbial N supply was observed in processed diets. Expander extrusion of SSB based complete diet resulted in improved (P < 0.01) efficiency of microbial protein synthesis. It is concluded that, when SSB was processed into complete diets, in terms of nutrient utilization and microbial N supply, the expander extruded pellet diet was better utilized than chopped or mash form by the growing ram lambs

Growth performance and carcass characteristics of growing ram lambs fed sweet sorghum bagasse-based complete rations varying in roughage-to-concentrate ratios

Different roughage-to-concentrate ratios of sweet sorghum bagasse (SSB) (a by-product of the biofuel industry)-based complete diets were assessed. Twenty four growing Nellore × Deccani ram lambs aged about 3 months (average body wt., 10.62 ± 0.25 kg) were randomly allotted to four complete rations (CR) varying in roughage-to-concentrate ratios viz. 60:40 (CR-I), 50:50 (CR-II), 40:60 (CR-III) and 30:70(CR-IV) for a period of 180 days. The feed intake was comparable among the lambs fed different experimental complete diets. Average daily weight gain (in grams) was 77.31 ± 4.90, 81.76 ± 5.16, 85.83 ± 2.83 and 86.30 ± 3.25, and feed conversion ratio (in kilograms of feed per kilogram gain) averaged 11.42 ± 0.68, 10.57 ± 0.64, 10.17 ± 0.37 and 9.96 ± 0.38 in ram lambs fed CR-I, CR-II, CR-III and CR-IV rations, respectively. Statistically, differences in daily weight gain and feed conversion ratio among the lambs fed four experimental rations were not significant (P > 0.05). The cost per kilogram gain was significantly (P < 0.01) higher in ram lambs fed CR-IV and CR-III rations compared to CR-I ration, and it was comparable between CR-I and CR-II rations. Dressing percentage averaged 44.90 ± 0.15, 42.57 ± 0.72, 43.67 ± 0.16 and 44.42 ± 0.76 for the respective diets. No significant difference and trend was observed in preslaughter weight, empty body weight, carcass weights, dressing percentage, wholesale cuts and edible and non-edible portions of experimental animals. Similarly, no significant variation could be seen in bone and meat yield (in per cent) and their ratios in various wholesale cuts among the dietary treatments. The roughage-to-concentrate ratio did not affect the chemical composition of meat; however, the fat content of meat was linearly increased with increase in the proportion of concentrate in the diets. The results of the experiment indicated that SSB can be included at 60 % level in the complete diet for economical mutton production from growing Nellore × Deccani ram lambs

A complete set of nascent transcription rates for yeast genes

The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell

Occupational exposure to dusts and risk of renal cell carcinoma

Background: Occupational exposures to dusts have generally been examined in relation to cancers of the respiratory system and have rarely been examined in relation to other cancers, such as renal cell carcinoma (RCC). Although previous epidemiological studies, though few, have shown certain dusts, such as asbestos, to increase renal cancer risk, the potential for other occupational dust exposures to cause kidney damage and/or cancer may exist. We investigated whether asbestos, as well as 20 other occupational dust exposures, were associated with RCC risk in a large European, multi-center, hospital-based renal case-control study.Methods: General occupational histories and job-specific questionnaires were reviewed by occupational hygienists for subject-specific information. Odds ratios (ORs) and 95% confidence intervals (95% CIs) between RCC risk and exposures were calculated using unconditional logistic regression. Results: Among participants ever exposed to dusts, significant associations were observed for glass fibres (OR: 2.1; 95% CI: 1.1-3.9), mineral wool fibres (OR: 2.5; 95% CI: 1.2-5.1), and brick dust (OR: 1.5; 95% CI: 1.0-2.4). Significant trends were also observed with exposure duration and cumulative exposure. No association between RCC risk and asbestos exposure was observed. Conclusion: Results suggest that increased RCC risk may be associated with occupational exposure to specific types of dusts. Additional studies are needed to replicate and extend findings. © 2011 Cancer Research UK All rights reserved

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

<p>Abstract</p> <p>Background</p> <p>Initiation and elongation of RNA polymerase II (RNAPII) transcription is regulated by both DNA sequence and chromatin signals. Recent breakthroughs make it possible to measure the chromatin state and activity of core promoters genome-wide, but dedicated computational strategies are needed to progress from descriptive annotation of data to quantitative, predictive models.</p> <p>Results</p> <p>Here, we describe a computational framework which with high accuracy can predict the locations of core promoters, the amount of recruited RNAPII at the promoter, the amount of elongating RNAPII in the gene body, the mRNA production originating from the promoter and finally also the stalling characteristics of RNAPII by considering both quantitative and spatial features of histone modifications around the transcription start site (TSS).</p> <p>As the model framework can also pinpoint the signals that are the most influential for prediction, it can be used to infer underlying regulatory biology. For example, we show that the H3K4 di- and tri- methylation signals are strongly predictive for promoter location while the acetylation marks H3K9 and H3K27 are highly important in estimating the promoter usage. All of these four marks are found to be necessary for recruitment of RNAPII but not sufficient for the elongation. We also show that the spatial distributions of histone marks are almost as predictive as the signal strength and that a set of histone marks immediately downstream of the TSS is highly predictive of RNAPII stalling.</p> <p>Conclusions</p> <p>In this study we introduce a general framework to accurately predict the level of RNAPII recruitment, elongation, stalling and mRNA expression from chromatin signals. The versatility of the method also makes it ideally suited to investigate other genomic data.</p

MicroRNA let-7c Is Downregulated in Prostate Cancer and Suppresses Prostate Cancer Growth

Prostate cancer (PCa) is characterized by deregulated expression of several tumor suppressor or oncogenic miRNAs. The objective of this study was the identification and characterization of miR-let-7c as a potential tumor suppressor in PCa.Levels of expression of miR-let-7c were examined in human PCa cell lines and tissues using qRT-PCR and in situ hybridization. Let-7c was overexpressed or suppressed to assess the effects on the growth of human PCa cell lines. Lentiviral-mediated re-expression of let-7c was utilized to assess the effects on human PCa xenografts.We identified miR-let-7c as a potential tumor suppressor in PCa. Expression of let-7c is downregulated in castration-resistant prostate cancer (CRPC) cells. Overexpression of let-7c decreased while downregulation of let-7c increased cell proliferation, clonogenicity and anchorage-independent growth of PCa cells in vitro. Suppression of let-7c expression enhanced the ability of androgen-sensitive PCa cells to grow in androgen-deprived conditions in vitro. Reconstitution of Let-7c by lentiviral-mediated intratumoral delivery significantly reduced tumor burden in xenografts of human PCa cells. Furthermore, let-7c expression is downregulated in clinical PCa specimens compared to their matched benign tissues, while the expression of Lin28, a master regulator of let-7 miRNA processing, is upregulated in clinical PCa specimens.These results demonstrate that microRNA let-7c is downregulated in PCa and functions as a tumor suppressor, and is a potential therapeutic target for PCa

Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks

A central challenge in genetics is to understand when and why mutations alter the phenotype of an organism. The consequences of gene inhibition have been systematically studied and can be predicted reasonably well across a genome. However, many sequence variants important for disease and evolution may alter gene regulation rather than gene function. The consequences of altering a regulatory interaction (or “edge”) rather than a gene (or “node”) in a network have not been as extensively studied. Here we use an integrative analysis and evolutionary conservation to identify features that predict when the loss of a regulatory interaction is detrimental in the extensively mapped transcription network of budding yeast. Properties such as the strength of an interaction, location and context in a promoter, regulator and target gene importance, and the potential for compensation (redundancy) associate to some extent with interaction importance. Combined, however, these features predict quite well whether the loss of a regulatory interaction is detrimental across many promoters and for many different transcription factors. Thus, despite the potential for regulatory diversity, common principles can be used to understand and predict when changes in regulation are most harmful to an organism

The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation

The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate their differences, we performed strand-specific, massively-parallel sequencing of RNA from C. albicans white and opaque cells. With these data we first annotated the C. albicans transcriptome, finding hundreds of novel differentially-expressed transcripts. Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by a master regulator of the white-opaque switch (Wor1). We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation. In particular, we can now resolve the poor concordance between binding of a master regulator and the differential expression of adjacent genes, a discrepancy observed in several other studies of cell differentiation. More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome. Many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts. We also find that 5′ and 3′ UTRs of mRNAs in the circuit are unusually long and that 5′ UTRs often differ in length between cell-types, suggesting UTRs encode important regulatory information and that use of alternative promoters is widespread. Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells. Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of heritable differentiation states in eukaryotes

Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions