Development of Appropriate Fibrolytic Enzyme Combination for Maize Stover and Its Effect on Rumen Fermentation in Sheep

In vitro studies were undertaken to develop an appropriate fibrolytic enzymes cocktail comprising of cellulase, xylanase and β-D-glucanase for maize stover with an aim to increase its nutrient utilization in sheep. Cellulase and xylanase added individually to ground maize stover at an increasing dose rates (0, 100, 200, 400, 800, 1,600, 3,200, 6,400, 12,800, 25,600, 32,000, 38,400, and 44,800 IU/g DM), increased (p<0.01) the in vitro dry matter digestibility and in vitro sugar release. The doses selected for studying the combination effect of enzymes were 6,400 to 32,000 IU/g of cellulase and 12,800 to 44,800 IU/g of xylanase. At cellulase concentration of 6,400 IU/g, IVDMD % was higher (p<0.01) at higher xylanase doses (25,600 to 44,800 IU/g). While at cellulase doses (12,800 to 32,000 IU/g), IVDMD % was higher at lower xylanase doses (12,800 and 25,600 IU/g) compared to higher xylanase doses (32,000 to 44,800 IU/g). At cellulase concentration of the 6,400 to 32,000 IU/g, the amount of sugar released increased (p<0.01) with increasing levels of xylanase concentrations except for the concentration of 44,800 IU/g. No effect of β-D-glucanase (100 to 300 IU/g) was observed at lower cellulase-xylanase dose (cellulase-xylanase 12,800 to 12,800 IU/g). Based on the IVDMD, the enzyme combination cellulase-xylanase 12,800 to 12,800 IU/g was selected to study its effect on feed intake and rumen fermentation pattern, conducted on 12 rams (6 to 8 months; 20.34±2.369 kg body weight) fed 50% maize stover based TMR. The total volatile fatty acids (p<0.01) and ammonia-N concentration was higher in enzyme supplemented group, while no effect was observed on dry matter intake, ruminal pH and total nitrogen concentration

Improving the value of public RNA-seq expression data by phenotype prediction.

Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data. We apply in silico phenotyping to a set of 70 000 RNA-seq samples we recently processed on a common pipeline as part of the recount2 project. We use gene expression data to build and evaluate predictors for both biological phenotypes (sex, tissue, sample source) and experimental conditions (sequencing strategy). We demonstrate how these predictions can be used to study cross-sample properties of public genomic data, select genomic projects with specific characteristics, and perform downstream analyses using predicted phenotypes. The methods to perform phenotype prediction are available in the phenopredict R package and the predictions for recount2 are available from the recount R package. With data and phenotype information available for 70,000 human samples, expression data is available for use on a scale that was not previously feasible

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

The Klein-Gordon equation with the Kratzer potential in d dimensions

We apply the Asymptotic Iteration Method to obtain the bound-state energy spectrum for the d-dimensional Klein-Gordon equation with scalar S(r) and vector potentials V(r). When S(r) and V(r) are both Coulombic, we obtain all the exact solutions; when the potentials are both of Kratzer type, we obtain all the exact solutions for S(r)=V(r); if S(r) > V(r) we obtain exact solutions under certain constraints on the potential parameters: in this case, a possible general solution is found in terms of a monic polynomial, whose coefficients form a set of elementary symmetric polynomials.Comment: 13 page

Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq

<p>Abstract</p> <p>Background</p> <p><it>Clostridium beijerinckii </it>is an important solvent producing microorganism. The genome of <it>C. beijerinckii </it>NCIMB 8052 has recently been sequenced. Although transcriptome structure is important in order to reveal the functional and regulatory architecture of the genome, the physical structure of transcriptome for this strain, such as the operon linkages and transcript boundaries are not well understood.</p> <p>Results</p> <p>In this study, we conducted a single-nucleotide resolution analysis of the <it>C. beijerinckii </it>NCIMB 8052 transcriptome using high-throughput RNA-Seq technology. We identified the transcription start sites and operon structure throughout the genome. We confirmed the structure of important gene operons involved in metabolic pathways for acid and solvent production in <it>C. beijerinckii </it>8052, including <it>pta</it>-<it>ack</it>, <it>ptb</it>-<it>buk</it>, <it>hbd</it>-<it>etfA</it>-<it>etfB</it>-<it>crt </it>(<it>bcs</it>) and <it>ald</it>-<it>ctfA</it>-<it>ctfB</it>-<it>adc </it>(<it>sol</it>) operons; we also defined important operons related to chemotaxis/motility, transcriptional regulation, stress response and fatty acids biosynthesis along with others. We discovered 20 previously non-annotated regions with significant transcriptional activities and 15 genes whose translation start codons were likely mis-annotated. As a consequence, the accuracy of existing genome annotation was significantly enhanced. Furthermore, we identified 78 putative silent genes and 177 putative housekeeping genes based on normalized transcription measurement with the sequence data. We also observed that more than 30% of pseudogenes had significant transcriptional activities during the fermentation process. Strong correlations exist between the expression values derived from RNA-Seq analysis and microarray data or qRT-PCR results.</p> <p>Conclusions</p> <p>Transcriptome structural profiling in this research provided important supplemental information on the accuracy of genome annotation, and revealed additional gene functions and regulation in <it>C. beijerinckii</it>.</p

Towards the reconstruction of integrated genome-scale models of metabolism and gene expression

The reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and weaknesses concerning the reconstruction of integrated models for multiple prokaryotic organisms. Additionally, the main resources of regulatory information were also surveyed, as the existence of novel sources of regulatory information and gene expression data may contribute for the improvement of methodologies referred herein.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit andBioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European RegionalDevelopment Fund under the scope of Norte2020-Programa Operacional Regional do Norte. Fernando Cruz holds a doctoral fellowship (SFRH/BD/139198/2018) funded by the FCT. The authors thank project SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway (814408) funded by the European Commission.info:eu-repo/semantics/publishedVersio

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

<p>Abstract</p> <p>Background</p> <p>DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations.</p> <p>Results</p> <p>Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads.</p> <p>Conclusion</p> <p>Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.</p