Observations on bacteria associated with pigeon crop

Lactobacilli, streptococci and coliforms of pigeon crop contents, 5th wash, macerate and those of first-day pigeon milk have been studied. Streptococci predominated in all the samples tested. Relatively higher counts of lactobacilli and streptococci in crop macerate than in the 5th wash suggested the adhesion of these bacteria to crop wall. Because of frequent occurrence in crop of partially digested fibrous food, its contents were tested for the presence of cellulolytic bacteria. The results indicated that four isolates were capable of utilizing cellulose with the resultant production of reducing sugars. It is inferred that the crop microflora is involved in the degradation of dietary fibre in the pigeon.     

Phenolic compounds present in rice husk

In a study on the phenolic distribution of rice husk (lemma, palea, rachilla and sterile lemmas), seven phenolic acids were detected in the alkali and alcoholie extracts. The total quantity of phenolic compounds in the husk differed with cultivars; however, no qualitative difference was noticed.     

Identification of potent,selective and orally bioavailable phenyl ((R)-3-phenylpyrrolidin-3-yl)sulfone analogues as RORγt inverse agonists

An X-ray crystal structure of one of our previously discovered RORγt inverse agonists bound to the RORγt ligand binding domain revealed that the cyclohexane carboxylic acid group of compound 2 plays a significant role in RORγt binding, forming four hydrogen bonding and ionic interactions with RORγt. SAR studies centered around the cyclohexane carboxylic acid group led to identification of several structurally diverse and more potent compounds, including new carboxylic acid analogues 7 and 20, and cyclic sulfone analogues 34 and 37. Notably, compounds 7 and 20 were found to maintain the desirable pharmacokinetic profile of 2.     

Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention

Genomic screens for small RNA candidates in Enterobacteriacae genomes were carried out with existing small RNA sequences, conserved flanking genes, and genomic backbone information. The small RNA sequences and contexts from E. coli K12 formed the basis of the search. Sequence identity identified 117 additional small RNA homologs in related genomes. Motifs of continuous sequence stretches added another 48 sRNA regions, termed partial homologs. However, this study is unique in identifying 160 nonhomologous sRNA loci in related genomes based on the conserved flanking gene synteny and the backbone retention information obtained from KEGG-SSDB. Gene synteny and genomic backbone continuity were observed to be correlated with all of the sRNAs in related genomes. This search is the first of its kind toward identification of functionally important regions using gene order and back-bone information. A disruption in flanking gene order or genomic backbone indicates a possible hotspot for alien gene pool integration. This study reports both occurrence of multiple copies of a sRNA and co-occurrence of different sRNAs between a pair of conserved flanking genes. In general, synteny and genomic backbone retention information can be added as additional search criteria toward the design of precise bioinformatics tools for sRNA, gene identification, and gene functional annotations in related genomes.     

Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex

Background  

The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by sleep:wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances.     

Genetic characterization of caffeine degradation by bacteria and its potential applications

The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N‐demethylation and C‐8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N‐demethylation and C‐8 oxidation. All of the genes for the N‐demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2‐kb genomic DNA fragment found in Pseudomonas putida CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C‐8 oxidation of caffeine have been located on a 25.2‐kb genomic DNA fragment of Pseudomonas sp. CBB1. The C‐8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio‐decaffeination, remediation of caffeine‐contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated.