Production of poly-3-hydroxybutyrate by Bacillus sp. JMa5 cultivated in molasses media

A strain of Bacillus sp. coded JMa5 was isolated from molasses contaminated soil. The strain was able to grow at a temperature as high as 45°C and in 250 g/l molasses although the optimal growth temperature was 35–37°C. Cell density reached 30 g/l 8 h after inoculation in a batch culture with an initial concentration of 210 g/l molasses. Under fed-batch conditions, the cells grew to a dry weight of 70 g/l after 30 h of fermentation. The strain accumulated 25–35%, (w/w) polyhydroxybutyrate (PHB) during fermentation. PHB accumulation was a growth-associated process. Factors that normally promote PHB production include high ratios of carbon to nitrogen, and carbon to phosphorus in growth media. Low dissolved oxygen supply resulted in sporulation, which reduced PHB contents and dry weights of the cells. It seems that sporulation induced by reduced supply of nutrients is the reason that PHB content is generally low in the Bacillus strain.     

Thermal enrichment of a reservoir and the effects on annulus formation and growth of largemouth bass, Micropterus salmoides

Analysis of largemouth bass scales, including those from 48 tagged and recaptured fish, revealed that many scales had more 'annuli' than possible for the age of Flint Creek Cooling Reservoir. The mark-recapture data indicated the formation of one supernumerary annulus per year for most bass. Time of formation of true and supernumerary annuli and the causative factors are discussed.
Growth of bass from this reservoir greatly exceeded that reported for thermally unaltered reservoirs of Northwest Arkansas, due to the existence of a nearly year-round growing season, a result of thermal enrichment. The relationship between the ratio of electric power output to reservoir surface area and growth offish was evaluated with reference to published data on cooling reservoirs.     

Food consumption, growth and survival of grass carp Ctenopharyngodon idella Val at four salinities

Grass carp were raised in 227-1 indoor tanks at 3,5,7 and 9%osalinities and 18·5 and 29·5°C temperatures at a density of five fish per tank. Growth rate did not differ under these conditions. Food consumption was similar between temperatures at a given salinity but differed among the salinities with most food intake at the 5%o salinity. An average of 40% of grass carp survived for 180 or more days.     

Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements.

Results

For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to β-lactam (n = 10) and multidrug efflux (n = 54). It also contained eight prophages, 17 other phage-related CDSs and 26 CDSs for transposases.

Conclusions

The L. hongkongensis genome possessed genes for acid and bile resistance, intestinal mucosa colonization, evasion of host defense and cytotoxicity and invasion. A broad variety of antibiotic resistance or multidrug resistance genes, a high number of prophages, other phage-related CDSs and CDSs for transposases, were also identified.     

Limited cell attachment time as a method to synchronize cells grown in monolayer culture

Summary A novel method of synchronizing monolayer tissue culture cells is described. By limiting the period of attachment of trypsinized cells and the subsequent removal of unattached cells a G₁ population of cells is isolated. Evaluation of the degree of synchrony has been carried out by measuring the labeling index and incorporation of [³H]thymidine into DNA. Further conformation of synchrony, as well as a comparison with synchrony by isoleucine deprivation, was obtained by flow cytometry. The expected peak in DNA synthesis rate following limited attachment was observed. This peak becomes more prominent and shifts to earlier times with shorter attachment intervals. The synchronization method described is simple, rapid, yields a substantial number of cells, and is applicable to many cell lines. This research was supported by a Basic Science Research Grant and a grant from the American Heart Foundation to K. Janakidevi. Paul Held and Christian Sell were also supported by predoctoral training grant HL07194 from the National Institutes of Health, Bethesda, MD.     

Computational assessment of the influence of vastus medialis obliquus function on patellofemoral pressures: Model evaluation

A study was performed to evaluate a computational model used to characterize the influence of vastus medialis obliquus (VMO) function on the patellofemoral pressure distribution. Ten knees were tested in vitro at 40°, 60° and 80° of knee flexion with quadriceps loads applied to represent a normal VMO, and with the VMO force decreased by approximately 50% to represent a weak VMO. The tests were performed with the cartilage intact and with a full thickness cartilage lesion centered on the lateral facet of the patella. The experimental tests were replicated computationally by applying discrete element analysis to a model of each knee constructed from MRI images. Repeated measures statistical comparisons were used to compare computational to experimental data and identify significant (p<0.05) differences due to the lesion and the applied VMO force. Neither the lateral force percentage nor the maximum lateral pressure varied significantly between the computational and experimental data. Creating a lesion significantly increased the maximum lateral pressure for all comparisons, except for the experimental data at 40°. Both computationally and experimentally, decrease in the VMO force increased the lateral force percentage by approximately 10% for all cases, and each increase was statistically significant. The maximum lateral pressure increase was typically less than 10% but was still significant for the majority of comparisons focused on the VMO strength. The results indicate that computational modeling can be used to characterize how varying quadriceps loading influences the patellofemoral force and pressure distributions while varying the condition of cartilage.     

Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with community-acquired gastroenteritis. The bacterium has been found in diverse freshwater environments including fish, frogs and drinking water reservoirs. Using the complete genome sequence data of L. hongkongensis, we performed a comprehensive analysis of putative transport-related genes and genes related to chemotaxis, motility and quorum sensing, which may help the bacterium adapt to the changing environments and combat harmful substances.

Results

A genome-wide analysis using Transport Classification Database TCDB, similarity and keyword searches revealed the presence of a large diversity of transporters (n = 457) and genes related to chemotaxis (n = 52) and flagellar biosynthesis (n = 40) in the L. hongkongensis genome. The transporters included those from all seven major transporter categories, which may allow the uptake of essential nutrients or ions, and extrusion of metabolic end products and hazardous substances. L. hongkongensis is unique among closely related members of Neisseriaceae family in possessing higher number of proteins related to transport of ammonium, urea and dicarboxylate, which may reflect the importance of nitrogen and dicarboxylate metabolism in this assacharolytic bacterium. Structural modeling of two C⁴-dicarboxylate transporters showed that they possessed similar structures to the determined structures of other DctP-TRAP transporters, with one having an unusual disulfide bond. Diverse mechanisms for iron transport, including hemin transporters for iron acquisition from host proteins, were also identified. In addition to the chemotaxis and flagella-related genes, the L. hongkongensis genome also contained two copies of qseB/qseC homologues of the AI-3 quorum sensing system.

Conclusions

The large number of diverse transporters and genes involved in chemotaxis, motility and quorum sensing suggested that the bacterium may utilize a complex system to adapt to different environments. Structural modeling will provide useful insights on the transporters in L. hongkongensis.     

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.