Bio-ethanol from water hyacinth biomass: An evaluation of enzymatic saccharification strategy

Biomass feedstock having less competition with food crops are desirable for bio-ethanol production and such resources may not be localized geographically. A distributed production strategy is therefore more suitable for feedstock like water hyacinth with a decentralized availability. In this study, we have demonstrated the suitability of this feedstock for production of fermentable sugars using cellulases produced on site. Testing of acid and alkali pretreatment methods indicated that alkali pretreatment was more efficient in making the sample susceptible to enzyme hydrolysis. Cellulase and β-glucosidase loading and the effect of surfactants were studied and optimized to improve saccharification. Redesigning of enzyme blends resulted in an improvement of saccharification from 57% to 71%. A crude trial on fermentation of the enzymatic hydrolysate using the common baker’s yeast Saccharomyces cerevisiae yielded an ethanol concentration of 4.4 g/L.     

Production of bio-ethanol from soybean molasses by Saccharomyces cerevisiae at laboratory, pilot and industrial scales

The aim of this work was to develop an economical bioprocess to produce the bio-ethanol from soybean molasses at laboratory, pilot and industrial scales. A strain of Saccharomyces cerevisiae (LPB-SC) was selected and fermentation conditions were defined at the laboratory scale, which included the medium with soluble solids concentration of 30% (w/v), without pH adjustment or supplementation with the mineral sources. The kinetic parameters - ethanol productivity of 8.08g/Lh, Y(P/S) 45.4%, Y(X/S) 0.815%, m 0.27h(-1) and mu(X) 0.0189h(-1) - were determined in a bench scale bioreactor. Ethanol production yields after the scale-up were satisfactory, with small decreases from 169.8L at the laboratory scale to 163.6 and 162.7L of absolute ethanol per ton of dry molasses, obtained at pilot and industrial scales, respectively.     

Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23

Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD.     

Interaction of thrombin with sucrose octasulfate

The serine protease thrombin plays multiple roles in many important physiological processes, especially coagulation, where it functions as both a pro- and anticoagulant. The polyanionic glycosaminoglycan heparin modulates thrombin's activity through binding at exosite II. Sucrose octasulfate (SOS) is often used as a surrogate for heparin, but it is not known whether it is an effective heparin mimic in its interaction with thrombin. We have characterized the interaction of SOS with thrombin in solution and determined a crystal structure of their complex. SOS binds thrombin with a K(d) of ~1.4 μM, comparable to that of the much larger polymeric heparin measured under the same conditions. Nonionic (hydrogen bonding) interactions make a larger contribution to thrombin binding of SOS than to heparin. SOS binding to exosite II inhibits thrombin's catalytic activity with high potency but with low efficacy. Analytical ultracentrifugation shows that bovine and human thrombins are monomers in solution in the presence of SOS, in contrast to their complexes with heparin, which are dimers. In the X-ray crystal structure, two molecules of SOS are bound nonequivalently to exosite II portions of a thrombin dimer, in contrast to the 1:2 stoichiometry of the heparin-thrombin complex, which has a different monomer association mode in the dimer. SOS and heparin binding to exosite II of thrombin differ on both chemical and structural levels and, perhaps most significantly, in thrombin inhibition. These differences may offer paths to the design of more potent exosite II binding, allosteric small molecules as modulators of thrombin function.     

The Making of the Women in Biology Forum (WiB) at Bioclues

The Women in Biology forum (WiB) of Bioclues (India) began in 2009 to promote and support women pursuing careers in bioinformatics and computational biology. WiB was formed in order to help women scientists deprived of basic research, boost the prominence of women scientists particularly from developing countries, and bridge the gender gap to innovation. WiB has also served as a platform to highlight the work of established female scientists in these fields. Several award-winning women researchers have shared their experiences and provided valuable suggestions to WiB. Headed by Mohanalatha Chandrasekharan and supported by Dr. Reeta Rani Singhania and Renuka Suravajhala, WiB has seen major progress in the last couple of years particularly in the two avenues Mentoring and Research, off the four avenues in Bioclues: Mentoring, Outreach, Research and Entrepreneurship (MORE).In line with the Bioclues vision for bioinformatics in India, the WiB Journal Club (JoC) recognizes women scientists working on functional genomics and bioinformatics, and provides scientific mentorship and support for project design and hypothesis formulation. As a part of Bioclues, WiB members practice the group''s open-desk policy and its belief that all members are free to express their own thoughts and opinions. The WiB forum appreciates suggestions and welcomes scientists from around the world to be a part of their mission to encourage women to pursue computational biology and bioinformatics.     

Modeling Patient-Derived Glioblastoma with Cerebral Organoids

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Transformation of applied phosphorus in soils under rice-wheat cropping sequence

Summary The transformation of phosphorus in a rice-wheat cropping sequence was studied on alluvial, black, red and laterite soils of India. Phosphorus applied to rice increased Al-P and Fe-P in all soils, R-P in alluvial, black and laterite, and Fe-P and Ca-P in laterite soil only, while it increased native Fe-P in black and red soils. Phosphorus applied to rice and recovered as Al-P was higher after wheat than after rice in alluvial, red and laterite soils. In alluvial and laterite soils, the sum of total inorganic phosphorus fractions in no-P treatment was almost the same after the harvest of rice or wheat, while in black and red soils it was lower after wheat than after rice.     

Gender and Age Differences in Hourly and Daily Patterns of Sedentary Time in Older Adults Living in Retirement Communities

Background

Total sedentary time varies across population groups with important health consequences. Patterns of sedentary time accumulation may vary and have differential health risks. The purpose of this study is to describe sedentary patterns of older adults living in retirement communities and illustrate gender and age differences in those patterns.

Methods

Baseline accelerometer data from 307 men and women (mean age = 84±6 years) who wore ActiGraph GT3X+ accelerometers for ≥ 4 days as part of a physical activity intervention were classified into bouts of sedentary time (<100 counts per minute). Linear mixed models were used to account for intra-person and site-level clustering. Daily and hourly summaries were examined in mutually non-exclusive bouts of sedentary time that were 1+, 5+, 10+, 20+, 30+, 40+, 50+, 60+, 90+ and 120+ minutes in duration. Variations by time of day, age and gender were explored.

Results

Men accumulated more sedentary time than women in 1+, 5+, 10+, 20+, 30+, 40+, 50+ and 60+ minute bouts; the largest gender-differences were observed in 10+ and 20+ minute bouts. Age was positively associated with sedentary time, but only in bouts of 10+, 20+, 30+, and 40+ minutes. Women had more daily 1+ minute sedentary bouts than men (71.8 vs. 65.2), indicating they break up sedentary time more often. For men and women, a greater proportion of time was spent being sedentary during later hours of the day than earlier. Gender differences in intra-day sedentary time were observed during morning hours with women accumulating less sedentary time overall and having more 1+ minute bouts.

Conclusions

Patterns identified using bouts of sedentary time revealed gender and age differences in the way in which sedentary time was accumulated by older adults in retirement communities. Awareness of these patterns can help interventionists better target sedentary time and may aid in the identification of health risks associated with sedentary behavior. Future studies should investigate the impact of patterns of sedentary time on healthy aging, disease, and mortality.