Evolutionary insights from suffix array-based genome sequence analysis

Gene and protein sequence analyses, central components of studies in modern biology are easily amenable to string matching and pattern recognition algorithms. The growing need of analysing whole genome sequences more efficiently and thoroughly, has led to the emergence of new computational methods. Suffix trees and suffix arrays are data structures, well known in many other areas and are highly suited for sequence analysis too. Here we report an improvement to the design of construction of suffix arrays. Enhancement in versatility and scalability, enabled by this approach, is demonstrated through the use of real-life examples.The scalability of the algorithm to whole genomes renders it suitable to address many biologically interesting problems. One example is the evolutionary insight gained by analysing unigrams, bi-grams and higher n-grams, indicating that the genetic code has a direct influence on the overall composition of the genome. Further, different proteomes have been analysed for the coverage of the possible peptide space, which indicate that as much as a quarter of the total space at the tetra-peptide level is left un-sampled in prokaryotic organisms, although almost all tri-peptides can be seen in one protein or another in a proteome. Besides, distinct patterns begin to emerge for the counts of particular tetra and higher peptides, indicative of a ‘meaning’ for tetra and higher n-grams.The toolkit has also been used to demonstrate the usefulness of identifying repeats in whole proteomes efficiently. As an example, 16 members of one COG, coded by the genome of Mycobacterium tuberculosis H37Rv have been found to contain a repeating sequence of 300 amino acids.     

Recent advances in biosensors for diagnosis of celiac disease: A review

Celiac disease (CD) is an intestinal issue activated by the inappropriate immune reaction towards gluten protein of wheat, rye, barley, oats, and autoantigen, tissue transglutaminase. Regardless of the accessibility of immunochemical conventions for research facility analysis of CD, there is as yet a need of speedier, less expensive, and simpler devices for diagnosing CD. This review concentrates on progresses in biosensors for diagnosing CD in perspective of the scaled down hardware, multianalyte discovery and low sample volume necessity. Various recently developed biosensors in this field are presented.     

A Genome-wide Haploid Genetic Screen Identifies Regulators of Glutathione Abundance and Ferroptosis Sensitivity

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Prenatal skeletal dysplasia phenotype in severe MLII alpha/beta with novel GNPTAB mutation

We report a neonate who was diagnosed as a case of skeletal dysplasia during pregnancy, and was subsequently diagnosed as a case of MLII alpha/beta on the basis of clinical and radiological findings and molecular testing of the parents. A novel GNPTAB mutation c.1701delC [p.F566LfsX5] was identified in the father. The case reiterates the severe prenatal phenotype of MLII alpha/beta which mimics skeletal dysplasia and illustrates the utility of molecular genetic analysis in confirmation of diagnosis and subsequent genetic counselling.     

Optical band gap enhancements of chemically synthesized α-Ni(OH)2 nanoparticles by a novel technique: Precipitator molarity variation

Nickel hydroxide nanoparticles (NHNPs) are extremely important semiconducting materials for applications in energy storage and energy harvesting devices. This study uses a novel variation in molarity of the sodium hydroxide (NaOH) precipitator solution to enhance the direct optical band gap in the NHNPs chemically synthesized by using nickel nitrate hexahydrate (Ni(NO₃)₂·6H₂O) as the precursor. The simple, energy benign chemical precipitation route involved the usage of 1 M (Ni(NO₃)₂·6H₂O) solutions as the precursor and 0.4 M, 0.6 M, and 0.8 M NaOH solutions as the precipitator solutions. The simple variation in precipitator molarity induces an increase in pH from about 6.9 to 7.5 of the reactant solution. As the molarity of the precursor solution does not change, the change in pH of the reactant solution is equivalent to the change in the pH of the precipitator solution. The NHNPs characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), dynamic light scattering (DLS), Fourier-transform infrared (FTIR) and ultraviolet-visible (UV-vis) techniques confirm a reduction of the nanocrystallite size from about 6.8 to 4.5 nm with a concomitant enhancement in the direct optical band gap energy from about 2.64 to 2.74 eV. The possible mechanisms that could be operative behind obtaining microstructurally tuned (MT)-NHNPs and band gap engineering (BGE) of the MT-NHNPs are discussed from both theoretical and physical process perspectives. Further, the implications of these novel results for possible future applications are briefly touched upon. The reported results might be useful to assess the material as an active electrode to improve the performance of batteries.     

Carbaryl-induced elevation of corticosterone level and cholinergic mechanism

Administration of a single dose (200 mg/kg, p.o.) of carbaryl to rats produced a significant rise in adrenal and plasma corticosterone levels and an increase of tyrosine alpha-ketoglutarate transaminase activity in the liver cytosol. Synaptosomal acetylcholinesterase activity of the hypothalamic and the striatal regions of rat brain was decreased by carbaryl treatment under similar conditions. Pretreatment (0.5 h) with atropine sulphate (10 mg/kg, i.p.) failed to counteract the carbaryl-induced elevation of adrenal and plasma corticosterone levels and hence the liver tyrosine alpha-ketoglutarate transaminase activity. Present results suggest that the carbaryl-induced rise in the corticosterone level in the adrenal gland and plasma is not due to a cholinergic mechanism.     

Long term effect of lithium on brain regional catecholamine metabolism

Administration of LiCl (2-4 mmol/kg/day, po) to adult male albino rats for 7 consecutive days increased the catabolism of dopamine (DA) in striatum (ST) and noradrenaline (NA) in hypothalamus (H). Extension of the period of treatment with LiCl (2-4 mmol/kg/day, po) to 14 consecutive days increased catabolism of DA in CX (cerebral cortex) and PM (pons-medulla) and NA in H, and decreased metabolism of DA in ST and NA in PM. Further prolongation of treatment with LiCl (2 or 4 mmol/kg/day, po) for 21 consecutive days greatly affected DA and NA metabolism in the respective brain regions. These results, thus suggest that LiCl produces region specific differential action depending on its dosage and duration of treatment in catecholaminergic activity in rat brain.