Breaking Lander-Waterman’s Coverage Bound

Lander-Waterman’s coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector’s problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman’s result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. Our approach also dramatically reduces the required computational power for the combined process. Simulation results are performed on real genomes with different sequencing error rates. The results support our theory predicting the log G improvement on coverage bound and corresponding reduction in the total number of bases required to be sequenced.     

Effect of Drought Stress on Certain Morphological and Physiological Characteristics of a Resistant and a Sensitive Canola Cultivar

Water stress is one of the main abiotic factors that reduces plant growth, mainly due to high evaporative demand and low water availability. In order to evaluate the effects of drought stress on certain morphological and physiological characteristics of two canola cultivars, we conducted a factorial experiment based on a completely randomized design. The findings show that drought stress exacerbations result in the plant's response to stress due to increased canola resistance caused by changes in plant pigments, proline, catalase, ascorbate peroxidase, peroxidase, superoxide dismutase and malondialdehyde, glucose, galactose, rhamnose and xylose. These in turn ultimately influence the morphological characteristics of canola. Drought stress reduces the concentration of carotenoids, chlorophyll a, chlorophyll b, total chlorophylls; however, glucose, galactose, rhamnose, xylose, proline, catalase, ascorbate peroxidase, peroxidase, superoxide dismutase, malondialdehyde (in leaves and roots) and the chlorophyll a and b ratios were increased. Reduction of plant height, stem height, root length, fresh and dry weight of canola treated with 300 g/l PEG compared to non‐treatment were 0.264, 0.236, 0.394, 0.183 and 0.395, respectively. From the two canola cultivars, the morphological characteristics of the NIMA increased compared to the Ks7 cultivar. Interaction effects of cultivar and drought stress showed that NIMA cultivar without treatment had the highest number of morphological characteristics such as carotenoid concentration, chlorophyll a, chlorophyll b, total chlorophylls a and b, whereas the cultivar with 300 g/l PEG (drought stress) had the highest amount of proline, malondialdehyde, soluble sugars and enzymes in leaves and roots. Increasing activity of oxidative enzymes and soluble sugars in canola under drought stress could be a sign of their relative tolerance to drought stress.     

The Human Cathelicidin LL-37, a Defensive Peptide Against Rotavirus Infection

International Journal of Peptide Research and Therapeutics - LL-37 is a 37 amino acid long cationic peptide belonging to the cathelicidin family of antimicrobial peptides. Limited investigations...     

Characterization of Aqueous Dispersions and Gels Made of Sodium Caseinate and Basil Seed Gum: Phase Behavior,Rheology, and Microstructure

The interactions between sodium caseinate (NaCas) and basil seed gum (BSG) in the presence of calcium chloride (CaCl₂) were investigated. The phase behavior of the mixed aqueous dispersions and their gels revealed a homogeneous mixture, obtained at the higher concentrations of both CaCl₂ and BSG. The Herschel-Bulkley model sufficiently fitted the flow behavior of the mixture solution data. Apparent viscosity increased significantly (p < 0.05) by increasing the concentration of BSG, where the addition of CaCl₂ had no significant effect on the viscosity of the samples (p > 0.05). Furthermore, there was an increase in thixotropy due to the higher concentrations of BSG and CaCl₂. Based on the frequency sweep test, at the low frequencies, a more gel-like behavior was observed in the case of the higher concentrations of either BSG or CaCl₂. The rheological and SEM data suggested that the stronger structure of NaCas-BSG gel in the presence of the higher concentrations of CaCl₂ was related to the induction of complex formation between the two biopolymers.

     

Single‐nucleotide polymorphism c.474G>A in the SEPT12 gene is a predisposing factor in male infertility

SEPT12 is a testis‐specific gene involved in the terminal differentiation of male germ cells. SEPT12 protein is required for sperm head‐tail formation and acts as a fundamental constituent of sperm tail annulus. In this study, we screened genetic variations in exons 5, 6, 7 of the SEPT12 and assessed the annulus status in teratozoospermic, globozoospermic, and patients with immotile short tail sperm. DNA sequencing was performed for 90 teratozoospermic and 30 normozoospermic individuals. Immunocytochemistry, transmission electron microscopy and western blotting were conducted to evaluate annulus status and the expression level of SEPT12 in patients with a distinct exonic variation (c.474G>A), respectively. Five polymorphisms identified within the desired regions of the SEPT12, among them c.474G>A had the potential to induce aberrant splicing results in the expression of a truncated protein. The annulus was detected in most of the spermatozoa from teratozoospermic and normozoospermic men with c.474G>A. In contrast, in the patient with short tail sperm defect carrying c.474G>A, 99% of spermatozoa were devoid of the annulus. Based on our findings there would be no association between exons 5, 6, 7 polymorphisms of the SEPT12 gene and the occurrence of mentioned disease but c.474G>A would be a predisposing factor in male infertility.     

Boosted Growth Performance,Mucosal and Serum Immunity,and Disease Resistance Nile Tilapia ( Oreochromis niloticus ) Fingerlings Using Corncob-Derived Xylooligosaccharide and Lactobacillus plantarum CR1T5

The present work, herein, studied the effects of corncob-derived xylooligosaccharides (CDXOS) and Lactobacillus plantarum CR1T5 (LP) integrated into fish d     

Research progress on gut health of farmers teleost fish: a viewpoint concerning the intestinal mucosal barrier and the impact of its damage

Reviews in Fish Biology and Fisheries - The intestinal mucosal barrier plays a critical role in the maintenance of host health. In farmed teleost fish, the intestinal epithelium is challenged by a...