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.     

Rapid natriuretic action of aldosterone in the rat.

Rapid, nongenomic actions of aldosterone have been demonstrated in a number of cell types in vitro, including renal cell lines, but there remains little direct evidence that it is able to exert rapid effects on the kidney in the whole animal. Accordingly, the aim of this study was to determine whether aldosterone induces rapid changes in the renal handling of electrolytes or acid-base balance in the anesthetized rat. With the use of a servo-controlled fluid replacement system, spontaneous urine output by anesthetized male Sprague-Dawley rats was replaced with 2.5% dextrose. After a 3-h equilibration and a 1-h control period, rats were infused with aldosterone (42 pmol/min) or vehicle for 1 h. Aldosterone infusion induced a rapid (within 15 min) increase in sodium excretion that peaked at 0.24 +/- 0.08 compared with 0.04 +/- 0.01 micromol x min(-1) 100 x body weight(-1) (P = 0.041) in the vehicle-infused rats. This natriuresis was not associated with changes in glomerular filtration rate; urine flow rate; potassium, chloride, or bicarbonate excretion; or urine pH. The mechanisms involved are unclear, but because we have previously shown that aldosterone stimulates a rapid (4 min) increase in cAMP generation in the rat inner medullary collecting duct (IMCD) (Sheader EA, Wargent ET, Ashton N, and Balment RJ. J Endocrinol 175: 343-347, 2002), they could involve cAMP-mediated activation of the cystic fibrosis transmembrane conductance regulator chloride channel, which drives sodium secretion in the IMCD.     

Truncatella angustata associated with grapevine trunk disease in northern Iran

In recent years, grapevine trunk diseases have gained growing attentions due to worldwide incidence of the disease. In a survey on fungal agents associated with grapevine trunk diseases in northern Iran, wood samples were collected from grapevines having the symptoms of declination. Isolation was made using routine plant pathology methods. A coelomycetous fungus with appendage-bearing conidia was recovered from symptomatic tissues. Based on morphological and cultural characteristics, the causal agent of the disease was identified as Truncatella angustata. The identity of the species was further confirmed by sequence data of internal transcribed spacer-rDNA region. A phylogeny inferred using sequence data obtained in this study, together with the sequences from GenBank, clustered our isolates together with T. angustata known from other host plant species. Pathogenicity tests performed on detached shoots of grapevines led to the same symptoms as observed in field conditions. This is first study on the pathogenicity of T. angustata on grapevine in Iran and first report on the occurrence of T. angustata on grapevine in Iran.     

A general and flexible methodology to define thresholds for heat health watch and warning systems, applied to the province of Québec (Canada)

Several watch and warning systems have been established in the world in recent years to prevent the effects of heat waves. However, many of these approaches can be applied only in regions with perfect conditions (e.g., enough data, stationary series or homogeneous regions). Furthermore, a number of these approaches do not account for possible trend in mortality and/or temperature series, whereas others are generally not adapted to regions with low population densities or low daily mortality levels. In addition, prediction based on multiple days preceding the event can be less accurate if it attributes the same importance to each of these days, since the forecasting accuracy actually decreases with the period. The aim of the present study was to identify appropriate indicators as well as flexible and general thresholds that can be applied to a variety of regions and conditions. From a practical point of view, the province of Québec constitutes a typical case where a number of the above-mentioned constraints are present. On the other hand, until recently, the province’s watch and warning system was based on a study conducted in 2005, covering only the city of Montreal and applied to the whole province. The proposed approach is applied to each one of the other health regions of the province often experiencing low daily counts of mortality and presenting trends. The first constraint led to grouping meteorologically homogeneous regions across the province in which the number of deaths is sufficient to carry out the appropriate data analyses. In each region, mortality trends are taken into account. In addition, the proposed indicators are defined by a 3-day weighted mean of maximal and minimal temperatures. The sensitivity of the results to the inclusion of traumatic deaths is also checked. The application shows that the proposed method improved the results in terms of sensitivity, specificity and number of yearly false alarms, compared to those of the existing and other classical approaches. An additional criterion based on the Humidex is applied in a second step and a local validation is applied to historical observations at reference forecasting stations. An integrated heat health watch and warning system with thresholds that are adapted to the regional climate has thus been established for each sub-region of the province of Quebec and became operational in June 2010.     

Immune response variations to Salmonella enterica serovar Typhi recombinant porin proteins in mice

ObjectivesTyphoid fever is caused by Salmonella enterica serovar Typhi. OmpC, OmpF and OmpA, the three major outer membrane proteins (OMPs), could serve as vaccine candidates.MethodsThe porins antigenicity was predicted in silico. The OMP genes were amplified, cloned and expressed. Sero-reactivities of the recombinant proteins purified by denaturing method were assayed by ELISA. BALB/c mice were immunized with the recombinant porins followed by bacterial challenge.ResultsBacterial challenge of the animal model brought about antibody triggering efficacy of the antigen in OmpF > OmpC > OmpA order. Experimental findings validated the in silico results. None of the antigens had synergic or antagonistic effects on each other from immune system induction points of view. Despite their high immunogenicity, none of the antigens was protective. However, administration of two or three antigens simultaneously resulted in retardation of lethal effect. Porins, in addition to their specific functions, share common functions. Hence, they can compensate for each other's functions.ConclusionsThe produced antibodies could not eliminate the pathogenicity by blockade of one or some of the antigens. Porin antigens are not suitable vaccine candidates alone or in denatured forms. Native forms of the antigens maybe studied for protective immunogenicity.     

Exosomes in tuberculosis: Still terra incognita?

Today, diagnosis, vaccination, and treatment of tuberculosis (TB) remain major clinical challenges. Therefore, an introduction of new diagnostic measures and biomarkers is necessary to improve infection control. The ideal biomarker for TB infection can be defined as a host or pathogen-derived biomolecule, which is potent for identifying infection and determining its clinical stage. Exosomes, defined as cell-derived nanovesicles released into biological fluids, are involved in cell–cell communication and immune modulation. These vesicles have emerged as a new platform for improving the clinical diagnosis and prognosis of different infectious diseases and cancers. The role of these nanovehicles, as alternative biomarkers for the improvement of TB diagnosis and treatment, has been demonstrated in a significant body of literature. In this review, we summarized recent progress in the clinical application of exosome-based biomarkers in TB infection.     

Melatonin,a toll-like receptor inhibitor: Current status and future perspectives

Toll-like receptors (TLRs) are crucial activators of inflammatory responses, they are considered immune receptors. TLRs are of fundamental importance in the pathophysiology of disorders related to inflammation including neurodegenerative diseases and cancer. Melatonin is a beneficial agent in the treatment of inflammatory and immune disorders. Melatonin is potent anti-inflammatory hormone that regulates various molecular pathways. Withal, limited studies have evaluated the inhibitory role of melatonin on TLRs. This review summarizes the current knowledge related to the effects of melatonin on TLRs in some common inflammatory and immunity disorders.     

microRNAs: Key players in virus-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is known as one of the major health problems worldwide. Pathological analysis indicated that a variety of risk factors including genetical (i.e., alteration of tumor suppressors and oncogenes) and environmental factors (i.e., viruses) are involved in beginning and development of HCC. The understanding of these risk factors could guide scientists and clinicians to design effective therapeutic options in HCC treatment. Various viruses such as hepatitis B virus (HBV) and hepatitis C virus (HCV) via targeting several cellular and molecular pathways involved in HCC pathogenesis. Among various cellular and molecular targets, microRNAs (miRNAs) have appeared as key players in HCC progression. miRNAs are short noncoding RNAs which could play important roles as oncogenes or tumor suppressors in several malignancies such as HCC. Deregulation of many miRNAs (i.e., miR-222, miR-25, miR-92a, miR-1, let-7f, and miR-21) could be associated with different stages of HCC. Besides miRNAs, exosomes are other particles which are involved in HCC pathogenesis via targeting different cargos, such as DNAs, RNAs, miRNAs, and proteins. In this review, we summarize the current knowledge of the role of miRNAs and exosomes as important players in HCC pathogenesis. Moreover, we highlighted HCV- and HBV-related miRNAs which led to HCC progression.     

Use of Coupled Al-Ag Bimetallic Cylindrical Nanoparticles to Improve the Photocurrent of a Thin-Film Silicon Solar Cell

In this paper, cylindrical shape coupled bimetallic plasmonic nanoparticles (NPs) were used to improve the performance of a thin-film silicon solar cell. Our design is based on the appropriate selection of the composition and morphology of the NPs to reach a cell with excellent optical properties. The specific interaction between the incident light and bimetallic NPs helps us to design better solar absorbers. Here, the FDTD method was used to evaluate the effect of cylindrical Al-Ag bimetallic NPs on the surface of a thin silicon absorber. At first, a unit cell with Al-Al paired nano-cylinders at the surface was evaluated and a photocurrent of 14.65 mA/cm² was obtained. In the case of a cell with paired Al-Ag bimetallic nano-cylinders, the photocurrent was increased to 16.15 mA/cm². This value was increased to 16.57 mA/cm² when paired polymetallic NPs were used. According to the results of this work, bimetallic and polymetallic nanoparticles can significantly improve the photocurrent of an ultra-thin silicon solar cell. The results of this work can be used to design better plasmonic-based light trapping systems for thin-film solar cells.

     

In vitro tetraploidy induction in Mexican lime and sour orange and evaluation of their morphological and physiological characteristics

Plant Cell, Tissue and Organ Culture (PCTOC) - In this research, the production of superior genotypes via the polyploidy induction method in two citrus species involved the tissue culture of stem...