Technical reproducibility of genotyping SNP arrays used in genome-wide association studies

During the last several years, high-density genotyping SNP arrays have facilitated genome-wide association studies (GWAS) that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small fraction of the underlying genetic contribution to the studied phenotypic trait. Moreover, discordance observed in results between independent GWAS indicates the potential for Type I and II errors. High reliability of genotyping technology is needed to have confidence in using SNP data and interpreting GWAS results. Therefore, reproducibility of two widely genotyping technology platforms from Affymetrix and Illumina was assessed by analyzing four technical replicates from each of the six individuals in five laboratories. Genotype concordance of 99.40% to 99.87% within a laboratory for the sample platform, 98.59% to 99.86% across laboratories for the same platform, and 98.80% across genotyping platforms was observed. Moreover, arrays with low quality data were detected when comparing genotyping data from technical replicates, but they could not be detected according to venders' quality control (QC) suggestions. Our results demonstrated the technical reliability of currently available genotyping platforms but also indicated the importance of incorporating some technical replicates for genotyping QC in order to improve the reliability of GWAS results. The impact of discordant genotypes on association analysis results was simulated and could explain, at least in part, the irreproducibility of some GWAS findings when the effect size (i.e. the odds ratio) and the minor allele frequencies are low.     

A fuzzy-genetic model for estimating forces from electromyographical activity of antagonistic muscles due to planar lower arm movements: the effect of nonlinear muscle properties

The aim of this paper is to create a model for mapping the surface electromyogram (EMG) signals to the force that generated by human arm muscles. Because the parameters of each person's muscle are individual, the model of the muscle must have two characteristics: (1) The model must be adjustable for each subject. (2) The relationship between the input and output of model must be affected by the force-length and the force-velocity behaviors are proven through Hill's experiments. Hill's model is a kinematic mechanistic model with three elements, i.e. one contractile component and two nonlinear spring elements.In this research, fuzzy systems are applied to improve the muscle model. The advantages of using fuzzy system are as follows: they are robust to noise, they prove an adjustable nonlinear mapping, and are able to model the uncertainties of the muscle.Three fuzzy coefficients have been added to the relationships of force-length (active and passive) and force-velocity existing in Hill's model. Then, a genetic algorithm (GA) has been used as a biological search method that can adjust the parameters of the model in order to achieve the optimal possible fit.Finally, the accuracy of the fuzzy genetic implementation Hill-based muscle model (FGIHM) is invested as following: the FGIHM results have 12.4% RMS error (in worse case) in comparison to the experimental data recorded from three healthy male subjects. Moreover, the FGIHM active force-length relationship which is the key characteristics of muscles has been compared to virtual muscle (VM) and Zajac muscle model. The sensitivity of the FGIHM has been evaluated by adding a white noise with zero mean to the input and FGIHM has proved to have lower sensitivity to input noise than the traditional Hill's muscle model.     

A new species of Leopoldia (Asparagaceae Scilloideae formerly Hyacinthaceae) from Iran

Leopoldia tabriziana Jafari (Hyacinthaceae) from northwest of Iran (East Azarbaijan province) is described here and illustrated by a line‐drawing. It is similar to L. comosa Parl . but differs in having violet (not cream) pedicels in the fresh fertile flowers, oblong‐campanulate (not oblong‐urceolate) fertile flowers, triangular‐obovate (not globose‐obovate) sterile flowers, dark violet (not beige) fertile flowers and dark violet (not pale violet) sterile flowers with much shorter pedicels. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

α-Bisabolol inhibits <Emphasis Type="Italic">Aspergillus fumigatus</Emphasis> Af239 growth via affecting microsomal ∆<Superscript>24</Superscript>-sterol methyltransferase as a crucial enzyme in ergosterol biosynthesis pathway

Finding new compounds with antifungal properties is an important task due to the side effects of common antifungal drugs and emerging antifungal resistance in fungal strains. ?²⁴-sterol methyltransferase (24-SMT) is a crucial enzyme that plays important roles in fungal ergosterol biosynthesis pathway and is not found in humans. In the present study, the effects of α-bisabolol on Aspergillus fumigatus Af239 growth and ergosterol synthesis on the base of 24-SMT enzyme activity were studied; in addition, the expression of erg6, the gene encoded 24-SMT, was considered. To our knowledge, this is the first report demonstrating that α-bisabolol inhibits A. fumigatus growth specifically via suppressing fungal 24-SMT. Since this enzyme is a specific fungal enzyme not reported to exist in mammalian cells, α-bisabolol may serve as a lead compound in the development of new antifungal drugs. Fungi were cultured in presence of serial concentrations of α-bisabolol (0.281–9 mM) for 3 days at 35?°C. Mycelia dry weight was determined as an index of fungal growth and ergosterol content was assessed. Microsomal 24-SMT activity was assayed in presence of α-bisabolol as an inhibitor, lanosterol as a substrate and [methyl-H³] AdoMet (S-Adenosyl methionin). In addition, the expression of erg 6 gene (24-SMT encoding gene) was determined after treatments with various concentrations of α-bisabolol. Our results demonstrated that α-bisabolol strongly inhibited A. fumigatus growth (35.53–77.17%) and ergosterol synthesis (26.31–73.77%) dose-dependently and suppressed the expression of erg 6 gene by 76.14% at the highest concentration of 9 mM. α-bisabolol inhibited the activity of 24-SMT by 99% at the concentration of 5 mM. Taken together, these results provides an evidence for the first time that α-bisabolol inhibits A. fumigatus Af239 growth via affecting microsomal ?²⁴-sterol methyltransferase as a crucial enzyme in ergosterol biosynthetic pathway.     

Treatment of old landfill leachate with high ammonium content using aerobic granular sludge

Background

Aerobic granular sludge has become an attractive alternative to the conventional activated sludge due to its high settling velocity, compact structure, and higher tolerance to toxic substances and adverse conditions. Aerobic granular sludge process has been studied intensively in the treatment of municipal and industrial wastewater. However, information on leachate treatment using aerobic granular sludge is very limited.

Methods

This study investigated the treatment performance of old landfill leachate with different levels of ammonium using two aerobic sequencing batch reactors (SBR): an activated sludge SBR (ASBR) and a granular sludge SBR (GSBR). Aerobic granules were successfully developed using old leachate with low ammonium concentration (136 mg L^?1 NH₄ ⁺-N).

Results

The GSBR obtained a stable chemical oxygen demand (COD) removal of 70% after 15 days of operation; while the ASBR required a start-up of at least 30 days and obtained unstable COD removal varying from 38 to 70%. Ammonium concentration was gradually increased in both reactors. Increasing influent ammonium concentration to 225 mg L^?1 N, the GSBR removed 73 ± 8% of COD; while COD removal of the ASBR was 59 ± 9%. The GSBR was also more efficient than the ASBR for nitrogen removal. The granular sludge could adapt to the increasing concentrations of ammonium, achieving 95 ± 7% removal efficiency at a maximum influent concentration of 465 mg L^?1 N. Ammonium removal of 96 ± 5% was obtained by the ASBR when it was fed with a maximum of 217 mg L^?1 NH₄ ⁺-N. However, the ASBR was partially inhibited by free-ammonia and nitrite accumulation rate increased up to 85%. Free-nitrous acid and the low biodegradability of organic carbon were likely the main factors affecting phosphorus removal.

Conclusion

The results from this research suggested that aerobic granular sludge have advantage over activated sludge in leachate treatment.

     

A multiscale cell‐based model of tumor growth for chemotherapy assessment and tumor‐targeted therapy through a 3D computational approach

ObjectivesComputational modeling of biological systems is a powerful tool to clarify diverse processes contributing to cancer. The aim is to clarify the complex biochemical and mechanical interactions between cells, the relevance of intracellular signaling pathways in tumor progression and related events to the cancer treatments, which are largely ignored in previous studies.Materials and MethodsA three‐dimensional multiscale cell‐based model is developed, covering multiple time and spatial scales, including intracellular, cellular, and extracellular processes. The model generates a realistic representation of the processes involved from an implementation of the signaling transduction network.ResultsConsidering a benign tumor development, results are in good agreement with the experimental ones, which identify three different phases in tumor growth. Simulating tumor vascular growth, results predict a highly vascularized tumor morphology in a lobulated form, a consequence of cells'' motile behavior. A novel systematic study of chemotherapy intervention, in combination with targeted therapy, is presented to address the capability of the model to evaluate typical clinical protocols. The model also performs a dose comparison study in order to optimize treatment efficacy and surveys the effect of chemotherapy initiation delays and different regimens.ConclusionsResults not only provide detailed insights into tumor progression, but also support suggestions for clinical implementation. This is a major step toward the goal of predicting the effects of not only traditional chemotherapy but also tumor‐targeted therapies.     

Reversing the trend of wildlife crime in Tanzania: challenges and opportunities

Wildlife crime is increasingly gaining prominence in global environmental debates. The crime, generating huge financial returns to few individuals, has far reaching implications on ecology, economy and global security. The seriousness of these implications provides sufficient rationale for reconsidering and intensifying efforts to combat this crime. However, these efforts are compromised by a number of challenges, though opportunities for success exist. This paper presents some of these challenges and opportunities available for reversing the trend of wildlife crime in Tanzania. The challenges presented include poverty, high profit associated with illicit trade on wildlife, poor governance and corruption, minimal budget and inadequate institutional support, political interference and low employee morale, minimal benefits to local communities, human population growth, climate change and HIV/AIDS pandemic. Opportunities identified include increased public awareness, growing global political concern and commitment, presence of relevant policies, programmes and strategies along with international agreements supportive to species protection. Before embarking on challenges and opportunities, the paper provides an overview of Tanzania’s wildlife resources, status and trend of this crime. In conclusion, the paper underscores the gravity of the problem and its implications and offers some recommendations for improving the situation.     

Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins

Aptamers are single stranded oligonucleotides, comparable to monoclonal antibodies (mAbs) in selectivity and affinity and have significant strategic properties in design, development and applications more than mAbs. Ease of design and development, simple chemical modification and the attachment of functional groups, easily handling and more adaptability with analytical methods, small size and adaptation with nanostructures are the valuable characteristics of aptamers in comparison to large protein based ligands. Among a broad range of targets that their specific aptamers developed, proteins and peptides have significant position according to the number of related studies performed so far. Since proteins control many of important physiological and pathological incidents in the living organisms, particularly human beings and because of the benefits of aptamers in clinical and analytical applications, aptamer related technologies in the field of proteins and peptides are under progress, exclusively. Currently, there is only one FDA approved therapeutic aptamer in the pharmaceutical market, which is specific to vascular endothelial growth factor and is prescribed for age related macular degenerative disease. Additionally, there are several aptamers in the different phases of clinical trials. Almost all of these aptamers are specific to clinically important peptide or protein targets. In addition, the application of protein specific aptamers in the design and development of targeted drug delivery systems and diagnostic biosensors is another intersting field of aptamer technology. In this review, significant efforts related to development and applications of aptamer technologies in proteins and peptides sciences were considered to emphasis on the importance of aptamers in medicinal and clinical applications.