Abstract: Background: Inter-individual variation in response to metformin, which has been considered as a first line therapy for T2DM treatment is considerable. In the current study, it was aimed to investigate the impact of two genetic variants Leu125Phe (rs77474263) and Gly64Asp (rs77630697) in gene SLC47A1 on the clinical efficacy of metformin in T2DM Pakistani patients. Methods: The study included 800 T2DM patients (400 metformin responders and 400 metformin non-responders) along with 400 ethnically matched healthy individuals. The genotypes were determined by allele-specific polymerase chain reaction. In-silico analysis was done to confirm the effect of the two SNPs on the structure of genes. Association was statistically determined using SPSS software. Results: Minor allele frequency for rs77474263 and rs77630697 was 0.13 and 0.12. For SLC47A1 rs77474263 the homozygotes of one mutant allele ‘T’ (CT) of rs77474263 variant were fewer in metformin responders than metformin non-responders (29.2% vs. 35.5 %). Likewise, the efficacy was further reduced (7.2% vs. 4.0 %) in homozygotes of two copies of ‘T’ allele (TT). Remarkably, T2DM cases with two copies of allele ‘C’ (CC) had 2.11 times more probability to respond towards metformin monotherapy. For SLC47A1 rs77630697 the homozygotes of one mutant allele ‘A’ (GA) of rs77630697 variant were fewer in metformin responders than metformin non-responders (33.5% vs. 43.0 %). Likewise, the efficacy was further reduced (8.5% vs. 4.5%) in homozygotes of two copies of ‘A’ allele (AA). Remarkably, T2DM cases with two copies of allele ‘G’ (GG) had 2.41 times more probability to respond towards metformin monotherapy. In-silico analysis revealed that these two variants affect the structure and stability of their corresponding proteins. Conclusion: The present data suggest that SLC47A1 Leu125Phe (rs77474263) and Gly64Asp (rs77630697) polymorphisms were associated with the therapeutic response of metformin in T2DM patients of Pakistan.
Abstract: Hyphal growth and the transcriptional regulation to the host environment are key issues during the pathogenesis of C. albicans. Tec1p is the C. albicans homolog of a TEA transcription factor family, which share a conserved DNA-binding TEA domain in their N-terminal. In order to define a structure-function relationship of the C. albicans Tec1p protein, we constructed several mutations on the N terminal, C terminal or in the TEA binding domain itself by homologous recombination technology. The modifications in the open reading frame of TEC1 were tested for reconstitution of the morphogenetic development of the tec1/tec1 mutant strain CaAS12. Mutation in the TEA consensus sequence did not confer transition to hyphae whereas the reconstitution of the full-length Tec1p has reconstituted hyphal development. A deletion in one of glutamine-rich regions either in the Tec1p N-terminal or the C-terminal in regions of 53-212 or 637–744 aa, respectively, did not restore morphological development in mutant CaAS12 strain. Whereas, the reconstitution with Tec1p mutants other than the glutamate-rich region has restored the morphogenetic switch. Additionally, the deletion of the glutamine-rich region has attenuated the invasive growth and the heat shock resistance of C. albicans. In conclusion, we show that a glutamine-rich region of Tec1p is essential for the hyphal development and mediating adaptation to the host environment of C. albicans.
Abstract: In recent years, interest in ecogenetic and biomedical problems related to the effects on the population of radon and its daughter decay products has increased significantly. Of particular interest is the assessment of the consequence of irradiation at hazardous radon areas, which includes the Almaty region due to the large number of tectonic faults that enhance radon emanation. In connection with the foregoing, the purpose of this work was to study the genetic effects of exposure to supernormal radon doses on the alpha-radiation model. Irradiation does not affect the growth of the cell, but rather its ability to differentiate. In addition, irradiation can lead to somatic mutations, morphoses and modifications. These damages most likely occur from changes in the composition of the substances of the cell. Such changes are epigenetic since they affect the regulatory processes of ontogenesis. Variability in the expression of regulatory genes refers to conditional mutations that modify the formation of signs of intraspecific similarity. Characteristic features of these conditional mutations are the dominant type of their manifestation, phenotypic asymmetry and their instability in the generations. Currently, the terms “morphosis” and “modification” are used to describe epigenetic variability, which are maintained in Drosophila melanogaster cultures using linkaged X- chromosomes, and the mutant X-chromosome is transmitted along the paternal line. In this paper, we investigated the epigenetic effects of alpha particles, whose source in nature is mainly radon and its daughter decay products. In the experiment, an isotope of plutonium-238 (Pu238), generating radiation with an energy of about 5500 eV, was used as a source of alpha particles. In an experiment in the first generation (F1), deformities or morphoses were found, which can be called "radiation syndromes" or mutations, the manifestation of which is similar to the pleiotropic action of genes. The proportion of morphoses in the experiment was 1.8%, and in control 0.4%. In this experiment, the morphoses in the flies of the first and second generation looked like black spots, or melanomas on different parts of the imago body; "generalized" melanomas; curled, curved wings; shortened wing; bubble on one wing; absence of one wing, deformation of thorax, interruption and violation of tergite patterns, disruption of distribution of ocular facets and bristles; absence of pigmentation of the second and third legs. Statistical analysis by the Chi-square method showed the reliability of the difference in experiment and control at P ≤ 0.01. On the basis of this, it can be considered that alpha particles, which in the environment are mainly generated by radon and its isotopes, have a mutagenic effect that manifests itself, mainly in the formation of morphoses or deformities.
Abstract: We analyze stochastic integrals associated with a mutation process. To be specific, we describe the cell population process and derive the differential equations for the joint generating functions for the number of mutants and their integrals in generating functions and their applications. We obtain first-order moments of the processes of the two-way mutation process in first-order moment structure of X (t) and Y (t) and the second-order moments of a one-way mutation process. In this paper, we obtain the limiting behaviour of the integrals in limiting distributions of X (t) and Y (t).
Abstract: Dunaliella salina has great potential as a system for generating commercially valuable products, including beta-carotene, pharmaceuticals, and biofuels. Our goal is to improve this potential by enhancing growth rate and other properties of D. salina under optimal growth conditions. We used ethyl methane sulfonate (EMS) to generate random mutants in D. salina KU11, a strain classified in Thailand. In a preliminary experiment, we first treated D. salina cells with 0%, 0.8%, 1.0%, 1.2%, 1.44% and 1.66% EMS to generate a killing curve. After that, we randomly picked 30 candidates from approximately 300 isolated survivor colonies from the 1.44% EMS treatment (which permitted 30% survival) as an initial test of the mutant screen. Among the 30 survivor lines, we found that 2 strains (mutant #17 and #24) had significantly improved growth rates and cell number accumulation at stationary phase approximately up to 1.8 and 1.45 fold, respectively, 2 strains (mutant #6 and #23) had significantly decreased growth rates and cell number accumulation at stationary phase approximately down to 1.4 and 1.35 fold, respectively, while 26 of 30 lines had similar growth rates compared with the wild type control. We also analyzed cell size for each strain and found there was no significant difference comparing all mutants with the wild type. In addition, mutant #24 had shown an increase of biomass accumulation approximately 1.65 fold compared with the wild type strain on day 5 that was entering early stationary phase. From these preliminary results, it could be feasible to identify D. salina mutants with significant improved growth rate, cell accumulation and biomass production compared to the wild type for the further study; this makes it possible to improve this microorganism as a platform for biotechnology application.
Abstract: Prediction of perturbations after genetic manipulation
(especially gene knockout) is one of the important challenges in
systems biology. In this paper, a new algorithm is introduced that
integrates microarray data into the metabolic model. The algorithm
was used to study the change in the cell phenotype after knockout of
Gss gene in Escherichia coli BW25113. Algorithm implementation
indicated that gene deletion resulted in more activation of the
metabolic network. Growth yield was more and less regulating gene
were identified for mutant in comparison with the wild-type strain.
Abstract: Due to its high computational cost, mutation testing has been neglected by researchers. Recently, many cost and mutants’ reduction techniques have been developed, improved, and experimented, but few of them has relied the possibility of reducing the cost of mutation testing on the program type of the application under test. This paper is a comparative study between four operators’ selection techniques (mutants sampling, class level operators, method level operators, and all operators’ selection) based on the program code type of each application under test. It aims at finding an alternative approach to reveal the effect of code type on mutation testing score. The result of our experiment shows that the program code type can affect the mutation score and that the programs using polymorphism are best suited to be tested with mutation testing.
Abstract: Fungal mutant strains have produced cellulase and
xylanase enzymes, and have induced high hydrolysis with enhanced
of rice straw. The mutants were obtained by exposing Penicillium
strain to UV-light treatments. Screening and selection after treatment
with UV-light were carried out using cellulolytic and xylanolytic
clear zones method to select the hypercellulolytic and
hyperxylanolytic mutants. These mutants were evaluated for their
cellulase and xylanase enzyme production as well as their abilities for
biodegradation of rice straw. The mutant 12 UV/1 produced 306.21%
and 209.91% cellulase and xylanase, respectively, as compared with
the original wild type strain. This mutant showed high capacity of
rice straw degradation. The effectiveness of tested mutant strain and
that of wild strain was compared in relation to enhancing the
composting process of rice straw and animal manures mixture. The
results obtained showed that the compost product of inoculated
mixture with mutant strain (12 UV/1) was the best compared to the
wild strain and un-inoculated mixture. Analysis of the composted
materials showed that the characteristics of the produced compost
were close to those of the high quality standard compost. The results
obtained in the present work suggest that the combination between
rice straw and animal manure could be used for enhancing the
composting process of rice straw and particularly when applied with
fungal decomposer accelerating the composting process.
Abstract: Microalgae lipid is a promising feedstock for biodiesel production. The objective of this work was to study growth factors affecting marine mutant Synechococcus sp. (PCC 7002) for high lipid production. Four growth factors were investigated; nitrogen-phosporus-potassium (NPK) concentration, light intensity, temperature and NaNO3 concentration on mutant strain growth and lipid production were studied. Design Expert v8.0 was used to design the experimental and analyze the data. The experimental design selected was Min-Run Res IV which consists of 12 runs and the response surfaces measured were specific growth rate and lipid concentration. The extraction of lipid was conducted by chloroform/methanol solvents system. Based on the study, mutant Synechococcus sp. PCC 7002 gave the highest specific growth rate of 0.0014 h-1 at 0% NPK, 2500 lux, 40oC and 0% NaNO3. On the other hand, the highest lipid concentration was obtained at 0% NPK, 3500 lux, 30oC and 1% NaNO3.
Abstract: Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.
Abstract: Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.
Abstract: Land with low pH soil spread widely in Indonesia
can be used for soybean (Glycine max) cultivation, however the
production is low. The use of acid tolerant soybean and acidaluminium
tolerant nitrogen-fixing bacteria formula was an
alternative way to increase soybean productivity on acid soils.
Bradyrhizobium japonicum is one of the nitrogen fixing bacteria
which can symbiose with soybean plants through root nodule
formation. Most of the nitrogen source required by soybean plants
can be provided by this symbiosis. This research was conducted to
study the influence of acid-aluminium tolerant B. japonicum strain
BJ 11 formula using peat as carrier on growth of Tanggamus and
Anjasmoro cultivar soybean planted on acid soil fields (pH 5.0-
5.5). The results showed that the inoculant was able to increase the
growth and production of soybean which were grown on fields acid
soil at Sukadana (Lampung) and Tanah Laut (South Kalimantan),
Indonesia.
Abstract: The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.
Abstract: Mutations of the telomeric copy of the survival motor neuron 1 (SMN1) gene cause spinal muscular atrophy. A deletion of the Eef1a2 gene leads to lower motor neuron degeneration in wasted mice. Indirect evidences have been shown that the eEF1A protein family may interact with SMN, and our previous study showed that abnormalities of neuromuscular junctions in wasted mice were similar to those of Smn mutant mice. To determine potential colocalization between SMN and tissue-specific translation elongation factor 1A2 (eEF1A2), an immunochemical analysis of HeLa cells transfected with the plasmid pcDNA3.1(+)C-hEEF1A2- myc and a new quantitative test of colocalization by intensity correlation analysis (ICA) was used to explore the association of SMN and eEF1A2. Here the results showed that eEF1A2 redistributed from the cytoplasm to the nucleus in response to serum and epidermal growth factor. In the cytoplasm, compelling evidence showed that staining for myc-tagged eEF1A2 varied in synchrony with that for SMN, consistent with the formation of a SMN-eEF1A2 complex in the cytoplasm of HeLa cells. These findings suggest that eEF1A2 may colocalize with SMN in the cytoplasm and may be a component of the SMN complex. However, the limitation of the ICA method is an inability to resolve colocalization in components of small organelles such as the nucleus.
Abstract: In order to find the particular interaction energy
between cylcloguanil and the amino acids surrounding the pocket of
wild type and quadruple mutant type PfDHFR enzymes, the MP2
method with basis set 6-31G(d,p) level of calculations was
performed. The obtained interaction energies found that Asp54 has
the strongest interaction energy to both wild type and mutant type of -
12.439 and -11.250 kcal/mol, respectively and three amino acids;
Asp54, Ile164 and Ile14 formed the H-bonding with cycloguanil
drug. Importantly, the mutation at Ser108Asn was the key important
of cycloguanil resistant with showing repulsive interaction energy.
Abstract: The objective of this research was to determine the
potency of indigenous acid-aluminium tolerant Bradyrhizobium
japonicum as producer of indole acetic acid (IAA) and applied it as
nitrogen fixation on local soybeans viz Anjasmoro, Tanggamus
(yellow soybean seeds), and Detam (black soybean seed). Three
isolates of acid-aluminium tolerant Bradyrhizobium japonicum (BJ)
were used in this research, i.e. BJ 11 (wt), BJ 11 (19) - BJ 11(wt)
mutant, and USDA 110 as a reference isolate. All of isolates tested to
produce the IAA by using Salkowsky method. Effect of IAA
production by each of B. japonicum was tested on growth pouch and
greenhouse using three varieties of soybean. All isolates could grow
well and produce IAA on yeast mannitol broth (YMB) medium in
the presence of 0.5 mM L-tryptophan. BJ 11 (19) produced the
highest of IAA at 4 days incubation compared to BJ 11 (wt) and
USDA 110. All tested isolates of Bradyrhizobium japonicum have
showed effect on stimulating the formation of root nodules in
soybean varieties grown on Leonard bottle. The concentration of
IAA on root nodules of soybean symbiotic with B. japonicum was
significantly different with control, except on the treatment using
Tanggamus soybean.
Abstract: Rice seed expression (cDNA) library in the Lambda
Zap 11® phage constructed from the developing grain 10-20 days
after flowering was transformed into yeast for functional
complementation assays in three salt sensitive yeast mutants S.
cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19
and Axt3K with pYES vector with cDNA inserts showed enhance
tolerance than those with empty pYes vector. Sequencing of the
cDNA inserts revealed that they encode for the putative proteins with
the sequence homologous to rice putative protein PROLM24
(Os06g31070), a prolamin precursor. Expression of this cDNA did
not affect yeast growth in absence of salt. Axt3k and G19 strains
expressing the PROLM24 were able to grow upto 400 mM and 600
mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24
expression showed comparatively higher growth rate in the medium
with excess LiCl (50 mM). The observation that expression of
PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k
indicates the existence of a regulatory system that ameliorates the
effect of salt stress in the transformed yeast mutants. However, the
exact function of the cDNA sequence, which shows partial sequence
homology to yeast UTR1 is not clear. Although UTR1 involved in
ferrous uptake and iron homeostasis in yeast cells, there is no
evidence to prove its role in Na+ homeostasis in yeast cells. Absence
of transmembrane regions in Os06g31070 protein indicates that salt
tolerance is achieved not through the direct functional
complementation of the mutant genes but through an alternative
mechanism.
Abstract: Every 2-3 years the influenza B virus serves
epidemics. Neuraminidase (NA) is an important target for influenza
drug design. Although, oseltamivir, an oral neuraminidase drug, has
been shown good inhibitory efficiency against wild-type of influenza
B virus, the lower susceptibility to the R152K mutation has been
reported. Better understanding of oseltamivir efficiency and
resistance toward the influenza B NA wild-type and R152K mutant,
respectively, could be useful for rational drug design. Here, two
complex systems of wild-type and R152K NAs with oseltamivir
bound were studied using molecular dynamics (MD) simulations.
Based on 5-ns MD simulation, the loss of notable hydrogen bond and
decrease in per-residue decomposition energy from the mutated
residue K152 contributed to drug compared to those of R152 in wildtype
were found to be a primary source of high-level of oseltamivir
resistance due to the R152K mutation.
Abstract: The subcellular organelles called oil bodies (OBs) are lipid-filled quasi-spherical droplets produced from the endoplasmic reticulum (ER) and then released into the cytoplasm during seed development. It is believed that an OB grows by coalescence with other OBs and that its stability depends on the composition of oleosins, major proteins inserted in the hemi membrane that covers OBs. In this study, we measured the OB-volume distribution from different genotypes of A. thaliana after 7, 8, 9, 10 and 11 days of seed development. In order to test the hypothesis of OBs dynamics, we developed a simple mathematical model using non-linear differential equations inspired from the theory of coagulation. The model describes the evolution of OB-volume distribution during the first steps of seed development by taking into consideration the production of OBs, the increase of triacylglycerol volume to be stored, and the growth by coalescence of OBs. Fitted parameters values show an increase in the OB production and coalescence rates in A. thaliana oleosin mutants compared to wild type.
Abstract: The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated.
Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP).Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest.
These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.