Iranian Strawberry crinkle cytorhabdovirus variation assessed using its movement protein (P3) gene

Background

Strawberry crinkle virus (SCV) is a member of the genus Cytorhabdovirus, family Rhabdovirida, and order Mononegavirales. SCV affects the production of various strawberry cultivars. In this study we investigated the genetic diversity of SCV in strawberry fields based on P3 (movement protein) gene.

Methods and results

The samples were collected from strawberry fields in the Kurdistan Province, Iran. P3 gene from 20 SCV isolates, representing 18 nucleic acid haplotypes, is composed of 729 nucleotides, encoding a protein with 243 amino acids. SCV-P3 sequences shared 98.77%–99.86% nucleotide and 97.5%–100% amino acid sequence identity. Phylogenetic analyses of the new P3 sequences with two previously published SCV-P3 sequences from the Czech Republic showed that there are two major phylogroups (I and II) and three minor phylogroups in the body of the phylogeny, I-1, I-2, II-1. Comparisons of P3 gene sequences revealed a mutational bias, with more differences being transitions than transversions. The ratio of non-synonymous/synonymous nucleotide changes was?<?1, indicating that SCV-P3 gene is under predominantly negative selection.

Conclusions

Phylogenetic and sequence identity analyses showed that SCV isolates from Iran are closely related and have not diverged more than 2% based on P3 gene despite geographical separation and strawberry cultivar. This is the first report of the genetic diversity of SCV worldwide.

     

Robust algorithm for brain magnetic resonance image (MRI) classification based on GARCH variances series

In this paper, a robust algorithm for disease type determination in brain magnetic resonance image (MRI) is presented. The proposed method classifies MRI into normal or one of the seven different diseases. At first two-level two-dimensional discrete wavelet transform (2D DWT) of input image is calculated. Our analysis show that the wavelet coefficients of detail sub-bands can be modeled by generalized autoregressive conditional heteroscedasticity (GARCH) statistical model. The parameters of GARCH model are considered as the primary feature vector. After feature vector normalization, principal component analysis (PCA) and linear discriminant analysis (LDA) are used to extract the proper features and remove the redundancy from the primary feature vector. Finally, the extracted features are applied to the K-nearest neighbor (KNN) and support vector machine (SVM) classifiers separately to determine the normal image or disease type. Experimental results indicate that the proposed algorithm achieves high classification rate and outperforms recently introduced methods while it needs less number of features for classification.     

A novel copper (II) complex activated both extrinsic and intrinsic apoptotic pathways in liver cancerous cells

Recent advances have put fundamental focus on the application of copper (II) (Cu [II]) complexes as agents for fighting against cancer. To determine whether [Cu(L)(2imi)] complex as a novel Cu complex can induce apoptosis in HepG2 as cancerous cells and L929 as normal cells via extrinsic or intrinsic apoptotic pathways, both cell lines were treated for 24 and 48 hours at IC₅₀ concentrations of [Cu(L)(2imi)] complex. Then, the expression of some apoptosis-related genes including p53, caspase-8, bcl-2, and bax were assayed by real-time polymerase chain reaction. The [Cu(L)(2imi)] complex seems to inhibit the expression of bcl-2 in complex-treated HepG2 cancerous cells following the 24- and 48-hour treatment. The complex upregulated the p53, bax, and caspase-8 genes, therefore treatment of HepG2 cancerous cells with [Cu(L)(2imi)] complex induces programmed cell death via the upregulation of relative bax/bcl-2 ratio. Finally, this copper complex triggered apoptosis in HepG2 cells via both intrinsic and extrinsic pathway, whereas treatment of normal L929 cells with this complex induce apoptosis only via intrinsic pathway with the upregulation of relative bax/bcl-2 ratio and does not affect the expression level of caspase-8 gene and does not trigger the extrinsic pathway. Finally, these results obtained from present study confirm the role of a novel Cu complex on the induction of apoptosis process in HepG2 and L929 cells by overexpression of bax, inhibition of bcl-2 and increase of the relative bax/bcl-2 ratio. These results support that the [Cu(L)(2imi)] complex is able to induce apoptosis in cancerous cells, therefore, it has a potential for development as a novel anticancer drug.     

Genetic and environmental determinants of menstrual characteristics

BACKGROUND:

The impact of women''s menstrual cycle on her quality of life, health, work, and community is substantial. Menstrual disturbance is linked with general ill conditions such as migraine, asthma, and endocrinopathies. The clinical significance of medical interventions to prevent these conditions becomes clear if the role of genetic or environment is clarified.

AIMS:

To identify the genetic and environmental contribution on menstrual characteristics.

SETTING AND DESIGN:

This was a cross-sectional study in 2 Asian countries.

MATERIALS AND METHODS:

2 cohorts of monozygotic and dizygotic twins born between (1945-1988, n = 122) and (1951-1993, n = 71) were taken. A standard questionnaire was designed inclusive of socio- demographic characteristics of subjects as well as menstrual history (duration, interval, amount, irregularity). Subjects were interviewed by phone.

STATISTICAL ANALYSIS:

Quantitative variables were analyzed using Falconars’ formula as well as maximum likelihood analysis. Structural modeling was then applied to twin correlations to provide estimates of the relative genetic and/or environmental factors contribution in determining the measured trait.

RESULTS:

Menstrual characteristics were found to be under environmental influence where the best fitting model for menstrual interval and duration was common environment. CDF plotting confirmed the results for both variables. Proband-wise concordance analysis for amount of menstruation, amenorrhea, and irregular menstruation revealed no genetic influence. The best fitting model for menstrual irregularity was CE (C73%, E27%). The same model was defined for amenorrhea (C48%, E52%).

CONCLUSIONS:

Environmental factors are most likely responsible to determine the menstrual flow, its integrity, and regularity. These factors need to be studied further.     

Assessment of metals in agricultural soil of surrounding areas of Urmia Lake,northwest Iran: A preliminary ecological risk assessment and source identification

The aim of this study was to quantify the levels of toxic heavy metals and sodium in topsoil of farmlands around the Urmia Lake. A total of 96 topsoil samples were collected, pre-treated, and analyzed for metals using ICP-AES.

Median concentrations of As, Cd, Cu, Ni, Pb, Zn, and Na in sampling sites were 5, 0.26, 30, 40, 13, 84, and 251 mg/kg, respectively. The enrichment factor, geoaccumulation index, and contamination factor of the metals ranked them in the order of: Na > Pb > Cu > As > Cd > Zn > Ni, indicating minor contamination for them except Na and Pb with moderate contamination. Furthermore, the spatial analysis indicated that Cd, Cu, Pb, Ni, and Zn had similar distribution patterns in the north and northwest lands of the lake. Principal component analysis revealed anthropogenic sources for Cd, Cu, Ni, Pb, and Zn in the soil, whereas, sources of As and Na were most likely related to the dust emitting from the dried bed of Urmia Lake and from a cement industry. Potential ecological risk index in 7% of the sampling sites was at serious or considerable pollution level, and Cd and Pb were identified as the main pollutants.     

Effects of Recruiting Midwives into a Family Physician Program on Women's Awareness and Preference for Mode of Delivery and Caesarean Section Rates in Rural Areas of Kurdistan

BackgroundThe accepted rate rate of caesarean section is 15%. It is expected that an increase in the density of midwives in the family physician program lead to a decrease in this indicator. This study aimed to compare the rates of caesarean section and women''s awareness and preference for mode of delivery before and after the implementation of the family physician program in health centres with and without an increase in midwives density.MethodsIn this cross-sectional study, using multistage cluster sampling method a total of 668 mothers with two-month-old children were selected from among all mothers with two-month-old children who were living in rural areas of Kurdistan province. Using the difference-in-differences model and Matchit statistical model, the factors associated with caesarean section rates and women''s awareness and preference for mode of delivery were compared in centres with and without an increase in midwives density after the implementation of the family physician program. To compare the changes before and after the program, we used the data collected from the same number of women in 2005 as the baseline.ResultsAfter adjusting for baseline data collected in 2005, the resutls showed no significant change in caesarean section rates and women''s awareness and preference for mode of delivery in the centres with and without an increase in midwives density after the implementation of the family physician program. The Matchit model showed a significant mean increase 14%(0.03–0.25) in women’s awareness of the benefits of natural childbirth between 2005 and 2013 in health centres where the density of midwives increased compared with health centres where it did not. The difference-in-differences model showed that the odds ratio of women’s preference for caesarean section decreased by 41% among participants who were aware of the benefits of natural childbirth, (OR = 0.59, 95% CI: (0.22–0.85); P>0.001).ConclusionsThe results of this study showed that an increase in the density of midwives in the family physician program led to an increase in women''s awareness of the benefits of natural childbirth. An increase in women’s awareness of the benefits of natural childbirth was associated with a decreased preference for caesarean section, however this reduction did not have a significant impact on caesarean section rates; possibly, this finding might be attributed to the complexity of this problem that needs a mixed strategy involving various stockholders.     

Ethnic and Geographic Differentiation of Helicobacter pylori within Iran

The bacterium Helicobacter pylori colonizes the human stomach, with individual infections persisting for decades. The spread of the bacterium has been shown to reflect both ancient and recent human migrations. We have sequenced housekeeping genes from H. pylori isolated from 147 Iranians with well-characterized geographical and ethnic origins sampled throughout Iran and compared them with sequences from strains from other locations. H. pylori from Iran are similar to others isolated from Western Eurasia and can be placed in the previously described HpEurope population. Despite the location of Iran at the crossroads of Eurasia, we found no evidence that the region been a major source of ancestry for strains across the continent. On a smaller scale, we found genetic affinities between the H. pylori isolated from particular Iranian populations and strains from Turks, Uzbeks, Palestinians and Israelis, reflecting documented historical contacts over the past two thousand years.     

The Effect of High-Frequency Electric Pulses on Tumor Blood Flow In Vivo

The aim of this study was to evaluate the effect of a 5-kHz repetition frequency of electroporating electric pulses in comparison to the standard 1-Hz frequency on blood flow of invasive ductal carcinoma tumors in Balb/C mice. Electroporation was performed by the delivery of eight electric pulses of 1,000 V cm⁻¹ and 100 μs duration at a repetition frequency of 1 Hz or 5 kHz. Blood flow changes in tumors were measured by laser Doppler flowmetry. Monitoring was performed continuously for 10 min before application of the electric pulses as well as immediately after application of the electric pulses for 40 min. The delivery of electric pulses to tumors induced changes in tumor blood flow. The reduction in blood flow started after the stimulation and continued for the 40-min period of observation. There was a significant difference in blood flow changes 3 min after application of the electric pulses at 1-Hz or 5-kHz repetition frequency. However, after 3 min the difference became nonsignificant. The findings showed that the high pulse frequency (5 kHz) had an effect comparable to the 1-Hz frequency on tumor blood flow except at very short times after pulse delivery, when pulses at 5 kHz produced a more intense reduction of blood flow.