Effect of BMP4 preceded by retinoic acid and co‐culturing ovarian somatic cells on differentiation of mouse embryonic stem cells into oocyte‐like cells

Bone morphogenetic protein 4 (BMP4) and retinoic acid (RA) signaling are the key regulators for germ cell and meiosis induction, respectively. Gonadal tissue also provides an appropriate microenvironment for oocyte differentiation in vivo. The current study aimed to determine whether mimicking in vivo niche is more efficient for oocyte differentiation from embryonic stem (ES) cells. Here, differentiation of mouse ES cells toward oocyte‐like cells using embryoid body (EB) and monolayer protocols was induced in the presence (+BMP4) or absence (‐BMP4) of BMP4. On day 5, each group was co‐cultured with ovarian somatic cells in the presence or absence of RA (+RA or –RA) for an additional 14 days. Our results showed a significant increase in expression of meiotic markers in the +BMP4 condition in EB differentiation protocol. Further differentiation with ovarian somatic cells led to a subpopulation of oocyte‐like cell formation. Compared to the controls, the +RA condition resulted in a significant elevation of the meiotic gene expression in contrast to Oct4 that significantly decreased in both protocols. In the cells pre‐treated with BMP4 and then exposed to RA in the monolayer differentiation protocol, the gene expression levels of germ cell, Mvh, and maturation markers, Cx37, Zp2, and Gdf9, were also upregulated significantly. Therefore, it can be concluded that +BMP4 and +RA along with ovarian somatic cell co‐culture improved the rate of in vitro oocyte differentiation.     

Bio- and sequence stratigraphy and microfacies analysis of the Oligocene Asmari Formation at Sepidar Anticline,Interior Fars sub-Basin,SW Iran

In this research, biostratigraphy, microfacies analysis and sequence stratigraphic framework of the Asmari Formation are discussed at Sepidar Anticline, Interior Fars sub-Basin. The strata are Rupelian to Chattian in age. According to the distribution of benthic foraminifera, two assemblage zones were recognised (I-) Nummulites vascus–Nummulites fichteli and (II-) Archaias asmaricus/hensoni–Miogypsinoides complanatus. Eight microfacies types which can be grouped into three depositional environments are recognised. Distribution of Oligocene foraminifera together with other constituents allowed the identification of three third-order sequences at Asmari Formation. Correlation of analysed sections through Interior Fars sub-Basin represents the development of a carbonate ramp with a deepening trend from SE to NW along the Rupelian/Chattian boundary.     

Prediction of HCV load using genotype,liver biomarkers,and clinical symptoms by a mathematical model in patients with HCV infection

Hepatitis C virus (HCV) infection is a major public health problem with about 1.75 million new HCV cases and 71 million chronic HCV infections worldwide. The study aimed to evaluate clinical, serological, molecular, and liver markers to develop a mathematical predictive model for the quantification of the HCV viral load in chronic HCV infected patients. In this cross‐sectional study, blood samples were taken from 249 recently diagnosed HCV‐infected subjects and were tested for liver condition, viral genotype, and HCV RNA load. Receiver operating characteristics (ROC) curves and multiple linear regression analysis were used to predict the HCV‐RNA load. Genotype 3 followed by genotype 1 were the most prevalent genotypes in Mashhad, Northeastern Iran. The maximum levels of viral load were detected in the mixed genotype group, and the lowest levels in the undetectable genotype group. The log of the HCV viral load was significantly associated with thrombocytopenia and higher serum levels of alanine transaminase (ALT). In addition, the log HCV RNA was significantly higher in patients with arthralgia, fatigue, fever, vomiting, or dizziness. Moreover, genotype 3 was significantly associated with icterus. A ROC curve analysis revealed that the best cut‐off points for serum levels of aspartate aminotransferase (AST), ALT, and alkaline phosphatase (ALP) were >31, >34, and ≤246 IU/L, respectively. Sensitivity, specificity, and positive predictive values for AST were 87.7%, 84.36%, and 44.6%, for ALT they were 83.51%, 81.11%, and 36%, and for ALP were 72.06%, 42.81%, and 8.3%, respectively. A mathematical regression model was developed that could estimate the HCV‐RNA load. Regression model: log viral load = 7.69 ? 1.01 × G3 ? 0.7 × G1 + 0.002 × ALT ? 0.86 × fatigue.     

Comparison of Diagnostic Methods in the Evaluation of Onychomycosis

Onychomycosis is a common nail problem, accounting for up to half of all nail diseases. Several nail disorders may mimic the onychomycosis clinically. Therefore, a sensitive, quick, and inexpensive test is essential for screening nail specimens for the administration of the proper drug. The aim of this study was to compare 4 different diagnostic methods in the evaluation of onychomycosis and to determine their sensitivity, specificity, positive predictive value, and negative predictive value. In a cross-sectional study, nail specimens were collected from 101 patients suspected to have onychomycosis during a 14-month period. The nail specimens were examined using potassium hydroxide (KOH) 20 %, KOH-treated nail clipping stained with periodic acid-Schiff (KONCPA), and calcofluor white (CFW) stain, and grew a fungal culture. The culture was chosen as the gold standard for statistical analysis using the McNemar and chi-square tests. Out of 101 patients, 100 (99 %) patients had at least 1 of the 4 diagnostic methods positive for the presence of organisms. The positive rates for the fungal culture, KOH preparation, CFW, and KONCPA were 74.2, 85.1, 91.09, and 99.01 %, respectively. The sensitivity and negative predictive value of KONCPA was 100 %. KONCPA was the most sensitive among the tests and was also superior to other methods in its negative predictive value. KONCPA was easy to perform, rapid, and gave significantly higher rates of detection of onychomycosis compared to the standard methods of KOH preparation and fungal culture. Therefore, KONCPA should be the single method of choice for the evaluation of onychomycosis.     

ncRNA consensus secondary structure derivation using grammar strings

Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.     

Autosomal recessive mental retardation: homozygosity mapping identifies 27 single linkage intervals, at least 14 novel loci and several mutation hotspots

Mental retardation (MR) has a worldwide prevalence of around 2% and is a frequent cause of severe disability. Significant excess of MR in the progeny of consanguineous matings as well as functional considerations suggest that autosomal recessive forms of MR (ARMR) must be relatively common. To shed more light on the causes of autosomal recessive MR (ARMR), we have set out in 2003 to perform systematic clinical studies and autozygosity mapping in large consanguineous Iranian families with non-syndromic ARMR (NS-ARMR). As previously reported (Najmabadi et al. in Hum Genet 121:43-48, 2007), this led us to the identification of 12 novel ARMR loci, 8 of which had a significant LOD score (OMIM: MRT5-12). In the meantime, we and others have found causative gene defects in two of these intervals. Moreover, as reported here, tripling the size of our cohort has enabled us to identify 27 additional unrelated families with NS-ARMR and single-linkage intervals; 14 of these define novel loci for non-syndromic ARMR. Altogether, 13 out of 39 single linkage intervals observed in our cohort were found to cluster at 6 different loci on chromosomes, i.e., 1p34, 4q27, 5p15, 9q34, 11p11-q13 and 19q13, respectively. Five of these clusters consist of two significantly overlapping linkage intervals, and on chr 1p34, three single linkage intervals coincide, including the previously described MRT12 locus. The probability for this distribution to be due to chance is only 1.14 × 10(-5), as shown by Monte Carlo simulation. Thus, in contrast to our previous conclusions, these novel data indicate that common molecular causes of NS-ARMR do exist, and in the Iranian population, the most frequent ones may well account for several percent of the patients. These findings will be instrumental in the identification of the underlying genes.