Prenatal diagnosis of chromosome abnormalities

Prenatal diagnosis of chromosome abnormalities can be performed on three different samples; chorion villi (CVS), amniotic fluid (AFS) and fetal blood (FBS). We are presenting data from our own experience on the chromosome analysis of 957 CVS, 1000 AFS and 927 FBS. A total of 69 chromosome abnormalities have been detected in the CVS, 38 in the AFS and 115 in the FBS. The type of abnormalities and their frequencies are compared between the three sampling methods. Our findings are in agreement with published data, and the higher incidence of chromosomal aberrations in the FBS group reflect the greater efficiency with which aneuploidies associated with more severe congenital malformation can be detected by ultrasound.Finally, we reported 18 cases of mosaicism in CVS, 76 in AFS and 31 in FBS. Of these cases, only 10 represented a true mosaicism of the fetus, 98 cases have been classified as pseudomosaicisms and 7 identified as maternal contamination. We have encountered 9 cases of mosaicism confined to the chorionic villi and 1 case limited to the amniotic fluid cells. There appeared to be a similarity between trisomies involved in chorion confined mosaicisms and pseudomosaicism cases of the AFS.The chromosome complement of the placenta may play an important role in the development of the pregnancy, and although a mosaic result in prenatal diagnosis could present difficulties in the prediction of the ffetal karyotype, it might give important information on the general condition of the fetus.     

Can fossil fuel energy be recovered and used without any CO2 emissions to the atmosphere?

Reviews in Environmental Science and Bio/Technology - The world’s energy system is still dominated by fossil fuels. While there is a rapid reduction in the cost of renewable energy and the...     

The first finding of chromosome variations in wild-born western hoolock gibbons

Hoolock gibbons (genus Hoolock) are a group of very endangered primate species that belong to the small ape family (family Hylobatidae). The entire population that is distributed in the northeast and southeast of Bangladesh is estimated to include only around 350 individuals. A conservation program is thus necessary as soon as possible. Genetic markers are significant tools for planning such programs. In this study, we examined chromosomal characteristics of two western hoolock gibbons that were captured in a Bangladesh forest. During chromosome analysis, we encountered two chromosome variations that were observed for the first time in the wild-born western hoolock gibbons (Hoolock hoolock). The first one was a nonhomologous centromere position in chromosome 8 that was observed in the two examined individuals. The alteration was identical in the two individuals, which were examined by G-band and DAPI-band analyses. Chromosome paint analyses revealed that the difference in the centromere position was due to a single small pericentric inversion. The second variation was a heterozygous elongation in chromosome 9. Analysis by sequential techniques of fluorescence in situ hybridization with 18S rDNA and silver nitrate staining revealed a single and an inverted tandem duplication, respectively, of the nucleolus organizer region in two individuals. These chromosome variations provide useful information for the next steps to consider the evolution and conservation of the hoolock gibbon.     

Metabolic engineering of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> for linalool production

Objectives

To engineer the yeast Saccharomyces cerevisiae for the heterologous production of linalool.

Results

Expression of linalool synthase gene from Lavandula angustifolia enabled heterologous production of linalool in S. cerevisiae. Downregulation of ERG9 gene, that encodes squalene synthase, by replacing its native promoter with the repressible MET3 promoter in the presence of methionine resulted in accumulation of 78 µg linalool l^?1 in the culture medium. This was more than twice that produced by the control strain. The highest linalool titer was obtained by combined repression of ERG9 and overexpression of tHMG1. The yeast strain harboring both modifications produced 95 μg linalool l^?1.

Conclusions

Although overexpression of tHMG1 and downregulation of ERG9 enhanced linalool titers threefold in the engineered yeast strain, alleviating linalool toxicity is necessary for further improvement of linalool biosynthesis in yeast.

     

HIPPI: highly accurate protein family classification with ensembles of HMMs

Background

Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics.

Results

We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification). HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy.

Conclusion

HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp.

     

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

Background

Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed.

Results

We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves.

Conclusions

We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.

     

Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function

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Detection of methicillin-resistance (mec-A) gene inStaphylococcus aureus strains by PCR and determination of antibiotic susceptibility

Methicillin-ResistantStaphylococcus aureus (MSRA) has become a frequent cause of serious infections. Extended hospitalization and antibiotic therapy have been identified as additional risk factors for MRSA carrier and infection. The aim of this study was to determine the incidence of MRSA infections in the hospitals affiliated to Hamedan University of Medical Sciences. SeventyS. aureus clinical strains were isolated from patients from June 2005 to June 2006 and examined by PCR and conventional microbiological tests. Then, the antibiotic susceptibility to methicillin/oxacillin and other antibiotics were performed by Disc Diffusion Agar (DDA). The results of this study showed that methicillin resistance gene was detected in 35 (50%) and 22 (31.4%) cases by PCR and DDA, respectively. The results of antibiotic susceptibility assays also showed there were high resistance MRSA strains to penicilin (100%), cloxacillin (91.4%), tetracycline (74.2%), cotrimoxazole (68.5%), erythromycin (68.5%) and less resistance to rifampin (11.4). Two MRSA also had decreased susceptibility to vancomycin. But the strains of Methicillin-SensitiveS. aureus (MSSA) showed high sensitivity to all antibiotics profiles except to penicillin (complete resistance). As a conclusion, the resistance to methicillin/oxacillin ofS. aureus in Hamedan hospitals has reached to 50% and they show multidrug resistance.     

Hexose monophosphate shunt,the role of its metabolites and associated disorders: A review

The hexose monophosphate (HMP) shunt acts as an essential component of cellular metabolism in maintaining carbon homeostasis. The HMP shunt comprises two phases viz. oxidative and nonoxidative, which provide different intermediates for the synthesis of biomolecules like nucleotides, DNA, RNA, amino acids, and so forth; reducing molecules for anabolism and detoxifying the reactive oxygen species during oxidative stress. The HMP shunt is significantly important in the liver, adipose tissue, erythrocytes, adrenal glands, lactating mammary glands and testes. We have researched the articles related to the HMP pathway, its metabolites and disorders related to its metabolic abnormalities. The literature for this paper was taken typically from a personal database, the Cochrane database of systemic reviews, PubMed publications, biochemistry textbooks, and electronic journals uptil date on the hexose monophosphate shunt. The HMP shunt is a tightly controlled metabolic pathway, which is also interconnected with other metabolic pathways in the body like glycolysis, gluconeogenesis, and glucuronic acid depending upon the metabolic needs of the body and depending upon the biochemical demand. The HMP shunt plays a significant role in NADPH₂ formation and in pentose sugars that are biosynthetic precursors of nucleic acids and amino acids. Cells can be protected from highly reactive oxygen species by NADPH ₂. Deficiency in the hexose monophosphate pathway is linked to numerous disorders. Furthermore, it was also reported that this metabolic pathway could act as a therapeutic target to treat different types of cancers, so treatments at the molecular level could be planned by limiting the synthesis of biomolecules required for proliferating cells provided by the HMP shunt, hence, more experiments still could be carried out to find additional discoveries.