Improved efficiency in cryo-em secondary structure topology determination from inaccurate data

The determination of the secondary structure topology is a critical step in deriving the atomic structure from the protein density map obtained from electron cryo-microscopy technique. This step often relies on the matching of two sources of information. One source comes from the secondary structures detected from the protein density map at the medium resolution, such as 5-10 ?. The other source comes from the predicted secondary structures from the amino acid sequence. Due to the inaccuracy in either source of information, a pool of possible secondary structure positions needs to be sampled. This paper studies the question, that is, how to reduce the computation of the mapping when the inaccuracy of the secondary structure predictions is considered. We present a method that combines the concept of dynamic graph with our previous work of using constrained shortest path to identify the topology of the secondary structures. We show a reduction of 34.55% of run-time as comparison to the na?ve way of handling the inaccuracies. We also show an improved accuracy when the potential secondary structure errors are explicitly sampled verses the use of one consensus prediction. Our framework demonstrated the potential of developing computationally effective exact algorithms to identify the optimal topology of the secondary structures when the inaccuracy of the predicted data is considered.     

Mouse Delta Opioid Receptors are Located on Presynaptic Afferents to Hippocampal Pyramidal Cells

Delta opioid receptors participate in the control of chronic pain and emotional responses. Recent data have also identified their implication in drug-context associations pointing to a modulatory role on hippocampal activity. We used fluorescent knock-in mice that express a functional delta opioid receptor fused at its carboxy terminus with the green fluorescent protein in place of the native receptor to investigate the receptor neuroanatomical distribution in this structure. Fine mapping of the pyramidal layer was performed in hippocampal acute brain slices and organotypic cultures using fluorescence confocal imaging, co-localization with pre- and postsynaptic markers and correlative light-electron microscopy. The different approaches concurred to identify delta opioid receptors on presynaptic afferents to glutamatergic principal cells. In the latter, only scarce receptors were detected that were confined within the Golgi or vesicular intracellular compartments with no receptor present at the cell surface. In the mouse hippocampus, expression of functional delta opioid receptors is therefore mostly associated with interneurons emphasizing a presynaptic modulatory effect on the pyramidal cell firing rate.     

A spectrum of novel NPHS1 and NPHS2 gene mutations in pediatric nephrotic syndrome patients from Pakistan

Background

Mutations in the NPHS1 and NPHS2 genes are among the main causes of early-onset and familial steroid resistant nephrotic syndrome respectively. This study was carried out to assess the frequencies of mutations in these two genes in a cohort of Pakistani pediatric NS patients.

Methods

Mutation analysis was carried out by direct sequencing of the NPHS1 and NPHS2 genes in 145 nephrotic syndrome (NS) patients. This cohort included 36 samples of congenital or infantile onset NS cases and 39 samples of familial cases obtained from 30 families.

Results

A total of 7 homozygous (6 novel) mutations were found in the NPHS1 gene and 4 homozygous mutations in the NPHS2 gene. All mutations in the NPHS1 gene were found in the early onset cases. Of these, one patient has a family history of NS. Homozygous p.R229Q mutation in the NPHS2 gene was found in two children with childhood-onset NS.

Conclusions

Our results show a low prevalence of disease causing mutations in the NPHS1 (22% early onset, 5.5% overall) and NPHS2 (3.3% early onset and 3.4% overall) genes in the Pakistani NS children as compared to the European populations. In contrast to the high frequency of the NPHS2 gene mutations reported for familial SRNS in Europe, no mutation was found in the familial Pakistani cases. To our knowledge, this is the first comprehensive screening of the NPHS1 and NPHS2 gene mutations in sporadic and familial NS cases from South Asia.     

Effect of periplasmic expression of recombinant mouse interleukin-4 on hydrogen peroxide concentration and catalase activity in Escherichia coli

Oxidative stress occurs as a result of imbalance between generation and detoxification of reactive oxygen species (ROS). This kind of stress was rarely discussed in connection with foreign protein production in Escherichia coli. Relation between cytoplasmic recombinant protein expression with H₂O₂ concentration and catalase activity variation was already reported. The periplasmic space of E. coli has different oxidative environment in relative to cytoplasm and there are some benefits in periplasmic expression of recombinant proteins. In this study, hydrogen peroxide concentration and catalase activity following periplasmic expression of mouse IL-4 were measured in E. coli. After construction of pET2mIL4 plasmid, the expression of recombinant mouse interleukin-4 (mIL-4) was confirmed. Then, the H₂O₂ concentration and catalase activity variation in the cells were studied in exponential and stationary phases at various ODs and were compared to those of wild type cells and empty vector transformed cells. It was revealed that empty vector introduction and periplasmic recombinant protein expression increased significantly the H₂O₂ concentration of the cells. However, the H₂O₂ concentration in mIL-4 expressing cells was significantly higher than its concentration in empty vector transformed cells, demonstrating more effects of recombinant mIL-4 expression on H₂O₂ elevation. Likewise, although catalase activity was reduced in foreign DNA introduced cells, it was more lowered following expression of recombinant proteins. Correlation between H₂O₂ concentration elevation and catalase activity reduction with cell growth depletion is also demonstrated. It was also found that recombinant protein expression results in cell size increase.     

Use of SRAP markers to assess genetic diversity and population structure of wild, cultivated, and ornamental pomegranates (Punica granatum L.) in different regions of Iran

Sequence-related amplified polymorphism (SRAP) was used to assess the genetic diversity of 63 cultivated, wild, and ornamental pomegranate genotypes from five different geographical regions of Iran. A total of 250 fragments were amplified using 13 primer combinations; among these, 133 bands (53?%) were polymorphic. The average PIC value was 0.28 over all PCs. The genetic distance among genotypes ranged from 0.10 to 0.37 with an average of 0.24. Cluster analysis using the neighbor-joining (NJ) method suggested there are close relationships between ornamental and some wild genotypes. Although AMOVA results revealed significant differences in the genetic diversity among the regions (P?=?0.0048), the genetic variation was mainly caused by variation of intra regions. The results indicated low genetic differentiation (Fst?=?0.025) and high gene flow (Nm?=?2.28) among regions. These results confirmed that SRAP markers could be powerful tools and an effective marker system for determining the genetic diversity and population genetic structure of the pomegranate.     

Genetic relatedness among some wild cherry (<Emphasis Type="Italic">Prunus</Emphasis> subgenus <Emphasis Type="Italic">Cerasus</Emphasis>) genotypes native to Iran assayed by morphological traits and random amplified polymorphic DNA analysis

Subgenus Cerasus species are useful genetic resources for cherry breeding programs. A total of 17 morphological traits together with 19 random amplified polymorphic DNA (RAPD) primers were used to study 39 accessions including 34 wild Cerasus subgenus genotypes belonging to Prunus avium L., P. cerasus L., P. mahaleb L., P. microcarpa Boiss., P. incana Pall., and P. brachypetala Boiss. species, along with an unknown wild Cerasus sample, two advanced cherry cultivars (‘Lambert’ and ‘Bulgar’), and two rootstocks (‘Colt’ and ‘Gisela 6’). Genotypes were separated into different groups according to their species and collection sites using cluster analysis performed by Ward’s clustering method based on morphological data. Nineteen RAPD primers from 60 screened produced 304 polymorphic reproducible bands (98.15% polymorphism). According to the similarity matrix, the lowest similarity was obtained between P. avium and P. microcarpa samples. A dendrogram was prepared by the unweighted pair-group method with arithmetic average (UPGMA), and the accessions were separated according to their species and geographic origin. In both morphological and molecular results, the advanced cultivars and rootstocks were separated from wild genotypes, and the unknown genotype was grouped with P. mahaleb accessions. Grouping by morphological characteristics was compared with the results of RAPD analysis, with no significant correlations between morphological and molecular data being found. This is the first report of molecular (RAPD) genetic diversity study in wild Cerasus subgenus genotypes from Iran, and the results demonstrate the high potential of RAPD analysis for discrimination of Cerasus subgenus genotypes.     

Predicting the Presence of Non-O157 Shiga Toxin-Producing Escherichia coli in Ground Beef by Using Molecular Tests for Shiga Toxins, Intimin, and O Serogroups

When 3,972 ground beef enrichments with 6 confirmed to contain a non-O157 Shiga toxin-producing intimin-positive Escherichia coli isolate were tested for Shiga toxin, intimin, and O group (O26, O45, O103, O111, O121, and O145) genes, 183 potential positives and only 2 of the 6 confirmed positives were identified.     

Productivity of greengram in tebuconazole-stressed soil, by using a tolerant and plant growth-promoting Bradyrhizobium sp. MRM6 strain

In this study, a total of 50 rhizobial isolates were recovered from the root nodules of greengram plants. Of the 50 isolates, 9 bradyrhizobial strains namely, MRM1, MRM2, MRM3, MRM4, MRM5, MRM6, MRM7, MRM8, and MRM9, exhibiting a higher tolerance levels of 600, 800, 1,200, 1,000, 1,000, 1,600, 1,400, 1,400, and 1,000 μg ml⁻¹, respectively, to triazole fungicide tebuconazole (chromatographically pure) were selected and tested for plant growth-promoting activities. Generally, the rhizobial strain with maximum fungicide-tolerance ability produced higher amounts of plant growth-promoting substances. Among the nine bacterial strains, Bradyrhizobium strain MRM6 was preferably selected due to its ability to tolerate tebuconazole maximally (up to 1,600 μg ml⁻¹) on minimal salt agar medium. In addition, the strain MRM6 grew well in minimal salts medium supplemented with 100 (recommended), 200 (two times of the recommended), and 300 μg tebuconazole l⁻¹ (three times of the recommended rate) and synthesized highest amounts of plant growth-promoting substances like indole acetic acid, siderophores, exopolysaccharides, hydrogen cyanate, and ammonia, both in the absence and presence of 100, 200, and 300 μg l⁻¹ of tebuconazole. Following these properties, the strain MRM6 was used as inoculant and the inoculated greengram plants was raised in soils treated separately with recommended, two and three times the recommended dose of tebuconazole. Generally, tebuconazole at recommended and the higher rates decreased biomass, nodulation, nutrient-uptake, and grain yield of uninoculated greengram plants. Interestingly, Bradyrhizobium sp. (vigna) strain MRM6 when used with any concentration of tebuconazole, significantly increased the measured phyto-chemical-parameters of greengram plants when compared with those grown in soils treated exclusively (without inoculant) with tebuconazole. This study inferred that the strain MRM6 of Bradyrhizobium sp. (vigna) was compatible with tebuconazole and may be co-inoculated with this fungicide for enhancing the production of legumes especially greengram in soils poisoned with fungicides.     

Spectroscopic characterization of furosemide binding to human carbonic anhydrase II

This study reports the interaction between furosemide and human carbonic anhydrase II (hCA II) using fluorescence, UV-vis and circular dichroism (CD) spectroscopy. Fluorescence data indicated that furosemide quenches the intrinsic fluorescence of the enzyme via a static mechanism and hydrogen bonding and van der Walls interactions play the major role in the drug binding. The binding average distance between furosemide and hCA II was estimated on the basis of the theory of F?rster energy transfer. Decrease of protein surface hydrophobicity was also documented upon furosemide binding. Chemical modification of hCA II using N-bromosuccinimide indicated decrease of the number of accessible tryptophans in the presence of furosemide. CD results suggested the occurance of some alterations in α-helical content as well as tertiary structure of hCA II upon drug binding.     

The inhibitory effect of ethylenediamine on mushroom tyrosinase

The inhibitory effect of ethylenediamine on both activities of mushroom tyrosinase (MT) at 20 °C in a 10 mM phosphate buffer solution (pH 6.8), was studied. L-DOPA and L-tyrosine were used as substrates of catecholase and cresolase activities, respectively. The results showed that ethylenediamine competitively inhibits both activities of the enzyme with inhibition constants (K(i)) of 0.18±0.05 and 0.14±0.01 μM for catecholase and cresolase respectively, which are lower than the reported values for other MT inhibitors. For further insight a docking study between tyrosinase and ethylenediamine was performed. The docking simulation showed that ethylenediamine binds in the active site of the enzyme near the Cu atoms and makes 3 hydrogen bonds with two histidine residues of active site.