Effect of sequential deletion of extra N-terminal residues on the structure and stability of yeast iso-1-cytochrome-c

A sequence alignment of yeast cytochrome-c (y-cyt-c) with mammalian cyts-c shows that the yeast protein has a five residue long N-terminal extension. A question arises: Does this N-terminal extension play any roles in the stability, structure, and folding of the yeast protein? To answer this question, in silico and in vitro studies were carried out on the wild type (WT) protein and its five deletants (Δ(?5/?5), Δ(?5/?4), Δ(?5/?3), Δ(?5/?2), and Δ(?5/?1) where Δ denotes the deletion and the numbers refer to the residues deleted, e.g. Δ(?5/?1) denotes the deletion of residues numbered from ?5 to ?1 (TEFKA), while Δ(?5/?2) denotes the deletion of resides numbered from ?5 to ?2 (TEFK) and so on). The main conclusion of the in silico study is that the order of stability of deletants and WT protein is Δ(?5/?4) > WT > Δ(?5/?3) > Δ(?5/?5) > Δ(?5/?1) ~ Δ(?5/?2). In vitro studies involved (i) measurements of thermodynamic stability of all proteins by differential scanning calorimetry and from sigmoidal curves of two different structural properties ([θ]₂₂₂, a probe for detecting change in secondary structure, and Δε₄₀₅, a probe for detecting alteration in the heme environment), and (ii) characterization of all proteins by various spectral properties. The main conclusions of the in vitro studies are as follows: (i) The order of thermodynamic stability of all proteins is in excellent agreement with that predicted by in silico studies, and (ii) A sequential deletion of the N-terminal extension has no effects on protein structure and folding.     

Molecular Variability in North Indian Isolates of Cylindrocladium quinquieseptatum Causing Eucalyptus Leaf and Seedling Blight

Cylindrocladium quinqueseptatum has been considered as the most destructive pathogen of Eucalyptus nurseries and plantations in north India. Genetic resistance has not been determined against this disease in Eucalyptus and genetic diversity among the fungal population in northern India is not known. Seventy three isolates from infected leaves and twigs of Eucalyptus were collected from different northern Indian state and analyzed through RAPD-PCR for screening genetic diversity. The UPGMA cluster analysis score of 284 loci permitted identification of 11 population lines and an outlier. This molecular variability prevalent among the north Indian population of the pathogen can used in identifying Cylindrocladium leaf and seedling blight resistant Eucalyptus germplasm.     

Determination of tranexamic acid concentration by solid phase microextraction and liquid chromatography-tandem mass spectrometry: first step to in vivo analysis

A solid phase microextraction (SPME) method followed by LC-MS/MS analysis was developed to determine the concentration of tranexamic acid (TA) in plasma. The use of a new biocompatible C18 coating allowed the direct extraction from complex biological samples without prior sample preparation; no matrix effect was observed. The results revealed that SPME was suitable for the analysis of polar drugs such as TA; such an application was previously inaccessible because of the limited availability of SPME coatings that can extract polar molecules. The proposed method was validated according to the bioanalytical method validation guidelines. LOD and LLOQ were 0.5 and 1.5 μg/ml, respectively. The recovery for the method was 0.19%, and the accuracy and precision of the method were <9 and <11%, respectively, with the exception of LLOQ, where the values were <16 and <13%, respectively. The performance of the proposed method was also compared against that of the standard techniques of protein precipitation and ultrafiltration. A statistical analysis indicated a clinically significant agreement among all assays. Another advantage of SPME over conventional techniques was the easy automation and feasibility of in vivo analysis; this advantage makes it possible to use the proposed method for an on-site analysis in clinical practice.     

DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria

Molecular Biology Reports - Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require...     

Discovery of Predictive Biomarkers for Litter Size in Boar Spermatozoa

Conventional semen analysis has been used for prognosis and diagnosis of male fertility. Although this tool is essential for providing initial quantitative information about semen, it remains a subject of debate. Therefore, development of new methods for the prognosis and diagnosis of male fertility should be seriously considered for animal species of economic importance as well as for humans. In the present study, we applied a comprehensive proteomic approach to identify global protein biomarkers in boar spermatozoa in order to increase the precision of male fertility prognoses and diagnoses. We determined that l-amino acid oxidase, mitochondrial malate dehydrogenase 2, NAD (MDH2), cytosolic 5′-nucleotidase 1B, lysozyme-like protein 4, and calmodulin (CALM) were significantly and abundantly expressed in high-litter size spermatozoa. We also found that equatorin, spermadhesin AWN, triosephosphate isomerase (TPI), Ras-related protein Rab-2A (RAB2A), spermadhesin AQN-3, and NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (NDUFS2) were significantly and abundantly expressed in low-litter size spermatozoa (>3-fold). Moreover, RAB2A, TPI, and NDUFS2 were negatively correlated with litter size, whereas CALM and MDH2 were positively correlated. This study provides novel biomarkers for the prediction of male fertility. To the best of our knowledge, this is the first work that shows significantly increased litter size using male fertility biomarkers in a field trial. Moreover, these protein markers may provide new developmental tools for the selection of superior sires as well as for the prognosis and diagnosis of male fertility.Prognosis and diagnosis of male fertility is a major concern in both animals and humans worldwide. In humans, about half of the fertility problems arise because of male factors. In addition, 50% of breeding system failures that are contributed by the sire lead to huge economic drawbacks in the animal industry (1 –5). Therefore, the development of new methods is needed to ensure more accurate prognosis and diagnosis of male fertility.Worldwide, artificial insemination (AI)¹ has been extensively performed in animal industries. Recent data revealed that more than 90% of the sows in Europe and the United States have been bred using AI during last three decades (6). The AI system sufficiently contributes to the achievement of high performance swine production through the selection of quality semen. Moreover, AI has been implemented extensively in swine industries for genetic up-grading (7, 8). However, the selection of high quality semen still depends on conventional sperm analyses such as the analysis of sperm morphology (9), motility (10), and sperm penetration assays (11, 12). Although these tests are commonly used to evaluate the male factor of fertility/infertility, the clinical value is still debated (13). Therefore, to evaluate the limits of conventional sperm analyses, the development of new methods to assess sperm function and fertility should be seriously considered for animal species of economic importance as well as for humans. Additionally, it is important to note that the optimization of sperm production will be possible when the methods to choose superior sires with greater efficiency become available. In this regard, the identification of global protein biomarkers using comprehensive proteomic tools represents a new method on the horizon that may facilitate the prediction of superior sires.Recently, several studies have reported that proteomics is an effective tool that has the potential to transform our understanding of spermatozoa (14 –16) by acquiring new biomarkers of male infertility and/or fertility. In addition, the development of mass spectrometry (MS) allows the potential identification of sperm proteins (17, 18). In fact, increased knowledge of the sperm proteome allows us to identify new molecular markers.In this study, we used high- and low-litter size boar spermatozoa to develop suitable biomarkers. First, sperm motility (%), motion characteristics, and capacitation status were evaluated by computer-assisted sperm analysis (CASA) and combined Hoechst 33258/chlortetracycline fluorescence assessment. Second, to find deferentially expressed proteins (>threefold) between high- and low-litter size boar spermatozoa, a 2-DE proteomic approach was applied following the identification of proteins by ESI-MS/MS and a MASCOT search. The 2-DE results were confirmed by a Western blot analysis that was performed with five commercially available antibodies. Third, to validate discovered markers for male fertility prediction, the expression levels of five proteins from 20 randomly selected boar spermatozoa with broad fertility ranges (i.e. litter size) were analyzed by enzyme-linked immunosorbent assay (ELISA), and the relationship between protein expression and male fertility was determined. Moreover, to represent the entire proteomic event, biological functions and interactions of the deferentially expressed proteins were schematized by a signaling pathway.     

Xtr, a plural tudor domain-containing protein, is involved in the translational regulation of maternal mRNA during oocyte maturation in Xenopus laevis

Xtr in the fertilized eggs of Xenopus has been demonstrated to be a member of a messenger ribonucleoprotein (mRNP) complex that plays a crucial role in karyokinesis during cleavage. Since the Xtr is also present both in oocytes and spermatocytes and its amount increases immediately after spematogenic cells enter into the meiotic phase, this protein was also predicted to act during meiotic progression. Taking advantage of Xenopus oocytes' large size to microinject anti-Xtr antibody into them for inhibition of Xtr function, we examined the role of Xtr in meiotic progression of oocytes. Microinjection of anti-Xtr antibody into immature oocytes followed by reinitiation of oocyte maturation did not affect germinal vesicle break down and the oscillation of Cdc2/cyclin B activity during meiotic progression but caused abnormal spindle formation and chromosomal alignment at meiotic metaphase I and II. Immunoprecipitation of Xtr showed the association of Xtr with FRGY2 and mRNAs such as RCC1 and XL-INCENP mRNAs, which are involved in the progression of karyokinesis. When anti-Xtr antibody was injected into oocytes, translation of XL-INCENP mRNA, which is known to be repressed in immature oocytes and induced after reinitiation of oocyte maturation, was inhibited even if the oocytes were treated with progesterone. A similar translational regulation was observed in oocytes injected with a reporter mRNA, which was composed of an enhanced green fluorescent protein open reading frame followed by the 3' untranslational region (3'UTR) of XL-INCENP mRNA. These results indicate that Xtr regulates the translation of XL-INCENP mRNA through its 3'UTR during meiotic progression of oocyte.     

ACC deaminase containing diazotrophic endophytic bacteria ameliorate salt stress in Catharanthus roseus through reduced ethylene levels and induction of antioxidative defense systems

Among a total of 27 cultivable salt tolerant endophytic bacteria isolated from Catharanthus roseus grown in highly salt affected coastal region of cuddalore district, Tamilnadu, India four isolates were found to be positive for nitrogenase activity. The isolates were evaluated for their stress tolerance efficiency and screened for different PGP traits. Based on the above studied parameters, and ability to produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase (4.24???mol ??-ketobutyrate mg^_1 protein h^_1) the salt tolerant diazotrophic isolate AUM54 was selected for further investigation and identified as Achromobacter xylosoxidans by 16S rRNA gene sequencing. The ability of this isolate to ameliorate salt stress in C. roseus was evaluated under gnotobiotic and pot culture conditions. At 150?mM NaCl level A. xylosoxidans AUM54 treated plants recorded ethylene level of 394.1 p mol ethylene g^?1 FW h^?1 compared to the ethylene level of 516.0 p mol ethylene g^?1 FW h^?1 recorded in the un inoculated control. A. xylosoxidans AUM54 inoculated plants recorded the maximum germination percentage of 98.3, vigor index of 2231.4, plant height of 120.4?cm, root dry weight of 53.24?g Plant^_1 and ajmalicine content of 1.60?mg?g^?1, compared to the germination percentage of 91.6%, vigour index of 1511.5, plant height of 105.8, root weight of 47.2?g Plant^?1, and ajmalicine content of 1.23?mg?g^?1 in uninoculated plants grown without NaCl treatment. This isolate also decreased plant ethylene levels by 11?C23% and increased the antioxidative enzyme content of inoculated C. roseus plants to the tune of 19?C32% for ascorbate peroxidase (APX) activity, 20?C30% for superoxide dismutase (SOD) activity and 4?C16% for catalase (CAT) under normal and salt affected conditions.     

Differential antioxidant/pro-oxidant activity of dimethoxycurcumin, a synthetic analogue of curcumin

Dimethoxycurcumin (Dimc), a metabolically stable analogue of curcumin, is under investigation as an anti-tumour agent. Recently a number of studies have been performed on Dimc in this laboratory and also by others. In the present article, all these results have been summarized and wherever possible compared with those of curcumin. Rate constant for reactions of Dimc with superoxide radicals was comparable with that of curcumin, while its reaction with peroxyl radicals was much slower. These results were further supported by the observations on the scavenging of basal ROS levels in lymphocytes and evaluation of antioxidant activities. In line with the earlier reports on curcumin, Dimc was a pro-oxidant and generated ROS in tumour cells. Both curcumin and Dimc were non-toxic to lymphocytes, while exhibiting comparable cytotoxicity to tumour cells. Additionally, these compounds showed higher uptake in tumour cells than in normal lymphocytes. Fluorescence studies on both the compounds revealed their binding to genomic DNA, similar sub-cellular distribution and nuclear localization. All these studies suggested that methylation of the phenolic-OH group in curcumin, although decreasing the antioxidant activity marginally, showed comparable pro-oxidant activity, making it a promising anti-tumour agent.     

Attenuated neuroprotective effect of riboflavin under UV-B irradiation via miR-203/c-Jun signaling pathway in vivo and in vitro

Background

Riboflavin (RF) or vitamin B2 is known to have neuroprotective effects. In the present study, we report the attenuation of the neuroprotective effects of RF under UV-B irradiation. Preconditioning of UV-B irradiated riboflavin (UV-B-RF) showed attenuated neuroprotective effects compared to that of RF in SH-SY5Y neuroblostoma cell line and primary cortical neurons in vitro and a rat model of cerebral ischemia in vivo.

Results

Results indicated that RF pretreatment significantly inhibited cell death and reduced LDH secretion compared to that of the UV-B-RF pretreatment in primary cortical neuron cultures subjected to oxygen glucose deprivation in vitro and cortical brain tissue subjected to ischemic injury in vivo. Further mechanistic studies using cortical neuron cultures revealed that RF treatment induced increased miR-203 expression which in turn inhibited c-Jun expression and increased neuronal cell survival. Functional assays clearly demonstrated that the UV-B-RF preconditioning failed to sustain the increased expression of miR-203 and the decreased levels of c-Jun, mediating the neuroprotective effects of RF. UV-B irradiation attenuated the neuroprotective effects of RF through modulation of the miR-203/c-Jun signaling pathway.

Conclusion

Thus, the ability of UV-B to serve as a modulator of this neuroprotective signaling pathway warrants further studies into its role as a regulator of other cytoprotective/neuroprotective signaling pathways.