A Convenient Method for the Synthesis of (Prop-2-Ynyloxy)Benzene Derivatives via Reaction with Propargyl Bromide,Their Optimization,Scope and Biological Evaluation

A highly convenient method has been developed for the synthesis of (prop-2-ynyloxy) benzene and its derivatives. Differently substituted phenol and aniline derivatives were allowed to react with propargyl bromide in the presence of K₂CO₃ base and acetone as solvent. The compounds were synthesized in good yields (53–85%). Low cost, high yields and easy availability of compounds helped in the synthesis. Electron withdrawing groups favor the formation of stable phenoxide ion thus in turn favors the formation of product while electron donating groups do not favor the reaction. Phenol derivatives gave good yields as compared to that of aniline. As aprotic polar solvents favor S_N2 type reactions so acetone provided best solvation for the reactions. K₂CO₃ was proved to be good for the synthesis. Antibacterial, Antiurease and NO scavenging activity of synthesized compounds were also examined. 4-bromo-2-chloro-1-(prop-2-ynyloxy)benzene 2a was found most active compound against urease enzyme with a percentage inhibition of 82.00±0.09 at 100 µg/mL with IC₅₀ value of 60.2. 2-bromo-4-methyl-1-(prop-2-ynyloxy)benzene 2d was found potent antibacterial against Bacillus subtillus showing excellent inhibitory action with percentage inhibition of 55.67±0.26 at 100 µg/ml wih IC₅₀ value of 79.9. Based on results, it can be concluded that some of the synthesized compounds may have potential antiurease and antibacterial effects against several harmful substances.     

Cloning, identification and accurate normalization expression analysis of PPARα gene by GeNorm in Megalobrama amblycephala

Megalobrama amblycephala suffers from serious liver diseases recently and PPARα gene has been reported to play an important role in the immune system of animal liver. On the basis of these facts, we have cloned and identified full-length cDNA of PPARα and examined its expression patterns at different embryo developmental stages and in different tissues of adult and young fish in order to improve liver disease immunity of M. amblycephala. We also accurately normalized seven reference genes by GeNorm and calculated their gene expression normalization factors. The total length of PPARα cDNA was 2021 bp, comprising of 214-bp 5'-untranslated region; 1404-bp open reading frame (encoding 467-amino acids); and 403-bp 3'-untranslated region. PPARα peptide was predicted to consist of 4 domains, i.e. A/B, C, D, and E/F. PPARα mRNAs were detected in different tissues of adult and young fish including adipose tissue, gill, heart, liver, spleen, kidney, white muscle, intestine, brain and gonad. In adult fish, the expression of PPARα in white muscles was highest followed by liver and it was lowest in gonads. Its expression in male gonads was significantly higher than female gonads. In young fish, the expression of PPARα was highest in brain, followed by intestines and it was lowest in spleen. At different embryo developmental stages, the expression of PPARα was highest at 2 cells stage and it was lowest at gastrula stage, but it increased on first day after hatching. In unfertilized spermatozoa, the expression of PPARα was higher than unfertilized ovum.     

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5-8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The ～380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover ～90% of genes and ～60% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.     

Mass spectrometry-based immuno-precipitation proteomics - the user's guide

Immuno-precipitation (IP) experiments using MS provide a sensitive and accurate way of characterising protein complexes and their response to regulatory mechanisms. Differences in stoichiometry can be determined as well as the reliable identification of specific binding partners. The quality control of IP and protein interaction studies has its basis in the biology that is being observed. Is that unusual protein identification a genuine novelty, or an experimental irregularity? Antibodies and the solid matrices used in these techniques isolate not only the target protein and its specific interaction partners but also many non-specific 'contaminants' requiring a structured analysis strategy. These methodological developments and the speed and accuracy of MS machines, which has been increasing consistently in the last 5 years, have expanded the number of proteins identified and complexity of analysis. The European Science Foundation's Frontiers in Functional Genomics programme 'Quality Control in Proteomics' Workshop provided a forum for disseminating knowledge and experience on this subject. Our aim in this technical brief is to outline clearly, for the scientists wanting to carry out this kind of experiment, and recommend what, in our experience, are the best potential ways to design an IP experiment, to help identify possible pitfalls, discuss important controls and outline how to manage and analyse the large amount of data generated. Detailed experimental methodologies have been referenced but not described in the form of protocols.     

Development of genetic transformation methodologies for an industrially-promising microalga: Scenedesmus almeriensis

The development of the microalgal industry requires advances in every aspect of microalgal biotechnology. In this regard, the availability of genetic engineering tools for industrially-promising species is key. As Scenedesmus almeriensis has promise for industrial use, we describe here an Agrobacterium-based methodology that allows stable genetic transformation of it for the first time, thus opening the way to its genetic manipulation. Transformation was accomplished using two different antibiotic resistance genes [hygromicine phophotransferase (hpt) and Shble] and it is credited by PCR amplification of both hpt/Shble and GUS genes and by the β-glucuronidase activity of transformed cells. Nevertheless, the single 35S promoter seems unable to direct gene expression to a convenient level in S. almeriensis as suggested by the low GUS enzymatic activity. Temperature was critical for the transformation efficiency.     

Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA

MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3′ region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3′ region of MALAT1 orchestrating AS.     

Population diversity of sheep bot fly,Oestrus ovis (Linné, 1758) (Diptera: Oestridae: Oestrinae), using SDS polyacrylamide gel electrophoresis

The study was planned to evaluate the inter, and intra population genetic variation in general protein banding pattern in Oestrus ovis larvae, by using 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). The larvae were collected from slaughtered goats head from five different locations (AAS, PN, LA, GM, and BC) of Karachi, Pakistan. The data obtained was subjected to POPGENE (Population Genetic Analysis) software for analysis. The polymorphic loci within populations ranged from 45.45% to 90.91%. Polymorphic loci observed in all populations were 90.91%. The expected heterozygosity observed was 0.182 ± 0.096 in all populations. The chi-square test showed 5 out of 11 loci at H-W equilibrium. The overall fixation index (FST) value was 0.108, showing that the likelihood of subpopulations being differentiated from one another is about 11 percent. The gene flow value (Nm = 2.065) was higher, showing that genes flow occurs between populations. The values of genetic identity were greater, and genetic distance were smaller among all the populations, which means that all the populations were more alike and closer to each other. It was concluded that there was no sympatric and parapatric population differentiation observed among all the population of O. ovis and the populations of the five different locations were not genetically and reproductively isolated from each other.     

Novel Methodology for the Detection of Chromosome 21-Specific α-Satellite DNA Sequences

We present a novel method, based on the hybridization of allele-specific oligonucleotide probes, that allows the specific detection of chromosome 21 α-satellite sequences. Absence of informative polymorphic markers from the centromeric region of chromosome 21 has constituted one of the difficulties in studying the centromere of this chromosome. The α-satellite subfamilies from chromosomes 21 and 13 are almost identical in sequence and thus cannot be distinguished using conventional hybridization techniques. Analysis using nuclear families showed that the centromeric polymorphism, detected using our specific probe and pulsed-field gel restriction analysis, segregates in a Mendelian fashion and exhibits a high degree of polymorphism among unrelated individuals. The alphoid DNA of chromosome 21 is highly polymorphic, useful not only as a definitive anchor for the genetic map, but also for studies of chromosome 21 nondisjunction, including the unequivocal assignment of meiotic origin.