POTENTIAL ANTIFUNGAL ACTIVITY OF DIFFERENT HONEY BRANDS FROM PAKISTAN: A QUEST FOR NATURAL REMEDY

Background: Besides a wholesome food, honey is known for its therapeutic implications. We investigated the antifungal activity of five honeys of different types from Pakistan against various pathogenic fungal strains. Antifungal properties of processed and non-processed honey were determined. Materials and Methods: The antifungal assay of honey was carried out against Aspergillus niger, Aspergillus flavus, Aspergillus fumigates, Alterneria alternata, Fusarium solanai, Microsporum canis, Penicillium funiculosium and Rhizopus solanai. Different dilutions of honey samples were used (20%, 50%, 70%, 90% and 100% w/v so as to find out the minimum effective concentration of each honey type. Results: It was observed that all of the honey samples were highly active, with percent inhibition range of (3-81%) for Aspergillus niger, (2-82%) for Aspergillus flavus, (1-76%) for Aspergillus fumigates, (1-84%) for Alterneria alternata, (2- 67%) for Fusarium solanai, (1-87%) Microsporum canis, (2-78%) Penicillium funiculosium and (1-86%) for Rhizopus solanai. Conclusion: The study of Pakistani honey brands reveals that they possess a substantial antifungal nature. Therefore, they may be used in curing fungal infections along with antifungal drugs as a cheaper alternative natural remedy with no side effects

The Structures and Abundance of Transposable Elements Contributing to Genome Diversity in the Diploid and Polyploid Brassica and Musa Crops

Mobile DNA sequences - transposable elements (TEs) that amplify and move within genomes represent a high proportion of the DNA in most eukaryotes. The present study aimed to define TE nature, structure and abundance in two contrasting groups of diploid and polyploids crop genera, Brassica (dicotyledon) and Musa (monocotyledon). Rather than starting with known TE sequences, a sequence-data driven approach was used, comparing homologous and homoeologous BAC pairs. Over ~100 kb regions, any stretch of sequence was characterized that was inserted or deleted in the evolutionary time since divergence of the two BAC genomic sequences. Almost all the sequences were indeed TEs, representatives of existing and a few novel superfamilies. Polymorphisms due to activity were measured by PCR with flanking primers in 40 (Brassica) or 96 (Musa) accessions, and some families were localized on chromosomes by fluorescent in situ hybridization. Autonomous and non-autonomous TEs were found; class I retrotransposons like Copia and Gypsy (LTR) predominated in both genera, while SINEs and LINEs (Non-LTR) were abundant in Brassica genomes. Large retrotransposon derivatives (LARDs) were in both genera, with a very few terminal-repeat in miniature (TRIM) elements. Class II DNA transposons included CACTA, hAT, Harbinger, Mariner and Mutator like MITEs in Brassica, while CACTA and Mutator were uncommon in Musa. Among miniature inverted-repeat transposable elements (MITEs), Stowaway, Tourist, and Mutator-like MITEs were abundant with several novel families identified and characterized. In diploid and allopolyploid Brassica species, A- or C-genome specific elements were found while others were more active. PCR enabled accession identification and phylogenetic reconstruction in Brassica and Musa. As well as known element families, few novel types of TEs were identified, including several variable, short elements with characteristic structural features. The analysis provides insight into the nature and diversity of TEs as an important genomic component; results are useful for genome annotation and understanding evolution and variation within these crops and the associated pool of wild germplasm

Natural killer cells enhance the immune surveillance of cancer

Immune system (IS) is comprised of molecules, cells, tissues and organs involved in host defense mechanism from infectious agents or tumor cells. On crossing the cell barriers by these infectious agents, the defense mechanism is alerted by the immune system to respond against these invading microbes. Innate immune response (IIR) and acquired immune response (AIR) are working in parallel to control these invading microbes. IIR is composed of various types of phagocytes and lymphocytes, while AIR is comprised of T and B lymphocytes. All the cells of the immune system cooperatively work against infectious agents and cancerous cells but Natural killer (NK) cells are playing an important role to respond to tumor by enhancing the expression of complementary domain (CD86) on dendritic cells (DCs) and production of IL-12. NK cells demolished tumor through perforin and granzyme, which are important for immune surveillance and death of tumor cells induced by cytokines such as tumor necrosis factor (TNF), Fas ligand (CD178), interferon-γ (IFN-γ) and IL-10. These cytokines have inhibited proliferation of tumor by inducing anti-angiogenic factors and maintaining cross talk with other immune cells. Natural products like transfer factor plus, immune modulator mix, ascorbic acid, Ganoderma lucidum, Agaricus blazei teas, nitrogenated soy extract, Andrographis paniculata and several phytochemicals enhanced the efficiency of NK cells in controlling cancers. Further studies will unravel the impact of NK cells in cancer control and how NK efficiency can be further enhanced

An overview on hepatitis C virus genotypes and its control

Hepatitis C virus (HCV) is a blood borne, circular and positive single stranded virus with high spread rates. With the passage of time the frequency of HCV is increasing in different parts of the world. HCV is a major cause, which may end in liver cirrhosis and hepatocellular carcinoma. HCV has six main genotypes with many subtypes, which have variable sequence homology with each other. Symptoms can appear anytime from 2 weeks to 6 months, which include jaundice, fatigue, gray-colored stool, joint pain, belly pain, weakness, anorexia, itchy skin and dark urine. Genotyping is more significant for planning of HCV treatment period and helps to cure HCV infections. For the quantification and identification of hepatitis C virus-ribonucleic acid, many molecular techniques are performed; the most significant are HCV ELISA, quantitative HCV-RNA PCR and recombinant immunoblot assay. PCR is the major technique targeting 5′ untranslated region (UTR). HCV can be transmitted by contaminated blood, ear and nose piercing and contaminated medical instruments. To overcome the rate of HCV, guidance should be provided to make aware the persons about risk factors, transmission and prevention. Discovery and designing of new therapies and vaccines to overcome this disease are the necessity of the present era. Four types of vaccines such as vector vaccines, peptide vaccines, DNA vaccines and recombinant protein vaccines are available in clinical trials

Molecular detection of <i>Candidatus</i> Scalindua flavia, study of anammox bacterial community structure, composition in the sediments of the East China Sea and the Yellow Sea

33-47In this study, the diversity, community structure and distribution of anammox bacteria in sediments from five sites of the ECS and YS were explored by using both the 16S rRNA and hzo functional gene biomarkers. A high diversity of anammox bacteria in the studied sites with Candidatus is observed. Scalindua being the dominant group of anammox bacteria. With 16S rRNA gene primers, an inimitable Candidatus. Scalindua phylotype was identified, putatively represented a novel species, and tentatively named “ Candidatus. Scalindua flavia”. In addition, three other distinct clades were also detected with a discrete clustering in the consensus tree. Statistical analysis of environmental variables indicated that NH4+ and PO43- are positively correlated to shape the differential distribution of anammox bacteria in different environments

Phylogenetic association of Cyprinid (Schizothorax) inferred from complete mitochondrial genome

Whole mitochondrial DNA (mtDNA) of S.esocinusand S. plagiostomus was found to be 16,591 and 16,564 bp respectively with 13 protein-coding genes, 2 rRNAs genes, 22 tRNA genes and 2 non-coding region. For valuing the phylogenetic relationship of a species on the basis of whole mitogenome are considered to be a great importance. In this study, we sequenced whole mitogenome of S.esocinusand S. plagiostomus and compared with the whole mitogenome sequences of members of other families (Balitoridae, Nemanchillidae and Cobatidae). The monophyly of the family Cyprinidae and a clade comprising Balitoridae and Nemanchillidae while Cobatidae with paraphyletic origin was strongly supported by the resultant phylogenies, recognized that Cyprinidae was closely related with the family Cobatidae than other ones. The results indicated that whole mitochondrial genome has a great importance in studying variation in genes and phylogenetic relationship in the subfamily Schizothoracinae. This data offering the molecular phylogenetic frame work of important Schizothorax species found in Swat

Identification and evolutionary genomics of novel LTR retrotransposons in Brassica

Retrotransposons (REs) are the most abundant and diverse elements identified from eukaryotic genomes. Using computational and molecular methods, 262 intact LTR retrotransposons were identified from Brassica genomes by dot plot analysis and data mining. The Copia superfamily was dominant (206 elements) over Gypsy (56), with estimated intact copies of ~1596 Copia and 540 Gypsy and ~7540 Copia and 780 Gypsy from Brassica rapa and Brassica oleracea whole genomes, respectively. Canonical Copia and Gypsy gag-pol polyprotein organizations were observed in most elements with a few displaying 1–3 additional or internally deleted domains. The PBS and PPT motifs were identified with tRNA complementary to tRNAMet or, rarely, other tRNA types. PCR amplification of RT regions revealed their abundance and distribution among A-, B-, and C-genome Brassicas indicating a common ancestor. The evolutionary relationship of Brassica REs resolved them into superfamily-specific (Copia/Gypsy) lineages. The phylogenetic analysis of 130 Brassica Copia clustered them into 2 clades and 10 sub-clades of 18 families; Gypsy elements clustered into 2 clades. The results enabled identification and understanding of the structure and nature of full-length REs and their derivatives in Brassica. The markers derived here will be useful for examining chromosome and genome evolution in Brassica

Characterization and Diversity of Novel PIF/Harbinger DNA Transposons in Brassica Genomes

Among DNA transposons, PIF/Harbinger is most recently identified superfamily characterized by 3 bp target site duplications (TSDs), flanked by 14-45 bp terminal inverted repeats (TIRs) and displaying DDD or DDE domain displaying transposase. Their autonomous elements contain two open reading frames, ORF1 and ORF2 encoding superfamily specific transposase and DNA-binding domain. Harbinger DNA transposons are recently identified in few plants. In present study, computational and molecular approaches were used for the identification of 8 Harbinger transposons, of which only 2 were complete with putative transposase, while rest 6 lack transposase and are considered as defective or non-autonomous elements. They ranged in size from 0.5-4 kb with 3 bp TSDs, 15-42 bp TIRs and internal AT rich regions. The PCR amplification of Brassica Harbinger transposase revealed diversity and ancient nature of these elements. The amplification polymorphism of some non-autonomous Harbingers showed species specific distribution. Phylogenetic analyses of transposase clustered them into two clades (monocot and dicot) and five sub-clades. The Brassica, Arabidopsis and Malus transposase clustered into genera specific sub-clades; although a lot of homology in transposase was observed. The multiple sequence alignment of Brassica and related transposase showed homology in five conserved blocks. The DD₃₅E triad and sequences showed similarity to already known Pong-like or Arabidopsis ATISI12 Harbinger transposase in contrast to other transposase having DD₄₇E or DD₄₈E motifs. The present study will be helpful in the characterization of Harbingers, their structural diversity in related genera and Harbinger based molecular markers for varietal/lines identifications

Molecular genetic analysis of Type II diabetes associated m.3243A>G mitochondrial DNA mutation in a Pakistani family

Background: Type II diabetes is the most often considered as maternally inherited disease and A>G transition at position 3243 of mitochondrial DNA (m.3243A>G) in the encoding tRNALeu (UUR) gene is thought to be strongly responsible for the pathogenesis of the disease in number of cases. Aim: Current study was conducted to investigate the family prevalence of m.3243A>G mutation in a Pakistani family with the context of insulin sensitivity and B-cell function. Subject and method This study was carried out in 6 suspected diabetic members of a Pakistani family. Mitochondrial DNA was extracted from saliva and after polymerase chain reaction, amplified DNA was subjected to direct sequencing. Results and conclusion: Sequencing results revealed absence of most common mtDNA m.3243A>G mutation in 6 subjects with devotedly congenital mitochondrial diabetes phenotype. Conclusively, the m.3243A>G mutation in mitochondrial tRNALeu gene was not found to be a frequent cause of Type II diabetes mellitus in a Pakistani (haripur) family. Our finding suggests that there might be some underlying genetic cause for Type II diabetes mellitus in the subjects under study

Prevalence of sputum smear positive pulmonary tuberculosis among the suspected visited patients in selected area of District Malakand, Pakistan

To control and stopped the progression of Tuberculosis (TB) epidemiological data as well as effective treatment are very necessary. This study was design to determine the prevalence of pulmonary tuberculosis sputum smear positive (PTB-SS+ve) cases among the total registered suspected cases of TB at different treatment center of district Malakand. This retrospective was carried out between 1st Janaury-25th June 2015. Overall prevalence of PTB-SS+ve in the district was 43.56%. The ratio of the disease was found slightly high 51.02% among the male patients while 48.98% in female. On the basis of age wise distribution the maximum amount cases 37.76% were recorded in age 16-30 years while the lowest No. of cases 8.16% were recorded in age 0-15 years. In conclusion, the PTB-SS+ve was prevalent disease in district Malakand mostly infected the individuals having age between 16-30 years. Early diagnosis and proper treatment are necessary to control the disease.Keywords:  Tuberculosis, Prevalence, Retrospective study, Smear positive Pulmonar