Morphological and biochemical variation in Sea buckthorn Hippophae rhamnoides ssp. turkestanica, a multipurpose plant for fragile mountains of Pakistan

Sea buckthorn (Hippophae rhamnoides ssp. turkestanica) a member of family Elaeagnaceae, is a very important multipurpose plant in the northern areas of Pakistan. It is an ideal plant for preventing soil erosion and land reclamation, can withstand extremes of temperature ranging from −43°C to 55°C and grows well under drought conditions and variable soil pH. The fruit is rich in nutrients and medicinal compounds such as vitamins, carotene, flavonoids, essential oil, carbohydrates, organic acids, amino acids, and soluble sugars. The plants are also important as fuel wood, fencing, fodder, soil erosion control, to make soil fertile by nitrogen fixation in roots and for the purpose of shelterbelts. In order to compare various populations of Sea buckthorn for morphological and biochemical composition, ten populations from different areas of northern Pakistan were compared using plant and fruit characters. The purpose of the investigation was to identify the variable populations for different valuable characteristics to develop improved varieties for commercial cultivation and easy fruit harvesting. The comparison indicated a significant amount of variability on morphological and biochemical basis. The variability will be utilised to develop commercial varieties of the plant utilising the conventional techniques of selection and hybridisation for economic activities on degraded land of mountainous regions of Pakistan

Characterization of RAPD markers in Vitis

A study was initiated to investigate the possibility of using RAPD markers in related populations of Vitis. We also sought to design primers that could amplify translation initiation sites (Kozak sequence) as a mean to maximize the production of RAPD markers from single copy DNA sequences in the genome. RAPD bands were labeled and used as probes on blots with either genomic DNA or RAPD products from cvs Aurore, Cayuga White, Horizon and Illinois 547-1. Reamplification of excised RAPD products produced either several bands of smaller size, a single band of smaller size or a single band of the same size as the original band. Among 16 probes hybridized to genomic DNA blots, three probes, including one from the Kozak primer amplification, hybridized to 1-2 bands, 5 probes hybridized to 3-8 bands and 8, including two from a Kozak primer reaction, to more than 10 bands on the genomic DNA blots. Twelve RAPD bands were also probed on RAPD blots derived from the RAPD reaction that produced each probe. Three of those probes hybridized to 1-2 bands, 8 hybridized to 3-8 and one hybridized to more than 10 bands indicating the presence of probe sequences in more than one RAPD band as amplified with the same primers. This result and the observations on reamplification of RAPD bands support the hypothesis that some of the longer RAPD fragments harbor internal priming sites that are either not amplified unless the reaction mixture is saturated with longer other primers indicating amplification from the same sequence but different sized repetitive DNA. RAPD reactions were also run with 16 primers on parental DNA of 2 crosses used in genetic mapping (Cayuga White x Aurore and Horizon x Illinois 547-1). These reactions rated 140 bands; 100 bands were shared by both populations, including 47 polymorphic bands. Ten polymorphic bands in Cayuga White x Aurore and 22 in Horizon x Illinois 547-1 were population specific. The RAPD analysis as well as hybridization of RAPD markers to the genomic blots suggest that linkage analysis could be used in related segregating populations with carefully chosen markers. Tagging single copy regions with Kozak-sequence-derived primers may be possible, but the low number of probes tested and lack of DNA sequence information prevents any definite conclusions

In vitro Maturation and Fertilization of Riverine Buffalo Follicular Oocytes in Media Supplemented with Oestrus Buffalo Serum and Hormones

Effects of two maturation media (TCM-199 and Ham's F-12) with and without the addition of oestrus buffalo serum (OBS) and hormones (FSH, LH, E2) on the maturation rate of buffalo follicular oocytes were evaluated. The results revealed a significant (P P 2+ free Tyrode's medium (63.72%) than in TALP (10.9%) and IVF-TL (32.18%). Thus, TCM-199 containing hormones and OBS appeared better for in vitro maturation, whereas modified Ca2+ free tyrode's medium was found to be more suitable for in vitro fertilization of buffalo follicular oocytes

Effect of Somatic Cell Types and Culture Medium on in vitro Maturation, Fertilization and Early Development Capability of Buffalo Oocytes

This study was designed to evaluate the efficacy of different somatic cell types and media in supporting in vitro maturation (IVM), in vitro fertilization (IVF) and early embryonic development competence of buffalo follicular oocytes. Cumulus oocyte complexes were collected for maturation from follicles (>6mm) of buffalo ovaries collected at the local abattoir. Oocytes were co-cultured in tissue culture medium (TCM-199) with either granulosa cells, cumulus cells, or buffalo oviductal epithelial cells (BOEC) @ 3x106 cells/ml or in TCM-199 without helper cells (control) at 39°C and 5%CO2 in humidified air. Fresh semen was prepared in modified Ca++ free Tyrode medium. Fertilization was carried out in four types of media: i) Tyrode lactate albumin pyruvate (TALP), ii) TALP+BOEC, iii) modified Ca++ free Tyrode and iv) modified Ca++ free Tyrode+BOEC. Fertilized oocytes were cultured for early embryonic development in TCM-199 with and without BOEC. Higher maturation rates were observed in the granulosa (84.24%) and cumulus cells (83.44%) than BOEC co culture system (73.37%). Highest fertilization rate was obtained in modified Ca++ free Tyrode with BOEC co culture (70.42%), followed by modified Ca++ free Tyrode alone (63.77%), TALP with BOEC (36.92%) and TALP alone (10.94%). Development of early embryos (8-cell stage) improved in TCM-199 with BOEC co culture than TCM-199 alone. From the results of this study, it can be concluded that addition of somatic cells (granulosa cells, cumulus cells) results in higher maturation rates of buffalo follicular oocytes than BOEC co culture system, while fertilization rate improved in modified Ca++ free Tyrode with and without BOEC. Addition of BOEC to TCM-199 improved the developmental capacity of early embryo

String pattern recognition using evolving spiking neural networks and quantum inspired particle swarm optimization

This paper proposes a novel method for string pattern recognition using an Evolving Spiking Neural Network (ESNN) with Quantum-inspired Particle Swarm Optimization (QiPSO). This study reveals an interesting concept of QiPSO by representing information as binary structures. The mechanism optimizes the ESNN parameters and relevant features using the wrapper approach simultaneously. The N-gram kernel is used to map Reuters string datasets into high dimensional feature matrix which acts as an input to the proposed method. The results show promising string classification results as well as satisfactory QiPSO performance in obtaining the best combination of ESNN parameters and in identifying the most relevant features

Evolving text classification rules with genetic programming

We describe a novel method for using genetic programming to create compact classification rules using combinations of N-grams (character strings). Genetic programs acquire fitness by producing rules that are effective classifiers in terms of precision and recall when evaluated against a set of training documents. We describe a set of functions and terminals and provide results from a classification task using the Reuters 21578 dataset. We also suggest that the rules may have a number of other uses beyond classification and provide a basis for text mining applications

EPIDEMIOLOGICAL SURVEY OF GENITAL PROLAPSE IN BUFFALOES KEPT UNDER DIFFERENT SYSTEMS AND SERUM MICRO MINERAL CONTENTS

The present project was planned to conduct an epidemiological survey of genital prolapse in buffaloes kept under different feeding and production systems and to study serum micro mineral contents in these animals. Data on 343 buffaloes were recorded for epidemiological studies, including 297 normal pregnant and 46 prolapsed cases. For serum micro mineral contents, blood samples were collected from 40 buffaloes comprising of 20 normal pregnant and 20 suffering from genital prolapse and analyzed for serum Cu, Zn, Fe and Mn contents. Occurrence of genital prolapse differed non significantly in animals kept under two feeding systems (stall fed and semi stall fed), three floor conditions (uneven floor, kacha/brick floor, sloppy floor) and two production systems (rural subsistence small holding and market oriented small holding). Its occurrence was higher during humid summer than other seasons. The mean values of serum copper and zinc were lower in prolapsed buffaloes compared to controls (P<0.01), while there was no difference in serum iron and manganese concentrations among animals of the two groups. Parity had no effect on serum concentration of any micro mineral. However, serum Zn level was higher in buffaloes suffering from vaginal prolapse compared to those with uterine prolapse (P<0.05)

Inferring Human Colonization History Using a Copying Model

Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single “Out-of-Africa” bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form

Serum ferritin levels, socio-demographic factors and desferrioxamine therapy in multi-transfused thalassemia major patients at a government tertiary care hospital of Karachi, Pakistan

<p>Abstract</p> <p>Background</p> <p>Beta thalassemia is the most frequent genetic disorder of haemoglobin synthesis in Pakistan. Recurrent transfusions lead to iron-overload manifested by increased serum Ferritin levels, for which chelation therapy is required.</p> <p>Findings</p> <p>The study was conducted in the Pediatric Emergency unit of Civil Hospital Karachi after ethical approval by the Institutional Review Board of Dow University of Health Sciences. Seventy nine cases of beta thalassemia major were included after a written consent. The care takers were interviewed for the socio-demographic variables and the use of Desferrioxamine therapy, after which a blood sample was drawn to assess the serum Ferritin level. SPSS 15.0 was employed for data entry and analysis.</p> <p>Of the seventy-nine patients included in the study, 46 (58.2%) were males while 33 (41.8%) were females. The mean age was 10.8 (± 4.5) years with the dominant age group (46.2%) being 10 to 14 years. In 62 (78.8%) cases, the care taker education was below the tenth grade. The mean serum Ferritin level in our study were 4236.5 ng/ml and showed a directly proportional relationship with age. Desferrioxamine was used by patients in 46 (58.2%) cases with monthly house hold income significant factor to the use of therapy.</p> <p>Conclusions</p> <p>The mean serum Ferritin levels are approximately ten times higher than the normal recommended levels for normal individuals, with two-fifths of the patients not receiving iron chelation therapy at all. Use of iron chelation therapy and titrating the dose according to the need can significantly lower the iron load reducing the risk of iron-overload related complications leading to a better quality of life and improving survival in Pakistani beta thalassemia major patients.</p> <p>Conflicts of Interest: None</p

Classification of heterogeneous microarray data by maximum entropy kernel

<p>Abstract</p> <p>Background</p> <p>There is a large amount of microarray data accumulating in public databases, providing various data waiting to be analyzed jointly. Powerful kernel-based methods are commonly used in microarray analyses with support vector machines (SVMs) to approach a wide range of classification problems. However, the standard vectorial data kernel family (linear, RBF, etc.) that takes vectorial data as input, often fails in prediction if the data come from different platforms or laboratories, due to the low gene overlaps or consistencies between the different datasets.</p> <p>Results</p> <p>We introduce a new type of kernel called maximum entropy (ME) kernel, which has no pre-defined function but is generated by kernel entropy maximization with sample distance matrices as constraints, into the field of SVM classification of microarray data. We assessed the performance of the ME kernel with three different data: heterogeneous kidney carcinoma, noise-introduced leukemia, and heterogeneous oral cavity carcinoma metastasis data. The results clearly show that the ME kernel is very robust for heterogeneous data containing missing values and high-noise, and gives higher prediction accuracies than the standard kernels, namely, linear, polynomial and RBF.</p> <p>Conclusion</p> <p>The results demonstrate its utility in effectively analyzing promiscuous microarray data of rare specimens, e.g., minor diseases or species, that present difficulty in compiling homogeneous data in a single laboratory.</p