FOOD HABITS OF ASIAN ELEPHANT (Elephas maximus maximus) IN HANDAPANAGALA , SOUTH EAST SRI LANKA

Handapanagala tank area is home for the largest Elephant aggregation(Elephas maxim us maxim us) in Wellawaya area during the dry season. Mostof these Elephants come from different areas mainly from adjacent protectedareas such as Yala, Udawalawe and Lunugamwehera National parks. Themain traditional migratory route lies across the study area connecting Yala -through Demodara. The local migration is mainly due to lack of food andwater within the protected areas.The study attempted to find the food habits of elephants in Handapanagalaarea during dry season. This study was carried out for six months. The mainobjectives were to determine both food availability and feeding habits inrelation to the habitats. Food availability and their Relative ImportanceValues (RIV) were estimated using line transect and direct observationmethod within study area. Relative importance values were comparativelyhigh in species like Bauhinia racemosa (12.39 %), Fleuggea leucocarpa(17.32 %), Securinrega leucopyrus (14.3 %). Relative frequency valueindicated that most common species distributed in the study area wereBauhinia racemosa, Dichrostachys cinera, Phyllanthus sp., Premna sp. Themicro histological analysis was done to determine food habits of elephants.The major food plant parts in dung samples were analyzed to identify thecategories of plants consumed by elephants. This study revealed that themajor food items consumed by elephant during dry season were themonocotyledon leaves (65 %), Culm (12 %), Sheath (6 %) and DicotylidensBark (7 %) and, Woody fiber (2%). The predominant grasses identified indung samples were Imperata cylindrica (Gini grass) and Panicum maximum(Illuk). The field observations revealed that the elephants were mainlyconsuming plants in families such as Leguminosae, Graminae,Euphorbiaceae and Verbenaceae. Majority of bark damages were seen inplants such as Bauhinia racemosa (RIV - 12.39), Treminalia arjuna(Kumbuk) and Phyllanthus spp. A total of 112 plant species were identifiedand 35 species (31% of the available plants) were consumed by elephants.The results indicate that the Elephants in the Handapanagala are grazers andmainly feed on tall grasses during the dry season. Results also indicated that there is an impact on forest tree species like Bauhinia racemosa, Fleuggealeucocarpa and Securinrega leucopyrus, which have high RIV. Since thepresent study was carried out during dry season, this should be continuedduring wet season to get a hroad idea about the seasonal changes in foodhabits of Elephants.

Networking the nucleus

The nuclei of differentiating cells exhibit several fundamental principles of self-organization. They are composed of many dynamical units connected physically and functionally to each other—a complex network—and the different parts of the system are mutually adapted and produce a characteristic end state. A unique cell-specific signature emerges over time from complex interactions among constituent elements that delineate coordinate gene expression and chromosome topology. Each element itself consists of many interacting components, all dynamical in nature. Self-organizing systems can be simplified while retaining complex information using approaches that examine the relationship between elements, such as spatial relationships and transcriptional information. These relationships can be represented using well-defined networks. We hypothesize that during the process of differentiation, networks within the cell nucleus rewire according to simple rules, from which a higher level of order emerges. Studying the interaction within and among networks provides a useful framework for investigating the complex organization and dynamic function of the nucleus

IMPACT OF SAMBAR DEER(Cervus unicoior unicoior) ON THE VEGETATION AT THE HORTON PLAINS NATIONAL PARK

A survey was carried out at the Horton Plains National Park to investigate the influenceof sambar deer on grassland and fares' vegetation. The method adopted was, comparisonof the dominant grassland communities and seedlings in the forested areas with andwithout the effect of deer. Three enclosures (20 m x 5 m) were erected in the grasslandand four enclosures (20 In x 15 m) were erected in the forest to serve as controls (nograzing). Similar areas adjoining the plots were marked with pegs as test areas (withgrazing). Field surveys were carried ou. during the years 1997 and 1998. Incidence andextent of bark damage by sambar deer \Y<JS also examined using a scoring method on sixtransects each measuring 250 lJ1. GSN (Grazing Susceptibility Number) was used as anindicator of the the phytosociological behaviour of sambar in the grassland SummedDominance Ratio (SDR)) was used to calculate the GSN. During the months of January,March. July and October 1997, GSN values for dominant species in the grassland vizPennicetum and Chrysopogon were 184,20,23.75, -3.06 and 18.6,8.1, 17.23, 19.0respectively. The minus GSN value of ).06 indicates that during October Pcnnicctumgrass was not damaged by deer which coincided with the flowering period of thatspecies. Grazing presusure values obtained during the periods July-Sep 97, Sep-Nov 97 .Nov-Jan 98, Jan-Mar 98 for Pennicetum and Chrysopogon were 17, 5.6, -17.6, 5.8 andI, I I, -0.5, 0.9 respectively. Here the minus values indicates heavy grazing. During theperiods of less rain and also during peak lactation periods of sambar, the grazingpressure is high (July-September and November-January) compared to positive values ofgrazing pressure which coincides well with the comparatively high rainfall periods Studiesof the forest vegetation revealed that after a period of two years (1997-1999) 88'% ofseedlings survived (N=1499) in the enclosure but only 73% of the seedlings survived(N= 1488) in the open area. Bark damage is distinct on plants like Cinnamomumovalifolium, Neolitsea fucata, Calopiiyllum walkeri, Eurya japonica, Eleocarpussubvillosus, Syzigium revolutum and rJedyotis lawsoniae all of which have high IV)(Importance Value Indices). Trees with average gbh 28 cm and average height 7 m weremore prone to damage by deer. Only S% of a total of 921 trees were dead due to barkdamage

Squamous cell carcinoma of the ampulla of vater – A case report

Introduction: Ampullary carcinoma comprises up to 2% of all gastrointestinal malignancies. Primary squamous cell carcinoma of the ampulla is a very rare neoplasm, with only three reported cases in literature. Due to its rarity, the biological behavior is largely unknown. We highlight such a case, and its diagnostic workup.Case Report: A 61 year old woman presented with painless obstructive jaundice of 2 months duration. MRI scan showed a stricture in the distal common bile duct suggestive of a neoplasm. Biopsy at ERCP showed a poorly differentiated ampullary carcinoma. The specimen received at Whipple’s surgery showed a white tumour surrounding the ampulla, 25 mm in maximum dimension. Histology and immunohistochemistry (CK 7+/20 -, CA 19-9+, CK5/6 focally+) pointed towards a poorly differentiated squamous cell carcinoma. A primary squamous carcinoma elsewhere was excluded. The patient is alive nine months after surgery.Discussion: Ampullary squamous cell carcinoma is most often metastatic from sites such as the larynx, esophagus, lung and uterus. A squamous carcinoma therefore requires ruing out of a primary site elsewhere or a glandular component (adenosquamous carcinoma). These were excluded in this patient. Immunohistochemistry differed from that of primary adenocarcinoma of the ampulla

SEWAL: an open-source platform for next-generation sequence analysis and visualization

Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼108 sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼107 sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal

A dynamical model reveals gene co-localizations in nucleus

Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency-or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Rosa26-GFP Direct Repeat (RaDR-GFP) Mice Reveal Tissue- and Age-Dependence of Homologous Recombination in Mammals In Vivo

Homologous recombination (HR) is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP) mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.National Institutes of Health (U.S.) (Program Project Grant P01-CA026731)National Institutes of Health (U.S.) (R33-CA112151)National Institute of Environmental Health Sciences (P30-ES002109)Singapore-MIT Alliance for Research and Technology CenterNational Institutes of Health (U.S.) (P41-EB015871)National Cancer Institute (U.S.) (P30-CA014051