HSM — a hybrid system based approach for modelling intracellular networks

The paper proposes a hybrid system based approach for modelling of intracellular networks and introduces a restricted subclass of hybrid systems – HSM – with an objective of still being able to provide sufficient power for the modelling of biological systems, while imposing some restrictions that facilitate analysis of systems described by such models.     

Systems biological approach to investigate the lack of familial link between Down's Syndrome & Neural Tube Disorders

Systems Biology involves the study of the interactions of biological systems and ultimately their functions. Down''s syndrome (DS) is one of the most common genetic disorders which are caused by complete, or occasionally partial, triplication of chromosome 21, characterized by cognitive and language dysfunction coupled with sensory and neuromotor deficits. Neural Tube Disorders (NTDs) are a group of congenital malformations of the central nervous system and neighboring structures related to defective neural tube closure during the first trimester of pregnancy usually occurring between days 18-29 of gestation. Several studies in the past have provided considerable evidence that abnormal folate and methyl metabolism are associated with onset of DS & NTDs. There is a possible common etiological pathway for both NTDs and Down''s syndrome. But, various research studies over the years have indicated very little evidence for familial link between the two disorders. Our research aimed at the gene expression profiling of microarray datasets pertaining to the two disorders to identify genes whose expression levels are significantly altered in these conditions. The genes which were 1.5 fold unregulated and having a p-value <0.05 were filtered out and gene interaction network were constructed for both NTDs and DS. The top ranked dense clique for both the disorders were recognized and over representation analysis was carried out for each of the constituent genes. The comprehensive manual analysis of these genes yields a hypothetical understanding of the lack of familial link between DS and NTDs. There were no genes involved with folic acid present in the dense cliques. Only – CBL, EGFR genes were commonly present, which makes the allelic variants of these genes – good candidates for future studies regarding the familial link between DS and NTDs.

Abbreviations

NTD - Neural Tube Disorders, DS - Down''s Syndrome, MTHFR - Methylenetetrahydrofolate reductase, MTRR– 5 - methyltetrahydrofolate-homocysteine methyltransferase reductase.     

Conceptual models for burrow-related, selective dolomitization with textural and isotopic evidence from the Tyndall Stone, Canada

The formation of dolomite is generally explained using models that reflect larger‐scale processes that describe the relationship between the supply and transport of Mg, and geochemical conditions that are amenable to the formation of dolomite. However, heterogeneities in the substrate, such as those made by bioturbating infauna, may play a more important role in dolomitization than has been previously considered. Burrow‐facilitated dolomitization is evident in the Ordovician Tyndall Stone (Red River Group, Selkirk Formation) of central Canada. The diagenetic fabrics present are attributed to dolomitizing fluids that both flowed through and evolved within burrow networks. Petrographic analysis suggests that two phases of dolomite formation took place. The first formed a fine‐grained, fabric‐destructive type that probably accompanied early burial; the second is a fine‐ to medium‐grained, locally sucrosic dolomite that is interpreted to have precipitated during later burial. Isotopic analysis supports the proposed paragenetic history: (1) an apparent linking of the stable isotopes ¹³C and ¹⁸O strongly suggests that the micrite matrix formed during very early diagenesis and was derived from seawater; (2) the initial phase of dolomitization is potentially microbially mediated, as evidenced by the enrichment of ¹³C; and (3) isotopic values for the second generation of dolomite reflect the mixing of ground water and resorbed early dolomite. This paper conceptualizes the physical and chemical conditions required for the formation of dolomite in association with burrow fabrics. The proposed model reveals a composite of biological and inorganic reactions that demonstrates the interdependence of sediment fabric, organic content and microbial interactions in the development of burrow‐mottled dolomitic limestone. It is suggested that where burrow‐associated dolomite occurs, it is most likely to develop in two stages: first, the byproducts of the degradation of organic material in burrows locally increase the permeability and porosity around burrow fabrics in shallow diagenetic depositional environments; and, second, the passing of burrowed media into deeper dysaerobic sediment is accompanied by the establishment of fermenting micro‐organisms whose byproducts mediate dolomitization.     

Procedure to Facilitate Chromosome Counts in Difficult Plant Material

Numerous mitotic plates of contracted and well-spread chromosomes may be obtained from root tips of plants set on melting ice or snow overnight at room temperature. After 1:3 acetic-alcohol fixation for 0.5 to 3 hours the material is mordanted in a mixture of 7 parts of alcohol plus 21/2 parts of 3% ferric ammonium sulfate for 3 hours to overnight. This solution may be used as storage fluid for flower buds. Deep chromosome coloration without precipitates is secured by staining in a few drops of aceto-carmine for 10-15 minutes after which the tissues are softened by heating in aceto-carmine diluted with 3 parts of 45% acetic acid.     

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.     

Sabkha and Burrow-Mediated Dolomitization in the Mississippian Debolt Formation,Northwestern Alberta,Canada

Dolomitized burrows in the Mississippian (Visean) Debolt Formation of northwestern Alberta, Canada form the primary reservoir intervals in the Dunvegan gas field. Sedimentological and ichnological analyses suggest a carbonate ramp setting that includes subenvironments such as sabkhas, hypersaline lagoons, restricted subtidal lagoons, intertidal mud flats, and peloidal shoals. Dolomitization occurs primarily within oxidized muds and highly bioturbated sediments, with the primary mode being sabkha-associated precipitation. In this context, dolomitization within the burrows also appears to be mediated by sulfate-reducing bacteria. δ¹⁸O values for dolomite within burrows (mean 2.4‰) are enriched by 1.3‰ relative to calcite values (mean 1.1‰) within the burrows. This degree of fractionation is similar for dolomite and calcite that have precipitated from the same solution. It is therefore suggested that the protodolomite precipitated in equilibrium with calcite rather than by replacement of pre-existing calcite. Isotopic values of δ¹³C measured for dolomite associated with burrows (mean 3.4‰) and matrix (mean 3.5‰) is slightly enriched relative to measured calcite values (mean 3.2‰ for matrix; mean 3.1‰ for burrows). These isotopic trends are common for modern dolomite that has precipitated in equilibrium with seawater where concomitant sulfate reduction and organic carbon-oxidation is inferred to occur near the surface.     

A new proposal concerning the botanical origin of Baltic amber

Baltic amber constitutes the largest known deposit of fossil plant resin and the richest repository of fossil insects of any age. Despite a remarkable legacy of archaeological, geochemical and palaeobiological investigation, the botanical origin of this exceptional resource remains controversial. Here, we use taxonomically explicit applications of solid-state Fourier-transform infrared (FTIR) microspectroscopy, coupled with multivariate clustering and palaeobotanical observations, to propose that conifers of the family Sciadopityaceae, closely allied to the sole extant representative, Sciadopitys verticillata, were involved in the genesis of Baltic amber. The fidelity of FTIR-based chemotaxonomic inferences is upheld by modern–fossil comparisons of resins from additional conifer families and genera (Cupressaceae: Metasequoia; Pinaceae: Pinus and Pseudolarix). Our conclusions challenge hypotheses advocating members of either of the families Araucariaceae or Pinaceae as the primary amber-producing trees and correlate favourably with the progressive demise of subtropical forest biomes from northern Europe as palaeotemperatures cooled following the Eocene climate optimum.     

Tolerability and efficacy of single dose albendazole,diethylcarbamazine citrate (DEC) or co-administration of albendazole with DEC in the clearance of <Emphasis Type="Italic">Wuchereria bancrofti</Emphasis>in asymptomatic microfilaraemic volunteers in Pondicherry,South India: a hospital-based study

Background  

The tolerability and efficacy of single dose albendazole (400 mg), diethylcarbamazine citrate (DEC) (6 mg/kg bodyweight) or co-administration of albendazole (400 mg) + DEC (6 mg/kg bodyweight) was studied in 54 asymptomatic Wuchereria bancrofti microfilaraemic volunteers in a double blind hospital-based clinical study.