Foraminiferal and Pteropod Records in the Late Quaternary Sequence off Northern Kerala and Their Oceanographic and Climatic Significance

In the present investigation, an attempt is made to study late Quaternary foraminiferal and pteropod records of the shelf of northern Kerala and to evaluate their potentiality in paleocenographic and paleoclimatic reconstruction. The study gives details of sediment cores, general characteristics of foraminifera and pteropod species recorded from the examined samples and their systematic classification, spatial distribution of Recent foraminifera and pteropods and their response to varying bathymetry, nature of substrate, organic matter content in sediment and hydrography across the shelf. An attempt is also made to establish an integrated chronostratigraphy for the examined core sections. An effort is also made to identify microfaunal criteria useful in biostratigraphic division in shallow marine core sections. An attempt is made to infer various factors responsible for the change in microfaunal assemblage. Reconstruction of sea level changes during the last 36,000 years was attempted based on the pteropod record. The study reveals a bathymetric control on benthic/planktic (BF/PF) foraminiferal and pteropods/planktic foraminiferal (Pt/PF) abundance ratio. Bathymetric distribution pattern of BF/PF ratio is opposite to the (Pt/PF) ratio with decreasing trend of former from the shore across the shelf. Quantitative benthic foraminiferal record in the surficial sediments reveals a positive correlation between the diversity and bathymetry. R-mode cluster analysis performed on 30n significant Recent benthic foraminiferal, determines three major assemblage.

Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

Background: Multi-drug resistance and severe/ complicated cases are the emerging phenotypes of vivax malaria, which may deteriorate current anti-malarial control measures. The emergence of these phenotypes could be associated with either of the two Plasmodium vivax lineages. The two lineages had been categorized as Old World and New World, based on geographical sub-division and genetic and phenotypical markers. This study revisited the lineage hypothesis of P. vivax by typing the distribution of lineages among global isolates and evaluated their genetic relatedness using a panel of new mini-satellite markers. Methods: 18S SSU rRNA S-type gene was amplified from 420 Plasmodium vivax field isolates collected from different geographical regions of India, Thailand and Colombia as well as four strains each of P. vivax originating from Nicaragua, Panama, Thailand (Pak Chang), and Vietnam (ONG). A mini-satellite marker panel was then developed to understand the population genetic parameters and tested on a sample subset of both lineages. Results: 18S SSU rRNA S-type gene typing revealed the distribution of both lineages (Old World and New World) in all geographical regions. However, distribution of Plasmodium vivax lineages was highly variable in every geographical region. The lack of geographical sub-division between lineages suggests that both lineages are globally distributed. Ten mini-satellites were scanned from the P. vivax genome sequence; these tandem repeats were located in eight of the chromosomes. Mini-satellites revealed substantial allelic diversity (7-21, AE = 14.6 +/- 2.0) and heterozygosity (He = 0.697-0.924, AE = 0.857 +/- 0.033) per locus. Mini-satellite comparison between the two lineages revealed high but similar pattern of genetic diversity, allele frequency, and high degree of allele sharing. A Neighbour-Joining phylogenetic tree derived from genetic distance data obtained from ten mini-satellites also placed both lineages together in every cluster. Conclusions: The global lineage distribution, lack of genetic distance, similar pattern of genetic diversity, and allele sharing strongly suggested that both lineages are a single species and thus new emerging phenotypes associated with vivax malaria could not be clearly classified as belonging to a particular lineage on basis of their geographical origin.

Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo

This article presents a statistical method for detecting recombination in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationship between the taxa, and (2) a site graph (hidden Markov model) representing interactions between different sites in the DNA sequence alignments. We adopt a Bayesian approach and sample the parameters of the model from the posterior distribution with Markov chain Monte Carlo, using a Metropolis-Hastings and Gibbs-within-Gibbs scheme. The proposed method is tested on various synthetic and real-world DNA sequence alignments, and we compare its performance with the established detection methods RECPARS, PLATO, and TOPAL, as well as with two alternative parameter estimation schemes.

Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding bla(CTX-M-14)

Antimicrobial drug resistance is a global challenge for the 21st century with the emergence of resistant bacterial strains worldwide. Transferable resistance to beta-lactam antimicrobial drugs, mediated by production of extended-spectrum beta-lactamases (ESBLs), is of particular concern. In 2004, an ESBL-carrying IncK plasmid (pCT) was isolated from cattle in the United Kingdom. The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla(CTX-M-14). From this information, PCRs identifying novel features of pCT were designed and applied to isolates from several countries, showing that the plasmid has disseminated worldwide in bacteria from humans and animals. Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals.

Distribution of β-amylase I haplotypes among European cultivated barleys

The barley β-amylase I (Bmy1) locus encodes a starch breakdown enzyme whose kinetic properties and thermostability are critical during malt production. Studies of allelic variation at the Bmy1 locus have shown that the encoded enzyme can be commonly found in at least three distinct thermostability classes and demonstrated the nucleotide sequence variations responsible for such phenotypic differences. In order to explore the extent of sequence diversity at the Bmy1 locus in cultivated European barley, 464 varieties representing a cross-section of popular varieties grown in western Europe over the past 60 years, were genotyped for three single nucleotide polymorphisms chosen to tag the four common alleles found in the collection. One of these haplotypes, which has not been explicitly recognised in the literature as a distinct allele, was found in 95% of winter varieties in the sample. When release dates of the varieties were considered, the lowest thermostability allele (Bmy1-Sd2L) appeared to decrease in abundance over time, while the highest thermostability allele (Bmy1-Sd2H) was the rarest allele at 5.4% of the sample and was virtually confined to two-row spring varieties. Pedigree analysis was used to track transmission of particular alleles over time and highlighted issues of genetic stratification of the sample.

Prevalence and nonrandom distribution of exonic mutations in interferon regulatory factor 6 in 307 families with Van der Woude syndrome and 37 families with popliteal pterygium syndrome

Purpose: Interferon regulatory factor 6 encodes a member of the IRF family of transcription factors. Mutations in interferon regulatory factor 6 cause Van der Woude and popliteal pterygium syndrome, two related orofacial clefting disorders. Here, we compared and contrasted the frequency and distribution of exonic Mutations in interferon regulatory factor 6 between two large geographically distinct collections of families with Van der Woude and between one collection of families with popliteal pterygium syndrome. Methods: We performed direct sequence analysis of interferon regulatory factor 6 exons oil samples from three collections, two with Van der Woude and one with popliteal pterygium syndrome. Results: We identified mutations in interferon regulatory factor 6 exons in 68% of families in both Van der Woude collections and in 97% of families with popliteal pterygium syndrome. In sum, 106 novel disease-causing variants were found. The distribution of mutations in the interferon regulatory factor 6 exons in each collection was not random; exons 3, 4, 7, and 9 accounted for 80%. In the Van der Woude collections, the mutations were evenly divided between protein truncation and missense, whereas most mutations identified in the popliteal pterygium syndrome collection were missense. Further, the missense mutations associated with popliteal pterygium syndrome were localized significantly to exon 4, at residues that are predicted to bind directly to DNA. Conclusion: The nonrandom distribution of mutations in the interferon regulatory factor 6 exons suggests a two-tier approach for efficient mutation screens for interferon regulatory factor 6. The type and distribution of mutations are consistent with the hypothesis that Van der Woude is caused by haploinsufficiency of interferon regulatory factor 6. Oil the other hand, the distribution of popliteal pterygium syndrome-associated mutations suggests a different, though not mutually exclusive, effect oil interferon regulatory factor 6 function. Genet Med 2009:11(4):241-247.

Towards the main sequence: detailed analysis of weak line and post-T Tauri stars

A detailed study was performed for a sample of low-mass pre-main-sequence (PMS) stars, previously identified as weak-line T Tauri stars, which are compared to members of the Tucanae and Horologium Associations. Aiming to verify if there is any pattern of abundances when comparing the young stars at different phases, we selected objects in the range from 1 to 100 Myr, which covers most of PMS evolution. High-resolution optical spectra were acquired at European Southern Observatory and Observatorio do Pico dos Dias. The stellar fundamental parameters effective temperature and gravity were calculated by excitation and ionization equilibria of iron absorption lines. Chemical abundances were obtained via equivalent width calculations and spectral synthesis for 44 per cent of the sample, which shows metallicities within 0.5 dex solar. A classification was developed based on equivalent width of Li I 6708 angstrom and Ha lines and spectral types of the studied stars. This classification allowed a separation of the sample into categories that correspond to different evolutive stages in the PMS. The position of these stars in the Hertzsprung-Russell diagram was also inspected in order to estimate their ages and masses. Among the studied objects, it was verified that our sample actually contains seven weak-line T Tauri stars, three are Classical T Tauri, 12 are Fe/Ge PMS stars and 21 are post-T Tauri or young main-sequence stars. An estimation of circumstellar luminosity was obtained using a disc model to reproduce the observed spectral energy distribution. Most of the stars show low levels of circumstellar emission, corresponding to less than 30 per cent of the total emission.

Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens

Plasmodium falciparum, the causative agent of human malaria, invades host erythrocytes using several proteins on the surface of the invasive merozoite, which have been proposed as potential vaccine candidates. Members of the multi-gene PfRh family are surface antigens that have been shown to play a central role in directing merozoites to alternative erythrocyte receptors for invasion. Recently, we identified a large structural polymorphism, a 0.58 Kb deletion, in the C-terminal region of the PfRh2b gene, present at a high frequency in parasite populations from Senegal. We hypothesize that this region is a target of humoral immunity. Here, by analyzing 371 P. falciparum isolates we show that this major allele is present at varying frequencies in different populations within Senegal, Africa, and throughout the world. For allelic dimorphisms in the asexual stage antigens, Msp-2 and EBA-175, we find minimal geographic differentiation among parasite populations from Senegal and other African localities, suggesting extensive gene flow among these populations and/or immune-mediated frequency-dependent balancing selection. In contrast, we observe a higher level of inter-population divergence (as measured by F(st)) for the PfRh2b deletion, similar to that observed for SNPs from the sexual stage Pfs45/48 loci, which is postulated to be under directional selection. We confirm that the region containing the PfRh2b polymorphism is a target of humoral immune responses by demonstrating antibody reactivity of endemic sera. Our analysis of inter-population divergence suggests that in contrast to the large allelic dimorphisms in EBA-175 and Msp-2, the presence or absence of the large PfRh2b deletion may not elicit frequency-dependent immune selection, but may be under positive immune selection, having important implications for the development of these proteins as vaccine candidates. (C) 2009 Elsevier B.V. All rights reserved.

The leptodus shales of central Peninsular Malaysia: distribution, age and palaeobiogeographical affinities

The terms ‘Leptodus Shales’ and ‘Leptodus Beds’ have been used to describe a rich brachiopod bearing unit within the Permian argillaceous facies of the Central Belt of Peninsular Malaysia. To date there has been no formal description of this unit regarding its age, spatial distribution or faunal composition. A review of previous literature, backed by recently collected data from our field surveys and biostratigraphical studies reveals that there is a sequence of fossiliferous assemblages within the Leptodus Shales, which range in age from Middle Permian to possibly early Late Permian and extend geographically from southern Kelantan to southern Pahang, Peninsular Malaysia. These assemblages are found in argillaceous sediments which are often highly tuffaceous, and in northern Pahang are associated with pyroclastic volcanics of probable island-arc origin. The faunas are of Palaeo-equatorial affinity and are taxonomically close to faunas in Indochina, such as the Sisophon fauna in Cambodia. Typical elements include Vediproductus cf. punctatiformis (Chao), Transennatia gratiosa (Waagen), T. termierorum Sone, Leman and Shi, Uncuninellina timorensis (Beyrich), Leptodus richthofeni Kayser, L. cf. tenuis (Waagen), Leptodus nobilis (Waagen), Gubleria aff. ninglangensis Fang and Jiang, and Spyridiophora gubleri Termier and Termier.

Frequency distribution of TATA box and extension sequences on human promoters

TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear yet. In this study, we conducted a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from TATA Box motif, TATAWAWN, were classified into three distribution patterns: peak, bottom-peak and bottom. Fourteen TATA extension sequences (up to two base extensions) were predicted to be the new TATA Box elements because of their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mouse, zebrafish and drosophila melanogaster verified seven of these elements. It was also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human.

Late Palaeozoic sequence stratigraphy and brachiopod faunas of the Tarim Basin, Northwest China

This thesis deals with the stratigraphy and brachiopod systematic palaeontology of the latest Devonian (Famennian) to Early Permian (Kungurian) sedimentary sequences of the Tarim Basin, NW China. Brachiopod faunas of latest Devonian and Carboniferous age have been published or currently in press in the course of the Ph.D candidature and are herein appendixed, while the Early Permian brachiopod faunas are systematically described in this thesis. The described Early Permian brachiopod faunas include 127 species, of which 29 are new and 12 indeterminate, and six new genera (subgenera) are proposed; Tarimella, Bmntonella, Marginifera (Arenaria), Marginifera (Nesiotia), Baliqliqia and Ustritskia. A new integrated brachiopod biostratigraphical zonation scheme is proposed, for the first time, for the latest Devonian-Early Permian sequences of the entire Tarim Basin on the basis of this study as well as previously published information (including the Candidate's own published papers). The scheme consists of twenty three brachiopod acm biozones, most of which replace previously proposed assemblage or assemblage zones. The age and distribution of these brachiopod zones within the Tarim Basin and their relationships with other important fossil groups are discussed. In terms of regional correlations and biostratigraphical affinities, the Late Devonian to Early Carboniferous brachiopod faunas of the Tarim Basin are closest to those from South China, while the Late Carboniferous faunas demonstrate strong similarities to coeval faunas from the Urals, central Asia, North China and South China. During the Asselian-Sakmarian, strong faunal links between the Tarim Basin and those of the Urals persisted, while at the same time links with central Asia, North China and South China weakened. On the other hand, during the Artinskian-Kungurian times, affinities of the Tarim faunas with the Urals/Russian Platform rapidly reduced, when those with peri-Gondwana (South Thailand, northern Tibet) and South China increased. Thirty lithofacies (or microfacies) types of four facies associations are recognised for the Late Devonian to early Permian sediments. Based on detailed lithostratigraphy, biostratigraphy and facies analysis, 23 third-order sequences belonging to four supcrsequences are identified for the Late Devonian to Early Permian successions, from which sea-level fluctuation curves are reconstructed. The sequence stratigraphical analysis reveals that four major regional regressions, each marking a distinct supersequence boundary, can be recognised; they correspond to the end-Serpukhovian, end-Moscovian, late Artinskian and end-Kungurian times, respectively. The development of these sequences is considered to have been formed and regulated by the interplay of both eustasy and tectonism. Using the system tract of a sequence as the mapping time unit, a succession of 47 palaeogeographical maps have been reconstructed through the Late Devonian to Early Permian. These maps reveal that the Tarim Basin was first immersed by southwest-directed (Recent geographical orientation) transgression in the late Famennian after the Caledonian Orogeny. Since then, the basin had maintained its geometry as a large, southwest-mouthed embayment until the late Moscovian when most areas were the uplifted above sea-level. The basin was flooded again in late Asselian-Artinskian times when a new transgression came from a large epicontinental sea lying to its northwest. Thereafter, marine deposition was restricted to local areas (southwestern and northwestern margins until the late Kungurian, while deposition of continental deposits prevailed and continued through the Middle and late Permian into the Triassic.

Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions

Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Prevalence and nonrandom distribution of exonic mutations in interferon regulatory factor 6 in 307 families with Van der Woude syndrome and 37 families with popliteal pterygium syndrome

Purpose: Interferon regulatory factor 6 encodes a member of the IRF family of transcription factors. Mutations in interferon regulatory factor 6 cause Van der Woude and popliteal pterygium syndrome, two related orofacial clefting disorders. Here, we compared and contrasted the frequency and distribution of exonic Mutations in interferon regulatory factor 6 between two large geographically distinct collections of families with Van der Woude and between one collection of families with popliteal pterygium syndrome. Methods: We performed direct sequence analysis of interferon regulatory factor 6 exons oil samples from three collections, two with Van der Woude and one with popliteal pterygium syndrome. Results: We identified mutations in interferon regulatory factor 6 exons in 68% of families in both Van der Woude collections and in 97% of families with popliteal pterygium syndrome. In sum, 106 novel disease-causing variants were found. The distribution of mutations in the interferon regulatory factor 6 exons in each collection was not random; exons 3, 4, 7, and 9 accounted for 80%. In the Van der Woude collections, the mutations were evenly divided between protein truncation and missense, whereas most mutations identified in the popliteal pterygium syndrome collection were missense. Further, the missense mutations associated with popliteal pterygium syndrome were localized significantly to exon 4, at residues that are predicted to bind directly to DNA. Conclusion: The nonrandom distribution of mutations in the interferon regulatory factor 6 exons suggests a two-tier approach for efficient mutation screens for interferon regulatory factor 6. The type and distribution of mutations are consistent with the hypothesis that Van der Woude is caused by haploinsufficiency of interferon regulatory factor 6. Oil the other hand, the distribution of popliteal pterygium syndrome-associated mutations suggests a different, though not mutually exclusive, effect oil interferon regulatory factor 6 function. Genet Med 2009:11(4):241-247.

5S rDNA chromosomal mapping and COI sequence analysis reveal differentiation among distinct populations of a characid fish Serrapinnus notomelas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)