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At least 199 records · Page 11Linked to original sources
PubMed2004

Arsenical resistance genes in Saccharomyces douglasii and other yeast species undergo rapid evolution involving genomic rearrangements and duplications.

We have isolated and characterized three adjacent Saccharomyces douglasii genes that share remarkable structural homology (97% amino acid sequence identity) with Saccharomyces cerevisiae ARR1 (ACR1), ARR2 (ACR2) and ARR3 (ACR3) genes involved in arsenical resistance. The ARR2 and ARR3 genes encoding the cytoplasmic arsenate reductase and the plasma membrane arsenite transporter are functionally interchangeable in both yeast species. In contrast, a single copy of S. douglasii ARR1 gene is not sufficient to complement the arsenic hypersensitivity of a S. cerevisiae mutant lacking the transcriptional activator Arr1p. This inability may be related to a deletion of a 35-bp sequence including the putative Yap-binding element in the ARR1 promoter of S. douglasii. Different mechanisms of regulation of ARR1 genes expression may therefore explain the increased tolerance of S. douglasii to arsenic in comparison with S. cerevisiae. The apparent duplication of the ARR gene cluster in the S. douglasii genome may constitute another factor contributing to the observed differences in arsenic sensitivity. Comparison of ARR genes from the genomes of several yeast species indicates that they are located in subtelomeric regions undergoing rapid evolution involving large-scale genomic rearrangements.

Amino Acid Sequence↗
PubMed2005

Distribution of Y chromosome lineages in Jerba island population.

We have analysed Y chromosome polymorphism on six STR markers (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393) and eight classical UEP markers (SRY10831a, YAP, SRY4064, M2, 92R7, M9, SRY2627 and 12f2) in three distinct ethnical, linguistic and cultural groups of Jerba island (Berbers, Arabs and a Jerban group of Sub-Saharan origin). Fst genetic distance and principal co-ordinate analysis based on STR haplotype frequencies, showed a genetic differentiation between the three Jerban groups and a genetic relationship between Jerban Berbers and Mozabites (a well defined Berber group in Algeria). Compound use of UEP and STR markers have increased discriminatory capacity. The detection of the most common haplotype (H9) in both Berbers and Mozabites may be useful in forensic special cases.

Chromosomes, Human, Y↗
PubMed2005

Geographical heterogeneity of Y-chromosomal lineages in Norway.

Y-chromosomal variation at five biallelic markers (Tat, YAP, 12f2, SRY(10831) and 92R7) and nine multiallelic short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II and DYS388) in a Norwegian population sample are presented. The material consists of 1766 unrelated males of Norwegian origin. The geographical distribution of the population sample reflects fairly well the population distribution around the year 1942, which is the median birth year of the index persons. Seven hundred and twenty-one different Y-STR haplotypes but 726 different lineages (Y-STRs plus biallelic markers) were encountered. We observed six known (P*(xR1a), BR(xDE, J, N3, P), R1a, N3, DE, J), and one previously undescribed haplogroup (probably a subgroup within haplogroup P*(xR1a)). Four of the haplogroups (P*(xR1a), BR(xDE, J, N3, P), R1a and N3) represented about 98% of the population sample. The analysis of population pairwise differences indicates that the Norwegian Y-chromosome distribution most closely resembles those observed in Iceland, Germany, the Netherlands and Denmark. Within Norway, geographical substructuring was observed between regions and counties. The substructuring reflects to some extent the European Y-chromosome gradients, with higher frequency of P*(xR1a) in the south-west and of R1a in the east. Heterogeneity in major founder groups, geographical isolation, severe epidemics, historical trading links and population movements may have led to population stratification and have most probably contributed to the observed regional differences in distribution of haplotypes within two of the major haplogroups.

Analysis of Variance↗
PubMed2005

Prospects for a self-sustainable sewage treatment system: a case study on full-scale UASB system in India's Yamuna River Basin.

The government of India decided to launch a project to implement 16 full-scale Upflow Anaerobic Sludge Blanket (UASB) reactors (with a total capacity of 598,000 m(3)/d) in the Yamuna River basin under its Yamuna Action Plan (YAP). A polishing pond called the Final Polishing Unit (FPU) was utilized for post-treatment. This paper evaluates the sewage treatment efficiency of the combined system of full-scale UASB reactors and polishing ponds under Indian climatic conditions. Results have shown that the effluent from the sewage treatment plants (STPs) investigated failed to comply with applicable discharge standards in terms of BOD, SS, and fecal coliform removal. Therefore, it is proposed that such proper operation and maintenance as removing excess sludge and scum be conducted in order to increase treatment efficiency. Moreover, trained and experienced workers are also required to operate and maintain the systems, along with a scientific approach.

Ammonia↗
PubMed2004

Resurrection of Bohadschia bivittata from B. marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence.

Behavior, color, body size, spicules, and mitochondrial DNA were examined in two morphs from the Bohadschia marmorata (Jaeger, 1833) species complex in Micronesia to test whether they are conspecific. This complex consists of eight morphs that have been described as separate species and combined in various ways for over a century. We examined the classic B. marmorata type and the type originally described as the species B. bivittata (Mitsukuri, 1912); B. bivittata was combined with B. marmorata by Panning (1944). Several observations and a phylogenetic analysis led us to conclude that B. marmorata and B. bivittata should return to their status as separate species. First, B. marmorata lives in shallow areas with strong currents, and B. bivittata lives on open sand between corals in deeper water. Second, the coloration of B. bivittata is distinct from B. marmorata, and although specimens collected on Yap Island differed from Mitsukuri's original description of B. bivittata, no specimens were collected with coloration intermediate between B. bivittata and B. marmorata. Third, spicules are more highly branched, perforated, and spiked in B. bivittata than in B. marmorata (and, in our study, spicule complexity did not correlate with body size). Finally, our phylogenetic analysis, based on partial nucleotide sequences of 16s, 12s, and COI mitochondrial genes, resulted in a tree--(Pearsonothuria graeffei (Bohadschia marmorata) (B. argus (B. bivittata)))--which shows that B. marmorata and B. bivittata are not even sister species, with B. bivittata more closely related to B. argus. Support for the clades for each Bohadschia species was strong, but the clade containing B. argus and B. bivittata had weaker support. Color and spicule examinations made of preserved B. marmorata-complex specimens from the Indo-Pacific as well as behavioral observations in the field also support the resurrection of B. bivittata.

Animals↗
PubMed1998

Importance of explicit salt ions for protein stability in molecular dynamics simulation.

The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.

Computer Simulation↗
PubMed1997

Adenosine 5'-triphosphate binding to bovine serum albumin.

Binding of ATP to bovine serum albumin was shown by ultrafiltration and NMR. The binding was pH dependent. Scatchard analysis revealed that at pH 5.4, 6.4 and 7.4, dissociation constant Kd was 13, 40 and 120 microM, respectively, and no binding was observed at pH 8.4. The binding stoichiometry was 1:1 for all pH. Dimer of BSA did not bind ATP. From chemical shifts of 31P-NMR, Kd was estimated to be 15 microM at pH 5.4, which is very close to that determined by ultrafiltration. While adenosine did not interfere with the binding. GTP, dCTP, ADP, UTP, AMP, phosphate and pyrophosphate were competitive inhibitors and their inhibition constants Ki were 25, 32, 36, 50, 130, 1000 and 186 microM, respectively. Fatty acids such as lauric acid and palmitic acid did not interfere with the binding. Warfarin was a non-competitive inhibitor. Cl- competitively inhibited the binding, and the inhibition constant was 20 mM. The dissociation constants of the Cl- binding were reported to be 0.42 mM for the first binding site, 10-5 mM for the second and 303-143 mM for the third [G. Scatchard, W.T. Yap, J. Am. Chem. Soc., 86 (1964) 3434; G. Scatchard et al., J. Am. Chem. Soc. 79 (1957) 12]. This suggests that the ATP binding site may be the second Cl- binding site.

Adenosine Triphosphate↗
PubMed2002

Jewish population genetic data in 20 polymorphic loci.

Frequency data of 20 polymorphisms (13 autosomal and 6 Y-chromosome STRs and the Alu-insertion YAP) were determined in a sample of 124 unrelated Jewish individuals from Ashkenazi, Sephardic, North African and Oriental origin. The a priori statistical power of the set of studied loci was highly discriminating (PD=1 in 2.393 E+15 individuals for autosomal STRs, and a probability of finding two unrelated males with the same haplotype of less than 0.01). Some significant population differences were registered between Jews and other Circummediterranean populations in Y-chromosome loci frequencies.

Forensic Medicine↗
PubMed2001

Characterizing Class I WW domains defines key specificity determinants and generates mutant domains with novel specificities.

INTRODUCTION: WW domains are small protein interaction modules found in a wide range of eukaryotic signaling and structural proteins. Five classes of WW domains have been annotated to date, where each class is largely defined by the type of peptide ligand selected, rather than by similarities within WW domains. Class I WW domains bind Pro-Pro-Xxx-Tyr containing ligands, and it would be of interest to determine residues within the domains that determine this specificity. RESULTS: Fourteen WW domains selected Leu/Pro-Pro-Xxx-Tyr containing peptides ligands via phage display and were thus designated as Class 1 WW domains. These domains include those present in human YAP (hYAP) and WWP3, as well as those found in ubiquitin protein ligases of the Nedd4 family, including mouse Nedd4 (mNedd4), WWP1, WWP2 and Rsp5. Comparing the primary structures of these WW domains highlighted a set of highly conserved residues, in addition to those originally noted to occur within WW domains. Substitutions at two of these conserved positions completely inhibited ligand binding, whereas substitution at a non-conserved position did not. Moreover, mutant WW domains containing substitutions at conserved positions bound novel peptide ligands. CONCLUSIONS: Class I WW domains contain a highly conserved set of residues that are important in selecting Pro-Xxx-Tyr containing peptide ligands. The presence of these residues within an uncharacterized WW domain can be used to predict its ability to bind Pro-Xxx-Tyr containing peptide ligands.

Amino Acid Sequence↗
PubMed2003

Comparative analysis of short tandem repeats and single nucleotide polymorphisms on the Y-chromosome in Germans, Chinese and Thais.

We have typed genomic DNA samples from 95 individuals from Western Germany, 78 individuals from Bangkok/Thailand and 56 individuals from Chengdu/China for 11 Y-chromosomal diallelic polymorphisms and eight short tandem repeat (STR) systems. For single nucleotide polymorphism (SNP) analysis, a rapid method was applied using the single base extension technology (minisequencing) in combination with capillary electrophoresis. PCR products for SRY-8299, Tat, SRY2627, 92R7, SRY1532, M9, M13, M17/M19 and M20 were pooled and used as templates for the commercially available SNaPshot kit. In addition to these ten SNPs we also tested the Y-chromosomal diallelic Alu repeat insertion DYS287 (YAP) by agarose gel electrophoresis as well as the Y-chromosomal STR systems DYS19, DYS389I+II, DYS390, DYS391, DYS392, DYS393 and DYS385 by fluorescent multiplex fragment analysis. Among the 11 diallelic SNP/Alu systems, only six were found to be polymorphic in the three population samples. From these a total number of seven different haplogroups could be identified in the three populations. Of these, five haplogroups were present in Germans, five in Thais, and only two in Chinese. These haplogroup trees clearly represent population-specific structures. Haplogroup 26 is represented at a high frequency in the Thai and Chinese populations whereas it is absent in Germans. The Y-STR data confirm a haplogroup-specific distribution of Y-STR haplotypes. Only a few cases of identical STR haplotypes in the same SNP haplogroups were detected in each of the three populations studied.

China↗
PubMed2001

Y chromosome microsatellite variation in three populations of Jerba Island (Tunisia).

Six Y-chromosome linked microsatellites were typed in a sample of 135 unrelated males representing three different ethnic groups: Arabs, Berbers and Blacks of Jerba Island (Tunisia). Analysis of variation at the six Y chromosome STRs showed significant differences in allele distributions between the Black group and the two other Islander groups. The Black group revealed the highest level of genetic diversity as compared to Arabs and Berbers, while the latter group was the most homogeneous. Allele frequencies obtained for the three islander groups analysed were compared to data available for some European, Mediterranean and African populations. Principal-coordinate analyses showed genetic differentiation between the three geographically closed groups of Jerba. The absence of the YAP insertion marker and the position of Arabs and Jerban Blacks near the European cluster would suggest their relative 'admixture' with European populations.

Alleles↗
PubMed2004

Novel betaines from a micronesian sponge Dysidea herbacea.

Three new betaines, dysibetaine PP (1), dysibetaine CPa (2), and dysibetaine CPb (3), were isolated from an aqueous extract of the marine sponge Dysidea herbacea collected in Yap state, Micronesia. The structure of 1 was determined by spectral methods as well as chemical degradation to be a novel dipeptide betaine, and those for 2 and 3 were determined to be unprecedented cyclopropane betaines. Compounds 2 and 3 showed weak affinity toward the N-methyl-D-aspartic acid-type and the kainic acid-type glutamate receptors, respectively, in a radioligand binding assay.

Animals↗
PubMed1999

Tamosterone Sulfates: A C-14 Epimeric Pair of Polyhydroxylated Sterols from a New Oceanapiid Sponge Genus.

Two novel, C-14 epimeric polyhydroxylated 15-keto steroid sulfates, tamosterone sulfate and 14beta-tamosterone sulfate (1 and 2), were isolated from a sponge belonging to a new genus collected in Yap, Federated States of Micronesia. Their structures were assigned by analysis of spectroscopic data and chemical conversions. 14beta-Tamosterone sulfate (2) has the rare naturally occurring C/D cis ring fusion and is the less stable epimer based on equilibration studies. Both compounds possess side-chain substitution patterns not observed previously in marine sterols.

Journal Article↗
PubMed2001

Milolides, new briarane diterpenoids from the western Pacific octocoral Briareum stechei.

Eleven new briarane-type diterpene lactones, designated milolides (1--8, 10--12), together with four known diterpene lactones (9, 13--15), were isolated from the Micronesian octocoral Briareum stechei collected at Yap, Federated States of Micronesia. One aspect of the stereochemistry of one of the known compounds, solenolide C (9), is revised. Structures of the new compounds were determined from spectral data.

Animals↗
PubMed2003

New sesquiterpene quinols from a Micronesian sponge, Aka sp.

Three new sesquiterpene quinols (1, 2, and 5) and two known ones (3 and 4) were isolated along with halistanol sulfate (6) from a marine sponge of the genus Aka collected from Yap Island, Federated States of Micronesia. Their structures were determined from spectral data, and the structure of siphonodictyal C (3) was revised. Sulfates 3 and 6 inhibit CDK4/cyclin D1 complexation, whereas 1 and 4 do not.

Animals↗