Intertidal clams exhibit population synchrony across spatial and temporal scales.

Long-term datasets can be particularly useful for parsing out factors influencing populations, yet few studies have utilized continuous datasets to quantify population dynamics in bivalve molluscs. We used dynamic factor analysis on a clam biomass dataset spanning 28 yr and five distinct regions in the southern Salish Sea to determine (1) if native intertidal clam populations exhibit synchrony and (2) what environmental covariates may be correlated with these population trends. Once covariates were accounted for, the model with the most data support included three predominant trends to describe multidecadal change in clam biomass.

Multimetallic complexes and functionalized nanoparticles based on unsymmetrical dithiocarbamate ligands with allyl and propargyl functionality.

The new, unsymmetrical dithiocarbamate ligands, KS2CN(CH2CH═CH2)Me and KS2CN(CH2C≡CH)Me, are formed from the respective amines on reaction with KOH and carbon disulfide. The homoleptic complexes [Ni{S2CN(CH2CH═CH2)Me}2] and [M{S2CN(CH2C≡CH)Me}2] (M = Ni, Pd, Pt) are formed on reaction with suitable metal precursors. Conversion between the two pendant functionalities was confirmed by hydrogenation of [Ni{S2CN(CH2C≡CH)Me}2] to yield [Ni{S2CN(CH2CH═CH2)Me}2].

An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry.

We have developed a tandem mass spectrometry (MS/MS) data analysis program for confirmation of sequence of chemically modified oligonucleotides. The method is based on the analysis of deconvoluted MS/MS data for fragment ions from three charge states and comparison of these data against a set of computer-generated masses from expected fragmentation patterns. The algorithm compares the experimental masses not only against the fragment set predicted for the expected sequence but also against a wider test set covering all next-neighbor position switches of the original sequence and all pairwise swaps of nucleosides, which in synthesis would result in molecules with masses within a preset mass tolerance.

Studies on the redox characteristics of ferrioxamine E.

Thermodynamic parameters for the reduction of ferrioxamine E as calculated from redox potentials determined at four different temperatures were found to be DeltaH( not equal)=7.1+/-3.4 kJ mol(-1) and DeltaS( not equal)=-146 J mol(-1) K(-1).

Nuclear Factor 90(NF90) targeted to TAR RNA inhibits transcriptional activation of HIV-1.

Background: Examination of host cell-based inhibitors of HIV-1 transcription may be important for attenuating viral replication. We describe properties of a cellular double-stranded RNA binding protein with intrinsic affinity for HIV-1 TAR RNA that interferes with Tat/TAR interaction and inhibits viral gene expression.

Results: Utilizing TAR affinity fractionation, North-Western blotting, and mobility-shift assays, we show that the C-terminal variant of nuclear factor 90 (NF90ctv) with strong affinity for the TAR RNA, competes with Tat/TAR interaction in vitro.

Formation of modified cytosine residues in the presence of depurinated DNA.

[Chemical reaction: See text] Depurination is an important degradation pathway for antisense phosphorothioate oligonucleotides under conditions of thermal stress. We present evidence showing that depurinated oligonucleotides react with cytosine-containing sequences giving products containing a 6-(2-deoxy-beta-D-erythro-pentofuranosyl)-3-(2-oxopropyl)imidazo[1,2-c]pyrimidin-5(6H)-one residue. Further, we demonstrate that the same product is formed upon treatment of 2'-deoxycytidine with 4-oxo-2-pentenal, the latter being an expected byproduct of serial elimination reactions at apurinic sites.

Characterization of high molecular weight impurities in synthetic phosphorothioate oligonucleotides.

Phosphorothioate oligonucleotides manufactured by standard phosphoramidite techniques using 2'-deoxyadenosine- or 2'-O-(2-methoxyethyl)-5-methylcytosine-loaded solid supports contain branched impurities consisting of two chains linked through the exocyclic amino group of the 3'-terminal nucleoside of one chain and the 3'-terminal hydroxyl group of another via a P(O)SH group. These impurities are not produced when a universal, non-nucleoside derivatized support is used.

Trichloroacetaldehyde modified oligonucleotides.

Some commercial batches of dichloroacetic acid (DCA) contain traces of chloral (trichloroacetaldehyde). Using such DCA to effect detritylation during solid-phase oligonucleotide synthesis results in the formation of a family of process impurities in which the atoms of chloral (Cl3CCHO) are incorporated between the 5'-oxygen and phosphorus atoms of an internucleotide linkage. The structure was elucidated by HPLC with UV and MS detection, digestion of the oligonucleotide, synthesis of model compounds, and 1H and 31P NMR spectroscopy.

Epidemiology of dengue and dengue hemorrhagic fever in a cohort of adults living in Bandung, West Java, Indonesia.

A prospective study of dengue fever (DF) and dengue hemorrhagic fever (DHF) was conducted in a cohort of adult volunteers from two textile factories located in West Java, Indonesia. Volunteers in the cohort were bled every three months and were actively followed for the occurrence of dengue (DEN) disease. The first two years of the study showed an incidence of symptomatic DEN disease of 18 cases per 1,000 person-years and an estimated asymptomatic/ mild infection rate of 56 cases per 1,000 person-years in areas of high disease transmission.

A serological study of Chikungunya virus transmission in Yogyakarta, Indonesia: evidence for the first outbreak since 1982.

A study of epidemic transmission of Chikungunya virus (CHIK) was initiated in April 1999 in Yogyakarta, Indonesia. Three hundred seventeen volunteers from three kelurahans (sub-districts) were recruited. Anti-CHIK IgG antibodies were detected in 68% to 74% of cases and 28% to 32% of controls.

Enhancing knowledge and awareness of dengue during a prospective study of dengue fever.

In 1992, the Indonesian CDC implemented strategies to control and prevent dengue fever (DF) by including community involvement to reduce larva breeding sites and a mass health education program. To contribute to this effort, we incorporated an educational component into a prospective study of DF conducted at two textile factories in Bandung. This education provided: a lecture on the signs and symptoms of dengue and ways to prevent the disease, posters in the health clinic at each factory and handouts given to each volunteer with an explanation of symptoms.

Influenza surveillance in Indonesia: 1999-2003.

Although influenza is recognized for its worldwide importance, little is known about the disease from tropical countries like Indonesia. From August 1999 through January 2003, a surveillance study was conducted in clinics at 6 sentinel locations. Adults (age, >14 years) and children (age, 4-14 years) presenting with respiratory symptoms suggestive of influenza were asked to enroll in the study.

Formation of 4,4'-dimethoxytrityl-C-phosphonate oligonucleotides.

Incomplete sulfurization during solid-phase synthesis of phosphorothioate oligonucleotides using phosphoramidite chemistry was identified as the cause of formation of two new classes of process-related oligonucleotide impurities containing a DMTr-C-phosphonate (DMTr=4,4'-dimethoxytrityl) moiety. Phosphite triester intermediates that failed to oxidize (sulfurize) to the corresponding phosphorothioate triester react during the subsequent acid-induced (dichloroacetic acid) detritylation with the DMTr cation or its equivalent in an Arbuzov-type reaction. This leads to formation of DMTr-C-phosphonate mono- and diesters resulting in oligonucleotides modified with a DMTr-C-phosphonate moiety located internally or at the 5'terminal hydroxy group.