Study of vaporization of sodium metaborate by transpiration thermogravimetry and Knudsen effusion mass spectrometry

The vaporization of solid sodium metaborate NaBO(2)(s) was studied by transpiration thermogravimetry (TTG) and Knudsen effusion mass spectrometry (KEMS). The transpiration measurements, performed for the first time on NaBO(2)(s), involved use of argon as the carrier gas for vapor transport and derivation of vapor pressure of NaBO(2)(g) (by assuming it as the sole vapor species) through many flow-dependence runs and temperature-dependence runs in the temperature range 1075-1218 K. The KEMS measurements performed in the temperature range 1060-1185 K confirmed NaBO(2)(g) as the principal vapor species over NaBO(2)(s), in accord with the previously reported KEMS studies. The values of p(NaBO(2)) obtained by both TTG and KEMS are consistent within the uncertainties associated with each method and so are the second- and third-law values of enthalpy of sublimation, the latter aspect consistently missing in all previous vaporization studies. The results of both TTG and KEMS were combined to recommend the following thermodynamic parameters pertinent to the sublimation reaction, NaBO(2)(s) = NaBO(2)(g): Log{p(NaBO(2))/Pa} = -(17056 ± 441)/(T/K) + (14.73 ± 0.35) for the temperature range 1060-1218 K; Δ(r)H°(m)(298.15 K) = (346.3 ± 9.4) kJ·mol(-1); and Δ(r)S°(m)(298.15 K) = (210.2 ± 6.8) J·mol(-1)·K(-1).

Stenotrophomonas maltophilia causing early onset neonatal sepsis

Stenotrophomonas maltophilia, a multi drug resistant non fermenting Gram negative bacillus is an increasingly common nosocomial pathogen, especially in intensive care units. Comparatively few cases of infection have been reported in neonatal population. We present two cases of early onset neonatal sepsis due to S.maltophilia and a brief review of documented isolation in neonates.

Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC

RSC (remodel the structure of chromatin) is an essential chromatin remodeler of Saccharomyces cerevisiae that has been shown to have DNA translocase properties. We studied the DNA binding properties of a "trimeric minimal RSC" (RSCt) of the RSC chromatin remodeling complex and the effect of nucleotides on this interaction using fluorescence anisotropy. RSCt binds to 20 bp fluorescein-labeled double-stranded DNA with a K(d) of ∼100 nM. The affinity of RSCt for DNA is reduced in the presence of AMP-PNP and ADP in a concentration-dependent manner with the addition of AMP-PNP having more pronounced effect. These differences in the magnitude at which the binding of ADP and AMP-PNP affects the affinity of DNA binding by RSCt suggest that the physical movement of the enzyme along DNA begins between the binding of ATP and its subsequent hydrolysis. Furthermore, the fact that the highest affinity for DNA binding by RSCt occurs in the absence of bound nucleotide offers a mechanistic explanation for the apparent low processivity of DNA translocation by the enzyme.

One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes?

The TATA-binding protein (TBP) is a major target for transcriptional regulation. Mot1, a Swi2/Snf2-related ATPase, dissociates TBP from DNA in an ATP dependent process. The experimental advantages of this relatively simple reaction have been exploited to learn more about how Swi2/Snf2 ATPases function biochemically. However, many unanswered questions remain and fundamental aspects of the Mot1 mechanism are still under debate. Here, we review the available data and integrate the results with structural and biochemical studies of related enzymes to derive a model for Mot1's catalytic action consistent with the broad literature on enzymes in this family. We propose that the Mot1 ATPase domain is tethered to TBP by a flexible, spring-like linker of alpha helical hairpins. The linker juxtaposes the ATPase domain such that it can engage duplex DNA on one side of the TBP-DNA complex. This allows the ATPase to employ short-range, nonprocessive ATP-driven DNA tracking to pull or push TBP off its DNA site. DNA translocation is a conserved property of ATPases in the broader enzyme family. As such, the model explains how a structurally and functionally conserved ATPase domain has been put to use in a very different context than other enzymes in the Swi2/Snf2 family. This article is part of a Special Issue entitled:Snf2/Swi2 ATPase structure and function.

The RSC chromatin remodelling ATPase translocates DNA with high force and small step size

ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to reposition and reconfigure nucleosomes. Despite their diverse functions, all remodellers share highly conserved ATPase domains, many shown to translocate DNA. Understanding remodelling requires biophysical knowledge of the DNA translocation process: how the ATPase moves DNA and generates force, and how translocation and force generation are coupled on nucleosomes. Here, we characterize the real-time activity of a minimal RSC translocase 'motor' on bare DNA, using high-resolution optical tweezers and a 'tethered' translocase system. We observe on dsDNA a processivity of ∼35 bp, a speed of ∼25 bp/s, and a step size of 2.0 (±0.4, s.e.m.) bp. Surprisingly, the motor is capable of moving against high force, up to 30 pN, making it one of the most force-resistant motors known. We also provide evidence for DNA 'buckling' at initiation. These observations reveal the ATPase as a powerful DNA translocating motor capable of disrupting DNA-histone interactions by mechanical force.

RNA synthesis precision is regulated by preinitiation complex turnover

TATA-binding protein (TBP) nucleates the assembly of the transcription preinitiation complex (PIC), and although TBP can bind promoters with high stability in vitro, recent results establish that virtually the entire TBP population is highly dynamic in yeast nuclei in vivo. This dynamic behavior is surprising in light of models that posit that a stable TBP-containing scaffold facilitates transcription reinitiation at active promoters. The dynamic behavior of TBP is a consequence of the enzymatic activity of the essential Snf2/Swi2 ATPase Mot1, suggesting that ensuring a highly mobile TBP population is critical for transcriptional regulation on a global scale. Here high-resolution tiling arrays were used to define how perturbed TBP dynamics impact the precision of RNA synthesis in Saccharomyces cerevisiae. We find that Mot1 plays a broad role in establishing the precision and efficiency of RNA synthesis: In mot1-42 cells, RNA length changes were observed for 713 genes, about twice the number observed in set2Δ cells, which display a previously reported propensity for spurious initiation within open reading frames. Loss of Mot1 led to both aberrant transcription initiation and termination, with prematurely terminated transcripts representing the largest class of events. Genetic and genomic analyses support the conclusion that these effects on RNA length are mechanistically tied to dynamic TBP occupancies at certain types of promoters. These results suggest a new model whereby dynamic disassembly of the PIC can influence productive RNA synthesis.

Pulmonary Scopulariopsis in a chronic tobacco smoker

A 70-year-old male smoker, with a three-month status of post-balloon angioplasty for ischaemic heart disease, presented with a one-week history of fever, haemoptysis and chest discomfort on coughing. The patient did not report any loss of weight or appetite. On examination, he was febrile. Pulmonary function tests revealed obstructive airway disease. High resolution computed tomography of the lungs revealed fibrosis with bronchiectasis in both the upper lobes, and a spiculating subpleural mass in the posterior aspect of the right lung apex. Subsequent bronchoalveolar lavage (BAL) culture yielded the Scopulariopsis species. Our patient was treated with a four-week course of amphotericin B, followed by itraconazole. At the 24-month follow-up, the patient was asymptomatic. Subsequent BAL cultures revealed no fungal growths, and radiological studies showed a regression in the lesion.

Influence of moisture content on physical properties of minor millets

Physical properties including 1000 kernel weight, bulk density, true density, porosity, angle of repose, coefficient of static friction, coefficient of internal friction and grain hardness were determined for foxtail millet, little millet, kodo millet, common millet, barnyard millet and finger millet in the moisture content range of 11.1 to 25% db. Thousand kernel weight increased from 2.3 to 6.1 g and angle of repose increased from 25.0 to 38.2°. Bulk density decreased from 868.1 to 477.1 kg/m(3) and true density from 1988.7 to 884.4 kg/m(3) for all minor millets when observed in the moisture range of 11.1 to 25%. Porosity decreased from 63.7 to 32.5%. Coefficient of static friction of minor millets against mild steel surface increased from 0.253 to 0.728 and coefficient of internal friction was in the range of 1.217 and 1.964 in the moisture range studied. Grain hardness decreased from 30.7 to 12.4 for all minor millets when moisture content was increased from 11.1 to 25% db.

Surface order and stability of langmuir-blodgett films

Angstrom-resolution atomic force microscope images of Langmuir-Blodgett monolayers and multilayers of cadmium arachidate in air and under water show a dramatic change from a disordered arrangement to a crystalline lattice by the addition or removal of a single layer of molecules. The disordered surface is less stable than the ordered one to mechanical stresses such as atomic force microscopy tip forces or at the air-water contact line during contact angle measurements. The difference in the degree of order in the alkyl chains is attributed to the strong attractive interaction between headgroups in the presence of the divalent cation.

Hydroxyapatite growth inhibition by osteopontin hexapeptide sequences

The effects of three acidic hexapeptides on in vitro hydroxyapatite growth were characterized by pH-stat kinetic studies, adsorption isotherms, and molecular modeling. The three peptides, pSDEpSDE, SDESDE, and DDDDDD, are equal-length model compounds for the acidic sequences in osteopontin, a protein that inhibits mineral formation in both calcified and noncalcified tissues. Growth rates from 1.67 mM calcium and 1.00 mM phosphate solution were measured at pH 7.4 and 37 degrees C in 150 mM NaCl. pSDEpSDE was a strong growth inhibitor when preadsorbed onto hydroxyapatite (HA) seeds from > or = 0.67 mM solutions, concentrations where adsorption isotherms showed relatively complete surface coverage. The nonphosphorylated SDESDE control showed no growth inhibition. Although it adsorbed to almost the same extent as pSDEpSDE, it rapidly desorbed under the pH-stat growth conditions while pSDEpSDE did not. DDDDDD exhibited weak inhibition as its concentration was increased and similar adsorption/desorption behavior to pSDEpSDE. Molecular modeling yielded binding energy trends based on simple adsorption of peptides on the [100] surface that were consistent with observed inhibition, but not for the [001] surface. The relatively unfavorable binding energies for peptides on the [001] surface suggest that their absorption will be primarily on the [100] face. The kinetic and adsorption data are consistent with phosphorylation of osteopontin acting to control mineral formation.

Identification of new variants of SCMV causing sugarcane mosaic in India and assessing their genetic diversity in relation to SCMV type strains

Sugarcane mosaic virus (SCMV) is one of the two causative viruses of mosaic in sugarcane, a sugar crop widely grown under tropical and subtropical conditions worldwide. Although molecular characterization of SCMV strains was reported from many countries, strains occurring in India, a major sugarcane producer have not been reported so far. Twenty-six sugarcane samples represented by seven major sugarcane growing states in India and USA were subjected to reverse-transcription polymerase chain reaction (RT-PCR) using a pair of newly designed coat protein specific primers. Among them 17 were found positive to the SCMV infection. The lengths of the sequences derived in this study using the new set of primers varied between 812 and 866 nt. The amino acid sequence comparison of 30 Indian SCMV isolates showed wide range of sequence similarities in core region (88.80-100%) and hyper variable region (51.3-100%). In the N-terminal region of the five Indian isolates, a deletion of 12 aa residues between aa 11 and 30 was observed, whereas the deletion was between aa 45 and 50 in SCMV-B and -D and between aa 61 and 70 in SCMV-A. The phylogenetic analyses performed with 46 SCMV CP sequences for both hyper variable region and core region separated the isolates mostly according to their geographical origin. The 30 Indian SCMV isolates were included exclusively in four groups besides SCMV-IND, which was grouped with SCMV-SC, a type of strain from Australia. Nearly 97.0% of the Indian isolates have no signs for close relationships with previously characterized SCMV type strains (SCMV-A, -B, -D, -E, and -SC) reported from other countries. Our studies revealed that the sugarcane mosaic in India are caused by at least nine new SCMV variants (IND-CC1, -CC2, -CC3, -CC4, -CO1, -CO2, -CP, -CS, and -J) and a type strain SCMV-SC represented by SCMV-IND. This is the first report on the variability and occurrence of new SCMV population in India.

Identification of three genotypes of sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization

Sugarcane yellow leaf virus (SCYLV) that causes yellow leaf disease (YLD) in sugarcane (recently reported in India) belongs to Polerovirus. Detailed studies were conducted to characterize the virus based on partial open reading frames (ORFs) 1 and 2 and complete ORFs 3 and 4 sequences in their genome. Reverse-transcriptase polymerase chain reaction (RT-PCR) was performed on 48 sugarcane leaf samples to detect the virus using a specific set of primers. Of the 48 samples, 36 samples (field samples with and without foliar symptoms) including 10 meristem culture derived plants were found to be positive to SCYLV infection. Additionally, an aphid colony collected from symptomatic sugarcane in the field was also found to be SCYLV positive. The amplicons from 22 samples were cloned, sequenced and acronymed as SCYLV-CB isolates. The nucleotide (nt) and amino acid (aa) sequence comparison showed a significant variation between SCYLV-CB and the database sequences at nt (3.7-5.1%) and aa (3.2-5.3%) sequence level in the CP coding region. However, the database sequences comprising isolates of three reported genotypes, viz., BRA, PER and REU, were observed with least nt and aa sequence dissimilarities (0.0-1.6%). The phylogenetic analyses of the overlapping ORFs (ORF 3 and ORF 4) of SCYLV encoding CP and MP determined in this study and additional sequences of 26 other isolates including an Indian isolate (SCYLV-IND) available from GenBank were distributed in four phylogenetic clusters. The SCYLV-CB isolates from this study lineated in two clusters (C1 and C2) and all the other isolates from the worldwide locations into another two clusters (C3 and C4). The sequence variation of the isolates in this study with the database isolates, even in the least variable region of the SCYLV genome, showed that the population existing in India is significantly different from rest of the world. Further, comparison of partial sequences encoding for ORFs 1 and 2 revealed that YLD in sugarcane in India is caused by at least three genotypes, viz., CUB, IND and BRA-PER, of which a majority of the samples were found infected with Cuban genotype (CUB) and lesser by IND and BRA-PER genotypes. The genotype IND was identified as a new genotype from this study, and this was found to have significant variation with the reported genotypes.