Benzene Forms Hydrogen Bonds with Water

Fully rotationally resolved spectra of three isotopic species of 1:1 clusters of benzene with water (H(2)O, D(2)O, and HDO) were fit to yield moments of inertia that demonstrate unambiguously that water is positioned above the benzene plane in nearly free internal rotation with both hydrogen atoms pointing toward the pi cloud. Ab initio calculations (MP2 level of electron correlation and 6-31 G(**) basis set with basis set superposition error corrections) predict a binding energy D(e) greater, similar 1.78 kilocalories per mole. In both the experimental and theoretical structures, water is situated nearly 1 angstrom within the van der Waals contacts of the monomers, a clear manifestation of hydrogen bond formation in this simple model of aqueous-pi electron interactions.

Cold plasma selectivity and the possibility of a paradigm shift in cancer therapy

Background:

Plasma is an ionised gas that is typically generated in high-temperature laboratory conditions. However, recent progress in atmospheric plasmas has led to the creation of cold plasmas with ion temperature close to room temperature.

Methods:

Both in-vitro and in-vivo studies revealed that cold plasmas selectively kill cancer cells.

Results:

We show that: (a) cold plasma application selectively eradicates cancer cells in vitro without damaging normal cells; and (b) significantly reduces tumour size in vivo. It is shown that reactive oxygen species metabolism and oxidative stress responsive genes are deregulated.

Conclusion:

The development of cold plasma tumour ablation has the potential of shifting the current paradigm of cancer treatment and enabling the transformation of cancer treatment technologies by utilisation of another state of matter.

Hypertonic stress induces alpha B-crystallin expression

Alpha B-crystallin, a major lens protein, was induced in primary cultures of dog lens epithelial cells and glomerular endothelial cells when they were grown under conditions of hypertonic stress. With Western blot analysis using a specific alpha B-crystallin antibody, we observed a significant increase in the concentration of alpha B-crystallin protein in cells grown for 4-6 days in media supplemented with 150 mM NaCl or 250 mM cellobiose. These supplements increased the osmolarity of the medium from 300 to 550-600 mosmol kg-1. Alpha B-crystallin mRNA was also increased reaching a maximum four-fold increase in lens and 16-fold increase in kidney cells within 1-2 days. These studies demonstrate a type of regulation of alpha B-crystallin expression in cells from lenticular and non-lenticular tissues.

Troger's base molecular scaffolds in dicarboxylic acid recognition

Artificial receptors (1-5) have been designed and synthesized from simple precursors. The chain length selectivity studies of dicarboxylic acids within the cavities of new fluorescent Troger's base molecular frameworks (1-3) have been carried out with a critical examination of their role of rigidity as well as flexibility in selective binding in comparison to receptor 5. The chiral resolution of the racemic Troger's base receptors (1 and 2) by chiral recognition with (+)- camphoric acid using hydrogen-bonding interactions has been studied.

Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers

A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contracts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue-residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue-residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy.

Multiple mechanisms for initiation of ColE1 DNA replication: DNA synthesis in the presence and absence of ribonuclease H

A transcript (RNA II) of plasmid ColE1 that hybridizes with the template DNA is cleaved by RNAase H and used as a primer by DNA polymerase I. However, the plasmid can replicate in bacteria lacking both enzymes, apparently using a different mechanism of initiation of replication. Here we report in vivo and in vitro studies on initiation of DNA replication in the presence or absence of either or both enzymes. Hybridization of RNA II with the template DNA is always required for initiation. Hybridized RNA II is cleaved by RNAase H to form a primer or used as a primer without cleavage by RNAase H. Hybridization also creates a single-stranded region on the nontranscribed strand that can serve as a template for synthesis of the lagging strand in a reaction that does not require DNA polymerase I. Lagging strand synthesis terminates 17 nucleotides upstream of the normal replication origin, forcing unidirectional replication.

Cell cycle arrest in Era GTPase mutants: a potential growth rate-regulated checkpoint in Escherichia coli

Era is a low-molecular-weight GTPase essential for Escherichia coli viability. The gene encoding Era is found in the rnc operon, and the synthesis of both RNase III and Era increases with growth rate. Mutants that are partially defective in Era GTPase activity or that are reduced in the synthesis of wild-type Era become arrested in the cell cycle at the predivisional two-cell stage. The partially defective Era GTPase mutation (era1) suppresses several temperature-sensitive lethal alleles that affect chromosome replication and chromosome partitioning but not cell division. Our results suggest that Era plays an important role in cell cycle progression at a specific point in the cycle, after chromosome partitioning but before cytokinesis. Possible functions for Era in cell cycle progression and the initiation of cell division are discussed.

The natural history of Niemann-Pick disease type C in the UK

Niemann-Pick disease type C (NPC) is an autosomal recessive, neurovisceral lipid storage disorder. Mutations in two genes (NPC1 and NPC2) produce indistinguishable clinical phenotypes by biochemical mechanisms that have not yet been entirely clarified. The wide spectrum of clinical presentations of NPC includes hepatic and pulmonary disease as well as a range of neuropsychiatric disorders. Late-onset disease has been increasingly recognized as the biochemical diagnosis of NPC has been more widely applied in adult neurology clinics. The clinical presentation and follow-up of 94 patients with NPC is described, 58 of whom were still alive at the time this report was prepared. The age at diagnosis ranged from the prenatal period (with hydrops fetalis) up to 51 years. This review of NPC patients in the UK confirms the phenotypic variability of this inherited lipid storage disorder reported elsewhere. Although a non-neuronopathic variant has been described, most patients in this series who survived childhood inevitably suffered neurological and in some cases neuropsychiatric deterioration. While symptomatic treatment, such as anticholinergic and antiepileptic drugs, can alleviate some aspects of the disease, there is a clear need to develop a specific treatment for this progressively debilitating neurodegenerative disorder.

Mutual suppression of mukB and seqA phenotypes might arise from their opposing influences on the Escherichia coli nucleoid structure

A strain of Escherichia coli in which both the seqA and mukB genes were inactivated displayed partial suppressions of their individual phenotypes. Temperature sensitivity, anucleate cell production and poor nucleoid folding seen in the mukB strain were suppressed by the seqA null mutation, whereas filamentation, asymmetric septation and compact folding of the nucleoids observed in the seqA strain were suppressed by inactivation of the mukB gene function. However, the asynchronous initiation of chromosome replication in the seqA strain was not reversed in the mukBseqA double mutant. Membrane-associated nucleoids were isolated from the wild-type, mukB, seqA and mukBseqA strains and their sedimentation rates were compared under identical conditions. Whereas the mukB mutation caused unfolding of the nucleoid, the seqA mutation led to a more compact packaging of the chromosome. The mukBseqA double mutant regained the wild-type nucleoid organization as revealed from its rate of sedimentation. Microscopic appearances of the nucleoids were consistent with the sedimentation profiles. The mukB mutant was oversensitive to novobiocin and this susceptibility was suppressed in the mukBseqA strain, suggesting possible roles of MukB and SeqA in maintaining chromosome topology. The mutual phenotypic suppression of mukB and seqA alleles thus suggests that these genes have opposing influences on the organization of the bacterial nucleoid.

Indoor air quality for poor families: new evidence from Bangladesh

Poor households in Bangladesh depend heavily on wood, dung and other biomass fuels for cooking. This paper provides a detailed analysis of the implications for indoor air pollution (IAP), drawing on new 24-h monitoring data for respirable airborne particulates (PM10). A stratified sample of 236 households was selected in Dhaka and Narayanganj, with a particular focus on fuel use, cooking locations, structural materials, ventilation practices, and other potential determinants of exposure to IAP. At each household, PM10 concentrations in the kitchen and living room were monitored for a 24-h period during December, 2003-February, 2004. Concentrations of 300 microg/m3 or greater are common in our sample, implying widespread exposure to a serious health hazard. A regression analysis for these 236 households was then conducted to explore the relationships between PM10 concentrations, fuel choices and a large set of variables that describe household cooking and ventilation practices, structure characteristics and building materials. As expected, our econometric results indicate that fuel choice significantly affects indoor pollution levels: natural gas and kerosene are significantly cleaner than biomass fuels. However, household-specific factors apparently matter more than fuel choice in determining PM10 concentrations. In some biomass-burning households, concentrations are scarcely higher than in households that use natural gas. Our results suggest that cross-household variation is strongly affected by structural arrangements: cooking locations, construction materials, and ventilation practices. A large variation in PM10 was also found during the 24-h cycle within households. For example, within the 'dirtiest' firewood-using household in our sample, readings over the 24-h cycle vary from 68 to 4864 microg/m3. Such variation occurs because houses can recycle air very quickly in Bangladesh. After the midday meal, when ventilation is common, air quality in many houses goes from very dirty to reasonably clean within an hour. Rapid change also occurs within households: diffusion of pollution from kitchens to living areas is nearly instantaneous in many cases, regardless of internal space configuration, and living-area concentrations are almost always in the same range as kitchen concentrations. By implication, exposure to dangerous indoor pollution levels is not confined to cooking areas. To assess the broader implications for poor Bangladeshi households, we extrapolate our regression results to representative 600 household samples from rural, peri-urban and urban areas in six regions: Rangpur in the north-west, Sylhet in the north-east, Rajshahi and Jessore in the west, Faridpur in the center, and Cox's Bazar in the south-east. Our results indicate great geographic variation, even for households in the same per capita income group. This variation reflects local differences in fuel use and, more significantly, construction practices that affect ventilation. For households with per capita income <US Dollars 1.00/day, rural PM10 concentrations vary from 410 microg/m3 in Cox's Bazar to 202 microg/m3 in Faridpur. In urban areas, concentrations for such households differ by almost 100 microg/m3 between the highest areas, Jessore and Rajshahi, and the lowest, Sylhet. Practical Implications Our analysis suggests that poor families may not have to wait for clean fuels or clean stoves to enjoy significantly cleaner air. Within our sample household population, some arrangements are already producing relatively clean conditions, even when 'dirty' biomass fuels are used, such as simple changes in ventilation characteristics of housing (construction materials, space configurations, cooking locations and placement of doors and windows) and ventilation behavior (keeping doors and windows open after cooking). As these arrangements are already within the means of poor families, the scope for cost-effective improvements may be larger than is commonly believed.

Genetic uncoupling of the dsRNA-binding and RNA cleavage activities of the Escherichia coli endoribonuclease RNase III--the effect of dsRNA binding on gene expression

RNase III, a double-stranded RNA-specific endonuclease, is proposed to be one of Escherichia coli's global regulators because of its ability to affect the expression of a large number of unrelated genes by influencing post-transcriptional control of mRNA stability or mRNA translational efficiency. Here, we describe the phenotypes of bacteria carrying point mutations in rnc, the gene encoding RNase III. The substrate recognition and RNA-processing properties of mutant proteins were analysed in vivo by measuring expression from known RNase III-modulated genes and in vitro from the proteins' binding and cleavage activities on known double-stranded RNA substrates. Our results show that although the point mutation rnc70 exhibited all the usual rnc null-like phenotypes, unlike other mutations, it was dominant over the wild-type allele. Multicopy expression of rnc70 could suppress a lethal phenotype of the wild-type rnc allele in a certain genetic background; it could also inhibit the RNase III-mediated activation of lambdaN gene translation by competing for the RNA-binding site of the wild-type endonuclease. The mutant protein failed to cleave the standard RNase III substrates in vitro but exhibited an affinity for double-stranded RNA when passed through poly(rI):poly(rC) columns. Filter binding and gel-shift assays with purified Rnc70 showed that the mutant protein binds to known RNase III mRNA substrates in a site-specific manner. In vitro processing reactions with purified enzyme and labelled RNA showed that the in vivo dominant effect of the mutant enzyme over the wild-type was not necessarily caused by formation of mixed dimers. Thus, the rnc70 mutation generates a mutant RNase III with impaired endonucleolytic activity but without blocking its ability to recognize and bind double-stranded RNA substrates.

Intracellular trafficking pathway of newly synthesized CD1b molecules

The intracellular trafficking of major histocompatibility complex (MHC) class I and class II molecules has evolved to support their function in peptide antigen presentation optimally. We have analyzed the intracellular trafficking of newly synthesized human CD1b, a lipid antigen-presenting molecule, to understand how this relates to its antigen-presenting function. Nascent CD1b was transported rapidly to the cell surface after leaving the Golgi, and then entered the endocytic system by internalization via AP-2-dependent sorting at the plasma membrane. A second sorting event, possibly involving AP-3 complexes, led to prominent accumulation of CD1b in MHC class II compartments (MIICs). Functional studies demonstrated the importance of nascent CD1b for the efficient presentation of a foreign lipid antigen. Therefore, the intracellular trafficking of nascent CD1b via the cell surface to reach MIICs may allow the efficient sampling of lipid antigens present in endocytic compartments.

Adenosine A2A receptors modulate the binding characteristics of dopamine D2 receptors in stably cotransfected fibroblast cells

In membrane preparations from rat striatum, where adenosine A2A and dopamine D2 receptors are coexpressed, stimulation of adenosine A2A receptors was found to decrease the affinity of dopamine D2 receptors for dopamine agonists. We now demonstrate the existence of this antagonistic interaction in a fibroblast cell line (Ltk-) stably transfected with the human dopamine D2 (long-form) receptor and the dog adenosine A2A receptor cDNAs (A2A-D2 cells). In A2A-D2 cells, but not in control cells only containing dopamine D2 receptors (D2 cells), the selective adenosine A2A agonist 2-[p-(2-carboxyethyl)-phenethylamino]-5'-N-ethyl-carboxamido adenosine (CGS 21680) induced a 2-3-fold decrease in the affinity of dopamine D2 receptors for dopamine, as shown in competition experiments with dopamine versus the selective dopamine D2 antagonist [3H]raclopride. By contrast, activation of the constitutively expressed adenosine A2B receptors with 5'-N-ethyl-carboxamidoadenosine (NECA) did not modify dopamine D2 receptor binding. In A2A-D2 cells CGS 21680 failed to induce or induced only a small increase in adenosine-3',5'-cyclic-monophosphate (cAMP) accumulation. In D2 cells NECA- or forskolin-induced adenylyl cyclase activation was not associated with any change in dopamine D2 receptor binding. These results indicate that adenylyl cyclase activation is not involved in the adenosine A2A receptor-mediated modulation of the binding characteristics of the dopamine D2 (long-form) receptor.

Shuttle cosmid vectors for the trypanosomatid parasite Leishmania

We have developed two shuttle cosmid vectors for the trypanosomatid protozoan parasite Leishmania. Cosmids cLHYG and cLNEO contain hyg and neo markers, conferring resistance to hygromycin B and G418, respectively, replicate extrachromosomally after transfection into promastigotes, and bear a unique BamHI cloning site. To ensure the representation of telomeric sequences, which represent about 5% of the Leishmania genome, random insert DNAs were prepared by shearing followed by blunt-end ligation with BamHI adapters. Representative genomic libraries from Leishmania species representing the four major pathogenic complexes were prepared using cosmid cLHYG. The cosmid libraries were efficiently transfected into Leishmania, and individual cosmids were readily recovered by transformation back into Escherichia coli. The relatively small size of the Leishmania genome (50 Mb) combined with the capacity and transfection efficiency of these cosmid libraries (> 1000 Leishmania transfectants/plate) suggests the feasibility of functional genetic complementation in this parasite.

Escherichia coli cell cycle control genes affect chromosome superhelicity

We have used ethidium bromide titration for direct measurement of the changes in the negative supercoiling of Escherichia coli chromosome caused by mutations inactivating the cell cycle functions mukB and seqA. The amounts of the intercalative agent required to relax the supercoiled chromosome in mukB and seqA mutants were lower and higher, respectively, than for the wild-type parent, confirming that these cell cycle genes modulate the topology of the E. coli chromosome. Plasmid superhelicity measured in these mutant strains showed similar effects albeit of reduced magnitude. As the effects of mukB and seqA mutations were not restricted to the chromosome alone, MukB and SeqA proteins possibly interact with factors involved in the maintenance of intracellular DNA topology. To our knowledge, this is the first direct demonstration of the influence of mukB and seqA genes on the superhelicity of the E. coli chromosome.

Mapping of the candidate tumor suppressor genes' loci on human chromosome 3 in head and neck squamous cell carcinoma of an Indian patient population

The candidate tumor suppressor genes' (TSG) loci on human chromosome 3 (chr.3) were mapped in six dysplastic lesions and 51 primary squamous cell carcinoma from head and neck region of an Indian patient population by using 20 highly polymorphic microsatellite markers. The two chromosomal regions 3p12-13 and 3p21.2-22 have shown the highest losses of heterozygosity (LOHs) of 34.6-38% and 37-46%, respectively with statistically significant clinical correlation's with tobacco habit, positive lymph node and tumor stages. In addition, high frequencies of microsatellite size alterations (MAs) of 16.2-28.5% and 23.8-28.2% were observed in the chromosomal 3p11-13 and 3p21.2-22 regions, respectively, with significant above-mentioned clinical correlation only in the 3p11-13 region. In the dysplastic lesions, the prevalence of LOHs compared to the MAs had indicated that LOHs might be the early events. Five tumors at stage-III/IV seemed to have lost an entire normal copy of chr.3. It was of particular note that 17% (10/57) of the samples showed rare bi-allelic alterations mainly in and around the high LOHs regions. Thus, (1) the gradual increase of LOHs/MAs during progression of the tumor, (2) high frequencies of MAs, (3) rare bi-allelic alterations in and around high LOHs regions and (4) loss of wild type chr.3 in the later stages of tumor development have suggested that such alterations might provide selective growth advantage to the tumors. Also, we propose from our data that the high LOHs regions (3p12-13 and 3p21.2-22) could harbour putative TSG(s), responsible for the development of head and neck squamous cell carcinoma.

Guaranteed convergence in a class of Hopfield networks

A class of symmetric Hopfield networks with nonpositive synapses and zero threshold is analyzed in detail. It is shown that all stationary points have a one-to-one correspondence with the minimal vertex covers of certain undirected graphs, that the sequential Hopfield algorithm as applied to this class of networks converges in at most 2n steps (n being the number of neurons), and that the parallel Hopfield algorithm either converges in one step or enters a two-cycle in one step. The necessary and sufficient condition on the initial iterate for the parallel algorithm to converge in one step are given. A modified parallel algorithm which is guaranteed to converge in [3n/2] steps ([x] being the integer part of x) for an n-neuron network of this particular class is also given. By way of application, it is shown that this class naturally solves the vertex cover problem. Simulations confirm that the solution provided by this method is better than those provided by other known methods.

Splenic marginal zone antigen-presenting cells are critical for the primary allo-immune response to therapeutic factor VIII in hemophilia A

BACKGROUND

Alloimmune responses to intravenously administered protein therapeutics are the most common cause of failure of replacement therapy in patients with defective levels of endogenous proteins. Such a situation is encountered in some patients with hemophilia A, who develop inhibitory anti-factor (F)VIII alloantibodies after administration of FVIII to treat hemorrhages.

OBJECTIVES

The nature of the secondary lymphoid organs involved in the initiation of immune responses to human therapeutic has not been studied. We therefore investigated this in the case of FVIII, a self-derived exogenous protein therapeutic.

METHODS

The distribution of intravenously administered FVIII was followed after FVIII-deficient mice were injected with radiolabeled FVIII and using immunohistochemistry. The role of the spleen and antigen-presenting cells (APC) in the onset of the anti-FVIII immune response was analyzed upon splenectomy or treatment of the mice with APC-depleting compounds.

RESULTS

FVIII preferentially accumulated in the spleen at the level of metallophilic macrophages in the marginal zone (MZ). Surgical removal of the spleen or selective in vivo depletion of macrophages and CD11c-positive CD8 alpha-negative dendritic cells resulted in a drastic reduction in anti-FVIII immune responses.

CONCLUSIONS

Using FVIII-deficient mice as a model for patients with hemophilia A, and human pro-coagulant FVIII as a model for immunogenic self-derived protein therapeutics, our results highlight the importance of the spleen and MZ APCs in the initiation of immune responses to protein therapeutics. Identification of the receptors implicated in retention of protein therapeutics in the MZ may pave the way towards novel strategies aimed at reducing their immunogenicity.

The predicted amino acid sequence of a centrosphere protein in dividing sea urchin eggs is similar to elongation factor (EF-1 alpha)

Monoclonal antibody (SU5), prepared from isolated mitotic spindles of sea urchin eggs, stained centrospheres preferentially and recognized a 50K (K = 10(3) Mr) polypeptide on immunoblots. Three positive clones were isolated by screening a lambda gt11 cDNA expression library prepared from sea urchin egg mRNA with SU5. One clone containing a 1.8-kb (1 kb = 10(3) base-pairs) insert was selected for further characterization. The beta-galactosidase fusion protein encoded by the cDNA clone had an apparent relative molecular mass of 150K, indicating that the inserted cDNA produced an estimated 34K of polypeptide. A single 2.2-kb RNA transcript was detected in sea urchin embryos using the cDNA clone as a probe. The cDNA fragment was sequenced and the nucleotide sequence was used to predict the amino acid sequence of the open reading frames in the clone. The putative gene product shows striking similarity to the peptide chain elongation factor (EF-1 alpha) from yeast, fungus, shrimp, insect, mouse and human.