The Gene Ontology (GO) database and informatics resource

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

Bacteria growing under different conditions experience a broad range of demand on the rate of protein synthesis, which profoundly affects cellular resource allocation. During fast growth, protein synthesis has long been known to be modulated by adjusting the ribosome content, with the vast majority of ribosomes engaged at a near-maximal rate of elongation. Here, we systematically characterize protein synthesis by Escherichia coli, focusing on slow-growth conditions. We establish that the translational elongation rate decreases as growth slows, exhibiting a Michaelis-Menten dependence on the abundance of the cellular translational apparatus. However, an appreciable elongation rate is maintained even towards zero growth, including the stationary phase. This maintenance, critical for timely protein synthesis in harsh environments, is accompanied by a drastic reduction in the fraction of active ribosomes. Interestingly, well-known antibiotics such as chloramphenicol also cause a substantial reduction in the pool of active ribosomes, instead of slowing down translational elongation as commonly thought.

The burden of smoking-related ill health in the UK

BACKGROUND

Smoking is one of the biggest avoidable causes of morbidity and mortality in the United Kingdom. This paper quantifies the current health and economic burden of smoking in the UK. It provides comparisons with previous studies of the burden of smoking in the UK and with the costs for other chronic disease risk factors.

METHODS

A systematic literature review to identify previous estimates of National Health Service costs attributable to smoking was undertaken. Information from the World Health Organization's Global Burden of Disease Project and routinely collected mortality data were used to calculate mortality due to smoking in the UK. Population-attributable fractions for smoking-related diseases from the Global Burden of Disease Project were applied to NHS cost data to estimate direct financial costs.

RESULTS

Previous studies estimated that smoking costs the NHS about 1.4 billion to 1.7 billion pound in 1991 and has been responsible for about 100,000 deaths per annum over the past 10 years. This paper estimates that the number of deaths attributable to smoking in 2005 was 109,164 (19% of all deaths, 27% deaths in men and 11% of deaths in women). Smoking was directly responsible for 12% of disability adjusted life years lost in 2002 (15.4% in men; 8.5% in women) and the direct cost to the NHS was 5.2 billion pound in 2005-6.

CONCLUSION

Smoking is still a considerable public health burden in the UK. Accurately establishing the burden in terms of death, disability and financial costs is important for informing national public health policy.

RUPTURE OF PATELLAR LIGAMENT AFTER STEROID INFILTRATION

1. A case of disruption of patellar ligament is described.

2. An association with previous steroid infiltration is present in this case.

Reverse engineering the (beta/alpha )8 barrel fold

The (beta/alpha)(8) barrel is the most commonly occurring fold among protein catalysts. To lay a groundwork for engineering novel barrel proteins, we investigated the amino acid sequence restrictions at 182 structural positions of the prototypical (beta/alpha)(8) barrel enzyme triosephosphate isomerase. Using combinatorial mutagenesis and functional selection, we find that turn sequences, alpha-helix capping and stop motifs, and residues that pack the interface between beta-strands and alpha-helices are highly mutable. Conversely, any mutation of residues in the central core of the beta-barrel, beta-strand stop motifs, and a single buried salt bridge between amino acids R189 and D227 substantially reduces catalytic activity. Four positions are effectively immutable: conservative single substitutions at these four positions prevent the mutant protein from complementing a triosephosphate isomerase knockout in Escherichia coli. At 142 of the 182 positions, mutation to at least one amino acid of a seven-letter amino acid alphabet produces a triosephosphate isomerase with wild-type activity. Consequently, it seems likely that (beta/alpha)(8) barrel structures can be encoded with a subset of the 20 amino acids. Such simplification would greatly decrease the computational burden of (beta/alpha)(8) barrel design.

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.

Binding of the origin of replication of Escherichia coli to the outer membrane

The replication origin of the Escherichia coli chromosome binds with high affinity to outer membrane preparations. This binding requires a 460 bp stretch of origin DNA between positions -40 and 420 of the oriC map. Specific binding can be detected by the use of a membrane filter retention assay in the presence of excess calf thymus DNA. This binding is enhanced by divalent cations and takes place specifically at a few (0.7-3.0) membrane sites per cell. The apparent affinity of origin DNA for membranes is enhanced by two peptides, (55 kilodaltons (kd) and 75 kd), which remain attached to the DNA through treatment with 5.5 M cesium chloride.

The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli

LepA is a paralog of EF-G found in all bacteria. Deletion of lepA confers no obvious growth defect in Escherichia coli, and the physiological role of LepA remains unknown. Here, we identify nine strains (ΔdksA, ΔmolR1, ΔrsgA, ΔtatB, ΔtonB, ΔtolR, ΔubiF, ΔubiG or ΔubiH) in which ΔlepA confers a synthetic growth phenotype. These strains are compromised for gene regulation, ribosome assembly, transport and/or respiration, indicating that LepA contributes to these functions in some way. We also use ribosome profiling to deduce the effects of LepA on translation. We find that loss of LepA alters the average ribosome density (ARD) for hundreds of mRNA coding regions in the cell, substantially reducing ARD in many cases. By contrast, only subtle and codon-specific changes in ribosome distribution along mRNA are seen. These data suggest that LepA contributes mainly to the initiation phase of translation. Consistent with this interpretation, the effect of LepA on ARD is related to the sequence of the Shine–Dalgarno region. Global perturbation of gene expression in the ΔlepA mutant likely explains most of its phenotypes.

The role of antennal sensory cues in female responses to courting males in the cricket Teleogryllus oceanicus

Courtship communication in the field cricket Teleogryllus oceanicus is multimodal, involving a minimum of both acoustic and chemical cues. The acoustic signal, or courtship song, is necessary to elicit normal levels of female mounting of the male during courtship. Antennal input is also crucial since antennectomized females show highly reduced levels of mounting. Immobilization of the scape­pedicel and pedicel­flagellum joints of female antennae had no effect on mounting probability, suggesting that mechanosensory input from chordotonal organs at the base of the antenna is not necessary. The antennal flagellum is a multimodal sensory organ, which contains both mechanoreceptors and chemoreceptors. In order to dissect the roles of different flagellar modalities, we treated antennae with zinc sulphate. This suppressed a well-characterized contact-chemosensory behaviour, initiation of courtship by males, and eliminated responsiveness of most chemosensory hairs as assayed electrophysiologically. Zinc sulphate treatment had no effect on a tactile antennal reflex, indicating that it selectively silenced chemoreceptors. Treatment of antennae with zinc sulphate reduced mounting levels nearly as much as antennectomy, suggesting that the main antennal cue required for the mounting responses is chemosensory, rather than mechanosensory, in nature.

Paromomycin and geneticin inhibit intracellular Cryptosporidium parvum without trafficking through the host cell cytoplasm: implications for drug delivery

Cryptosporidium parvum, which causes intractable diarrhea and lethal wasting in people with AIDS, occupies an unusual intracellular but extracytoplasmic niche. No reliable therapy for cryptosporidiosis exists, though the aminoglycoside paromomycin is somewhat effective. We report that paromomycin and the related compound geneticin manifest their major in vitro anti-C. parvum activity against intracellular parasites via a mechanism that does not require drug trafficking through the host cell cytoplasm. We used both normal and transformed aminoglycoside-resistant Caco-2 or MDBK cells in these studies. Timed-exposure experiments demonstrated that these drugs inhibit intracellular but not extracellular parasites. Apical but not basolateral exposure of infected cells to these drugs led to very significant parasite inhibition, indicating an apical topological restriction of action. We estimated intracytoplasmic concentrations of paromomycin, using an intracellular bacterial killing assay, and found that C. parvum infection did not lead to increased paromomycin concentrations compared to those in uninfected cells. Global [3H]paromomycin uptake by Caco-2 cells was approximately 200-fold higher than the estimated intracytoplasmic paromomycin concentration, suggestive of host cell vesicular uptake and concentration (as has been reported with other cell lines). However, preinfection exposure of Caco-2 cells to paromomycin did not result in subsequent inhibition of parasite development, indicating that if exogenous paromomycin enters the infected host cell vesicular compartment, it does not effectively communicate with the parasite. Thus, the apical membranes overlying the parasite and parasitophorous vacuole may be the unsuspected major route of entry for paromomycin and may be of importance in the design and discovery of novel drug therapies for the otherwise untreatable C. parvum.

Dual ectopic thyroid: a report of two cases

Ectopic thyroid is an uncommon embryological aberration characterized by the presence of thyroid tissue at a site other than in its usual pretracheal region. Usually it occurs along the path of descent of the developing thyroid primodium from the foramen caecum, commonest being lingual followed by sublingual and in the anterior midline of neck at, or below, the level of the hyoid bone. It is unusual for lingual thyroid to present simultaneously with another ectopic thyroid; reported here are two such cases.

Cellular perception of growth rate and the mechanistic origin of bacterial growth law

Many cellular activities in bacteria are organized according to their growth rate. The notion that ppGpp measures the cell’s growth rate is well accepted in the field of bacterial physiology. However, despite decades of interrogation and the identification of multiple molecular interactions that connects ppGpp to some aspects of cell growth, we lack a system-level, quantitative picture of how this alleged “measurement” is performed. Through quantitative experiments, we show that the ppGpp pool responds inversely to the rate of translational elongation in Escherichia coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole.

Song pattern recognition in the grasshopper Chorthippus biguttulus: the mechanism of syllable onset and offset detection

The male song of the duetting grasshopper Chorthippus biguttulus consists of syllables alternating with noisy pauses. The syllable-pause structure is important for song recognition by the female. Using playback experiments we investigated the mechanism by which intensity modulations within the song pattern are used to detect syllable onsets and offsets. We varied the relative onset level (level of the syllable beginning relative to the noisy pause) and the relative offset level (level of the noisy pause relative to the syllable end) independently in different experiments. For all females, an increase in intensity defining the syllable onset was necessary to evoke responses. Syllable offset cues were not always necessary: some females responded to continuous noise stimuli wherein only syllable onsets were marked by short pulses of high intensity. Those females that did not require syllable offset cues did not, however, lack a functional pause detection mechanism, since their responses to model songs containing silent pauses were restricted to a given range of pause durations. We propose that syllable-pause detection involves two independent processes: (1) syllable onset detection by a phasic neuronal unit that can be re-activated only after a short pause, and (2) the rejection of unacceptably long pauses by a second unit.

Allele and genotype frequency of CYP2C9 in Tamilnadu population

OBJECTIVES

To identify the frequency of CYP2C9*1, *2 and *3 alleles and the genotype of CYP2C9 gene in the Tamilian population.

METHODS

The study was conducted on 135 unrelated healthy human volunteers. DNA was extracted from the peripheral leukocytes samples and was analyzed using the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) protocol. The PCR products were digested with AvaII, KpnI or NsiI restriction enzymes. The digested products were separated using 8% polyacrylamide gel and stained by ethidium bromide. Genotyping of the subjects was done based on DNA fragment size.

RESULTS

The frequencies of CYP2C9*1, *2 and *3 alleles in the Tamilian population were 0.907, 0.026 and 0.067, respectively. The distribution of CYP2C9*1/*1, *1/*2, *1/*3 and *2/*3 genotypes were 0.823, 0.044, 0.126 and 0.007, respectively.

CONCLUSION

CYP2C9*3 is the most frequent mutant allele found in the Tamilian population. The distribution of this mutant allele in the Tamilian population was found to be lesser than in Caucasians but higher than in Chinese.

Hyalinizing clear cell carcinoma of the base of the tongue

Clear cell carcinoma of the salivary glands is a rare tumour that represents less than one per cent of all salivary tumours. They are divided into a biphasic, epithelial-myoepithelial carcinoma and a monophasic pattern which may be myoepithelial or ductal in origin. The latter is accompanied by prominent fibrohyaline stroma and has been described recently as hyalinizing clear cell carcinoma (HCCC). Most of the HCCC occur in the oral cavity, and are associated with minor salivary glands, unlike the biphasic pattern which is more common in the major salivary glands. In the oral cavity, the commonest site is the palate followed by the lips and the buccal mucosa. Its occurrence in the oropharynx and the larynx is extremely rare.

An endoscopic approach to the deviated nasal septum--a preliminary study

The authors have used the nasal endoscope for the precise identification of pathological abnormalities of the nasal septum in relation to the lateral nasal wall including the osteo-metal complex and in its ultraconservative management. The aim of the study was to compare the efficacies of endoscope-aided septoplasty (EAS) over traditional septoplasty (TS) in treating the pathological septum and turbinates, performed in 30 cases each. The subjective assessment was carried out by visual analogue scores and objective assessment by nasal endoscopy. This study demonstrates the superiority and limitations of the endoscopic approach in managing a deviated nasal septum and the turbinates. The endoscope-aided technique was found to be more effective in relieving the contact areas and nasal obstruction (p = < or = 0.05). The authors advocate a combined approach--an endoscopic approach for inaccessible posterior deviation and the conservative traditional technique for accessible anterior deviation of the nasal septum.

Suboptimal resource allocation in changing environments constrains response and growth in bacteria

To respond to fluctuating conditions, microbes typically need to synthesize novel proteins. As this synthesis relies on sufficient biosynthetic precursors, microbes must devise effective response strategies to manage depleting precursors. To better understand these strategies, we investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene expression to growth phenotypes. By synthetically modifying gene expression during changing conditions, we show how the competition by genes for the limited protein synthesis capacity constrains cellular response. Despite this constraint cells substantially express genes that are not required, trapping them in states where precursor levels are low and the genes needed to replenish the precursors are outcompeted. Contrary to common modeling assumptions, our findings highlight that cells do not optimize growth under changing environments but rather exhibit hardwired response strategies that may have evolved to promote fitness in their native environment. The constraint and the suboptimality of the cellular response uncovered provide a conceptual framework relevant for many research applications, from the prediction of evolution to the improvement of gene circuits in biotechnology.

Cloning and identification of bacteriophage T4 gene 2 product gp2 and action of gp2 on infecting DNA in vivo

We sequenced bacteriophage T4 genes 2 and 3 and the putative C-terminal portion of gene 50. They were found to have appropriate open reading frames directed counterclockwise on the T4 map. Mutations in genes 2 and 64 were shown to be in the same open reading frame, which we now call gene 2. This gene codes for a protein of 27,068 daltons. The open reading frame corresponding to gene 3 codes for a protein of 20,634 daltons. Appropriate bands on polyacrylamide gels were identified at 30 and 20 kilodaltons, respectively. We found that the product of the cloned gene 2 can protect T4 DNA double-stranded ends from exonuclease V action.

Isolation of a replication origin complex from Escherichia coli

A complex consisting of replicative origin DNA and several proteins was isolated from Escherichia coli. Cells of temperature-sensitive mutants were labeled at the origin and fractionated by sucrose gradient centrifugation. A complex highly purified in origin DNA sedimented as a unique band. This complex dissociated at high concentration, above 0.2 M KCl. Upon dialysis, the complex reformed, allowing further purification of its constituents. Three major protein bands were found, corresponding to proteins of the outer membrane. The complex did not sediment with membrane fractions, but adhered to the outer membrane in the presence of magnesium.

Taste sensilla of flies: function, central neuronal projections, and development

Taste sensilla of flies are composed of only a few cells, all of which have different functions. Depending on the species and on the sensillum type, there are from 2-5 neurons, each of which has its own stimulus specificity, and each of which makes a different contribution to the fly's behavior. In addition, taste sensilla include several nonneuronal cells that are important both for the development of the sensillum and for its functioning. The component cells of a sensillum derive from a single epidermal precursor according to a stereotyped sequence of mitoses. This review focuses on the different phenotypes of the component cells of taste sensilla, particularly the stimulus sensitivity and central neuronal anatomy of the receptor neurons, and on the development of this multicellular organ from a single precursor cell.

Mutations in masquerade, a novel serine-protease-like molecule, affect axonal guidance and taste behavior in Drosophila

The masquerade (mas) locus encodes an extracellular molecule with a striking similarity to serine proteases. The serine residue, which is essential for enzymatic activity, has been substituted by glycine, suggesting that MAS could serve to antagonize serine protease activity [Murugasu-Oei et al. (1995), Genes Dev. 9, 139-154]. We describe the expression pattern of mas mRNA and protein in the developing embryonic, larval and pupal nervous system and in the epidermis. Total loss of mas function is lethal and results in aberrations in the embryonic central and peripheral nervous systems, consistent with a role in axonal guidance. The possibility that the observed deficits in taste behavior, exhibited by animals with partial loss of mas function, are a result of defects in the adult brain are discussed.