Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

MOTIVATION: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring. RESULTS: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive analysis of the possible simplified amino acid alphabets, using a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the simplified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the performance becomes worse, taking up to several hours, for highly simplified alphabets. AVAILABILITY: AlphaSimp and other accessory programs are available at http://bioinformatics.cribi.unipd.it/alphasimp     

PrPC is sorted to the basolateral membrane of epithelial cells independently of its association with rafts

PrP(C) is a glycosylphosphatidylinositol-anchored protein expressed in neurons as well as in the cells of several peripheral tissues. Although the normal function of PrP(C) remains unknown, a conformational isoform called PrP(Sc) (scrapie) has been proposed to be the infectious agent of transmissible spongiform encephalopathies in animals and humans. Where and how the PrP(C) to PrP(Sc) conversion occurs in the cells is not yet known. Therefore, dissecting the intracellular trafficking of the wild-type prion protein, as well as of the scrapie isoform, can be of major relevance to the pathogenesis of the diseases. In this report we have analyzed the exocytic pathway of transfected mouse PrP(C) in thyroid and kidney polarized epithelial cells. In contrast to the majority of glycosylphosphatidylinositol-anchored proteins, we found that PrP(C) is localized mainly on the basolateral domain of the plasma membrane of both cell lines. This is reminiscent of the predominant somatodendritic localization found in neurons. However, similarly to apical glycosylphosphatidylinositol-proteins, PrP(C) associates with detergent-resistant microdomains, which have been suggested to have a role in apical sorting of glycosylphosphatidylinositol-proteins, as well as in the conversion process of PrP(C) to PrP(Sc). In order to discriminate whether detergent-resistant microdomains have a direct role in PrP(Sc) conversion, or whether they are involved in the transport of the protein to the site of its conversion, we have examined the effect of disruption of detergent-resistant microdomain association on PrP(C) intracellular traffic. Consistent with the unusual basolateral localization of this glycosylphosphatidylinositol-linked protein, our data exclude a classical role for detergent-resistant microdomains in the post-trans-Golgi network sorting and transport of PrP(C) to the plasma membrane.     

Lipovitellins and phosvitins of the fertilized eggs during embryo growth in the oviparous lizard Podarcis sicula

In the lizard Podarcis sicula, the major vitellogenin (VTG)-derived yolk proteins, lipovitellins and phosvitins, were extracted from the yolk globules of laid and fertilized eggs at different periods of incubation up to 44 days close to hatching. Embryonic development was almost over at this time. Yolk proteins were isolated by precipitation in saturated (NH(4))(2)SO(4), separated on SDS-PAGE and detected by Western blotting with homologous polyclonal anti/VTG antibody. Two lipovitellins of 110 and 116 kDa were always present in the yolk of laid eggs after 1, 10, 18, and 44 days from oviposition. Both these proteins were glycosylated and were recognized by the anti/VTG antibody; their N-terminal sequences were analyzed. Four phosvitins were detected in freshly laid eggs, but their number decreased during incubation, and after 44 days only a single protein of approximately 6.5 kDa was present. The results indicated that, in this lizard, during embryonic development, lipovitellins remain unchanged, whereas the phosphorylated components of yolk undergo continuous degradation.     

Risk factors for elevated HIV incidence rates among female injection drug users in Vancouver

Background

In 1997, we found a higher prevalence of HIV among female than among male injection drug users in Vancouver. Factors associated with HIV incidence among women in this setting were unknown. In the present study, we sought to compare HIV incidence rates among male and female injection drug users in Vancouver and to compare factors associated with HIV seroconversion.

Methods

This analysis was based on 939 participants recruited between May 1996 and December 2000 who were seronegative at enrolment with at least one follow-up visit completed, and who were studied prospectively until March 2001. Incidence rates were calculated using the Kaplan–Meier method. The Cox proportional hazards regression model was used to identify independent predictors of time to HIV seroconversion.

Results

As of March 2001, seroconversion had occurred in 110 of 939 participants (64 men, 46 women), yielding a cumulative incidence rate of HIV at 48 months of 13.4% (95% confidence interval [CI] 11.0%–15.8%). Incidence was higher among women than among men (16.6% v. 11.7%, p = 0.074). Multivariate analysis of the female participants'' practices revealed injecting cocaine once or more per day compared with injecting less than once per day (adjusted relative risk [RR] 2.6, 95% CI 1.4–4.8), requiring help injecting compared with not requiring such assistance (adjusted RR 2.1, 95% CI 1.1–3.8), having unsafe sex with a regular partner compared with not having unsafe sex with a regular partner (adjusted RR 2.9, 95% CI 0.9–9.5) and having an HIV-positive sex partner compared with not having an HIV-positive sex partner (adjusted RR 2.7, 95% CI 1.0–7.7) to be independent predictors of time to HIV seroconversion. Among male participants, injecting cocaine once or more per day compared with injecting less than once per day (adjusted RR 3.3, 95% CI 1.9–5.6), self-reporting identification as an Aboriginal compared with not self-reporting identification as an Aboriginal (adjusted RR 2.5, 95% CI 1.4–4.2) and borrowing needles compared with not borrowing needles (adjusted RR 2.0, 95% CI 1.1–3.4) were independent predictors of HIV infection.

Interpretation

HIV incidence rates among female injection drug users in Vancouver are about 40% higher than those of male injection drug users. Different risk factors for seroconversion for women as opposed to men suggest that sex-specific prevention initiatives are urgently required.Recent reports in Canada and numerous other countries indicate that HIV is increasingly affecting women.¹ Before 1995, adult women in Canada had 9.6% of all positive HIV tests for which the age and sex of the person being tested were known. By 1995, this proportion had increased to 18.5% and reached 23.9% in 2000. In addition, 39% of all new HIV infections among women in 2000 were attributed to injection drug use.² These data are consistent with findings in the United States where, in 1999, women accounted for 23% of all reported AIDS cases in adults, of which 42% were attributed to injection drug use.³These data clearly indicate that the face of the epidemic is changing. Whereas some factors unique to the transmission of HIV to women are known, basic and behavioural research efforts addressing sex-related and drug-related vulnerabilities among female injection drug users (IDUs) are lacking.⁴ At a time when women''s vulnerability to HIV infection is becoming increasingly apparent worldwide,^5,6 a better understanding of the processes and factors that cause drug-related harm among women in industrialized countries is urgently required.Since the mid-1990s, the Downtown Eastside of Vancouver, British Columbia, has experienced an explosive and ongoing HIV epidemic among IDUs with annual HIV incidence rates reaching as high as 19% in 1997.^7,8 When subjects were enrolled in the Vancouver Injection Drug User Study (VIDUS), it was found that the baseline HIV prevalence was higher among women than men (35.2% v. 25.8%).⁷ Follow-up of this cohort now allows an investigation aimed at identifying the predictors of HIV seroconversion among female and male IDUs. Therefore, we sought to compare HIV incidence rates among male and female IDUs in Vancouver and to compare risk factors associated with HIV seroconversion.     

Relaxation kinetics following sudden Ca(2+) reduction in single myofibrils from skeletal muscle

To investigate the roles of cross-bridge dissociation and cross-bridge-induced thin filament activation in the time course of muscle relaxation, we initiated force relaxation in single myofibrils from skeletal muscles by rapidly (approximately 10 ms) switching from high to low [Ca(2+)] solutions. Full force decay from maximal activation occurs in two phases: a slow one followed by a rapid one. The latter is initiated by sarcomere "give" and dominated by inter-sarcomere dynamics (see the companion paper, Stehle, R., M. Krueger, and G. Pfitzer. 2002. Biophys. J. 83:2152-2161), while the former occurs under nearly isometric conditions and is sensitive to mechanical perturbations. Decreasing the Ca(2+)-activated force preceding the start of relaxation does not increase the rate of the slow isometric phase, suggesting that cycling force-generating cross-bridges do not significantly sustain activation during relaxation. This conclusion is strengthened by the finding that the rate of isometric relaxation from maximum force to any given Ca(2+)-activated force level is similar to that of Ca(2+)-activation from rest to that given force. It is likely, therefore, that the slow rate of force decay in full relaxation simply reflects the rate at which cross-bridges leave force-generating states. Because increasing [P(i)] accelerates relaxation while increasing [MgADP] slows relaxation, both forward and backward transitions of cross-bridges from force-generating to non-force-generating states contribute to muscle relaxation.     

K+ channel cAMP activated in guinea pig gallbladder epithelial cells

In guinea pig gallbladder epithelial cells, an increase in intracellular cAMP levels elicits the rise of anion channel activity. We investigated by patch-clamp techniques whether K(+) channels were also activated. In a cell-attached configuration and in the presence of theophylline and forskolin or 8-Br-cAMP in the cellular incubation bath, an increase of the open probability (P(o)) values for Ca(2+)-activated K(+) channels with a single-channel conductance of about 160 pS, for inward current, was observed. The increase in P(o) of these channels was also seen in an inside-out configuration and in the presence of PKA, ATP, and cAMP, but not with cAMP alone; phosphorylation did not influence single-channel conductance. In the inside-out configuration, the opioid loperamide (10(-5) M) was able to reduce P(o) when it was present either in the microelectrode filling solution or on the cytoplasmic side. Detection in the epithelial cells by RT-PCR of the mRNA corresponding to the alpha subunit of large-conductance Ca(2+)-activated K(+) channels (BK(Ca)) indicates that this gallbladder channel could belong to the BK family. Immunohistochemistry experiments confirm that these cells express the BK alpha subunit, which is located on the apical membrane. Other K(+) channels with lower conductance (40 pS) were not activated either by 8-Br-cAMP (cell-attached) or by PKA + ATP + cAMP (inside-out). These channels were insensitive to TEA(+) and loperamide. The data demonstrate that under conditions that induce secretion, phosphorylation activates anion channels as well as Ca(2+)-dependent, loperamide-sensitive K(+) channels present on the apical membrane.     

Mechanisms controlling the integrity of replicating chromosomes in budding yeast

Cells are continually challenged by genomic insults that originate from chemical and physical agents diffused in the environment, but also normal cellular metabolism produces genotoxic effects. Moreover, DNA replication and recombination generate intermediates potentially dangerous for genome stability. Growing evidence show that many genetic disorders are characterized by high levels of chromosome alterations due to genomic instability, which is also a hallmark of cancer cells. Recent work shed some light on the molecular events that maintain the integrity of chromosomes during unperturbed S phase and in the face of odds.     

Proteins from bovine tissues and biological fluids: defining a reference electrophoresis map for liver,kidney, muscle,plasma and red blood cells

A number of high resolution two-dimensional electrophoresis (2-DE) reference maps for bovine tissues and biological fluids have been determined for animals in basal state. Among the 1863 distinct protein features detected in samples of liver, kidney, muscle, plasma and red blood cells, 509 species were identified and associated to 209 different genes. Difficulties in the identification were related to the poorly characterized Bos taurus genome and were solved by a combined matrix-assisted laser desorption/ionisation-mass spectrometry and liquid chromatography-electrospray ionization tandem mass spectrometry approach. The experimental output allowed us to establish a 2-DE database accessible through the World Wide Web network at the URL address (http://www.iabbam.na.cnr.it/Biochem). These reference maps may serve as a tool in future veterinary medical studies aimed at the evaluation of changes in protein repertoire for altered animal physiological conditions and infectious diseases, to the definition of molecular markers for novel diagnostic kits and vaccines, as well as the characterization of protein modifications in bovine materials following technological processes used in the food industry.