Servers for sequence-structure relationship analysis and prediction

We describe several algorithms and public servers that were developed to analyze and predict various features of protein structures. These servers provide information about the covalent state of cysteine (CYSREDOX), as well as about residues involved in non-covalent cross links that play an important role in the structural stability of proteins (SCIDE and SCPRED). We also discuss methods and servers developed to identify helical transmembrane proteins from large databases and rough genomic data, including two of the most popular transmembrane prediction methods, DAS and HMMTOP. Several biologically interesting applications of these servers are also presented. The servers are available through http://www.enzim.hu/servers.html.     

Delayed arteriolar relaxation after prolonged agonist exposure: functional remodeling involving tyrosine phosphorylation

Although arteriolar contraction is dependent on Ca2+-induced myosin phosphorylation, other mechanisms including Ca2+ sensitization and time-dependent phenomena such as cytoskeletal and cellular reorganization may contribute to contractile events. We hypothesized that if arteriolar smooth muscle exhibits time-dependent behavior this may be manifested in differences in relaxation after short- and long-term exposure to contractile agonists. Studies were conducted in isolated arterioles pressurized to 70 mmHg. In initial experiments (n = 10), rate of relaxation was measured after acute (5 min) or prolonged (4 h) exposure to 5 microM norepinephrine (NE). Prolonged exposure to NE resulted in significantly (P < 0.05) increased time for relaxation in physiological salt solution. Rapid relaxation of vessels exposed to NE for 4 h was observed after superfusion with 0 mM Ca2+ buffer, indicating that the alteration in relaxation was reversible and Ca2+ dependent. A similarly impaired dilation was not observed with 4-h exposure to KCl (75 mM). To determine mechanisms contributing to the effects of prolonged NE exposure, studies were performed in the presence of the microtubule depolymerizing agent demecolcine (10 microM) or a series of tyrosine phosphorylation inhibitors. Although demecolcine caused significant vasoconstriction (P < 0.05) and potentiated NE vasoconstriction, it did not prevent the effect of long-term NE exposure on relaxation. Genistein, although having no effect on acute NE-induced contraction, concentration-dependently inhibited prolonged NE constriction. Similarly, Src (PP1) and p42/44 MAP kinase (PD-98059) inhibitors prevented maintenance of long-term NE contraction. The data indicate that prolonged exposure to NE induces biochemical alterations that impair relaxation after removal of the agonist. The contractile effects are Ca2+ dependent and involve tyrosine phosphorylation but do not appear to involve the polymerization state of the microtubule network.     

Higher order structure of the PCM adjacent to the centriole

The centrosome is the major microtubule organizing center in most animal cells. This cytoplasmic organelle consists of two components : a mature centriole (or a pair of centrioles) and a mass of pericentriolar material (PCM). The PCM has been described as either a cloud of material that encases the entire centriole or as a cluster of proteins divided into two subsets, one that adheres to the lateral surface of the centriole and another that extends outward from this region as a cloud of material. In contrast to these protein distribution patterns, we demonstrated in a previous study that a subset of proteins present within the PCM is integrated together to form a tube (PCM tube) with an open and closed end that is duplicated in concert with centrosome duplication. The present study was undertaken to determine if this tubular conformation represents proteins that are confined to the surface of the centriole or if it represents a subset of proteins within the cloud of material that extends outward from the centriole. We document that : (1) the PCM tube represents a portion of the PCM directly associated with the centriole; (2) the PCM tube has a specific and reproducible relationship to the polar structure of the centriole; (3) the tube is a site of cytoplasmic microtubule organization, and has a structure that influences the initial pattern of microtubule assembly within the juxta-centriolar region; and (4) the PCM tube has a structural relationship with respect to the centriole, which allows the simultaneous expression of centriole- and PCM-based functions (e.g., ciliogenesis and cytoplasmic microtubule organization). Based on these findings, we propose a new model of the PCM at the centriole. This model highlights the role played by the proximal end of the centriole in the nucleation and organization of centriole-associated PCM, and indicates that the centrosome has an overall polarity in the region of the centriole.     

Keratinocyte differentiation is regulated by the Rho and ROCK signaling pathway

The epidermis comprises multiple layers of specialized epithelial cells called keratinocytes. As cells are lost from the outermost epidermal layers, they are replaced through terminal differentiation, in which keratinocytes of the basal layer cease proliferating, migrate upwards, and eventually reach the outermost cornified layers. Normal homeostasis of the epidermis requires that the balance between proliferation and differentiation be tightly regulated. The GTP binding protein RhoA plays a fundamental role in the regulation of the actin cytoskeleton and in the adhesion events that are critically important to normal tissue homeostasis. Two central mediators of the signals from RhoA are the ROCK serine/threonine kinases ROCK-I and ROCK-II. We have analyzed ROCK's role in the regulation of epidermal keratinocyte function by using a pharmacological inhibitor and expressing conditionally active or inactive forms of ROCK-II in primary human keratinocytes. We report that blocking ROCK function results in inhibition of keratinocyte terminal differentiation and an increase in cell proliferation. In contrast, activation of ROCK-II in keratinocytes results in cell cycle arrest and an increase in the expression of a number of genes associated with terminal differentiation. Thus, these results indicate that ROCK plays a critical role in regulating the balance between proliferation and differentiation in human keratinocytes.     

A novel domain in AMP-activated protein kinase causes glycogen storage bodies similar to those seen in hereditary cardiac arrhythmias

The AMP-activated protein kinase (AMPK) is an alphabetagamma heterotrimer that is activated by low cellular energy status and affects a switch away from energy-requiring processes and toward catabolism. While it is primarily regulated by AMP and ATP, high muscle glycogen has also been shown to repress its activation. Mutations in the gamma2 and gamma3 subunit isoforms lead to arrhythmias associated with abnormal glycogen storage in human heart and elevated glycogen in pig muscle, respectively. A putative glycogen binding domain (GBD) has now been identified in the beta subunits. Coexpression of truncated beta subunits lacking the GBD with alpha and gamma subunits yielded complexes that were active and normally regulated. However, coexpression of alpha and gamma with full-length beta caused accumulation of AMPK in large cytoplasmic inclusions that could be counterstained with anti-glycogen or anti-glycogen synthase antibodies. These inclusions were not affected by mutations that increased or abolished the kinase activity and were not observed by using truncated beta subunits lacking the GBD. Our results suggest that the GBD binds glycogen and can lead to abnormal glycogen-containing inclusions when the kinase is overexpressed. These may be related to the abnormal glycogen storage bodies seen in heart disease patients with gamma2 mutations.     

Prevalence of scrapie infection in Great Britain: interpreting the results of the 1997-1998 abattoir survey

An accurate estimate of the prevalence of scrapie infection in the Great Britain (GB) sheep flock is essential when assessing any potential risk to human health through exposure to sheep transmissible spongiform encephalopathies (TSEs). One method for assessing the prevalence is to sample sheep intended for human consumption using a diagnostic test capable of detecting infected animals prior to the onset of clinical signs. An abattoir survey conducted in Great Britain in 1997-1998 tested brain samples from 2809 apparently healthy sheep of which none was found to be positive for scrapie by histopathology or immunohistochemistry (IHC) although 10 were positive for scrapie-associated fibrils (SAF). Subsequently, the tonsils from a subset of the animals sampled were examined using IHC, one of which tested positive. To interpret these results we use a likelihood-based approach, which accounts for the variation in the prevalence of infection with age and test sensitivity and specificity with stage of infection. Combining the results for all of the diagnostic tests yields an estimate of the prevalence of scrapie infection in the GB sheep flock of 0.22% (95% confidence interval: 0.01-0.97%). Moreover, our analysis suggests that all of the diagnostic tests used are very specific (greater than 99%). Indeed, only SAF detection yields a specificity estimate of less than 100%, which helps to account for the high number of samples found to be positive for SAF.     

Host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts

In North America, the pea aphid Acyrthosiphon pisum encompasses ecologically and genetically distinct host races that offer an ideal biological system for studies on sympatric speciation. In addition to its obligate symbiont Buchnera, pea aphids harbour several facultative and phylogenetically distant symbionts. We explored the relationships between host races of A. pisum and their symbiotic microbiota to gain insights into the historical process of ecological specialization and symbiotic acquisition in this aphid. We used allozyme and microsatellite markers to analyse the extent of genetic differentiation between populations of A. pisum on pea, alfalfa and clover in France. In parallel, we examined: (i) the distribution of four facultative symbionts; and (ii) the genetic variation in the Buchnera genome across host-associated populations of A. pisum. Our study clearly demonstrates that populations of A. pisum on pea, clover and alfalfa in France are genetically divergent, which indicates that they constitute distinct host races. We also found a very strong association between host races of A. pisum and their symbiotic microbiota. We stress the need for phylogeographic studies to shed light on the process of host-race formation and acquisition of facultative symbionts in A. pisum. We also question the effects of these symbionts on aphid host fitness, including their role in adaptation to a host plant.     

The systemizing quotient: an investigation of adults with Asperger syndrome or high-functioning autism,and normal sex differences

Systemizing is the drive to analyse systems or construct systems. A recent model of psychological sex differences suggests that this is a major dimension in which the sexes differ, with males being more drawn to systemize than females. Currently, there are no self-report measures to assess this important dimension. A second major dimension of sex differences is empathizing (the drive to identify mental states and respond to these with an appropriate emotion). Previous studies find females score higher on empathy measures. We report a new self-report questionnaire, the Systemizing Quotient (SQ), for use with adults of normal intelligence. It contains 40 systemizing items and 20 control items. On each systemizing item, a person can score 2, 1 or 0, so the SQ has a maximum score of 80 and a minimum of zero. In Study 1, we measured the SQ of n = 278 adults (114 males, 164 females) from a general population, to test for predicted sex differences (male superiority) in systemizing. All subjects were also given the Empathy Quotient (EQ) to test if previous reports of female superiority would be replicated. In Study 2 we employed the SQ and the EQ with n = 47 adults (33 males, 14 females) with Asperger syndrome (AS) or high-functioning autism (HFA), who are predicted to be either normal or superior at systemizing, but impaired at empathizing. Their scores were compared with n = 47 matched adults from the general population in Study 1. In Study 1, as predicted, normal adult males scored significantly higher than females on the SQ and significantly lower on the EQ. In Study 2, again as predicted, adults with AS/HFA scored significantly higher on the SQ than matched controls, and significantly lower on the EQ than matched controls. The SQ reveals both a sex difference in systemizing in the general population and an unusually strong drive to systemize in AS/HFA. These results are discussed in relation to two linked theories: the 'empathizing-systemizing' (E-S) theory of sex differences and the extreme male brain (EMB) theory of autism.