Influence of exon duplication on intron and exon phase distribution

A combination of small angle X-ray scattering and gel techniques was used to follow the kinetics of protein crystal growth as a function of time. Hen egg white lysozyme, at different protein concentrations, was used as a model system. A new sample holder was designed, in which supersaturation is induced in the presence of salt by decreasing the temperature. It had been shown previously that a decrease in temperature and/or an increase in crystallizing agent induces an increase in the attractive interactions present in the lysozyme solutions, the lysozyme remaining monomeric. In the present paper we show that similar behaviour is observed in NaCl when agarose gels are used. During crystal growth, special attention was paid to determine whether oligomers were formed as the protein in solution was incorporated in the newly formed crystals. From these first series of experiments, we did not find any indication of oligomer formation between monomer in solution and crystal. The results obtained are in agreement with the hypothesis that lysozyme crystals in NaCl grow by addition of monomeric particles.     

Finding and using hyperthermophilic enzymes

Recent developments have enhanced the prospects for the discovery of hyperthermophilic enzymes. This is important because the intrinsic basis underlying the extraordinary thermostability of hyperthermophilic enzymes has yet to be revealed, and so engineering this characteristic into less thermophilic enzymes is not possible at this time. Successful efforts to clone and express the genes encoding hyperthermophilic enzymes in mesophilic hosts have improved the availability of high-temperature biocatalysts. The remaining task is the identification of opportunities to make strategic use of the thermoactivity and thermostability of hyperthermophilic enzymes.     

The role of branchpoint-3' splice site spacing and interaction between intron terminal nucleotides in 3' splice site selection in Saccharomyces cerevisiae

A conserved 3' splice site YAG is essential for the second step of pre-mRNA splicing but no trans-acting factor recognizing this sequence has been found. A direct, non-Watson-Crick interaction between the intron terminal nucleotides was suggested to affect YAG selection. The mechanism of YAG recognition was proposed to involve 5' to 3' scanning originating from the branchpoint or the polypyrimidine tract. We have constructed a yeast intron harbouring two closely spaced 3' splice sites. Preferential selection of a wild-type site over mutant ones indicated that the two sites are competing. For two identical sequences, the proximal site is selected. As previously observed, an A at the first intron nucleotide spliced most efficiently with a 3' splice site UAC. In this context, UAA or UAU were also more efficient 3' splice sites than UAG and competed more efficiently than the wild-type sequence with a 3' splice site UAC. We observed that a U at the first intron nucleotide is used for splicing in combination with 3' splice sites UAG, UAA or UAU. Our data indicate that the 3' splice site is not primarily selected through an interaction with the first intron nucleotide. Selection of the 3' splice site depends critically on its distance from the branchpoint but does not occur by a simple leaky scanning mechanism.     

A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human beta-glucuronidase gene

BACKGROUND: Allergen-specific IgE antibodies have been considered to play an important role in the pathogenesis of atopic asthma. However, studies on allergen-specific IgE antibodies in airway secretion from asthmatic patients are very rare compared with those in serum. OBJECTIVES: The present study was undertaken to determine whether induced sputum might provide a useful method for analysing allergen-specific IgE antibodies in airway secretions from asthmatic patients. METHODS: Specific IgE antibodies to house dust mite (HDM) antigen were measured in induced sputum from 10 HDM-sensitive asthmatic patients and 12 non-allergic controls by enzyme-linked immunosorbent assay. HDM-specific IgE was regarded as positive when the absorbance value was higher than mean + 2SD of controls. Their antigen-binding characteristics were determined by immunoblot analysis. RESULTS: HDM-specific IgE was positive in induced sputum from seven of 10 HDM-sensitive asthmatics. The IgE binding to HDM antigen could be inhibited by fluid phase HDM antigen in a dose-dependent manner, not by mugwort antigen. Treatment of induced sputum with dithiothreitol decreased the antigen-specific bindings, and increased the non-specific bindings on the measurement of HDM-specific IgE. These effects were significant in a concentration of dithiothreitol greater than 0.05%. Immunoblot analysis revealed that HDM-specific IgE antibodies in induced sputum recognized the HDM antigens with molecular weights of 42, 34, 32, 25 and 14 kDa. These antigen binding characteristics were similar to those in serum. CONCLUSION: We conclude that analysis of induced sputum is a useful non-invasive method for studying allergen-specific IgE antibodies in airway secretion from asthmatic patients.     

The exon/intron organization and chromosomal mapping of the mouse ADAMTS-1 gene encoding an ADAM family protein with TSP motifs

ADAM is a recently discovered gene family that encodes proteins with a disintegrin and metalloproteinase. ADAMTS-1 is a gene encoding a new member protein of the ADAM family with the thrombospondin (TSP) type I motif, the expression of which is associated with inflammatory processes. In the present study, we have characterized the exon/intron organization of the mouse ADAMTS-1 gene. The ADAMTS-1 gene is composed of nine exons, all of which are present within the 9.2-kb genomic region. Among the nine exons, exons 1, 5, and 6 encode a proprotein domain, a disintegrin-like domain, and a TSP type I motif, respectively, of the ADAMTS-1 protein, suggesting that there is a correlation between exon/intron organization and functional domains. In addition, the exon/ intron organization of the ADAMTS-1 gene is very different from that of the metalloproteinase-like/disintegrin-like/ cysteine-rich protein gene (MDC) (ADAM11), suggesting that the genomic structure of ADAM family genes is not necessarily conserved. Furthermore, fluorescence in situ hybridization revealed that the ADAMTS-1 gene is located in region C3-C5 of chromosome 16, to which none of the previously identified ADAM genes have been mapped.     

Finding the target in search tasks using detection, localization, and identification responses.

Visual search is a favourite paradigm for researchers interested in attention because of its ease of implementation and interpretation. Typically, visual search requires the participant to indicate the presence or absence of a prespecified target. Although the slope ratio for present versus absent trials is no longer considered to be indicative of whether search is serial or not, target detection remains a staple amongst studies examining theoretical and empirical aspects of attention. The current study sought to compare within subjects three tasks in a visual search paradigm, detection, localisation, and identification, using identical stimuli. Detection differed in both pattern of error rates and slope from both identification and localisation. Moreover, the slopes from identification and localisation were significantly correlated, whilst neither was significantly correlated with slopes from the detection task. These results suggest that researchers interested in using slopes to estimate search efficiency should use localisation or identification, rather than target detection. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Intron definition is required for excision of the minute virus of mice small intron and definition of the upstream exon

Alternative splicing of pre-mRNAs plays a critical role in maximizing the coding capacity of the small parvovirus genome. The small-intron region of minute virus of mice (MVM) pre-mRNAs undergoes an unusual pattern of overlapping alternative splicing--using two donors (D1 and D2) and two acceptors (A1 and A2) within a region of 120 nucleotides--that determines the steady-state ratios of the various viral mRNAs. In this report, we show that the determinants that govern excision of the small intron are complex and are also required for efficient definition of the upstream exon. For the MVM small intron in its natural context, the two donors appear to compete for the splicing machinery: the position of D1 favors its usage, while the primary sequence of D2 must be more like the consensus sequence than is D1 to be used efficiently. We have genetically defined the branch points that are used for generation of the major and minor spliced forms and show that recognition of components of the small-intron acceptors is likely to be the dominant determinant in alternative small-intron excision. We have also identified a G-rich intronic enhancer sequence within the small intron that is essential for splicing of the minor form (D2 to A2) but not the major form (D1 to A1) of MVM mRNAs and is required for efficient definition of the upstream NS2-specific exon. In its natural context, the small intron appears to be excised by a mechanism consistent with intron definition. When the MVM small intron is expanded, various parameters of its excision are altered, indicating that critical cis-acting signals are context dependent. Relative use of the donors and acceptors is altered, and the upstream NS2-specific exon is no longer efficiently defined. The fact that definition of the upstream NS2-specific exon can be achieved by the MVM small intron in its natural context, but not when it is expanded, suggests that the multiple determinants that govern definition and excision of the small intron are required, in concert, for upstream exon definition. Our data are consistent with a model in which alternative splicing of the MVM P4-generated pre-mRNAs is governed by a hybrid of intron- and exon-defining mechanisms.     

Control of human immunodeficiency virus type 1 RNA metabolism: role of splice sites and intron sequences in unspliced viral RNA subcellular distribution

In the course of examining the various factors which affect the metabolism of human immunodeficiency virus type 1 (HIV-1) RNA, we examined the role of intron sequences and splice sites in determining the subcellular distribution of the RNA. Using in situ hybridization, we demonstrated that in the absence of Rev, unspliced RNA generated with an HIV-1 env expression construct displayed discrete localization in the nucleus, coincident with the location of the gene and not associated with SC35-containing nuclear speckles. Expression of Rev resulted in a disperse signal for the unspliced RNA throughout both the nucleus and the cytoplasm. Subsequent fractionation of the nucleus revealed that the majority of unspliced viral RNA within the nucleus is associated with the nuclear matrix and that upon expression of Rev, a small proportion of the unspliced RNA is found within the nucleoplasm. Mutations which altered splice site utilization did not alter the sequestration of unspliced RNA into discrete nuclear regions. In contrast, a 2.2-kb deletion of intron sequence resulted in a shift from discrete regions within the nucleus to a disperse signal throughout the cell, indicating that intron sequences, and not just splice sites, are required for the observed nuclear sequestration of unspliced viral RNA.     

Finding meaning, perceiving growth, and acceptance of tinnitus.

Objectives: The authors test hypotheses derived from current models of growth following adversity in a sample of people with tinnitus. These models assume a process whereby adversity or trauma threatens major assumptions, which, in turn, promotes a search for meaning in the adversity and subsequently growth. Method: Data from a sample of 315 people with tinnitus who completed an online survey were used to assess the relations of reports of negative changes to asking "Why me?" and answering the Why me? question with reports of growth, acceptance, and well-being. Results: indicate that reports of negative changes in goals and philosophy of life predict a search for meaning and that finding meaning is associated with perceived growth. Those who report never searching for meaning are less likely to report growth but report better adjustment and acceptance of their tinnitus than those who have searched for meaning. Discussion: The data are consistent with models of growth that give a central role to meaning-making processes, but they also suggest that a significant minority of people with tinnitus do not report searching for meaning or perceiving growth--yet appear to be coping well. Acceptance of tinnitus is identified as a key construct for future research. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Finding equilibrium: Mentoring, sexual orientation, and gender identity.

The authors explore mentoring relationships in which one or both members are lesbian, gay, bisexual, or transgender (LGBT). They highlight the role of stigma, in its variable presentations, as an important underpinning of these relationships. They argue that explicit attention to stigma, both within the mentoring relationship and beyond, is of value to the mentoring process and outcome. The authors offer a developmental perspective on mentoring needs, and they suggest specific considerations for LGBT and heterosexual mentors of LGBT students. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Endothelial nitric oxide synthase exon 7 polymorphism, ischemic cerebrovascular disease, and carotid atheroma

BACKGROUND AND PURPOSE: The role of endothelial nitric oxide synthase (eNOS) in normal physiology suggests that it could be a potential candidate gene for stroke. Reduced eNOS activity could mediate an increased stroke risk through hypertension or independent of hypertension through abnormal vasomotor responses, promoting atherogenesis, or increased platelet adhesion and aggregation. Recently, a common polymorphism in exon 7 of the eNOS gene (894G-->T) has been reported to be a strong risk factor for coronary artery disease. We determined whether it was also a risk factor for transient ischemic attack (TIA) and ischemic stroke and for carotid atheroma. METHODS: We studied 361 consecutive white patients presenting with ischemic stroke or TIA to a neurological cerebrovascular disease service and 236 normal white controls. In all patients CT and/or MR head imaging and high-resolution carotid duplex ultrasound were performed. The presence of the polymorphism (N/n) was determined by polymerase chain reaction and restriction with the enzyme BanII. RESULTS: There was no difference in the frequency of the NN genotype between patients and controls (13.0% versus 15.3%; P=0.44) or in N allele frequency (39% versus 37%; P=0.57). There was no association with genotype when only patients with stroke (excluding those with TIA) or when only individuals aged < or =65 years were considered. In contrast, there was a highly significant independent association between cerebrovascular disease and hypertension (odds ratio, 2.87; 95% CI, 2.0 to 4.15; P<0.00001), smoking (odds ratio, 2.58; 95% CI, 1.80 to 3.70; P<0.00001), and diabetes (odds ratio, 2.68; 95% CI, 1.38 to 5.24; P=0.004). There was no relationship between the polymorphism and any particular stroke subtype: large-vessel disease, for NN, 15 of 105 (14.3%); lacunar disease, 10 of 75 (13.3%); cardioembolic and unknown, 18 of 151 (11.9%); and tandem pathology, 4 of 30 (13.3%) (P=0.68, chi2). There was no difference in the mean degree of carotid stenosis between the 3 genotypes: NN, 31.1% (SD, 27.1); Nn, 30.1% (29.0); and nn, 31.2% (26.3) (P=0.9). There was no association between the NN genotype or the N allele and hypertension. CONCLUSIONS: We failed to find a relationship between this exon 7 polymorphism and ischemic cerebrovascular disease. In particular, it was not associated with stroke and TIA secondary to large-vessel atherosclerosis or with the degree of carotid stenosis in patients with cerebrovascular disease. It is unlikely that this particular polymorphism or any closely linked polymorphism is a major risk factor in the majority of white patients with stroke.     

Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy

A 32-base-pair model of the Holliday junction (HJ) intermediate in genetic recombination has been prepared and analyzed in-depth by 2D and 3D (1)H NMR spectroscopy. This HJ (J2P1) corresponds to a cyclic permutation of the base pairs at the junction relative to a previously studied HJ [J2; Chen, S.-M., & Chazin, W.J. (1994) Biochemistry 33, 11453-11459], designed to probe the effect of the sequence at the n - 1 position (where n is the residue directly at the branch point) on the stacking geometry. Observation of several interbase nuclear Overhauser effects (NOEs) clearly indicates a strong preference for the isomer opposite that observed for J2, confirming the dependence of stacking isomer preference on the sequence at the junction. As for other model HJs studied, a small equilibrium distribution of the alternate isomer could be identified. A sample of J2P1 was prepared with a single (15)N-labeled thymine residue at the branch point. 1D (15)n-filtered (1)H-detected experiments on this sample at low temperature give strong support for the co-existence of the two stacking isomers and provide a much more direct and accurate measure of the crossover isomer distribution. The comparative analysis of our immobile HJs and a model cruciform structure [Pikkemaat, J.A., van den Elst, H., van Boom, J.H., & Altona, C. (1994) Biochemistry 33, 14896-14907] sheds new light on the issue of the relevance of crossover isomer preference in vivo.     

Proteolytic processing of the adherens junctions components beta-catenin and gamma-catenin/plakoglobin during apoptosis

Apoptotic cells undergo specific morphological changes that include loss of cell-cell interactions. Cellular adhesiveness is dependent on members of the cadherin family of adhesion receptors and on the cytoplasmic adaptor proteins alpha-catenin, beta-catenin and gamma-catenin/plakoglobin. The caspase family of cystein proteases play a key role during the execution phase of the apoptotic program. These proteolytic enzymes, once activated, cleave cellular proteins which are important for the maintenance of cell integrity. Here we report that gamma-catenin is cleaved at different sites during apoptosis in various cell lines. The major apoptotic product of gamma-catenin still retains the ability to bind alpha-catenin but loses the carboxy-terminal region. We also show that gamma-catenin is cleaved by caspase-3 in vitro although with lower affinity when compared to PARP or beta-catenin. These findings indicate that multiple proteolytic events regulate the dismantling of the cell-cell junctional complexes during apoptosis.     

'Module'-substituted globins: artificial exon shuffling among myoglobin, hemoglobin alpha- and beta-subunits

Based on the detailed structural analysis of proteins, Go [M. Go, Nature 291 (1981) 90-92] found that protein structures can be divided into some structural units, 'modules,' which correspond to peptides coded by exons. In the present study, to investigate functional and structural roles of modular structures in proteins, we have engineered eight chimera globins, in which the exons are shuffled among human myoglobin, human hemoglobin alpha- and beta-subunits, in addition to the chimera beta beta alpha-globin described previously [K. Wakasugi, K. Ishimori, K. Imai, Y. Wada, I. Morishima, J. Biol. Chem. 269 (1994) 18750-18756]. Although all of the chimera globins stoichiometrically bound the heme and their alpha-helical contents increased by heme incorporation as found for native globins, the alpha-helical contents of the chimera globins were significantly lower than those of native globins, suggesting that 'module' substitutions seriously affect the protein folding and stability in globins. The comparisons among several chimera globins demonstrated that such structural alterations are mainly attributed to loss of some key intermodular interactions for protein folding. By simultaneous substitution of the modules M1 and M4 from the same globin, the protein structure was stabilized, which indicates that the module packing between modules M1 and M4 would be one of the crucial interaction to stabilize the globin fold. Present results allow us to conclude that module substitutions would be available for designing and producing novel functional proteins if we can reproduce the stable modular packing in the 'module'-substituted proteins.     

Functional differences in the interaction of arrestin and its splice variant, p44, with rhodopsin

Arrestin quenches signal transduction in rod photoreceptors by blocking the catalytic activity of photoactivated phosphorylated rhodopsin toward the G protein, transducin (Gt). Rod cells also express a splice variant of arrestin, termed p44, in which the last 35 amino acids are replaced by a single Ala. In contrast to arrestin, this protein has been reported to bind to both the phosphorylated and nonphosphorylated forms of the activated receptor. In this study, we analyzed formation of the rhodopsin-p44 complex in vitro. Like arrestin, p44 stabilized the meta II (MII) photoproduct relative to forms MI and MIII and did not interact measurably with the apoprotein opsin. However, several differences between p44 and its parent protein were found: (i) p44 binds to nonphosphorylated MII with a much lower affinity (KD = 0.24 microM) than to phosphorylated MII (P-MII) (KD = 12 nM); arrestin binds only to P-MII (KD = 20 nM); (ii) p44 interacted also with truncated MII (329G-Rho MII), which lacked the sites of phosphorylation; (iii) with both MII and P-MII, the activation energy of complex formation with p44 was lower than that found for arrestin (70 kJ/mol instead of 140 kJ/mol); and (iv) InsP6 inhibited poorly the interaction between p44 and P-MII, but it strongly inhibited the interaction between arrestin and P-MII. Extrapolation of the measured on-rates to physiological conditions yielded reaction times for the binding of p44 to activated rhodopsin. The data suggest that the splice variant, p44, and its parent protein, arrestin, play different roles in phototransduction. The physiological significance of these differences remains to be determined.     

Finding groups using model-based cluster analysis: Heterogeneous emotional self-regulatory processes and heavy alcohol use risk.

Model-based cluster analysis is a new clustering procedure to investigate population heterogeneity utilizing finite mixture multivariate normal densities. It is an inferentially based, statistically principled procedure that allows comparison of nonnested models using the Bayesian information criterion to compare multiple models and identify the optimum number of clusters. The current study clustered 36 young men and women on the basis of their baseline heart rate and heart rate variability (HRV), chronic alcohol use, and reasons for drinking. Two cluster groups were identified and labeled the high alcohol risk and normative groups. Compared to the normative group, individuals in the high alcohol risk group had higher levels of alcohol use and more strongly endorsed disinhibition and suppression reasons for use. The high alcohol risk group showed significant HRV changes in response to positive and negative emotional and appetitive picture cues, compared to neutral cues. In contrast, the normative group showed a significant HRV change only to negative cues. Findings suggest that individuals with autonomic self-regulatory difficulties may be more susceptible to heavy alcohol use and use of alcohol for emotional regulation. (PsycINFO Database Record (c) 2010 APA, all rights reserved)