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PubMed1993

Time-resolved infrared spectral analysis of the KL-to-L conversion in the photocycle of bacteriorhodopsin.

Time-resolved infrared spectra of the hydrated film of light-adapted bacteriorhodopsin were recorded from earlier than 200 ns to 450 microseconds after light excitation in the 1800-900-cm-1 region on a newly designed dispersive-type infrared spectrometer [Iwata & Hamaguchi (1989) Appl. Spectrosc. 44, 1431-1437]. Both the KL-to-L and L-to-M conversions were detected in this time range. The spectral shape of KL is similar to K measured at 77 K except for the intense hydrogen out-of-plane vibrational band at 984 cm-1. The kinetics of this band are different from those of the other KL-specific bands at 1510, 1296, and 956 cm-1. Since the hydrogen out-of-plane vibrational bands are intensified by twists of the polyene chain, a change in the twist of the chromophore is suggested within the lifetime of KL. During the decaying process of L, the KL-specific vibrational bands are observed in parallel with L, indicating that KL and L are in equilibrium.

Bacteriorhodopsins↗
PubMed2006

Reaction coordinate analysis of the S1-S0 internal conversion of azulene.

The reaction coordinate of the S(1)-S(0) internal conversion of azulene has been analyzed using ab initio complete active space self-consistent field method. The stable geometry in S(0) (S(0) geometry) takes a bond-equalized structure where all the peripheral skeletal bond distances are similar to an aromatic CC bond distance. The transannular bond is similar to a normal C-C single bond. The first event upon electronic excitation into S(1) at S(0) geometry is characterized by the following two simultaneous changes in the skeletal bonds; the transannular bond in S(1) increases its double bond character and the aromaticity of the peripheral bonds disappears. In consequence, the most stable azulene in S(1) (S(1) geometry) has a biradical character. To reach the conical intersection between S(1) and S(0) (S(1)S(0)-CIX) where radiationless relaxation takes place, the seven-membered ring greatly deviates from a planar structure. After a transition into S(0) at S(1)S(0)-CIX, the bond-equalized structure is recovered immediately and then the nonplanarity decreases so that azulene again takes the stable planar S(0) geometry. In order to deepen the understanding of the S(1)-S(0) internal conversion, the dipole moments along the reaction coordinate have been analyzed.

Journal Article↗
PubMed1994

Analysis of a recombination hotspot for gene conversion occurring at the HIS2 gene of Saccharomyces cerevisiae.

The properties of gene conversion as measured in fungi that generate asci containing all the products of meiosis imply that meiotic recombination initiates at specific sites. The HIS2 gene of Saccharomyces cerevisiae displays a high frequency of gene conversion, indicating that it is a recombination hotspot. The HIS2 gene was cloned and sequenced, and the cloned DNA was used to make several different types of alterations in the yeast chromosome by transformation; these alterations were used to determine the location of the sequences necessary for the high levels of meiotic conversion observed at HIS2. Previous work indicated that the gene conversion polarity gradient is high at the 3' end of the gene, and that the promoter of the gene is not necessary for the high frequency of conversion observed. Data presented here suggest that at least some of the sequences necessary for high levels of conversion at HIS2 are located over 700 bp downstream of the end of the coding region, extend over (at least) several hundred base pairs, and may be quite complex, perhaps involving chromatin structure. Additional data indicate that multiple single base heterologies within a 1-kb interval contribute little to the frequency of gene conversion. This contrasts with other reports about the role of heterologies at the MAT locus.

Amino Acid Sequence↗
PubMed1985

Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion.

Simple but exact statistical tests for detecting a cluster of associated nucleotide changes in DNA are presented. The tests are based on the linear distribution of a set of s sites among a total of n sites, where the s sites may be the variable sites, sites of insertion/deletion, or categorized in some other way. These tests are especially useful for detecting gene conversion and intragenic recombination in a sample of DNA sequences. In this case, the sites of interest are those that correspond to particular ways of splitting the sequences into two groups (e.g., sequences A and D vs. sequences B, C, and E-J). Each such split is termed a phylogenetic partition. Application of these methods to a well-documented case of gene conversion in human gamma-globin genes shows that sites corresponding to two of the three observed partitions are significantly clustered, whereas application to hominoid mitochondrial DNA sequences--among which no recombination is expected to occur--shows no evidence of such clustering. This indicates that clustering of partition-specific sites is largely due to intragenic recombination or gene conversion. Alternative hypotheses explaining the observed clustering of sites, such as biased selection or mutation, are discussed.

Animals↗
PubMed1999

Expression of vascular endothelial growth factor in patients with testicular germ cell tumors as an indicator of metastatic disease.

BACKGROUND: Angiogenesis is essential for tumor growth and metastasis. Vascular endothelial growth factor (VEGF) and thymidine phosphorylase (TP)/platelet-derived endothelial cell growth factor (PD-ECGF) are involved in increased angiogenic activity and disease progression in solid tumors. However, there is no information regarding the association of these angiogenic factors with clinicopathologic findings in testicular germ cell tumors (GCTs). METHODS: The authors examined the expression of VEGF and TP as well as microvessel density in GCTs and their association with clinicopathologic findings. Expression of VEGF and TP and microvessel density were examined immunohistochemically in 80 GCTs, including 33 seminomas (25 tumors with organ-confined disease and 8 with metastasis) and 47 nonseminomatous testicular GCTs (NSGCTs) (20 tumors with organ-confined disease and 27 with metastasis). Expression of VEGF also was examined in four GCTs and one nonneoplastic testis by immunoblotting. RESULTS: VEGF protein was expressed more highly in GCTs compared with nonneoplastic testes. VEGF expression in GCTs was correlated significantly with microvessel count (P < 0.001). Both VEGF expression and microvessel count were correlated with metastasis in seminoma (P = 0.008 and P < 0.001, respectively), but only VEGF expression was identified as statistically significant by multiple regression analysis (P = 0.006). Conversely, four variables (VEGF expression, microvessel count, the presence of venous invasion, and the presence of embryonal carcinoma elements in the primary tumor) were correlated with metastasis in NSGCT (P < 0.001, P < 0.001, P = 0.004, and P = 0.029, respectively). However, multiple regression analysis revealed that only VEGF expression and microvessel count were significant factors for metastasis (P < 0.007 and P < 0.001, respectively). In contrast, high levels of TP were observed in infiltrating cells, but not in the majority of cancer cells. CONCLUSIONS: The findings of the current study suggest that VEGF expression is involved in tumor development, angiogenesis, and metastasis in GCT.

Adolescent↗
PubMed1992

[Conversion of forensic paternity determination to DNA analysis].

For many years, the resolution of disputed paternity cases by genetic means relied on laboratory blood tests of red cell antigens and red cell and serum protein electrophoresis. These systems are generally characterized as lacking polymorphism and having low powers of exclusion, therefore it was necessary to use a panel of up to 23 marker systems. Over the past five years, a variety of DNA restriction fragment length polymorphism (RFLP) systems have been developed that characterize individuals at the DNA level. In this paper we describe the implementation of a Hae III RFLP system utilized in our laboratory for the resolution of disputed parentage cases as well as forensic casework. Since the analysis of highly polymorphic VNTR loci has proven to be the most powerful method to date for the determination of biological relatedness the utilization of the conventional methodologies should be completely replaced.

Adult↗
PubMed1990

A practical method for the analysis of osmotic-and-diffusive energy conversion.

A practical method for the study of osmotic- and-diffusive conversion of free energy of solutions with different concentrations is presented. Equations for effective power, dissipative power, total power and energetic efficiency have been derived for fixed membrane systems. These equations allow energetic evaluation of these systems. The significance of the method for biological studies is also suggested.

Diffusion↗
PubMed1998

LDLR Database (second edition): new additions to the database and the software, and results of the first molecular analysis.

Mutations in the LDL receptor gene (LDLR) cause familial hypercholesterolemia (FH), a common autosomal dominant disorder. The LDLR database is a computerized tool that has been developed to provide tools to analyse the numerous mutations that have been identified in the LDLR gene. The second version of the LDLR database contains 140 new entries and the software has been modified to accommodate four new routines. The analysis of the updated data (350 mutations) gives the following informations: (i) 63% of the mutations are missense, and only 20% occur in CpG dinucleotides; (ii) although the mutations are widely distributed throughout the gene, there is an excess of mutations in exons 4 and 9, and a deficit in exons 13 and 15; (iii) the analysis of the distribution of mutations located within the ligand-binding domain shows that 74% of the mutations in this domain affect a conserved amino-acid, and that they are mostly confined in the C-terminal region of the repeats. Conversely, the same analysis in the EGF-like domain shows that 64% of the mutations in this domain affect a non-conserved amino-acid, and, that they are mostly confined in the N-terminal half of the repeats. The database is now accessible on the World Wide Web at http://www.umd.necker.fr

Computer Communication Networks↗
PubMed1996

Specificity and kinetics of haloalkane dehalogenase.

Haloalkane dehalogenase converts halogenated alkanes to their corresponding alcohols. The active site is buried inside the protein and lined with hydrophobic residues. The reaction proceeds via a covalent substrate-enzyme complex. This paper describes a steady-state and pre-steady-state kinetic analysis of the conversion of a number of substrates of the dehalogenase. The kinetic mechanism for the "natural" substrate 1,2-dichloroethane and for the brominated analog and nematocide 1,2-dibromoethane are given. In general, brominated substrates had a lower Km, but a similar kcat than the chlorinated analogs. The rate of C-Br bond cleavage was higher than the rate of C-Cl bond cleavage, which is in agreement with the leaving group abilities of these halogens. The lower Km for brominated compounds therefore originates both from the higher rate of C-Br bond cleavage and from a lower Ks for bromo-compounds. However, the rate-determining step in the conversion (kcat) of 1, 2-dibromoethane and 1,2-dichloroethane was found to be release of the charged halide ion out of the active site cavity, explaining the different Km but similar kcat values for these compounds. The study provides a basis for the analysis of rate-determining steps in the hydrolysis of various environmentally important substrates.

Binding Sites↗
PubMed1995

The measurement of team process.

The construct validity of measures of team process was evaluated using predictive, known groups and multitrait-multimethod (MTMM) validation strategies. Military air crews (N = 51) flew two simulated missions. Independent judges provided evaluations of the same six team process variables in both scenarios. An MTMM analysis of judges' ratings treating judges as a method variable showed good convergent and discriminant validity. Judges' mean ratings of the six process variables were correlated with mission effectiveness. Some process measures discriminated between student and instructor teams, thus showing discrimination between known groups. Conversely, an MTMM analysis of ratings treating scenarios as a method showed poor convergent validity. We concluded that important team process behaviors have been identified and can be rated validly but that multiple observations are necessary to assess characteristics of individual teams with any accuracy. The discussion includes implications for practice and future research.

Aircraft↗
PubMed1997

Analyzing predictive models following definitive radiotherapy for prostate carcinoma.

BACKGROUND: As we approach the 21st century, clinically useful predictive models for prostate carcinoma are urgently needed to stratify patients reliably for future treatment strategies. Recently, many investigators have developed models that employ prostate specific antigen (PSA)-based constructs or groupings in an attempt to predict outcome accurately following definitive radiotherapy. This investigation was conducted to determine which of these models provides the closest "fit" to independent clinical outcome data measuring biochemical freedom from failure (bNED control), thereby warranting further exploration. METHODS: Six models were analyzed in a definitive radiotherapy series of 421 patients with localized prostate carcinoma treated with a median dose of 74 Gray (Gy) between March 1988 and November 1994. A stepwise Cox proportional hazards multivariate analysis (MVA) was performed to predict for bNED control using the following covariates: PSA, Gleason's score, stage, dose, PSA density, and perineural invasion. Subsequent MVAs were performed for each model incorporating the new construct or prognostic groupings. The adequacy of the models was confirmed using plots of score residuals against time to bNED failure and comparisons were made used Akaike's Information Criteria (AIC) in which a smaller value corresponds to a statistically improved model based on explained variation and the number of predictors. Because PSA was distributed in a log-normal fashion in the current study population, the model-building process was duplicated using a logarithmic transformation analysis. Biochemical failure was defined as 2 consecutive elevations in the PSA > or = 1.5 ng/mL. The median follow-up time was 34 months (range, 2-87 months). RESULTS: Initially, the model developed by Pisansky et al. appeared the most predictive due to the parsimony in their risk estimate, which is the sole predictor of outcome, as well as its associated lowest AIC value. However, after the logarithmic transformation analysis, all the models appeared to be equally predictive of bNED outcome. CONCLUSIONS: A plethora of accurate models for predicting outcome following definitive radiotherapy for prostate carcinoma recently have been engineered, all of which are essentially equally predictive in this data base (via a logarithmic conversion process). This analysis should be corroborated in other large radiotherapy series.

Follow-Up Studies↗
PubMed2005

Are Victorian elective surgery cases still converting from overnight to same day cases?

The conversion rate on a diagnosis related group (DRG)-standardised basis of Victorian private overnight (ON) elective surgery cases to same day (SD) cases declined from 4.7% per annum over 1996-97 to 1998-99 to 2.5% per annum over 1998-99 to 2002-03. Similar analysis within the Victorian public sector shows a decline from 3.8% per annum over 1996-97 to 1998-99 to 1.9% over 1998-99 to 2002-03. Comparison on a DRG-standardised basis shows while the public sector continued to show a higher incidence of elective surgery SD cases than the private sector in 2002-03 (by 1.6%). The difference has declined since 1998-99 when it was 2.4%. DRG-based analysis suggests the conversion rate in both sectors and the difference in SD surgery cases between the two sectors will continue to decline. Future savings in recurrent and capital cost due to ON surgery cases becoming SD cases are likely to be much lower than savings in recent years.

Ambulatory Surgical Procedures↗
PubMed2001

Conversion from laparoscopic to open appendicectomy: a possible drawback of the laparoscopic technique?

OBJECTIVE: To analyse the reasons for, and outcome of, conversion from laparoscopic to open appendicectomy and to identify factors that may predict the need for conversion. DESIGN: Subgroup analysis from a randomised multicentre study. SETTING: One university hospital and four county hospitals, Sweden. SUBJECTS: A total of 500 patients were randomised to laparoscopic (n = 244) or open (n = 256) appendicectomy. Thirty operations (12%) were converted to open appendicectomy. MAIN OUTCOME MEASURES: Reasons for conversion, outcome, and preoperative predictive variables. RESULTS: Difficult anatomy or the presence of an abscess were the main reasons for conversion (25/30). The incidence of perforated appendicitis was higher among patients who required conversion compared with both the open and laparoscopic group. Operating time, anaesthetic time, and duration of hospital stay were longer after conversion. Time to full recovery and length of sick leave were also longer, except for patients with perforated appendicitis. There was no difference in the complication rate. No predictive factors were identified. CONCLUSION: The main reasons for conversion were difficult anatomy and the presence of an abscess. After conversion patients recovered more slowly than those operated on laparoscopically or by primary open operation.

Adolescent↗