Overview of the gene ontology task at BioCreative IV

Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation.

Database URL:http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/.

QSAR studies on imidazopyrazine derivatives as Aurora A kinase inhibitors

Aurora kinases have emerged as attractive targets for the development of novel anti-cancer agents. A combined study of molecular docking, pharmacophore modelling and 3D-QSAR was performed on a series of imidazo [1, 2-a] pyrazines as novel Aurora kinase inhibitors to gain insights into the structural determinants and their structure-activity relationship. An ensemble of conformations based on molecular docking was used for PHASE pharmacophore studies. The developed best-fitted pharmacophore model was validated by diverse chemotypes of Aurora A kinase inhibitors and was consistent with the structural requirements for the docked binding mechanism. Subsequently, the pharmacophore-based alignment was used to develop PHASE and comparative molecular similarity indices analysis (CoMSIA) 3D-QSAR models. The best CoMSIA model showed good statistics (q (2 )= 0.567, r (2 )= 0.992), and the predictive ability of the model was validated using an external test set of 13 compounds giving a satisfactory prediction ([Formula: see text]). The 3D contour maps provided insight into the binding mechanism and highlighted key structural features that are essential to the inhibitory activity. Based on the PHASE and CoMSIA 3D-QSAR results, a set of novel Aurora A inhibitors were designed that showed excellent potencies.

The usefulness of phosphorylated-signal transduction and activators of transcription 3 in detecting prostate cancer from negative biopsies

AIMS

To avoid the misdiagnosis of prostate cancer (PCA), many patients receive repeated biopsies, despite receiving prior negative biopsies for PCA. Signal transduction and activators of transcription 3 (STAT3), a component of the JAK-STAT signaling pathway, can be activated by tyrosine phosphorylation as P-STAT3 and involved in the regulation of cellular growth, survival and oncogenesis. We aimed to assess the reliability of detecting PCA from the expression of P-STAT3 in prostate tissue previously designated as a negative biopsy.

METHODS

Prostate tissues were obtained from the biopsies of 52 patients with localized PCA as well as from the biopsies of 80 patients free of PCA. Expression of P-STAT3 in these specimens was examined by immunohistochemical staining (IHC) and used to distinguish tissue with PCA from tissue designated as benign during a biopsy procedure.

RESULTS

P-STAT3 staining intensities in all samples (initial negative biopsies, cancer positive cores and other negative cores from the same-batch biopsies) of PCA patients was significantly higher than that of benign patients (F = 23.664, P < 0.001). Analysis of the receiver operating characteristics (ROC) curve showed that the area under curve (AUC) for P-STAT3 staining was 0.785. When positive immuno-labeling of P-STAT3 in samples from initial biopsies was used as a marker for PCA, it showed relatively high sensitivity (80.8%) and specificity (76.3%).

CONCLUSIONS

IHC of P-STAT3 could be utilized to detect PCA patients with initial negative biopsies. As a result, it can be a potential adjunctive tool for current PCA diagnostic programs. P-STAT3 can predict the onset of PCA up to 40 months earlier than currently used diagnostic approaches.

Free energy of nascent-chain folding in the translocon

During their synthesis, many water-soluble proteins and nearly all membrane proteins transit through a protein-conducting channel in the membrane, the Sec translocon, from where they are inserted into the lipid bilayer. Increasing evidence indicates that folding of the nascent protein begins already within the ribosomal exit tunnel in a sequence- and environment-dependent fashion. To examine the effects of the translocon on the nascent-chain folding, we have calculated the potential of mean force for α-helix formation of a 10-alanine oligopeptide as a function of its position within the translocon channel. We find that the predominant conformational states, α-helical and extended, reflect those found for the peptide in water. However, the translocon, via its surface properties and its variable diameter, shifts the equilibrium in favor of the α-helical state. Thus, we suggest that the translocon facilitates not only the insertion of membrane proteins into the bilayer but also their folding.

Recent progress in the identification and development of InhA direct inhibitors of Mycobacterium tuberculosis

The InhA-related enoyl-ACP reductase, an enzyme involved in fatty acid synthesis, is one of the best validated targets for the development of anti-tubercular agents. However, the majority of isoniazid (INH)-resistant clinical strains are observed mainly due to the emergence of KatG mutants that do not form an INH-NAD adduct. Thus compounds that directly inhibit InhA avoiding activation by KatG would be promising candidates for combating MDR-TB. Herein, some predominant examples of InhA direct inhibitors recently developed are reviewed and special attention is paid to 3D-structures of InhA in drug design process.

Anomalous properties of a simple small-volume membrane transport system at steady state

We investigate the transport of a single ligand L, between two macroscopic baths with different concentrations of L, by a simple membrane system. The center of this system is a very small volume V that might contain N = 0, 1, 2,... molecules of L. Access to V from either bath is by means of a single binding site for L. The steady-state properties of this simple system are studied exactly by a discrete-N master-equation approach. It is found that the mean concentration of L in V, c = N/V, is not a significant quantity either kinetically or thermodynamically. Further, the chemical potential of L in V is not defined and hence the overall thermodynamic force on L between the two baths cannot be subdivided at V. In fact, because V is small, the transport system must be treated as an indivisible system with interdependent parts. In the limit when V and N are very large, V becomes in effect a third macroscopic bath and two well-defined transport subsystems emerge (between V and either bath).

Three-state, steady-state Ising systems: Monte Carlo and Bragg-Williams treatments

In two earlier papers, the steady-state critical and phase-transition properties of a lattice of three-state enzyme molecules were studied by using the "closed" Bragg-Williams (BW), or mean field, approximation. The "open" BW and Monte Carlo methods are applied to the same problem in this paper by using finite lattices. The open BW treatment provides a way of locating the cut across a van der Waals type of loop encountered in a phase transition in the closed BW system. Thermodynamic-like methods cannot be used for this purpose as they can with two-state, steady-state systems.

Study comparing the double kissing (DK) crush with classical crush for the treatment of coronary bifurcation lesions: the DKCRUSH-1 Bifurcation Study with drug-eluting stents

BACKGROUND

Classical crush has a lower rate of final kissing balloon inflation (FKBI) immediately after percutaneous coronary intervention (PCI). The double kissing (DK) crush technique has the potential to increase the FKBI rate, and no prospective studies on the comparison of classical with DK crush techniques have been reported.

MATERIALS AND METHODS

Three hundred and eleven patients with true bifurcation lesions were randomly divided into classical (n = 156) and DK crush (n = 155) groups. Clinical and angiographic details at follow-up at 8 months were indexed. The primary end point was major adverse cardiac events (MACE) including myocardial infarction, cardiac death and target lesion revascularization (TLR) at 8 months.

RESULTS

FKBI was 76% in the classical crush group and 100% in the DK group (P < 0.001). The incidence of stent thrombosis was 3.2% in the classical crush group (5.1% in without- and 1.7% in with-FKBI) and 1.3% in the DK crush group. Cumulative 8 month MACE was 24.4% in the classical crush group and 11.4% in the DK crush group (P = 0.02). The TLR-free survival rate was 75.4% in the classical crush group and 89.5% in the DK crush group (P = 0.002).

CONCLUSIONS

DK crush technique has the potential of increasing FKBI rate and reducing stent thrombosis, with a further reduction of TLR and cumulative MACE rate at 8 months.

Inverted papilloma of urinary bladder: Is long-term cystoscopic surveillance needed? A single center’s experience

OBJECTIVES

To review all cases of urinary bladder inverted papilloma (IP) in our institution and determine the need for cystoscopic surveillance. IP is an uncommon benign tumor of the urinary tract. Its multiplicity, recurrence, and association with transitional cell carcinoma (TCC) suggest possible malignant potential, leading to conflicting clinical conclusions regarding the need for surveillance.

METHODS

All consecutive patients from January 1991 to December 2004 with IP were included in this study. A single pathologist performed the histologic review. The patients had undergone cystoscopy and ultrasound evaluation of the kidneys every 6 months.

RESULTS

Of the 52 patients, 45 were men and 7 were women. The average age at presentation was 58.9 +/- 11.8 years (range 30 to 79). No patient had a synchronous or previous bladder tumor. The most common complaint was macroscopic hematuria. Ten cases were incidental findings during bladder ultrasonography or cystoscopy. All were solitary tumors, most commonly found at the bladder neck. The average follow-up period was 62 +/- 23 months, with no recurrence. One case of subsequent noninvasive papillary TCC developed 15 months later. The initial histologic findings had revealed cytologic atypia, with suspicious urine cytology findings. On review, it was more compatible with TCC with an inverted pattern.

CONCLUSIONS

Although our cases exhibited benign biologic behavior, the presence of cytologic atypia and suspicious urine cytology require exclusion of TCC with an inverted pattern. Thus, in histologically proven solitary bladder IP with no associated TCC, cystoscopic surveillance may not be necessary.

[Time trends, estimates and projects for breast cancer incidence and mortality in China]

OBJECTIVE

Using comprehensive available data on women breast cancer in China, to describe the mortality trends from late 1970s, estimate and project the profile in 2000 and 2005, and to aim to provide a reference for clinic, basic research and prevention and control strategy making for breast cancer in China.

METHODS

Using Joinpoint model, the mortality trends were analyzed on the basis of routine surveillance data. Combining with the data from the second national mortality survey and several cancer registries, using the log-linear model (based on Poisson distribution), the breast cancer profile in 2000 and 2005 were estimated and projected.

RESULTS

Although there was a slight decline in mortality between early 1970s and 1990s, the age-specific mortality rates among young and middle age women increased dramatically which followed a continuing increase trend on both rates and absolute numbers, in both urban and rural areas in recent 15 years. Compared with 2000, there are 470 thousands more new breast cancer cases and 130 thousands more deaths from breast cancer in 2005.

CONCLUSION

Due to the double effects of both increasing risk factors and population growth and ageing, breast cancer will be one of the most extensively increasing cancers in Chinese women. The prevention and control of breast cancer will be of great emphasis for future cancer control strategy in China.

Estimation and projection of the national profile of cancer mortality in China: 1991-2005

There are no national-level data on cancer mortality in China since two surveys in 1973–1975 and 1990–1992 (a 10% sample), but ongoing surveillance systems, based on nonrandom selected populations, give an indication as to the trends for major cancers. Based on a log-linear regression model with Poisson errors, the annual rates of change for 10 cancers and all other cancers combined, by age, sex and urban/rural residence were estimated from the data of the surveillance system of the Center for Health Information and Statistics, covering about 10% of the national population. These rates of change were applied to the survey data of 1990–1992 to estimate national mortality in the year 2000, and to make projections for 2005. Mortality rates for all cancers combined, adjusted for age, are predicted to change little between 1991 and 2005 (−0.8% in men and +2.5% in women), but population growth and ageing will result in an increasing number of deaths, from 1.2 to 1.8 million. The largest predicted increases are for the numbers of female breast (+155.4%) and lung cancers (+112.1% in men, +153.5% in women). For these two sites, mortality rates will almost double. Cancer will make an increasing contribution to the burden of diseases in China in the 21st century. The marked increases in risk of cancers of the lung, female breast and large bowel indicate priorities for prevention and control. The increasing trends in young age groups for cancers of the cervix, lung and female breast suggest that their predicted increases may be underestimated, and that more attention should be paid to strategies for their prevention and control.

Estimation and projection of the national profile of cancer mortality in China: 1991-2005

There are no national-level data on cancer mortality in China since two surveys in 1973-1975 and 1990-1992 (a 10% sample), but ongoing surveillance systems, based on nonrandom selected populations, give an indication as to the trends for major cancers. Based on a log-linear regression model with Poisson errors, the annual rates of change for 10 cancers and all other cancers combined, by age, sex and urban/rural residence were estimated from the data of the surveillance system of the Center for Health Information and Statistics, covering about 10% of the national population. These rates of change were applied to the survey data of 1990-1992 to estimate national mortality in the year 2000, and to make projections for 2005. Mortality rates for all cancers combined, adjusted for age, are predicted to change little between 1991 and 2005 (-0.8% in men and +2.5% in women), but population growth and ageing will result in an increasing number of deaths, from 1.2 to 1.8 million. The largest predicted increases are for the numbers of female breast (+155.4%) and lung cancers (+112.1% in men, +153.5% in women). For these two sites, mortality rates will almost double. Cancer will make an increasing contribution to the burden of diseases in China in the 21st century. The marked increases in risk of cancers of the lung, female breast and large bowel indicate priorities for prevention and control. The increasing trends in young age groups for cancers of the cervix, lung and female breast suggest that their predicted increases may be underestimated, and that more attention should be paid to strategies for their prevention and control.

Long-term temporal-spatial dynamics of marine coastal water quality in the Tolo Harbor, Hong Kong, China

The long-term temporal and spatial dynamics of marine coastal water quality in Tolo Harbor, Hong Kong were explored. The Harbor is divided into three zones represented as Harbor, Buffer, and Channel Subzones. The time range for the study covers the period from the 1970s to the 1990s. The selected indicators for the comprehensive assessment of water quality consist of physical, chemical and biological aspects, including suspended solids(SS), Secchi disk depth(SD), 5-day biochemical oxygen demand(BOD5), total nitrogen (TN), total phosphorus(TP), faecal coliform, chlorophyll-a(Chl-a), and the number of red tide occurrences. The results indicated the presence of obvious temporal and spatial trends with regard to changes in water quality. Spatially, water quality in the Channel Subzone is the best, while that in the Harbor Subzone is the worst. On a temporal basis, the average trend from bad to good was 1980s > 1990s > 1970s as indicated by most of the selected water quality indicators. Water quality during the late 1980s reached its worst level with the lowest SD, the highest BOD5, TN, TP, Chl-a concentrations, and the number of red tide occurrences. These long-term temporal-spatial water quality trends were also found in other studies of the Tolo Harbor. The large quantity of pollutants produced as a result of increasing population, industrial and commercial actives, and urbanization and industrialization trends in both Shatin and Tai Po seem to be primarily responsible for the changes in marine coastal water quality.

[Analysis on karyotypes of ANKA strain of Plasmodium berghei]

OBJECTIVE

To analyze the molecular karyotypes of ANKA strain of Plasmodium berghei and demonstrate the size and number of chromosomes.

METHODS

To isolate the genome DNA of P. berghei ANKA strain and analyze molecular karyotypes through CHEF-III pulsed field gel electrophoresis (PFGE).

RESULTS

The number of chromosomes was found to be 14, and their size ranged from 0.6 Mb to 3 Mb. Chromosomes number 5 to 7 and 9 to 12 appeared co-migrated in the gel.

CONCLUSION

PFGE technique is useful for analyzing the molecular karyotypes and may be also useful for further study to locate the special gene on chromosomes and carry out the genetic characters and mechanism of drug resistance.

The glycine allele of a glycine/arginine polymorphism in the beta2-adrenergic receptor gene is associated with essential hypertension in a population of Chinese origin

BACKGROUND

Several studies implicate polymorphisms in the human beta-adrenergic receptor gene (ADRB2) in the susceptibility to hypertension. We sought to replicate these results in a population of Chinese origin primarily from Taiwan and the San Francisco Bay area.

METHODS

We genotyped >800 hypertensive subjects and individuals with low-normal blood pressure that were derived largely from the same families as the hypertensive patients for three polymorphisms in the ADRB2 gene: a C/T transition at position 47 (C-47T) in the 5' leader cistron; another C/T transition that results in a glycine/ arginine substitution at codon 16 (Gly16Arg), and a G/C transversion that causes a glutamate/glutamine substitution at codon 27 (Glu27Gln).

RESULTS

The Gly16Arg was significantly associated with hypertension (P < .03). Under a dominant model, for hypertension the relative risk for the Gly/Gly and Gly/Arg genotypes versus the Arg/Arg genotype was 1.35 (95% confidence limits [CL] 1.08, 1.70); for low-normal blood pressure the relative risk was 0.79 (95% CL 0.66, 0.94). This polymorphism explained approximately 1% of the variance in systolic and diastolic blood pressures in our study population. There was no evidence of association between the C-47T and Glu27Gln polymorphisms and hypertension in this population.

CONCLUSIONS

The Glyl6 allele in the beta2-adrenergic receptor gene is a susceptibility allele for essential hypertension in a population of Chinese origin.

Genetic variation in aldosterone synthase predicts plasma glucose levels

The mineralocorticoid hormone, aldosterone, is known to play a role in sodium homeostasis. We serendipitously found, however, highly significant association between single-nucleotide polymorphisms in the aldosterone synthase gene and plasma glucose levels in a large population of Chinese and Japanese origin. Two polymorphisms--one in the putative promoter (T-344C) and another resulting in a lysine/arginine substitution at amino acid 173, which are in complete linkage disequilibrium in this population--were associated with fasting plasma glucose levels (P = 0.000017) and those 60 (P = 0.017) and 120 (P = 0.0019) min after an oral glucose challenge. A C/T variant in intron 1, between these polymorphisms, was not associated with glucose levels. Arg-173 and -344C homozygotes were most likely to be diabetic [odds ratio 2.51; 95% confidence interval (C.I.) 1.39-3.92; P = 0.0015] and have impaired fasting glucose levels (odds ratio 3.53; 95% C.I. 2.02-5.5; P = 0.0000036). These results suggest a new role for aldosterone in glucose homeostasis.

Sibling-based association study of the PPARgamma2 Pro12Ala polymorphism and metabolic variables in Chinese and Japanese hypertension families: a SAPPHIRe study. Stanford Asian-Pacific Program in Hypertension and Insulin Resistance

The peroxisome proliferator activated receptor (PPAR) gamma2 is a transcription factor that has been shown to be involved in adipocyte differentiation, adipogenesis, and insulin sensitivity. To address the role of PPARgamma2 in glucose homeostasis and insulin sensitivity, among many other objectives, we conducted a sibling-controlled association study in a multicenter program - the Stanford Asian-Pacific Program in Hypertension and Insulin Resistance (SAPPHIRe). Approximately 2525 subjects in 734 Chinese and Japanese families have been recruited from six field centers for SAPPHIRe. In total, 1702 subjects including parents and siblings from 449 families have been genotyped for PPARgamma2, of which 328 families were Chinese and 121 Japanese. Only 88 subjects of the 1525 siblings screened for the P12A polymorphism were found to be carriers of the A variant, the most common variant of the PPARgamma2 gene. A variant frequencies of the siblings were 4.27% in Chinese and 2.72% in Japanese. A sibling-controlled association study was performed through genetically discordant sibships (i.e., P/P genotype vs. P/A + A/A genotypes). Specifically, we examined whether there were differences in metabolic variables between the discordant siblings within families. In total, 88 subjects carrying either 1 or 2 A alleles had at least one sibling who was discordant for the P12A polymorphism, yielding a total of 180 individuals from 47 families for analyses, among which 92 siblings were homozygous for wild-type P allele. Siblings with the A variant tended to have lower levels of fasting plasma glucose (OG-10), and lower glucose levels at 60 min following oral glucose loading after adjusting for age, gender, and body mass index. Using a mixed model treating family as a random effect, we found that P12A polymorphism of the PPARgamma2 gene contributes significantly to the variance in fasting plasma glucose, glucose level at 60 min, and insulin-resistance homeostasis model assessment. Our results suggest that within families siblings with the A variant in the PPARgamma2 gene may be more likely to have better glucose tolerance and insulin sensitivity independent of obesity in Chinese and Japanese populations.

Stiff-Baby--an unusual manifestation of cytoplasmic body myopathy: report of one case

A 2-month-old male baby was admitted to our hospital with episodic cyanosis and respiratory failure which required mechanical ventilation. He was found to have upper limb flexion rigidity and poor weight gain since one month old. Progressive muscle stiffness over the abdomen, chest wall, back and four limbs were also noted. He could not be weaned from the ventilator smoothly due to recurrent CO2 retention. Laboratory tests revealed a high serum creatine kinase level. Cytoplasmic body myopathy was confirmed by muscle biopsy. The unusual initial presentations of generalized stiffness and early onset of respiratory failure were quite different from those of patients reported in the literature, who had floppiness, muscular atrophy and weakness. Prednisolone and Vigabatrin were given and the patient showed slight improvement in muscle stiffness and spontaneous movement.

Genetic variation in the human urea transporter-2 is associated with variation in blood pressure

The kidney, by regulating the volume of fluid in the body, plays a key role in regulating blood pressure (BP). The kidney uses primarily sodium and, to a lesser extent, urea to maintain the appropriate volume of fluid. Genetic variation in proteins that determine sodium reabsorption and excretion is known to significantly influence BP. However, the influence of genetic variation in urea transporters on BP has not been examined. We determined therefore whether nucleotide variation in the kidney-specific human urea transporter, HUT2, is associated with variation in BP. After determining the genomic structure of the coding sequence, seven single nucleotide polymorphisms (SNPs) were identified. Two of the SNPs result in Val/Ile and Ala/Thr amino acid substitutions at positions 227 and 357 in the HUT2 open reading frame, respectively. Another SNP is silent and four others are in introns or the 3' untranslated region. Over 1000 hypertensive and low-normotensive individuals of Chinese origin were typed for five of these SNPs using a high-throughput genotyping method. The Ile227 and Ala357 alleles were associated with low diastolic BP in men but not women, with odds ratios 2.1 [95% confidence interval (CI) 1.5-2.7, P < 0.001] and 1.5 (95% CI 1.2-1.8, P < 0.001), respectively. There was a similar trend for systolic BP, and odds ratios for the Ile227 and Ala357 alleles were 1.7 (95% CI 1.2-2.3, P = 0.002) and 1.3 (95% CI 1.1-1.6, P = 0.007), respectively, in men.

Growth response and final height in growth hormone-deficient patients treated with biosynthetic growth hormone

Twenty-three patients with growth hormone deficiency (GHD) followed until their final heights (FH) were reported by retrospective review. Seven patients had spontaneous puberty (group 1) and sixteen required induction of puberty (group 2). Their heights prior to growth hormone (GH) therapy were -3.7 +/- 1.4 and -2.8 +/- 1.4 SDS in men and women respectively. The mean ages at initiation of GH therapy were 17.2 +/- 3.3 in men and 13.0 +/- 1.7 years in women, with a growth velocity < 4 cm/year and a mean bone age (BA) of 12.6 +/- 0.7 years (men) and 9.8 +/- 1.2 years (women). The dose of GH was 0.27-0.83 IU/kg/week, with a total duration of 2.5 +/- 1.0 years. Their consecutive annual mean growth velocities on GH therapy were: 10.6 cm/year, 8.0 cm/year, 6.1 cm/year, 5.1 cm/year and 4.6 cm/year respectively. They reached a mean final height of 167.1 +/- 5.3 cm (-0.4 +/- 1.0 SDS) in men and 157.9 +/- 3.5 cm (-0.1 +/- 0.7 SDS) in women, which is slightly taller than their target height. Demographic factors related to growth response and final heights were analyzed. We conclude that GH therapy is very effective in linear growth promotion. Their final height was correlated with initial height SDS, target height SDS, predicted adult height SDS according to the bone age at the start of GH therapy and height SDS at the onset of puberty.

High-throughput genotyping with single nucleotide polymorphisms

To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5' nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To demonstrate the utility of these methods, we typed >1600 individuals for a G-to-T transversion that results in a glutamate-to-aspartate substitution at position 298 in the endothelial nitric oxide synthase gene, and a G/C polymorphism (newly identified in our laboratory) in intron 8 of the 11-beta hydroxylase gene. The genotyping method is accurate-we estimate an error rate of fewer than 1 in 2000 genotypes, rapid-with five 96-well PCR machines, one fluorescent reader, and no automated pipetting, over one thousand genotypes can be generated by one person in one day, and flexible-a new SNP can be tested for association in less than one week. Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three "pseudo-SNPs" (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication.

Precocious puberty associated with growth hormone deficiency in a patient with craniopharyngioma: report of one case

Isosexual precocious puberty in girls is not uncommon, but its association with craniopharyngioma and growth hormone deficiency is rarely reported. We present a patient with this combination. An 8-year-old girl developed breasts and then had menarche at 7 9/12 years old. Growth hormone deficiency was suspected due to inappropriate height and growth velocity in association with idiopathic precocity and a poor predicted adult height of 138.8 cm. Growth hormone deficiency was confirmed by clonidine and insulin stimulation tests. Intracranial lesion was suspected due to precocity associated with GH deficiency. MRI of the sella's region revealed a 1 cm mass in the hypothalamus. After surgical resection, pathology of the tumor disclosed a craniopharyngioma which has rarely been reported to cause precocious puberty. The precocious puberty regressed after surgery. Growth hormone deficiency persisted and GH therapy was given to improve growth. The growth rate of patients with both growth hormone deficiency and precocious puberty may be maintained within the normal prepubertal range by the effect of sex steroid. We suggest that in patients with central type precocity in association with an inappropriate growth status, physicians should investigate the underlying intracranial lesion, and the possibility of growth hormone deficiency.

Theoretical formalism for bead movement powered by single two-headed motors in a motility assay

Kinesins and dyneins are protein motors that can use the free energy of ATP hydrolysis to carry a cargo and move uni-directionally along a microtubule filament. The purpose of this paper is to derive the formalism connecting the ATP-driven translocation reactions of these motors on microtubule filaments and the movement of the bead carried by the motor in a motility assay in which the bead is clamped at an arbitrary constant force. The formalism is thus useful in elucidating the load-dependent kinetic mechanism of the free-energy transduction of the motor using the mechanical data obtained from the motility assay. The formalism is also useful in assessing the effect on the measured motility data of various physical and hydrodynamic parameters of the assay, such as the size of the bead, the viscosity of the medium, the stiffness of the elastic element connecting the motor and the bead, etc. In a previous paper [Biophys. J. 67 (2000) 313] (hereafter referred to as paper I), we have derived the formalism for the case that the motor in the assay has only one head. In this paper we extend the derivation to the case that the motor is two-headed. The formalism is derived based on a simple two-state hand-over-hand model for the movement of the motor on microtubule, but can be easily extended to more complicated kinetic models. Effects of various hydrodynamic parameters on the velocity of the bead are studied with numerical calculations of the model. The difference between the formalism presented in this paper and the widely used "chemical" formalism, in which the movement of the kinesin and the bead is described by pure chemical reactions, is discussed.

Caldesmon reduces the apparent rate of binding of myosin S1 to actin-tropomyosin

Equilibrium measurements of the rate of binding of caldesmon and myosin S1 to actin-tropomyosin from different laboratories have yielded different results and have led to different models of caldesmon function. An alternate approach to answering these questions is to study the kinetics of binding of both caldesmon and S1 to actin. We observed that caldesmon decreased the rate of binding of S1 to actin in a concentration-dependent manner. The inhibition of the rate of S1 binding was enhanced by tropomyosin, but the effect of tropomyosin on the binding was small. Premixing actin with S1 reduced the amplitude (extent) of caldesmon binding in proportion to the fraction of actin that contained bound S1, but the rate of binding of caldesmon to free sites was not greatly altered. No evidence for a stable caldesmon-actin-tropomyosin-S1 complex was observed, although S1 did apparently bind to gaps between caldesmon molecules. These results indicate that experiments involving caldesmon, actin, tropomyosin, and myosin are inherently complex. When the concentration of either S1 or caldesmon is varied, the amount of the other component bound to actin-tropomyosin cannot be assumed to remain fixed. The results are not readily explained by a mechanism in which caldesmon acts only by stabilizing an inactive state of actin-tropomyosin. The results support regulatory mechanisms that involve changes in the actin-S1 interaction.