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PubMed2002

Time-frequency distribution of neuronal activity in the gerbil inferior colliculus responding to auditory stimuli.

We classified the firing pattern of neurons in the central nucleus of the inferior colliculus (ICc) in a time-frequency coordinate, except for simple phasic onset responses, into four groups using tone bursts with a wide frequency range. The ICc is the major nucleus in the auditory midbrain. Single-unit recordings were made from ICc contralateral to the monaurally stimulated ear in anesthetized gerbils. Neurons of three out of the four groups (53.8%) demonstrated that the firing distribution changed depending on time and frequency, which was not shown previously. Neurons of one group (37.6%) exhibited a frequency response range that changed little with time. The remaining neurons (8.6%) belonged to none of the above classifications. The time-frequency-sensitive neurons in ICc may be good candidates for coding communication sounds, which comprise complex temporal changes in frequency.

Acoustic Stimulation↗
PubMed2004

The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 2. Cooperative free energies of (alphaFeCObetaFe)2 and (alphaFebetaFeCO)2 T-state tetramers.

Ligand photodissociation experiments are used to measure the prephotolysis equilibria between doubly liganded R and T quaternary conformers of the symmetric Fe-Co HbCO hybrids, (alpha(FeCO)beta(Co))(2) and (alpha(Co)beta(FeCO))(2). The free energies obtained from these data are used to calculate the cooperative free energies of the (alpha(FeCO)beta(Fe))(2) and (alpha(Fe)beta(FeCO))(2) intermediate CO-ligation states of normal hemoglobin in the T conformation, quantities important to the evaluation of current models of cooperativity. The symmetry rule model, incorporating sequential cooperativity of T-state ligand binding within an alphabeta dimer in addition to the traditional two-state cooperativity of the tetramer, predicts a larger free energy penalty for disturbing both dimers in a doubly liganded T tetramer than would be expected in the two-state model as currently formulated. (Cooperative energy penalties are simply proportional to the number of tetramer-bound ligands in the traditional two-state model.) The value found here for the energies of doubly liganded T microstates in which both dimers are perturbed, 7.9 +/- 0.3 kcal/mol, is consistent with the symmetry rule model but significantly higher than that expected (5-6 kcal/mol) in the two-state model of cooperativity.

Allosteric Regulation↗
PubMed2004

The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 1. Microstate linear free energy relations.

A novel model linking the thermodynamics and kinetics of hemoglobin's allosteric (R --> T) and ligand binding reactions is applied to photolysis data for human HbCO. To describe hemoglobin's kinetics at the microscopic level of structural transitions and ligand-binding events for individual [ij]-ligation microstates ((ij)R --> (ij)T, (ij)R + CO --> ((i)(+1))(k)R, and (ij)T + CO --> ((i)(+1))(k)T), the model calculates activation energies, (ij)DeltaG(++), from previously measured cooperative free energies of the equilibrium microstates (Huang, Y., and Ackers, G. K. (1996) Biochemistry 35, 704-718) by using linear free energy relations ((ij)DeltaG(++) - (01)DeltaG(++) = alpha[(ij)DeltaG - (01)DeltaG], where the parameter alpha, describing the variation of activation energy with reaction energy perturbation, can depend on the natures of both the reaction and the perturbation). The alpha value measured here for the allosteric dynamics, 0.21 +/- 0.03, corresponds closely to values observed previously, strongly suggesting that the thermodynamic microstate energies directly underlie the allosteric kinetics (as opposed to the alpha((ij)DeltaG(RT)) serving merely as arbitrary fitting parameters). Besides systematizing the study of hemoglobin kinetics, the utility of the microstate linear free energy model lies in the ability to test microscopic aspects of allosteric dynamics such as the "symmetry rule" for quaternary change deduced previously from thermodynamic evidence (Ackers, G. K., et al. (1992) Science 255, 54-63). Reflecting a remarkably detailed correspondence between thermodynamics and kinetics, we find that a kinetic model that includes the large free energy splitting between doubly ligated T microstates implied by the symmetry rule fits the data significantly better than one that does not.

Allosteric Regulation↗
PubMed2006

Validity of International Classification of Diseases, Ninth Revision, Clinical Modification Codes for Acute Renal Failure.

Administrative and claims databases may be useful for the study of acute renal failure (ARF) and ARF that requires dialysis (ARF-D), but the validity of the corresponding diagnosis and procedure codes is unknown. The performance characteristics of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes for ARF were assessed against serum creatinine-based definitions of ARF in 97,705 adult discharges from three Boston hospitals in 2004. For ARF-D, ICD-9-CM codes were compared with review of medical records in 150 patients with ARF-D and 150 control patients. As compared with a diagnostic standard of a 100% change in serum creatinine, ICD-9-CM codes for ARF had a sensitivity of 35.4%, specificity of 97.7%, positive predictive value of 47.9%, and negative predictive value of 96.1%. As compared with review of medical records, ICD-9-CM codes for ARF-D had positive predictive value of 94.0% and negative predictive value of 90.0%. It is concluded that administrative databases may be a powerful tool for the study of ARF, although the low sensitivity of ARF codes is an important caveat. The excellent performance characteristics of ICD-9-CM codes for ARF-D suggest that administrative data sets may be particularly well suited for research endeavors that involve patients with ARF-D.

Acute Kidney Injury↗
PubMed2002

Polymorphisms in the human xeroderma pigmentosum group A gene and their impact on cell survival and nucleotide excision repair.

Polymorphisms in DNA repair genes may contribute to defects in DNA repair and increased susceptibility to cancer. The xeroderma pigmentosum group A (XPA) gene is required for nucleotide excision repair (NER) and mutations in XPA highly predispose humans to skin cancer. We examined DNA samples from 189 individuals for polymorphisms in the XPA gene. First, SSCP analysis was used to examine each of the six exons and their intron boundaries. One frequent single nucleotide polymorphism (SNP) in the untranslated region of exon 1 and two rare SNPs which produce the changes Arg228Gln and Val234Leu in the coding region of exon 6 were identified. Quite surprisingly, no sequence variants were found within the coding regions or the adjacent intron boundaries of exons 1-5. Ecdysone-inducible expression vectors containing wild type XPA cDNA or cDNAs representing the two polymorphisms that we identified in exon 6 were created and independently introduced into the XPA deficient cell line XP12RO-SV. Transcription-coupled repair (TCR), global genome repair (GGR) and cell survival following UV irradiation were studied in each cell line in the absence or presence of the ecdysone hormone analog, ponasterone A. No substantial difference in repair or cell survival was found in cells complemented with wild type or polymorphic alleles of XPA. A 10-fold increase in the expression of XPA by addition of ponasterone A resulted in faster removal of 6-4 photoproducts from the total genomes of cells complemented with wild type or polymorphic alleles of XPA but had no significant impact on TCR or global genome repair of cyclobutane pyrimidine dimers (CPDs). Since our SSCP analysis failed to detect significant numbers of polymorphisms we directly sequenced exons 4-6 in a subset of our samples. One additional rare SNP, which produces the change Leu252Val was found in exon 6 and four rare SNPs and one rare single nucleotide deletion were found in intron 4. Hence, the XPA gene appears to be a cold spot for genetic variation and rare polymorphisms in the coding region of the gene do not reduce NER or cell survival after UV irradiation.

Cell Survival↗
PubMed2006

Genetic architecture of the F7 gene in a Spanish population: implication for mapping complex diseases and for functional assays.

Delineating the genetic variability of loci coding for complex diseases helps to understand the individual variation in disease susceptibility and drug response. We present the allelic architecture of the F7 gene. This gene is the major determinant of FVII plasma levels, and these plasma levels constitute an important intermediate risk factor for cardiovascular disease. As part of the Genetic Analysis of Idiopathic Thrombophila Project, we completely re-sequenced the F7 locus (promoter, exons, introns, and 3'-untranslated region) in 40 unrelated individuals. We found 49 polymorphisms with only two amino acid changes suggesting that regulatory non-coding and intronic variants are responsible for the FVII variability. These results are important for mapping susceptibility alleles of complex diseases, because differences in pair-wise linkage disequilibrium patterns between DNA variants and haplotype frequency distributions may help to detect disease-associated alleles. In addition, we present the results of an in silico search that established genomic comparisons among different species. In conclusion, our study of the F7 DNA sequence variations is an example of a strategy for analyzing the genetic architecture of a quantitative trait locus. Furthermore, it provides a model for future analyses of genetic factors that contribute to the susceptibility of complex diseases in humans.

Alleles↗
PubMed1996

Experience with color-coded duplex sonography after combined kidney/pancreas transplantation--preliminary results.

The value of color-coded duplex sonography in the assessment of combined kidney and pancreatic transplantations (KTX/PTX) was studied in 9 patients. In normal graft function the median resistive index (RI) was 0.69 (range 0.60-0.80) for the kidney and 0.61 (range 0.55-0.70) for the pancreas. Ten episodes of graft dysfunction (kidney n = 4; pancreas n = 6) were observed. During renal rejection and hemolytic uremic syndrome the RI was above 0.80. In pancreatic rejection the RI exceeded 0.80 while all other causes of pancreatic dysfunction were not associated with changes in the RI. Color-coded duplex sonography may prove to be a reliable noninvasive diagnostic method in the evaluation of the posttransplant course after combined KTX/PTX, in particular in the diagnosis of pancreatic rejection.

Diabetes Mellitus, Type 1↗
PubMed2003

[Study on the gene mutation of TIGR in primary open angle glaucoma, their relatives and normal controls in Chongqing].

OBJECTIVE: To study trabecular meshwork induced glucocorticoid response protein (TIGR) gene mutation in primary open angle glaucoma (POAG), their relatives and normal controls in Chongqing. METHODS: (1) The coding sequence of TIGR was screened for sequence alterations using polymerase chain reaction (PCR) followed by single-strand conformation polymorphism (SSCP). (2) Samples corresponding to bands of altered mobility were sequenced. (3) The sequence alterations were analyzed by bioinformatics. RESULTS: (1) In 15 POAG, TIGR gene mutation was found in 5 cases. In 10 POAG relatives, 2 TIGR gene mutations were found. No TIGR gene mutation was found in 20 normal persons in Chongqing. (2) The mutation sites Ser55Thr, Asp247Stop and in 49021 c-t alteration discovered in the present study have not been reported previously. The 63155 c-t alternation has been reported as a polymorphism site previously. (3) Bioinformatics analysis indicated that the mutations in structural domain could lead to the changes in the amino acid sequence coded, second structure of protein, isoelectric point and antigen binding site. CONCLUSIONS: We found that the TIGR gene mutations is closely related to the occurrence of JOAG in Chongqing. The relatives of POAG patients may have a higher incidence of TIGR gene mutation as compared with the controls. Furthermore, after analyzed by bioinformatics, we found that the alteration of structure and biological activity of TIGR protein resulted from gene mutation may be one of the important changes that leading to the occurrence of POAG.

Adolescent↗
PubMed1983

Gödel's arithmetization procedure as the basis for a pattern recognition system: a nascent theory mapping pattern into number and number into phenomenal experience.

Prime numbers are used to code various dimensions of an input matrix (receptor surface), i.e., prime numbers code the position of each cell in the matrix, the position of each column and row constituted by the cells of the matrix, and the orientation of each such column or row. The coding permits any pattern or stimulus configuration to be changed into a single, unique number, viz., the serial product of the prime numbers which code the relevant dimensions of the pattern. Storage of a pattern is effected by storage of the serial product. By factoring the serial product, the pattern or stimulus configuration is analyzed into the dimensions (features) specified by the code. The factorization is also utilized in abstracting a schema, in approximating a feature count model, and in presenting a strategy for holistic vs sequential pattern processing. Finally, the relationship between the serial product representing a pattern and the phenomenal experience of a pattern is explored.

Computers↗
PubMed2006

Candidate gene mutation analysis in idiopathic acquired sideroblastic anemia (refractory anemia with ringed sideroblasts).

BACKGROUND: For most cases of idiopathic acquired sideroblastic anemia (IASA), the molecular pathogenesis is unknown, despite the consistent morphological signature of abundant pathological ringed sideroblasts with their characteristic iron-engorged mitochondria. Moderately elevated free erythrocyte protoporphyrin (FEP) levels have been described in IASA, suggesting that the activity of ferrochelatase, the enzyme that catalyzes the final step in heme biosynthesis (incorporation of ferrous iron into protoporphyrin), might be diminished in erythroid progenitor cells from IASA patients. METHODS: We confirmed FEP elevation in IASA, then pursued a candidate gene approach that included screening the gene encoding ferrochelatase, FECH, for promoter and coding region mutations and mRNA expression changes in bone marrow from 37 patients with IASA. RESULTS: The analytical techniques employed detected mutations in a test cohort of previously undiagnosed patients with biochemical evidence for erythropoietic protoporphyria, a condition resulting from germline mutations in FECH, but somatic missense mutations of FECH and its promoter were not observed in IASA patients. FECH was modestly overexpressed in progenitor cells from patients with IASA, compared with MDS patients without sideroblasts and healthy controls. In addition, we analyzed ABCB7 and PUS1, genes implicated in congenital sideroblastic anemia syndromes, but again found no coding mutations in acquired cases. CONCLUSION: We conclude that acquired mutations in the factors currently known to cause inherited sideroblastic anemias are uncommon in IASA.

ATP-Binding Cassette Transporters↗
PubMed2001

Epidemiology of pulmonary embolism.

The diagnosis of venous thromboembolism (VTE) has notoriously been challenging because the disease often has no specific clinical presentation, can at times be completely asymptomatic, and can masquerade as other illnesses. To further complicate matters, the rules for coding VTE in the presence of other illnesses changed in 1983 so that among patients who died of VTE and other causes, VTE was omitted from the coding. The International Cooperative Pulmonary Embolism Registry enrolled 2454 consecutive pulmonary embolism (PE) patients from 52 participating hospitals in 7 countries. The aim was to establish the 3-month all-cause mortality rate and to identify factors associated with death. Three-month follow-up was completed in 98% of the patients. The all-cause mortality rate was 11.4% during the first 2 weeks after diagnosis and 17.4% at 3 months. Especially troubling among survivors was the high rate of recurrent VTE after anticoagulation was discontinued. Age is a potent risk factor for the development of VTE. The two most common genetic mutations that predispose to VTE are the factor V Leiden and the prothrombin gene. VTE can be precipitated by oral contraceptives, pregnancy, or hormone replacement therapy.

Contraceptives, Oral, Hormonal↗
PubMed1996

An iterative algorithm for correcting sequencing errors in DNA coding regions.

Insertion and deletion (indel) sequencing errors in DNA coding regions disrupt DNA-to-protein translation frames, and hence make most frame-sensitive coding recognition approaches fail. This paper extends the authors' previous work on indel detection and "correction" algorithms, and presents a more effective algorithm for localizing indels that appear in DNA coding regions and "correcting" the located indels by inserting or deleting DNA bases. The algorithm localizes indels by discovering changes of the preferred translation frames within presumed coding regions, and then "corrects" them to restore a consistent translation frame within each coding region. An iterative strategy is exploited to repeatedly localize and "correct" indels until no more indels can be found. Test results have shown that this improved algorithm can detect and "correct" more indels while not worsening the rate of introduction of false indels when compared to the authors' previous work.

Algorithms↗
PubMed2006

Investigation of the role of the agouti signaling protein gene (ASIP) in coat color evolution in primates.

We investigated variation in the gene encoding the agouti signaling protein (ASIP) in relation to coat color evolution in primates. We found little evidence that mutations in the coding region of ASIP have been involved in color changes among closely related primate species. Among many closely related species with differing coat color, the coding region of ASIP was identical. In two cases (Sulawesi macaque and black lion tamarin) where species with almost completely black coat color had derived point mutations in exon 4 of the ASIP coding sequence, the same mutations did not alter coloration in other mammals and so probably do not affect ASIP function. Evolutionary reconstructions of two key phenotypes that are typically related to ASIP function--transverse phaeomelanin bands on hairs and pale ventral coloration--showed that these usually evolved concurrently, suggesting that loci acting downstream of ASIP may be involved. Analysis of dN/dS ratios revealed a likely change in functional constraint on ASIP following loss of agouti-banded hairs + pale ventral coloration, particularly in catarrhine primates (humans, apes, and Old World monkeys). Together with previous results on a lack of association of coat color with MC1R variation, these results suggest that other loci probably have an important role in primate coat color evolution.

Agouti Signaling Protein↗
PubMed1990

Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria.

Yeast mitochondria use UUR as the sole leucine codons. CUN, universal leucine codons, are read as threonine by aberrant threonine tRNA with anticodon sequence (UAG). The reassignment of CUN codons to threonine during yeast mitochondrial evolution could have proceeded by the disappearance of CUN codons from the reading frames of messenger RNA, through mutation mainly to UUR leucine codons as a result of AT pressure. We suggest that this was accompanied by a loss of leucine-accepting ability of tRNA Leu(UAG). This tRNA could have then acquired threonine-accepting activity through the appearance of an additional threonyl-tRNA synthetase. CUN codons that subsequently appeared from mutations of various other codons would have been translated as threonine. This change in the yeast mitochondrial genetic code is likely to have evolved through a series of nondisruptive nucleotide substitutions that produced no widespread replacement of leucine by threonine in proteins as a consequence.

Adenine↗
PubMed2006

Spike-timing codes enhance the representation of multiple simultaneous sound-localization cues in the inferior colliculus.

To preserve multiple streams of independent information that converge onto a neuron, the information must be re-represented more efficiently in the neural response. Here we analyze the increase in the representational capacity of spike timing over rate codes using sound localization cues as an example. The inferior colliculus receives convergent input from multiple auditory brainstem nuclei, including sound localization information such as interaural level differences (ILDs), interaural timing differences (ITDs), and spectral cues. Virtual space techniques were used to create stimulus sets varying in two sound-localization parameters each. Information about the cues was quantified using a spike distance metric that allows one to separate contributions to the information arising from spike rate and spike timing. Spike timing enhances the representation of spectral and ILD cues at timescales averaging 12 ms. ITD information, however, is carried by a rate code. Comparing responses to frozen and random noise shows that the temporal information is mainly attributable to phase locking to temporal stimulus features, with an additional first-spike latency component. With rate-based codes, there is significant confounding of information about two cues presented simultaneously, meaning that the cues cannot be decoded independently. Spike-timing-based codes reduce this confounded information. Furthermore, the relative representation of the cues often changes as a function of the time resolution of the code, implying that information about multiple cues can be multiplexed onto individual spike trains.

Acoustic Stimulation↗
PubMed2002

The aquaporin-2 water channel in autosomal dominant primary nocturnal enuresis.

PURPOSE: Nocturnal enuresis is one of the most common diagnoses in a pediatric clinic. Recently, linkage analysis revealed a 2-point lod score of 4.2 in 6 families with dominant primary nocturnal enuresis around the aquaporin-2 (AQP2) water channel locus. Since primary nocturnal enuresis is ameliorated by desmopressin, AQP2 expression is increased by desmopressin and AQP2 is essential for concentrating urine, we determined whether a mutation in the AQP2 gene could cause primary nocturnal enuresis in these families. MATERIALS AND METHODS: Genomic DNAs of several patients from the 6 families were analyzed for disease causing mutations in the 4 exons of the AQP2 genes. RESULTS: In 1 family a G to A transition in the intron 1 splice donor site was found but it was also found in healthy subjects. In another family a C to T transition in the intron 1 splice acceptor region was identified but it was often found in splice acceptor sites. In 2 families a C to T transition was identified in the coding region of exon 3 but this mutation did not lead to a changed amino acid. CONCLUSIONS: Since no mutation in the AQP2 coding sequence was found, while this is essential for involvement in dominant primary nocturnal enuresis, the AQP2 gene is excluded as a candidate for autosomal dominant PNE in these families in which the disease co-segregates with chromosome 12q.

Aquaporin 2↗
PubMed2000

Mutation screening of a neutral amino acid transporter, ASCT1, and its potential role in schizophrenia.

In a previous study, a genome scan of a subset of schizophrenia families from Palau, Micronesia gave evidence suggestive of linkage to microsatellite markers at 2p13-14. In addition, in a large extended multiplex pedigree (K1583), an 11 cM 2p13-14 haplotype segregated with the illness in eight distantly related schizophrenics. The haplotype region includes a neutral amino acid transporter, ASCT1. We mutation-screened the coding region, flanking intronic sequence and 5'-untranslated region of this transporter in affected members of K1583, two Palauan controls and one Caucasian control. Most polymorphisms were found to be silent or common to all samples scanned. A G/A heterozygote within intron 3 was found in one schizophrenic member of K1583, but was not found in any of the other affected members of K1583. A G/A heterozygote within intron 6 was found in two of six schizophrenics tested in K1583, and in one control. As none of the sequence polymorphisms segregated with illness in the eight schizophrenics, it is unlikely that changes in the 5'-untranslated region, coding sequence or flanking intronic sequence of the ASCT gene predispose to schizophrenia in these families.

Amino Acid Transport Systems↗
PubMedDate not supplied

Preoperative colour-coded duplex scanning in varicose veins of the lower extremity.

OBJECTIVE: To evaluate the role of colour-coded duplex scanning in the preoperative assessment of varicose veins of the lower extremity. DESIGN: Open study. SETTING: District hospital. SUBJECTS: 48 patients who were due to be operated on for varicose veins (20 bilateral); 10 were being operated on for the second time. MAIN OUTCOME MEASURES: The planned operation was changed according to the results of the colour-coded duplex scan if they differed from those of physical examination and continuous wave Doppler flow, and its accuracy was verified at operation. RESULTS: The use of colour-coded duplex scanning resulted in a change in the plan of operation in 18 of the 68 legs. Escape points between the superficial and deep venous system would have been left intact in 14, the long saphenous vein would have been stripped unnecessarily in three, and one exploration to find an incompetent perforating vein would have been unnecessary. In 6 of the 10 having reoperations colour-coded duplex scanning showed that the recurrences were caused by incompetent perforating veins; this indicated that ligation of perforating veins had been inadequate at the first operation. In the remaining four the duplex scan showed that the recurrence was caused either by a patent incompetent long saphenous vein (n = 2) or by an incompetent saphenofemoral junction (n = 2). CONCLUSION: Colour-coded duplex scanning is more accurate than physical examination and continuous wave Doppler flow studies in the preoperative assessment of varicose veins of the lower limb.

Adolescent↗