An acenocoumarol dosing algorithm using clinical and pharmacogenetic data in spanish patients with thromboembolic disease

Appropriate dosing of coumarins is difficult to establish, due to significant inter-individual variability in the dose required to obtain stable anticoagulation. Several genetic and other clinical factors have been associated with the coumarins dose, and some pharmacogenetic-guided dosing algorithms for warfarin and acenocoumarol have been developed for mixed populations. We recruited 147 patients with thromboembolic disease who were on stable doses and with an international normalized ratio (INR) between 2 and 3. We ascertained the influence of clinical and genetic variables on the stable acenocoumarol dose by multiple linear regression analysis in a derivation cohort (DC; n = 117) and developed an algorithm for dosing that included clinical factors (age, body mass index and concomitant drugs) and genetic variations of VKORC1, CYP2C9, CYP4F2 and APOE. For purposes of comparison, a model including only clinical data was created. The clinical factors explained 22% of the dose variability, which increased to 60.6% when pharmacogenetic information was included (p<0.001); CYP4F2 and APOE variants explained 4.9% of this variability. The mean absolute error of the predicted acenocoumarol dose (mg/week) obtained with the pharmacogenetic algorithm was 3.63 vs. 5.08 mg/week with the clinical algorithm (95% CI: 0.88 to 2.04). In the testing cohort (n = 30), clinical factors explained a mere 7% of the dose variability, compared to 39% explained by the pharmacogenetic algorithm. Considering a more clinically relevant parameter, the pharmacogenetic algorithm correctly predicted the real stable dose in 59.8% of the cases (DC) vs. only 37.6% predicted by the clinical algorithm (95% CI: 10 to 35). Therefore the number of patients needed to genotype to avoid one over- or under-dosing was estimated to be 5.     

The signal peptide of pro-opiomelancortin: validation of a specific radioimmunoassay

The N-terminus portion of the POMC leader sequence (signal peptide) was synthesized, and an antiserum was raised against it. A radioimmunoassay was developed which is effective at a dilution of 1:500,000, and sensitive at less than 1 fmole/tube. Since leader sequences often exhibit structural homologies, and since synthetic peptides are not readily available, we resorted to an unusual procedure to establish specificity. This involved extraction of pituitary RNA, cell-free translation to produce the pre-prohormones, and purification by B-END and signal antibody affinity columns. The eluates were then tested by SDS gel electrophoresis and by multiple immunoprecipitations. All results showed that the signal antibody captured a single molecular species, approximately 30,000 in MW, which was also captured by the B-END column, and was immunoprecipitable by B-END and ACTH antisera. It therefore appears that this antibody selectively measures the POMC leader sequence and should be valuable in measuring the newly synthesized pre-prohormone.     

Admixture and population replacement of the sells Papago Indians: Three strategies

Abstract

Changes in rates of admixture on the Sells Papago Indian reservation over the last century are shown to reflect ethnohistorically recorded events of extra‐tribal contact. Three distinct strategies providing, in varying degrees, for the preservation of group identity were identified. It is argued that strategies favoring maximum preservation of ethnic identity have threatened the survival of the reservation breeding units because traditional patterns of mate selection are inconsistent with present settlement patterns and result in delay of mate selection and childbearing early in reproductive life.     

Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications

Understanding the role of inheritance in individual variation in drug response is the focus of pharmacogenetics (PGx). A key part of this understanding is quantifying the role of genetic ancestry in this phenotypic outcome. To provide insight into the relationship between ethnicity and drug response, this study first infers the global distribution of PGx variation and defines its structure. Second, the study evaluates if geographic population structure stems from all PGx loci in general, or if structure is caused by specific genes. Lastly, we identify the genetic variants contributing the greatest proportion of such structure. Our study describes the global genetic structure of PGx loci across the 52 populations of the Human Genome Diversity Cell-Line Panel, the most inclusive set of human populations freely available for studies on human genetic variation. By analysing genetic variation at 1,001 single nucleotide polymorphisms (SNPs) involved in biotransformation of exogenous substances, we describe the between-populations PGx variation, as well geographical groupings of diversity. In addition, with discriminant analysis of principal component (DAPC), we infer how many and which groups of populations are supported by PGx variation, and identify which SNPs actually contribute to the PGx structure between such groups. Our results show that intergenic, synonymous and non-synonymous SNPs show similar levels of genetic variation across the globe. Conversely, loci coding for Cytochrome P450s (mainly metabolizing exogenous substances) show significantly higher levels of genetic diversity between populations than the other gene categories. Overall, genetic variation at PGx loci correlates with geographic distances between populations, and the apportionment of genetic variation is similar to that observed for the rest of the genome. In other words, the pattern of PGx variation has been mainly shaped by the demographic history of our species, as in the case of most of our genes. The population structure defined by PGx loci supports the presence of six genetic clusters reflecting geographic location of samples. In particular, the results of the DAPC analyses show that 27 SNPs substantially contribute to the first three discriminant functions. Among these SNPs, some, such as the intronic rs1403527 of NR1I2 and the non-synonymous rs699 of AGT, are known to be associated with specific drug responses. Their substantial variation between different groups of populations may have important implications for PGx practical applications.     

Development and validation of a consistency based multiple structure alignment algorithm

SUMMARY: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments (MSTAs). Consistency-based alignment (CBA) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA's alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif. RESULTS: CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and it outperforms a number of previously reported MSTA algorithms.     

Lung cancer risk in north Indian population: role of genetic polymorphisms and smoking

Lung cancer (LC) is the leading cause of cancer-related mortality in developing as well as developed countries. Life style choices, particularly tobacco smoking, have been implicated as the main cause in the development of the LC. Despite the fact that majority cases of the LC occur among smokers, only 1–15% of smokers develop LC. In the present study, we have explored the role of genetic polymorphism, smoking habit and their association to LC in a cohort of north Indian population. The polymorphic genes explored were CYP1A1, GSTM1, GSTP1 and GSTT1 using techniques of Polymerase chain reaction (PCR), Restriction Fragment Length Polymorphism (RFLP), Real Time PCR (RT PCR), and gene sequencing. Genetic polymorphism was analysed in 253 normal participants (control) and 93 LC patients originating from Lucknow, India. Data were compared using odds ratio and Fisher Exact Test. We found that smoking increases the susceptibility to LC threefold (OR = 2.9; 95% CI: 0.9–2.8). The most significant risk for LC (OR = 3.2; 95% CI: 0.7–3.8) was found in the association of the homozygous variant of CYP1A1 gene at A2455G base change at Exon 7 (Val/Val) genotype. There was a marginally significant association between LC and GSTT1 null genotype (OR = 1.3; 95% CI: 1.0–1.7) while no significant risk association was found between GSTP1 polymorphism and LC. The present study demonstrates that the presence of null genotype of GSTM1/GSTT1 taken together with CYP1A1 (Val/Val) genotype increases the susceptibility to LC eightfold in comparison to CYP1A1 (Ile/Ile) and GSTM1/ GSTT1 genotype.     

Gene pool of the Novgorod population: Between the north and the south

We studied the Y-chromosome pool of the ethnic Russian population of Novgorod oblast (Russia) by 49 SNP and 17 STR markers. The total sample (N = 191) consists of four populations of the Novgorod region, including its southwestern (Shelon Pyatina) and eastern (Bezhetsk Pyatina) parts. Altogether, these four populations represent both the area of the Sopki archaeological culture (supposedly linked with the Novgorod Slovens tribe known from the chronicles) and the area of the Long Barrows culture (supposedly linked with the Krivichi Slavic tribe or with Balts). The pronounced genetic differences between southern and northern Russian populations are well known from previous studies; however, the Novgorod gene pool turned out to be neither northern nor southern, but a representative of the intermediate buffer zone. This zone was identified in this study and included a set of regional Russian populations from Pskov in the west to Kostroma in the east. All four studied populations of Novgorod region are genetically similar. The minor differences among them might represent the medieval Slavic migrations along the rivers, which survived despite the massive demographic shifts during the following history. Haplogroup N3 comprises one-fifth of the Novgorod pool of paternal lineages, with conditionally “Finnic” N3a4 and conditionally “East Baltic Sea Coast” N3a3 clades being almost equally frequent. The N3a3 phylogenetic network revealed the specific “Balto-Slavic” cluster of STR haplotypes, which is frequent in Baltic-speaking Lithuanians but infrequent in Finno-Ugric speaking Estonians. The Novgorod haplotypes lie outside this cluster, indicating that the Novgorod population received both N3a3 and N3a4 from Finno-Ugric speaking populations of the region, which, in turn, acquired the Mesolithic gene pool of the Northeastern Europe.     

The muskoxen Ovibos moschatus in north and northeast Greenland: population trends and the influence of abiotic parameters on population dynamics

This paper presents the first long term (1960–89) data set on both muskox Ovibos moschatus density and weather parameters in north and northeast Greenland The muskoxen appear to have expenenced a 25 yr favourable period from the early 1960 'ies to the mid 1980' ies, in which density increased and reached a maximum level The population minimum around 1960 probably represents a long term minimum, following a long, generally unfavourable period between 1940–60 Variation in the local population trends from the southern parts of the muskox distribution m northeast Greenland to the northeast parts, can be divided into three geographical areas (72°–75°N, 75°–77°30 'N, and north of 79°30' N), where density dependent and density independent factors affecting muskox populations are apparently different Regional population stability does not increase towards the north Two density independent (abiotic) factors seem to be of prime importance in determining the muskox population density and distribution in northeast Greenland 1) the amount of winter precipitation affects the distribution of muskoxen negatively, inducing local migrations, but does not have a direct negative effect on large scale variation in density,11) ablation (i.e melting of the upper snow layer) and concomitant ice crust formation in winter have a highly negative effect on muskox density in the southern range, but not in the northern range The two abiotic factors, which show a considerable variation from north to south, are statistically independent and seem to be triggered by different weather conditions The predictions that follow from a climatic model both with respect to the direct influence of abiotic factors on muskox density and the indirect influence of climatic fluctuation, are not fully supported by the data presented here     

Estimating population cause-specific mortality fractions from in-hospital mortality: validation of a new method

Background

Cause-of-death data for many developing countries are not available. Information on deaths in hospital by cause is available in many low- and middle-income countries but is not a representative sample of deaths in the population. We propose a method to estimate population cause-specific mortality fractions (CSMFs) using data already collected in many middle-income and some low-income developing nations, yet rarely used: in-hospital death records.

Methods and Findings

For a given cause of death, a community''s hospital deaths are equal to total community deaths multiplied by the proportion of deaths occurring in hospital. If we can estimate the proportion dying in hospital, we can estimate the proportion dying in the population using deaths in hospital. We propose to estimate the proportion of deaths for an age, sex, and cause group that die in hospital from the subset of the population where vital registration systems function or from another population. We evaluated our method using nearly complete vital registration (VR) data from Mexico 1998–2005, which records whether a death occurred in a hospital. In this validation test, we used 45 disease categories. We validated our method in two ways: nationally and between communities. First, we investigated how the method''s accuracy changes as we decrease the amount of Mexican VR used to estimate the proportion of each age, sex, and cause group dying in hospital. Decreasing VR data used for this first step from 100% to 9% produces only a 12% maximum relative error between estimated and true CSMFs. Even if Mexico collected full VR information only in its capital city with 9% of its population, our estimation method would produce an average relative error in CSMFs across the 45 causes of just over 10%. Second, we used VR data for the capital zone (Distrito Federal and Estado de Mexico) and estimated CSMFs for the three lowest-development states. Our estimation method gave an average relative error of 20%, 23%, and 31% for Guerrero, Chiapas, and Oaxaca, respectively.

Conclusions

Where accurate International Classification of Diseases (ICD)-coded cause-of-death data are available for deaths in hospital and for VR covering a subset of the population, we demonstrated that population CSMFs can be estimated with low average error. In addition, we showed in the case of Mexico that this method can substantially reduce error from biased hospital data, even when applied to areas with widely different levels of development. For countries with ICD-coded deaths in hospital, this method potentially allows the use of existing data to inform health policy.     

VEGF and IL-4 gene variability and its association with the risk of coronary heart disease in north Indian population

Vascular endothelial growth factor (VEGF) is a potent angiogenic growth factor that has been shown to play a significant role in neovascularization during inflammation in atherosclerotic plaques, formation of collateral vessels to an area of ischemic myocardium and neovascularization at the edges of a myocardial infarction during its repair. Interleukin-4 (IL-4) has important role in immune cell chemotaxis, formation of endothelial cell adhesion molecules and has numerous anti-inflammatory effects which prevent the complications of atherosclerosis, the primary cause of coronary heart disease (CHD). In this study, we have analyzed the effect of 1154 A/G polymorphism of VEGF and 70 bp VNTR polymorphism of intron 3 in IL-4 genes in coronary heart disease (CHD) patients (n = 300) and their age matched controls (n = 300). To analyze polymorphic alleles, ARMS-PCR and RFLP techniques were used. Multiple logistic regression analysis was carried out with statistical software. GG genotype was associated with a decreased risk of development of CHD (OR 0.22, 95% CI 0.12–0.38, P < 0.001). However, A allele showed an increased risk whereas G allele decreased the risk of CHD with diabetes mellitus, hypertension, chronic mental stress and positive familial history of myocardial infarction (MI)/CHD. GG genotype was found to have protective effect with alcohol intake (OR 0.34, 95% CI 0.14–0.82, P < 0.01) and central obesity (OR 0.15, 95% CI 0.04–0.56, P < 0.001). GG genotype of VEGF has also shown significant association with IL-4 (P2P2 and P1P2) genotypes.     

Sub-mitochondrial location of Ruthenium Red-sensitive calcium-ion transport and evidence for its enrichment in a specific population of rat liver mitochondria

1. Seven fractions sedimenting at between 3000 and 120000g-min were prepared from a rat liver homogenate by differential centrifugation in buffered iso-osmotic sucrose. The following measurements were carried out on each of these fractions: Ruthenium Red-sensitive Ca²⁺ transport in the absence and in the presence of P_i as well as in the presence of N-ethylmaleimide to prevent P_i cycling, succinate-supported respiration in the absence and in the presence of ADP, the ΔE and −59 ΔpH components of the protonmotive force, cytochrome oxidase, uncoupler-stimulated adenosine triphosphatase, α-glycerophosphate dehydrogenase, P_i content and the effect on the `resting' rate of respiration of repeated additions of a fixed Ca²⁺ concentration. 2. Ca²⁺ transport either in the presence or in the absence of added P_i and in the presence of N-ethylmaleimide exhibits significantly higher rates in the fraction sedimenting at 8000g-min. By contrast, respiration in the presence or in the absence of added ADP and the values for ΔE and −59 ΔpH were similar in those fractions sedimenting between 4000 and 20000g-min, indicating that the driving force for Ca²⁺ transport was similar in each of these fractions. 3. Experiments designed to determine the capacity of the individual fractions for Ca²⁺, as measured by the effect of repeated additions of Ca²⁺ on the resting rate of respiration, showed that fraction 2, i.e. that sedimenting at 8000g-min, also exhibited the greatest tolerance towards the uncoupling action of the ion. 4. Of the three enzyme activity profiles, only that of α-glycerophosphate dehydrogenase was similar to that of Ca²⁺ transport. Because previous workers have assigned this enzyme to loci in the inner peripheral membrane [Werner & Neupert (1972) Eur. J. Biochem. 25, 379–396], it is concluded that the Ruthenium Red-sensitive Ca²⁺- transport system also is located in this domain of the inner membrane. The relation of these findings to the mechanisms of mitochondrial Ca²⁺ transport and the biogenesis of mitochondria is discussed.     

Isolation and characterization of a specific antibody population against human fibrinogen

A specific antibody population against human fibrinogen was isolated from a rabbit antiserum by affinity chromatography on fibrinogen-bound Sepharose gel. Using a sensitive competitive radioimmunoassay, the antibody population was found to recognize epitopes on native fibrinogen but crossreacted minimally with fibrinogen fragment D and an early plasmin-degraded fibrinogen A alpha-chain product, but not at all with fragment E or fibrinopeptides A and B. Fibrin monomers shared part of these epitopes. The antibody population crossreacted to a small extent with bovine, horse and baboon fibrinogens and not at all with fibrinogens from sheep, rat, pig, goat, guinea pig, dog and rabbit.     

A model of stem cell population dynamics: in silico analysis and in vivo validation

The proper renewal and maintenance of tissues by stem cell populations is simultaneously influenced by anatomical constraints, cell proliferation dynamics and cell fate specification. However, their relative influence is difficult to examine in vivo. To address this difficulty we built, as a test case, a cell-centered state-based computational model of key behaviors that govern germline development in C. elegans, and used it to drive simulations of cell population dynamics under a variety of perturbations. Our analysis provided unexpected possible explanations for laboratory observations, including certain 'all-or-none' phenotypes and complex differentiation patterns. The simulations also offered insights into niche-association dynamics and the interplay between cell cycle and cell fate. Subsequent experiments validated several predictions generated by the simulations. Notably, we found that early cell cycle defects influence later maintenance of the progenitor cell population. This general modeling approach is potentially applicable to other stem cell systems.     

Vocal communications and the maintenance of population specific songs in a contact zone

Bird song has been hypothesized to play a role in several important aspects of the biology of songbirds, including the generation of taxonomic diversity by speciation; however, the role that song plays in speciation within this group may be dependent upon the ability of populations to maintain population specific songs or calls in the face of gene flow and external cultural influences. Here, in an exploratory study, we construct a spatially explicit model of population movement to examine the consequences of secondary contact of populations singing distinct songs. We concentrate on two broad questions: 1) will population specific songs be maintained in a contact zone or will they be replaced by shared song, and 2) what spatial patterns in the distribution of songs may result from contact? We examine the effects of multiple factors including song-based mating preferences and movement probabilities, oblique versus paternal learning of song, and both cultural and genetic mutations. We find a variety of conditions under which population specific songs can be maintained, particularly when females have preferences for their population specific songs, and we document many distinct patterns of song distribution within the contact zone, including clines, banding, and mosaics.     

Diabetes mellitus and its complications in a Hungarian population

The aim of this study was to examine the disease characteristics and complications of diabetes mellitus in patients in a Hungarian rural community. Data relating to age, sex, date of onset of diabetes, fasting blood glucose values and all diseases associated with diabetics were retrieved from the medical records of patients. Almost six percent (5.7%) of the population has diabetes mellitus. The percentage of Type I diabetic patients in this population was 5.8 percent. The prevalence of diabetes was slightly but not significantly higher in females than in males. The mean age of the diabetic population was 52.1 +/- 11.3 for male and 53.47 +/- 15.7 for the female patients. The peak age of onset of diabetes mellitus was in the sixth decade of life. The mean fasting blood sugar value was 10.64 +/- 0.6 and 10.57 +/- 0.5 mmol L(-1), in male and female diabetic patients (n = 103), respectively. Diabetic patients presented with many signs and symptoms in the general practice setting. The findings of this study showed that diabetics present with many disease conditions and signs and symptoms in the general practice setting. Many of these conditions are known to be associated with diabetes while others are not. As a result of the adverse effects of diabetes mellitus on the cardiovascular system and on body metabolism as a whole, the damage and morbidity caused by diabetes mellitus may have been underestimated. The results of this study have shed light on the unrecognised complications of diabetes mellitus.     

A proposal for a specific double-helical structure in which the polynucleotide strands intercalate instead of forming base-pairs

Double helices, since the discovery of the DNA structure by Watson and Crick, represent the single most important secondary structural form of nucleic acids. The secondary structures of a variety of polynucleotide helices have now been well characterised with hydrogen-bonded base-pairs as building blocks. We wish to propose here the possibility, in a specific case, of a double stranded helical structure without any base-pair, but having a repeat unit of two nucleotides with their bases stacked through intercalation. The proposal comes from the initial models we have built for poly(dC) using the stacking patterns found in the crystal structures of 5'-dCMPNa2 which crystallises in two forms depending on the degree of hydration. These structures have pairs of nucleotides with the cytosine rings partially overlapping and separated by 3.3A. Using these as repeat units one could generate a model for poly(dC) with parallel strands, having a turn angle of 30 degrees and a base separation of 6.6A along each strand. Both right and left handed models with these parameters can be built in a smooth fashion without any obviously unreasonable stereochemical contacts. The helix diameter is about 13.5A, much smaller than that of normal helices with base-pair repeats. The changes in the sugar-phosphate backbone conformation in the present models compared to normal duplexes only reflect the torsional flexibility available for extension of polynucleotide chains as manifested by the crystal structures of drug-inserted oligonucleotide complexes. Intercalation proposed here could have some structural relevance elsewhere, for instance to the base-mismatched regions on the double helix and the packing of noncomplementary single strands as found in the filamentous bacteriophage Pf1.     

Serum aldosterone and protein-binding variables in Yanomama Indians: a no-salt culture as compared to partially acculturated Guaymi Indians

Yanomama Indians from the jungles of southern Venezuela and northern Brazil excreted 1 +/- 1.5 mEq of Na and 203 +/- 109 mEq of K and had low blood pressure (BP), 102/62 mm Hg). In comparison, Guaymi Indians of Panama excreted 103 +/- 50 mEq of Na and 118 +/- 52 mEq of K and had significantly higher BP (114/75 mm Hg, p less than 0.001). Elucidating the renin-aldosterone axis, total upright serum aldosterone in 34 Yanomama was high (85.6 +/- 78 ng/100 ml). The binding capacities of thermolabile (ABG) and thermostable (ABG-Ts) serum globulins for aldosterone were elevated at 23.8 +/- 6 and 14.9 +/- 2.6%, respectively; consequently, total ABG- plus ABG-Ts- bound aldosterone was as high as 38.6 +/- 6.3%. Plasma renin activity (PRA 10.3 +/- 2.4 ng/ml/h) and urinary aldosterone 18-glucuronide (70.3 +/- 30 micrograms/24 h) in 17 Yanomama were also very high. In contrast, total serum corticosteroids and corticosteroid-binding globulin (CBG) binding capacity were normal, suggesting normal ACTH activity. PRA correlated positively with total (r = 0.47, p less than 0.05) and free (r = 0.47, p less than 0.05) serum aldosterone, which in turn showed a negative trend with Na (r = 0.33, NS) excretion. The effect of high dietary K appeared less important to aldosterone stimulation and PRA suppression. ABG-bound aldosterone (r = 0.43, p less than 0.01) as well as ABG-Ts (r = 0.56, p less than 0.05) were negatively correlated with diastolic but not systolic BP. The total ABG- and ABG-Ts-bound fraction correlated with diastolic BP (r = 0.43, p less than 0.05) in contrast to the free fraction (r = 0.08, NS) or total aldosterone (r = -0.09). Apparently, only bound serum aldosterone is important for the maintenance of diastolic BP. High serum aldosterone, with elevated excretion, indicates an increased secretion rate; increased serum protein binding suggests an increased tissular activity and alterations in aldosterone metabolism. In Guaymi Indians both total plasma aldosterone (14.5 +/- 65 ng/100 ml) and urinary aldosterone (8.1 +/- 4.8 micrograms/creatinine excretion) were normal. ABG-binding capacity for aldosterone was moderately elevated (17.8 +/- 4.8) and of ABG-Ts normal (10.2 +/- 1.2) suggesting a nearly normal aldosterone metabolism and regulation. The BP of Guaymi was significantly higher than that of the Yanomama.     

DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool

There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes.