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At least 217 records · Page 12Linked to original sources

Predictive value of drug levels, HIV genotyping, and the genotypic inhibitory quotient (GIQ) on response to saquinavir/ritonavir in antiretroviral-experienced HIV-infected patients.

Plasma levels of HIV protease inhibitors (PI) are often close to IC50 values of wild-type viruses when administered without ritonavir boosting. The impact of drug levels, resistance mutations, and the genotypic inhibitory quotient (GIQ) were examined on the response to saquinavir/ritonavir (SQV/r)-based salvage therapy. Patients with prior exposure to PI other than SQV and currently failing virologically were recruited prospectively in a multicenter trial. All patients began SQV/r 1000/100 mg bid plus another two antiretrovirals. A total of 139 patients was enrolled. At month 12, virological response (VR), defined as plasma HIV-RNA decline >1 log, was recorded in 68.2% of patients on treatment (41.7% in the intent-to-treat analysis). The median baseline number of protease resistance mutations was three. The VR was significantly lower in patients with >5 protease resistance mutations and in those with plasma SQV Cmin<0.1 microg/ml. At week 48, the VR was seen in 77.1% of patients with a GIQ>0.04 compared to 18.2% of those with a lower GIQ (P=0.001). In the multivariate analysis, 0.1 microg/ml were independently associated with VR. Interestingly, drug levels had their highest predictive value of the VR at week 12, since low SQV plasma levels often permitted ruling out poorly adherent patients. In contrast, the number of protease resistance mutations had the highest impact on the VR at week 24, suggesting that for those taking the drugs, the VR is highly dependent of the presence of resistance mutations. At any time, nevertheless, the GIQ provided the most accurate prediction of the VR.

Antiretroviral Therapy, Highly Active↗

A new inactivated BVDV genotype I and II vaccine. An immunisation and challenge study with BVDV genotype I.

An inactivated vaccine containing BVDV I and II strains (PT810; BVDV I, and 890; BVDV II) and using different adjuvants and antigen dosages was tested in a cattle challenge model. Groups of six healthy, seronegative cattle were vaccinated twice with a low dose (10(6.6) TCID(50) PT810 and 10(7.2) TCID(50) 890) vaccine with the adjuvant Bay R1005 or a high dose (10(7.8) TCID(50) PT810 and 10(8. 2) TCID(50) 890) vaccine with two different adjuvants (Bay R1005 or Polygen). Thirty-eight days after the second vaccination, immunised animals (n=18) and non-vaccinated control animals (n=3) were challenged intranasally with 10(6) TCID(50) BVDV strain PT810. For a period of 16 days, virus was isolated from blood leukocytes and nasal swabs, and neutralising antibody titres were determined.The induction of antibodies following immunisation was strongly dependent on the antigen dosage in the vaccine. The high dose formulation induced high serum neutralising antibody titres against both genotypes of up to 32000 after the second immunisation. Animals with neutralising antibody titres >512 (n=14) did not show any marked leukopenia after challenge and only very little or no virus could be isolated from blood leukocytes and/or nasal swabs when compared to control cattle. Furthermore, some of these animals did not show any boost of neutralising or even NS3-specific antibodies, which renders viral replication unlikely and thus would prevent infection of the fetus. Both adjuvants (Bay R1005 or Polygen) were similarly efficient and induced nearly identical antibody responses. In contrast, four of the six low dosage vaccinates had a marked leukopenia and viraemia as well as detectable nasal virus shedding for several days. We conclude that the selected strains and the system of vaccine preparation with high BVDV antigen dosages and highly efficient new adjuvants provide an effective means of protection against BVDV I infections. Investigations to demonstrate the protection against BVDV II infections, the duration of immunity and the ability of fetal protection by using the high dose vaccine in a fetal challenge model will follow.

Animals↗

Genotype-by-environment interaction with broiler genotypes differing in growth rate. 3. Growth rate and water consumption of broiler progeny from weight-selected versus nonselected parents under normal and high ambient temperatures.

One cycle of high-intensity selection on BW was conducted to study correlated effects on performance under high ambient temperature (AT). From a large flock of a commercial sire-line, 3 males and 15 females with the highest BW at 35 d of age were mated and produced a group of 120 BW-selected chicks. Three average-BW males and 15 average-BW females from the same flock were mated to produce a control group of 120 chicks. On Day 17, the two groups were equally divided between two temperature-controlled chambers and housed in individual cages. One chamber was set to a normal AT (NAT; constant 22 C) and the second chamber to high AT (HAT; constant 32 C). Under NAT, the relative advantage of the selected broilers over the controls did not change from 17 to 42 d of age, averaging about 15% for BW gain and 9.7% for feed consumption. These differences were halved under HAT from Days 17 to 28 and were reversed from 28 to 42 d of age, when the selected broilers consumed significantly less feed and gained less BW than the controls. Water-to-feed ratio was measured in each AT treatment. From 28 to 42 d of age, averaged over the two groups, birds under HAT consumed 2.5 g water/g of feed compared to only 1.5 g water/g feed under NAT. The diminished superiority of the selected broilers under HAT led to a substantial genotype-by-environment interaction involving high AT and within-stock genetic differences in growth rate. It appears that broilers selected for rapid growth under optimal conditions do not achieve their genetic potential under high AT. Thus, specific indicators of adaptation to heat, possibly water consumption or body temperature, should be added to commercial selection for rapid growth to improve broiler performance in hot climates.

Aging↗

Geographical genotypes (geotypes) of poliovirus case isolates from the former Soviet Union: relatedness to other known poliovirus genotypes.

A 150 nucleotide long region corresponding to adjoining segments of the genes encoding polypeptides VP1 and 2A of 84 poliovirus strains recently isolated from patients with paralytic poliomyelitis over the territory of the former Soviet Union (FSU) were characterized by sequencing and/or PCR amplification using specially designed primers. Eighteen isolates were found to be very closely related to one or another of the three Sabin vaccine strains. Three distinct classes of geographical genotypes (geotypes) were discerned among 42 wild-type (non-Sabin) strains of serotype 1. One such geotype (called A) was widely circulating in 1990-91 in the Caucasian (Azerbaijan and Georgia) as well as Asian (Kyrgyzstan and Turkmenistan) Republics; this geotype exhibited only weak relatedness to known strains isolated outside the FSU. On the other hand, a subset of strains belonging to another geotype (T) of serotype 1, which circulated in 1991 in Tajikistan, demonstrated very close relatedness to contemporaneous strains isolated in Pakistan, India and Jordan. Strains that were somewhat different, but belonging to the same T-geotype, were found also in Moldova and Georgia. Strikingly, the primary structure of the VP1/2A junction of certain T-geotype isolates differed from the corresponding region of Sabin 1 only in 13-15% of positions, thereby not reaching the upper limit accepted for a geotype. This observation raises, though does not prove, the possibility that at least the relevant segment of the T-geotype RNA originated from the vaccine strain. The third geotype of serotype 1 was represented by a single, perhaps imported, isolate. Four distinct subsets of a common geotype (C) were discerned among 24 wild-type isolates belonging to serotype 3. These strains exhibited a broad geographical distribution being found, in particular, in Armenia, Azerbaijan, Georgia, Turkmenistan and Tajikistan; on the other hand, the C-geotype strains exhibited only a relatively distant relatedness to a strain isolated outside of the FSU (in Oman).

Amino Acid Sequence↗

Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.

Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of approximately 90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high multiplex levels. The results of this study demonstrate the suitability of this technology for comprehensive association studies that use targeted SNPs in indirect linkage disequilibrium studies or that directly screen for causative mutations.

Chromosome Inversion↗

Efficient computation of lod scores: genotype elimination, genotype redefinition, and hybrid maximum likelihood algorithms.

Calculation of multilocus lod scores presents challenging problems in numerical analysis, combinatories, programming, and genetics. It is possible to accelerate these computations by exploiting the simple pedigree structure of a CEPH-type pedigree consisting of a nuclear family plus all four grandparents. Lathrop et al. (1986) have done this by introducing likelihood factorization and transformation rules and Lander & Green (1987) by the method of 'hidden Markov chains'. The present paper explores an alternative approach based on genotype redefinition in the grandparents and systematic phase elimination in all pedigree members. All three approaches accelerate the computation of a single likelihood. Equally relevant to multilocus mapping are search strategies for finding the maximum likelihood estimates of recombination fractions. Hybrid algorithms that start with the EM algorithm and switch midway to quasi-Newton algorithms show promise. These issues are investigated in the context of a simulated 10 locus example. This same example allows us to illustrate a simple strategy for determining locus order.

Algorithms↗

Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.

Potato (Solanum tuberosum L.) is an important food crop that is sensitive to high temperatures, which cause major changes in the transcriptome and a reduction in yield. In several plant species, DNA methylation has been reported to influence gene expression, particularly under abiotic stress conditions. However, the role of DNA methylation in regulating gene expression in heat-tolerant and heat-sensitive potato genotypes is still poorly understood. In this study, we conducted genome-wide DNA methylome and transcriptome analyses of leaves from two contrasting potato cultivars, Annabelle (moderately heat-tolerant) and Camel (heat-sensitive), before and after heat stress (HS). Genome-wide differential methylation analysis revealed that most identified differentially methylated regions (DMRs) were constitutive, reflecting variation between cultivars rather than being induced by HS. While thousands of heat-responsive differentially expressed genes (DEGs) were identified, only a small fraction coincided with heat-induced DMRs. Despite substantial constitutive DNA methylation and transcriptome differences between the cultivars, we found no consistent association between DMRs and DEGs, indicating that DNA methylation does not play a widespread direct regulatory role in gene expression. Surprisingly, hypermethylated genomic regions were associated with lower alternative allele frequencies, whereas hypomethylated regions showed the opposite trend. These findings indicate that the potato DNA methylome is largely stable under HS and that constitutive DNA methylation variation contributes rather to genetic diversity than to the direct regulation of gene expression.

DNA Methylation↗

Assessment of the clinical and virological protection provided by a commercial inactivated bovine viral diarrhoea virus genotype 1 vaccine against a BVDV genotype 2 challenge.

A new genotype of bovine viral diarrhoea virus (BVDV), designated BVDV-2, has emerged in the last decade and in recent years the prevalence of BVDV-2 strains has increased. A vaccination-challenge study was carried out to determine the cross-protective efficacy of a commercial inactivated vaccine containing a BVDV-1 strain. A group of five BVDV-free calves was vaccinated twice and a second group of five calves served as negative controls. Two months after the first vaccination, all the calves were challenged intranasally with BVDV-2 strain BVD890. The clinical signs of disease, the changes in haematological variables and the level of viraemia were significantly less in the vaccinated group.

Animals↗

Prevalence of bovine viral diarrhea virus genotypes and antibody against those viral genotypes in fetal bovine serum.

One thousand lots of pooled fetal bovine serum (FBS) were tested for contamination with bovine viral diarrhea virus (BVDV) and/or for contamination with neutralizing antibody against BVDV. Noncytopathic or cytopathic BVDV was isolated from 203 lots of FBS. Analysis of the viral isolates identified 115 type 1 and 65 type 2 BVDV isolates. An additional 23 virus isolates were mixtures of > or = 2 BVDV isolates and were not classified to viral genotype. Further characterization of the type 1 viruses identified 51 subgenotype 1a and 64 subgenotype 1b BVDV isolates. Viral neutralizing antibody was detected in 113 lots of FBS. Differential viral neutralization indicated that type 1 BVDV induced the antibody detected in 48 lots of FBS and type 2 BVDV induced the antibody detected in 16 lots of FBS.

Animals↗

Comparison of two CYP2D6 genotyping methods and assessment of genotype-phenotype relationships.

BACKGROUND: There have been no published reports comparing the CYP450 GeneChip microarray assay with more standard methods of genetic testing. METHODS: We collected 20-mL blood samples from 236 volunteers for DNA isolation and testing before each individual ingested 60 mg of dextromethorphan, and collected their urine. CYP2D6 alleles *3 to *7, *9, *17, and *41, and multiple CYP2D6 gene copies were tested by allele-specific PCR (AS-PCR), whereas alleles *2 to *4 and *6 to *11 were tested by the Affymetrix CYP450 GeneChip assay. Five of the CYP2D6 alleles (*3, *4, *6, *7, and *9) were tested by both AS-PCR and the CYP450 GeneChip assay in an independent and blinded fashion in 232 of the 236 healthy volunteers. The combined CYP2D6 genotype from both methods was used to divide the population into four subgroups, poor metabolizers (PMs), intermediate metabolizers (IMs), extensive metabolizers (EMs), and ultrarapid metabolizers (UMs), based on their relative function and ability to express the CYP2D6 gene. The urinary elimination of dextromethorphan was assessed in each of these CYP2D6 subgroups. RESULTS: The CYP2D6*3, *4, *6, *7, and *9 alleles showed a high degree of concordance between the CYP450 GeneChip and AS-PCR methods (>99% concordance). The mean (SD) of the log[dextromethorphan metabolic ratio (MR)] in the four CYP2D6 subgroups was PM = 0.49 (0.38); IM = -1.24 (0.53); EM = -2.35 (0.61); and UM = -2.43 (0.38). CONCLUSIONS: Oligonucleotide microarray technology is an efficient and reliable way to test for CYP2D6 gene variation based on five alleles compared by separate methods. The methodology is influenced by the quality and amount of DNA present. The log(dextromethorphan MR) is a highly variable index that appears to reflect the crude nature of the dextromethorphan MR as an indicator of CYP2D6 in vivo enzyme activity.

Cytochrome P-450 CYP2D6↗

Toward fully automated genotyping: genotyping microsatellite markers by deconvolution.

Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements.

Algorithms↗

HLA class II genotypic frequencies in atopic asthma: association of DRB1*01-DQB1*0501 genotype with Artemisia vulgaris allergic asthma.

Different human leukocyte antigen (HLA) class II alleles have been associated with the development of atopic asthma. To determine whether HLA class II alleles are associated with atopic asthma in a population from southeast Spain (Murcia region), 213 atopic asthmatic patients and 150 controls were selected for HLA typing. Significant association of the DRB1*01 and DQB1*0501 alleles was found in Artemisia vulgaris allergic patients (p(c) = 0.00052 and p(c) = 0.00023, respectively). No significant correlation was found in other atopic patients allergic to pollens (Phleum pratense, Olea europaea, and Salsola kali), house dust mites (Dermatophagoides pteronyssinus, D. farinae), molds (Alternaria alternata, Cladosporium herbarum), or animal danders (dog, cat). The results reveal that the DRB1*01-DQB1*0501 genotype is strongly associated with a positive response to Artemisia vulgaris in the population studied.

Alleles↗

Analysis of the entire nucleotide sequence of hepatitis B virus genotype B in the Philippines reveals a new subgenotype of genotype B.

The entire nucleotide sequences were determined for hepatitis B virus (HBV) genotype B (HBV/B) genomes extracted from five patients in the Philippines and designated GenBank AB219426, AB219427, AB219428, AB219429 and AB219430. The serotype of the first four isolates was ayw and that of GenBank AB219430 was adw. Divergences of entire sequences were 1.0-2.0 % between the first four isolates and 3.8-4.2 % between these four and GenBank AB219430. Phylogenetic-tree analysis revealed that, worldwide, HBV/B comprises five subgenotypes: B1, B2, B3, B4 and the new Philippines group, designated B5. Divergences of the entire genome sequences between four isolates in subgenotype B5 and isolates from other countries (subgenotypes) were 4.4-4.8 % with Vietnam (B4), 2.9-3.5 % with Indonesia (B3), 4.7-5.1 % with China (B2) and 5.4-6.0 % with Japan (B1). Similarly, GenBank AB219430 showed the lowest divergences: 3.4 % with the isolate from Indonesia (B3), 5.0 % with Vietnam (B4), 5.4 % with China (B2) and 6.1 % with Japan (B1). This is the first report of entire nucleotide sequences of HBV/B from the Philippines and the results show that these sequences belong to a new subgenotype, B5. The present study identified that HBV/B isolates throughout the world are divided genetically into five subgenotypes, the relationships between geographical distances and the genetic distances of HBV/B being well-correlated.

Adult↗

Rep-PCR--a variant to RAPD or an independent technique of bacteria genotyping? A comparison of the typing properties of rep-PCR with other recognised methods of genotyping of microorganisms.

The paper presents technical aspects of rep-PCR fingerprinting technique and compares its typing abilities, differentiation power and reproducibility with other recognised and recommended genotyping methods. Although rep-PCR fingerprinting is similar to MAAP techniques, it demonstrates some essentially different elements. The data presented in this review, indicate a rep-PCR genomic fingerprinting technique as a highly discriminating, independent screening method for determining the taxonomical diversity of bacterial population.

Bacteria↗

Genotyping--from genomic DNA to genotype in a single tube.

Nucleotide variations in the human genome, such as single-nucleotide polymorphisms, have been researched more intensively since it became apparent that these deviations are linked to various diseases and also several side effects of drugs. The investigation of genomic DNA in the laboratory requires routine methods that are time-, labour-, and cost-effective. These criteria are fulfilled by so-called closed-tube methods, which are applied directly to isolated genomic DNA without any preamplification.

Cytogenetic Analysis↗