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Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas.

B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression profiling has revealed two distinct tumor subtypes of B-DLCL: germinal center B cell-like DLCL and activated B cell-like DLCL. In a separate study, we determined that B-DLCL can also be subdivided into two groups based on the presence or absence of ongoing Ig gene hypermutation. Here, we evaluated the correlation between these B-DLCL subtypes established by the two different methods. Fourteen primary B-DLCL cases were studied by gene expression profiling using DNA microarrays and for the presence of ongoing mutations in their Ig heavy chain gene. All seven cases classified as germinal center B cell-like DLCL by gene expression showed the presence of ongoing mutations in the Ig genes. Five of the seven cases classified by gene expression as activated B cell-like DLCL had no ongoing somatic mutations, whereas, in the remaining two cases, a single point mutation was observed in only 2 of 15 and 21 examined molecular clones of variable heavy (V(H)) chain gene, respectively. These two cases were distantly related to the rest of the activated B cell-like DLCL tumors by gene expression. Our findings validate the concept that lymphoid malignancies are derived from cells at discrete stages of normal lymphocyte maturation and that the malignant cells retain the genetic program of those normal cells.

Biopsy↗

Improving the efficiency of artificial selection: more selection pressure with less inbreeding.

The use of population genetic variability in present-day selection schemes can be improved to reduce inbreeding rate and inbreeding depression without impairing genetic progress. We performed an experiment with Drosophila melanogaster to test mate selection, an optimizing method that uses linear programming to maximize the selection differential applied while at the same time respecting a restriction on the increase in inbreeding expected in the next generation. Previous studies about mate selection used computer simulation on simple additive genetic models, and no experiment with a real character in a real population had been carried out. After six selection generations, the optimized lines showed an increase in cumulated phenotypic selection differential of 10.76%, and at the same time, a reduction of 19.91 and 60.47% in inbreeding coefficient mean and variance, respectively. The increased selection pressure would bring greater selection response, and in fact, the observed change in the selected trait was on average 31.03% greater in the optimized lines. These improvements in the selection scheme were not made at the expense of the long-term expectations of genetic variability in the population, as these expectations were very similar for both mate selection and conventionally selected lines in our experiment.

Animals↗

The Tay-Sachs disease gene in North American Jewish populations: geographic variations and origin.

From data collected in a North American Tay-Sachs disease (TSD) heterozygote screening program, the TSD carrier frequency among 46,304 Jewish individuals was found to be .0324 (1 in 31 individuals). This frequency is consistent with earlier estimates based on TSD incidence data. TSD carrier frequencies were then examined by single country and single region of origin in 28,029 Jews within this sample for whom such data were available for analysis. Jews with Polish and/or Russian ancestry constituted 88% of this sample and had a TSD carrier frequency of .0327. No TSD carriers were observed among the 166 Jews of Near Eastern origins. Relative to Jews of Polish and Russian origins, there was at least a twofold increase in the TSD carrier frequency in Jews of Austrian, Hungarian, and Czechoslovakian origins (P less than .005). These findings suggest that the TSD gene proliferated among the antecedents of modern Ashkenazi Jewry after the Second Diaspora (70 A.D.) and before their major migrations to regions of Poland and Russia (before 1100 A.D.).

Female↗

Comparison of lifestyle and risk factors among Japanese with and without gastric cancer family history.

To find specific risk factors of gastric cancer (GC) independent of GC family history (GCFH), 2 studies were conducted using the database of the Hospital-based Epidemiological Research Program at Aichi Cancer Center: (i) a comparison of lifestyles between non-cancer cases with positive and negative GCFH status and (ii) a case-reference investigation of subjects with and without GCFH, treated separately. The first showed no significant variation of GCFH status with regard to smoking, drinking and most food habits. Multivariate analyses in the case-referent studies revealed odds ratios (ORs) for GC associated with habitual smoking of 2.78 (95% CI 1.22-6.28) for those with and 2.74 (95% CI 1.76-4.26) for those without GCFH. In individuals with GCFH, an independently lowered OR (0.52, 95% CI 0.27-0.99) was evident for frequent consumption of raw vegetables, whereas the opposite was noted for pickled vegetables (2. 39, 95% CI 1.28-4.45). No statistically significant interaction was found between GCFH and selected lifestyle items. In conclusion, our results suggest a limited influence of GCFH on risk factors for GC.

Adult↗

A comparative method for identification of gene structures and alternatively spliced variants.

MOTIVATION: Alternative splicing (AS) serves as a mechanism to create diversity among functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures. RESULTS: A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on expressed sequence tag (EST)-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extraction and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate approximately 88% of potential overprediction. The overall accuracy of PSEP is better than or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2 and SLAM, when tested on three benchmark datasets (the ELN gene region, the HoxA cluster and the ROSETTA set). In addition, 76.2 and 76.0% of multiple-exon genes in the ROSETTA dataset and human chromosome 20, respectively, are found to have AS forms. Approximately 23% of the 210 elementary alternatives identified in the ROSETTA dataset are not conserved between the human and mouse genomes, and none of the 210 transcripts is found in the RefSeq annotation. With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features.

Algorithms↗

Variation between ASP-1 molecules from Ancylostoma caninum in China and the United States.

Hookworm infection continues to be a serious problem in rural areas of China. Rapid reinfection and high cost limit the effectiveness of deworming programs. Vaccination offers an attractive alternative to mass chemotherapy. However, variation in vaccine antigens from field hookworm populations could conceivably limit efficacy of a vaccine developed from laboratory strains. Reported here are initial experiments to ascertain levels of molecular variation in a promising vaccine antigen, ASP-1, from the dog hookworm Ancylostoma caninum. ASP-1 from a Chinese strain of A. caninum was isolated from a third-stage larval cDNA library and compared to ASP-1 from a U.S. strain. There was 97% and 98% similarity in the DNA and amino acid sequences, respectively. There were 42 polymorphic sites between the sequences, 30 of which were synonymous. The 12 nonsynonymous substitutions resulted in 10 changes in the deduced amino acid sequence. Five of the amino acid changes were in the N-terminal domain, whereas the C-terminal domain was more highly conserved, containing only 2 amino acid changes. The results suggest that the effect of molecular variation in antigens from geographically separated parasite populations should be considered during vaccine development.

Amino Acid Sequence↗

Multiple regression analysis of pharmacogenetic variability of carvedilol disposition in 54 healthy Japanese volunteers.

The aim of this study was to evaluate the pharmacogenetic variability in the disposition of carvedilol in the Japanese population. Five or 10 mg of carvedilol was orally administered to 54 healthy Japanese subjects (22-44 years old), and blood samples were taken at 2 and 6 h after dosing. We determined the polymorphic alleles of CYP2D6, CYP2C9, CYP2C19, CYP3A5, UGT2B7, and MDR1 in each subject. The whole blood concentration of R- and S-carvedilol was measured by an HPLC method. The pharmacokinetic parameters in individual subjects were estimated by the Bayesian method using the nonlinear mixed effects model (NONMEM) program. We then examined the effect of the genetic polymorphisms on the variability in the pharmacokinetics of carvedilol using a multiple regression analysis. The oral clearance (CL/F) and also apparent volume of distribution (V/F) of both enantiomers were significantly lower in the subjects with the CYP2D6*10 allele than those with the CYP2D6*1/*1, *1/*2, or *2/*2 genotype, confirming our previous finding that the bioavailability (F) and systemic clearance (CL) of R- and S-carvedilol in the liver is significantly altered in Japanese with the CYP2D6*10 allele. On the other hand, CYP2C9*3, CYP2C19*2, CYP2C19*3, CYP3A5*3, UGT2B7*2, and MDR1 C3435T did not significantly affect the pharmacokinetics of carvedilol in Japanese subjects.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Sequence microheterogeneity is generated at junctions of programmed DNA deletions in Tetrahymena thermophila.

Regulated DNA deletions are known to occur to thousands of specific DNA segments in Tetrahymena during macronuclear development. In this study we determined the precision of this event by examining the junction sequences produced by three different deletions in many independent caryonidal lines. 0.9 kb deletions in region M produce at least 3 types of junction sequences, of which two have been determined and found to be different by 4 bp. The alternative 0.6 kb deletions in this region are much less variable. 1.1 kb deletions in region R, known from a previous study to be slightly variable, produce two types of junction sequences which are different from each other by 3 bp. Thus, developmentally regulated deletions in Tetrahymena can produce sequence microheterogeneity at their junctions. This process contributes significantly to the diversification of Tetrahymena's somatic genome.

Animals↗

Linkage analysis of quantitative traits in randomly ascertained pedigrees: comparison of penetrance-based and variance component analysis.

Penetrance-based linkage analysis and variance component linkage analysis are two methods that are widely used to localize genes influencing quantitative traits. Using computer programs PAP and SOLAR as representative software implementations, we have conducted an empirical comparison of both methods' power to map quantitative trait loci in extended, randomly ascertained pedigrees, using simulated data. Two-point linkage analyses were conducted on several quantitative traits of different genetic and environmental etiology using both programs, and the lod scores were compared. The two methods appear to have similar power when the underlying quantitative trait locus is diallelic, with one or the other method being slightly more powerful depending on the characteristics of the quantitative trait and the quantitative trait locus. In the case of a multiallelic quantitative trait locus, however, the variance component approach has much greater power. These findings suggest that one should give careful thought to the likely allelic architecture of the quantitative trait to be analyzed when choosing between these two analytical approaches. It may be the case in general that linkage methods which explicitly or implicitly rely on the assumption of a diallelic trait locus fare poorly when this assumption is incorrect.

Chromosome Mapping↗

Nucleoprotein gene analysis of fixed and street rabies virus variants using RT-PCR.

A simple and rapid single-step reverse transcriptase-polymerase chain reaction (RT-PCR) was used to investigate the nucleoprotein (N) gene of 11 rabies viruses. A conserved set of RT-PCR primers was designed to amplify the most variable region in the N gene. N gene regions were amplified from 6 fixed laboratory viruses, 4 street viruses from dogs in Thailand, and a horse in Zambia. Sequences of the amplified products, together with the database of 91 additional sequences, were analyzed by using PILEUP program of the GCG package. The rabies viruses grouped into at least 9 distinct clusters by < 90% nucleotide similarity of the N gene region: I (4 isolates, USA), II (2 isolates, South America), III (3 isolates, Africa), IV (52 strains, Europe, Middle East, Africa and South America), V (16 isolates, North America and Arctic), VI (17 isolates, Africa), VII (1 isolate, Africa), VIII (6 isolates, Thailand and Malaysia) and IX (1 isolate, Sri Lanka). A unique group of rabies viruses from Thailand and clusters of isolates corresponding to their geographic origin also were determined. The simple and rapid single-step RT-PCR proved to be useful for identifying rabies viruses, and for grouping the viruses into clades by sequence analysis.

Animals↗

On the origin of Ser/Thr kinases in a prokaryote.

The family of Ser/Thr and/or Tyr kinases and that of His kinases play essential roles in signal transduction. For a long time, the former has been found in eukaryotes, the latter in prokaryotes. Studies in the last decade have shown, however, that most bacteria possess from one to more than 10 genes encoding Ser/Thr kinases. This observation raises an important question concerning the evolutionary origin of Ser/Thr kinases found in bacteria. To answer this question, we have analyzed a family of 11 genes encoding Ser/Thr kinases in the cyanobacterium Synechocystis sp. PCC 6803. This bacterium contains the largest number of Ser/Thr kinases among all bacteria whose genomic sequences have been released so far. In this study, we have developed a user-friendly computer program for statistical analysis of codon usages and GC content. The results demonstrate that Ser/Thr kinases have similar codon usages and GC contents as the average of all possible open reading frames (ORFs) deduced from the genome. In contrast, ORFs encoding transposases, as a control in our analysis, display a disparity in both codon usage and GC content, confirming their multiple origin and genetic promiscuity. In light of our results, we propose that Ser/Thr kinases existed before the divergence between prokaryotes and eukaryotes during evolution, or were laterally transferred into prokaryotes at the early stages of bacterial evolution. If Ser/Thr kinases have persisted ever since in prokaryotes under evolutionary pressure, it is then expected that they play important, possibly even essential roles in regulating bacterial activities as do their counterparts in eukaryotes.

Base Composition↗

Autism and the serotonin transporter: the long and short of it.

Autism is a neurodevelopmental disorder manifesting early in childhood. Some symptoms of autism are alleviated by treatment with selective serotonin reuptake inhibitors, which are known to interact with the serotonin transporter. Moreover, variation in the gene that encodes the transporter (SLC6A4), especially the HTTLPR locus, is known to modulate its expression. It is natural, therefore, to evaluate whether this variation plays a role in liability to autism. We investigated the impact of alleles at HTTLPR and three other loci in SLC6A4 by using a large, independent family-based sample (390 families, 1528 individuals) from the NIH Collaborative Programs of Excellence in Autism (CPEA) network. Allele transmissions to individuals diagnosed with autism were biased only for HTTLPR, both for the narrow diagnosis of autism (P=0.035) and for the broader diagnosis of autism spectrum (P=0.007). The short allele of HTTLPR was significantly overtransmitted. Investigation of haplotype transmissions suggested that, in our data, biased transmission was only due to HTTLPR. With respect to this locus, there are now seven of 12 studies reporting significant transmission bias of HTTLPR alleles, a noteworthy result in itself. However, the studies with significant findings are almost equally divided between overtransmission of short and overtransmission of long alleles. We place our results within this extremely heterogeneous field of studies. Determining the factors influencing the relationship between autism phenotypes and HTTLPR variation, as well as other loci in SLC6A4, could be an important advance in our understanding of this complex disorder.

Adult↗

Rationale for the use of dietary control in toxicity studies--B6C3F1 mouse.

Significant variability in critical study parameters such as tumor incidences and survival, increasing tumor incidence and decreasing survival in common toxicity test models, and agent-induced changes in body weight (BW) and BW distribution all generate concern about the reproducibility, consistency, and equity of chronic toxicity tests used in regulation. These concerns have led to suggestions to control BW in chronic tests by the modulation of dietary intake without inducing malnutrition [dietary control (DC)] thereby minimizing tumor and survival variability both between and within studies. Evaluating the reports of the best controlled set of chronic experiments, the National Toxicology Program bioassay series, from studies initiated from 1981 to 1990, there is an increase in tumor incidence, especially liver tumors, with a consistent increase in BW. The studies are classified as to whether normal or aberrant BW growth curves occur. When the studies with normal growth curves are considered, the variance in the BW at 12 mo on test (BW12) can account for over 50% of the variance in liver tumor incidence. Additional stratification by study type, which alter tumor prevalences, as well as appreciation of housing effects [group housing decreases survival (in male mice) and induces tumors in males and females when compared to individual housing], further increase the strength of the correlations, accounting for up to 90% of the variance seen in tumor incidences. These updated analyses further support the hypothesis that it is the BW variation that is resulting in much of the variability seen in tumor incidences and refine the suggestions for the BW curves used as the desired targets for DC.

Animals↗

Atypical changes in chromatin structure during development in the sea urchin, Lytechinus variegatus.

Embryos of several sea urchin species express three distinct sets of developmental-stage-specific histone variants: cleavage stage, early and late variants. Urchins also contain sperm-specific histone variants. We have found that the sea urchin Lytechinus variegatus, common in shallow coastal waters of the southeastern United States, also contains these four distinct sets of variants. The number and electrophoretic characteristics of L. variegatus variants are similar to those of the related species, Lytechinus pictus, but changes in variant populations are delayed in relation to stage in L. variegatus relative to L. pictus and other species. The cleavage-stage-like variants of H2a and perhaps H1 in L. variegatus are much more abundant in pre-blastula and blastula embryos than cleavage-stage variants in other species; and the appearance of L. variegatus late variants is delayed, relative to the program in L. pictus. Likewise the nucleosome repeat length in L. variegatus embryos increases from 191 to 210 base pairs (bp) upon gastrulation, while major increases in repeat length in other urchins occur before or during blastulation. In addition, the nucleosome repeat length in L. variegatus sperm is anomalously low, 201 +/- 2 bp - lower than observed in L. variegatus gastrula to pluteus stage embryos (210 bp), and much lower than previously observed in sperm of other urchins (more than 233 bp). Direct comparisons showed that Strongylocentrotus purpuratus and L. variegatus sperm contained electrophoretically identical core histones, including two high-molecular-weight H2b variants characteristic of all urchin sperm, but nucleosome repeat lengths of 240 and 201 bp, respectively. Differences in nucleosome repeats of these species appear to be due to differences in H1 variants.

Animals↗

Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry.

Amino acid sequence variations resulting from single-nucleotide polymorphisms (SNPs) were identified using a novel mass spectrometric method. This method obtains 99+% protein sequence coverage for human hemoglobin in a single LC-microspray tandem mass spectrometry (microLC-MS/MS) experiment. Tandem mass spectrometry data was analyzed using a modified version of the computer program SEQUEST to identify the sequence variations. Conditions of sample preparation, chromatographic separation, and data collection were optimized to correctly identify amino acid changes in six variants of human hemoglobin (Hb C, Hb E, Hb D-Los Angeles, Hb G-Philadelphia, Hb Hope, and Hb S). Hemoglobin proteins were isolated and purified, dehemed, (S)-carboxyami-domethylated, and then subjected to a combination proteolytic digestion to obtain a complex peptide mixture with multiple overlaps in sequence. Reversed-phase chromatographic separation of peptides was achieved on-line with MS utilizing a robust fritless microelectrospray interface. Tandem mass spectrometry was performed on an ion trap mass spectrometer using automated data-dependent MS/MS procedures. Tandem mass spectra were collected from the five most abundant ions in each scan using dynamic and isotopic exclusion to minimize redundancy. The spectra were analyzed by a version of the SEQUEST algorithm modified to identify amino acid substations resulting from SNPs.

Amino Acid Sequence↗

Subroutines in the programme of Chlamydomonas gene expression induced by flagellar regeneration.

The unicellular green alga Chlamydomonas reinhardtii possesses two anterior flagella that are rapidly replaced if they are lost. A cytoplasmic pool of flagellar precursors supports regeneration of partial length flagella, but complete regeneration requires de novo synthesis of flagellar proteins. This increase in protein synthesis is transient and is programmed by changes in the physical abundance of a set of RNAs. These changes were measured using cloned cDNAs. The curves that were generated with probes for a number of different RNAs were variations-on-the-theme of a rapid accumulation following deflagellation of the cells, followed by similarly rapid degradation. Differences in the characteristics of the accumulation curves suggest that several 'subroutines' for RNA metabolism appear to run concurrently during flagellar regeneration. A significant portion of the mRNA abundance regulation occurs at the transcriptional level. A group of cDNAs that encode mRNAs whose abundance remains at constant levels during regeneration provides an important internal control for the abundance and transcription measurements. Flagella contain over 200 different proteins, so the possibility exists that the cells coordinately and rapidly alter the transcription of the same number of genes. Chlamydomonas flagellar regeneration thus provides an opportunity to study cellular mechanisms for coordinating the expression of a large set of genes, and correlating these changes with an easily monitored morphogenetic process.

Chlamydomonas↗

InSNP: a tool for automated detection and visualization of SNPs and InDels.

Availability of high quality SNP data is a rate-limiting factor in understanding the impact of genetic variability on gene function and phenotype. Although global projects like HAPMAP generate large numbers of SNPs in an even spacing throughout the human genome, many variation studies have a more focused approach: in the follow-up of positional association findings, candidate gene studies, and functional genomics experiments, knowledge of all variations in a limited amount of sequence (e.g., a gene) is needed. This leads to a large number of resequencing experiments, for which there is a surprising lack of analysis software. We have thus developed specialized software (InSNP) for targeted mutation detection and compared its performance to Polyphred and Mutation Surveyor using 28 amplicons. Out of a total of 579 (InSNP), 644 (Polyphred), and 526 (Mutation Surveyor) SNP predictions, 39 SNPs were confirmed by human expert inspection, with five SNPs missed by Polyphred and one missed by InSNP using the default settings. For InDel detection, out of 70 (InSNP), 28 (Polyphred), and 693 (Mutation Surveyor) InDel predictions, two InDels were confirmed by human expert inspection, with one InDel missed by Polyphred. InSNP provides a user-friendly interface with better functionality for mutation detection than general-purpose sequence handling software. It provides similar SNP detection sensitivity and specificity as the public domain and commercial alternatives in the investigated dataset. We hope that InSNP lowers the barriers to the use of automated mutation detection software and aids in the improvement of the efficiency of such experiments. The Windows installer (setup) program and sample datasets are available at www.mucosa.de/insnp/.

Algorithms↗

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.

Algorithms↗