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PubMed2001

Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments.

AIMS: The objectives of this work were to explore the diversity in Fe (III)-reducing enrichment cultures from the deep subsurface and to identify strains involved in metal reduction. METHODS AND RESULTS: Analyses of 16S ribosomal RNA (rRNA) of enrichments, supplemented with hydrogen, acetate or pyruvate as an electron donor, identified three dominant operational taxonomic units (OTUs). All cultures exhibited considerable diversity (36-24 OTUs), even after being transferred at least nine times. Two OTUs were present in all three cultures, constituting about 65% of the total clones examined. CONCLUSION: Dominant OTUs appeared to be most closely related to Thermoanaerobacter ethanolicus or T. kivui. One OTU, which is potentially responsible for autotrophic Fe (III) reduction, was only about 95% similar to T. ethanolicus and may represent a new species. SIGNIFICANCE AND IMPACT OF THE STUDY: An unexpectedly high diversity was found in these enrichments and this diversity may be a feature that can be exploited.

Acetic Acid↗
PubMed2003

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important contribution to the study of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We identified 7206 separate clones that satisfied stringent criteria for tissue-specific expression. Gene Ontology terms were assigned for these 7206 clones, and the proportion of 'molecular function' ontology for each tissue-specific clone was examined. These data will provide insights into the function of each tissue. Tissue-specific gene expression profiles obtained using our cDNA microarrays were also compared with the data extracted from the GNF Expression Atlas based on Affymetrix microarrays. One major outcome of the RIKEN transcriptome analysis is the identification of numerous nonprotein-coding mRNAs. The expression profile was also used to obtain evidence of expression for putative noncoding RNAs. In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed.

Animals↗
PubMed1996

The rho 1 GABA receptor cloned from rat retina is down-modulated by protons.

We have cloned and sequenced the full-length cDNA of the rat GABA (gamma-aminobutyric acid) rho 1 receptor subunit. The deduced amino acid sequence (474 amino acids) of the rat rho 1 receptor is 95% homologous to the previously cloned human rho 1 receptor. The rho 1 cDNA includes a 5' 129 bp and a 3' 2.6 kb untranslated region, which contains a sequence homologous to the human medium reiteration frequency repetitive sequence, MER18. The rat rho 1 receptor shows 45-50% similarity to the GABAA receptor beta subunits. This similarity is among the highest between all GABAA receptor subunit classes, giving no support at the molecular level to the classification of the rho subunits to a novel GABAC receptor class. The rat rho 1 cDNA formed functional GABA receptors insensitive to bicuculline, but sensitive to blockade by picrotoxin, when transiently expressed in the human embryonic kidney cell line HEK 293. We studied the sensitivity of the rho 1-mediated GABA current to variations in extracellular pH (pH0), and found that these receptors are strongly down-modulated by H+ ions. A decrease in pH0 from 7.4 to 6.4 decreased the GABA current by 51 +/- 8%, whereas an increase in pH0 from 7.4 to 8.4 increased the current by 77 +/- 8%. In view of the up-regulatory effect of protons on the GABA current observed in a number of preparations, the rho 1 receptors may contain a novel down-regulatory binding site for protons characteristic to these receptors.

Amino Acid Sequence↗
PubMed2005

[Role of molecular screening for common fusion genes in the diagnosis and classification of leukemia].

OBJECTIVE: To assess the value of common fusion genes analysis in the diagnosis and classification of leukemia by multiplex RT-PCR. METHODS: The multiplex RT-PCR, including 8 parallel PCR reactions, could screen 86 mRNA breakpoints or splice variants at the same time, which was important for the diagnosis and prognosis of leukemia. Bone marrow samples from 161 cases of leukemia and 8 cases of myelodysplastic syndrome (MDS) were involved in the study. The distribution of common fusion genes in leukemia was analyzed by the method mentioned above in combination with clinical and morphological features. RESULTS: Ten fusion genes were detected in 115 cases of leukemia, including AML1/ETO, PML/RAR alpha, PLZF/RAR alpha, dupMLL, MLL/AF6, MLL/AF10, CBFbeta/MYH11, BCR/ABL, Hox11, and EVI1 BCR/ABL was positive in all the 52 cases of chronic myeloid leukemia; PML/RAR alpha was found in 21 of 25 acute promyelocytic leukemia (APL), and PLZF/RAR alpha was detected in one case of APL. Sixteen cases of 17 AML1/ETO-positive acute leukemia (AL) belonged to FAB-M2 subtype, and one case was mixed leukemia. Three of 4 AL cases carrying CBFbeta/MYH11 were M4 subtype, and one was M5 subtype. MLL aberrations were found in 16 AL, in which all MLL/AF6 translocation existed in M5 subtype with classic monoblastic characters. Furthermore, BCR/ABL was detected in 5 acute lymphoblastic leukemia (ALL) cases. Fusion genes were also found in 2 MDS cases, of which AML1/ETO positive-MDS-RAEB progressed to AML rapidly. CONCLUSION: Screening of common fusion genes by multiplex RT-PCR is an important tool which could provide useful and reliable molecular genetic information for the diagnosis and treatment of leukemia.

Adolescent↗
PubMed2004

Column sorting: rapid calculation of the phylogenetic likelihood function.

Likelihood applications have become a central approach for molecular evolutionary analyses since the first computationally tractable treatment two decades ago. Although Felsenstein's original pruning algorithm makes likelihood calculations feasible, it is usually possible to take advantage of repetitive structure present in the data to arrive at even greater computational reductions. In particular, alignment columns with certain similarities have components of the likelihood calculation that are identical and need not be recomputed if columns are evaluated in an optimal order. We develop an algorithm for exploiting this speed improvement via an application of graph theory. The reductions provided by the method depend on both the tree and the data, but typical savings range between 15%and 50%. Real-data examples with time reductions of 80%have been identified. The overhead costs associated with implementing the algorithm are minimal, and they are recovered in all but the smallest data sets. The modifications will provide faster likelihood algorithms, which will allow likelihood methods to be applied to larger sets of taxa and to include more thorough searches of the tree topology space.

Algorithms↗
PubMed2004

Bayesian phylogenetic analysis of combined data.

The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.

Animals↗
PubMed2004

Impaired glucose transport into the brain: the expanding spectrum of glucose transporter type 1 deficiency syndrome.

PURPOSE OF REVIEW: Glucose transporter type 1 deficiency syndrome (OMIM 606777) is a treatable epileptic encephalopathy resulting from impaired glucose transport into the brain. In recent years, the increasing number of patients has generated substantial insights into the manifestations and mechanisms of this disease. Current understanding of this novel disorder is reviewed, and recent advances in diagnosis and treatment are highlighted. RECENT FINDINGS: The syndrome is now understood to be a complex neurological disorder. The clinical spectrum has recently been extended by infants with 'benign' transient hypoglycorrhachia, glucose transporter type 1 deficiency syndrome without seizures, and by adult cases. Other key findings in the last couple of years include (1) the description of electroencephalogram abnormalities, (2) a characteristic cerebral metabolic footprint in positron emission tomography imaging, and (3) the definition of molecular mechanisms and functional domains within the glucose transporter type 1 protein by in-vitro mutagenesis. The disease has also shed a new light on the mechanisms and the effectiveness of the ketogenic diet for seizure control. SUMMARY: The syndrome is now well characterized in children and should be considered in any patient with intractable epilepsy. An effective therapy is available. The clinical spectrum and the molecular basis of the disease are increasingly heterogeneous and indicate complex pathogenic mechanisms that will ultimately lead to a classification on clinical, biochemical, and molecular grounds.

Adult↗
PubMedDate not supplied

Ontogeny and homoplasy in the papionin monkey face.

Recent molecular research has provided a consistent estimate of phylogeny for the living papionin monkeys (Cercocebus, Lophocebus, Macaca, Mandrillus, Papio, and Theropithecus). This phylogeny differs from morphological phylogenies regarding the relationships of the mangabeys (Cercocebus and Lophocebus) and baboons (Mandrillus, Papio, and Theropithecus). Under the likely assumption that the molecular estimate is correct, the incongruence between the molecular and morphological data sets indicates that the latter include numerous homoplasies. Knowledge of how these homoplasies emerge through development is important for understanding the morphological evolution of the living papionins, and also for reconstructing the phylogenetic relationships and adaptations of their fossil relatives. Accordingly, we have used geometric morphometric techniques and the molecular phylogeny to investigate the ontogeny of a key area of morphological homoplasy in papionins, the face. Two analyses were carried out. The first compared allometric vectors of Cercocebus, Lophocebus, Macaca, Mandrillus, and Papioto determine which of the facial resemblances among the genera are homoplasic and which are plesiomorphic. The second analysis focused on early post-natal facial form in order to establish whether the facial homoplasies exhibited by the adult papionins are to some degree present early in the post-natal period or whether they develop only later in ontogeny. The results of our analyses go some way to resolving the debate over which papionin genera display homoplasic facial similarities. They strongly suggest that the homoplasic facial similarities are exhibited by Mandrillus and Papio and not by Cercocebus and Lophocebus, which share the putative primitive state with Macaca. Our results also indicate that Mandrillus and Papio achieve their homoplasic similarities in facial form not through simple extension of the ancestral allometric trajectory but through a combination of an extension of allometry into larger size ranges and a change in direction of allometry away from the ancestral trajectory. Thus, the face of Mandrillus is not simply a hypermorphic version of the face of its sister taxon, Cercocebus, and the face of Papio is not merely a scaled-up version of the face of its sister taxon, Lophocebus. Lastly, our results show that facial homoplasy is not restricted to adult papionins; it is also manifest in infant and juvenile papionins. This suggests that the homoplasic facial similarities between Mandrillus and Papio are unlikely to be a result of sexual selection.

Animals↗
PubMed1999

Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification.

Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.

Amino Acid Sequence↗
PubMed1996

A revised and extended classification of the distal arthrogryposes.

Since the group of disorders known as the distal arthrogryposes (DAs) were defined, additional disorders characterized by multiple congenital contractures of the distal limbs were described, and the distribution of phenotypic findings in the DAs has been expanded. The breadth of disorders labeled as DAs has diminished the usefulness of the DA classification. We propose a strict definition of DA and diagnostic criteria for DA disorders. Subsequently, we use these standards and propose a revised classification of discrete conditions that should be labeled DAs. Optimally, this serves as a framework for a DA classification based on underlying molecular and physiologic abnormalities.

Arthrogryposis↗
PubMed1992

Future directions for the American Joint Committee on Cancer.

This report summarizes future directions for the American Joint Committee on Cancer (AJCC). It was presented at the Workshop on Molecular Markers in the Classification and Staging of Cancer that was sponsored by the AJCC and supported by a grant from the American Cancer Society.

Forecasting↗
PubMed1994

A variety of genetic mechanisms are associated with the Prader-Willi syndrome.

An extensive set of chromosome 15 DNA polymorphisms and densitometric analysis with four markers mapping to the Prader-Willi chromosome region (PWCR) of chromosome 15 have been used to characterize a cohort of 30 subjects with classical Prader-Willi syndrome (PWS). Molecular analysis enabled the classification of the PWS subjects into four groups: (A) 18 subjects (60%) had deletions of paternal 15q11-13 involving a common set of DNA markers. Two subjects had differently sized deletions, one larger and one smaller than the other cases. (B) Eight (27%) had maternal uniparental disomy for chromosome 15. (C) One (3%) had a marker chromosome carrying an extra copy of the PWCR. The marker chromosome was demonstrated to be of paternal origin and the two intact chromosomes were maternally derived. This case represents an apparent exception to the generally held view that PWS is associated with an absence of paternally inherited gene(s) located in the PWCR. (D) The remaining three cases (10%) had none of the above abnormalities. This last subgroup of patients has not previously been well characterized but could represent limited deletions not detectable with the markers used or abnormalities in the imprinting process. These cases represent potentially valuable resources to elucidate more precisely the fundamental disorders responsible for PWS.

Adolescent↗
PubMed2007

Prognostic significance of vascular endothelial growth factor protein levels in T1-2 N0 laryngeal cancer treated with primary radiation therapy.

BACKGROUND: The purpose of this study was to assess the prognostic value of vascular endothelial growth factor protein levels in a large cohort of patients with T1-T2 N0 laryngeal cancer treated with primary radiation therapy (XRT). METHODS: Primary tumor specimens from a cohort of 123 patients with T1-T2 N0 laryngeal cancer treated with XRT between 1975 and 2000 were constructed into a tissue microarray. Clinical prognostic factors included age, sex, T classification, and tumor subsite. Molecular prognostic factors included vascular endothelial growth factor, epidermal growth factor receptor, and p53 expression, determined by using immunohistochemistry on tissue microarrays. The association between vascular endothelial growth factor status, covariables, and outcome was assessed. RESULTS: With a median follow-up of 9.9 years, 32 (26%) were diagnosed with local relapse (5-year local relapse-free rate, 70.4%). T2 tumor stage (31.7%) was a significant predictor of local relapse (relative risk [RR], 1.71; 95% confidence interval [CI], 1.21-2.43; P<.05). Positive expression of vascular endothelial growth factor, epidermal growth factor receptor, and p53 were: 8.5%, 58.7%, and 36.4%, respectively. In univariate analysis, vascular endothelial growth factor positivity was a significant predictor of overall survival (RR = 1.62; 95% CI, 0.99-2.42; P = .05). In multivariate analysis, positive vascular endothelial growth factor status maintained significant correlation with overall survival (RR, 2.79; 95% CI, 1.49-4.95; P = .002). CONCLUSIONS: Vascular endothelial growth factor positivity appeared to be a significant predictor of overall survival in a multivariate model. Further evaluation of vascular endothelial growth factor-positive laryngeal cancers treated with primary XRT is warranted.

Adult↗
PubMed1988

Evaluation of the L5178Y mouse lymphoma cell mutagenesis assay: methods used and chemicals evaluated.

A general protocol, modified from the one described by Clive and Spector (Mutat Res 31:17-29, 1975), was followed by two laboratories, Litton Bionetics, Inc., and SRI International, to evaluate 63 coded chemicals from 16 chemical classes for mutagenic activity at the thymidine kinase locus in L5178Y TK+/- 3.7.2C mouse lymphoma cells. The general protocol is discussed. Some procedural variations introduced by both laboratories are described and discussed in terms of their potential effect on the comparative results of the assay. Also included are the chemical structures, molecular weights, and functional classifications of the 63 chemicals. The assay appeared to tolerate the specific procedural variations in each laboratory without changing its reliability.

Animals↗
PubMed2000

PCR-RFLP and sequence analysis of a non-ribosomal fragment for genetic characterization of European stone fruit yellows phytoplasmas infecting various Prunus species.

A 927 bp non-ribosomal fragment was used to assess the genetic variability of the European stone fruit yellows (ESFY) phytoplasma infecting 14 different Prunus species. For this, 175 isolates originating from four different Mediterranean countries were tested by PCR-RFLP analysis with seven restriction enzymes. No polymorphism among the ESFY phytoplasma could be observed but 12 out of 18 restriction sites differed between the homologous fragments of ESFY and apple proliferation (AP) phytoplasmas. An 846 bp fragment of a French ESFY isolate was sequenced, it included the 3'-end of a putative nitroreductase gene, an intergenic region and a truncated open reading frame. This ESFY phytoplasma sequence showed 89.7% identity with the equivalent AP phytoplasma nucleotide sequence (83. 9% identity at the amino acid level). The G+C content of the entire sequence was extremely low (15.4%) and A+T-rich codons were highly preferred in codon usage. In this paper, we report the presence of the ESFY phytoplasma for the first time in Turkey and in five Prunus hosts never reported previously. Our results also indicate that the ESFY phytoplasma isolates affecting various Prunus species are genetically homogenous but can be distinguished from the AP phytoplasma. Therefore, they are likely to represent different taxons.

Amino Acid Sequence↗
PubMed1998

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences.

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.

Acanthocephala↗
PubMed2000

The granule-bound starch synthase (GBSSI) gene in the Rosaceae: multiple loci and phylogenetic utility.

We sampled the 5' end of the granule-bound starch synthase gene (GBSSI or waxy) in Rosaceae, sequencing 108 clones from 18 species in 14 genera representing all four subfamilies (Amygdaloideae, Maloideae, Rosoideae, and Spiraeoideae), as well as four clones from Rhamnus catharticus (Rhamnaceae). This is the first phylogenetic study to use the 5' portion of this nuclear gene. Parsimony and maximum-likelihood analyses of 941 bases from seven complete and two partial exons demonstrate the presence of two loci (GBSSI-1 and GBSSI-2) in the Rosaceae. Southern hybridization analyses with locus-specific probes confirm that all four Rosaceae subfamilies have at least two GBSSI loci, even though only one locus has been reported in all previously studied diploid flowering plants. Phylogenetic analyses also identify four clades representing four loci in the Maloideae. Phylogenetic relationships inferred from GBSSI sequences are largely compatible with those from chloroplast (cpDNA: ndhF, rbcL) and nuclear ribosomal internal transcribed spacer (nrITS) DNA. Large clades are marked by significant intron variation: a long first intron plus no sixth intron in Maloideae GBSSI-1, a long fourth intron in Rosoideae GBSSI-1, and a GT to GC mutation in the 5' splice site of the fourth intron in all GBSSI-2 sequences. Our data do not support the long-held hypothesis that Maloideae originated from an ancient hybridization between amygdaloid and spiraeoid ancestors. Instead, Spiraeoideae genera (Kageneckia and Vauquelinia) are their closest relatives in all four GBSSI clades.

Base Sequence↗
PubMed1995

Phylogenetic analysis of primate foamy viruses by comparison of pol sequences.

The relationship between primate foamy viruses was determined by comparing a 425-bp DNA segment obtained by PCR using primers homologous to highly conserved portions of the pol gene. The phylogenetic tree of 14 foamy viruses investigated reflects the relationship between their host species: A cluster of Asian Old World monkey foamy viruses including simian foamy virus (SFV) prototypes 1 and 2 (isolated from Macaca cyclopsis) is separated from African Old World foamy viruses including prototype SFV-3 and SFV-3 strain LK-3 (isolated from African green monkeys, Cercopithecus aethiops). These two clusters of Old World monkey foamy viruses are more distantly related to a cluster of ape and human foamy viruses including prototypes SFV-6, SFV-7, SFV cpz (all isolated from chimpanzees), and human foamy virus (HFV). The New World prototype SFV-8 (isolated from a spider monkey, Ateles sp.) is distinct from the Old World cluster. Our own foamy virus isolates from a rhesus monkey (Macaca mulatta) and an African green monkey were grouped to the Asian or the African Old World monkey foamy virus cluster, respectively. The foamy virus sequences obtained from lymphocytes of two humans, one exposed to African green monkeys and the other to cultured HFV, were compared. The first sequence was closely related to the African Old World monkey foamy virus cluster, whereas the second was identical to HFV, except for a single mismatch. We conclude that limited sequencing of amplified DNA is a powerful tool for classification as well as molecular epidemiology of foamy viruses.

Animals↗