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At least 1,171 records · Page 65Linked to original sources
PubMed1999

The Leishmania genome comes of Age.

The Leishmania Genome Network (LGN) was born in Rio de Janeiro, Brazil in 1994. In the short period that has elapsed since then, the LGN has focused solely on the acquisition of the resources, and hence data, that have enabled a rational approach to genomic sequencing of the reference strain, Leishmania major Friedlin. This has now been achieved. In this review, Alasdair Ivens and Jennie Blackwell, secretary and chairman of the LGN, respectively, re-examine the approaches that were adopted, comment on some of the interesting data that have been obtained and introduce some genome-wide approaches that will facilitate functional studies of the parasite.

Animals↗
PubMed2006

Correlation analysis between single-nucleotide polymorphism of malate dehydrogenase gene 5'-flanking region and growth and body composition traits in chicken.

Malate dehydrogenase (MD) is a key enzyme that plays an important role in energy metabolism. It catalyzes the oxidative decarboxylation of L-malate to yield CO2 and pyruvate, while simultaneously generating NADPH from NADP+. The NADPH generated can be utilized in de novo synthesis of palmitate, which is the precursor molecule for the formation of other long-chain fatty acids. And high levels of MD will also activate muscle development. The current study was designed to investigate the effects of MD gene on growth and body-composition traits in chicken. The eighth generation population of Northeast Agricultural University broiler lines divergently selected for its abdominal fat and Northeast Agricultural University F2 resource population were used in the research. Polymorphisms were detected by DNA sequencing and PCR-RFLP method was then developed to screen the population. A single mutation at the position of the 235 bp (Accession No. U49693) of MD 5'-flanking region was found. The correlation analysis between the polymorphism of the MD gene and growth and body composition traits was carried out using the appropriate statistic model. Least-square analysis showed that the BB genotype birds had much higher pectoralis major weight and percentage of pectoralis major than AA genotype birds (P<0.05). The abdominal fat weight, percentage of abdominal fat, the liver weight and percentage of liver weight of the AA genotype birds were much higher than those of BB genotype birds (P<0.05). These results indicate that MD gene is the major gene or is linked to the major gene that affects the growth and body composition traits in chicken.

5' Flanking Region↗
PubMed2025

Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.

Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n&#x2009;=&#x2009;8) was obtained between April 2014 and January 2015 from two depths (1&#x2009;m and 50&#x2009;m) in four different seasons, while the second set (n&#x2009;=&#x2009;20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90&#x2009;m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.

Republic of Korea↗
PubMed2006

2-(4-Tolylsulfonyl)ethoxymethyl (TEM)-a new 2'-OH protecting group for solid-supported RNA synthesis.

The 2-(4-tolylsulfonyl)ethoxymethyl (TEM) as a new 2'-OH protecting group is reported for solid-supported RNA synthesis using phosphoramidite chemistry. The usefulness of the 2'-O-TEM group is exemplified by the synthesis of 12 different oligo-RNAs of various sizes (14-38 nucleotides long). The stepwise coupling yield varied from 97-99% with an optimized coupling time of 120 s. The synthesis of all four pure phosphoramidite building blocks is also described. Two new reliable parameters, delta(C2')-delta(C3') and delta(H2')-delta(H3'), have been suggested for the characterization of isomeric 2'-O-TEM and 3'-O-TEM as well as other isomeric mono 2'/3'-protected ribonucleoside derivatives. The most striking feature of this strategy is that the crude RNA prepared using our 2'-O-TEM strategy is sufficiently pure (>90%) for molecular biology research without any additional purification step, thereby making oligo-RNAs easily available at a relatively low cost, saving both time and lab resources.

Base Sequence↗
PubMed1989

Recombinant inbred strain and interspecific backcross analysis of molecular markers flanking the murine agouti coat color locus.

Recombinant inbred strain and interspecific backcross mice were used to create a molecular genetic linkage map of the distal portion of mouse chromosome 2. The orientation and distance of the Ada, Emv-13, Emv-15, Hck-1, Il-1a, Pck-1, Psp, Src-1 and Svp-1 loci from the beta 2-microglobulin locus and the agouti locus were established. Our mapping results have provided the identification of molecular markers both proximal and distal to the agouti locus. The recombinants obtained provide valuable resources for determining the direction of chromosome walking experiments designed to clone sequences at the agouti locus. Comparisons between the mouse and human genome maps suggest that the human homolog of the agouti locus resides on human chromosome 20q. Three loci not present on mouse chromosome 2 were also identified and were provisionally named Psp-2, Hck-2 and Hck-3. The Psp-2 locus maps to mouse chromosome 14. The Hck-2 locus maps near the centromere of mouse chromosome 4 and may identify the Lyn locus. The Hck-3 locus maps near the distal end of mouse chromosome 4 and may identify the Lck locus.

Animals↗
PubMed2003

Practical imaging of the spine and spinal cord.

Magnetic resonance imaging is the imaging method of choice in most diseases of the spinal canal and cord. Many pulse sequences are available, and in this era of increased expectations and diminishing resources, a practical approach to the most efficient spine imaging is needed. Our strategy is a series of protocols tailored to the particular area of the spine and the disease process suspected.

Cervical Vertebrae↗
PubMedDate not supplied

Turning point and public health institutes: vehicles for systems change.

Public Health Institutes are free-standing multisector entities able to function as conveners to improve health status and foster innovations in health systems. Turning Point is a program funded by The Robert Wood Johnson Foundation, involving 21 statewide initiatives and 2 "linked" states that formed multisector collaborative partnerships for public health systems change. In 18 of the Turning Point states, there are also Public Health Institutes, some formed by Turning Point partnerships and some established independently. Both Turning Point and Public Health Institutes represent efforts to reform and enhance public health systems. What has been the relationship between these two organizational forms? This descriptive, qualitative study examined the relationships between state-level Turning Point partnerships and Public Health Institutes in states that have both. Key participants in both institutions were interviewed, and models were developed to represent those relationships. Principal findings suggest that the relationships of Turning Point state partnerships with Public Health Institutes have taken many shapes. Factors that influence the choices and sequencing of these options are largely related to the political and economic resources of each state. Turning Point participants perceived Public Health Institutes to be a useful organizational form for sustaining public health systems change. Public Health Institutes have more administrative and fiscal flexibility than state government and greater opportunities for policy development and advocacy. However, free-standing institutes also have greater financial uncertainty.

Academies and Institutes↗
PubMed2006

Sequence diversity and rates of molecular evolution between sheep and cattle genes.

Experiments that aim to identify genes of importance in sheep are currently inhibited by a paucity of genomic resources. One approach, therefore, is to exploit the wealth of data and associated capabilities becoming available for the bovine genome. Cross-species application of microarrays and comparative sequencing to identify single nucleotide polymorphisms are two possibilities; however, both are dependant on the level of nucleotide sequence similarity between the two species. This study used 120 gene orthologues consisting of over 60 kb of aligned sequence to estimate the gene diversity between cattle and sheep. Less than 3% of protein-coding nucleotide positions were found to be different, indicating that the prospect for successfully using cross-species strategies is high. Substitution at synonymous sites ranged between 6.9 and 7.7% (+/- 0.3%), and was higher than at non-synonymous sites (1.4-1.7 +/- 0.1%). The relative rate test was used to determine whether the observed mutation rates were constant between the two lineages. While the rate at synonymous sites appeared constant, the rate at non-synonymous sites was significantly higher within the caprinae lineage (sheep) when compared with bovinae (cattle; chi2 = 10.03; d.f. = 1, P < 0.01). This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Animals↗
PubMed2006

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

Animals↗
PubMed2006

6S RNA regulation of pspF transcription leads to altered cell survival at high pH.

6S RNA is a highly abundant small RNA that regulates transcription through direct interaction with RNA polymerase. Here we show that 6S RNA directly inhibits transcription of pspF, which subsequently leads to inhibition of pspABCDE and pspG expression. Cells without 6S RNA are able to survive at elevated pH better than wild-type cells due to loss of 6S RNA-regulation of pspF. This 6S RNA-dependent phenotype is eliminated in pspF-null cells, indicating that 6S RNA effects are conferred through PspF. Similar growth phenotypes are seen when PspF levels are increased in a 6S RNA-independent manner, signifying that changes to pspF expression are sufficient. Changes in survival at elevated pH most likely result from altered expression of pspABCDE and/or pspG, both of which require PspF for transcription and are indirectly regulated by 6S RNA. 6S RNA provides another layer of regulation in response to high pH during stationary phase. We propose that the normal role of 6S RNA at elevated pH is to limit the extent of the psp response under conditions of nutrient deprivation, perhaps facilitating appropriate allocation of diminishing resources.

Base Sequence↗
PubMed2026

Mechanistic Perspectives From Genomics and Pangenomics of Medicinal and Aromatic Plants: Linking Genome Architecture to Phytochemical Diversity.

Medicinal and aromatic plants (MAPs) produce a remarkable diversity of specialized metabolites with significant pharmaceutical, nutraceutical, and industrial value. Although advances in long-read sequencing, chromosome-scale genome assembly, and pangenomics have greatly expanded genomic resources, the mechanistic links between genome architecture and phytochemical diversity remain incompletely understood. The present review synthesizes current evidence describing how structural genomic variation may contribute to phytochemical diversity, while acknowledging that many proposed genome-to-metabolite relationships require further experimental validation. Examples illustrate how genome architecture is associated with specialized-metabolite biosynthesis through multiple regulatory processes. However, the strength of supporting evidence varies considerably among MAP species. Moreover, relatively few genome-to-metabolite relationships have been confirmed through direct functional validation. We further discuss how pangenomics, multiomics integration, genome editing, synthetic biology, and artificial intelligence support the discovery, validation, and engineering of specialized metabolic pathways. Casual conclusions are evaluated according to the strength of available evidence, highlighting where causal relationships have been experimentally established and where conclusions remain primarily association-based. Overall, this review provides an integrated conceptual and evidence-based perspective summarizing proposed relationships between genome architecture and phytochemical diversity and outlines future priorities for functional genomics, precision breeding, metabolic engineering, and sustainable utilization of MAPs.

artificial intelligence↗
PubMed2002

Clinicopathologic significance of structural alterations of p53 protein in papillary thyroid carcinoma.

OBJECTIVE: To make a thorough study on the clinicopathologic significance of the three-dimensional structural alteration of the p53 protein in papillary thyroid carcinomas and to provide an objective criterion for the evaluation of PTC prognosis. METHODS: A total of 41 PTC cases were enrolled. Techniques including polymerase chain reaction with single strand conformational polymorphism (PCR-SSCP), DNA sequencing, computerized three-dimensional protein modeling by means of international shared resources and related software analysis were used. RESULTS: 15 cases with p53 gene mutation defined as Group I were detected in totally 41 PTC cases. No p53 gene mutation was found in the rest 26 cases which were classified as Group II. The differences in lymph node metastatic rate, distant metastatic rate, age, sex, size of the lesion between Group I and Group II were not significant (P > 0.05). The alterations of the amino acid residues of 9 PTC cases out of the 15 p53-gene mutated patients (Group I) were either located in the p53-protein domains, mainly the core domain and the non-specific DNA binding basic domain, or the severely defect cases with the formation of widely divergent structures. It was found that the alterations of the structure of the core domain could directly check the binding of p53 protein to its target DNA molecules. In addition, the alterations of the structure of the basic domain could indirectly prohibit the binding. The ones mentioned above were classified as Group Ib. The rest of six cases with their p53 protein amino acid residues mutated beyond the domains were grouped as Group Ia. The differences in lymph node metastatic rate, distant metastatic rate between Group Ib and Group Ia were statistically significant (P < 0.01, P < 0.05) respectively. CONCLUSIONS: The alterations of the three-dimensional structure of p53-protein is considered as one of the morphological basis of the progression and heterogeneity of PTC. They render an authentic evidence for the selection of the clinical cases with a poor risk for metastasis.

Humans↗
PubMed2003

The human genome and comparative genomics: understanding human evolution, biology, and medicine.

The entire 2.9-billion-letter sequence (nucleotide base pairs) of the human genome is available as a resource for scientific discovery. Some of the findings from the completion of the human genome were expected, confirming knowledge anticipated by many years of research and analysis in both human and comparative genetics. Other findings were not expected. In either case, the availability of the human genome is likely to have significant implications on basic research, clinical investigation, and ultimately the practice of medicine.

Biological Evolution↗
PubMed1988

[The context of dental education].

The author suggests a series of points for reflection and discussion about dental education, beginning with an analysis of the educational process: "why," "for what purpose" (goals), "how" (strategies), and "what" (content). He also explores various aspects of the target population, the sequence, location in time and space, and problems related to financing and resources. He proposes some ideas about the orientation and structure of the curriculum, for discussion by the university and dental care communities.

Curriculum↗
PubMed2002

A bioinformatic strategy to rapidly characterize cDNA libraries.

MOTIVATION: Complementary DNA libraries can define the genetic constituents of specific cells and/or tissues. Their sequencing will illuminate the transcriptome but it is a monumental task requiring considerable resources. RESULTS: We have employed a computational search in conjunction with a microarray-based strategy to alleviate the impediments of deriving a consensus of records that describe testis gene expression. This strategy identified 5681 unique testes-expressed genes of which 3265 were previously portrayed in the UniGene database. Interestingly, a total of 2416 novel testes-expressed genes were identified. This clearly demonstrates that microarrays can be used to rapidly discover a large number of new transcripts.

Adolescent↗
PubMed2005

Molecular analysis of unknown beta-globin gene mutations using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique and its application in Thai families with beta-thalassemias and beta-globin variants.

OBJECTIVES: Approximately 40 beta-globin gene mutations have been identified in Thailand. The detection of these mutations is currently performed by the reverse dot blot (RDB) hybridization technique, which could detect only known mutations. We describe here the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) assay for detecting unknown mutations of the beta-globin genes. DESIGN AND METHODS: Six PCR fragments covering the promoter, entire coding region, and intervening sequences were amplified before separation by the SSCP technique. Fifteen known mutations and two polymorphisms were analyzed by this technique in various gel mixtures and temperatures to compare their mobility shift patterns. RESULTS: The clear patterns of mobility shift were demonstrated when a 10% polyacrylamide gel with 5% glycerol was used. The sensitivity was found to be 100% when electrophoreses were performed at both room temperature and 6 degrees C. This technique was then applied to screen beta-globin gene mutations in Thai families with similar profiles of abnormal hemoglobins. The distinct patterns of mobility shifts were observed in which further sequencing analysis revealed an AC insertion at codon 146, causing hemoglobin Tak. CONCLUSION: The PCR-SSCP technique might be a useful molecular technique to minimize the requirement of direct genomic sequencing to identify beta-globin gene mutations and could be applied in several developing countries where resources are limited but genetic hemoglobin disorders are highly prevalent.

Adolescent↗