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At least 955 records · Page 53Linked to original sources
PubMed2005

Genomic structure and alternative transcript of bovine fatty acid synthase gene (FASN): comparative analysis of the FASN gene between monogastric and ruminant species.

Fatty acid synthesis differs considerably between monogastric and ruminant species. Fatty acid synthase (FASN) plays a central role in de novo lipogenesis in mammals. FASN has seven active sites which help to catalyse all the reaction steps in the conversion of acetyl-CoA and malonyl-CoA to palmitate. In this work, the bovine fatty acid synthase gene (FASN) was cloned, characterized and compared to the human and rat orthologs. Comparative analysis reveals evolutionarily conserved exon regions and gene flanking sequences. Analysis of the DNA sequence in the 5' flanking region of the FASN bovine gene revealed a potential TATA box, CAAT box and 5 Sp1 binding sites located in a CpG island. RT-PCR and Western blot analysis showed that FASN expression was higher in brain, testis and adipose tissue than in liver and heart. The longer form of the FASN cDNA includes a 7,542-bp sequence which encodes a protein with 2,513 amino acids. An alternative transcript was discovered in bovine and ovine tissues devoid of part of exon 9. The removal of part of exon 9 by post-transcriptional splicing causes a frameshift in the open reading frame and results in a premature termination codon. We hypothesize that in ruminants, FASN may be regulated by the ratio between the two transcripts. The small transcript is mostly produced in tissues with low fatty acid synthesis.

Alternative Splicing↗
PubMed1984

A frequent restriction fragment length polymorphism in the human metallothionein-II processed gene region is evolutionarily conserved.

Genomic blot analysis of human DNA indicated that metallothioneins are represented by a multi-gene family. Clones containing metallothionein sequences have been isolated and two of these have been identified as metallothionein-I and metallothionein-II processed genes by sequence analysis. The metallothionein-II processed gene in humans shows two restriction fragment length polymorphisms of 4.5 and 4.8 kb (10(3) bases) when EcoRI-digested genomic DNA from various individuals was analysed by Southern blotting. All the three genotypes are found at a high frequency and thus the metallothionein-II processed gene represents a true polymorphic marker. Familial studies also indicate that these restriction fragment length polymorphisms follow the classical Mendelian inheritance. Detailed Southern blot analyses show that this restriction fragment length polymorphism is due to a restriction site polymorphism and is localized at the 5'-flanking region of the metallothionein-II processed gene. Sequence analysis of the suspected region in the 4.8 kb fragment shows that the sequence G*GATTC, which is found 371 nucleotides downstream from the EcoRI site on the 5' end of the 4.8 kb fragment, makes a HinfI site. A transition of *G to A in this sequence in the 4.5 kb allele has resulted in loss of the HinfI site and created an EcoRI site. Thus, this mutation has given rise to this restriction fragment length polymorphism.

Alleles↗
PubMed2001

Comparison of Vif sequences from diverse geographical isolates of HIV type 1 and SIV(cpz) identifies substitutions common to subtype C isolates and extensive variation in a proposed nuclear transport inhibition signal.

We compared the Vif sequences from more than 100 group M and O strains of HIV-1 isolated from diverse geographical regions and various subtypes, in order to identify regions of high variability and those amino acid residues that were highly conserved or invariant. Our analysis found that there were 10 highly conserved domains with additional invariant residues located throughout the protein. Our analysis revealed that in the highly conserved amino-terminal domain, all subtype C isolates examined had a methionine-to-leucine substitution at position 8 and most subtype C isolates had an arginine-to-lysine substitution at position 17 of the protein. Our analysis revealed that the MAP kinase phosphorylation sites, and the cysteine residues at positions 114 and 133, were conserved in Vif sequences from group M, group O, and SIV cpz isolates. Our analysis also shows that the RKKR motif at positions 90--93, proposed as a nuclear transport inhibition signal (NTIS), was conserved neither in different geographical group M and O HIV-1 isolates nor in SIVcpz.

Amino Acid Sequence↗
PubMed2006

Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea.

The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition, large-scale gene expression data for Arabidopsis (Arabidopsis thaliana) have recently become available. Coexpression and evolutionarily conserved sequences are criteria widely used to identify shared cis-regulatory elements. In our study, we employ an integrated approach to combine two sources of information, coexpression and sequence conservation. Best-candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes coexpressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified binding sites and showed strong enrichment of shared cis-elements within functionally related genes. This study demonstrates the value of partially shotgun sequenced genomes and their combinatorial use with functional genomics data to address complex questions in comparative genomics.

Arabidopsis↗
PubMed2005

The prognosis of conservative treatments for lumbar spinal stenosis: analysis of patients over 70 years of age.

STUDY DESIGN: A prospective study. OBJECTIVES: To identify outcomes of aged patients with lumbar spinal stenosis (LSS) treated conservatively and to examine factors that control the prognosis. SUMMARY AND BACKGROUND DATA: There have been no reports evaluating the outcomes of conservative treatments for elderly LSS patients. METHODS: A total of 89 patients, 70 years of age and older, who underwent in-hospital conservative treatment were included. The Japanese Orthopedic Association's score (JOA score) and the disturbance level of activities of daily living (ADL) were used for evaluation. Nerve involvement was classified into radicular, cauda equina, and mixed type. Myelographic findings were classified into central defect with or without block and root defect. Associations between disturbance level of ADL, nerve involvement, and myelographic classifications were investigated. RESULTS: The mean JOA score increased from 11.1 points at admission to 15.9 points at discharge, with 14.3 points maintained at the follow-up; 48.8% of radicular type showed no obstacle in ADL at the follow-up compared with 33.3% of the other types; 13.3% of central defect with block showed no obstacle in ADL compared with 47.8% of the other types with significant difference. CONCLUSION: The prognosis of conservative treatment for aged LSS was relatively good. Radicular type may be a candidate for conservative treatment. However, patients with complete block in the myelogram may not respond favorably to conservative treatment.

Activities of Daily Living↗
PubMed1994

Analysis of the nucleotide sequence of 48 kbp of the variola major virus strain India-1967 located on the right terminus of the conservative genome region.

Computer analysis of a variola major virus (VAR) genomic fragment bounded by the open reading frames (ORFs) D1R and A33L, which is 47,961 bp long, revealed 46 potential ORFs. The VAR proteins were compared to the analogous proteins of vaccinia virus strain Copenhagen. The subunits of DNA-dependent RNA polymerase, as well as the transcription factors, mRNA-capping enzymes, and proteins necessary for the virion morphogenesis proved to be highly conservative within orthopoxviruses. The most pronounced differences between the VAR genome fragment under study and the corresponding vaccinia virus fragment were revealed in the vicinity of the gene encoding the A-type inclusion bodies protein. Possible functions of the analysed viral proteins are discussed.

Amino Acid Sequence↗
PubMed2002

An analysis of 11,196 burn admissions and evaluation of conservative management techniques.

We present an 8-year analysis (1993-2000) of 11,196 burn admissions with an average of 116.6 patients per month. Patients were largely treated by conservative techniques. The mean burn percentage was 50.35. Almost 80% of admissions were in the 16-55 years age group. Paediatric and geriatric burns were 17.1 and 3.1%, respectively. Flame burns accounted for 82.15% of admissions and of these 77.5% were sustained in the kitchen. A total of 35.32% of flame accidents were due to malfunctioning kerosene pressure stove. The overall mortality was 51.80%. These figures need further qualification because 46.8% of patients had more than 50% BSA burns and 50.72% patients reported to the hospital more than 6h after sustaining burns. Patients with <60% BSA burns, and who were received within 6h of injury had a mortality of 23% only. Significantly, 1078/1952 deaths (55.23%) of patients <60% BSA burns took place in first 6 days of admission when 3639 patients with <60% BSA injury were received more than 6h after burn injury. This reflects that even if economic constraints preclude one from having the best infrastructure reasonable mortality rates are still achievable with conservative line of management, even in face of a heavy work load. This also makes one question the cost effectiveness of high cost technology in burn management.

Accidents↗
PubMed1996

Amino acid pair interchanges at spatially conserved locations.

Here we study the pattern of amino acid interchanges at spatially, locally conserved regions in globally dissimilar and unrelated proteins. By using a method which completely separates the amino acid sequence from its respective structure, this work addresses the question of which properties of the amino acids are the most crucial for the stability of conserved structural motifs. The proteins are taken from a structurally non-redundant dataset. The spatially conserved substructural motifs are defined as consisting of a "large enough" number of Calpha atoms found to provide a geometric match between two proteins, regardless of the order of the Calpha atoms in the sequence, or of the sequence composition of the substructures. This approach can apply to proteins with little or no sequence similarity but with sufficient structural similarity, and is unique in its ability to handle local, non-topological matches between pairs of dissimilar proteins. The method uses a computer-version based algorithm, the Geometric Hashing. Since the Geometric Hashing ignores sequence information it lends itself to answer the question posed above. The interchanges at geometrically similar positions that have been obtained with our method demonstrate the expected behaviour. Yet, a closer inspection reveals some distant characteristics, as compared with interchanges based upon sequence-order based techniques, or from energy-contact-based considerations. First, a pronounced division of the amino acids into two classes is displayed: Lys, Glu, Arg, Gln, Asp, Asn, Pro, Gly, Thr, Ser and His on the one hand, and Ile, Val, Leu, Phe, Met, Tyr, Trp, Cys and Ala on the other. These groups further cluster into subgroups: Lys, Glu, Arg, Gln; Asp Asn; Pro, Gly; Ile, Val, Leu, Phe. The other amino acids stand alone. Analysis of the conservation among amino acids indicates proline to be consistently, by far, the most conserved. Next are Asp, Glu, Lys and Gly. Cys is also highly conserved. Interestingly, oppositely charged amino acids are interchanged roughly as frequently as those of the same charge. These observations can be explained in terms of the three-dimensional structures of the proteins. Most of all, there is a clear distinction between residues which prefer to be on the protein surfaces, compared to those frequently buried in the interiors. Analysis of the interchanges indicates their low information content. This, together with the separation into two groups, suggest that the predictive value of the spatial positions of the Calpha+ atoms is not much greater than the sequence alone, aside from their hydrophobicity/hydrophillicity classification.

Amino Acid Sequence↗
PubMed2003

Molecular cloning of feline CD34.

In humans, baboons, dogs and mice CD34 is a cell surface molecule that is expressed on primitive hematopoietic cells and in all these species CD34 positive cells can be used to effect long-term haematopoietic reconstitution. CD34 positive haematopoietic cells therefore provide a convenient and relatively small cell population to target when attempting gene therapy via the haematopoietic system. In order to develop the mucopolysaccharidosis type VI (MPS VI) cat as a model for haematopoietic cell-mediated gene therapy we have isolated the feline CD34 gene as a first step in the generation of antibodies for purification of feline CD34 positive cells. The coding sequence for feline CD34 was isolated from brain cDNA using the polymerase chain reaction (PCR) with oligonucleotides designed to conserved regions of known CD34 gene sequences as primers. Sequence analysis of PCR products revealed the complete amino acid sequence of feline CD34 and allowed analysis of sequence conservation with CD34 from other species. Northern blot analysis showed a 2.6 kb CD34 transcript was present in feline brain, spleen, heart, testis and thymus, and to a lesser extent, in liver. A full-length cDNA clone of the feline CD34 coding sequence was assembled and expressed in CHO-K1 cells. The isolation and expression of the feline CD34 cDNA should facilitate the production of antibodies suitable for the purification of CD34 positive cells.

Amino Acid Sequence↗
PubMed1997

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.

Computer analysis of a conserved domain, BRCT, first described at the carboxyl terminus of the breast cancer protein BRCA1, a p53 binding protein (53BP1), and the yeast cell cycle checkpoint protein RAD9 revealed a large superfamily of domains that occur predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain consists of approximately 95 amino acid residues and occurs as a tandem repeat at the carboxyl terminus of numerous proteins, but has been observed also as a tandem repeat at the amino terminus or as a single copy. The BRCT superfamily presently includes approximately 40 nonorthologous proteins, namely, BRCA1, 53BP1, and RAD9; a protein family that consists of the fission yeast replication checkpoint protein Rad4, the oncoprotein ECT2, the DNA repair protein XRCC1, and yeast DNA polymerase subunit DPB11; DNA binding enzymes such as terminal deoxynucleotidyltransferases, deoxycytidyl transferase involved in DNA repair, and DNA-ligases III and IV; yeast multifunctional transcription factor RAP1; and several uncharacterized gene products. Another previously described domain that is shared by bacterial NAD-dependent DNA-ligases, the large subunits of eukaryotic replication factor C, and poly(ADP-ribose) polymerases appears to be a distinct version of the BRCT domain. The retinoblastoma protein (a universal tumor suppressor) and related proteins may contain a distant relative of the BRCT domain. Despite the functional diversity of all these proteins, participation in DNA damage-responsive checkpoints appears to be a unifying theme. Thus, the BRCT domain is likely to perform critical, yet uncharacterized, functions in the cell cycle control of organisms from bacteria to humans. The carboxyterminal BRCT domain of BRCA1 corresponds precisely to the recently identified minimal transcription activation domain of this protein, indicating one such function.

Amino Acid Sequence↗
PubMed2006

Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs.

BACKGROUND: The canonical core promoter elements consist of the TATA box, initiator (Inr), downstream core promoter element (DPE), TFIIB recognition element (BRE) and the newly-discovered motif 10 element (MTE). The motifs for these core promoter elements are highly degenerate, which tends to lead to a high false discovery rate when attempting to detect them in promoter sequences. RESULTS: In this study, we have performed the first analysis of these core promoter elements in orthologous mouse and human promoters with experimentally-supported transcription start sites. We have identified these various elements using a combination of positional weight matrices (PWMs) and the degree of conservation of orthologous mouse and human sequences--a procedure that significantly reduces the false positive rate of motif discovery. Our analysis of 9,010 orthologous mouse-human promoter pairs revealed two combinations of three-way synergistic effects, TATA-Inr-MTE and BRE-Inr-MTE. The former has previously been putatively identified in human, but the latter represents a novel synergistic relationship. CONCLUSION: Our results demonstrate that DNA sequence conservation can greatly improve the identification of functional core promoter elements in the human genome. The data also underscores the importance of synergistic occurrence of two or more core promoter elements. Furthermore, the sequence data and results presented here can help build better computational models for predicting the transcription start sites in the promoter regions, which remains one of the most challenging problems.

Animals↗
PubMed2003

Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis.

Francisella tularensis is a potent pathogen and a possible bioterrorism agent. Little is known, however, to explain the molecular basis for its virulence and the distinct differences in virulence found between the four recognized subspecies, F. tularensis subsp. tularensis, F. tularensis subsp. mediasiatica, F. tularensis subsp. holarctica, and F. tularensis subsp. novicida. We developed a DNA microarray based on 1,832 clones from a shotgun library used for sequencing of the highly virulent strain F. tularensis subsp. tularensis Schu S4. This allowed a genome-wide analysis of 27 strains representing all four subspecies. Overall, the microarray analysis confirmed a limited genetic variation within the species F. tularensis, and when the strains were compared, at most 3.7% of the probes showed differential hybridization. Cluster analysis of the hybridization data revealed that the causative agents of type A and type B tularemia, i.e., F. tularensis subsp. tularensis and F. tularensis subsp. holarctica, respectively, formed distinct clusters. Despite marked differences in their virulence and geographical origin, a high degree of genomic similarity between strains of F. tularensis subsp. tularensis and F. tularensis subsp. mediasiatica was apparent. Strains from Japan clustered separately, as did strains of F. tularensis subsp. novicida. Eight regions of difference (RD) 0.6 to 11.5 kb in size, altogether comprising 21 open reading frames, were identified that distinguished strains of the moderately virulent subspecies F. tularensis subsp. holarctica and the highly virulent subspecies F. tularensis subsp. tularensis. One of these regions, RD1, allowed for the first time the development of an F. tularensis-specific PCR assay that discriminates each of the four subspecies.

Bacterial Proteins↗
PubMed2005

Terrestrial metapopulation dynamics: a nonlinear bioeconomic model analysis.

This paper presents a spatially explicit bioeconomic analysis of species conservation in agricultural areas. Wild species in fragmented agricultural landscapes are best approached as metapopulations consisting of a finite number of local populations. Economic analysis of species conservation in fragmented habitat needs to deal with metapopulation theory and its theoretical implications. This paper presents a spatially explicit bioeconomic model consisting of a straightforward economic land use model and an applied metapopulation model. This paper demonstrates that multiple equilibria and multiple local optima in metapopulations might lead to nonconvexities in the production possibilities set of agricultural profits and species conservation.

Agriculture↗
PubMed2004

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Animals↗
PubMed1992

Analysis of the murine Hox-2.7 gene: conserved alternative transcripts with differential distributions in the nervous system and the potential for shared regulatory regions.

In this study we have investigated the organization and regulation of the mouse Hox-2.7 gene. There are several alternative transcripts some of which are conserved between mouse and humans. By Northern and in situ analysis we are able to identify at least three types of transcripts which are different in size and splicing pattern and have distinctly different boundaries of expression in the nervous system. One subset of the endogenous transcripts has a boundary of expression that corresponds to the adjacent Hox-2.8 gene instead of Hox-2.7. In another type of transcript there is an alternative reading frame which predicts a protein that has homology to an enzyme ATPase and suggests that a non-homeobox containing gene may be located in the Hox-2 cluster. A Hox-2.7-lacZ transgene is expressed in a similar pattern to the endogenous gene in that spatially-restricted domains of expression are seen in the branchial arches, neural tube, paraxial mesoderm (somites), cranial ganglia, neural crest and gut. However, the anterior boundaries of transgene expression only correspond to the subset of Hox-2.7 transcripts which map to the Hox-2.8 boundary. The proximity of a Hox-2.7 promoter to regions which regulate the adjacent Hox-2.6 gene and the expression of transgenic and endogenous transcripts in a Hox-2.8 pattern, suggest that regulatory elements may be shared by neighbouring genes to establish the complete expression pattern.

Amino Acid Sequence↗
PubMed2003

[Phylogenetic diversity of microbes and its perspectives in conservation biology].

Molecular phylogenetic analysis plays a very important role in the study of microbial diversity. For both cultivated and uncultivated microbes, the comparative sequence analysis of 16S rRNA enabled the investigation of phylogenetic relationships among microorganisms in a manner that was not feasible through traditional microbiological methods. As a result, there are drastic revisions in our understanding of microbiology. The phylogenetic diversity based on the comparative sequence analysis of 16S rRNA produced new insights into the biodiversity conservation. It provides a method for biodiversity judgment and a guideline for biodiversity conservation. Also, it produces the aim of conservation, which is to keep the phylogenetic information as much as possible. In this review, some characters of microbial phylogenetic diversity and the perspectives in conservation biology are outlined.

Conservation of Natural Resources↗
PubMedDate not supplied

Multifactorial analysis of exchanger efficiency and liquid conservation during perfluorochemical liquid-assisted ventilation.

Liquid-assisted ventilation (LAV) of the lung with perfluorochemical (PFC) requires a method of oxygenating and removing CO2 from the liquid. Current PFC LAV techniques consist of total liquid ventilation, PFC lavage, and partial liquid ventilation. Because PFC liquid is volatile, it may be lost from the lung or ventilator circuit in the expired gas. This study evaluated the efficiencies of two types of exchangers (spray bubbler and membrane oxygenator) with respect to CO2 elimination from the PFC liquid and prevention of the loss of PFC liquid. A multifactorial analysis of exchanger efficiency was performed with respect to liquid conservation and CO2 removal. PFC losses and relative efficiencies of two types of exchangers to eliminate CO2 from expired PFC liquid were evaluated, along with two types of PFC liquids. Gas (100% O2 at 4 and 8 L/min) and PFC liquid were circulated countercurrently through the exchangers (oxygenator and bubbler) through a temperature-controlled (25 degrees or 37 degrees C) open circuit. To evaluate effectiveness of CO2 elimination, an exchanger efficiency index (EEI) for CO2 was calculated applying mass-transfer theory to characterize gas transport down a concentration gradient where EEI equals: [PPFCCO2 out--PPFCCO2 in]/PgasCO2 in--PPFCCO2 in]. Rate of PFC loss from the circuit was calculated from mixed expired gas samples using a thermal detector analyzer. EEI and PFC loss rate were analyzed with respect to gas: PFC liquid flow ratios (analogous to the V/Q ratio). The results showed that 1) PFC loss rate and exchanger efficiency to remove CO2 increased with increasing gas: PFC liquid flow rates independent of the type of exchanger or PFC liquid; 2) PFC loss rate at any gas or liquid flow rate was greater for the bubbler than for the oxygenator; 3) the oxygenator was more efficient than the bubbler with respect to CO2 elimination; 4) although PFC loss rate increased with temperature and vapor pressure, there was little difference in the EEIs for the temperatures studied. These results 1) identify exchanger requirements necessary to maintain effective CO2 elimination up to four times normal CO2 loading conditions during LAV; 2) suggest that using a membrane oxygenator as the gas exchanger, in concert with stringent fluid temperature control, improves PFC liquid conservation and CO2 elimination relative to bubbler exchanger configurations; 3) highlight the importance of matching the exchanger type to the physiocochemical properties of the specific PFC liquid to optimize CO2 elimination while reducing PFC liquid loss by minimizing gas relative to PFC liquid flow rates. Because PFC liquid loss occurs with all current means of oxygenating and removing CO2, this study raises the importance of developing alternative, bulk-gas-flow-independent, means to recondition PFC liquids.

Carbon Dioxide↗