PubMed Health⌕ Search

Biomedical subjects

T M Fink

Publications and source records attributed to T M Fink.

17 recordsLinked to original sources

How many conformations can a protein remember?

We show that a protein can be trained to recognize multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield network, the number of conformations which can be remembered by a protein sequence depends on the size of the amino acid alphabet as lnA, independent of protein length. This admits the possibility of certain proteins, such as prions, evolving to fold to independent stable conformations, as well as novel possibilities for protein and heteropolymer design.

Protein Conformation↗

Occurrence of Anopheles hermsi (Diptera: Culicidae) in Arizona and Colorado.

Historically, malaria was a significant cause of morbidity and mortality throughout the western United States, and Anopheles freeborni Aitken was thought to be the vector west of the Continental Divide. In 1989, Anopheles hermsi Barr & Guptavanij was described and subsequently found to be an effective laboratory vector of Plasmodium. The adults of these two species are morphologically indistinguishable, and therefore polymerase chain reaction was used to analyze the DNA from 48 mosquitoes collected in Arizona and Colorado (identified morphologically as An. freeborni). All specimens were identified as An. hermsi. This was the first report of An. hermsi in Arizona and Colorado and indicated that this Anopheles species historically may have been a malaria vector in these two western states.

Animals↗

Short report: Decrease in seroprevalence of antibodies to hantavirus in rodents from 1993-1994 hantavirus pulmonary syndrome case sites.

Rodent trapping was conducted at seven hantavirus pulmonary syndrome (HPS) case sites from June 1993 to March 1994 during the HPS outbreak in the southwestern United States. To determine if there were changes in the rodent population or the hantavirus seroprevalence in rodents since the HPS outbreak, rodents were trapped at the same sites three years later using the same trapping protocol. The trap success decreased from the numbers trapped during the outbreak, however, the number of Peromyscus, as a percentage of the total rodents captured, did not noticeably decrease. In addition, the seroprevalence of hantavirus antibodies in Peromyscus decreased significantly (P < 0.0001).

Animals↗

Rodents, human remains, and North American hantaviruses: risk factors and prevention measures for forensic science personnel--a review.

In 1993, a previously unrecognized hantavirus was identified as the cause for a severe form of respiratory distress later termed Hantavirus Pulmonary Syndrome (HPS). In the past two years, several distinct hantaviruses, of which many are pathogenic, have been found in rodent populations in the US. Rodents shed the virus in their saliva, urine, and feces. Humans usually become infected after inhaling either aerosolized droplets of urine or particulates contaminated with rodent excreta. Rodents, including those identified as hantavirus reservoirs, will often infest and disturb human remains. Forensic science personnel should recognize the potential HPS risks associated with rodent contaminated remains and consider using High Efficiency Particulate Air-filter respirators, disinfectants, and insecticides to minimize risks.

Animals↗

Cloning and structure of the gene encoding the human N-methyl-D-aspartate receptor (NMDAR1).

The complete gene encoding the human N-methyl-D-aspartate receptor subunit NR1 (NMDAR1) has been isolated on a single cosmid clone. The gene is composed of 21 exons distributed over a total length of about 31 kb. More than 24 kb were sequenced. Exons 4, 20 and 21 are identical in their amino-acid sequence to those exons that are subject to alternative splicing in rat, indicating that all eight NMDAR1 isoforms found in rat will also be expressed in the human brain. Computer analysis of the pre-mRNA sequence revealed no secondary structures stable enough to explain alternative splicing. We suggest that cell-specific factors control expression of different isoforms. The promoter region contains two perfect copies of the recognition sequence for the Drosophila even-skipped protein, indicating that the developmentally regulated expression of NMDAR1 is controlled by a homeobox protein. The complete cosmid clone covering NMDAR1 was mapped to chromosome 9q34.3-qter by fluorescent in situ hybridization (FISH). The telomeric location is supported by an imperfect (CA)n repeat homologous to a subtelomeric repeat on chromosome 16p.

Alternative Splicing↗

Sequence data and chromosomal localization of human type I and type II hair keratin genes.

A cDNA library constructed with poly(A)+ RNA from human scalp was screened with selected fragments of both murine type I and type II hair keratin cDNAs. Two keratin clones, one type I, phKI-2, and one type II, phKII-1, were isolated and sequenced. In Northern blots, cDNA probes containing the 3'-noncoding sequences of the clones specifically hybridized to scalp mRNA species. Based on sequence homology comparisons with the four known murine type I hair keratins mHa1-4, the phKI-2 encoded keratin could be identified as human hair keratin hHa2. Similarly, sequence comparison with the four type II sheep wool keratins K2.9-12 revealed an orthologous relationship between the largest member of the type II wool keratin subfamily, K2.9 (i.e., sHb1) and the phKII-1 encoded human hair keratin (hHb1). The specific 3'-noncoding sequences of hHa2 and hHb1 were also used to isolate genomic fragments for both keratins from human genomic libraries which were than used for fluorescence in situ hybridization to human metaphase chromosomes. The hHa2 gene could be mapped to the long arm of chromosome 17, whereas the hHb1 gene was found on the long arm of chromosome 12. DAPI banding of the chromosomes allowed sublocalization of the hHa2 gene to 17q12-q21 and the hHb1 gene to 12q13, i.e., gene loci that have also been previously determined for human type I and type II epithelial keratins.

Amino Acid Sequence↗

A large duplicated area in the polycystic kidney disease 1 (PKD1) region of chromosome 16 is prone to rearrangement.

An area of 500 kb at the proximal end of the polycystic kidney disease 1 (PKD1) region has been mapped in detail, with 260 kb cloned in cosmids. The area cloned from normal individuals contains two homologous but divergent regions each of 75 kb, including the previously described marker 26-6. Pulsed-field gel electrophoresis identified a duplication of 75 kb of this region, referred to as the OX duplication (OXdup), in three patients with PKD1. The OXdup probably arose by an unequal exchange promoted by misalignment of partially homologous areas. Study of the OXdup in a large PKD1 family showed that it segregated with PKD1 in just one-half of the family, indicating that a recent crossover had occurred between the OXdup and PKD1 and showing that it was not a PKD1 mutation. Further analysis identified an OXdup breakpoint fragment: the OXdup was subsequently identified in 2 normal individuals of 110 assayed. The finding of the OXdup and in other individuals an 11-kb deletion (OXdel) at a similar point within this duplicated area indicates that this is an unusually unstable genomic region.

Chromosome Mapping↗

Mapping and chromosome analysis: the potential of fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) is a method widely used for the delineation of chromosomal DNA. FISH is applied in many areas of basic research as well as in clinical cytogenetics. In this review important technical improvements as well as the various applications of this method are summarized. In the first part different labeling and detection procedures are described and the potential of various kinds of probes are discussed. Recent developments in optical instrumentation and digital imaging procedures are outlined in the second part. The following important applications of FISH are discussed: (a) new strategies for high resolution mapping of DNA sequences; (b) detection of chromosomal aberrations in clinical material; (c) techniques allowing the simultaneous detection of numerous probes by multiple color FISH; and (d) the new approach of comparative genomic hybridization, allowing a rapid and comprehensive analysis of chromosomal imbalances in cell populations, which is particularly useful for the cytogenetic analysis of tumor samples.

Animals↗

The human gene for nuclear protein BM28 (CDCL1), a new member of the early S-phase family of proteins, maps to chromosome band 3q21.

BM28, a newly recognized human nuclear protein, possibly plays an important role in two crucial steps of the cell cycle e.g. the onset of DNA replication and cell division. It shows significant similarity to members of a recently defined family of early S-phase proteins. Using total plasmid DNA containing the complete coding sequence of the BM28 gene (CDCL1, for cdc-like 1) as a probe for fluorescence in situ hybridization, we have mapped the gene to chromosome band 3q21. This region is involved in specific structural chromosome aberrations found in acute myeloid leukemia (AML). Based on the function of BM28 and the chromosomal location of its gene, CDCL1 might prove to be a candidate for an oncogene affected by the chromosomal breaks and playing a pathogenetic role in AML.

Cell Cycle Proteins↗

Human clusterin (CLI) maps to 8p21 in proximity to the lipoprotein lipase (LPL) gene.

Clusterin (gene symbol: CLI) is a post-translationally nicked, two-chain plasma and tissue glycoprotein of 80 kDa. It forms high-density lipoprotein complexes with apolipoprotein A-I in plasma, functions as an inhibitor of the cytolytic reaction of the terminal complement proteins C5 to C9, and is secreted by Sertoli cells in large amounts into the seminal fluid. By isolating and characterizing three partially overlapping cosmid clones, we have established the complete physical map of the clusterin gene which spans about 20 kb. The subchromosomal position of the clusterin gene (CLI) and the order of CLI and the lipoprotein lipase (LPL) gene were determined by fluorescence in situ hybridization. We show that CLI, previously assigned to chromosome 8, is located on 8p21 proximal to the LPL locus. Based on this localization we consider clusterin as a novel candidate gene determining susceptibility to atherosclerosis.

Arteriosclerosis↗

The human granzyme A (HFSP, CTLA3) gene maps to 5q11-q12 and defines a new locus of the serine protease superfamily.

Human granzyme A (HFSP, Hanukah factor serine protease; CTLA3, cytotoxic T-lymphocyte-associated serine esterase-3), a homodimeric, trypsin-like serine protease of 60 kDa found in granules of cytolytic T cells and natural killer cells, is implicated in lymphocyte-mediated target cell lysis. It contributes to DNA fragmentation in perforin (PRF1)-lysed target cells through an unknown mechanism. We have isolated a cosmid clone for the functional gene of human granzyme A and established its complete exon-intron map of 10 kb. Using an 11-kb subfragment of the cloned genomic DNA as a probe, we have identified the chromosomal position of human granzyme A on 5q11-q12. Thus, the human granzyme A gene falls into a region of homology between human chromosome 5 and mouse chromosome 13, band D, where the mouse granzyme A gene has been located previously. The granzyme A gene is not linked to known members of the large superfamily of serine proteases.

Animals↗

Three human elastase-like genes coordinately expressed in the myelomonocyte lineage are organized as a single genetic locus on 19pter.

The human neutrophil and monocyte-derived serine protease homologues neutrophil elastase (NE), proteinase 3 (PR3), and azurocidin (AZU) are involved in a variety of immune defense reactions. NE and PR3 assist in the destruction of phagocytosed microorganisms, cleave the important connective-tissue protein elastin, and generate chemotactic activities by forming alpha 1-proteinase inhibitor complexes and elastin peptides. AZU is cytotoxic to certain microorganisms and chemotactic for monocytes. All three proteins are produced and packaged into azurophil granules in large quantities during neutrophil differentiation. We have isolated several cosmid clones each of which contains the functional genes for AZU, PR3, and NE in this order. The PR3 gene is separated by 8 kilobases from the 3' end of the AZU gene and by 3 kilobases from the 5' end of the NE gene. We report a physical map of the gene cluster, its location on chromosome 19pter, and the exon-intron organization of the AZU and PR3 genes. Our fluorescence in situ hybridization studies disprove the previous chromosomal assignment of the human NE gene to 11q14. The five exons of AZU and PR3 are organized like those of NE and other granule-associated serine proteases of hematopoietic cells. NE, PR3, and AZU are coordinately downregulated in the premonocytic cell line U937 during induced terminal differentiation. The cluster-like physical organization of these genes and concerted regulation during hematopoietic differentiation suggests that they are located in a developmentally activated chromatin domain promoting high-level, cell-specific expression in the monocyte-myelocyte lineage.

Amino Acid Sequence↗

The human vitronectin (complement S-protein) gene maps to the centromeric region of 17q.

Vitronectin (complement S-protein, serum-spreading factor, epibolin) is a multifunctional glycoprotein that mediates cell-to-substrate adhesion, inhibits the cytolytic action of the terminal complement cascade in vitro and binds to several serine protease inhibitors of the serpin family, viz. antithrombin III, plasminogen activator inhibitor I (PAI-1) and II (PAI-2), heparin cofactor II and protease nexin. Using high resolution fluorescence in situ hybridization, we mapped the vitronectin gene to the centromeric region of the long arm of chromosome 17 corresponding to 17q11. The location was confirmed by co-hybridization with the centromere-specific alphoid probe p17H8 (D17Z1) and by chromosome banding with 4,6-diamidino-2-phenylindole-dihydrochloride (DAPI). None of the previously mapped genes that are evolutionary related to vitronectin are located on the same chromosome.

Centromere↗

Human perforin (PRF1) maps to 10q22, a region that is syntenic with mouse chromosome 10.

Perforin (PRF1) is a cytolytic, channel-forming protein of cytolytic T cells, natural killer cells, and granulated metrial gland cells and plays a crucial role in the killer cell-mediated elimination of virally infected host cells, tumor cells, and allotransplants. Two-thirds of the perforin sequence is homologous to the lytic, channel-forming complement proteins C6, C7, C8 alpha, C8 beta, and C9. Using cosmid DNA containing the PRF1 gene as a probe for fluorescence in situ hybridization, we have reevaluated its chromosomal location. Previously assigned to chromosome 17q11-q21, it has now been mapped to 10q22. The human PRF1 locus lies within a conserved synteny segment present on mouse chromosome 10, consistent with the previous chromosomal assignment of mouse perforin. The perforin locus is not linked to any of the genes of the terminal complement system.

Animals↗