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A M Martin

Publications and source records attributed to A M Martin.

At least 37 records · Page 2Linked to original sources

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.

Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.

Base Sequence↗

Non-major histocompatibility complex-linked diabetes susceptibility loci on chromosomes 4 and 13 in a backcross of the DP-BB/Wor rat to the WF rat.

BB rats are used as models of autoimmune human IDDM. Genetic control of IDDM in both species is complex, including both major histocompatibility complex (MHC)-linked and non-MHC-linked genes. DP-BB rats develop IDDM spontaneously. Expression of disease in these animals requires homozygosity at the lyp locus, which causes lymphopenia. All genetic analyses of BB rat diabetes to date have backcrossed to the DP-BB strain or used (DP-BB x non-BB)F2 animals to ensure that a fraction of progeny are homozygous for lyp. Here we report the analysis of a backcross of the DP-BB rat to the histocompatible WF rat. Neither WF nor (WF x DP-BB)F1 animals develop spontaneous IDDM. However, 95% of (WF x DP-BB)F1 rats and a fraction of (WF x DP-BB) x WF backcross animals readily develop IDDM after treatment with polyinosinic:polycytidylic acid and a cytotoxic anti-RT6.1 monoclonal antibody. Using simple sequence length polymorphism analysis, we have mapped loci on chromosomes 4 and 13 that show significant linkage to IDDM expression and insulitis. The susceptibility locus on chromosome 4 is linked to, but not identical to, lyp. We propose a disease model for the BB rat that requires 1) the RT1u MHC haplotype for disease susceptibility, 2) a new locus on chromosome 4 for disease initiation (as measured by insulitis), 3) a new locus on chromosome 13 for disease progression in response to environmental perturbation, and 4) lyp for spontaneous expression of disease.

Animals↗

Diabetes-prone and diabetes-resistant BB rats share a common major diabetes susceptibility locus, iddm4: additional evidence for a "universal autoimmunity locus" on rat chromosome 4.

Diabetes-prone (DP) BB rats develop autoimmune type 1 diabetes spontaneously. At least five loci are linked to disease expression: the major histocompatibility complex (iddm2), two susceptibility loci (iddm4, iddm5), and, possibly, a resistance locus (iddm3). Spontaneous disease also requires homozygosity for lyp/iddm1, which causes lymphopenia. It has not been determined whether lyp/iddm1 is required for predisposition to diabetes autoimmunity in addition to being required for its spontaneous expression. We analyzed backcross rats segregating for diabetes but not lymphopenia using Wistar-Furth (WF) and diabetes-resistant (DR) BB animals. The latter are nonlymphopenic (lyp+/+) and develop diabetes only in response to immunological perturbants. Treatment of (DR-BB x WF)F1 x WF animals (all lyp+/+) using a standard induction protocol caused type 1 diabetes in 58% of progeny. Expression of type 1 diabetes was strongly linked to iddm4. The results suggest that lyp/iddm1 does not determine the predisposition to autoimmunity in BB rats and that iddm4 is a major diabetogenic locus in both DP- and DR-BB animals. The iddm4 gene maps to a region containing several major autoimmunity loci, including aia2, aia3, and cia3. We propose that BB rat diabetes requires 1) class II RT1u (iddm2) for susceptibility, 2) additional loci for disease initiation and progression in response to perturbants, and 3) lyp for spontaneous disease.

Age of Onset↗

A comparison of some clinical features of visual reinforcement audiometry and the distraction test.

The aim of this study was to compare aspects of visual reinforcement audiometry (VRA) and the distraction test (DT), the two most commonly used behavioural tests of hearing for young children. The number of assessments completed, time taken, parental opinion and levels of minimum responses were compared in a group of 20 infants (mean age 17.7 months; SD 4.7 months; range 12-25 months) who had been selected from those referred from a local second-tier community audiology service. Each infant was assessed with each test following set protocols and a balanced design on two occasions separated by one week. Parental opinion was determined by application of two questionnaires, one after each session. There was no difference in the number of minimum response levels (MRLs) measured by the two tests. However, if a VRA protocol using three MRLs was assumed then the assessment was completed successfully in a significantly greater number of subjects with VRA. VRA took, on average, two minutes less than the DT to measure six MRLs. Most of the subject sample had normal hearing as defined by both tests. However, where MRLs were >30 dB HL for at least one of the tests, the DT elicited responses at significantly higher levels than VRA, suggesting that in these subjects the DT under-estimated hearing sensitivity. Seventy per cent of parents selected VRA when asked to choose between the tests.

Attention↗

Classifying a protein in the CATH database of domain structures.

The CATH database of protein domain structures classifies structures according to their (C)lass, (A)rchitecture, (T)opology or fold and (H)omologous family (http://www.biochem.ucl.ac.uk/bsm/cath). Although the protocol used is mostly automatic, manual inspection is used to check assignments at some critical stages, such as the detection of very distantly related homologues and anologues and the assignment of novel architectures. Described in this article is a recently established facility to search the database with the coordinates of a newly determined structure. The CATH server first locates domain boundaries and then uses automatic sequence and structure comparison methods to assign this new structure to one or more of the domain families within CATH. Diagnostic reports are generated, together with multiple structural alignments for close relatives. The Server can be accessed over the World Wide Web (WWW) and mirror sites are planned to improve access.

Amino Acid Sequence↗

Monocyte chemoattractant protein-1-induced CCR2B receptor desensitization mediated by the G protein-coupled receptor kinase 2.

Monocyte chemoattractant protein 1 (MCP-1) is a member of the chemokine cytokine family, whose physiological function is mediated by binding to the CCR2 and CCR4 receptors, which are members of the G protein-coupled receptor family. MCP-1 plays a critical role in both activation and migration of leukocytes. Rapid chemokine receptor desensitization is very likely essential for accurate chemotaxis. In this report, we show that MCP-1 binding to the CCR2 receptor in Mono Mac 1 cells promotes the rapid desensitization of MCP-1-induced calcium flux responses. This desensitization correlates with the Ser/Thr phosphorylation of the receptor and with the transient translocation of the G protein-coupled receptor kinase 2 (GRK2, also called beta-adrenergic kinase 1 or betaARK1) to the membrane. We also demonstrate that GRK2 and the uncoupling protein beta-arrestin associate with the receptor, forming a macromolecular complex shortly after MCP-1 binding. Calcium flux responses to MCP-1 in HEK293 cells expressing the CCR2B receptor were also markedly reduced upon cotransfection with GRK2 or the homologous kinase GRK3. Nevertheless, expression of the GRK2 dominant-negative mutant betaARK-K220R did not affect the initial calcium response, but favored receptor response to a subsequent challenge by agonists. The modulation of the CCR2B receptor by GRK2 suggests an important role for this kinase in the regulation of monocyte and lymphocyte response to chemokines.

Arrestin↗

Optimization of Phaffia rhodozyma continuous culture through response surface methodology.

Response surface methodology was applied to optimize the growth of the yeast Phaffia rhodozyma in continuous fermentation using peat hydrolysates as substrate. A second-order, complete, factorial design of the experiments was used to develop empirical models providing a quantitative interpretation of the relationships between the two variables studied, dilution rate and pH. Maximum biomass concentration in the fermentor was obtained by employing the following predicted optimum fermentation conditions: a dilution rate of 0.017/h and a pH level of 7.19. A verification experiment, conducted at previously optimized conditions for maximum biomass volumetric productivity (a dilution rate of 0.022/h, and a pH level of 6.90), produced values for biomass concentration, residual substrate concentration, biomass yield, and biomass volumetric productivity that were very close to the predicted values, indicating the reliability of the empirical model. The concentration of the pigment astaxanthin produced by the yeast under the optimized growth conditions was found to be 544 mg astaxanthin/kg dry cell biomass.

Basidiomycota↗

Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.

The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have been determined at 2.4 A resolution in a new crystal lattice. Comparison of these structures with that of the free enzyme determined with different packing constraints shows that the conformations of the domain interfaces are not conserved between crystal forms. The unliganded enzyme and the enzyme-DNA complex delineate two distinct quaternary states separated by a 25 degrees intersubunit rotation, but considerable conformational heterogeneity, of the order of 10 degrees domain rotations, exists within each of these states. Comparison of the free enzyme structure between the two crystal forms further reveals that the C-terminal 28 amino acid residues are disordered and undergo an extensive local folding transition upon DNA binding. Introduction of the mutation T93A at the DNA-binding cleft causes large-scale effects on the protein conformation. Structural changes in the mutated unliganded enzyme propagate some 20 to 25 A to the dimerization interface and lead to a rearrangement of monomer subunits. Comparative analysis of these structures, a new structure of the enzyme cocrystallized with DNA and calcium ions, and previously determined cocrystal structures suggests important roles for a number of amino acid residues in facilitating the intersubunit motions and local folding transitions. In particular, the T93A structure reveals a pathway through the protein, by which DNA-binding may cause the domain movements required for proper alignment of catalytic groups. The key active-site residue Glu45 is located on a flexible helix inside this pathway, and this provides a direct means by which essential catalytic functions are coupled to the protein conformational change. It appears that indirect perturbation of the Glu45 conformation via an altered quaternary structure may be a contributing factor to the decreased catalytic efficiency of T93A, and this mechanism may also explain the diminished activities of other active site variants of EcoRV.

Binding Sites↗

Influence of wholesale lamb marketing options and merchandising styles on retail yield and fabrication time.

Lamb carcasses (n = 94) from five packing plants, selected to vary in weight class and fat thickness, were used to determine retail yield and labor requirements of wholesale lamb fabrication. Carcasses were allotted randomly according to weight class to be fabricated as whole carcasses (n = 20), three-piece boxes (n = 22), or subprimals (n = 52). Processing times (seconds) were recorded and wholesale and retail weights (kilograms) were obtained to calculate retail yield. Subprimals were fabricated into bone-in retail cuts or boneless or semi-boneless retail cuts. Retail yield for subprimal lamb legs decreased from 85.3 +/- .6% for bone-in to 68.0 +/- .7% for a completely boneless retail product. Correspondingly, processing times increased from 126.1 +/- 5.4 s to 542.0 +/- 19.2 s for bone-in and boneless legs, respectively. For all subprimals, retail yield percentage tended to decrease and total processing time increase as cuts were fabricated to boneless or semi-boneless end points compared with a bone-in end point. Percentage retail yield did not differ (P > .05) among whole carcass, three-piece box, and subprimal marketing methods. Total processing time was shorter for subprimals (P < .05) than for the other two marketing methods.

Animals↗

Optimization of nitrogen recovery in the enzymatic hydrolysis of dogfish (Squalus acanthias) protein. Composition of the hydrolysates.

The recovery of nitrogen in the enzymatic hydrolysis of dogfish shark muscle was optimized by the use of response surface methodology. The optimum values for enzyme/substrate ratio, temperature and pH were found to be 3.7% (w/w), 55.3 degrees C, and 8.3, respectively. The dogfish protein hydrolysate produced under these conditions contained a high crude protein concentration (> 85%), and its high nutritional value was indicated by the presence of all essential amino acids, and by high PER values. These results indicate the potential for dogfish protein hydrolysate to be used in lieu of vegetable proteins as a protein supplement in foods.

Amino Acids, Essential↗

Studies on the composition and properties of thermophilic Bacillus populations in subterranean thermal waters of Budapest (Hungary).

A collection of 148 thermophilic Bacillus isolates were obtained from two thermal wells (water temperature at about 70 degrees C) in the area of Budapest (Hungary). These isolates, furthermore seven authentic thermophilic reference strains of Bacillus spp. were submitted to detailed comparative biochemical-physiological studies. Overall similarities of these strains for 134 unit characters were determined by the SSM coefficient and clustering achieved using the UPGMA algorithm. According to the results of our computer aided numerical taxonomic analyses, numerous metabolic types, varieties and mutants of a single Bacillus sp. not identical with the known thermophilic Bacillus species constitute the major fraction of the indigenous thermophilic microbial communities in the thermal waters of the Pascal and Széchenyi wells. The data also revealed, (1) that the most adapted varieties of this Bacillus sp. can form the most dense local populations in these subterranean ecological systems. Furthermore, it seems to be probable (2) that the cells of the most commonly occurring varieties of this Bacillus sp. may be able to migrate in the underground thermal water systems between diverse subterranean regions located more or less far from one another.

Bacillus↗

Possible mechanism for the TCR beta-chain associated EAE resistance of LER rats.

LER rats are resistant to the active induction of experimental allergic encephalomyelitis (EAE). The mechanism of their resistance to EAE has yet to be defined, although LER rats are susceptible to adoptively transferred EAE. Genetic analysis of LER and the susceptible LEW rat suggests that a gene linked to the T cell receptor (TCR) beta-chain complex contributes to EAE resistance. This result is consistent with the fact that EAE is a T cell mediated disease and one characterized in EAE-susceptible animals by an oligoclonal TCR V beta 8.2+ response. In this report, analysis of TCR transcripts by reverse transcriptase polymerase chain reaction (RT-PCR) and restriction digestion demonstrates that LER lymph nodes, collected on day 10 post-immunization with myelin basic protein (MBP), express both TCR-V beta 8.2 and other TCR beta chains, usually V beta 8.4, whereas LEW animals demonstrate preferential and almost exclusive use of V beta 8.2 TCR. Fluorescence-activated cell sorting (FACS) analyses of anti-MBP T cells confirm that LER T cells express V beta 8.2 TCR to a lesser degree than LEW T cells. Finally, experiments examining the oligo- or polyclonality of the TCRV beta CDR3 region show that the LER response to MBP is polyclonal, while the LEW response to MBP is oligoclonal. Therefore, the cumulative data on the TCR usage profiles in this report suggest that the choice of TCR variable beta-chain may contribute to the resistance seen in the LER rat.

Alleles↗

Monomeric base damage products from adenine, guanine, and thymine induced by exposure of DNA to ultraviolet radiation.

The formation of monomeric products in DNA upon exposure to UV radiation was investigated. Three novel products were identified in DNA in aqueous solution upon exposure to UV radiation at 254 nm in a dose range from 100 to 10,000 J/m2. These were 4,6-diamino-5-formamidopyrimidine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 5-hydroxy-5,6-dihydrothymine. These three products are known to be substrates for base excision repair enzymes involved in the reversal of oxidative DNA damage. The dependence of the yields of formamidopyrimidines on UV radiation dose was nonlinear, whereas the yield of 5-hydroxy-5,6-dihydrothymine was increased linearly in the entire dose range. Of these products, 4,6-diamino-5-formamidopyrimidine was the only compound produced in appreciable amounts at 310 nm. At the highest dose used, the formation of other pyrimidine- and purine-derived products was also observed. Their amounts, however, were increased above control levels up to 2-fold only. The hydroxyl radical scavenger dimethyl sulfoxide had no effect on product yields excluding the involvement of hydroxyl radical in product formation. 4,6-Diamino-5-formamidopyrimidine and 2,6-diamino-4-hydroxy-5-formamidopyrimidine may be produced by hydration of adenine and guanine, respectively, across the N(7)-C(8) double bond by mechanisms similar to those proposed previously for well-known formation of pyrimidine hydrates with the hydroxyl group located at C(6). Formation of 5-hydroxy-5,6-dihydrothymine indicates that hydration of thymine with the hydroxyl group located at C(5) of the pyrimidine ring also occurs.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA↗

Kinetic studies on the yeast Phaffia rhodozyma.

The yeast Phaffia rhodozyma, a promising microbial producer of the carotenoid astaxanthin, was cultivated in batch and continuous processes in an agitated and aerated fermenter using an acid peat extract based culture medium. For the accelerated growth phase, the mean specific growth rate and doubling time were found to be 0.038 h-1, and 18.24 hours, respectively. The production of astaxanthin was found to be basically growth associated, the maximum concentrations of the pigment produced in batch culture and continuous cultivation being similar.

Biomass↗

Cloning of myelin basic protein-reactive T cells from the experimental allergic encephalomyelitis-resistant rat strain, LER.

Rats of the LER inbred strain are resistant to the active induction of experimental allergic encephalomyelitis (EAE), although they are susceptible to adoptively transferred EAE when they are injected with encephalitogenic T cells from EAE-susceptible Lewis rats. The mechanism of resistance remains to be elucidated. We report here that myelin basic protein (MBP)-specific T cells can be cloned from LER rats immunized with MBP, that these CD4+ LER T cells can recognize the encephalitogenic peptide (MBP-EP) and will divide vigorously when it is presented to them, and that these T cells bear V beta 8 + TCR chains. Nevertheless, in contrast to Lewis T cells with the same specificity and TCR beta chains, LER T cells from MBP-EP-specific clones cannot induce EAE when adoptively transferred into naive rats of either strain. Thus, LER T cells can assemble and use a TCR with the canonical encephalitogenic V beta 8.2-D beta-J beta region in response to immunization with MBP, yet they continue to display resistance to EAE.

Amino Acid Sequence↗

An alternative eukaryotic DNA excision repair pathway.

DNA lesions induced by UV light, cyclobutane pyrimidine dimers, and (6-4)pyrimidine pyrimidones are known to be repaired by the process of nucleotide excision repair (NER). However, in the fission yeast Schizosaccharomyces pombe, studies have demonstrated that at least two mechanisms for excising UV photo-products exist; NER and a second, previously unidentified process. Recently we reported that S. pombe contains a DNA endonuclease, SPDE, which recognizes and cleaves at a position immediately adjacent to cyclobutane pyrimidine dimers and (6-4)pyrimidine pyrimidones. Here we report that the UV-sensitive S. pombe rad12-502 mutant lacks SPDE activity. In addition, extracts prepared from the rad12-502 mutant are deficient in DNA excision repair, as demonstrated in an in vitro excision repair assay. DNA repair activity was restored to wild-type levels in extracts prepared from rad12-502 cells by the addition of partially purified SPDE to in vitro repair reaction mixtures. When the rad12-502 mutant was crossed with the NER rad13-A mutant, the resulting double mutant was much more sensitive to UV radiation than either single mutant, demonstrating that the rad12 gene product functions in a DNA repair pathway distinct from NER. These data directly link SPDE to this alternative excision repair process. We propose that the SPDE-dependent DNA repair pathway is the second DNA excision repair process present in S. pombe.

Base Sequence↗

Every mother is a working mother: breastfeeding and women's work.

Working and breastfeeding can be very complicated because of the kinds of work women are doing; the settings in which they are working; recent changes which have made breastfeeding and work less compatible; trade-offs that working mothers must make; the importance of breastfeeding for the working woman; and the range of feeding options for working mothers. To adequately address these and other issues, several initiatives are needed: (1) additional research on breast pumping and breastmilk storage, and the social and emotional benefits of breastfeeding for working mothers and their infants; (2) protective legislation and strategies for its implementation and monitoring; (3) information and support for breastfeeding mothers and families, policy markers, and the general public; and (4) an alliance between breastfeeding advocates and feminists to promote this intrinsically female issue.

Breast Feeding↗