Publications

head-to-head linkage of carp alpha- and beta-globin genes.	the alpha- and beta-globin gene variants are believed to have diverged from a single ancestral globin gene, and the divergence was primed by the duplication of the ancestral globin gene. to understand the process of gene duplication, we investigated the alpha- and beta-globin gene arrangement of a bony fish (carp). from a southern analysis of seven previously prepared lambda phage clones (lambdacg1-7) using radio-labelled alpha- or beta-globin gene probes, it was found that the clones included b ...	1997	9396629
assembly of the n-dependent antitermination complex of phage lambda: nusa and rna bind independently to different unfolded domains of the n protein.	the n protein of bacteriophage lambda activates expression of the delayed early genes of this phage by modifying rna polymerase (rnap) into a form that is resistant to termination signals. n binds to the boxb hairpin that forms in the nascent rna transcript upon transcription of the nut regulatory element, and then interacts with rnap by rna looping. the binding of the n-boxb subassembly to the transcription complex is further stabilized by interaction with the escherichia coli nusa protein. n, ...	1997	9398524
comparative analysis of the genomic dna terminal regions of the lactococcal bacteriophages from species c2.	in an attempt to compare the cos intergenic region and bordering orfs from lactococcus lactis bacteriophages of the species c2, the nucleotide sequence of a 2479-bp fragment containing the cos site of phage p001 dna was determined and compared with the corresponding regions of phages c2, bil67 and p6 (partial sequence), which belong to species c2. this comparative analysis revealed that some characteristic features of the cos intergenic region are conserved in all members of species c2. some of ...	1997	9765842
image contrast of biological macromolecules in electron microscopy under accelerated voltage.	image contrast in the tilted beam mode of dark field (df) imaging with a conventional transmission electron microscope has been estimated theoretically for two well-known biological macromolecules viz. lambda-phage dna and bsa precursor protein. the df contrast for electron accelerating voltage 0.1 to 3.0 mv has been compared with the corresponding bright field (bf) contrast. the df contrast is seen to be so overwhelmingly greater than the bf contrast, for a wide range of accelerating voltage (p ...	1997	9491650
regulation of protein synthesis by minigene expression.	peptidyl-trna hydrolase (pth), an enzyme essential for escherichia coli viability, scavenges peptidyl-trna released during abortive polypeptide chain elongation. bacterial strains of e coli partially defective in pth activity are unable to maintain bacteriophage lambda growth. phage mutations that overcome the bacterial defect have been located to several regions in the lambda genome named bar. plasmid constructs expressing just the bar region are toxic and cause a general arrest of protein synt ...	1997	9451455
cloning and characterization of a mouse sensory neuron tetrodotoxin-resistant voltage-gated sodium channel gene, scn10a.	small-diameter sensory neurons associated with unmyelinated axons express a tetrodotoxin-insensitive (ttxi) voltage-gated sodium channel (vgsc) that may play an important role in the transmission of nociceptive information to the spinal cord. a ttxi vgsc, named sns, that accounts for the tetrodotoxin-resistant sodium current described in sensory neurons has been cloned from rat dorsal root ganglia. using recombinant lambda phage clones encoding a mouse 129/sv genomic library, we have determined ...	1997	9143495
evidence for phosphorylation and oligomeric assembly of presenilin 1.	pathogenic mutations in presenilin 1 (ps1) are associated with approximately 50% of early-onset familial alzheimer disease. ps1 is endoproteolytically cleaved to yield a 30-kda n-terminal fragment (ntf) and an 18-kda c-terminal fragment (ctf). using cos7 cells transfected with human ps1, we have found that phorbol 12, 13-dibutyrate and forskolin increase the state of phosphorylation of serine residues of the human ctf. phosphorylation of the human ctf resulted in a shift in electrophoretic mobil ...	1997	9144195
crystallization and preliminary x-ray analysis of bacteriophage lambda lysozyme in which all tryptophans have been replaced by aza-tryptophans.	after many unsuccessful attempts to crystallize the bacteriophage lambda lysozyme, a mutant where all the tryptophan residues have been replaced by aza-tryptophans has been crystallized by the vapor-diffusion method. the crystals are orthorhombic and belong to space group p2(1)2(1)2(1) with cell dimensions a = 73.01, b = 78.80, c = 82.31 a. diffraction data were collected using synchrotron radiation sources. crystals diffract to a resolution of 2.3 a. data from two different platinum derivatives ...	1997	15299961
combinatorial mutagenesis analysis of residues in the channel constriction loop l3 and neighbouring beta-strands in the lamb glycoporin of escherichia coli.	members of the lamb family of sugar-selective porins (glycoporins) are beta-barrel proteins in the outer membrane of gram-negative bacteria. to study the determinants of structure and sugar selectivity, 68 non-identical single amino acid substitutions were introduced into the stretch of sequence consisting of residues 106 through 125 in escherichia coli lamb. this region includes all bar one residue of the channel constriction loop l3 and extends into the transmembrane beta 6 strand in the lamb ...	1996	9147661
irs-bubble pcr: an effective method for representative amplification of human genomic dna sequences from complex sources	a rate-limiting step in the analysis of large segments of genomic dna is the generation of a set of representative short single-copy sequences that can be used for development of fine-structure maps. in direct response to this need, we have developed interspersed repetitive dna sequence (irs)-bubble pcr. irs-bubble pcr was designed to amplify the human dna content of somatic cell hybrids, yeast artificial chromosomes (yacs), bacs, pacs, cosmids, and lambda phage and to result in greater complexi ...	1996	9245349
mammalian cell binding and transfection mediated by surface-modified bacteriophage lambda.	bacteriophage lambda virions whose tail tube major subunit (v) proteins are modified with a cyclizable arg-gly-asp (rgd) peptide are able to promote the binding of certain mammalian cells to a solid surface. this effect was shown to be specific by peptide competition experiments, and control phage lacking the rgd peptide showed no significant cellular interaction. rgd-modified but not control phage bearing a reporter gene could transfect cos cells at a significant frequency. phage-mediated trans ...	1996	9116055
[the role of bacteriophage lambda coded proteins in destruction of the bacterial cell wall and the control of lysis timing].		1996	9102634
[assessment of genetic toxicity of the exposure to clomiphene citrate, with various bacterial test systems].	clomiphene citrate (cc) induces framshift mutations on the salmonella typhimurium ames strains ta1538, ta97 and ta100 employing in vitro metabolic activation with s9 aerochlor 1254 induced rat livers, but not base pair substitution mutations with neither the standard or the preincubation method. cc induced genolethal dna damages on the escherichia coli pola-/pola+ with s9 on the preincubation method or without s9 on the disk diffusion one. the severe primary dna damages produced b cc was verifie ...	1996	9091425
telomere-homologous sequences occur near the centromeres of many tomato chromosomes.	several bacteriophage lambda clones containing interstitial telomere repeats (itr) were isolated from a library of tomato genomic dna by plaque hybridization with the cloned arabidopsis thaliana telomere repeat. restriction fragments lacking highly repetitive dna were identified and used as probes to map 14 of the 20 lambda clones. all of these markers mapped near the centromere on eight of the twelve tomato chromosomes. the exact centromere location of chromosomes 7 and 9 has recently been dete ...	1996	8709958
cloning and analysis of the mnn4 gene required for phosphorylation of n-linked oligosaccharides in saccharomyces cerevisiae.	the saccharomyces cerevisiae mnn4 gene, which is involved in mannosylphosphate transfer from gdp-mannose to n-linked oligosaccharide, has been cloned from a lambda phage containing a yeast chromosome xi dna fragment. the mnn4 orf encodes a protein of 1178 amino acids. the deduced amino acid sequence shows a topology of type ii membrane proteins and has a unique repeated sequence of lysine and glutamic acid at the c-terminus. disruption and overexpression of mnn4 led to a decrease and increase, r ...	1996	9023541
protein inheritance: lambda plasmid replication perpetuated by the heritable replication complex.	replication of a plasmid derived from the escherichia coli phage lambda initiates by binding of the lambda o protein initiator to the origin of lambda dna replication, ori lambda. the lambda p protein participates in subsequent steps of assembly of the lambda replication complex. a function of lambda p required for replication complex assembly is inactivated at 43 degrees c by the ts1 mutation.	1996	9077459
architectural flexibility in lambda site-specific recombination: three alternate conformations channel the attl site into three distinct pathways.	in the phage lambda life cycle, the integrase (int) protein carries out recombination between two different sets of dna substrates: attp and attb in integration, attl and attr in excision. in each case, the partners are very different in structure from each other and the recombination reaction between them is effectively irreversible. for comparison, we have studied the recombination mediated by int between two identical attl sites. both in vitro and in vivo, recombination between two attl sites ...	1996	9078377
in vitro alpha-complementation of beta-galactosidase on a bacteriophage surface.	surface display of large multimeric non-secreted proteins is advantageous on the bacteriophage lambda compared with the widely used filamentous phage systems. a model system, the alpha-complementation of beta-galactosidase, was used for both further general characterization of protein-protein interactions on the lambda tail tube surface and for specifically probing the structure of the phage-displayed beta-galactosidase tetramer. in this complementation system, dimeric enzymatically inactive n-t ...	1996	9022702
tissue specificity of spontaneous point mutations in lambda supf transgenic mice.	transgenic mice carrying multiple copies of a recoverable lambda phage shuttle vector carrying the supf mutation reporter gene (lambda supf) were constructed for the purpose of studying mutagenesis in a whole animal. spontaneous mutations in rescued supf target genes from mouse liver and skin were analyzed. the mutation frequency was similar in both tissues (in the range of 2 x 10(-5)), but the spectrum of point mutations was distinct, with transitions common in the skin and transversions more p ...	1996	8991078
total modification of the bacteriophage lambda tail tube major subunit protein with foreign peptides.	the bacteriophage lambda has been shown previously to tolerate a high multiplicity of peptide additions to the c-terminus of the major tail tube subunit protein (gpv, the product of the v gene). however, it was not clear whether all gpv copies within a functional virion could tolerate such modification. complementation tests with phage bearing either v gene amber mutations or a precisely deleted v gene were used to test the extent of possible tail tube peptide display. expression of plasmid-enco ...	1996	8996081
characterization of the dna-binding domain of beta protein, a component of phage lambda red-pathway, by uv catalyzed cross-linking.	beta protein, a key component of red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of escherichia coli. to facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. a chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. a 67-kda band, corresponding to homodimer, was identified after separation ...	1996	8982071
sura, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins.	little is known about either the process of periplasmic protein folding or how information concerning the folding state in this compartment is communicated. we present evidence that sura, a periplasmic protein with peptidyl-prolyl isomerase activity, is involved in the maturation and assembly of lamb. lamb is a trimeric outer membrane porin for maltodextrins as well as the bacteriophage lambda receptor in escherichia coli. we demonstrate that sura is involved in the conversion of unfolded monome ...	1996	8985185
molecular cloning of cdna that encodes chymotrypsin inhibitor eci from erythrina variegata seeds and its expression in escherichia coli.	synthetic oligonucleotides representing all possible sequences of the n-terminal and internal amino acid sequences of the chymotrypsin inhibitor eci from erythrina variegata seeds were used to generate a probe specific for eci-related sequences by the polymerase chain reaction on the e. variegata genomic dna. a lambda phage cdna library constructed from poly(a+) rna from maturing seeds was screened with the eci gene thus obtained as a probe and characterized by dna sequencing. the cloned eci cdn ...	1996	8987596
bioreactor studies on temperature induction of the q- mutant of bacteriophage lambda in escherichia coli.	the parasite-host interactions between bacteriophage lambda (denoted as lambda) and escherichia coli bacteria were studied in different bioreactor systems. although the replicated lambda-dna of q- mutant remains naked for a longer time to reach a high gene expression, the epidemic of lambda-infection and the coevolutionary host-phage relations limit the temperature induction efficiency. the temperature induction is strongly dependent upon the susceptible population density at which lambda-infect ...	1996	8987627
molecular analysis of the dla dr region.	the dog is an important model for studying organ transplantation. in order to develop a dna-based typing system, a genomic analysis of the canine dr region of the mhc was undertaken. southern analysis suggests the presence of two drb genes in most dogs and all have one dra gene. one dog out of 200 examined contains only one drb gene. the dra gene was mapped in one lambda phage clone. one drb gene (drbb1) was localized to two overlapping phage clones. another drb gene (drbb2) was localized to two ...	1996	8988537
structural distortions induced by integration host factor (ihf) at the h' site of phage lambda probed by (+)-cc-1065, pluramycin, and kmno4 and by dna cyclization studies.	integration host factor (ihf) is a sequence-specific dna-bending protein that is proposed to interact with dna primarily through the minor groove. we have used various chemical probes [(+)-cc-1065, a minor-groove-specific agent that alkylates n3 of adenine and traps bends into the minor groove; pluramycin, a minor-major-groove threading intercalator that alkylates n7 of guanine; kmno4, which reacts more strongly with bases in denatured dna] to gain more information on the interaction of ihf with ...	1996	8718873
[expression of hiv-1 epitopes included in particles formed by human hepatitis b virus nucleocapsid protein].	hybrids of the core protein of hepatitis b virus (hbcag) have been designed which carry n-terminal insertions of b- and t-cell epitopes of hiv-1 an immunodominant b-epitope from gp41, a t-cell epitope from p34 pol, and a cluster of b- and t-cell epitopes from p17 gag. the hybrids have been synthesized using two expression systems-one based on the thermoinducible pr promoter of bacteriophage lambda and the other one based on phi 10 promoter of bacteriophage t7 with 3-5% and 7-14% yields, respecti ...	1996	8724609
the reactivity of sera from patients with systemic lupus erythematosus to seven different species of single and double stranded deoxyribonucleic acids.	anti-dna antibodies are frequently found in the serum of patients with systemic lupus erythematosus (sle). to understand whether the avidity of sle sera to different species of single-stranded (ss) and double-stranded (ds) dna is different or not, the reactivity of active sle sera to seven species of dna from viral, bacterial, piscine, and mammalian sources was compared.	1996	8737719
identification, localization, and functional implications of an abundant nematode annexin.	cultures of the nematode c. elegans were examined for the presence of calcium-dependent, phospholipid-binding proteins of the annexin class. a single protein of apparent mass on sds-polyacrylamide gels of 32 kd was isolated from soluble extracts of nematode cultures on the basis of its ability to bind to phospholipids in a calcium-dependent manner. after verification of the protein as an annexin by peptide sequencing, an antiserum to the protein was prepared and used to isolate a corresponding c ...	1996	8601586
nucleotide sequence and expression of the gene encoding nadp+- dependent glutamate dehydrogenase (gdha) from agaricus bisporus.	the gene encoding nadp+-dependent glutamate dehydrogenase (gdha) was isolated from an agaricus bisporus recombinant phage lambda library. the deduced amino acid sequence would specify a 457-amino acid protein that is highly homologous in sequence to those derived from previously isolated and characterized genes coding for microbial nadp+-gdh. the open reading frame is interrupted by six introns. none of the introns is located at either one of the positions of the two introns conserved in the cor ...	1996	8602149
cysticercosis: identification and cloning of protective recombinant antigens.	we describe the cloning and the evaluation of the protective capacity of 5 recombinant antigens expressed during the cysticercus stage of both taenia crassiceps and taenia solium. a cdna library was constructed in bacteriophage lambda zap using mrna isolated from larvae of t. crassiceps of the orf strain. the recombinant phage library was screened with polyclonal antibodies against 56- and 74-kda protective antigen fractions. this screening identified 13 recombinant clones, 5 of which were also ...	1996	8604092
computer-aided discrimination between active and inactive mutants of the n-terminal domain of the bacteriophage lambda repressor.	binding of the n-terminal domain of the lambda repressor to dna is coupled to dimerization. hydrophobic interactions between helix-5 and helix-5' drive the packing at the dimer interface. we have carried out computations of the conformational energy of packing of the fifth helices (and of the helix-4-loop-helix-5 portions) of variants of the lambda repressor operator binding domain, using an ecepp/3-based packing algorithm. here, we report the results for 26 mutants chosen among those that hve b ...	1996	8604135
cooperativity mutants of bacteriophage lambda ci repressor: temperature dependence of self-assembly.	analytical ultracentrifugation was used to study higher order self-assembly of lambda ci repressors, including eight mutants whose monomer to dimer reactions were recently characterized [burz et al. (1994) biochemistry 33, 8399]. six of the mutants were found to remain dimeric up to 50 microm total protein; the remaining mutants (ek102 and pt158) were found to undergo higher order oligomerization, as does wild-type ci. for these three repressors, we determined the stoichiometries and energetics ...	1996	8605172
identification of new fis binding sites by dna scission with fis-1,10-phenanthroline-copper(i) chimeras.	the chimeric nuclease fis-op has been used to identify novel fis binding sites. tethering the chemical nuclease op-cu+ to position 73 of the protein with a newly developed longer acetyl-beta-alanylamino spacer has facilitated the localization of two high-affinity fis binding sequences in a 3 kb puc19 plasmid. the shorter acetamido linker has allowed the chimeric nuclease to locate two strong fis binding sites in the 50 kb phage lambda genome. all four sites reside in biologically interesting loc ...	1996	8605181
exclusion of t4 phage by the hok/sok killer locus from plasmid r1.	the hok (host killing) and sok (suppressor of killing) genes (hok/sok) efficiently maintain the low-copy-number plasmid r1. to investigate whether the hok/sok locus evolved as a phage-exclusion mechanism, escherichia coli cells that contain hok/sok on a pbr322-based plasmid were challenged with t1, t4, t5, t7, and lambda phage. upon infection with t4, the optical density of cells containing hok/sok on a high-copy-number plasmid continued to increase whereas the optical density for those lacking ...	1996	8606182
role of escherichia coli rna polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor nusa.	the alpha subunit (alpha) of rna polymerase (rnap) is critical for assembly of polymerase and positive control of transcription initiation in escherichia coli. here, we report that alpha also plays a role in transcription elongation, and this involves a direct interaction between alpha and nusa factor. during in vitro transcription without nusa, alpha interacts with the nascent rna, as revealed by photocrosslinking. when nusa is present, rna crosslinks to nusa rather than to alpha. we show that ...	1996	8598198
high pressure represses expression of the malb operon in escherichia coli.	the formation of plaques by lambda phage in escherichia coli was prevented by elevated hydrostatic pressure; phage plaques were not detected at 30 mpa. furthermore, using promoter fragments derived from the malb operon, we showed that gene expression initiated from both promoters (malk-lamb and malefg) was repressed by elevated hydrostatic pressure. our findings suggest that high pressure affects gene expression directed by the malb regulatory interval, and this may cause a decrease in the quant ...	1996	8598266
cleavage by rnase p of gene n mrna reduces bacteriophage lambda burst size.	rnase p, an enzyme essential for trna biosynthesis, can be directed to cleave any rna when the target rna is in a complex with a short, complementary oligonucleotide called an external guide sequence (egs). rnase p from escherichia coli can cleave phage lambda n mrna in vitro or in vivo when the mrna is in a complex with an egs. the egs can either be separate from or covalently linked to m1 rna, the catalytic rna subunit of rnase p. the requirement for mg2+ in the reaction in vitro is lower when ...	1996	8600449
nondisruptive detection of activity of catabolic promoters of pseudomonas putida with an antigenic surface reporter system.	a simple procedure to detect the switching on and off of catabolic promoters of pseudomonas putida, at the level of single cells based on the immunodetection of a reporter epitope expressed on the surface of bacterial cells, has been developed. to do this, the antigenic sequence asp-leu-pro-pro-asn-ser-asp-val-val-asp, from a coronavirus, was inserted genetically in the permissive site around amino acid position 153 of the lamb protein (maltose and lambda phage receptor) of escherichia coli. whe ...	1996	8572699
disassembly of the coliphage lambda replication complex due to heat shock induction of the groe operon.	we have found previously that, in contrast to the free o initiator protein of lambda phage or plasmid rapidly degraded by the escherichia coli clpp/clpx protease, the lambda o present in the replication complex (rc) is protected from proteolysis. in amino acid-starved e. coli rela cells, a temperature shift from 30 to 43 degrees did not affect rc integrity, as judged from the unchanged level of stable lambda o observed; however, the same temperature shift in a complete medium resulted in the dec ...	1996	8610451
long-circulating bacteriophage as antibacterial agents.	the increased prevalence of multidrug-resistant bacterial pathogens motivated us to attempt to enhance the therapeutic efficacy of bacteriophages. the therapeutic application of phages as antibacterial agents was impeded by several factors: (i) the failure to recognize the relatively narrow host range of phages; (ii) the presence of toxins in crude phage lysates; and (iii) a lack of appreciation for the capacity of mammalian host defense systems, particularly the organs of the reticuloendothelia ...	1996	8622911
conservation of the rd-bf-c2 organization in the pig mhc class-iii region: mapping and cloning of the pig rd gene.	the rd gene, named after the arginine (r) and aspartic acid (d) repeat in the central part of its protein, was initially mapped in the mouse h-2s subregion between c4 and bf. it was later mapped in the same position in the human mhc and here we show it is also conserved in the pig mhc class iii region, close to the complement bf gene. a pig rd genomic clone was isolated from a lambda-phage library. hybridizations on genomic dna separated with pulsed field gel electrophoresis identified common 22 ...	1996	8624034
the rz1 gene product of bacteriophage lambda is a lipoprotein localized in the outer membrane of escherichia coli.	the rz1 gene of bacteriophage lambda is located within the rz1 lysis gene. it codes for the 6.5-kda prolipoprotein (rz1) which undergoes n-terminal signal sequence cleavage and post-translational lipid modification of the n-terminal cys of the mature protein. globomycin, the antibiotic which inhibits bacterial signal peptidase ii, specific for prolipoproteins containing diacylglyceryl cysteine [hayashi and wu, j. bioenerg. biomembr. 22 (1990) 451-471] inhibits the n-terminal sequence cleavage of ...	1996	8626053
a bipartite signaling mechanism involved in dnaj-mediated activation of the escherichia coli dnak protein.	the dnak and dnaj heat shock proteins function as the primary hsp70 and hsp40 homologues, respectively, of escherichia coli. intensive studies of various hsp70 and dnaj-like proteins over the past decade have led to the suggestion that interactions between specific pairs of these two types of proteins permit them to serve as molecular chaperones in a diverse array of protein metabolic events, including protein folding, protein trafficking, and assembly and disassembly of multisubunit protein com ...	1996	8626673
precise limitation of concerted evolution to orfs in mosquito hsp82 genes.	two hsp82 genes were isolated from the malaria vector anopheles albimanus in a single lambda phage clone. the two genes are in a head-to-head arrangement separated by approx. 0.9 kbp. northern hybridizations and 5' race demonstrate that both genes are transcribed, have moderate levels of constitutive transcription, and are also heat-inducible with maximum transcript accumulation occurring after 40 degrees c heat shocks. both genes have typical heat-shock promoters and conserved intron boundaries ...	1996	8630537
escherichia coli thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding tmk locus.	thymidylate kinase (dtmp kinase; ec 2.7.4.9) catalyzes the phosphorylation of dtmp to form dtdp in both de novo and salvage pathways of dttp synthesis. the nucleotide sequence of the tmk gene encoding this essential escherichia coli enzyme is the last one among all the e. coli nucleoside and nucleotide kinase genes which has not yet been reported. by subcloning the 24.0-min region where the tmk gene has been previously mapped from the lambda phage 236 (e9g1) of the kohara e. coli genomic library ...	1996	8631667
overexpression of an mrna dependent on rare codons inhibits protein synthesis and cell growth.	lambda's int gene contains an unusually high frequency of the rare arginine codons aga and agg, as well as dual rare arg codons at three positions. related work has demonstrated that int protein expression depends on the rare aga trna. strong transcription of the int mrna with a highly efficient ribosome-binding site leads to inhibition of int protein synthesis, alteration of the overall pattern of cellular protein synthesis, and cell death. synthesis or stability of int and ampicillin resistanc ...	1996	8631683
a family of genes coding for two serologically distinct chicken interferons.	southern blot analysis and screening of a genomic lambda phage library with the previously cloned chicken interferon (ifn) cdna indicated that the chicken genome contains at least 10 ifn genes. a particularly strongly hybridizing phage clone that we analyzed in more detail carried a head to tail arrangement of three intron-less ifn genes that differed from each other and from the cloned chicken ifn cdna by only a few base changes. the primary translation products of these three ifn genes consist ...	1996	8631799
identification of functional regions of the nun transcription termination protein of phage hk022 and the n antitermination protein of phage lambda using hybrid nun-n genes.	phages lambda and hk022 express proteins n and nun, respectively, each of which acts with a number of escherichia coli host nus factors at lambda nut rna sites, to influence transcription elongation. the lambda nut sites, nearly identical sequences located downstream of the early promoters, pl and pr, were first identified as cis-acting signals required for the action of n in forming termination-resistant transcription complexes. surprisingly, the nun protein, resembling n and expressed by anoth ...	1996	8632463
a refined vector system for the in vitro construction of single-copy transcriptional or translational fusions to lacz.	new single-copy vectors based on lambda phage have been developed for creating either transcriptional (operon) or translational (gene) fusions to the lacz gene. the improvements of these vectors over the previous lambda tl61 vector include: (i) incorporation of a tetracycline-resistance-encoding gene (tcr) to permit direct selection of lysogens, (ii) low-background beta-galactosidase activity, (iii) the ability to accept dna inserts up to 8 kb in size, and (iv) an expanded multiple cloning site ...	1996	8635751
use of genomic dna probes for the diagnosis of acute sarcocystosis in experimentally infected cattle.	two clones of 1.4 and 4.33 kilobase pairs (kbp) dna inserts, were selected from a sarcocystis cruzi sporozoite genomic library constructed in bacteriophage lambda gt10. these clones strongly hybridized with sporozoite and merozoite dna and were evaluated as probes for detection of merozoite dna in clinical samples. of five calves in the experiment, four were each orally dosed with approximately 200,000 s. cruzi sporocysts; one calf served as non-infected control. subsequently, blood was collecte ...	1996	8638397
epitope-specific tolerance induction with an engineered immunoglobulin.	isologous and heterologous immunoglobulins have been shown to be extremely effective as tolerogenic carriers for nearly 30 years. the efficacy of these proteins is due in part to their long half-life in vivo, as well as their ability to crosslink surface igm with fc receptors. the concept of using igg as a carrier molecule to induce unresponsiveness in the adult immune system has been exploited for simple haptens, such as nucleosides, as well as for peptides. to further evaluate the in vivo pote ...	1996	8643522
topology of the membrane protein lamb by epitope tagging and a comparison with the x-ray model.	we previously developed a genetic approach to study, with a single antibody, the topology of the outer membrane protein lamb, an escherichia coli porin with specificity towards maltodextrins and a receptor for bacteriophage lambda. our initial procedure consisted of inserting at random the same reporter epitope (the c3 neutralization epitope from poliovirus) into permissive sites of lamb (i.e., sites which tolerate insertions without deleterious effects on the protein activities or the cell). a ...	1996	8655540
tsp49i (acgt/), a thermostable neoschizomer of the type ii restriction endonuclease maeii (a/cgt), discovered in isolates of the genus thermus from the azores, iceland and new zealand.	one hundred and forty eight isolates of the genus thermus, from neutral and alkaline hot water springs on four continents, have been screened for the presence of restriction endonuclease activity. an isolate (sm49) from the island of sao miguel, in the azores, showed a high level of restriction endonuclease activity when a cell-free extract was incubated with lambda phage dna at 65 degrees c. a type ii restriction endonuclease (tsp49i) has been partially purified from this isolate and the recogn ...	1996	8657557
amphimeric mitochondrial genomes of petite mutants of yeast. i. flip-flop amphimers make up the mitochondrial genomes of "palindromic" petite mutants of yeast.	the mitochondrial (mt) genomes of three spontaneous cytoplasmic "palindromic" petite mutants of yeast were studied by restriction-enzyme analysis. these mt genomes were shown to be made up of an amplified "master basic unit" consisting of two inverted segments (a and a) and of two different unique segments (d and t) separating them. the basic unit was called "amphimeric", this term having been first proposed for certain lambda-phage mutants. we propose that in the mt genomes of the petite mutant ...	1996	8660459
structure of the human type iv collagen col4a6 gene, which is mutated in alport syndrome-associated leiomyomatosis.	basement membrane (type iv) collagen, a subfamily of the collagen protein family, is encoded by six distinct genes in mammals. three of those, col4a3, col4a4, and col4a5, are linked with alport syndrome (hereditary nephritis). patients with leimoyomatosis associated with alport syndrome have been shown to have deletions in the 5' end of the col4a6 gene, in addition to having deletions in col4a5 (zhou et al., science 261: 1167-1169, 1993). the human col4a6 gene is reported to be 425 kb as determi ...	1996	8661006
physical assignments of 68 porcine cosmid and lambda clones containing polymorphic microsatellites.	two lambda phage and 66 cosmids containing informative porcine microsatellites were assigned to 17 of 18 porcine autosomes and the x chromosome (chr) by fluorescence in situ hybridization (fish). these assignments provide additional physically anchored markers to integrate the porcine physical and genetic maps.	1996	8661726
cloning and sequencing analysis of three amylase cdnas in the shrimp penaeus vannamei (crustacea decapoda): evolutionary aspects.	in penaeus vannamei, alpha-amylase is the most important glucosidase and is present as at least two major isoenzymes which have been purified. in order to obtain information on their structure, a hepatopancreas cdna library constructed in phage lambda-zap ii (strategene) was screened using a synthetic oligonucleotide based on the amino acid sequence of a v8 staphylococcal protease peptide of p. vannamei alpha-amylase. three clones were selected: amy sk 37 (embl sequence accession number: x 77318 ...	1996	8661999
structure-function analysis of the zinc finger region of the dnaj molecular chaperone.	dnaj is a molecular chaperone, which not only binds to its various protein substrates, but can also activate the dnak cochaperone to bind to its various protein substrates as well. dnaj is a modular protein, which contains a putative zinc finger motif of unknown function. quantitation of the released zn(ii) ions, upon challenge with p-hydroxymercuriphenylsulfonic acid, and by atomic absorption showed that two zn(ii) ions interact with each monomer of dnaj. following the release of zn(ii) ions, t ...	1996	8662861
the rna chain elongation rate of the lambda late mrna is unaffected by high levels of ppgpp in the absence of amino acid starvation.	in this study, the effects of high levels of guanosine tetraphosphate (ppgpp) on the decay and rna chain elongation kinetics of the bacteriophage lambda late transcript in escherichia coli were examined in the absence of amino acid starvation. the accumulation, mrna decay kinetics, and rna chain elongation rate of the lambda late mrna were determined after heat induction of lambdaci857 lysogens in the presence of high levels of ppgpp induced from a relaalpha fragment-overproducing plasmid. the a ...	1996	8663373
a multicopy suppressor of nin1-1 of the yeast saccharomyces cerevisiae is a counterpart of the drosophila melanogaster diphenol oxidase a2 gene, dox-a2.	nin1 is an essential gene for growth of the yeast saccharomyces cerevisiae and was recently found to encode a component of the regulatory subunit of the 26s proteasome. the nin1-1 mutant is temperature sensitive and its main defect is in g1/s progression and g2/m progression at non-permissive temperatures. one of the two multicopy suppressors of nin1-1, sun2 (suppressor of nin1-1), was found to encode a protein of 523 amino acids whose sequence is similar to those of drosophila melanogaster diph ...	1996	8668124
synthesis of the bacteriophage lambda p protein in amino acid-starved escherichia coli cells.	it was demonstrated previously that in isoleucine-starved escherichia coli rela mutants harboring a plasmid derived from bacteriophage lambda the lambda o protein is not synthesized. however, a protein which coprecipited with the lambda o during immunoprecipitation with anti-lambda o serum was synthesized during the relaxed response. here we found that this protein is the lambda p gene product. despite significant inhibition of transcription from the pr promoter (which produces mrna for the lamb ...	1996	8670253
frequent spontaneous deletions at a shuttle vector locus in transgenic mice.	transgenic mice carrying multiple copies of a recoverable lambda phage shuttle vector (lambda supf) were constructed for the purpose of studying mutagenesis in a whole animal. spontaneous mutations in rescued supf target genes from several different lines of transgenic mice were analyzed. one mouse line, 1139, was identified in which the frequency of spontaneous mutations was unusually high (3.15 x 10(-4)), 20-fold higher than in other transgenic mice carrying a similar number of copies of the l ...	1996	8671715
evaluation of a plasmid-based transgenic mouse model for detecting in vivo mutations.	to study in vivo somatic mutations a c57bl/6 transgenic mouse model was constructed harboring multiple chromosomally integrated copies of the plasmid pur288, which carried the lacz reporter gene as the mutational target. we previously demonstrated that lacz-containing plasmids could be rescued from their integrated state efficient enough to detect mutations in lacz by positive selection. the smaller size of the plasmid vector, as compared with our earlier transgenic mouse model based on bacterio ...	1996	8671725
specificity mechanisms in the control of transcription.	in this overview we analyze and illustrate the principles underlying some of the specificity mechanisms that control the initiation, elongation, and termination phases of transcription. thermodynamic mechanisms dominate in the first steps of initiation, where promoters at various levels of activation can be considered to be in competition for a limiting supply of core rna polymerase. in the later stages of initiation, as well as in elongation and termination, the regulatory mechanisms that contr ...	1996	8672714
interaction between camp-dependent protein kinase catalytic subunit and peptide inhibitors analyzed with lambda repressor fusions.	the lambda phage repressor is currently used as a genetic tool to analyze homodimeric interactions in escherichia coli. we have applied this system to detect the interaction that takes place within an enzyme-protein inhibitor complex. the sequences encoding the catalytic subunit of the camp-dependent protein kinase and the active portion of the natural thermostable protein kinase inhibitor have been fused to the carboxy terminus of the repressor dna binding domain and introduced into compatible ...	1996	8683565
systematic mapping of autonomously replicating sequences on chromosome v of saccharomyces cerevisiae using a novel strategy.	we have developed a new procedure for easy and rapid identification of autonomously replicating sequences (arss) and have applied it to the analysis of chromosome v of saccharomyces cerevisiae. the procedure makes use of the ordered lambda phage clone bank of this chromosome that we have constructed, and includes transposition of a mini-transposon and selection of transposon-containing derivatives, isolation of their dna and circularization at their cos-ends, transformation of yeast cells with t ...	1996	8686374
detection of dna damage induced by human carcinogens in acellular assays: potential application for determining genotoxic mechanisms.	positive outcomes of in vitro genotoxicity tests may not always occur as a consequence of direct reaction of a compound or a metabolite with dna. to follow-up positive responses in in vitro tests, we developed two supplemental, cell-free assays to examine the potential of compounds and metabolites to directly damage dna. calf thymus dna was used as the target for the direct detection of adducts by 32p-postlabeling/tlc and electrochemical detection, and alkaline gel electrophoresis was used to de ...	1996	8692229
effect of eugenol on the mutagenicity of benzo[a]pyrene and the formation of benzo[a]pyrene-dna adducts in the lambda-lacz-transgenic mouse.	to study the possible reduction by eugenol of the mutagenicity and genotoxicity of benzo[a]pyrene (b[a]p) in vivo, the lambda-lacz-transgenic mouse strain 40.6 (muta mouse) was used. male mice were fed a diet containing 0.4% (w/w) eugenol or a control diet for 58 days. on day 10, half of the mice received an i.p. dose of 100 mg/kg b.w. b[a]p. the lacz mutants were recovered by packaging of dna isolated from liver into lambda phage, and expressed in e. coli c lacz-reca-gale- bacteria. in both con ...	1996	8700188
rho-dependent termination of transcription is governed primarily by the upstream rho utilization (rut) sequences of a terminator.	a rho-dependent transcription terminator in escherichia coli dna consists of an upstream part for rho utilization (rut) and the transcription stop point (tsp) region. to test the role of the tsp region variants of the coliphage lambda cro gene terminator, tr1, containing inserts of non-terminator sequences between its rut and tsp regions were tested for termination function. the results showed that termination occurred with high efficiency at multiple sites in each of the new sequences with the ...	1996	8702947
bacteriophage lambda lysis gene product modified and inserted into escherichia coli outer membrane: rz1 lipoprotein.	lysis proteins of bacteriophage lambda were localized in different parts of the host envelope: s in the inner membrane,36 rz in the membrane adhesion sites,14 and rz1 in the outer membrane. the r gene product, the transglycosylase destroying bacterial murein, is a soluble protein. computer-assisted analysis of the rz1 protein amino acids sequence revealed that its n-terminal part contained the site 15vvvg [symbol: see text] c20, which could be recognizable for the spase ii and cleaved leaving li ...	1996	9158738
a one-hybrid system for detecting rna-protein interactions.	mrna translation, stability, and localization are controlled by regulatory proteins that bind to specific rna motifs. since biochemical isolation of such proteins has often proven to be difficult, a genetic system for studying rna-protein interactions would be of great utility in the identification of novel rna binding proteins and in understanding how these proteins recognize particular rna sequences. the bacteriophage lambda gene product n protein is a sequence specific rna binding protein tha ...	1996	9133665
high-resolution structure of an engineered cro monomer shows changes in conformation relative to the native dimer.	a rationally designed, genetically engineered, monomeric form of the cro protein from bacteriophage lambda has been crystallized and its structure determined by isomorphous replacement and refined to a resolution of 1.54 a. the structure confirms the rationale of the design but, at the same time, reveals 1-2 a shifts throughout the monomer structure relative to the previously determined structure of the dimeric wild-type protein. these changes include a 1.6 a main-chain shift in part of the beta ...	1996	8547253
regulation of the shiga-like toxin ii operon in escherichia coli.	investigations of the regulation of the bacteriophage-encoded shiga-like toxin ii (slt-ii) in escherichia coli demonstrated that bacteriophages exhibit a regulatory impact on toxin production by two mechanisms. firstly, replication of the toxin-converting bacteriophages brings about an increase in toxin production due to concomitant multiplication of toxin gene copies. secondly, an influence of a phage-encoded regulatory molecule was demonstrated by using low-copy-number plasmid padr-28, carryin ...	1996	8550198
bacteriophage lambda n protein alone can induce transcription antitermination in vitro.	specific and processive antitermination by bacteriophage lambda n protein in vivo and in vitro requires the participation of a large number of escherichia coli proteins (nus factors), as well as an rna hairpin (boxb) within the nut site of the nascent transcript. in this study we show that efficient, though nonprocessive, antitermination can be induced by large concentrations of n alone, even in the absence of a nut site. by adding back individual components of the system, we also show that n wi ...	1996	8552635
second-site reversion of a structural defect in bacteriophage t4 lysozyme.	a plasmid-borne gene encoding bacteriophage t4 lysozyme with a structural mutation, tyr161-ala, was mutagenized by by the use of polymerase chain reaction. the mutagenized gene was inserted into a specialized bacteriophage lambda cloning vector that must acquire a functional lysozyme gene in order to form plaques. functional variants of the mutant lysozyme were selected. three compensatory second-site revertants were obtained: thr152-met, lys43-ile, and thr151-ala. the effects of these mutations ...	1996	8566537
structural analysis of mitochondrial dna molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis.	the size and structure of mitochondrial dna (mtdna) molecules was investigated by conventional and pulsed-field gel electrophoresis (pfge) and by analyzing moving pictures during electrophoresis of individual fluorescently labelled mtdna molecules. little or no mtdna that migrated into the gel was found in circular form for fungi (schizosaccharomyces pombe, saccharomyces cerevisiae and neurospora crassa) or plants (brassica hirta, tobacco, voodoo lily and maize). most mtdna migrated as a smear o ...	1996	8568898
ribose catabolism of escherichia coli: characterization of the rpib gene encoding ribose phosphate isomerase b and of the rpir gene, which is involved in regulation of rpib expression.	escherichia coli strains defective in the rpia gene, encoding ribose phosphate isomerase a, are ribose auxotrophs, despite the presence of the wild-type rpib gene, which encodes ribose phosphate isomerase b. ribose prototrophs of an rpia genetic background were isolated by two different approaches. firstly, spontaneous ribose-independent mutants were isolated. the locus for this lesion, rpir, was mapped to 93 min on the linkage map, and the gene order zje::tn10-rpir-mel-zjd::tn10-psd-pura was es ...	1996	8576032
interleukin-5 receptor alpha subunit gene regulation in human eosinophil development: identification of a unique cis-element that acts lie an enhancer in regulating activity of the il-5r alpha promoter.	further functional and biochemical characterization of the nuclear factor(s) which interacts with the eos1 enhancer-like element in the il-5r alpha promoter is currently in progress. since different transcription factors recognize and interact with dna in distinct fashions and with distinct structural motifs, we have modeled potential binding of the eos1 factor to its cis-element based upon its methylation interference pattern (fig. 2), using a cylindrical dna helical projection (fig. 6). over a ...	1996	8585949
construction and characterization of a potential live oral carrier-based vaccine against vibrio cholerae o139.	the rfb region from vibrio cholerae o139 strain mo45 was cloned from cosmid gene banks established in escherichia coli hb101, using an immunoblot assay for screening of the correct clones. immunoblot analysis of lipopolysaccharide (lps) preparations revealed the presence of two types of positive clones: (i) those expressing only a short core-linked o polysaccharide (sops) and (ii) those also expressing a highly polymerized capsular polysaccharide (cps) not bound to the e. coli k-12 lps core. in ...	1996	8751900
cloning and analysis of igg kappa and igg lambda anti-thyroglobulin autoantibodies from a patient with hashimoto's thyroiditis: evidence for in vivo antigen-driven repertoire selection.	antibodies to thyroglobulin (tg) are commonly found in patients with the autoimmune thyroid diseases graves' disease and hashimoto's thyroiditis as well as in individuals with apparently normal thyroid function. although it is not clear how tg abs are involved in the pathology of the diseases, the study and analysis of these abs may nevertheless be instructive in allowing the development of an ab response to an autoimmune disease-associated self ag to be followed. we have prepared igg kappa and ...	1996	8752947
complete structure of the human alpha-albumin gene, a new member of the serum albumin multigene family.	the nucleotide sequence of the human alpha-albumin gene, including 887 bp of the 5'-flanking region and 1311 bp of the 3-flanking region (24,454 in total), was determined from three overlapping lambda phage clones. the sequence spans 22,256 bp from the cap site to the polyadenylylation site, revealing a gene structure of 15 exons separated by 14 introns. the methionine initiation codon atg is within exon 1; the termination codon tga is within exon 14. exon 15 is entirely untranslated and contain ...	1996	8755513
raman spectroscopy of the ff gene v protein and complexes with poly(da): nonspecific dna recognition and binding.	raman spectra of crystals and solutions of the single-stranded dna binding protein of bacteriophage ff (gene v protein, gvp) and of solution complexes of gvp with single-stranded poly-(deoxyadenylic acid) [poly(da)] reveal the following: (i) the gvp secondary and tertiary structures are similar in solution and in the crystal and are dominated by beta-sheet domains, in agreement with nmr and x-ray findings. (ii) subunit conformation and side chain environments of gvp are virtually unchanged over ...	1996	8755742
function of e. coli rna polymerase sigma factor sigma 70 in promoter-proximal pausing.	the sigma factor sigma 70 of e. coli rna polymerase acts not only in initiation, but also at an early stage of elongation to induce a transcription pause, and simultaneously to allow the phage lambda gene q transcription antiterminator to act. we identify the signal in dna that induces early pausing to be a version of the sigma 70 -10 promoter consensus, and we show that sigma 70 is both necessary for pausing and present in the paused transcription complex. regions 2 and 3 of sigma 70 suffice to ...	1996	8756730
identification of an up element within the ihf binding site at the pl1-pl2 tandem promoter of bacteriophage lambda.	an up element defines a supplementary promoter element located upstream of the -35 region that stimulates transcription by interacting with the c-terminal domain of the rna polymerase alpha subunit (alpha ctd). the alpha ctd also responds to various transcription activators, including the integration host factor protein, ihf, in the stimulation of the bacteriophage lambda pl promoter. pl consists of the tandem pl1-pl2 promoters where pl1 is stimulated and pl2 is repressed by ihf. we identified a ...	1996	8759315
cloning, restriction endonuclease mapping and partial sequence analysis of the genome of human herpesvirus 7 strain ji.	human herpesvirus 7 (hhv-7) is a recently isolated herpesvirus that has been shown to be related to human cytomegalovirus and human herpesvirus 6 and to be a member of the betaherpesvirus subgroup. here we report the cloning, restriction endonuclease mapping and partial sequence analysis of hhv-7 strain ji dna. virus particles were obtained from the supernatant of infected supt1 cells, the dna isolated by proteinase k treatment-phenol extraction, and full-length viral dna was purified and isolat ...	1996	8760442
characterization of the rat glutathione s-transferase yc2 subunit gene, gsta5: identification of a putative antioxidant-responsive element in the 5'-flanking region of rat gsta5 that may mediate chemoprotection against aflatoxin b1.	we have isolated and characterized genomic dna encoding the rat glutathione s-transferase yc2 subunit. this protein is now referred to as rgsta5 and is noteworthy because of its high activity towards aflatoxin b1-8,9-epoxide, its marked inducibility by chemoprotectors, its sex-specific regulation, and its over-expression in hepatoma and preneoplastic nodules. the rgsta5 gene, which was isolated on two overlapping bacteriophage lambda clones, is approx. 12 kb in length and, unlike other class alp ...	1996	8761455
a proposal for using modified site-specific recombination systems for making insertions into a chosen chromosomal site in vivo based on the analysis of lambda phage integration.	a proposal is presented here to use modified mobile genetic elements for making chromosomal insertions in vivo, into any desired chromosomal site. the idea lies in replacing the sequences which direct specificity of integration of those elements with other dna sequences, homologous to the desired target chromosomal site. the idea is analysed on the basis of a lambda phage integration system. a design for a universal system for making chromosomal insertions into any site of choice is proposed.	1996	8763358
[organization of the gene for the beta-subunit of human photoreceptor cyclic gmp phosphodiesterase].	two recombinant bacteriophage lambda clones encoding a 27.8-kb fragment of the human phosphodiesterase beta-subunit gene were isolated from a human genomic library. the nucleotide sequences of 19 exons (from the 4th to 22nd), 18 introns, and the 3'-flanking region were determined. the analysis of the nucleotide sequence of the phosphodiesterase beta-subunit gene revealed four alu repeats and four minisatellite regions.	1996	8768262
device for the simultaneous screening of bacteriophage lambda clones.		1996	8770396
membrane topology of the mannose transporter of escherichia coli k12.	the mannose transporter of the bacterial phosphotransferase system mediates carbohydrate transport across the cytoplasmic membrane concomitant with carbohydrate phosphorylation. it also functions as a receptor for bacterial chemotaxis [adler.j. & epstein, w. (1974) proc. natl acad. sci. usa 71. 2895-2899] and is required for infection of the cell by bacteriophage lambda where it most likely functions as a pore for penetration of phage dna [elliott, j. & arber, w. (1978) mol. & gen. genet. 161, 1 ...	1996	8774730
conserved structure and adjacent location of the thrombin receptor and protease-activated receptor 2 genes define a protease-activated receptor gene cluster.	thrombin is a serine protease that elicits a variety of cellular responses. molecular cloning of a thrombin receptor revealed a g protein-coupled receptor that is activated by a novel proteolytic mechanism. recently, a second protease-activated receptor was discovered and dubbed par2. par2 is highly related to the thrombin receptor by sequence and, like the thrombin receptor, is activated by cleavage of its amino terminal exodomain. also like the thrombin receptor, par2 can be activated by the h ...	1996	8784787
structure of the human laminin gamma 2 chain gene (lamc2): alternative splicing with different tissue distribution of two transcripts.	we have determined the structure of the human laminin gamma 2 chain gene (lamc2), which is mutated in some patients with junctional epidermolysis bullosa. eight lambda phage clones isolated from a genomic library and three subgenomic lambda phage clones made from a plasmid artificial chromosome clone spanned 75 kb, including the 55-kb gene. the lamc2 gene contains 23 exons and is structurally highly homologous with the 28-exon lamc1 gene (kallunki et al., 1991, j. biol. chem. 266: 221-228), with ...	1996	8786121
characterization of a translocation-associated deletion defines the candidate region for the gene responsible for branchio-oto-renal syndrome.	fluorescence in situ hybridization analysis of an 8q translocation breakpoint, dir ins(8)(q24.11;q13.3;q21.13), carried by an individual presenting with branchio-oto-renal (bor) syndrome, resulted in the identification of an associated deletion. the generation of a yac contig and the isolation of overlapping recombinant p1 and lambda phage clones from the region allowed further characterization of this deletion. its size was estimated to be between 470 and 650 kb, and it was flanked by the two p ...	1996	8786145
structural prediction of a- and b-dna duplexes based on coordinates of the phosphorus atoms.	the sequence-dependent structure of dna double helices was studied extensively during the past 10 years. how the backbone structure correlates with the base structure in a duplex conformation is still an important yet open question. using a set of reduced coordinates and a least-squares fitting procedure, we have developed a method to predict structures for b-dna duplexes based on coordinates of the phosphorus atoms. this method can be used to predict all-atom structures for both bent and straig ...	1996	8789108
sequencing of a 23 kb fragment from saccharomyces cerevisiae chromosome vi.	plasmid clone gapb and lambda phage clone 4682, which contain fragments of saccharomyces cerevisiae chromosome vi, were analysed. a 23 kb sequence was determined and ten open reading frames (orfs) were revealed. among them, five orfs were identical to five yeast genes (sec4, msh4, spb4, deg1 and nic96), two were identical to transposable elements (tya and tyb), one (gapborff003) was highly homologous to a yeast expressed sequence tag, and another (4682orff002) was predicted to be a nuclear prote ...	1996	8789262
thi1, a thiamine biosynthetic gene in arabidopsis thaliana, complements bacterial defects in dna repair.	an arabidopsis thaliana cdna was isolated by complementation of the escherichia coli mutant strain bw535 (xth, nfo, nth), which is defective in dna base excision repair pathways. this cdna partially complements the methyl methane sulfonate (mms) sensitive phenotype of bw535. it also partially corrects the uv-sensitive phenotype of e. coli ab1886 (uvra) and restores its ability to reactivate uv-irradiated lambda phage. it has an insert of ca. 1.3 kb with an open reading frame of 1047 bp (predicti ...	1996	8790291
isolation and subcloning of chitinase clone from chickpea genomic library.	chickpea genomic library constructed earlier in phage lambda (embl-3) was screened for the presence of chitinase clone using tobacco chitinase cdna as a probe. positive clones obtained by primary screening of plaques (2 x 10(6)) were ascertained by secondary and tertiary screening. presence of chitinase insert in the positive clones obtained, was further confirmed by restricting phage dna with sal i and then doing southern with tobacco chitinase. the insert band was eluted out and subcloned in p ...	1996	8792650
mutations affecting the high affinity atpase center of gpa, the large subunit of bacteriophage lambda terminase, inactivate the endonuclease activity of terminase.	phage lambda terminase carries out the cos cleavage reaction that generates mature chromosomes from immature concatemeric dna. the atp-stimulated endonuclease activity of terminase is located in gpa, the large terminase subunit. there is a high affinity atpase center in gpa, and a match to the conserved p-loop of known atpases is found starting near residue 490. changing the conserved p-loop lysine at residue 497 of gpa affects the high affinity atpase activity of terminase. in the present work, ...	1996	8794874
interactions between a minimal protein serine/threonine phosphatase and its phosphopeptide substrate sequence.	the protein phosphatase encoded by coliphage lambda (pplambda) was found to be the equivalent of the minimal catalytic core of serine/threonine protein phosphatases (pp) by biochemical and mutational criteria. bacterially expressed truncated versions of pp1 and pp5 phosphatases, representing the catalytic cores homologous to pplambda, exhibited potent phosphatase activity. unlike full-length pp1, but like pplambda, the recombinant cores could use casein, p-nitrophenyl phosphate, and a wide varie ...	1996	8798696