... in paleoparasitology. However, aDNA is especially subject to degradation (especially nuclear aDNA) and contamination; therefore, PCR and sequencing results ... ...
NBII National Biological Information Infrastructure
... 4. TITLE AND SUBTITLE DNA as Part of Identity Management for the Department of Defense 5a. ... DNA as Part of Identity Management for the ...
DTIC Science & Technology
In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA) report from a medieval ...
PubMed
The problems of tuberculosis (TB) and its drug resistances are very severe in China. New therapeutic agents or regimens to treat multi-drug-resistant tuberculosis (MDR-TB) are urgently needed. We studied the effects of Ag85A DNA vaccine alone or in combination with rifampin (RFP) or pyrazinamide (PZA) for the treatment of MDR-TB in mice. ...
There could still be a residual abundance bias in flares 1a dna 1b if the ... and that some of the 3-parameter events are degraded to 2-parameter events. ...
NASA Website
... a) Milk b) Orange Juice c) Tomato d) Egg; Which of these is not a cause of emerging pathogens? a) DNA Mapping b) Transduction c) Transformation d) Conjugation. ...
Center for Food Safety and Applied Nutrition (CFSAN)
... test tube resembles a translucent glob of mucous. Ribonucleic acid (RNA) (Figure 1-A) DNA can be extracted from ... ...
... without ampicillin. These cells will be used for competent cell preparation the following day (one plate required ... then incubated at 37°C overnight. If the competent E. coli cells are not going to be ...
...DISTRICT OF COLUMBIA COLLECTION AND USE OF DNA INFORMATION § 812.4 Collection procedures. (a) DNA samples will be collected, handled, preserved...misdemeanor pursuant to section 4(a)(5) of the DNA Analysis Backlog Elimination Act of...
Code of Federal Regulations, 2011
...DISTRICT OF COLUMBIA COLLECTION AND USE OF DNA INFORMATION § 812.4 Collection procedures. (a) DNA samples will be collected, handled, preserved...pursuant to section 4(a)(5) of the DNA Analysis Backlog Elimination Act of...
Code of Federal Regulations, 2010
Vaccine development for severe acute respiratory syndrome coronavirus (SARS-CoV) has mainly focused on the spike (S) protein. However, the variation of the S gene between viruses may affect the efficacy of a vaccine, particularly for cross-protection against SARS-like CoV (SL-CoV). Recently, a more conserved group-specific open reading frame (ORF), the 3a gene, was found in both SARS-CoV and ...
Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in ...
PubMed Central
The paucity of ancient DNA (aDNA) studies in insects can be traced to the dismissal of the 1990s reports of DNA isolation from amber-entombed insects. In retrospect, amber was an obvious place to start, but it has since been demonstrated that DNA preservation is not necessarily correlated with physical preservation. The discipline of aDNA is rapidly progressing as issues ...
NASA Astrophysics Data System (ADS)
A-DNA and B-DNA are two secondary molecular conformations (among other allomorphs) that double-stranded DNA drawn into a fiber can assume, depending on the relative water content and other chemical parameters of the fiber. They were the first two forms to be observed by X-ray fiber diffraction in the early 1950s, respectively by Wilkins and Gosling and by Franklin and Gosling. ...
ERIC Educational Resources Information Center
� 2006 Nature Publishing Group Mechanism of DNA translocation in a replicative hexameric helicase around the ring from one subunit to the next. Replication initiation only occurs at specific DNA sites three proteins (DnaA, DnaB and DnaC)1 are required just to establish the replicative helicase at ori
E-print Network
bp of each of 13 housekeeping genes (arcA, aroE, aspC, clpX, cyaA, dnaG, fadD, grpE, icdA, lysP, mdh
of topologies. Potential unimolecular (i.e. intramolecular) G- quadruplex forming sequences can be described ................................................................................... 11 1.2.4 G-Quadruplex: a potential target for anti-cancer drug design-handed double helix, the Z-form of DNA (Fig. 1). [2] Fig. 1 A) A-DNA; B) B-DNA; C) Z-DNA; D) 4-Stranded G-quadruplex
... two archaeological sites on the Alaska Peninsula (the Hot Springs site near Port Moller, Alaska; and samples from ... Figure 1). The oldest material comes from the Hot Springs site located on the Bering c...
and Cordilleran ice sheets Dryas integrifolia (plant) [33] Ovis spp. (mountain sheep) [36] Lagopus mutus (rock suggested for the rock ptarmigan Lagopus mutus [37], the plant Dryas integrifolia [33] and the collared. A study on the Arctic fox Alopex lagopus (Box 2, Figure I) using aDNA [46] suggests that populations did
The primary accomplishments of the previous funding period were: 1) RACE analysis of the 5' end of Navl.8/Scn10a murine DRG aDNA confirmed the presence of one intron splice site in the 200 bp 5'UTR of the Scn10a transcript; 2) Three BAC clones were isolat...
National Technical Information Service (NTIS)
you extracted. However, since we are doing the scat samples the majority of the DNA you would be measuring will be bacterial. We will quantify the other DNA you extracted (Badger and your hair samples1 PCR: a background and some Uses. Introduction A. DNA and Genetic Identity Every person who ever
) are consistent with a phylogenetic rate derived from Bison�Bos divergence 1 Myr before present (Troy et al. 2001 rein- terpretation. For example, the Bison aDNA (0�60 kyr) rates reported by Ho, Shapiro, et al. (2007 bison. Science. 306:1561�1565. Singh LJ. 1994. Late Quaternary history of Pelorus Sound from shallow
AL. TABLE 1. Glossary of molecular terms and acronyms cDNA Complementary DNA (a cloned DNA version of a cDNA clone). BAC Bacterial artificial chromosome (a DNA plasmid engineered to allow stable homologs of genes of interest, cDNA clones were picked individually from a mixed organ cDNA library, grown
after translation � For attenuation in different cases - RNA binding proteins that stabilize base is a hexameric protein around which a 70- to 80-base segment of the growing RNA transcript wraps � Rho then moves, which binds downstream of the transcription unit (A DNA-binding protein not a RNA binding as Rho) � RNA
The gene encoding the human glucagon receptor (GCGR) was mapped to chromosome band 17q25 by fluorescence in situ hybridization to metaphase chromosomes. An Alu variable poly(A) DNA polymorphism was identified in this gene. Studies of the CEPH families showed significant evidence of linkage between this DNA polymorphism and markers localized to the distal ...
Energy Citations Database
A-DNA conformation is favored by guanine-rich sequences, such as (dG)n x (dC)n, or under low-humidity conditions. Earlier A-DNA crystal structures revealed some conformational variations which may be the result of sequence-dependent effects and/or crystal packing forces. Here we report the high-resolution crystal structure of d(AGGGGCCCCT) in two crystal ...
establishing different interactions with their animal and plant hosts, the bubonic plague agent Yersinia pestis in S. enterica and Y. pestis. The Salmonella- specific ugtL gene has no homolog in YersiniaCB transcription in Y. pestis. A) DNA sequence of the Yersinia mgtCB promoter region. The transcription start site
Ancient DNA (aDNA) samples extracted from the bone remains of six equids buried by the Vesuvius eruption in 79 AD were investigated to test pre-amplification and enzymatic repair procedures designed to enhance the rescue of nuclear genes. The extracts, which proved all positive for Equidae mtDNA amplification, proved positive only four times out of 18 when tested for ...
of nonspecific protein-DNA interactions. For nonspecific DNA binding, similar intermolecular 1 H-PRE profiles for comparison. We show that the 1HN-PRE profiles for the non- specific HMGB-1A/DNA and specific SRY/DNA-terminus, the 1HN-PRE profiles for the two complexes should be essentially identical if the DNA- binding
resolution of the methylation pattern of each allele, the DNA samples were subjected to further diges- tion+ Figure 2. Variation of Allelic Methylation in Two Human Tissues (A) DNA isolated from peripheral blood Figure 3. Inheritance of Variant Methylation Patterns of the JCZ67 Locus EaN@&r DNA samples isolated from
Recombinant Human VEGF Source: A DNA sequence encoding the 165 amino acid residue variant of human VEGF (Leung, D.W. et al., 1989, Science 246:1306) was expressed in Sf 21 cells using a baculovirus expression system and the protein purified by sequential
Cancer.gov
Identifying the causes of past epidemics depends on the specific detection of pathogens in buried individuals; this field of research is known as paleomicrobiology, an emerging field that has benefited from technological advances in microbiology. For almost 15 years, the detection, identification, and characterization of microbes in ancient environmental and human specimens emerged on the basis of ...
blotting has 2 main drawbacks. First, the DNA must be intact or at least not badly degraded. The molecules are amplified, the PCR test works with partially degraded DNA; however, some DNA samples can be degraded1 BIOL 101 H Lab DNA FINGERPRINTING LABORATORY EXERCISE Introduction A. DNA and Genetic Identity
aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing. PMID:9647790
Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) ...
...the real-time polymerase chain reaction test for Mycoplasma gallisepticum (MGLP ReTi). (a) DNA extraction . Use Qiagen Qiamp Mini Kit for DNA extraction or equivalent validated technique/procedure. This kit utilizes the following...
...Mycoplasma gallisepticum and M. synoviae. (a) DNA isolation. Isolate DNA from 1 mL of eluate from tracheal swabs in PBS...Centrifuge as above and transfer the supernatant DNA to a nuclease-free tube. Estimate the DNA...
Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that ...
Conservation biologists understand that linking demographic histories of species at risk with causal biotic and abiotic events should help us predict the effects of ongoing biotic and abiotic change. In parallel, researchers have started to use ancient genetic information (aDNA) to explore the demographic histories of a number of species present in the Pleistocene fossil ...
Inappropriate expression of 3-methyladenine (3MeA) DNA glycosylases has been shown to have harmful effects on microbial and mammalian cells. To understand the underlying reasons for this phenomenon, we have determined how DNA glycosylase activity and substrate specificity modulate glycosylase effects in Escherichia coli. We compared the effects of two ...
Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by postmortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide ...
Details of the mechanism of DNA replication in the slow growing pathogen Mycobacterium tuberculosis (M. tb) are unknown. The dnaA and dnaN gene products are essential for chromosome replication and growth of a bacterium. Here we analyzed the transcriptional activity at the oriC locus in M. tb that includes dnaA, dnaN and recF. dnaA and dnaN are each ...
Alterations in the epigenetic programming of sex differences in the brain may underlie sexually dimorphic neurodevelopmental disorders. Sex differences have been found in DNA methyltransferases 3a, DNA methylation patterns, MeCP2, and nuclear corepressor within the developing brain. Natural variations in these epigenetic mechanisms have profound ...
-affinity variant of MS2 coat protein, fused to a monomer of the LexA DNA-binding protein. We show that the use, this protein consists of a LexA/MS2 coat protein fusion. A hybrid RNA binds to the MS2 por- tion via tandem MS2 this problem. The common strains used in the three-hybrid system, such as L40coat, contain a fusion protein
gclAtc*AtPAy�Ay*AQcIA#L*A0kDA> iAV�*A�.PA�OA�pAFj}AS9&AWr*ALk*A8*P A2 ...... A�9*A �B*M^A2$Ac�*A�N�A*\\gA*�WASe*A��AT�dA **AѫA Y ...
development. Nat Rev Genet 2002; 3:662-73. 3 Bird A. DNA methylation patterns and epigenetic memory. Genes Dev I, et al. Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene:129-32. 18 Kawasaki H, Taira K. Induction of DNA methylation and gene silencing by short interfering RNAs
Construction of Expression Plasmid DNA GUS ( 2.1) pBluescript SK (-) gusA ( uidA) pQE31 T5 promoter gusA (inducible gene) GUS (glucuronides) gus operon GUS, glucuronide-specific permease, GusC GUS gusA (reporter gene) GUS 2.1 DNA E. coli pBlueGus (pBluescript gusA DNA
DNAs from the genomes of Clostridium perfringens and Cytophaga johnsonii display orthodox A-DNA and B-DNA structures despite their high (A+L) nucleotide content. Unique structures, such as those found for synthetic DNAs having specific special sequences, do therefore not necessarily occur for DNAs having more random base sequence even if these have unusual base compositions. ...
The LADI-III diffractometer at the Institut Laue�Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)2 in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion�water networks that ...
TF aTF degrade degrade DNA TF RNA TF DNA A RNA A Andrew Phillips - BioConcur 2004 17 #12;Gene Regulation_TF() protein_A RNA_TF rna_TF() !RNA_TF degrade'() translate() protein_TF degrade() degrade() DNA() degrade() DNA_A transcribe() tail() transcribe'() rna_A DNA_TF transcribe() tail() transcribe'() rna
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in ...
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from �modern� DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be �gold ...
BackgroundLeprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae ...
Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed ...
We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from ...
Increased spontaneous mutation is associated with increased cancer risk. Here, by using a model system, we show that spontaneous mutation can be increased several hundred-fold by a simple imbalance between the first two enzymes involved in DNA base excision repair. The Saccharomyces cerevisiae MAG1 3-methyladenine (3MeA) DNA glycosylase, when expressed at ...
Escherichia coli has two DNA glycosylases for repair of DNA damage caused by simple alkylating agents. The inducible AlkA DNA glycosylase (3-methyladenine [m3A] DNA glycosylase II) removes several different alkylated bases including m3A and 3-methylguanine (m3G) from DNA, whereas the constitutively expressed Tag ...
Anaplasma organisms are observed in erythrocytes from goats with anemia and weight loss in Kenya. Three anaplasmas have been isolated in nature, Anaplasma ovis, Anaplasma marginale, and Anaplasma centrale. The two recognized species, A. ovis and A. marginale, are known to infect goats. Since only A. ovis causes clinical disease in goats, the Anaplasma species in goats in Kenya were identified. To ...
As a significant association has been established between residual ancient DNA (aDNA) and histological preservation, the morphological identification or confirmation of preserved cell residue in ancient tissues would greatly facilitate aDNA studies and enhance the definitiveness of their conclusions. However, morphological differentiation of cell residue ...
In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA ...
The environmental bacterium Listeria monocytogenes survives and replicates in a variety of diverse ecological niches that range from the soil to the cytosol of infected mammalian cells. The ability of L. monocytogenes to replicate within an infected host requires the expression of a number of secreted bacterial gene products whose expression is regulated by the transcriptional activator PrfA. PrfA ...
Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad ...
BackgroundThe GP5+/GP6+ PCR assay is a well-established HPV detection technique. This study has examined the effects of incorporating 'hot start' and 'touchdown' steps into the protocol. In addition, dTTP was substituted with dUTP to permit contamination control measures against carry-over PCR product.MethodsFirstly, HPV-16 was amplified from SiHa cell DNA (0.1 ng�100 ng) diluted in a background ...
Alterations in the epigenetic programming of sex differences in the brain may underlie sexually dimorphic neurodevelopmental disorders. Sex differences have been found in DNA methyltransferase 3a, DNA methylation patterns, MeCP2 and nuclear co-repressors within the developing brain. Variations in these epigenetic mechanisms can have profound consequences ...
Teeth, the hardest substance in the human body, are frequently all that remain of a mortuary population from which direct human presence can be gleaned. As such their morphology is invaluable to physical anthropologists and investigators in allied disciplines. Methods currently used for purposes of extracting DNA from dental remains--e.g. bone-milling, crushing, and sectioning--result in total ...
US Patent & Trademark Office Database
A dual approach for studying the dynamics and function of DNA is proposed. Soliton-like excitations may occur under certain conditions and, via an electromagnetic signal that can modulate the soliton energy, the transition B-DNA (resting state) ..-->.. A-DNA (active state) can take place. On the other hand, the Hamiltonian describing this transition can be used to construct ...
Nocardia species are ubiquitous in the environment and can be found worldwide. Direct inhalation remains the most commonly attributed route of infection with Nocardia asteroides complex, causing 50% of invasive infections. Improved molecular methods have identified a significant proportion of N. asteroides complex isolates to be Nocardia cyriacigeorgica. We report a case of a 58-year-old male ...
Concanavalin A (con A) bound to Sepharose beads stimulates human peripheral blood lymphocytes and as with soluble con A, DNA synthesis can be prevented by the addition of methyl-..cap alpha..-mannoside (MAM) 1 hr after exposure to mitogen. In contrast to the response of cells stimulated with soluble con A, addition of MAM 24 hr after the start of ...
Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep biosynthesis under mild conditions with all reactants simultaneously present in solution. If the latter approach could be applied in the laboratory, it could improve the ease, speed ...
DNA damage incurred during the process of chromosomal replication has a particularly high possibility of resulting in mutagenesis or lethality for the cell. The SOS response of Escherichia coli appears to be well adapted for this particular situation and involves the coordinated up-regulation of genes whose products center upon the tasks of maintaining the integrity of the replication fork when it ...
The ability to predict macromolecular conformations from sequence and thermodynamic principles has long been coveted but generally has not been achieved. We show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From this, a "triplet code" of A-DNA propensities was derived as energetic rules for predicting ...
A generally applicable approach for amplification and subsequent sequencing using commercially available dye primers is described. The polymerase chain reaction primers, one of which is biotinylated, are tagged at their 5' end with sequences of commercial sequencing primers. After purification and strand separation on streptavidin-coated magnetic beads, both strands are sequenced automatically on ...
BackgroundNew polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. ...
Specific and sensitive amplification of major outer membrane protein (MOMP) gene (ompA) DNA sequences of Chlamydia species with various MOMP genotypes was achieved by a two-step polymerase chain reaction (PCR). Degenerate, inosine-containing oligonucleotide primers homologous to the 5' and 3' ends of the translated regions of all chlamydial MOMP genes were ...
The putative two-component system BfrAB is involved in Streptococcus gordonii biofilm development. Here, we provide evidence that BfrAB regulates the expression of bfrCD and bfrEFG, which encode two ABC transporters, and bfrH, which encodes a CAAX amino-terminal protease family protein. BfrC and BfrE are ATP-binding proteins and BfrD, BfrF and BfrG are homologous membrane- spanning polypeptides. ...
Nucleosomes from chicken erythrocytes, with DNA containing an average of 144 base pairs, were alkylated with (/sup 3/H)methylnitrosourea. The level of alkylation of the nucleosomal DNA was 48% of that of free DNA. The histones had approximately one tenth the radioactivity of the DNA. There was no statistically significant difference between alkylation of nucleosome bases in the major vs. minor ...
The initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. DnaA also binds to many sites around the chromosome, outside oriC, and acts as a transcription factor at several of these. In low-G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, ...
We recently identified 21 structural proteins in the virion of Spodoptera frugiperda ascovirus 1a (SfAV1a), a virus with a large, double-stranded DNA genome of 157 kbp, which attacks species of the lepidopteran family Noctuidae. The two most abundant virion proteins were the major capsid protein and a novel protein (P64) of 64 kDa that contained two distinct domains not known previously to occur ...
Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic ...
A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the ...
Rickettsioses are recognized as important emerging vector-borne infections of humans worldwide. Previous reports documented the presence of two spotted fever group rickettsiae in Israel, Rickettsia conorii israelensis and Rickettsia felis. The aim of this study was to characterize the diversity of rickettsiae in ticks collected from vegetation and the ground, from different parts of Israel. ...
Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. One form of CMT, CMT type 1A, is characterized by uniformly decreased nerve conduction velocities, usually shows autosomal dominant inheritance, and is associated with a large submicroscopic duplication of the p11.2-p12 region of chromosome 17. A cohort of 75 unrelated patients diagnosed clinically with CMT and ...
Hydration around the DNA fragment d(C5T5).(A5G5) is presented from two molecular dynamics simulations of 10 and 12 ns total simulation time. The DNA has been simulated as a flexible molecule with both the CHARMM and AMBER force fields in explicit solvent including counterions and 0.8 M additional NaCl salt. From the previous analysis of the DNA structure B-DNA conformations were found with the ...
The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based ...
The question of the origins of the dog has been much debated. The dog is descended from the wolf that at the end of the last glaciation (the archaeologically hypothesized period of dog domestication) was one of the most widespread among Holarctic mammals. Scenarios provided by genetic studies range from multiple dog-founding events to a single origin in East Asia. The earliest fossil dogs, dated ...
Although exosites 1 and 2 regulate thrombin activity by binding substrates and cofactors and by allosterically modulating the active site, it is unclear whether there is direct allosteric linkage between the two exosites. To begin to address this, we first titrated a thrombin variant fluorescently labeled at exosite 1 with exosite 2 ligands, HD22 (a DNA ...
Porcine circovirus type 2 (PCV2) is an economically important pathogen. It has been demonstrated that PCV2 DNA can be detected in boar semen by PCR; however, the biological relevance of this is unknown. The objectives of this study were to determine if semen positive for PCV2 DNA is infectious (1) in a swine bioassay, or (2) when used for artificial insemination. For the first objective, ...
BackgroundProgress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible ...
Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. ...
N-Methylpurine-DNA glycosylase (MPG) initiates base excision repair in DNA by removing a wide variety of alkylated, deaminated, and lipid peroxidation-induced purine adducts. In this study, we tested the role of excised base on MPG�s enzymatic activity. After the reaction, MPG produced two products: free damaged base and AP-site containing DNA. Our results showed that MPG excises 1, ...
The E2A proteins, E12 and E47, are basic helix-loop-helix (bHLH) proteins essential for the B-cell lineage. Initially identified as immunoglobulin enhancer-binding proteins, they have also been shown to activate immunoglobulin enhancer-based reporters in transient transfection assays. Here, we examine the relationship between E2A DNA binding activity and ...
In buffers containing selected transition metal salts, DNA binds to mica tightly enough to be directly imaged in the buffer in the atomic force microscope (AFM, also known as scanning force microscope). The binding of DNA to mica, as measured by AFM-imaging, is correlated with the radius of the transition metal cation. The transition metal cations that effectively bind DNA to mica are Ni(II), ...
DNA glycosylases, such as the Mag1 3-methyladenine (3MeA) DNA glycosylase, initiate the base excision repair (BER) pathway by removing damaged bases to create abasic apurinic/apyrimidinic (AP) sites that are subsequently repaired by downstream BER enzymes. Although unrepaired base damage may be mutagenic or recombinogenic, BER intermediates (e.g. AP sites ...
Dnmt3a-C, the catalytic domain of the Dnmt3a DNA-(cytosine-C5)-methyltransferase, is active in an isolated form but, like the full-length Dnmt3a, shows only weak DNA methylation activity. To improve this activity by directed evolution, we set up a selection system in which Dnmt3a-C methylated its own expression plasmid in E. coli, and protected it from ...
The platination processes of DNA bases with second- and third-generation Pt(II) anticancer drugs have been investigated using density functional theory (DFT) combined with the conductor-like dielectric continuum model (CPCM) approach, in order to describe their binding mechanisms and to obtain detailed data on the reaction energy profiles. Although there is no doubt that a Pt-N7 bond forms during ...
Objective: To describe the clinical and pathological findings of two large mainland Chinese kindreds with vitreous amyloidosis and associated transthyretin mutation. Methods: Twenty individuals from two kindreds with vitreous amyloidosis were ascertained. The transtheretin (TTR) gene of each individual was analyzed, and a clinical examination was obtained on the index patient. Results: Vitreous ...
BackgroundThis study reports progress in assembling a DNA barcode reference library for Ephemeroptera, Plecoptera, and Trichoptera ("EPTs") from a Canadian subarctic site, which is the focus of a comprehensive biodiversity inventory using DNA barcoding. These three groups of aquatic insects exhibit a moderate level of species diversity, making them ideal for testing the feasibility of DNA ...
LysR-type transcriptional regulators (LTTRs) form the largest family of bacterial regulators acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes. The LTTR, CrgA, from the human pathogen Neisseria meningitidis, is upregulated during bacterial�host cell contact. Here, we report the crystal structures of both ...
Oligonucleotide-directed site-specific mutagenesis was used to systematically shorten the hydrophobic region within the signal peptide of the Escherichia coli outer membrane protein OmpA. DNA encoding the wild type and mutant OmpA signal peptides were then fused in frame to DNA encoding the mature regions of Staphylococcus aureus nuclease A and TEM ...
The Aleutian Islands were colonized, perhaps several times, from the Alaskan mainland. Earlier work documented transitions in the relative frequencies of mtDNA haplogroups over time, but little is known about potential source populations for prehistoric Aleut migrants. As part of a pilot investigation, we sequenced the mtDNA first hypervariable region (HVRI) in samples from two archaeological ...
To ensure proper timing of chromosome duplication during the cell cycle, bacteria must carefully regulate the activity of initiator protein DnaA and its interactions with the unique replication origin oriC. Although several protein regulators of DnaA are known, recent evidence suggests that DnaA recognition sites, in multiple genomic locations, also play an important role in controlling assembly ...
The polymerization of RecA on individual double-stranded DNA molecules is studied. A linear DNA (? DNA, 48.5 Kb), anchored at one end to a cover glass and at the other end to an optically trapped 3-?m diameter polystyrene bead, serves as a template. The elongation caused by RecA assembly is measured in the presence of ATP and ATP[?S]. By using force extension and hydrodynamic recoil, a value of ...
Outer membrane protein P1 from Haemophilus influenzae type b MinnA was purified and partially characterized. Antiserum was generated against the purified protein and was used to immunologically screen a lamba EMBL3 genomic library prepared from strain MinnA DNA. A 4.2-kilobase-pair EcoRI-BamHI fragment containing the P1 gene was subcloned into pBR322. The ...
We report on a novel approach to predict the mode of genotoxic action of chemicals using a series of DNA damage specific bioluminescent bacteria. For this, a group of seven different DNA damage sensing recombinant bioluminescent strains were employed. Each of these strains was tested against model DNA damaging agents, such as mitomycin C (MMC), 1-methyl-1-nitroso-N-methylguanidine (MNNG), ...
Poly(ADP-ribose) polymerase 1 (PARP-1) is a DNA-binding enzyme that is activated by DNA breaks, converting them into an intracellular signal via poly(ADP-ribosyl)ation of nuclear proteins. Negatively charged polymers of ADP-ribose (PAR) attached to PARP-1 itself and histones lead to chromatin relaxation, facilitating the access of base excision/single strand break repair proteins and activating ...
SummaryThe essential proteins DnaB, DnaD, and DnaI of Bacillus subtilis are required for initiation, but not elongation, of DNA replication, and for replication restart at stalled forks. The interactions and functions of these proteins have largely been determined in vitro based on their roles in replication restart. During replication initiation in vivo, it is not known if these proteins, and the ...
Structural studies showed that Dnmt3a has two interfaces for protein-protein interaction in the heterotetrameric Dnmt3a/3L C-terminal domain complex: the RD interface (mediating the Dnmt3a-3a contact) and the FF interface (mediating the Dnmt3a-3L contact). Here, we demonstrate that Dnmt3a-C forms dimers via the FF interface as well, which further oligomerize via their RD interfaces. Each RD ...
We have investigated the effect of nitrogen laser irradiation (337 nm) on viability of clinical isolates of Mycobacterium tuberculosis. Bacteria were exposed to a nitrogen laser (average power 2.0 mW) in vitro at power density of 70 +/- 0.7 W/m2 for 0-30 min, and the cell viability was determined by luciferase reporter phage (LRP) assay. Immediately after laser exposure, all the clinical isolates ...
Moraxella bovis expresses an iron-repressible 79-kDa outer-membrane protein, IrpA. DNA and N-terminal amino acid sequence analysis indicate that IrpA is closely related to FrpB of Neisseria meningitidis, FetA of Neisseria gonorrhoeae and CopB of Moraxella catarrhalis. The results of manganese mutagenesis and a gel-shift assay suggested that the ...
Helicases are ubiquitous enzymes involved in nucleic acid metabolism. The PcrA DNA helicase is an essential bacterial protein involved in rolling circle plasmid replication and DNA repair. Recent crystal structures of PcrA bound to DNA indicate that a flexible loop mediates a functionally important rigid-body-domain rotation. In this study, we report ...
There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV, the RecA DNA repair protein in bacteria, and all proteins involved in mRNA splicing and translation. We extend the Vienna Package for quantitatively modeling the secondary structure of nucleic acids to include proteins which bind to unpaired ...
The human androgen-receptor gene (HUMARA; GenBank) contains a highly polymorphic trinucleotide repeat in the first exon. The authors have found that the methylation of HpaII and HhaI sites less than 100 pb away from this polymorphic short tandem repeat (STR) correlates with X inactivation. The close proximity of the restriction-enzyme sites to the STR allows the development of a PCR assay that ...
Simple and novel nuclease models have been synthesized. These involve metal-binding ligand 1,4,7,10-tetraazlcyclododecane (cyclen) tethered to an acridine ring (a DNA-binding group) by amide linkers of various lengths. Binding of these probes to DNA was studied by monitoring changes in their UV-visible spectra affected by the presence of DNA. Titration of ...
Far-UV irradiation of DNA leads to the dimerization of pyrimidine bases, resulting in the formation of cyclobutane type dimers and (6�4) photoproducts. In the dry state, an additional thymine dimeric photolesion, the spore photoproduct, is also generated. While most photoproducts are expected to be produced between adjacent pyrimidines, little attention has been paid to lesions involving bases ...
BackgroundA DNA vaccine expressing glycoprotein C (gC) of duck plague virus (DPV) was evaluated for inducing immunity in ducks. The plasmid encoding gC of DPV was administered via intramuscular (IM) injection and gene gun bombardment.ResultsAfter immunization by both routes virus-specific serum antibody and T-cell responses developed. Vaccination of ducks ...
UV mutability of Salmonella typhimurium LT2 was eliminated in the presence of a multicopy plasmid carrying the Escherichia coli lexA/sup +/ gene. This result suggests that inducible, SOS-like functions are required for UV mutagenesis in S. typhimurium. S. typhimurium strains carrying either point or deletion mutations in topA had previously been shown to lose their mutability by UV or methyl ...
Human herpesvirus 6 and 7 (HHV-6, HHV-7) have been associated with several neurologic syndromes and have been detected in nervous tissue from healthy persons; however, only two cases of HHV-6A have been reported to be associated with intraocular inflammatory disease. Vitreous fluid was tested from 101 patients, including 69 samples from patients with ocular inflammation including CMV retinitis, ...
The addition of various metabolic inhibitors (uncouplers, cyanide, arsenate, ionophores) separately or together (for example, arsenate and an uncoupler) or even harsher methods of energy depletion did not prevent bacteriophage T5 from injecting its first-step-transfer DNA (a DNA segment 3 micron long) into the cytoplasm of host cells. The same indifference ...
A 68-kDa heat-stress protein (HSP68) has been purified from cell-suspension cultures of tomato (Lycopersicon peruvianum L.). Antibodies raised against HSP68 cross-react with the Escherichia coli heat-stress protein DnaK. HSP68 was found to be a hydrophilic, ATP-binding protein. Immunological analysis of subcellular fractions and immunogold-labelling of ultrathin sections showed consistently that ...
HIV integration predominantly occurs in introns of transcriptionally active genes. To study the impact of the integration site on HIV gene expression, a complete HIV-1 provirus (with GFP as a fusion with Nef) was inserted into bacterial artificial chromosomes (BACs) at three sites previously identified in latent T cells of patients: topoisomerase II (Top2A), ...
The sloppy paired (slp) locus consists of two genes, slp1 and slp2, both of which encode proteins containing a forkhead domain (a DNA-binding motif). Previous work has shown that a severe segmentation phenotype is obtained only when both slp genes are deleted. Here we examine the functional redundancy of the locus in more detail. The phenotypes of embryos ...
Generic primers are available for detecting bacterial genes required for almost every reaction of the biological nitrogen cycle, the one notable exception being napA (gene for the molybdoprotein of the periplasmic nitrate reductase) encoding periplasmic nitrate reductases. Using an iterative approach, we report the first successful design of three forward oligonucleotide primers and one reverse ...
A molecular fingerprinting assay was developed to assess the diversity of copA genes, one of the genetic determinants involved in bacterial resistance to copper. Consensus primers of the copA genes were deduced from an alignment of sequences from proteobacterial strains. A PCR detection procedure was optimized for bacterial strains and allowed the description of a novel copA genetic determinant in ...
Infectious bursal disease (IBD) is an economically important immunosuppressive disease of chickens. The IBD virus (IBDV) actively replicates in B cells and causes severe bursal damage. Generally, T cells are refractory to infection with IBDV but are known to promote virus clearance. However, the mechanisms of T cell mediated viral clearance are not well understood. In this study, we evaluated the ...
Four species of marine purple sulfur bacteria of the genus Marichromatium have been validly described. A recent re-analysis of the 16S rRNA-based similarity and genomic DNA-DNA hybridizations (DDH) of the type strains [33] suggested that some of them are so closely related that they can be considered heterotypic synonyms. Here, we report on the evaluation of the multilocus sequence analysis ...
In the present study, we investigated the effect of exposure to A static magnetic field (SMF) on cell growth, viability, and gene expression of Salmonella enterica subsp. enterica serovar Hadar. Our results indicated that SMF exposure (200 mT, 13 hours) failed to alter cellular growth but induced a decrease of colony-forming units (CFU) between 3 and 6 hours followed by an increase from 6 to 9 ...
Before an oxic cell sensitizer such as beta-ara A (a DNA-dependent DNA polymerase inhibitor) can be used in cancer treatment, it is essential to know both the influence of this type of drug on certain critical normal tissues and the role of proliferation kinetics in the radiosensitizing capacity. The biological system chosen for this in vitro study was the ...
We have analyzed DNA conformations in a series of protein-DNA complexes, and we find that a distinctive conformation--with an enlarged major groove--occurs in a number of different complexes. During this analysis, we also developed a simplified model of DNA structure that illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double-helical axis. This ...
Micro-RNAs are a class of small non-coding regulatory RNAs that impair translation by imperfect base pairing to mRNAs. For analysis of their cellular function we injected different miRNA-specific DNA antisense oligonucleotides in Drosophila embryos. In four cases we observed severe interference with normal development, one had a moderate impact and six oligonucleotides did not cause detectable ...
The psbA gene is the coding locus for a polypeptide of 32 kilodaltons that is involved in electron transport through photosystem II. The 4.9 kilobasepair (kbp) EcoRI restriction endonuclease fragment EcoI from the 145 kbp Euglena gracilis chloroplast DNA was shown to encode psbA. Five transcripts of size 3.1, 2.8, 2.3, 1.8, and 1.2 kilobases were detected by hybridization of psbA probes to ...
A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double-helical domain is connected to each of its neighbors via two or more Holliday-junction-like reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a ...
A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double-helical domain is connected to each of its neighbors via two or more Holliday-junctionlike reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a five-parameter ...
Complementation of Rhizobium leguminosarum dct mutants with a cosmid bank yielded Rhizobium meliloti homologs of the dctA, dctB, and dctD genes. The genes dctB and dctD are thought to form a two-component system which responds to the presence of C4-dicarboxylates to regulate expression of a transport protein encoded by dctA. DNA sequence analysis showed ...
In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the ...
In 2003 a variety of crafts and bone specimens were found during excavations of a Neolithic settlement near Freising, the southernmost site of the Linear Pottery Culture in Bavaria. Six cattle bones were used to extract ancient DNA (aDNA). Applying nested and touchdown PCR, two fragments of the mitochondrial (mt) DNA control region could be amplified from specimen 533/III ...
A glutamine synthetase (GS) gene, glnA, from the gram-positive obligate anaerobe Clostridium acetobutylicum was cloned on recombinant plasmid pHZ200 and enabled Escherichia coli glnA deletion mutants to utilize (NH/sub 4/)/sub 2/ as a sole source of nitrogen. The cloned C. acetobutylicum gene was expressed from a regulatory region contained within the cloned DNA fragment. glnA expression was ...
Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic ...
Conformation-sensitive gel electrophoresis (CSGE) has been introduced as the most reliable method for the screening of large and multi-exon genes because of its simplicity, sensitivity and specificity. Based on heteroduplex formation and with the use of mildly denaturing solvents, it allows detection of single-base mutations with accuracy. This is important in genes such as BRCA1 and BRCA2, in ...
P1 ParA is a member of the Walker-type family of partition ATPases involved in the segregation of plasmids and bacterial chromosomes. ATPases of this class interact with DNA non-specifically in vitro and colocalize with the bacterial nucleoid to generate a variety of reported patterns in vivo. Here, we directly visualize ParA binding to DNA using total internal reflection fluorescence microscopy. ...
The first molecular dynamics study of a series of heterospacer-expanded tricyclic bases in DNA using modified force field parameters in AMBER is detailed. The expanded purine nucleoside monomers have been designed to probe the effects of a heteroaromatic spacer ring on the structure, function, and dynamics of the DNA helix. The heterobase scaffold has been expanded with a furan, pyrrole, or ...
Background and AimsBarley (Hordeum vulgare ssp. vulgare) cultivation started between 9500 and 8400 years ago, and was a major part of ancient agriculture in the Near East. The brittle rachis is a critical trait in the domestication process.MethodsA DNA sequence closely linked to the brittle rachis complex was amplified and resequenced in a collection of ...
The DNAs of four human papillomaviruses (HPVs) that were found in the benign lesions of three patients suffering from epidermodysplasia verruciformis have been characterized. The flat wart-like lesions and the macular lesions of patient 1 contained two viruses, HPV-3a and HPV-8, respectively, whose genomes had previously been only partially characterized. The flat wart-like lesions of patient 2 ...
Previously we showed that infection of human type II airway epithelial (A549) cells with purified respiratory syncytial virus (pRSV) induced interleukin-8 transcription by a mechanism involving cytokine-inducible cytoplasmic-nuclear translocation of the RelA transcription factor. In unstimulated cells, RelA is tethered in the cytoplasm by association with the I?B inhibitor and can be released only ...
A leaching experiment, where liquid manure spiked with Salmonella enterica serovar Typhimurium (Tet(+)) DSM554 was applied to soil surfaces, was conducted on intact soil monoliths (60 cm in diameter and 100 cm long). A total of 6.5 x 10(10) CFU was applied to each column. We found that Salmonella serovar Typhimurium could be transported to a 1-m depth in loamy soil at concentrations reaching 1.3 x ...
Bacteriophage Mu DNA synthesis is initiated during transposition by replication restart proteins PriA, DnaT and either PriB or PriC. The PriA-PriC pathway requires PriA's helicase activity and other host factors that promote the orderly transition from transpososome to replisome on the Mu DNA template. The host factor MRFalpha-PR, which removes obstacles ...
SUMMARY Using cDNA microarray analysis, we isolated a cDNA clone, CaATL1 (Capsicum annuum L. Bukang AT-hook-Like gene 1), from a chili pepper plant incompatibly interacting with bacterial pathogens. The deduced amino acid sequence has a potential nuclear localization sequence and an AT-hook DNA binding motif which can bind AT-rich sequence elements. Expression of CaATL1 was specifically induced in ...
BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal ...
While increasing knowledge is accumulating about the molecular mechanisms allowing the human pathogen Helicobacter pylori to survive and to subvert host defenses, much less is known about fundamental aspects of its biology, including DNA replication. We have studied the initiation step of chromosome replication of H. pylori and particularly the interaction between the initiator protein DnaA and ...
Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine ...
The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, ...
Recently, we have proposed a novel strategy for a cell-specific gene therapy system based on responses to intracellular signals. In this system, an intracellular signal that is specifically and abnormally activated in the diseased cells is used for the activation of transgene expression. In this study, we used protein kinase C (PKC)? as a trigger to activate transgene expression. We prepared a ...
Poly(ADP-ribose) polymerase 1 (PARP-1) is a zinc-finger DNA-binding enzyme that is activated by binding to DNA breaks. Poly(ADP-ribosyl)ation of nuclear proteins by PARP-1 converts DNA damage into intracellular signals that activate either DNA repair by the base-excision pathway or cell death. A family of 18 PARPs has been identified, but only the most abundant, PARP-1 and PARP-2, which are both ...
A bank of 892 human autoimmune serum samples was screened by indirect immunofluorescence on human tissue culture HT-29 cells. Seven serum samples that stain 4 to 10 bright dots in cell lines of several different mammals, including humans, monkeys, rats, and pigs, were identified. Immunofluorescence experiments indicate that these antigens, called nuclear dot (ND) antigens, are distinct from ...
BackgroundA major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens ...
The protective effect of cyclic stable nitroxide free radicals, having SOD-like activity, against oxidative damage was studied by using Escherichia coli xthA DNA repair-deficient mutant hypersensitive to H{sub 2}O{sub 2}. Oxidative damage induced by H{sub 2}O{sub 2} was assayed by monitoring cell survival. The metal chelator 1,10-phenanthroline (OP), which ...
The diazotrophic bacteria collectively known as "rhizobia" are important for establishing symbiotic N(2)-fixing associations with many legumes. These microbes have been used for over a century as an environmentally beneficial and cost-effective means of ensuring acceptable yields of agricultural legumes. The most widely used phylogenetic marker for identification and classification of rhizobia has ...
Since their first detection in 1988, penicillin-resistant Streptococcus pneumoniae isolates have rapidly spread in Iceland to account for close to 20% of all pneumococcal disease in that country by 1993. The major component (70%) of the resistant pneumococci identified from 1989 to 1992 was the progeny of a single multidrug-resistant clone (Icelandic clone) with a homogeneous chromosomal ...
The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) ...
High mobility group box-1 A box (HMGB1A) is an anti-inflammatory peptide originating from HMGB1. A previous report demonstrated that recombinant HMGB1A could deliver DNA into cells. Lung epithelial-specific gene delivery is required for the gene therapy of various lung diseases such as acute lung injury. In this study, a lung epithelial-specific DNA carrier was produced by linking the lung ...
An aerobic, spore-forming, moderately halophilic bacterium, strain BH260(T), was isolated from a salt lake in China. Cells of this strain were found to be motile rods with flagella. The organism grew optimally at 30-32 degrees C and pH 8.0 in the presence of 12-15% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a clade with the type strains of the ...
Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To investigate, we characterized yeast Rad51 H352A and H352Y mutants, and solved the ...
Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding properties essential for partition; it binds sopC to form a partition complex, which recruits SopA, and it also coats DNA to prevent non-specific ...
Tomato leaf curl virus (ToLCV) is a member of family geminiviridae that constitute rapidly emerging group of phytopathogens posing threat to a large number of vegetable crops worldwide. Three different genomes are found to be associated with ToLCV viz., DNA-A, DNA-B and beta satellite DNA. MicroRNAs (miRs) are known to govern several fundamental processes ...
Heterologous prime-boost regimens utilizing BCG as a prime vaccine probably represent the best hope for the development of novel tuberculosis (TB) vaccines. In this study, we examined the immunogenicity and protective efficacy of DNA vaccine (pcD685A) expressing the fusion protein of Ag85A and ESAT-6 (r685A) and its booster effects in BCG-immunized mice. The recombinant r685A fusion protein ...
Expression of the lysine decarboxylase gene (cadA) of Escherichia coli is induced upon external acidification. To dissect the molecular mechanisms responsible for this regulation, we analyzed a 4.2-kbp region upstream from cadA. DNA sequencing revealed two long open reading frames upstream of and on the same strand as cadA. One of these, cadB, is 444 ...
Preclinical biodistribution studies with INGN 007, an oncolytic adenovirus (Ad) vector, supporting an early stage clinical trial were conducted in Syrian hamsters, which are permissive for Ad replication, and mice, which are a standard model for assessing toxicity and biodistribution of replication-defective (RD) Ad vectors. Vector dissemination and pharmacokinetics following intravenous ...
Glycogen storage disease type la (GSD1a) is an autosomal recessive metabolic disorder caused by a deficiency in glucose-6-phosphatase (G6Pase). We analyzed the G6Pase genes of two unrelated Chinese families with GSD1a. DNA sequencing of all five exons and the exon-intron boundaries revealed a G T transversion at nucleotide 727 (727G-->T) in exon 5, ...
Residues of the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) are ubiquitously found in aquatic biota but potential adverse effects in fish are fairly unknown. To identify molecular effects and modes of action of EHMC we applied a gene expression profiling in zebrafish using whole genome microarrays. Transcriptome analysis and validation of targeted genes were performed after 14 days of ...
The purpose of the current study was to determine whether heat shock protein 70 (Hsp70) directly regulates forkhead box O (FOXO) signaling in skeletal muscle. This aim stems from previous work demonstrating that Hsp70 overexpression inhibits disuse-induced FOXO transactivation and prevents muscle fiber atrophy. However, although FOXO is sufficient to cause muscle wasting, no data currently exist ...
As an inhibitor of cyclin-dependent kinases, p16(INK4A) is an important tumour suppressor and inducer of cellular senescence that is often inactivated during the development of cancer by promoter DNA methylation. Using newly established lymphoblastoid cell lines (LCLs) expressing a conditional EBNA3C from recombinant EBV, we demonstrate that EBNA3C inactivation initiates chromatin remodelling that ...
From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18(th) century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to ...
From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by ...
When CHO-K1 cells monolayers are grown in Ham's F-12 culture medium containing 10% fetal calf serum (medium A) exogenous thymidine (dThd) is degraded to thymine by a putative dThd phosphorylase. Thymine is then poorly incorporated into cellular DNA. When 2 mM deoxycytidine (dCyd) is added to medium A (medium B) no degradation of exogenous dThd occurs; rather dThd is consumed in the ...
Despite the widespread use of bones in ancient DNA (aDNA) studies, relatively little concrete information exists in regard to how the DNA in mineralised collagen degrades, or where it survives in the material's architecture. While, at the macrostructural level, physical exclusion of microbes and other external contaminants may be an important feature, and, at the ...
CCR4, an evolutionarily conserved member of the CCR4-NOT complex, is the main cytoplasmic deadenylase. It contains a C-terminal nuclease domain with homology to the endonuclease-exonuclease-phosphatase (EEP) family of enzymes. We have determined the high-resolution three-dimensional structure of the nuclease domain of CNOT6L, a human homologue of CCR4, by X-ray crystallography using the ...
Complementation group A of xeroderma pigmentosum (XP) represents one of the most prevalent and serious forms of this cancer-prone disorder. Because of a marked defect in DNA excision repair, cells from individuals with XP-A are hypersensitive to the toxic and mutagenic effects of ultraviolet light and many chemical agents. We report here the isolation of the XP-A ...
The Rhodobacter sphaeroides cytochrome c/sub 2/ functions as a mobile electron carrier in both aerobic and photosynthetic electron transport chains. Synthetic deoxyoligonucleotide probes, based on the known amino acid sequence of this protein (M/sub r/ 14,000), were used to identify and clone the cytochrome c/sub 2/ structural gene (cycA). DNA sequence ...
In iron-limited environments plant-growth-stimulating Pseudomonas putida WCS358 produces a yellow-green fluorescent siderophore called pseudobactin 358. Ferric pseudobactin 358 is efficiently taken up by cells of WCS358 but not by cells of another rhizophere-colonizing strain, Pseudomonas fluorescens WCS374. A gene bank containing partial Sau3A DNA ...
Microarray gene expression profiling studies have demonstrated immune response gene signatures that appear predictive of outcome in follicular lymphoma (FL). However, measurement of these marker genes in routine practice remains difficult. We have therefore investigated the immune response in FL using real-time polymerase chain reaction (PCR) to measure expression levels of 35 candidate Indicator ...
Chemical epigenetic manipulation of Penicillium citreonigrum led to profound changes in the secondary metabolite profile of its guttate. While guttate from control cultures exhibited a relatively simple assemblage of secondary metabolites, the guttate collected from cultures treated with 50 ?M 5-azacytidine (a DNA methyltransferase inhibitor) were highly ...
To identify Rhodobacter capsulatus nif genes necessary for the alternative nitrogenase, strains carrying defined mutations in 32 genes and open reading frames of nif region A, B or C were constructed. The ability of these mutants to grow on nitrogen-free medium with molybdenum (Nif phenotype) or in a nifHDK deletion background on medium without molybdenum (Anf phenotype) was tested. Nine nif genes ...
Use of electricity is a hallmark of the industrialization process, but there has been no suspicion that electricity could increase the risk of cancer. Recently, however, a number of epidemiologic studies have suggested that electromagnetic fields (EMF) may do just that. Although few cancer experiments have been done yet, there are a number of biological effects of EMF reported in the literature ...
Vanadate induces DNA strand breaks in cultured human fibroblasts at doses that are relative to the occupational exposure. Oxovanadium compounds also exert preventive effects against chemical carcinogenesis in animals and form complexes with DNA in vivo. This study was designed to examine the interaction of calf-thymus DNA with VO2+ and VO3 ions in aqueous solution at physiological pH, with a ...
The SeqA protein regulates chromosome initiation and is involved in segregation in Escherichia coli. One SeqA protein binds to two hemi-methylated GATC sequences to form a stable SeqA-DNA complex. We found that binding induced DNA bending, which was pronounced when the two sequences were on the same face of the DNA. Two SeqA molecules bound cooperatively to each pair of ...
During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10?000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cytb) DNA fragments from 4200 to 800?000 y.a. specimens ...
The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still ...
A high-angle neutron fibre diffraction study of the hydration of A-DNA has been performed using the single-crystal diffractometer D19 at the Institut Laue-Langevin (Grenoble, France). The sample was prepared using deuterated DNA extracted from E. Coli cells cultured on deuterated nutrients. In common with our previous neutron fibre diffraction studies of DNA, this work exploits the ability to ...
Prostate cancer exhibits tremendous variability in clinical behavior, ranging from indolent to lethal disease. Better prognostic markers are needed to stratify patients for appropriately aggressive therapy. By expression profiling, we can identify a proliferation signature variably expressed in prostate cancers. Here, ...
Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance the basic helical frame to show the shapes and ...
