Search For DNA Sequences Research Articles

Molecular Detection of Anaplasma phagocytophilum, Babesia odocoilei, Babesia species and Borrelia burgdorferi Sensu Lato in Songbirds

The blacklegged tick, Ixodes scapularis, is known to carry various tick-borne zoonotic pathogens with the potential to cause debilitating human and animal diseases. Juvenile I. scapularis parasitize songbirds and, perhaps, these avifauna are competent hosts of common microbial pathogens. We extracted brachial venous blood from 18 ground-foraging passerine birds that were parasitized by I. scapularis larvae and nymphs. Using molecular identification, namely PCR, DNA sequencing, and Basic Local Alignment Search Tool (BLAST), we targeted Anaplasma phagocytophilum, Babesia spp. and Borrelia burgdorferi sensu lato. Overall, 15 (83%) of 18 passerine birds were positive for 3 microbial zoonotic pathogens that comprised of A. phagocytophilum (n = 8), Babesia odocoilei (n = 6), Babesia spp. 20-5A74 (n = 1), and B. burgdorferi sensu lato (n = 9). The pathogen load consisted of 8 singles, 5 doubles, and 2 triples. One novel Babesia sp. (Babesia spp. 20-5A74) was found, and the remaining Babesia infections were B. odocoilei. Our findings reveal that ground-foraging, passerine birds are avian hosts of zoonotic pathogens. We provide the first-ever documentation that songbirds are hosts of B. odocoilei. Based on our data, B. odocoilei outnumbered other Babesia spp., and elucidated the authentic fact that B. odocoilei is the predominant Babesia sp. in North America. As avian hosts, passerine birds play a significant role in the enzootic transmission cycle of B. burgdorferi sensu lato, A. phagocytophilum, and Babesia species.

Stretch Profile: A pruning technique to accelerate DNA sequence search

Abstract DNA sequence similarity search has been used by scientists to facilitate biological research. Over the years, more sequences are added to databases, making them constantly larger. Existing sequence search techniques usually focus on the improvement of sequence search algorithms to make the search faster, ignoring the possibility of reducing unrelated sequences from the search. This paper presents a pruning technique to accelerate DNA sequence search based on a novel Stretch Profile created from stretches of consecutive base characters: A-Stretch, C-Stretch, G-Stretch, and T-Stretch. The Stretch Profile is pre-generated for each sequence in a sequence database. During the search, the Stretch Profile of the query sequence is generated for comparison. The sequences in the database whose profiles do not match the Stretch Profile of the query sequence are excluded from the search, resulting in the reduction of search space, and consequently, search time. For evaluation, we compare sequence retrievals from the Greengenes database and processing time when using only BLAST and when using the proposed pruning technique with BLAST. The results show that the proposed pruning technique can reduce the search time by 30.43% up to 63.74% depending on the length of input query, while maintaining a sensitivity of 1.00 when compared to the result of the original BLAST search.

RhopH3, rhoptry gene conserved in the free-living alveolate flagellate Colpodella sp. (Apicomplexa)

In this study, we investigated morphological, immunological and molecular characteristics of Colpodella sp. (American Type Culture Collection 50594) in a diprotist culture containing Bodo caudatus as prey using Plasmodium rhoptry specific antibodies and oligonucleotide primers targeting Plasmodium falciparum rhoptry genes. In culture, Colpodella sp. attached to its prey using the apical end with attachment lasting for approximately 20 min while the cytoplasmic contents of the prey were aspirated into the posterior food vacuole of Colpodella sp. Encystment of Colpodella sp. was observed following feeding. Indirect immunofluorescence assay (IFA) and confocal microscopy using P. falciparum rhoptry specific antibodies showed intense reactivity with cytoplasmic vesicles of Colpodella sp. Bodo caudatus from diprotist and monoprotist (ATCC 30395) cultures showed weak background reactivity. Giemsa staining permitted differentiation of both protists. Genomic DNA isolated from the diprotist culture was used in polymerase chain reaction (PCR) with oligonucleotide primers targeting the P. falciparum rhoptry genes RhopH3, RhopH1/Clag3.2 and RAMA. Primers targeting exon 7 of the P. falciparum RhopH3 gene amplified an approximately 2 kb DNA fragment from the diprotist DNA template. DNA sequence and BLAST search analysis of the amplified product from diprotist DNA identified the RhopH3 gene demonstrating that the RhopH3 gene is conserved in Colpodella sp.

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

Dynamics of nuclear proteins in crowded chromatin has only been poorly understood. Here, we address the diffusion, target search, and structural dynamics of three proteins in a model chromatin using coarse-grained molecular simulations run on the K computer. We prepared two structures of chromatin made of 20 nucleosomes with different nucleosome densities and investigated dynamics of two transcription factors, HMGB1 and p53, and one signaling protein, ERK, embedded in the chromatin. We found fast and normal diffusion of the nuclear proteins in the low-density chromatins and slow and subdiffusional movements in the high-density chromatin. The diffusion of the largest transcription factor, p53, is slowed by high-density chromatin most markedly. The on rates and off rates for DNA binding are increased and decreased, respectively, in the high-density chromatin. To our surprise, the DNA sequence search was faster in chromatin with high nucleosome density, though the diffusion is slower. We also found that the three nuclear proteins preferred to bind on the linker DNA and the entry and exit regions of nucleosomal DNA. In addition to these regions, HMGB1 and p53 also bound to the dyad.

Molecular identification of a root apical cell-specific and stress-responsive enhancer from an Arabidopsis enhancer trap line

BackgroundPlant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment.ResultsUsing nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line. Subsequently, a 2000 bp plant DNA-fragment (Ertip1) upstream of the insert position of the coding T-DNA was in silico analysed, revealing certain putative promoter/enhancer cis-regulatory elements. Cloning and transformation of this DNA fragment and its truncated segments tagged with or without 35S minimal promoter (35Smini), all of which were fused with a GFP or GUS reporter, allowed to detect GFP and GUS expression mediated only by Ertip1 + 35mini (PErtip1+35Smini) specifically in the Arabidopsis root tip region. The PErtip1+35Smini activity was further tested to be strong and stable under many different growth conditions but suppressed by cold, salt, alkaline pH and higher ammonium and phosphorus.ConclusionThis work describes a promising strategy to isolate a tissue-/cell-specific enhancer sequence from the enhancer trap lines, which are publically available. The reported synthetic promoter i.e. PErtip1+35Smini may provide a valuable and potent molecular-tool for comprehensive investigation of a gene function related to root growth and development as well as molecular engineering of root-architectural formation aiming to improve plant growth.

Identification of Bacteria in Raindrops from Daegu and Pohang Area

산업화가 가속화되며 대기 오염으로 인한 각종 문제들이 끊임없이 제기되고 있다. 또한 미세먼지 및 황사로 인한 문제들이 심각한 수준에 이르렀다. 대기 오염은 인간 생활에 큰 변화를 가져오고 있으며, 오염된 대기가 빗물에 섞여 내리면서 수질 오염으로도 이어질 수 있다. 우리는 대기와 수질 오염의 매개 역할을 할 수 있는 빗물의 오염 여부에 대해 연구할 필요가 있다고 생각했다. 일반적인 빗물의 오염으로 알려진 산성비에 대해서는 잘 알려져 있지만 대기 오염으로 인해 빗물의 미생물에 변화가 있는지는 잘 알려져 있지 않다. 이에 우리는 대구 및 포항 지역 4개 장소 (대구 북구 복현동, 대현동, 수성구 황금동, 포항 북구 우현동)에서 빗물을 수집하여 각 빗물 샘플에서 미생물을 배양하였다. 이후 유전자증폭 (PCR)을 통해 각 미생물의 16S rDNA 획득하고, DNA 염기서열 분석 (DNA sequencing)과 유사 DNA 검색 (BLAST search) 을 진행하여 미생물을 동정하였다. 또한 각 미생물의 서식지, 특성 및 병원성 유무 등을 조사하였다. 배양 결과 18종의 미생물이 동정 되었으며, 이 중 병원성을 지니는 미생물도 8종 확인되었다. 이 연구결과는 빗물의 오염에 대한 미생물학적 정보를 제공할 수 있을 것으로 기대한다.Currently, air pollutions such as micro-dust and yellow dust have reached a critical level that negatively affect on human health in Korea. Moreover, air pollution makes a big difference in human life style, and polluted air can also lead to water pollution by merged to raindrops. We thought we needed to elucidate the contamination of rainwater that could serve as a bridge for air and water pollution. Acid rain is commonly known as the contamination of rainwater as well. However, there are little information if air pollution causes changes in the microbial life of rain. In response, we collected raindrops from four locations in Daegu and Pohang cities; Bokhyeon-dong, Daehyeon-dong, Hwanggeum-dong in Daegu, and Woohyeon-dong in Pohang. Each of the raindrop samples were incubated at 37°C for cultivating microorganisms using two types of media LB and R2A. Afterwards, 16S rDNA of each microorganism was amplified through PCR, and DNA sequencing and DNA BLAST search was performed. We also examined the habitat, characteristics, and pathogenic presence of each microorganism. Eight microorganisms were identified as pathogenic from eighteen samples. This study may provide the microbiological information about the contamination of rainwater.

Abstract 674: HPV16 was the preponderant type of HPV infection in cutaneous squamous cell carcinoma

Abstract Purpose: Human papillomavirus (HPV) has been well established as a causative factor in mucosal oropharyngeal cancer and anogenital surface malignancies. However, its etiological role in cutaneous squamous cell carcinoma (cSCC) is still debated. The aim of this study is to identify the presence of HPV types in cSCC and identify their associations with cSCC. Methods: 77 cSCC blocks from 54 patients underwent DNA isolation and a broad spectrum of HPV PCR tests to detect the presence of HPV genotypes by the use of a universal primer pair GP5+/GP6+. The resultant PCR products were cloned to T Vectors and subsequently underwent DNA sequencing and Nucleotide BLAST search to identify the HPV types in cSCC. To ensure the accuracy of the HPV PCR test, 16 blocks from 10 head and neck SCC (oropharyngeal) patients were also included in the HPV presence and type analyses. Cutaneous SCC patients’ demographics, pathology and clinical parameters were compared and analyzed statistically in conjunction with the HPV test results. Results: HPV DNA was found in 37 of 77 (48.1%) blocks representing 32 of 54 (59.3%) cSCC patients. HPV16 was the preponderant type of HPV Infection, accounting for 28 of 32 (87.5%) and 30 of 37 (81.08%) HPV positive patients and blocks. Other HPV genotypes found included HPV18, 57, 10, 2, accounting for 4 of 32 (12.5%), 2 of 32 (6.25%), 2 of 32 (6.25%), 2 of 32 (6.25%) of the HPV positive patients and 4 of 37 (10.81%), 2 of 37 (5.41%), 2 of 37 (5.41%), 2 of 37 (5.41%) of the HPV positive blocks, respectively. HPV infection was significantly associated with the cSCC tumor size in this cohort of patients. Tumors with a size of ≤20mm were more frequently associated with HPV. Moreover, the average tumor size of the HPV positive group was also significantly smaller than that of the HPV negative group. Conclusions: HPV infection is very commonly found in cSCC patients and HPV16 is the major type of HPV involved in cSCC oncogenesis, accounting for >80% of HPV infections. HPV is a contributing factor, which appears to be contributing to a smaller size of cSCC, which may improve the prognostic classification of patients to provide a new insight into tumorigenesis. Citation Format: Gang Shi, Anne C. Fischer, Jonathan M. Zenilman, Patti E. Gravitt, Max Fischer, Inbal B. Sander, Jonathan D. Cuda, Janis M. Taube, Mohammed Lilo, W P Andrew Lee, Anthony P. Tufaro. HPV16 was the preponderant type of HPV infection in cutaneous squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 674. doi:10.1158/1538-7445.AM2017-674

Abstract 2718: Genomic and microRNAome subtraction identifies pathogenic viral sequences in pancreatic ductal adenocarcinoma

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is by far the most common type of pancreatic cancer. It constitutes about 90% of tumors of the exocrine pancreas. The aggressive nature of PDAC along with its poor diagnostic markers contributes to a high lethality of this disease. Studies from other cancer entities implicate the role of viruses in tumor development. However, there have been no established reports about virus(es) associated with pancreatic cancer. The present study identified a virus by genomic and digital microRNAome subtraction between healthy and PDAC patients, suggesting that this virus may play a role in carcinogenesis. Experimental procedures: Representational difference analysis (RDA) was utilized to perform an experimental genome-wide search for DNA sequences that occur in PDAC but not in normal tissues. Ten healthy and ten PDAC tissue DNA samples were used for the generation of representations and subtractive hybridization. The difference products (DPs) so obtained were paired end sequenced on the Illumina MiSeq platform. The sequencing data were aligned against the viral RefSeq database. We also did in silico subtraction of microRNA content (miRNA-seq) of PDAC samples. Eight PDAC samples were analyzed for viral sequences using relevant RefSeq databases. The two approaches (RDA and miRNA-seq) were pursued in parallel. RT-qPCR analysis and the in vitro functional characterization of viral sequences in PDAC cell lines were respectively performed using hydrolysis probes and second generation microRNA mimic systems. Stable cell lines expressing viral microRNA and luciferase were produced using lentivirus for mice in vivo studies. Results and Summary: We found DNA sequences of a virus in the difference products of RDA whose signature was also implicated in the microRNA analysis. Further, using RT-qPCR, we identified that a particular microRNA from this virus is expressed at significantly higher levels in PDAC samples than in normal tissue. This observation was also verified by droplet digital PCR analysis. Non-metastatic PDAC cell lines overexpressing viral microRNA showed significant invasion against relevant controls, interestingly with no significant change in proliferation. We are currently analyzing the functional consequences of these viral sequences and their involvement in carcinogenesis. Conclusion: From two different robust approaches, these findings strongly indicate viral sequences associated with PDAC that could affect pathways relevant to tumor development. Citation Format: Mohanachary Amaravadi, Agnes Hotz-Wagenblatt, Sandeep Kumar Botla, Pouria Jandaghi, Mehdi Manoochehri, Nathalia Giese, Markus W. Büchler, Andrea S. Bauer, Jörg D. Hoheisel. Genomic and microRNAome subtraction identifies pathogenic viral sequences in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2718. doi:10.1158/1538-7445.AM2015-2718

Are the Available DNA Sequence Alignments and Search Tools Reliable for Alu Research?

The results of most bioinformatics and microbiology research studies that use SINEs depend entirely on the mechanism used to detect and count these element instances in the genome. Hence, the reliability and accuracy of the DNA sequence alignment and search tool is vital for genetic researches. This research report presents the findings from testing the reliability of some popular DNA Sequence alignment and search (SA&S) tools using a test/known genomic sequence. The findings reveal the need for novel tool design.

Lower esophageal microbiota species are affected by the eradication of Helicobacter pylori infection using antibiotics.

The aim of this study was to investigate the effect of Helicobacter pylori (H. pylori) infection on the lower esophageal microbiota and the eradication of H. pylori through the use of antibiotics. Forty-five BALB/C mice were randomly divided into negative control, infection and treatment groups. The mice were sacrificed and DNA was extracted from the lower esophageal microbiota. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was performed to determine the composition of the microbiota. Quantity One® 1-D Analysis Software was used for the analysis of the DGGE profiles. The different bands from the groups were amplified with 16S rDNA V6 region primers. DNA sequencing and Basic Local Alignment Search Tool analysis were performed for the identification of the bands. H. pylori colonization led to severe ulcers in the stomachs of the mice, and these ulcers were alleviated by antibiotic treatment. The infection group had an increased number of bacterial species in the stomach compared with the control and treatment groups. DGGE fingerprinting of the lower esophagus showed that there were significant differences in the number of bands (P<0.05), diversity index and abundance among the groups (P<0.05); however, no significant differences in homogeneity were observed (P>0.05). Although the composition of flora species in the lower espohagus varied, the dominant species, and their relative contents, were similar in the control, infection and treatment groups. The present study provided a microecological basis for the understanding of the pathogenesis of lower esophageal diseases, following the eradication of H. pylori infection with antibiotics.

Detection and characterization of class 1 integron-associated gene cassettes from Pseudomonas aeruginosa isolates in southern Taiwan

In this study, detection and characterization of class 1 integron-associated gene cassettes from Pseudomonas aeruginosa isolates in southern Taiwan were investigated. The study focused on the association between integron-associated resistance gene cassettes and multidrug resistance in P. aeruginosa isolates. Using polymerase chain reaction amplification, DNA sequencing, and basic local alignment search tool analysis, a total of 22 different types of gene cassette arrays were detected in 162 class 1 integron-positive P. aeruginosa isolates. We first identified 11 different types of new gene cassette arrays within class 1 integron in P. aeruginosa isolates, including aac(6′)-II-catB2-aadA2, aac(6′)-II-aadA2, aac(6′)-II-catB2, aacA4-aadA15, aacC1-orfA-orfB-aadA1, cm1A-aadA1, catB3-blaOxA-10-aadA15, aacA4-catB8-aadA1, aadB-orfF1-aadA11, dfrB1, and dfrB4a-aacA4-aacA4-aadA1. Of these, aac(6′)-II-catB2-aadA2 was the most frequently found gene cassette. Twenty-one (21/162, 12.9%) strains carrying two different types of gene cassette arrays of catB3-blaOxA-10-aadA15 and aac(6′)-II-catB2-aadA2 were also simultaneously present in the P. aeruginosa isolates. A novel dfrB4a gene, different from the dfrB4 gene detected in the gene cassette array of dfrB4a-aacA4-aacA4-aadA, was characterized. A metallo-β-lactamaseo gene was also found to be carried on the gene cassette of blaVIM-3-orf2a-aacA4-aadB-aacA4 inserted in a class 1 integron obtained from meropenem-resistant P. aeruginosa isolates.

Specific DNA Sequence Search Dynamics of p53 and Effect of Acetylation of its C-Terminal Domain: Multi-Scale Simulation Study

A transcription factor p53 is composed of ordered Core and Teramerization domain and of intrinsically disordered N-terminal domain, C-terminal domain and the linker region, which prevent to elucidate the functional mechanism based on static structural analyses. In order to model the linker region supposed to play an important role, first, we performed all atom (AA) multi-canonical MD simulation of this 40 amino acid residues long region. Second, we decided the parameters of CG model so that the contact map of the CG structural ensemble was marginally same as that from the AA simulation. The SAXS profile obtained from the CG simulation using these parameters reproduces the previous experiment. Finally, we conducted the CG simulation of the system containing a full-length p53 quaternary structure and a 100 bp DNA including a p53 binding site. In the production simulation, p53 spontaneously binds to its binding site and forms a complex structure that is consistent with the electron microscopic model obtained previously. The result also revealed that p53 slides along nonspecific dsDNA with its CTD before it binds to REs, whereas, upon acetylation of the CTD, it repeats dissociation from and association to dsDNA, suggesting that previously suggested inhibitory effect of the CTD on binding of p53 to its binding site and the nullification of the inhibitory effect upon acetylation are largely attributed to the change of main search mechanism from sliding to 3D diffusion. Taken together, the result of this multi-scale simulation shed light on the problem that is difficult for conventional experimental technique to address due to the flexibility of this protein.

An Enhanced Version of Pattern Matching Algorithm using Bitwise XOR Operation

this study, a new algorithm for the traditional pattern matching problem has been proposed. This algorithm is a modified version of KMP algorithm and using bitwise XOR operation to process two characters (or bytes) in parallel, to speed up the pattern matching process. An additional loop to avoid the undesirable comparison(s) also been introduced and let the algorithm to initiate, and continue only the essential comparisons from the required location. As the new algorithm uses the principle of Finite automata which is used by KMP algorithm and Bitwise XOR operation to speed up the character match, it shows some reasonable performance improvement. Also this new algorithm is easy to implement as it doesn't require any additional/complex data structure(s) and suitable for DNA sequence search. KeywordsAlgorithm, Pattern Matching. Exact Pattern Matching.

Structure of a filament of stacked octamers of human DMC1 recombinase.

Eukaryal DMC1 proteins play a central role in homologous recombination in meiosis by assembling at the sites of programmed DNA double-strand breaks and carrying out a search for allelic DNA sequences located on homologous chromatids. They are close homologs of eukaryal Rad51 and archaeal RadA proteins and are remote homologs of bacterial RecA proteins. These recombinases (also called DNA strand-exchange proteins) promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. An octameric form of a truncated human DMC1 devoid of its small N-terminal domain (residues 1-83) has been crystallized. The structure of the truncated DMC1 octamer is similar to that of the previously reported full-length DMC1 octamer, which has disordered N-terminal domains. In each protomer, only the ATP cap regions (Asp317-Glu323) show a noticeable conformational difference. The truncated DMC1 octamers further stack with alternate polarity into a filament. Similar filamentous assemblies of DMC1 have been observed to form on DNA by electron microscopy.

3P118 転写因子p53の特異的結合部位探索・認識機構 : マルチスケールシミュレーション研究(04.核酸結合蛋白質,ポスター,日本生物物理学会年会第51回(2013年度))

3P118 転写因子p53の特異的結合部位探索・認識機構 : マルチスケールシミュレーション研究(04.核酸結合蛋白質,ポスター,日本生物物理学会年会第51回(2013年度))

DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii.

In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination.

A FAST LOCAL SEARCH ALGORITHM USING HISTOGRAM FEATURES FOR DNA SEQUENCE DATABASE

DNA sequence search is a very important topic in bioinformatics algorithm development. However, this task usually spends much computational time to search on large DNA sequence database. In this paper, we propose an efficient hierarchical DNA sequence search algorithm to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search algorithm using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the algorithm. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank se- quence data show the proposed algorithm combining histogram information and Smith-Waterman algorithm is more efficient for DNA se- quence search. Keywords- Fast search, DNA sequence, Histogram feature, Smith-Waterman algorithm, Local search.

English

DNA sequence search is a fundamental topic in bioinformatics. The Smith-Waterman algorithm achieved highest accuracy among various sequence alignment tools, but it usually spends much computational time to search on large DNA sequence database. On the contrary, BLAST and FASTA have improved the search speed by using heuristic approaches, by there is a possibility of missing an alignment or giving inaccurate output. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram based method is used to scan the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith- Waterman algorithm is then applied to each remainder sequences. Experimental results show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence search.

The RecA/RAD51 protein drives migration of Holliday junctions via polymerization on DNA

The Holliday junction (HJ), a cross-shaped structure that physically links the two DNA helices, is a key intermediate in homologous recombination, DNA repair, and replication. Several helicase-like proteins are known to bind HJs and promote their branch migration (BM) by translocating along DNA at the expense of ATP hydrolysis. Surprisingly, the bacterial recombinase protein RecA and its eukaryotic homologue Rad51 also promote BM of HJs despite the fact they do not bind HJs preferentially and do not translocate along DNA. RecA/Rad51 plays a key role in DNA double-stranded break repair and homologous recombination. RecA/Rad51 binds to ssDNA and forms contiguous filaments that promote the search for homologous DNA sequences and DNA strand exchange. The mechanism of BM promoted by RecA/RAD51 is unknown. Here, we demonstrate that cycles of RecA/Rad51 polymerization and dissociation coupled with ATP hydrolysis drives the BM of HJs.

Marcadores genéticos en hipertensión esencial

Essential hypertension (HTA) is a multifactorial disease and in Chile, its prevalence is 33.7%. There is a genetic predisposition to develop hypertension, whose magnitude is approximately 30 to 50%. At present, some factors are known to increase the risk for cardiovascular disease, but widely accepted biomarkers for screening are missing. The first studies that looked for candidate genes have focused on the renin-angiotensin--aldosterone, aducina, adrenoreceptors beta, G protein subunits, G protein signaling regulators, kinases associated with G proteins and Rho kinases. Studies of DNA sequencing search for polymorphisms and variants through single nucleotide polymorphisms, have been used to seek partnerships with complex or multifactorial diseases, like HTA. Examples of these are: components of collagen proteins, genes related to cell myocardial proteins belonging to cytochrome P450 and growth factors, among others. It is still unlikely to count in a near future with a universal marker. Most probably, a series of markers that confer susceptibility to a specific individual will have to be used in prevention programs or personalized therapy.