Multiple DNA Sequences Research Articles

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.

RFLP-kenzy: a new bioinformatics tool for in silico detection of key restriction enzyme in RFLP technique

BackgroundToday, several bioinformatics tools are available for analyzing restriction fragment length data. RFLP-kenzy is a new bioinformatic tool for identifying restriction key enzyme that cut at least 1 sequence and a maximum of n-1 sequence.ResultsThis bioinformatic tool helps researchers to select appropriate enzymes that yield different RFLP patterns, especially from overly identical sequences with single nucleotide mutation or other small variations. By using RFLP-kenzy, multiple DNA sequences could be analyzed simultaneously and the key enzymes list is provided. The present paper also demonstrates the ability of RFLP-kenzy to identify the key enzymes through the analysis of 16S rRNA sequences and the complete genome of various genera of microorganisms.ConclusionFrom the results, several key enzymes were provided indicating the importance of this new tool in the selection of appropriate restriction enzymes.

The Methods and Strategies to Improve the Stability of Nano Antibody

Because of the advantages of simple structure, easy modification, low immunogenicity, good stability, strong specificity and strong affinity, nano-antibodies have broad development space in clinical practice. Compared with traditional antibodies, nano antibodies are easier to store and transport, and after denaturation in high temperature, chemical, pressure and other environments, they can still be efficiently recombined, thereby regaining affinity for antigens. The structure and stability of nano antibody were studied. Multiple DNA sequence repair with the same sequence, easily modified amino acid replacement, protein net charge change, unnatural disulfide bond introduction and CDR supervariable region transfer was used to control the stability of the protein. The implementation of this project is expected to lay a foundation for improving its application in the fields of drug therapy, diagnosis and biosensing.

Biological Control Activities of Rhizosphere Fungus Trichoderma virens T1-02 in Suppressing Flower Blight of Flamingo Flower (Anthurium andraeanum Lind.).

Flower blight caused by Neopestalotiopsis clavispora is an emerging disease of flamingo flower (Anthurium andraeanum Lind.) that negatively impacts flower production. The use of rhizosphere fungi as biocontrol agents is an alternative way to control this disease instead of using synthetic fungicides. This research aimed to screen the potential of rhizosphere fungi, Trichoderma spp., with diverse antifungal abilities to control N. clavispora and to reduce flower blight in flamingo flowers. A total of ten isolates were tested against N. clavispora by dual culture assay, and T1-02 was found to be the most effective isolate against N. clavispora, with inhibition of 78.21%. Morphology and molecular phylogeny of multiple DNA sequences of the genes, the internal transcribed spacer (ITS), translation elongation factor 1-α (tef1-α), and RNA polymerase 2 (rpb2) identified isolate T1-02 as Trichoderma virens. Sealed plate method revealed T. virens T1-02 produced volatile antifungal compounds (VOCs) against N. clavispora, with inhibition of 51.28%. Solid-phase microextraction (SPME) was applied to trap volatiles, and GC/MS profiling showed VOCs emitted from T. virens T1-02 contained a sesquiterpene antifungal compound-germacrene D. The pre-colonized plate method showed that T. virens T1-02 aggressively colonized in tested plates with inhibition of 100% against N. clavispora, and microscopy revealed direct parasitism onto fungal hyphae. Furthermore, the application of T. virens T1-02 spore suspension reduced the disease severity index (DSI) of flower blight in flamingo flowers. Based on the results from this study, T. virens T1-02 displays multiple antagonistic mechanisms and has the potential ability to control flower blight of flamingo flowers caused by N. clavispora.

Multiplexed DNA and Protease Detection with Orthogonal Energy Transfer on a Single Quantum Dot Scaffolded Biosensor.

Almost all pathogens, whether viral or bacterial, utilize key proteolytic steps in their pathogenesis. The ability to detect a pathogen's genomic material along with its proteolytic activity represents one approach to identifying the pathogen and providing initial evidence of its viability. Here, we report on a prototype biosensor design assembled around a single semiconductor quantum dot (QD) scaffold that is capable of detecting both nucleic acid sequences and proteolytic activity by using orthogonal energy transfer (ET) processes. The sensor consists of a central QD assembled via peptidyl-PNA linkers with multiple DNA sequences that encode complements to genomic sequences originating from the Ebola, Influenza, and COVID-19 viruses, which we use as surrogate targets. These are hybridized to complement strands labeled with a terbium (Tb) chelate, AlexaFluor647 (AF647), and Cy5.5 dyes, giving rise to two potential FRET cascades: the first includes Tb → QD → AF647 → Cy5.5 (→ = ET step), which is detected in a time-gated modality, and QD → AF647 → Cy5.5, which is detected from direct excitation. The labeled DNA-displaying QD construct is then further assembled with a RuII-modified peptide, which quenches QD photoluminescence by charge transfer and is recognized by a protease to yield the full biosensor. Each of the labeled DNAs and peptides can be ratiometrically assembled to the QD in a controllable manner to tune each of the ET pathways. Addition of a given target DNA displaces its labeled complement on the QD, disrupting that FRET channel, while protease addition disrupts charge transfer quenching of the central QD scaffold and boosts its photoluminescence and FRET relay capabilities. Along with characterizing the ET pathways and verifying biosensing in both individual and multiplexed formats, we also demonstrate the ability of this construct to function in molecular logic and perform Boolean operations; this highlights the construct's ability to discriminate and transduce signals between different inputs or pathogens. The potential application space for such a sensor device is discussed.

Development of First in Class DNA-Zip Code Drug Conjugate (ZDC) in Multiple Myeloma

Multiple myeloma is a heterogeneous malignant plasma cell disorder with complex molecular and genetic abnormalities. Significant advances have been made in the treatment of multiple myeloma; however, a large proportion of patients fail to attain a favorable response and relapse. Due to efficacy and toxicity, the development of drug conjugates for multiple myeloma has been limited. Our lab discovered that circulating tumor DNA (ctDNA) serves as a cell-specific mechanism for genetic transmission. Certain retrotransposon sequences within the ctDNA were identified as being crucial for the tropism of ctDNA to target tumor cells (Cinar et al bioRxiv.2022). We therefore query whether these transposons can be exploited for the targeted drug delivery. To do so, chemically synthetize and CY5-labeled multiple retrotransposons DNA sequences (a.k.a Zip Codes, ZC) to perform high through put screening assessing for cell targeting. Our findings showed that the AluSp and MER11c DNA sequences (MM-ZC1 and 2) with unique MM mutations were the most efficient and specific DNA sequences for targeting myeloma cells. Furthermore, Flow cytometry and CYTOF validated the specific MM cell targeting on full bone marrow samples from MM patients. Based on this analysis we used MMZC1 for further drug development. We design a drug conjugation approach for the MMZC and screen various drugs for their killing potential. Two potent MM ZC drug conjugates (ZDC) were identified by high throughput viability screening assay: ZC-DM4, a microtubule inhibitor, and ZC-Carfilzomib, an irreversible proteasome inhibitor. We move forward exploration with ZC-DM4 due to limited carfilzomib-linker drug availability. Experiments cancer cell lines in vitro demonstrated that MMZC-DM4 had a potent killing effect on MM cells (IC50: 3.25 nM) but not on other cancer cell lines. These results were the validated in vivo. Maximum tolerated dosing studies (MTD) demonstrated excellent tolerability in all doses (ranges from 1 to 20 mg of MMZC-DM4/Kg (equivalent to 0.007-0.149 mg of DM4/kg). To look for an efficacy signal of MMZC-DM4, MM xenograft mice were given MMZC-DM4 twice a week for three weeks. Due to limitations in production, we treated the animals biweekly with three distinct low doses of MMZC-DM4: 1.9, 3.75, and 7.5 mg/kg (equivalent to 0.014, 0.028, and 0.056 mg of DM4/kg) and compared their response to mice not treated with MMZC-DM4 and mice treated weekly with bortezomib. MMZC-DM4 at such small doses reduced the tumor by 30% without affecting body weight, WBC, HB, AST, or platelets. In contrast, Bortezomib was associated with 90% growth inhibition at the expense of significant weight loss that required treatment interruptions and thrombocytopenia. Currently, investigations are being conducted to examine the therapeutic efficacy of greater doses of MMZC-DM4. This study described the first-in-class MM targeted medicine delivery employing an MM zic code drug conjugate. Our findings suggest new method for targeted delivery therapeutic cargo material directly to cancer cells that could revolutionize cancer treatment.

Nuclear DNA segments homologous to mitochondrial DNA are obstacles for detecting heteroplasmy in sugar beet (Beta vulgaris L.).

Heteroplasmy, the coexistence of multiple mitochondrial DNA (mtDNA) sequences in a cell, is well documented in plants. Next-generation sequencing technology (NGS) has made it feasible to sequence entire genomes. Thus, NGS has the potential to detect heteroplasmy; however, the methods and pitfalls in heteroplasmy detection have not been fully investigated and identified. One obstacle for heteroplasmy detection is the sequence homology between mitochondrial-, plastid-, and nuclear DNA, of which the influence of nuclear DNA segments homologous to mtDNA (numt) need to be minimized. To detect heteroplasmy, we first excluded nuclear DNA sequences of sugar beet (Beta vulgaris) line EL10 from the sugar beet mtDNA sequence. NGS reads were obtained from single plants of sugar beet lines NK-195BRmm-O and NK-291BRmm-O and mapped to the unexcluded mtDNA regions. More than 1000 sites exhibited intra-individual polymorphism as detected by genome browsing analysis. We focused on a 309-bp region where 12 intra-individual polymorphic sites were closely linked to each other. Although the existence of DNA molecules having variant alleles at the 12 sites was confirmed by PCR amplification from NK-195BRmm-O and NK-291BRmm-O, these variants were not always called by six variant-calling programs, suggesting that these programs are inappropriate for intra-individual polymorphism detection. When we changed the nuclear DNA reference, a numt absent from EL10 was found to include the 309-bp region. Genetic segregation of an F2 population from NK-195BRmm-O x NK-291BRmm-O supported the numt origin of the variant alleles. Using four references, we found that numt detection exhibited reference dependency, and extreme polymorphism of numts exists among sugar beet lines. One of the identified numts absent from EL10 is also associated with another intra-individual polymorphic site in NK-195mm-O. Our data suggest that polymorphism among numts is unexpectedly high within sugar beets, leading to confusion about the true degree of heteroplasmy.

Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate.

Novel enzymatic methods are poised to become the dominant processes for de novo synthesis of DNA, promising functional, economic, and environmental advantages over the longstanding approach of phosphoramidite synthesis. Before this can occur, however, enzymatic synthesis methods must be parallelized to enable production of multiple DNA sequences simultaneously. As a means to this parallelization, we report a polymerase-nucleotide conjugate that is cleaved using electrochemical oxidation on a microelectrode array. The developed conjugate maintains polymerase activity toward surface-bound substrates with single-base control and detaches from the surface at mild oxidative voltages, leaving an extendable oligonucleotide behind. Our approach readies the way for enzymatic DNA synthesis on the scale necessary for DNA-intensive applications such as DNA data storage or gene synthesis.

Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications.

The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species. The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica. The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.

Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae

Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.

A New Species of Neoscytalidium hylocereum sp. nov. Causing Canker on Red-Fleshed Dragon Fruit (Hylocereus polyrhizus) in Southern Thailand.

During 2020-2021, cultivated red-fleshed dragon fruit (Hylocereus polyrhizus) in Phatthalung province, southern Thailand, was infected with canker disease in all stages of growth. Small, circular, sunken, orange cankers first developed on the cladodes of H. polyrhizus and later expanded and became gray scabs with masses of pycnidia. The fungi were isolated using the tissue transplanting method and identified based on the growth of the fungal colony, and the dimensions of the conidia were measured. Their species level was confirmed with the molecular study of multiple DNA sequences, and their pathogenicity was tested using the agar plug method. Morphological characterization and molecular identification of the internal transcribed spacer (ITS), translation elongation factor 1-α (tef1-α) and β-tubulin (tub) sequences revealed the fungal pathogen to be a new species. It was named Neoscytalidium hylocereum sp. nov. The biota of the new species, N. hylocereum, was deposited in Mycobank, and the species was assigned accession number 838004. The pathogenicity test was performed to fulfil Koch's postulates. N. hylocereum showed sunken orange cankers with a mass of conidia similar to those observed in the field. To our knowledge, this is the first report of H. polyrhizus as a host of the new species N. hylocereum causing stem cankers in Thailand.

Biosensor model based on single hairpin structure for highly sensitive detection of multiple targets.

Nowadays, due to the genetic information carried by nucleic acids, they can serve as a biomarker for the early diagnosis of diseases, including tumors and cardiovascular disease, among others, making genetic testing a hotspot of biomedicine. Therefore, we have designed a universal fluorescence biosensor that can detect multiple DNA sequences with good performance. In our designed biosensor, λ exonuclease is used due to its ability to digest double-stranded DNA from the phosphorylated 5'- end and promote the targeted cycle. The exonuclease is introduced into a DNA hairpin containing a target recognition sequence. Hence, with the target, λ exonuclease-assisted targeted recycling can be activated. The hydrolyzed DNA hairpin triggers a strand displacement reaction between the hairpin probe (H1) and F-Q double DNA strand (F-Q), increasing the distance between the fluorescent chain (F) and quenching chain (Q); thus the fluorescence signal is emitted. It is exciting that the detection limit of the biosensor is 300 fM, which is relatively low, and there is an excellent linear relationship between fluorescence intensity and target concentration. Moreover, the biosensor we designed has universal applicability in the detection of other genes, and the range of RSD is 1.28-2.45%. Hence, it has good application prospects and practical value in the early detection of some diseases and the design of fluorescent biosensors.

Ultrasensitive Fluorescence Detection and Imaging of MicroRNA in Cells Based on a Hyperbranched RCA-Assisted Multiposition SDR Signal Amplification Strategy.

Herein, an innovative fluorescent sensor was courageously empoldered for precise and ultrasensitive detection and imaging of target miRNA-21 through the agency of a dextrous target-motivated polymerization/nicking DNA nanomachineries based on a hyperbranched rolling circle amplification (HB-RCA)-assisted multiposition strand displacement reaction (SDR) signal amplification approach. Impressively, the ingenious technique not only realized target recycling via polymerization/nicking DNA nanomachineries but also involved HB-RCA amplification induced by the released transformation target as the repeated signal amplification. Most importantly, HB-RCA was firstly exploited to remarkably increase the local concentration and collision efficiency of the templates and primers, which could simultaneously generate multiple repeated DNA sequences as initiators to supply substantial banding positions for SDR, removing the massive fluorescence-resonance-energy-transfer (FRET) DNA duplexes from the repeated DNA sequences to remarkably avert the self-quenching of the fluorescence signal due to self-aggregation caused by the winding of the HB-RCA products, thereby leading to a conspicuously improved signal amplification multiplier. As proof of concept, an ingenious technique effectively and accurately distinguished target miRNA-21 even with a tiny change in cells compared to the conventional fluorescence in situ hybridization (FISH) approach. Moreover, the proposed fluorescent method apparently discriminated drug-manipulative miRNA expression level abnormities. Therefore, the proposed cascade nucleic acid amplification strategy could provide an epigamic avenue for ultrasensitive imaging of diverse biomarkers, which help researchers to better study the tumor mechanism, thereby unambiguously increasing cancer cure rates and reducing the risk of recurrence.

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein.

Protein-DNA binding is of a great interest due to its importance in many biological processes. Previous studies have presented many factors responsible for the recognition and specificity, but understanding the minimal informational requirements for proteins that bind to multiple DNA-sites is still an understudied area of bioinformatics. Here we focus on the hydrogen bonds displayed by the target DNA in the major groove that take part in protein-binding. We show that analyses focused on the base pair identity may overlook key hydrogen bonds. We have developed an algorithm that converts a nucleotide sequence into an array of hydrogen bond donors and acceptors and methyl groups. It then aligns these non-covalent interaction arrays to identify what information is being maintained among multiple DNA sequences. For three different DNA-binding proteins, Lactose repressor, controller protein and λ-CI repressor, we uncovered the minimal pattern of hydrogen bonds that are common amongst all the binding sequences. Notably in the three proteins, key interacting hydrogen bonds are maintained despite nucleobase mutations in the corresponding binding sites. We believe this work will be useful for developing new DNA binding proteins and shed new light on evolutionary relationships.

Rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses

BackgroundThis paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping.ResultsThe assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation.ConclusionsAn R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development.

Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.

Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.

Parallel multiple DNA sequence alignment using genetic algorithm and asynchronous advantage actor critic model

Multiple sequence alignment plays a crucial role in bioinformatics field. In this process, sequences are compared by establishing residue-residue correspondence among related sequences. In this paper, we present a novel framework that uses genetic algorithm and asynchronous advantage actor critic model to look for the optimal multiple DNA sequence alignment. In the first step, we generate initial alignments by applying the T-COFFEE method. Then, we recursively use a genetic algorithm to find the optimal fragmentation of the pre-aligned sequences. At this stage, the obtained short sub alignments are introduced to the A3C model for parallel alignments. So, the optimal multiple alignment of the original sequences represents the fusion of sub-alignments. To evaluate the performances of the proposed approach, we used the Balibase 3.0 benchmark and compared to TCOFFEE, MAFFT and RLALIGN methods. The obtained experimental results show that the proposed approach can achieve solutions of competitive quality.

Design of Effective Lossless Data Compression Technique for Multiple Genomic DNA Sequences

Design of Effective Lossless Data Compression Technique for Multiple Genomic DNA Sequences

1447Gastric histopathology by Helicobacter pylori cagA status in Arctic Canada

Abstract Background Our community-driven projects address concerns of Canadian Arctic Indigenous communities about Helicobacter pylori (Hp) infection, responsible for elevated gastric cancer mortality in the region. Community research partners wished to learn whether bacterial characteristics determine severity of Hp-related disease in their communities. We aimed to describe gastric histopathology by cagA genotype of Hp isolated from residents of 7 Indigenous communities in the Northwest Territories and Yukon. Methods Participants underwent gastroscopy with 5-6 biopsies taken for histopathological assessment and 2 biopsies taken for tissue culture during 2008-2017. We used multiple PCR reactions and DNA sequence analysis to classify Hp genotypes as cagA+ or cagA-. A single pathologist used the updated Sydney classification system to grade severity of 5 gastric pathology outcomes: Hp density; chronic gastritis; active gastritis; atrophy; and intestinal metaplasia. We estimated prevalence of each outcome with 95% confidence intervals (CI) by gastric subsite and cagA status. Results Of 262 Hp isolates assessed, 142 (54%) were cagA+. Prevalence of moderate-high Hp density, severe chronic gastritis, moderate-severe active gastritis, atrophy, and metaplasia were (%[CI]): respectively, 78[70-85], 44[36-53], 65[56-72], 55[46-63], 25[18-33] in cagA+ participants and 61[52-70], 35[27-44], 31[23-40], 32[23-41], 8[4-15] in cagA- participants. cagA+ participants had higher prevalence of all outcomes in antrum and corpus. Conclusion Hp-infected Indigenous residents of Arctic Canada who harbored cagA-positive strains had higher prevalence of more severe gastric pathology than those with cagA-negative strains. Key messages Community-driven research answers questions posed by those who bear the disease burden.

Multiple DNA Sequence Alignment Based on Genetic Algorithms and Divide-and-Conquer Techniques

Multiple DNA sequence alignment is one of the important research topics of bioin- formatics. Because of the huge length of DNA sequences of advanced organisms, some re- searchers used divide-and-conquer techniques to cut the sequences for decreasing the space complexity for sequence alignment. Because the cutting points of sequences of the existing methods are fixed at the middle or the near-middle points, the performance of sequence align- ment of the existing methods is not good enough. In this paper, we present a new method for multiple DNA sequence alignment using genetic algorithms and divide-and-conquer techniques to choose optimal cut points of multiple DNA sequences. The experimental results show that the proposed method is better than the existing method for dealing with multiple DNA sequence alignment.