Comparison Of DNA Sequences Research Articles

Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering

A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence’s 3D chaos game representation can be used to compare DNA sequences without prior alignment and without truncating or padding any of the sequences. Two proposed methods inspired by shape-similarity comparison techniques show that this form of encoding can perform as well as alignment-based techniques for building phylogenetic trees. The first method uses the volume overlap of intersecting spheres and the second uses shape signatures by summarizing the coordinates, oriented angles, and oriented distances of the 3D chaos game trajectory. The methods are tested using: (1) the first exon of the beta-globin gene for 11 species, (2) mitochondrial DNA from four groups of primates, and (3) a set of synthetic DNA sequences. Simulations show that the proposed methods produce distances that reflect the number of mutation events; additionally, on average, distances resulting from deletion mutations are comparable to those produced by substitution mutations.

Graph-based analysis of DNA sequence comparison in closed cotton species: A generalized method to unveil genetic connections.

Graph theory provides a systematic method for modeling and analysing complicated biological data as an effective bioinformatics tool. Based on current trends, the number of DNA sequences in the DNA database is growing quickly. To determine the origin of a species and identify homologous sequences, it is crucial to detect similarities in DNA sequences. Alignment-free techniques are required for accurate measures of sequence similarity, which has been one of the main issues facing computational biologists. The current study provides a mathematical technique for comparing DNA sequences that are constructed in graph theory. The sequences of each DNA were divided into pairs of nucleotides, from which weighted loop digraphs and corresponding weighted vectors were computed. To check the sequence similarity, distance measures like Cosine, Correlation, and Jaccard were employed. To verify the method, DNA segments from the genomes of ten species of cotton were tested. Furthermore, to evaluate the efficacy of the proposed methodology, a K-means clustering method was performed. This study proposes a proof-of-model that utilises a distance matrix approach that promises impressive outcomes with future optimisations to be made to the suggested solution to get the hundred percent accurate result. In the realm of bioinformatics, this paper highlights the use of graph theory as an effective tool for biological data study and sequence comparison. It's expected that further optimization in the proposed solution can bring remarkable results, as this paper presents a proof-of-concept implementation for a given set of data using the proposed distance matrix technique.

Comparison of Six Measures of Genetic Similarity of Interspecific Brassicaceae Hybrids F2 Generation and Their Parental Forms Estimated on the Basis of ISSR Markers.

Genetic similarity determines the extent to which two genotypes share common genetic material. It can be measured in various ways, such as by comparing DNA sequences, proteins, or other genetic markers. The significance of genetic similarity is multifaceted and encompasses various fields, including evolutionary biology, medicine, forensic science, animal and plant breeding, and anthropology. Genetic similarity is an important concept with wide application across different scientific disciplines. The research material included 21 rapeseed genotypes (ten interspecific Brassicaceae hybrids of F2 generation and 11 of their parental forms) and 146 alleles obtained using 21 ISSR molecular markers. In the presented study, six measures for calculating genetic similarity were compared: Euclidean, Jaccard, Kulczyński, Sokal and Michener, Nei, and Rogers. Genetic similarity values were estimated between all pairs of examined genotypes using the six measures proposed above. For each genetic similarity measure, the average, minimum, maximum values, and coefficient of variation were calculated. Correlation coefficients between the genetic similarity values obtained from each measure were determined. The obtained genetic similarity coefficients were used for the hierarchical clustering of objects using the unweighted pair group method with an arithmetic mean. A multiple regression model was written for each method, where the independent variables were the remaining methods. For each model, the coefficient of multiple determination was calculated. Genetic similarity values ranged from 0.486 to 0.993 (for the Euclidean method), from 0.157 to 0.986 (for the Jaccard method), from 0.275 to 0.993 (for the Kulczyński method), from 0.272 to 0.993 (for the Nei method), from 0.801 to 1.000 (for the Rogers method) and from 0.486 to 0.993 (for the Sokal and Michener method). The results indicate that the research material was divided into two identical groups using any of the proposed methods despite differences in the values of genetic similarity coefficients. Two of the presented measures of genetic similarity (the Sokal and Michener method and the Euclidean method) were the same.

Fusarium andiyazi, a Pathogenic Species Associated with Rice Bakanae Disease in Malaysia.

Rice is the main staple food crops for the Malaysian population. Rice is also susceptible to bakanae diseases caused by some Fusarium species and reducing yield, and quality of rice also profit. In this study, several rice fields were surveyed to collect Fusarium isolates associated with bakanae disease. The morphological features of Fusarium andiyazi isolates found on infected rice plants were identified in this investigation. For biological species identification, MAT-1 (Mating type idiomorphs) bearing isolates were crossed with MAT-2 isolates. Crossing was succeeded between cross of two different mating type bearing field isolates. Consequently, there is a possibility of exchange of genetic material within the F. andiyazi population in Malaysia. The identity of the isolates was further determined up to the species level by comparing DNA sequences and phylogenetic analysis of two genes. The phylogenetic analyses of the joined dataset of translation elongation factor 1-alpha (TEF1-α) and RNA polymerase subunit II (RPB2) revealed that all the isolates were F. andiyazi. In pathogenicity tests, F. andiyazi were found to be pathogenic on the susceptible rice cultivars MR211 and MR220. Inoculated rice seedling produced typical bakanae symptom like elongation, thin and yellow leaves. F. andiyazi was further confirmed as pathogenic species by Ultra High-Performance Liquid Chromatography (UPLC) detection of Gibberellic acid (GA3) and Fusaric acid. In this study, F. andiyazi strains have been identified as the responsible pathogen for causing rice bakanae disease in Malaysia and it is the first report of F. andiyazi, as a pathogenic species on rice in Malaysia.

Fecal IgE Analyses Reveal a Role for Stratifying Peanut-Allergic Patients.

Peanut allergy (PA) is an IgE-mediated food allergy with variable clinical outcomes. Mild-to-severe symptoms affect various organs and, often, the gastrointestinal tract. The role of intestine-derived IgE antibodies in astrointestinal PA symptoms is poorly understood. This study aimed to examine fecal IgE responses in PA as a novel approach to patient endotyping. Feces and serum samples were collected from peanut-allergic and healthy children (n=26) to identify IgE and cytokines using multiplex assays. Shotgun metagenomics DNA sequencing and allergen database comparisons made it possible to identify microbial peptides with homology to known allergens. Compared to controls, fecal IgE signatures showed broad diversity and increased levels for 13 allergens, including food, venom, contact, and respiratory allergens (P<.01-.0001). Overall, fecal IgE patterns were negatively correlated compared to sera IgE patterns in PA patients, with the greatest differences recorded for peanut allergens (P<.0001). For 83% of the allergens recognized by fecal IgE, we found bacterial homologs from PA patients' gut microbiome (eg, thaumatin-like protein Acinetobacter baumannii vs Act d 2, 109/124 aa identical). Compared to controls, PA patients had higher levels of fecal IgA, IL-22, and auto-IgE binding to their own fecal proteins (P<.001). Finally, levels of fecal IgE correlated with abdominal pain scores (P<.0001), suggesting a link between local IgE production and clinical outcomes. Fecal IgE release from the intestinal mucosa could be an underlying mechanism of severe abdominal pain through the association between leaky gut epithelia and anticommensal TH2 responses in PA.

Diversity of Calonectria species from leaves and soils in diseased southern China Eucalyptus plantation

Calonectria leaf blight (CLB) is one of the best-known diseases of Eucalyptus spp., particularly in Asia and South America. Recently, typical symptoms of leaf and shoot blight caused by Calonectria spp. Were observed in a Eucalyptus plantation in the YunNan Province of southwestern China. Isolations were made from diseased leaves and top soil collected below the diseased trees to determine the causal agent of the disease and to consider the distribution characteristics of the Calonectria species. This resulted in 417 isolates, of which 228 were from leaves and 189 were from soil. Based on comparisons of DNA sequences for the act (actin), cmdA (calmodulin), his3 (histone H3), rpb2 (the second largest subunit of RNA polymerase), tef1 (translation elongation factor 1-alpha) and tub2 (β-tubulin) gene regions, as well as morphological characteristics, 11 Calonectria species were identified. These included Calonectria aciculata (0.7 %), Ca. colhounii (1.2 %), Ca. eucalypti (10.6 %) and Ca. honghensis (43.2 %) in the Ca. colhounii species complex, and Ca. aconidialis (15.3 %), Ca. asiatica (9.8 %), Ca. hongkongensis (1.0 %), Ca. ilicicola (6.0 %), Ca. kyotensis (0.5 %), and Ca. yunnanensis (11.3 %) in the Ca. kyotensis species complex. In addition, a novel species, accounting for 0.5 % of the isolates, was discovered and is described here as Ca. dianii sp. nov. in the Ca colhounii species complex. Most (99.1 %) of the isolates collected from the leaves resided in the Ca. colhounii species complex and a majority (95.8 %) of those from the soils were in Ca. kyotensis species complex. These results suggest that Calonectria spp. in the Ca. colhounii species complex infecting leaves might be adapted to that niche and that those in the Ca. kyotensis species complex are better adapted to a soil habitat.

Description of Babesia galileei sp. nov. A Piroplasmid species causing severe disease in domestic cats

BackgroundBabesiosis is a tick-borne infection caused by piroplasmid protozoa and associated with anemia and severe disease in humans, domestic animals and wildlife. Domestic cats are infected by at least six Babesia spp. that cause clinical disease.MethodsInfection with a piroplasmid species was detected by microscopy of stained blood smears in three sick cats from Israel. Genetic characterization of the piroplasmid was performed by PCR amplification of the 18S rRNA, cytochorme B (CytB) and heat shock protein 70 (HSP70) genes and the internal transcribed spacer (ITS) locus, DNA sequencing and phylogenetic analysis. In addition, Haemaphysalis adleri ticks collected from two cats were analyzed by PCR for piroplasmids.ResultsThe infected cats presented with anemia and thrombocytopenia (3/3), fever (2/3) and icterus (1/3). Comparison of gene and loci sequences found 99–100% identity between sequences amplified from different cats and ticks. Constructed phylogenetic trees and DNA sequence comparisons demonstrated a previously undescribed Babesia sp. belonging to the Babesia sensu stricto (clade X). The piroplasm forms detected included pear-shaped merozoite and round-to-oval trophozoite stages with average sizes larger than those of Babesia felis, B. leo and B. lengau and smaller than canine Babesia s.s. spp. Four of 11 H. adleri adult ticks analyzed from cat # 3 were PCR positive for Babesia sp. with a DNA sequence identical to that found in the cats. Of these, two ticks were PCR positive in their salivary glands, suggesting that the parasite reached these glands and could possibly be transmitted by H. adleri.ConclusionsThis study describes genetic and morphological findings of a new Babesia sp. which we propose to name Babesia galileei sp. nov. after the Galilee region in northern Israel where two of the infected cats originated from. The salivary gland PCR suggests that this Babesia sp. may be transmitted by H. adleri. However, incriminating this tick sp. as the vector of B. galilee sp. nov. would require further studies.Graphical

Identification and pathogenicity of Ceratocystis manginecans causing wilt disease on Acacia mangium in Sabah, Malaysia

Abstract. Yunus NM, Maid M, Yong WTL, Anthony FE, Sudin M, Taylor PWJ. 2024. Identification and pathogenicity of Ceratocystis manginecans causing wilt disease on Acacia mangium in Sabah, Malaysia. Biodiversitas 25: 2170-2182. An alarming incidence of wilt disease has been reported in an Acacia mangium plantation in Ulu Kukut, Kota Belud District, Sabah, Malaysia. Infected trees exhibited symptoms such as severe wilting, sapwood discoloration or black lesion, and a fruity-sweet odor emanating from the fermentation exudate at the wound lesion. This is the first investigation of the causal wilt pathogen in a commercial A. mangium plantation in Ulu Kukut, located in the western region of Sabah. This study aimed to identify the causal fungal pathogen from infected A. mangium trees using morphological characterization and DNA sequence comparisons for the regions of Internal Transcribed Spacer (ITS), beta-tubulin 1 (bt1), transcription elongation factor-1 alpha (tef1), guanine nucleotide-binding protein subunit beta-like protein (ms204), and second largest subunits of RNA polymerase II (rpb2). The fungal isolates shared morphological characteristics with the wilt pathogen Ceratocystis sp., including a globose base with a long neck-ended tip with ostiolar hyphae. Sequence-based phylogenetic analysis confirmed the identity of Ceratocystis manginecans, distinguishing them from all other Ceratocystis species. Bioassays inoculating phyllodes and twigs of 1-year-old A. mangium trees confirmed that C. manginecans was the cause of wilt disease. Confirming the identity of the causal agent of the increasingly destructive and severe wilt disease aids in developing effective disease management strategies for Acacia-based plantations.

How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders.

Large-scale barcoding projects help to aggregate information on genetic variability of multiple species throughout their ranges. Comparing DNA sequences of both non-conspecific and conspecific individuals from distant parts of their ranges helps to compare level of genetic isolation-by-distance patterns in different species and adaptive types. We compared mitochondrial CO1 gene sequences of 223 spiders from Georgia (Caucasus), representing 124 species and eight families, with 3097 homological sequences from spiders mostly from Europe, but also from other parts of the World. In most families, a significant isolation-by distance pattern was observed on family level. On species level, a significant isolation-by-distance was observed in 40 species, although this low proportion is most likely related to a lack of data. Simultaneously, remarkable differences in spatial structure were shown for different species. Although the majority of the studied species have a broad western Palearctic range, web-building spiders from families Araneidae, Theridiidae, and Linyphiidae are less isolated spatially than flower spiders (Thomisidae), jumping spiders (Salticidae), wolf spiders (Lycosidae), sac spiders (Clubionidae), and ground spiders (Gnaphosidae). This pattern is related with more common ballooning in web building than in actively hunting spiders, which commonly remain isolated since preglacial time. Ground spiders build the most isolated populations in the Caucasus.

Evolutionary Computation in bioinformatics: A survey

Bioinformatics is a subject that studies life phenomena by using mathematical and information science theories and techniques. Its main tasks, such as DNA sequence comparison, protein structure prediction and cell metabolism analysis, can be regarded as complex optimization problems with different characteristics. Evolutionary computing is a kind of global optimization algorithm inspired by nature. Over the years, scholars have accumulated fruitful results in solving complex optimization problems such as large-scale, dynamic, multi-modal, multi-objective and multi-constrained problems by using Evolutionary Computation algorithms, and have successfully applied to the above optimization tasks in bioinformatics. This paper mainly summarizes the work of Evolutionary Computation technologies in bioinformatics from 2019 to 2023 at multiple levels, including Genomics, Proteomics, metabolomics and molecular networks related optimization tasks, as well as further applications in disease diagnosis and drug development.

When standard DNA barcodes do not work for species identification: intermixed mitochondrial haplotypes in the Jaera albifrons complex (Crustacea: Isopoda)

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species.

Distribution of the invasive ambrosia beetle Anisandrus maiche (Coleoptera, Scolytinae) in Switzerland and first record in Europe of its ambrosia fungus Ambrosiella cleistominuta

Ambrosia beetles are highly successful as invaders because they are often transported internationally with wood packaging and other wood products and because their inbreeding mating systems facilitates establishment of invading populations. In 2022, two independent insect surveys in canton Ticino (southern Switzerland) revealed the widespread occurrence of the invasive ambrosia beetle Anisandrus maiche (Kurentzov, 1941) from southern to central-upper Ticino. This species is native to east Asia and has previously been found as a non-native invasive species in the United States, Canada, western Russia, Ukraine and, in 2021, in northern Italy. Here, we present the results of several trapping studies using different trap types (bottle traps, funnel traps and Polytrap intercept traps) and attractants and a map of the distribution of the species. In total, 715 specimens of A. maiche, all female, were trapped, and the identity of selected individuals was confirmed by morphological and molecular identification based on three mitochondrial and nuclear markers (COI, 28S and CAD). Trap samples from early April to early September 2022 in intervals of two to four weeks showed that flights of A. maiche occurred mainly from June to mid-August. Isolation of fungal associates of A. maiche from beetles trapped alive revealed the presence of four fungal species, including the ambrosia fungus Ambrosiella cleistominuta, the known mutualist of A. maiche. The identity of A. cleistominuta was confirmed by comparing DNA sequences of its nuclear, internal transcribed spacer (ITS) gene with reference sequences in NCBI and BOLDSYSTEMS. This represents the first record of A. cleistominuta in Europe. Of the other fungal associates isolated from A. maiche in Ticino, Fusarium lateritium is of note as there is a possibility that A. maiche could act as a vector of this plant pathogen. We highlight several research needs that should be addressed to gain insight into the potential impact of these non-native species and to overcome problems with heteroplasmy in COI sequences in studies of invasion and population genetics of ambrosia beetles.

Comparison of genomic DNA sequencing to anerobic cultures to detect efficacy of hydrogen peroxide at reducing cutibacterium acnes bacterial burden during primary shoulder arthroplasty

BackgroundThe purpose of this investigation is to compare Cutibacterium acnes diagnosis using culturing vs. genomic DNA sequencing (NextGen) at various timepoints and locations during primary total shoulder arthroplasty. Additionally, we intend to compare the effects of hydrogen peroxide on standard culture technique results with genomic DNA sequencing. MethodsA prospective diagnostic study of 40 patients undergoing primary total shoulder arthroplasty was performed. Intraoperatively, 4 tissue samples were collected per patient: subdermal skin edge following initial skin incision, subdermal skin edge following hydrogen peroxide soak for 5 minutes, glenohumeral joint capsule, and subdermal skin edge prior to wound closure. Each tissue specimen was collected twice (one for culture analysis and the other for genomic (NextGen) DNA sequencing analysis) for a total of 8 specimens per patient and 320 tissue specimens in total. All anaerobic cultures were held for 14 days. Each culture plate was divided into quadrants and the amount of growth was quantified. Tissue samples were collected for genomic sequencing DNA analysis. Genomic sequencing results provided relative percentage of bacteria for each specimen detected. ResultsThere were 18/40 males (45%) and no postoperative complications. Average age was 72.2 ± 11.8. Overall, 18% (29/160) of standard anaerobic cultures were positive for C. Acnes and 26% (942/160) were positive with genomic (Nextgen) DNA sequencing. When comparing the NextGen results with anaerobic standard cultures, there was a calculated negative predictive value of 85.6% and positive predictive value of 28.6%. Sensitivity of the NextGen was 41.4% and specificity was 77.1%. Bacterial culture rates did not significantly change from the beginning to the end of surgery as demonstrated on standard culturing and the NextGen analysis (P > .05). After treatment with hydrogen peroxide, the standard culturing technique showed no significant difference between the samples; however, there was a significant increase in bacterial burden (12.4%) noted with NextGen analysis (P = .0147). ConclusionNextGen culturing is a novel technique to help identify shoulder prosthetic joint infections. These results show that, NextGen is better at identifying the absence of infection, but has a high false positive rate indicative of its ability to identify contaminants as compared to standard anaerobic culturing methods. The increase in bacterial burden after peroxide treatment noted with NextGen could also be secondary to the test’s increased ability to identify both living and dead bacterial pathogens.

A novel Bartonella-like bacterium forms an interdependent mutualistic symbiosis with its host, the stored-product mite Tyrophagus putrescentiae.

A novel Bartonella-like symbiont (BLS) of Tyrophagus putrescentiae was characterized. BLS formed a separate cluster from the Bartonella clade together with an ant symbiont. BLS was present in mite bodies (103 16S DNA copies/mite) and feces but was absent in eggs. This indicated the presence of the BLS in mite guts. The BLS showed a reduction in genome size (1.6 Mb) and indicates gene loss compared to Bartonella apis. The BLS can be interacted with its host by using host metabolic pathways (e.g., the histidine and arginine metabolic pathways) as well as by providing its own metabolic pathways (pantothenate and lipoic acid) to the host, suggesting the existence of a mutualistic association. Our experimental data further confirmed these potential mutualistic nutritional associations, as cultures of T. putrescentiae with low BLS abundance showed the strongest response after the addition of vitamins. Despite developing an arguably tight dependency on its host, the BLS has probably retained flagellar mobility, as evidenced by the 32 proteins enriched in KEGG pathways associated with flagellar assembly or chemotaxis (e.g., fliC, flgE, and flgK, as highly expressed genes). Some of these proteins probably also facilitate adhesion to host gut cells. The microcin C transporter was identified in the BLS, suggesting that microcin C may be used in competition with other gut bacteria. The 16S DNA sequence comparison indicated a mite clade of BLSs with a broad host range, including house dust and stored-product mites. Our phylogenomic analyses identified a unique lineage of arachnid specific BLSs in mites and scorpions.IMPORTANCEA Bartonella-like symbiont was found in an astigmatid mite of allergenic importance. We assembled the genome of the bacterium from metagenomes of different stored-product mite (T. putrescentiae) cultures. The bacterium provides pantothenate and lipoic acid to the mite host. The vitamin supply explains the changes in the relative abundance of BLSs in T. putrescentiae as the microbiome response to nutritional or pesticide stress, as observed previously. The phylogenomic analyses of available 16S DNA sequences originating from mite, scorpion, and insect samples identified a unique lineage of arachnid specific forming large Bartonella clade. BLSs associated with mites and a scorpion. The Bartonella clade included the previously described Ca. Tokpelaia symbionts of ants.

Wide Distribution of Teratosphaeria epicoccoides and T. destructans Associated with Diseased Eucalyptus Leaves in Plantations in Southern China.

Species of Mycosphaerellaceae and Teratosphaeriaceae represent over 40% of the fungi identified on eucalypt leaves worldwide. These include some important pathogens that mainly cause leaf blight and spot, and result in increasingly negative impacts on global commercial eucalypt industries. Eucalyptus plantations are commonly cultivated in southern China for solid wood and pulp products. However, the species diversity and geographic distribution of Mycosphaerellaceae and Teratosphaeriaceae, associated with diseased plantation Eucalyptus leaves in China, have not been clarified. In this study, we conducted the first systematic surveys and sample collections of Mycosphaerellaceae- and Teratosphaeriaceae-like fungi from diseased plantation Eucalyptus leaves in southern China. In total, 558 isolates were obtained from 59 sampled sites in five provinces. One isolate was isolated from each tree. According to the disease symptoms, conidia morphological characteristics, and DNA sequence comparisons of ITS, tef1 and tub2 gene regions. The 558 isolates were identified as Teratosphaeria epicoccoides (312 isolates; 55.9%) and T. destructans (246 isolates, 44.1%). Both species were widely distributed in the sampled regions in southern China. The genotypes of T. epicoccoides and T. destructans were determined based on ITS, tef1, and tub2 sequences. The results showed that multiple genotypes of each species of T. epicoccoides and T. destructans exist in China. Additionally, isolates with multiple genotypes were obtained in all five sampled provinces. These results suggest that both T. epicoccoides and T. destructans are not clonal. This study proved that both T. epicoccoides and T. destructans are dominant species and widely distributed on diseased Eucalyptus leaves in southern China. The wide geographic distribution and potential high genetic diversity pose challenges for the disease management of Teratosphaeria leaf blight and leaf spot in China.

MAS-Cloud+: A novel multi-agent architecture with reasoning models for resource management in multiple providers

Nowadays, scientific and commercial applications are often deployed to cloud environments requiring multiple resource types. This scenario increases the necessity for efficient resource management. However, efficient resource management remains challenging due to the complex nature of modern cloud-distributed systems since resources involve different characteristics, technologies, and financial costs. Thus, optimized cloud resource management to support the heterogeneous nature of applications balancing cost, time, and waste remains a challenge. Multi-agent technologies can offer noticeable improvements for resource management, with intelligent agents deciding on Virtual Machine (VM) resources. This article proposes MAS-Cloud+, a novel agent-based architecture for predicting, provisioning, and monitoring optimized cloud computing resources. MAS-Cloud+ implements agents with three reasoning models including heuristic, formal optimization, and metaheuristic. MAS-Cloud+ instantiates VMs considering Service Level Agreement (SLA) on cloud platforms, prioritizing user needs considering time, cost, and waste of resources providing appropriate selection for evaluated workloads. To validate MAS-Cloud+, we use a DNA sequence comparison application subjected to different workload sizes and a comparative study with state-of-the-art work with Apache Spark benchmark applications executed on the AWS EC2. Our results show that to execute the sequence comparison application, the best performance was obtained by the optimization model, whereas the heuristic model presented the best cost. By providing the choice among multiple reasoning models, our results show that MAS-Cloud+ could provide a more cost-effective selection of the instances reducing ≈58% of execution average cost of WorkdCount, Sort, and PageRank BigDataBench benchmarking workloads. As for the execution time, the WorkdCount and PageRank present reduction, the latter with ≈58%. The results indicate a promising solution for efficient cloud resource management.

Detection of Cotton Leaf Curl Disease using Betasatellite-based Molecular Marker

Cotton leaf curl disease (CLCuD) caused by whitefly-transmitted begomoviruses has hampered cotton production across the Punjab and Sindh provinces of Pakistan and northeastern India. Eight species of begomoviruses in association with a single betasatellite “Cotton leaf curl Multan betasatellite (CLCuMB)” have been reported to cause CLCuD. Objective: To detect early and efficiently Cotton leaf curl disease (CLCuD) using betasatellite-based molecular marker. Methods: 3-7 samples leaves were collected from symptomatic cotton fields in selected five areas of cotton production in Pakistan. Total DNA was extracted from collected leaves using the Cetyl trimethylammonium bromide (CTAB) method. Primers were designed by MUSCLE alignment tool and target region was amplified by PCR and amplification confirmed by performing gel electrophoresis. After DNA sequencing Phylogenetic analysis of the was carried out using software MEGA-X. Results: Amplified target region of483bp was observed by running 1% agarose gel. Comparison of DNA sequences revealed two nucleotide substitutions in DNA sequence from samples collected from Multan, Sakrand, Rahim Yar Khan and, while four nucleotide substations in sample collected from Vehari. High nucleotide substation in DNA sequence from Vehari as compared to other regions. Conclusions: In conclusion all of eight distinct begomoviruses causing CLCuD with CLCuMB is indicative of the fact that CLCuMB based molecular marker can be developed for detection of the disease. Early detection of disease will help the breeders and farmers to manage the disease.

Characterization of ?-1,3-GLUCANASE gene associated with resistance to anthracnose disease in mango (Mangifera indica L.)

?-1,3-Glucanase plays key roles in plants and have been studied in a wide range of plant species. It has many functions including defene plants against fungal pathogens either alone or in association with chitinases and other antifungal proteins. The structure of ?-1,3-Glucanase in mango has been incomplete. Thus, our study proposed to characterize this gene and compare DNA sequences in exon 2 of mango cultivars. The DNA was extracted from mango leaves and Colletotrichum asianum hypha, then this gene in exons 2, 3 and 4 were amplified by PCR and only sequences of exon 2 were sequenced and compared to database. The results presented that ?-1,3-Glucanase gene is composed of 4 exons which exon 2 is the largest region. Exons 2 (1254 bp) and 3 (27 bp) were interrupted by intron 2 at about 180 bp while exons 3 and 4 (153 bp) were separated with intron 3 at about 16 bp in size. Sequences in exon 2 pointed that mango in Thailand is different with mango in database from Philippine. Moreover, there were 31 SNPs in exon 2 amplified from GLU2F and GLU2R. These SNPs may be the pathogenesis-related resistance against C. asianum.

Identification of Lasiodiplodia species inciting stem rot of dragon fruit in India through polyphasic approach.

Lasiodiplodia species commonly thrive as endophytes, saprobes, and plant pathogens in tropical and subtropical regions. Association of Lasiodiplodia species causing stem rot in dragon fruit in the coastal belt of Odisha, eastern India, has been illustrated here. The stem rot disease was characterized by yellowing of the stem, followed by softening of the stem tissues with fungal fructifications of the pathogen in the affected tissues. On the basis of macro- and micromorphological characteristics, the four fungal isolates recovered from diseased stems were identified initially as Lasiodiplodia species. By comparing DNA sequences within the NCBI GenBank database as well as performing a multigene phylogenetic analysis involving the internal transcribed spacer region (ITS-rDNA), β-tubulin (β-tub), and elongation factor-alpha (EF1-α) genes, the identity of Lasiodiplodia isolates was determined. The isolate CHES-21-DFCA was identified as Lasiodiplodia iraniensis (syn: L. iranensis) and the remaining three isolates, namely CHES-22-DFCA-1, CHES-22-DFCA-2, and CHES-22-DFCA-3, as L. theobromae. Although pathogenicity studies confirmed both L. iraniensisand L. theobromae were responsible for stem rot in dragon fruit, L. iraniensis was more virulent than L. theobromae. This study established the association of Lasiodiplodia species with stem rot in dragon fruit using a polyphasic approach. Further investigations are required, particularly related to on host-pathogen-weather interaction and spatiotemporal distribution across the major dragon fruit-growing areas of the country to formulate prospective disease management strategies. This is the first report on these two species of Lasiodiplodia inflicting stem rot in Hylocereus species in India.

Population genetic diversity in Nezara viridula by analysis of mitochondrial control region sequences

Abstract Here, we examine genetic diversity and dispersal patterns in populations of the agricultural pest Nezara viridula from Argentina using mitochondrial control region sequences. The DNA sequence comparisons of 1837 base pairs of the control region revealed 60 haplotypes determined by a total of 108 variable sites. The observed total haplotype diversity (Hd) value was 0.99, and the nucleotide diversity was 0.00423 and 0.00571 according to π and θW, respectively. The high haplotype diversity and low nucleotide diversity, as well as both neutrality tests and unimodal mismatch distributions, suggested a recent expansion in the populations of N. viridula from Argentina. The expansion of the populations of this insect is probably due to the recent agricultural expansion and intensification of soybean cultivation in this country. No significant levels of genetic differentiation were detected, suggesting that gene flow predominates over genetic drift. In addition, the Bayesian individual assignment analysis revealed that all populations share ancestry. It is probable that the growth in the area cultivated with soybean has generated stable and continuous habitats that allow gene flow among populations of N. viridula. The results of demographic history analysis suggest that the direction of migration of N. viridula would be associated with the growth pattern of soybean crops in Argentina.