Sequence Distance Research Articles

Viral genetic diversity and protective efficacy of a tetravalent dengue vaccine in two phase 3 trials

Two phase 3 placebo-controlled trials of the CYD-TDV vaccine, evaluated in children aged 2-14 y (CYD14) and 9-16 y (CYD15), demonstrated vaccine efficacy (VE) of 56.5% and 60.8%, respectively, against symptomatic virologically confirmed dengue (VCD). Sieve analyses were conducted to evaluate whether and how VE varied with amino acid sequence features of dengue viruses (DENVs). DENV premembrane/envelope amino acid sequences from VCD endpoint cases were aligned with the vaccine insert sequences, and extensions of the proportional hazards model were applied to assess variation in VE with amino acid mismatch proportion distances from vaccine strains, individual amino acid residues, and phylogenetic genotypes. In CYD14, VE against VCD of any serotype (DENV-Any) decreased significantly with increasing amino acid distance from the vaccine, whereas in CYD15, VE against DENV-Any was distance-invariant. Restricting to the common age range and amino acid distance range between the trials and accounting for differential VE by serotype, however, showed no evidence of VE variation with distance in either trial. In serotype-specific analyses, VE against DENV4 decreased significantly with increasing amino acid distance from the DENV4 vaccine insert and was significantly greater against residue-matched DENV4 at eight signature positions. These effects were restricted to 2- to 8-y-olds, potentially because greater seropositivity of older children at baseline might facilitate a broader protective immune response. The relevance of an antigenic match between vaccine strains and circulating DENVs was also supported by greater estimated VE against serotypes and genotypes for which the circulating DENVs had shorter amino acid sequence distances from the vaccine.

A Novel Marsupial Hepatitis A Virus Corroborates Complex Evolutionary Patterns Shaping the Genus Hepatovirus.

ABSTRACTThe discovery of highly diverse nonprimate hepatoviruses illuminated the evolutionary origins of hepatitis A virus (HAV) ancestors in mammals other than primates. Marsupials are ancient mammals that diverged from other Eutheria during the Jurassic. Viruses from marsupials may thus provide important insight into virus evolution. To investigate Hepatovirus macroevolutionary patterns, we sampled 112 opossums in northeastern Brazil. A novel marsupial HAV (MHAV) in the Brazilian common opossum (Didelphis aurita) was detected by nested reverse transcription-PCR (RT-PCR). MHAV concentration in the liver was high, at 2.5 × 109 RNA copies/g, and at least 300-fold higher than those in other solid organs, suggesting hepatotropism. Hepatovirus seroprevalence in D. aurita was 26.6% as determined using an enzyme-linked immunosorbent assay (ELISA). Endpoint titers in confirmatory immunofluorescence assays were high, and marsupial antibodies colocalized with anti-HAV control sera, suggesting specificity of serological detection and considerable antigenic relatedness between HAV and MHAV. MHAV showed all genomic hallmarks defining hepatoviruses, including late-domain motifs likely involved in quasi-envelope acquisition, a predicted C-terminal pX extension of VP1, strong avoidance of CpG dinucleotides, and a type 3 internal ribosomal entry site. Translated polyprotein gene sequence distances of at least 23.7% from other hepatoviruses suggested that MHAV represents a novel Hepatovirus species. Conserved predicted cleavage sites suggested similarities in polyprotein processing between HAV and MHAV. MHAV was nested within rodent hepatoviruses in phylogenetic reconstructions, suggesting an ancestral hepatovirus host switch from rodents into marsupials. Cophylogenetic reconciliations of host and hepatovirus phylogenies confirmed that host-independent macroevolutionary patterns shaped the phylogenetic relationships of extant hepatoviruses. Although marsupials are synanthropic and consumed as wild game in Brazil, HAV community protective immunity may limit the zoonotic potential of MHAV.IMPORTANCE Hepatitis A virus (HAV) is a ubiquitous cause of acute hepatitis in humans. Recent findings revealed the evolutionary origins of HAV and the genus Hepatovirus defined by HAV in mammals other than primates in general and in small mammals in particular. The factors shaping the genealogy of extant hepatoviruses are unclear. We sampled marsupials, one of the most ancient mammalian lineages, and identified a novel marsupial HAV (MHAV). The novel MHAV shared specific features with HAV, including hepatotropism, antigenicity, genome structure, and a common ancestor in phylogenetic reconstructions. Coevolutionary analyses revealed that host-independent evolutionary patterns contributed most to the current phylogeny of hepatoviruses and that MHAV was the most drastic example of a cross-order host switch of any hepatovirus observed so far. The divergence of marsupials from other mammals offers unique opportunities to investigate HAV species barriers and whether mechanisms of HAV immune control are evolutionarily conserved.

Microscopic and molecular identification of pine needles

To identify pine needles from different plant origins by microscopic and molecular approaches. The characteristics of pine needles of Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were investigated via plant morphology and microscopic characteristics. ITS2 and rbcL were analyzed with PCR amplification and bi-directional sequencing. MEGA 6.0 was used to calculate the intra-and inter-specific Kimura-2-Parameter (K2P) distances, and the phylogenetic tree was constructed by using the neighbor-joining (NJ) method. There were significant differences in the number and length of pine needles, number of vascular bundles, distribution of stomatal lines, number and distribution of resin channels among three kinds of pine needles. The lengths of ITS2 sequences of Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were 470, 469 and 470 bp, respectively. The lengths of rbcL sequences in three kinds of pine needles were 553 bp. The intraspecific variation rates of ITS2 sequences in Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were 0%, 0.2%, and 2.8%, respectively; and the intraspecific variation rates of rbcL sequences were 0%, 2.4%, and 1.1%, respectively. There was no significant barcoding gap in intraspecific and interspecific genetic distances of ITS2 sequences. The intraspecific and interspecific distances of rbcL sequences were clearly separated in the barcoding gap test. The NJ tree based on rbcL showed that the three pine needles clustered into three separate groups, indicating that rbcL DNA marker could distinguish the Pinus massoniana Lamb., Pinus thunbergii Parl., Pinus armandii Franch. and its close relative species. s The three types of pine needles can be distinguished accurately and rapidly by microscopic and molecular identification. The study provides methodology and experimental basis for the quality evaluation and classification of pine needles.

A curve based cryptography for wireless security in MANET

Mobile Ad hoc Network (MANET) is a mobile and infrastructure less network, widely used in various applications. In this paper, we study the major security issues in MANET to reduce the malicious activity at the nodes. To reduce the unsecured network, Enhanced Adaptive Acknowledgement Scheme (EAACK) is proposed and it involves Acknowledgement (ACK), Secure Acknowledgement (SACK), and Misbehavior Report Authentication (MRA) schemes. In EAACK scheme, the 2b (2-Bit) packet header is used and it overcomes some of the disadvantages of Watchdog behavior. In this work, the sender has to digitally sign the ACK packets and the receiver has to verify it. The proposed Scheme is applied to 40% of malicious nodes and Routing overhead (Ro) hits the value 0.6. The Network performance is better when the value of Ro is 0. In order to secure more, Credibility Based Sequence Distance Vector Routing (CBSDV) and Curve based cryptographic technique is used. Simulation results show that proposed scheme provides better secure network and CBSDV, hop count, time duration, energy values and trust scores play a deciding factor between the source and destination in the network.

A new freshwater alga, Ulvella shanxiensis (Chlorophyta) described from China

A new freshwater alga species of Ulvella shanxiensis, is found in the circulating neutral water spring in China (Shanxi Province), growing epilithic and epiphytic on other substrates. This new species is characterized by olive-green, disc-shaped hollow thallus with irregularly vesicular morphology, which composed of 2–3 layers cells. Most characteristics were in agreement with Ulvella, but distinguished from the other freshwater members by thalli dimensions and cell diameter. In addition to describing the morphological structures of U. shanxiensis in detail, phylogenetic analysis based on sequences of the rbcL and 18S rDNA gene placed the algae in single clade with two samples, and demonstrated the separation between U. shanxiensis and other Ulvella species with a considerable sequence distance. Comparing with U. bullata, the internal transcribed spacer secondary structure of the new species has some compensatory base changes in 1 Helix and hemi-CBCs in 2–3 Helix, differed in several ways from that of other Ulvella algae. Consequently, these results of morphological observation and phylogenetic analysis suggest this alga as a new species, and bring a new record in the total number of recognized freshwater Ulvella species in China.

Psychrophrynella glauca sp. n., a new species of terrestrial-breeding frogs (Amphibia, Anura, Strabomantidae) from the montane forests of the Amazonian Andes of Puno, Peru.

We describe a new species of small strabomantid frog (genus Psychrophrynella) from a humid montane forest in the Peruvian Department of Puno. Specimens were collected at 2,225 m a.s.l. in the leaf litter of primary montane forest near Thiuni, along the Macusani–San Gabán road, in the province of Carabaya. The new species is assigned to Psychrophrynella on the basis of morphological similarity, including presence of a tubercle on the inner edge of the tarsus, and call composed of multiple notes. We also include genetic distances for 16S rRNA partial sequences between the new species and other strabomantid frogs. The species with lowest genetic distances are Psychrophrynella chirihampatu and Psychrophrynella usurpator. Psychrophrynella glauca sp. n. is readily distinguished from the three other species of Psychrophrynella (Psychrophrynella bagrecito, P. chirihampatu, and P. usurpator) by its small size, and by having belly and ventral surfaces of legs reddish-brown or red, and chest and throat brown to dark brown with a profusion of bluish-gray flecks. The new species is only known from its type locality. With the discovery of P. glauca, the geographic distribution of Psychrophrynella is extended to the Department of Puno, where it was no longer represented after the description of the genus Microkayla. Furthermore, the Cordillera de Carabaya is the only mountain range known to be home to four of the seven genera of Holoadeninae (Bryophryne, Microkayla, Noblella, and Psychrophrynella), suggesting an intriguing evolutionary history for this group in southern Peru.

Isolation and Characterization of GDP-L-Galactose Phosphorylase Gene of Vitamin C Biosynthesis Pathway from Kiwi

Introduction: Vitamin C is a major antioxidant in plants and plays an important role in reducing the activity of reactive oxygen species. In humans, the main role of this molecule is the elimination of activity of active oxygen species along with being cofactor for many enzymes. Human is one of the few mammalian species that can not synthesize this vitamin and needs to get it through food sources. The GDP-L-galactose phosphorylase (GGP) gene is one of the most important genes in the biosynthetic pathway of vitamin C, which codes for the GDPL-galactose phosphorylase enzyme. Isolation of GGP gene is an important step in transferring it to elevate vitamin C biosynthesis in plants. Materials and Methods: In current study, the isolation of this gene from kiwi plant was carried out and then was cloned in the pTG19-T plasmid via T/A cloning and subsequently sequenced to confirm it. Results: Sequencing analysis of the GGP gene showed that this fragment contains 1383 bp and the start and stop codons were ATG and TGA, respectively. The bioinformatics analysis of this gene can provide important information on gene and protein structure. The alignment of cloned sequence was done with other Actinidia DNA sequences. The results based on neighbor-joining alignment showed that some of the mutations in nucleotides were related to the third nucleotide in a specific codon. Also, the minimum distance of protein sequences was observed between isolated GGP and Actinidia chinensis. Conclusions: Based on analyses, isolated gene (GGP) can be used for increase vitamin C content in other plants such as cucumber and for resistance to environmental stresses in different plants.

A novel hepatitis B virus species discovered in capuchin monkeys sheds new light on the evolution of primate hepadnaviruses

All known hepatitis B virus (HBV) genotypes occur in humans and hominoid Old World non-human primates (NHPs). The divergent woolly monkey HBV (WMHBV) forms another orthohepadnavirus species. The evolutionary origins of HBV are unclear. We analysed sera from 124 Brazilian monkeys collected during 2012-2016 for hepadnaviruses using molecular and serological tools, and conducted evolutionary analyses. We identified a novel orthohepadnavirus species in capuchin monkeys (capuchin monkey hepatitis B virus [CMHBV]). We found CMHBV-specific antibodies in five animals and high CMHBV concentrations in one animal. Non-inflammatory, probably chronic infection was consistent with an intact preCore domain, low genetic variability, core deletions in deep sequencing, and no elevated liver enzymes. Cross-reactivity of antisera against surface antigens suggested antigenic relatedness of HBV, CMHBV, and WMHBV. Infection-determining CMHBV surface peptides bound to the human HBV receptor (human sodium taurocholate co-transporting polypeptide), but preferentially interacted with the capuchin monkey receptor homologue. CMHBV and WMHBV pseudotypes infected human hepatoma cells via the human sodium taurocholate co-transporting polypeptide, and were poorly neutralised by HBV vaccine-derived antibodies, suggesting that cross-species infections may be possible. Ancestral state reconstructions and sequence distance comparisons associated HBV with humans, whereas primate hepadnaviruses as a whole were projected to NHP ancestors. Co-phylogenetic analyses yielded evidence for co-speciation of hepadnaviruses and New World NHP. Bayesian hypothesis testing yielded strong support for an association of the HBV stem lineage with hominoid ancestors. Neither CMHBV nor WMHBV was likely the ancestor of the divergent human HBV genotypes F/H found in American natives. Our data suggest ancestral co-speciation of hepadnaviruses and NHP, and an Old World origin of the divergent HBV genotypes F/H. The identification of a novel primate hepadnavirus offers new perspectives for urgently needed animal models of chronic hepatitis B. The origins of HBV are unclear. The new orthohepadnavirus species from Brazilian capuchin monkeys resembled HBV in elicited infection patterns and could infect human liver cells using the same receptor as HBV. Evolutionary analyses suggested that primate HBV-related viruses might have emerged in African ancestors of New World monkeys millions of years ago. HBV was associated with hominoid primates, including humans and apes, suggesting evolutionary origins of HBV before the formation of modern humans. HBV genotypes found in American natives were divergent from those found in American monkeys, and likely introduced along prehistoric human migration. Our results elucidate the evolutionary origins and dispersal of primate HBV, identify a new orthohepadnavirus reservoir, and enable new perspectives for animal models of hepatitis B.

Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults.

BackgroundIdentifying pre-ART factors associated with the emergence of HIV-1 drug resistance is critical for optimizing strategies to prevent virologic failure. A previous study reported that lower pre-ART HIV-1 pol diversity was associated with higher risk of virologic failure in HIV-1-infected children. To investigate this association in adults, we measured HIV-1 diversity with deep sequencing in pre-ART samples from adults with well-characterized virologic outcomes in a study (A5142) of initial ART conducted by the AIDS Clinical Trials Group (ACTG).MethodsWe identified 22 cases in ACTG A5142 who experienced virologic failure with drug resistance mutations in RT and 44 matched controls who did not experience virologic failure. cDNA was synthesized from plasma HIV-1 RNA. Each cDNA molecule was tagged with a unique primer ID and RT codons 41–103 were amplified and deep sequenced. Sequences with the same tag were aligned and a consensus was generated to reduce PCR and sequencing errors. Diversity was calculated by measuring average pairwise distance (APD) of the consensus sequences. An exact conditional logistic regression model with percent APD as the risk factor estimated the odds ratio for VF and the corresponding 95% confidence interval.ResultsConsensus single-genome sequences and diversity estimates of pol were obtained for pre-ART samples from 21 cases and 42 controls. The median (IQR) pre-ART percent APD was 0.71 (0.31–1.13) in cases and 0.58 (0.32–0.94) in controls. A possible trend was found for higher diversity being associated with greater risk of virologic failure in adults (OR = 2.2 per one percent APD increase, 95% CI = [0.8, 7.2]; p = 0.15).ConclusionsThis study in adults suggests there is a positive association between higher pre-ART pol diversity and the risk of virologic failure in adults rather than an inverse relationship reported in children.

How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?

Global coevolutionary models of homologous protein families, as constructed by direct coupling analysis (DCA), have recently gained popularity in particular due to their capacity to accurately predict residue-residue contacts from sequence information alone, and thereby to facilitate tertiary and quaternary protein structure prediction. More recently, they have also been used to predict fitness effects of amino-acid substitutions in proteins, and to predict evolutionary conserved protein-protein interactions. These models are based on two currently unjustified hypotheses: 1) correlations in the amino-acid usage of different positions are resulting collectively from networks of direct couplings; and 2) pairwise couplings are sufficient to capture the amino-acid variability. Here, we propose a highly precise inference scheme based on Boltzmann-machine learning, which allows us to systematically address these hypotheses. We show how correlations are built up in a highly collective way by a large number of coupling paths, which are based on the proteins three-dimensional structure. We further find that pairwise coevolutionary models capture the collective residue variability across homologous proteins even for quantities which are not imposed by the inference procedure, like three-residue correlations, the clustered structure of protein families in sequence space or the sequence distances between homologs. These findings strongly suggest that pairwise coevolutionary models are actually sufficient to accurately capture the residue variability in homologous protein families.

A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs.

Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3–V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3–V4 ribotypes had greater divergence than predominant V1–V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.

New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants.

MicroRNAs (miRNAs) are a family of short non-coding RNAs that play significant roles as post-transcriptional regulators. Consequently, various methods have been proposed to identify precursor miRNAs (pre-miRNAs), among which the comparative studies of miRNA structures are the most important. To measure and classify the structural similarity of miRNAs, we propose a new three-dimensional (3D) graphical representation of the secondary structure of miRNAs, in which an miRNA secondary structure is initially transformed into a characteristic sequence based on physicochemical properties and frequency of base. A numerical characterization of the 3D graph is used to represent the miRNA secondary structure. We then utilize a novel Euclidean distance method based on this expression to compute the distance of different miRNA sequences for the sequence similarity analysis. Finally, we use this sequence similarity analysis method to identify plant pre-miRNAs among three commonly used datasets. Results show that the method is reasonable and effective.

Generalised distances of sequences I: $B$-distances

Generalised distances of sequences I: $B$-distances

Sequence diversification and phylogenetic analysis of selfincompatibility specific determinant genes in Brassicaceae

It is a long history of theoretical interest in understanding the genetic causes and consequences of shifts between outcrossing and inbreeding in plant mating systems. Selfincompatibility (SI) systems genetically promote outcrossing, and its transitions to inbreeding potentially changes genetic diversity in the evolution of species. SI in the Brassicaceae family is sporophytically controlled by a single locus (S-locus), which locates the female determinant gene SRK (S-locus receptor kinase) and the male determinant gene SCR (S-locus cysteine rich). Operation of diversifying selection maintains the diversity of SRK and SCR during the evolutionary course of S haplotypes. Here we used deduced amino acid sequences of SRK and/or SCR publicly available from seven species in three genera, Brassica, Arabidopsis and Raphanus, to investigate the sequence diversification and phylogenetic distribution of S haplotypes in the Brassicaceae family. The results reveal that SCR shows higher sequence distance than SRK within or between genera, and also in the interspecific pairs of S haplotypes. Phylogenetic analysis supports the conclusion that SI has a single origin but evolves differently within the Brassicaceae. The genetic mechanisms and consequences of the loss of SI in the Brassicaceae family are discussed.

Performance comparision of mobile Ad-Hoc network using routing protocols

Selection of the protocols and path routing are the most common strategies that are to be focused while designing any kind of wireless networks such as MANETs and VANETs. MANETs are basically characterized as frequently changing network topology, multi-hop wireless connectivity and an efficient dynamic routing protocol. In MANETs, the protocol is selected on the basis of how the data is delivered and how its integrity is maintained. Hence, before making the selection of any routing protocol we should make the performance analysis of various routing protocol. In this paper, performance analysis of various routing protocols Ad-hoc On-Demand Distance Vector (AODV), Distance source routing (DSR) and Destination Sequenced Distance Vector (DSDV) are carried out using NS2 simulator. We compare the performance of these routing protocols on the basis of various parameters such as throughput, packet delivery ratio, delay and energy consumption.

MANET Routing Protocols Evaluation: AODV, DSR and DSDV Perspective

Mobile Ad Hoc Network (MANET) is a set of mobile nodes that communicate with each other to configure an immediate network without utilizing any of infrastructure, the centralized access point or centralized administration in multiple hop manner. There are a lot of routing protocols have been proposed in MANET which are different from each other in the performance and the mechanism. Therefore, the performance study of those protocols in different scenarios is needed. This paper presents the performance comparison between Dynamic Source Routing (DSR), Ad hoc on demand distance Vector Routing (AODV) as reactive routing protocols and Destination Sequenced Distance Vector (DSDV) as a proactive routing protocol to precisely determine which protocol is more effective. Network Simulator (NS) version 2.35 has used to simulate and evaluate the performance of these protocols in terms of the packet delivery ratio, average throughput, average end-to-end delay, and packet loss ratio with respect to the variable number of nodes.

Fitness cost of reassortment in human influenza.

Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10−2 in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage.

Molecular evolution of types in non-polio enteroviruses.

Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10-2 to 3.07×10-2 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.

Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences

Mitochondrial genome (mitogenome) is a small and extra-chromosomal DNA, located in cytoplasm and presents an ideal model to study evolution and genetic similarity due to genomic rearrangement. In the present study, mitochondrial DNA sequences of 14 farm animal species including, Bos indicus, Bos taurus, Ovis aries, Capra hircus, Equus caballus, Camelus bactrianus, Camelus dromedaries, Sus scrofa domesticus, Gallus gallus, Meleagris gallopavo, Struthio camelus, Anser anser, Anas platyrhynchos and Oncorhynchus mykiss were retrieved from NCBI databases and compared with the sequence of Homo sapiens. Sequence distance analysis showed a high similarity (74.4%) between Homo sapiens and Equus caballus, while the Oncorhynchus mykiss had the lowest similarity (64.1%) to the Homo sapiens. The highest similarities among the studied species were observed between Anser anser and Anas platyrhynchos (100%) and Bos taurus and Bos indicus (98.5%). In phylogenetic analysis, the Homo sapiens fell in a same cluster with Equus caballus, Bos indicus, Bos taurus, Ovis aries, Capra hircus, Camelus bactrianus, Camelus dromedaries and Sus scrofa domesticus. Poultry species (Gallus gallus, Meleagris gallopavo and Struthio camelus, Anser anser and Anas platyrhynchos) and rainbow trout (Oncorhynchus mykiss) formed a distinct cluster with the lowest similarity to the human. The D-loop regions showed the most obvious differences, while other parts including tRNA, rRNA, STSs and CDSs for different genes, had more similarities. Based on the results of the present study, the mitogenomic sequences could be used for accurate phylogenetic analysis and clustering of different species. Moreover, use of mitogenomic sequence in mammalian farm animals, as biomedical model species would not be far-fetched for genetic control of zoonotic diseases.

A Survey Study on Attacks in MANET Ad-Hoc Network

In this time of instant units, Mobile Ad-hoc Network(MANET) has become an indivisible part for transmission for mobile devices. Therefore, curiosity about study of Mobile Ad-hoc Network has been growing because last several years. In this report we have mentioned some simple routing protocols in MANET like Destination Sequenced Distance Vector, Active Source Redirecting, Temporally-Ordered Redirecting Algorithm and Ad-hoc On Need Distance Vector. Protection is just a serious problem in MANETs because they are infrastructure-less and autonomous. Principal target of writing this report is to handle some simple problems and security considerations in MANET, operation of wormhole strike and acquiring the well-known routing protocol Ad-hoc On Need Distance Vector. This short article will be a great help for the people performing study on real world problems in MANET security.