Percent Sequence Similarity Research Articles

Abstract 3274: Targeting NSD family histone methyltransferase activity with irreversible inhibitors

Abstract Nuclear SET domain containing (NSD) family member proteins are histone methyltransferases that mono- and di-methylate histone 3 at lysine 36 (H3K36) to alter gene expression in a context-dependent manner. NSD1 and NSD3 are two members of this family which share greater than 80 percent sequence similarity in the catalytic SET domain. NSD1 is found as a fusion with NUP98 in aggressive cases of pediatric leukemia, and the lysine methyltransferase (KMTase) activity of NUP98-NSD1 drives bone marrow progenitor proliferation. Similarly, high levels of enzymatically active NSD3 mRNA are correlated with reduced disease-free survival in breast cancer and catalytic NSD3 expression is sufficient to rescue tumor growth in a xenograft model of triple negative breast cancer. Selective and potent inhibitors of NSD1 and NSD3 KMTase activity are needed to further investigate the therapeutic potential of targeting this function in leukemia and/or solid cancers. Here, we report the development of irreversible small molecule inhibitors of the NSD1 and NSD3 SET domains. We utilized a NMR-based fragment screen of the NSD1 SET domain to identify the hit BT1, which binds reversibly to the SET domain of NSD1. BT1 was extensively optimized into a series of potent irreversible ligands. Mass spectrometry and structural studies revealed that these compounds react with a cysteine near the autoinhibitory loop, providing a rational for the strong inhibition of KMTase activity we observe in biochemical assays. These inhibitors also bind to the NSD1 and NSD3 SET domains in cells and exhibit potent anti-proliferative effects against leukemia cells containing NUP98-NSD1 and breast cancer cells with high levels of NSD3 expression. In summary, we present novel irreversible inhibitors of NSD1 and NSD3 KMTase activity which represent important chemical probes that can be used to investigate the therapeutic potential of targeting NSD family member catalytic activity in cancers. Citation Format: Christina Howard, Sergei Zari, Shuangjiang Li, Huang Huang, EunGi Kim, Se Ra Park, Trupta Purohit, Hongzhi Miao, Xiaotian Zhang, Caroline Nikolaidis, Hao Li, Juliano Ndoj, HyoJe Cho, Jolanta Grembecka, Tomasz Cierpicki. Targeting NSD family histone methyltransferase activity with irreversible inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3274.

Isolation and characterization of Ureaplasma parvum from the semen of infertile men and detection of virulence factors genes

The bacterial infection of seminal fluid is one of the most important factors behind infertility in many cases. The biological diversity of the Ureaplasma and Mycoplasma have widely been reported to be associated with the infertility grade in many cases. The purpose of this research was to identify and characterize and the phylogenetic positioning of twenty-one isolates of Ureaplasma in seminal fluids. Two genetic loci were included in this study ureB/ureA and upV for Ureaplasma. Each amplified locus was investigated in both bacterial infections to identify the identity of the possible bacterial infection of those patients and to assess the pattern of the genetic variation for each genetic locus in investigated patients. The results of the DNA sequence analysis of the urease and upv gene extracted from these bacteria showed that Ureaplasma parvum serovar 3 was the cause of infections in the studied samples. The studied isolates were also matched with the global isolates registered in the gene bank. After NCBI matching for these gene segments, polymerase chain experiments confirmed the diagnosis. The NCBI BLASTn The algorithm discovered up to 99.5 percent sequence similarity. between the studied samples and the reference samples for these gene.

Hydrogenophaga crocea sp. nov. associated with cyanobacterial mat isolated from farmland mud.

A catalase and oxidase-positive strain BA0156T was isolated from a cyanobacterial mat collected from the farmland mud cultivated with sugarcane from Ahmednagar, India. The 16S rRNA gene of strain BA0156T showed the highest percent sequence similarity with Hydrogenophaga borbori LMG 30805T (98.5%), followed by H. flava DSM 619T (98.3%) and H. intermedia DSM 5680T (98.2%). The strain BA0156T contained the major fatty acids, C16:0 (25.1%) and C17:0 cyclo (3.9%), whereas phosphatidylethanolamine and diphosphatidylglycerol were the major polar lipids. The OrthoANI and dDDH values between strain BA0156T and its closest relative H. borbori LMG 30805T were 84.6% and 28.3%, respectively. The DNA G+C content of strain BA0156T was 69.4mol %. Furthermore, the biochemical and physiological features of strain BA0156T showed a distinct pattern from their closest phylogenetic neighbours. The phenotypic, genotypic and chemotaxonomic characteristics indicated that the strain BA0156T represents a new species for which the name Hydrogenophaga crocea (type strain BA0156T = MCC 3062T = KCTC 72452T = JCM 34507T) is proposed.

FIRST DESCRIPTION ON MOLECULAR CHARACTERISATION OF HEMIURID TREMATODE Lecithocladium excisum FROM BLOCH,1795: Apolectus niger (PISCES: CARANGIDAE:) USING 18S RIBOSOMAL DNA MARKER

A total of 55 specimens of Bloch: Apolectus niger (Pisces: Carangidae) were obtained during the current inquiry from the sea beach of Puri, Orissa, India. It is a commercially significant marine fish, since it is a highly valued source of nutrition for human consumption. One type of the digenetic trematodes was collected from the gut of the affected fish, which belong to the genus, Lecithocladium, of the family Hemiuridae. Partial nucleotide sequences of the 18S ribosomal gene were acquired from this trematode species and deposited in the GenBank. Molecular analysis of the parasites using 18s small subunit rDNA was undertaken to evaluate their phylogenetic position with respect to previously known species in GenBank, which strikingly confirmed their molecular phylogeny revealed here. The hemiurid species from the genus, Lecithocladium are found to be L. excisum. A comparison of 18S rDNA sequences indicated that they exhibited 98.0 percent sequence similarity with Dinurus longisinus.

Molecular detection and genomic characterization of Torque teno canis virus in domestic dogs in Guangxi Province, China

The Torque teno canis virus (TTCaV) is a small virus with circular single-stranded DNA that has been reported to cause infections in dogs. The present study aimed to identify the presence of TTCaV in blood samples obtained from domestic dogs, and examine its diversity and evolution of the genomes. Five strains of TTCaV were detected, and the overall prevalence was found to be 7% (28/400). Phylogenetic analysis showed that the five genomes were closely clustered with the previously known Cf-TTV10 and LDL strains and formed a Thetatorque virus. Homology analysis of the whole genome showed a sequence identity of 94.6%–96.8% among the five genomes. The percent sequence similarity among the five complete genomes ranged from 95.3% to 97.4% and from 95.1% to 97% compared to the Cf-TTV10 and LDL strains respectively. The ORF1-encoded amino acid sequences showed 94.4%–97.2% identity among the five isolates. Our findings suggest that the TTCaV has a large genetic diversity and showed that TTCaV and canine parvovirus (CPV) co-infection exists in China. Further studies on the pathogenicity of TTCaV are required.

Phylogenetic Relationships among Whiteflies in the Bemisia tabaci (Gennadius) Species Complex from Major Cassava Growing Areas in Kenya.

Whiteflies, Bemisia tabaci (Gennadius) are major insect pests that affect many crops such as cassava, tomato, beans, cotton, cucurbits, potato, sweet potato, and ornamental crops. Bemisia tabaci transmits viral diseases, namely cassava mosaic and cassava brown streak diseases, which are the main constraints to cassava production, causing huge losses to many small-scale farmers. The aim of this work was to determine the phylogenetic relationships among Bemisia tabaci species in major cassava growing areas of Kenya. Surveys were carried out between 2013 and 2015 in major cassava growing areas (Western, Nyanza, Eastern, and Coast regions), for cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Mitochondrial cytochrome oxidase I (mtCOI-DNA) was used to determine the genetic diversity of B. tabaci. Phylogenetic trees were constructed using Bayesian methods to understand the genetic diversity across the study regions. Phylogenetic analysis revealed two B. tabaci species present in Kenya, sub-Saharan Africa 1 and 2 comprising five distinct clades (A–E) with percent sequence similarity ranging from 97.7 % to 99.5%. Clades B, C, D, and E are predominantly distributed in the Western and Nyanza regions of Kenya whereas clade B is dominantly found along the coast, the eastern region, and parts of Nyanza. Our B. tabaci clade A groups with sub-Saharan Africa 2-(SSA2) recorded a percent sequence similarity of 99.5%. In this study, we also report the identification of SSA2 after a 15 year absence in Kenya. The SSA2 species associated with CMD has been found in the Western region of Kenya bordering Uganda. More information is needed to determine if these species are differentially involved in the epidemiology of the cassava viruses.

A Segmentation-Based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition.

Protein fold recognition (PFR) is considered as an important step towards the protein structure prediction problem. Despite all the efforts that have been made so far, finding an accurate and fast computational approach to solve the PFR still remains a challenging problem for bioinformatics and computational biology. In this study, we propose the concept of segmented-based feature extraction technique to provide local evolutionary information embedded in position specific scoring matrix (PSSM) and structural information embedded in the predicted secondary structure of proteins using SPINE-X. We also employ the concept of occurrence feature to extract global discriminatory information from PSSM and SPINE-X. By applying a support vector machine (SVM) to our extracted features, we enhance the protein fold prediction accuracy for 7.4 percent over the best results reported in the literature. We also report 73.8 percent prediction accuracy for a data set consisting of proteins with less than 25 percent sequence similarity rates and 80.7 percent prediction accuracy for a data set with proteins belonging to 110 folds with less than 40 percent sequence similarity rates. We also investigate the relation between the number of folds and the number of features being used and show that the number of features should be increased to get better protein fold prediction results when the number of folds is relatively large.

Sequence and apoptotic activity of VacA cytotoxin cloned from a Helicobacter pylori Thai clinical isolate.

The vacuolating cytotoxin VacA produced by Helicobacter pylori induces the formation of large cytoplasmic vacuoles in host gastric epithelial cells as well as a release of cytochrome C from mitochondria resulting in cell apoptosis. Considerable sequence diversity in VacA relating to different degrees of disease severity is observed with clinical samples from a multitude of geographic places. In this study we describe expression in Escherichia coli, purification to homogeneity and in vitro assay of its apoptotic activity of a VacA toxin from a H. pylori isolate of a Thai patient with gastrointestinal lymphoma. Sequencing revealed that the deduced amino acid sequence of the cloned Thai isolate VacA is similar to H. pylori s1/m2 type strains. The percent sequence similarity to the model strain 60190 was lower due to the presence of extra amino acids in the mid (m) region. The purified VacA toxin exhibited significant apoptotic activity on both T84 and MDCK epithelial cell lines, as revealed by DAPI staining, whereby the observed activity was significantly higher on MDCK cells. These findings could relate to a modulation of VacA activity on host cells in the Thai isolate-VacA toxin that may differ from those of the model strain.

Identification of aBartonellaSpecies in the Harbor Seal (Phoca vitulina) and in Seal Lice (Echinophtirius horridus)

To explore whether harbor seals (Phoca vitulina) are exposed to Bartonella spp., 35 seal lice (Echinophtirius horridus) were collected from seven seals, during their rehabilitation period in the Seal Rehabilitation and Research Center at Pieterburen, The Netherlands. Forty-eight spleen samples were collected during necropsies of other harbor seals that died during rehabilitation, or had stranded dead and were brought to the Seal Rehabilitation and Research Center for postmortem investigation. Lice were grouped into six pools, and DNA was extracted from each pool and from all the seals' spleen samples. One of the six lice pools and one spleen sample were found positive by high-resolution melt, real-time PCR amplifying partial loci of the rpoB gene, and the intergenic spacer (ITS) region. The Bartonella spp. identified in the spleen and lice were found to be identical to each other. One hundred percent sequence similarity with Bartonella henselae was found in the ITS, and 97% sequence similarity with Bartonella grahamii was detected in the rpoB gene. To the best of the authors' knowledge, this is the first report describing the detection of Bartonella spp. from a seal or any other pinniped, and from seal lice, E. horridus. The 100% sequence similarity in the ITS of the Bartonella sp. identified with the zoonotic B. henselae warrants further investigation and characterization of this organism, which may be found to be of public health importance.

Classification of <i>Rhizoctonia</i> spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping

Currently, rDNA-ITS sequence analysis seems to be the most appropriate method for comprehensive classification of Rhizoctonia spp. Our previous review article was concerned with detailed analysis of multinucleate Rhizoctonia (MNR), and the current review complements the previous one with detailed analysis of binucleate Rhizoctonia (BNR) (teleomorphs: Ceratobasidium spp. and Tulasnella spp.) and uninucleate Rhizoctonia (UNR) (teleomorph: C. bicorne). Data of all the appropriate BNR and UNR accumulated in GenBank were analyzed together in neighborjoining (NJ) trees supplemented with percent sequence similarity within and among the anastomosis groups (AGs) and subgroups. Generally, the clusters of the isolate sequences supported the genetic basis for the AG based on hyphal fusion anastomosis. Comprehensive interrelationships among all the currently available MNR, BNR, and UNR groups and subgroups in GenBank were subsequently analyzed in NJ and maximum-parsimony (MP) trees, showing the genetic relatedness among the different groups and indicating possible bridging groups between MNR, BNR, and UNR. The review also indicates serious inaccuracies in designation of sequences of some isolates deposited in GenBank. Several additional teleomorph genera with Rhizoctonia spp. anamorphs have also been reported in the literature. However, as they have not been intensively studied, there were no available data on their rDNA-ITS sequences that could be included in this review.

Conserved sequence patterns in the non-coding ribosomal ITS-1 of distantly related snail taxa

The ensuing contribution gives an insight into the evolution of non-coding ribosomal DNA of two distantly related groups of snails. The non-coding sequences of the ribosomal DNA comprise the First Internal Transcribed Spacer (ITS-1), the Second Internal Transcribed Spacer (ITS-2), and the NonTranscribed Spacer (NTS). These spacers are known to evolve faster than the coding 18S, 5.8S and 28S ribosomal DNA1,2,3. The fast evolution of the spacers can be used to investigate the genetic relationships of closely related genera, species and other lower taxonomic units with a divergence time of less than 50 million years3,4,5. The focus of our analysis is on the evolution of the ITS-1 of land snails (Stylommatophora) and of freshwater snails (Basommatophora). These two snail groups have their origin in the Mesozoic. Consequently, we expected their ITS-1 sequences to show strong differences. However, the ITS-1 of stylommatophoran and basommatophoran gastropods is consecutively divided into conserved and variable regions. The detection of conserved ITS-1 regions among distantly related animals gives further insight into the functional significance of non-coding ribosomal RNA. In the analysis, all published ITS-1 sequences of stylommatophoran and basommatophoran gastropods are taken into consideration. These include the sequences of two species of Albinaria, two species of Isabellaria (Stylommatophora; Clausiliidae)6, three species of Bulinus (Basommatophora; Planorbidae)7, and four species of Stagnicola (Basommatophora; Lymnaeidae)8. In addition, we sequenced the ITS-1 of the following five species (protocols are available on request): three species of Cochlicopa (Stylommatophora; Cochlicopidae), Azeca goodalli (Stylommatophora; Cochlicopidae), and two specimens of Arianta arbustorum (Stylommatophora; Helicidae) (accession numbers: Y16755–Y16765; AF124052–AF124053). The sequences were aligned with the program CLUSTAL W, version 1.5, in order to find homologous regions in all taxa see 9. The sequence alignment clearly shows that conserved sequence regions and variable regions occur inthe ITS-1 of stylommatophoran and basommatophoran gastropods. Only a few alignment positions had to be corrected manually. Six conserved blocks, I to VI, ranging in size from 15 to 28 nucleotides were found. Both the relative position (Figure 1) and the respective sequences are highly similar among the taxa (over 80 percent sequence similarity in pairwise RESEARCH NOTES

Sequence Analysis of One Major Basic β-Crystallin (β-Bp) of Amphibian Lenses - Evolutionary Comparison and Phylogenetic Relatedness Between β-Crystallin and γ-Crystallin

βBp-Crystailin a major basic β-crystallin of vertebrate eye lens, is developmentally regulated during the process of amphibian metamorphosis. In order to facilitate the determination of the primary sequence of this ubiquitous crystallin present in all vertebrate species, cDNA mixture was synthesized from the poly(A)+ mRNA isolated from bullfrog eye lenses. A protocol of Rapid Amplification of cDNA Ends (RACE) was used to amplify cDNAs encoding βBp-crystallin by polymerase chain reaction (PCR). PCR-amplified product corresponding to βBp-crystallin was then ligated into pGEM-T vector and then transformed into E. coli strain JM109. One complete full-length reading frame of 615 base pairs, which covers a deduced protein sequence of 205 amino acids, including the universal initiating methionine, was revealed by automatic nucleotide sequencing with a fluorescence-based dideoxynucleotide chain-termination method. It shows 83, 74, 78 and 80 percent sequence similarity to the homologous β2 crystallins of chicken, rat, bovine, and human species, respectively, revealing the close structural relationship among βBp-crystallins even from remotely related species. In this study phylogenetic trees based on nucleotide and protein sequences of various β- and γ-crystallins from different vertebrate classes are constructed using a combination of distance matrix and approximate parsimony methods. which corroborate the previous supposition that β- and γ-crystallins form a superfamily with a common ancestry.

Sequence-Analysis of Frog ρ-Crystallin by cDNA Cloning and Sequencing: A Member of the Aldo-Keto Reductase Family

ρ-Crystallin is a major enzyme crystallin present in the lenses of amphibian species with a blocked amino terminus. In order to facilitate the determination of the primary sequence of this taxon-specific crystallin, cDNA mixture was synthesized from the poly(A) +mRNA of bullfrog eye lenses. cDNAs encoding ρ-crystallin were then amplified by polymerase chain reaction (PCR) using a new protocol of Rapid Amplification of cDNA Ends (RACE). PCR-amplified product corresponding to ρ-crystallin was obtained, which was then subcloned into pUC18 vector and then transformed into E. coli strain JM109. Plasmids purified from the positive clones were prepared for nucleotide sequencing by the automatic fluorescence-based dideoxynucleotide chain-termination method. Sequencing more than 15 clones containing DNA inserts coding for ρ-crystallin constructed only one unique and complete full-length reading frame of 975 base pairs covering a deduced protein sequence of 324 amino acids including the universal initiating methionine. It shows 96, 59, 46 and 37 percent sequence similarity to another ρ-crystallin from European common frog, bovine prostaglandin-F synthase, human aldose reductase and human aldehyde reductase, respectively, revealing the close relationship between ρ-crystallins from related amphibian species and its possible evolutionary relatedness with various aldo-keto reductases. In this study a phylogenetic tree for ρ-crystallin and related enzymes is constructed based on multiple-sequence alignment program using a combination of distance matrix and approximate parsimony methods. We have thus established the remote phylogenetic relationship between ρ-crystallin and some aldehyde/aldose reductases, which may provide a possible link for the recruitment of this crystallin from detoxification-related enzymes and its physiological role in maintaining a transparent and clear lens.

Organization of a Solatium brevidens repetitive sequence related to the TGRI subtelomeric repeats of Lycopersicon esculentum

A species-specific repetitive DNA fragment has been isolated from a genomic library of Solanum brevidens. Sequence analysis revealed a regular organization of three non-homologous subrepeats forming tandemly-arranged composite repetitive units. Interpretation of Southern hybridization patterns based on the known sequence data suggests that the isolated sequence element represents an abundant organization type, although the presence of simple tandem arrays of the subrepeats is also indicated. Seventy-four percent sequence similarity was found between one of the S. brevidens subrepeats (Sb4AX) and a satellite DNA (TGRI) localized as a subtelomeric repeat on almost all Lycopersicon esculentum chromosomes. Insitu hybridization indicated that, similarly to TGRI, the S. brevidens-specific repeats are located at the ends of the arms of several chromosomes. On the basis of the data obtained, a common ancestral sequence can be proposed for the tomato (TGRI) and the S. brevidens (Sb4AX) repeat however, the molecular organization of this element in these two species evolved in a basically different manner.