scholarly journals The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Geng Zou ◽  
Bernardo Bello-Orti ◽  
Virginia Aragon ◽  
Alexander W. Tucker ◽  
Rui Luo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Simple Sequence Repeats ◽  
Potential Role ◽  
Gc Content ◽  
Nucleotide Metabolism ◽  
Coding Regions ◽  
Purine Nucleotide Metabolism ◽  
Go Terms ◽  
Simple Sequence

Abstract Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

scholarly journals A potential role of extended simple sequence repeats in competing endogenous RNA crosstalk

RNA Biology ◽  
2018 ◽  
Vol 15 (11) ◽  
pp. 1399-1409 ◽  
Author(s):  
Tomasz M. Witkos ◽  
Wlodzimierz J. Krzyzosiak ◽  
Agnieszka Fiszer ◽  
Edyta Koscianska
Keyword(s):  
Simple Sequence Repeats ◽  
Potential Role ◽  
Competing Endogenous Rna ◽  
Simple Sequence

scholarly journals Genome-wide investigation and analysis of microsatellites and compound microsatellites in Leptolyngbya species, Cyanobacteria

2021 ◽  
Author(s):  
Dan Yao ◽  
Lian-Ming Du ◽  
Meijin Li ◽  
Maurycy Daroch ◽  
Jie Tang
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeats ◽  
Gc Content ◽  
The Other ◽  
Closely Related Species ◽  
Coding Regions ◽  
Genome Wide ◽  
Almost All ◽  
Insight Into ◽  
Simple Sequence

Abstract Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in 36 genomes of Leptolyngbya. The results disclosed diversified patterns of distribution, abundance, density and diversity of SSRs and CSSRs in Leptolyngbya genomes. The numbers of SSRs and CSSRs were extremely uneven distributed among genomes, ranging from 11,086 to 27,292 and from 286 to 1,102, respectively. Mononucleotide SSRs were the most abundant category in 14 genomes, while the other 22 genomes followed the pattern: di- > mono- > trinucleotide SSRs. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly correlated with genome size (P < 0.01) and but not closely correlated with GC content (P > 0.05). Moreover, the motif (A/T)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 33 genomes. This study provides the first insight into SSRs and CSSRs in Leptolyngbya genomes and will be useful to contribute to future use as molecular markers in closely-related species.

scholarly journals Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

2020 ◽  
Author(s):  
Albert Maibam ◽  
Sunil Nigombam ◽  
Harinder Vishwakarma ◽  
Showkat Ahmad Lone ◽  
Kishor Gaikwad ◽  
...  
Keyword(s):  
Heat Stress ◽  
Pearl Millet ◽  
Stress Responses ◽  
Simple Sequence Repeats ◽  
Pennisetum Glaucum ◽  
Average Length ◽  
Gc Content ◽  
Functional Markers ◽  
Sequencing Data ◽  
Simple Sequence

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

Characterization of Italian populations ofLoliumspp. resistant and susceptible to diclofop by inter simple sequence repeat

Weed Science ◽  
2004 ◽  
Vol 52 (4) ◽  
pp. 554-563 ◽  
Author(s):  
Giovanni Dinelli ◽  
Alessandra Bonetti ◽  
Ilaria Marotti ◽  
Maurizio Minelli ◽  
Pietro Catizone
Keyword(s):  
Potential Role ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Intergeneric Hybridization ◽  
Banding Patterns ◽  
Inter Simple Sequence Repeats ◽  
Range Of Variation ◽  
Simple Sequence

Three ItalianLoliumweed populations, one susceptible and two resistant to diclofop, were characterized by the technique of inter simple sequence repeats (ISSR). The goal of this study was to taxonomically identify theseLoliumpopulations as well as to evaluate evidence for introgression of ISSR fragments fromFestucaand the potential role of this introgression in the diclofop response. ISSR analysis confirmed the genomic background of the weed populations to be consistent with that ofLolium. However, the great range of variation in ISSR banding patterns highlighted that the three ryegrass accessions are mixed populations made up of individuals resulting presumably from intrageneric and intergeneric hybridization in theLolium–Festucacomplex. TwoFestucagenus-discriminating and 20Festucaspecies-discriminating ISSR markers were screened among all the three ryegrass populations. The resistant Tuscania population carried the highest percentage ofFestucagenome (16.8%) followed by the resistant Roma (13.6%) and susceptible Vetralla (7.6%) populations. On the basis of these data some influence ofFestucagenome in diclofop resistance levels of studied ryegrass populations could be hypothesized.

scholarly journals Endothelin in health and disease

2004 ◽  
Vol 4 (3) ◽  
pp. 31-34 ◽  
Author(s):  
Emina Nakaš-Ićindić ◽  
Asija Začiragić ◽  
Almira Hadžović ◽  
Nešina Avdagić
Keyword(s):  
Nitric Oxide ◽  
Amino Acids ◽  
Calcium Ions ◽  
Potential Role ◽  
Cyclic Guanosine Monophosphate ◽  
Guanosine Monophosphate ◽  
Health And Disease ◽  
Endothelin 3 ◽  
Stimulation Of

Endothelin is a recently discovered peptide composed of 21 amino acids. There are three endothelin isomers: endothelin -1 (ET-1), endothelin -2 (ET-2) and endothelin - 3 (ET-3). In humans and animals levels of ET-1, ET-2, ET-3 and big endothelin in blood range from 0,3 to 3 pg/ml. ET-1, ET-2 and ET-3 act by binding to receptors. Two main types of the receptors for endothelins exist and they are referred to as A and B type receptors. Different factors can stimulate or inhibit production of endothelin by endothelial cells. Mechanical stimulation of endothehum, thrombin, calcium ions, epinephrine, angiotensin II, vasopressin, dopamine, cytokines, growth factors stimulate the production of endothelin whereas nitric oxide, cyclic guanosine monophosphate, atrial natriuretic peptide, prostacyclin, bradykinin inhibit its production. Endothelins have different physiological roles in human body but at the same time their actions are involved in the pathogenesis of many diseases.The aim of this review was to present some of, so far, the best studied physiological roles of endothelin and to summarize evidence supporting the potential role of ET in the pathogenesis of certain diseases.

Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 413-419 ◽  
Author(s):  
Jin-Feng Chen ◽  
Fei Lu ◽  
Su-Shing Chen ◽  
Shi-Heng Tao
Keyword(s):  
Recombination Rate ◽  
Base Composition ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Pseudoautosomal Region ◽  
Positive Correlation ◽  
Coding Regions ◽  
Ideal System ◽  
Fixation Bias

This paper establishes that recombination drives the evolution of GC content in a significant way. Because the human P-arm pseudoautosomal region (PAR1) has been shown to have a high recombination rate, at least 20-fold more frequent than the genomic average of ~1 cM/Mb, this region provides an ideal system to study the role of recombination in the evolution of base composition. Nine non-coding regions of PAR1 are analyzed in this study. We have observed a highly significant positive correlation between the recombination rate and GC content (ρ = 0.837, p ≤ 0.005). Five regions that lie in the distal part of PAR1 are shown to be significantly higher than genomic average divergence. By comparing the intra- and inter-specific AT→GC – GC→AT ratios, we have detected no fixation bias toward GC alleles except for L254915, which has excessive AT→GC changes in the human lineage. Thus, we conclude that the high GC content of the PAR1 genes better fits the biased gene conversion (BGC) model.Key words: pseudoautosomal region, GC content, base composition, evolution, recombination.

scholarly journals Internal Point Mutations of the Capsid Modify the Serotype of Rice Yellow Mottle Virus

2005 ◽  
Vol 79 (7) ◽  
pp. 4407-4414 ◽  
Author(s):  
Eugénie Hébrard ◽  
Agnès Pinel-Galzi ◽  
Vincent Catherinot ◽  
Gilles Labesse ◽  
Christophe Brugidou ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Diversity ◽  
Potential Role ◽  
Infectious Clone ◽  
Point Mutations ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Internal Point ◽  
Yellow Mottle

ABSTRACT Rice yellow mottle virus is classified in five major serotypes; the molecular diversity of the coat protein (CP) is well established, but the amino acids involved in the recognition by discriminant monoclonal antibodies (MAbs) remain unknown. Reconstruction of a phylogenetic tree and sequence alignment of the CP gene of a sample representative of the continental-large diversity were used to identify 10 serospecific amino acids (i.e., conserved in all isolates belonging to the same serotype and distinct in other serotypes). Positions occupied by serospecific residues were localized on the crystal structure of the CP monomer and on modeled capsomers. Structural, molecular, and serological properties of each serotype were analyzed, and subsequently, hypotheses on the potential role of amino acids in discriminating reactions with antibodies were formulated. The residues 114 and 115 (serospecific of Sr1) and 190 (serospecific of Sr2) were localized on the outer surface of the capsid and might be directly involved in the immunoreactivity with MAb D and MAb A, respectively. In contrast, residues 180 (Sr3) and 178 (Sr5) lay within the inner surface of the capsid. To understand the role of these internal positions in the recognition with the antibodies, two substitutions (T180K and G178D) were introduced in the CP of an infectious clone. These mutations modified the antigenicity with MAb G and MAb E discriminating Sr3 and Sr5, respectively, while the reaction with MAb D remained unaffected. This result suggests an indirect effect of these two internal mutations on local immunostructure while the global structure was maintained.

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