Guanine-cytosine Research Articles

Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine-Cytosine Base Pair.

In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine-cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

The RCAN1.4 Metastasis Suppressor Is Hypermethylated at Intron 1 in Thyroid Cancer.

Background: Regulator of calcineurin 1.4 (RCAN1.4) is a functionally downregulated metastasis progression suppressor (MPS) in thyroid cancer; however, the mechanisms for RCAN1.4 loss in thyroid cancer have not yet been reported. The RCAN1.4 promoter and gene contain several cytosine-guanine (CG)-rich regions, some of which are reported to be hypermethylated in nonthyroid tissues. We, therefore, hypothesized that RCAN1.4 downregulation in thyroid cancer was in part due to hypermethylation. Methods: Studies were performed in 5 thyroid cancer cell lines (TPC1, FTC133, BCPAP, C643, and 8505C) with different genetic drivers, and in 18 paired normal and thyroid cancer human thyroid cancer tissues. Basal RCAN1.4 messenger RNA (mRNA) and protein levels were assessed in all of the cell lines. Cell lines with lowest RCAN1.4 expression levels were treated with the DNA methyl transferase inhibitor, decitabine. Normal/tumor tissue pairs were analyzed for methylation of three CG-rich regions both by capture of methylated DNA by MBD2 protein and by methylation-specific polymerase chain reaction (MSPCR). Results: In all assessed cell lines, RCAN1.4 mRNA and protein levels increased after decitabine treatment. In silico analysis of the RCAN1.4 gene identified 3 CG-rich regions as possible methylation targets: 1 in the proximal promoter and 2 in intron 1. Hypermethylation of the intron 1 CG-rich regions was identified by both the capture method and MSPCR. In contrast, hypermethylation of the CG-rich region of the proximal promoter was not identified. Gene expression confirmed that hypermethylation in thyroid cancer samples in intron 1 of RCAN1.4 was associated with lower levels of RCAN1.4 mRNA. Finally, the cancer samples demonstrated increased NFE2L3 expression, a downstream marker of functional RCAN1.4 loss. Conclusions: The MPS gene, RCAN1.4, is downregulated in thyroid cancer cells and human thyroid cancer in part by hypermethylation of CG-rich regions in intron 1.

The molecular mechanisms of the bacterial iron sensor IdeR.

Life came to depend on iron as a cofactor for many essential enzymatic reactions. However, once the atmosphere was oxygenated, iron became both scarce and toxic. Therefore, complex mechanisms have evolved to scavenge iron from an environment in which it is poorly bioavailable, and to tightly regulate intracellular iron contents. In bacteria, this is typically accomplished with the help of one key regulator, an iron-sensing transcription factor. While Gram-negative bacteria and Gram-positive species with low guanine-cytosine (GC) content generally use Fur (ferric uptake regulator) proteins to regulate iron homeostasis, Gram-positive species with high GC content use the functional homolog IdeR (iron-dependent regulator). IdeR controls the expression of iron acquisition and storage genes, repressing the former, and activating the latter in an iron-dependent manner. In bacterial pathogens such as Corynebacterium diphtheriae and Mycobacterium tuberculosis, IdeR is also involved in virulence, whereas in non-pathogenic species such as Streptomyces, it regulates secondary metabolism as well. Although in recent years the focus of research on IdeR has shifted towards drug development, there is much left to learn about the molecular mechanisms of IdeR. Here, we summarize our current understanding of how this important bacterial transcriptional regulator represses and activates transcription, how it is allosterically activated by iron binding, and how it recognizes its DNA target sites, highlighting the open questions that remain to be addressed.

Complete genome sequence of Lactococcus taiwanensis strain K_LL004, encoding hydrolytic enzymes of plant polysaccharides isolated from grasshopper (Oxya chinensis sinuosa).

The Lactococcus taiwanensis strain K_LL004 was isolated from the gut of a grasshopper (Oxya chinensis sinuosa) collected from local farm in Korea. L. taiwanensis strain K_LL004 is the functional probiotic candidate with an ability to hydrolyse plant polysaccharides. The complete genome of the L. taiwanensis strain K_LL004 contains one circular chromosome (1,995,099 bp) with a guanine + cytosine (GC) content of 38.8%. Moreover, 1,929 Protein-coding sequence, 19 rRNA genes, and 62 tRNA genes were identified based on results of annotation. L. taiwanensis strain K_LL004 has a gene, which encodes hydrolytic enzymes such as beta-glucosidase and beta-xylosidase, that hydrolyzes plant polysaccharides.

Phenotype and genotype of Boerka goats raised in Bali.

Boerka goats are the new breed in Bali targeted at meeting the increasing demand for lamb. They are meat-type goats created by crossing male Boer and female Kacang breeds. This new breed is expected to have good adaptation in a poor environment, such as Kacang goats and produce good quality lamb as Boer goats. Therefore, this study aimed to examine phenotypic and genotypic characteristics of Boerka goats raised in Bali. A total of 16 female Boerka goats at 2 years old collected from a group of livestock farmers in Sanda Village were used as samples. This observational study began with observations of qualitative characteristics and morphometric measurements of goats, followed by polymerase chain reaction (PCR) of the growth hormone (GH) gene using GH5F and GH5R primers. Polymerase chain reaction products were then sequenced and analyzed with the MEGA 11 program. The results showed that all Boerka goats had stuck-down ears, the heads were predominantly brown in color (62.5%), the body color pattern tends to be white (87.50%), and the tail color pattern was also dominated by white (62.5%). In morphometric terms, the samples were close to Kacang goats based on the body weight, head length, head width, chest width, depth, and circumference, left front leg circumference, ear length, ear width, tail length, tail width, and flank height except for head height, body length, horn length, and shoulder height. Analysis of the GH gene showed that Boerka goats had a nucleotide composition dominated by the purine base guanine (26.5%) and pyrimidine cytosine (31.8%). Furthermore, they formed a separate cluster with a genetic distance of 14.1% to the Anhui White breed from China, the Tibetan breed, and the Swiss Saanen breed. Boerka goats raised in Bali have phenotypes, including qualitative characteristics and morphometric measurements close to Kacang goats. As meat-type goats, they also form a separate cluster distinct from similar types worldwide.

A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator

BackgroundThe field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, research now utilises DNA methylation measures at cytosine–guanine dinucleotides (CpG) to detect disease and estimate biological traits such as aging. Given the challenge of high dimensionality of DNA methylation data, feature-selection techniques are commonly employed to reduce dimensionality and identify the most important subset of features. In this study, our aim was to test and compare a range of feature-selection methods and ML algorithms in the development of a novel DNA methylation-based telomere length (TL) estimator. We utilised both nested cross-validation and two independent test sets for the comparisons.ResultsWe found that principal component analysis in advance of elastic net regression led to the overall best performing estimator when evaluated using a nested cross-validation analysis and two independent test cohorts. This approach achieved a correlation between estimated and actual TL of 0.295 (83.4% CI [0.201, 0.384]) on the EXTEND test data set. Contrastingly, the baseline model of elastic net regression with no prior feature reduction stage performed less well in general—suggesting a prior feature-selection stage may have important utility. A previously developed TL estimator, DNAmTL, achieved a correlation of 0.216 (83.4% CI [0.118, 0.310]) on the EXTEND data. Additionally, we observed that different DNA methylation-based TL estimators, which have few common CpGs, are associated with many of the same biological entities.ConclusionsThe variance in performance across tested approaches shows that estimators are sensitive to data set heterogeneity and the development of an optimal DNA methylation-based estimator should benefit from the robust methodological approach used in this study. Moreover, our methodology which utilises a range of feature-selection approaches and ML algorithms could be applied to other biological markers and disease phenotypes, to examine their relationship with DNA methylation and predictive value.

Oligonucleotides as Inhibitors of Ice Recrystallization.

Oligonucleotides of adenine (A20), guanine (G20), cytosine (C20), thymine (T20), cytosine-guanine ((CG)20), and adenine-thymine ((AT)20) were investigated as model compounds for ice recrystallization inhibition (IRI). Dehydroxy uracil (dU20), U20, and T20 were also compared to investigate the effect of minute changes in the hydrophobicity of the oligonucleotides on the IRI activity. Among the oligonucleotides considered in this study, T20 exhibited the best performance for IRI. In addition, the degree of polymerization of oligothymines varied over 5, 10, 20, 30, 50, and 100, and T20 was found to be the most effective for IRI. The IRI mechanism was investigated by comparing U20 and T20, which exhibited the lowest and highest IRI activity, respectively, among the oligonucleotides for their dynamic ice-shaping, thermal hysteresis, and ice nucleation inhibition. Little or no dynamic ice-shaping activity and small thermal hysteresis were observed for both nucleotides. All of the findings suggest that not the ice-polymer adhesion but the hydrophobic interactions of T20 in the interface layer might interfere with the water deposition on the ice crystal surfaces and contribute to the IRI activity of the T20 oligonucleotide.

Development and validation of DNA methylation scores in two European cohorts augment 10-year risk prediction of type 2 diabetes.

Type 2 diabetes mellitus (T2D) presents a major health and economic burden that could be alleviated with improved early prediction and intervention. While standard risk factors have shown good predictive performance, we show that the use of blood-based DNA methylation information leads to a significant improvement in the prediction of 10-year T2D incidence risk. Previous studies have been largely constrained by linear assumptions, the use of cytosine-guanine pairs one-at-a-time and binary outcomes. We present a flexible approach (via an R package, MethylPipeR) based on a range of linear and tree-ensemble models that incorporate time-to-event data for prediction. Using the Generation Scotland cohort (training set ncases = 374, ncontrols = 9,461; test set ncases = 252, ncontrols = 4,526) our best-performing model (area under the receiver operating characteristic curve (AUC) = 0.872, area under the precision-recall curve (PRAUC) = 0.302) showed notable improvement in 10-year onset prediction beyond standard risk factors (AUC = 0.839, precision-recall AUC = 0.227). Replication was observed in the German-based KORA study (n = 1,451, ncases = 142, P = 1.6 × 10-5).

High-Yield Natural Vanillin Production by Amycolatopsis sp. after CRISPR-Cas12a-Mediated Gene Deletion.

Vanillin is an aromatic compound, which is widely used in food flavoring, beverages, perfumes, and pharmaceuticals. Amycolatopsis sp. is considered a good strain for the production of vanillin from ferulic acid by fermentation; however, its high genomic guanine-cytosine (GC) content (>70%) and low transformation and recombination efficiency limit its genetic modification potential to improve vanillin production. Efficient genome editing of Amycolatopsis sp. has been challenging, but this study developed a CRISPR-Cas12a system for efficient, markerless, and scarless genome editing of Amycolatopsis sp. CCTCC NO: M2011265. A mutant, ΔvdhΔphdB, was obtained by the deletion of two genes coding byproduct enzymes from the vanillin biosynthetic pathway. The gene deletion increased vanillin production from 10.60 g/L (wild-type) to 20.44 g/L and reduced byproduct vanillic acid from 2.45 to 0.15 g/L in a 3 L fed-batch fermentation, markedly enhancing vanillin production and reducing byproduct formation; the mutant has great potential for industrial application.

A multi-objective butterfly optimization algorithm for protein encoding

The integration of multiple genes to maximize protein expression levels represents an important challenge in synthetic biology. This task relies on the definition of multiple protein-coding sequences, which must be as different as possible to avoid information loss. Proteins can be encoded in different ways, using synonymous codons that translate into the same amino acid. Some codons are better suited to the host than others, thus being preferable the use of the most fitting ones. However, adopting only the most highly adapted codons would lead to very similar coding sequences. An additional criterion is given by the fact that the designed sequences must contain a suitable guanine–cytosine (GC) ratio in accordance with the characteristics of the host organism. Therefore, this biological task requires the simultaneous optimization of several, conflicting objectives. This work proposes a novel multi-objective approach for protein encoding, which tackles the problem according to a new formulation based on three objective functions: codon adaptation index, Hamming distance between sequences, and GC content. Our work extends the recent Butterfly Optimization Algorithm to multi-objective contexts, integrating problem-specific operators to boost solution quality by covering the different aspects required for accurate protein encoding. Two key structures, a taboo list and a best solution list, are defined to conduct improved searches attending to the potential improvements that each solution in the population can promote. Experiments conducted on nine real-world proteins reveal the attainment of relevant solutions from different evaluation perspectives, showing significant improvements over other single and multi-objective methods from the literature.

Methylation of BDNF gene in association with episodic memory in women.

Brain-derived neurotrophic factor (BDNF) gene regulation plays an important role in long-term memory formation, and the DNA methylation (DNAm) level of BDNF promoters has been associated with episodic memory deficits. Our aim was to explore the association between DNAm levels in BDNF promoter IV with verbal learning and memory performance in healthy women. We conducted a cross-sectional study by recruiting 53 individuals. Episodic memory was assessed by using the Rey Auditory Verbal Learning Test (RAVLT). Clinical interviews, RAVLT, and blood sample collection were assessed in all participants. DNAm was measured on DNA from whole peripheral blood using pyrosequencing. According to generalized linear model (GzLM) analyses, cytosine guanine dinucleotide (CpG) site 5 showed significant associations between learning capacity (LC, p < 0.035), that is, every 1% of DNA methylation at CpG site 5 results in a 0.068 reduction in verbal learning performance. To the best of our knowledge, the current study is the first to show that BDNF DNAm plays an important role in episodic memory.

Comparison of the DNA-binding interactions of 5-hydroxymethylfurfural and its synthesized derivative, 5, 5’[oxy-bis(methylene)]bis-2-furfural: experimental, DFT and docking studies

In this study, the in vitro DNA-binding interactions of the food/drug additive, 5-hydroxymethylfurfural (HMF) and its major degradant, 5, 5'[oxy-bis(methylene)]bis-2-furfural (OBMF) were investigated. OBMF was synthesized and characterized using IR, NMR and mass spectrometry. Photometric titrations revealed OBMF induced more extensive perturbations in the 258 nm band of DNA and exhibited binding constants that were 5–12-folds higher than those of HMF. The greatest net changes in viscosity of DNA induced by HMF and OBMF were 10.5 and 8.9%, respectively which confirmed both compounds as minor groove binders. Docking revealed that OBMF and HMF bound to the guanine–cytosine regions of minor groove of DNA with global binding energies of −36.36 and −26.12 kcal/mol, respectively. DFT calculations revealed the higher electrophilicity of OBMF contributed to its increased interaction with the negatively charged DNA backbone. There is a need for stricter control of permissible levels of OBMF in food and drug products.

Global concerns about camel flu: outbreak, etiology, genomic structure, transmission, symptoms, diagnostic tests, prevention, and treatment - correspondence.

Global concerns about camel flu: outbreak, etiology, genomic structure, transmission, symptoms, diagnostic tests, prevention, and treatment - correspondence.

De Novo Hybrid Assembled Draft Genome of Commiphora wightii (Arnott) Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis

Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine-cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.

Genome survey and genetic characterization of Acacia pachyceras O. Schwartz.

Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation.

Whole-genome sequencing of Histophilus somni strains isolated in Russia.

Histophilus somni is a Gram-negative bacterium belonging to the Pasteurellaceae family that can cause bovine histophilosis. Histophilus may act as a commensal or opportunistic bacterial cattle pathogen. Comparing genomes of the pathogenic strain 2336 with the non-pathogenic preputial 129Pt isolate revealed some putative virulence factors. The study of the complete genomes of H. somni strains circulating in Russia has never been conducted before. This study aimed to identify genetic features of the H. somni strains isolated in Russia and evaluate the possibility of using strains for vaccine development. Three strains of H. somni were isolated from different sources. Strain 188-VIEV was isolated from a vaginal swab sample of cattle with endometritis. 532-VIEV and 551-VIEV were cultured from the cryopreserved bull semen samples imported from Canada. Histophilus somni strain ATCC 700025 provided by ATCC (American Type Culture Collection) was also used in the study. DNA extraction was performed using QIAamp DNA Mini Kit (QIAGEN, USA). The whole-genome sequencing of the four strains was performed using Illumina Miseq. The comparison of the resulting sequences with the complete genomes of H. somni 2336 and 129Pt, and detection of the resistance genes and virulence factors, was performed using the ResFinder and Virulence Factor Database web services. The genome size of the samples varied from 1.9 to 2.3 Mb. The number of coding sequences varied from 1795 to 2256. The average sequence density was 90%. The total guanine-cytosine (GC) content was 36.8%-37.2%, which coincided with data previously obtained for H. somni. Three out of four studied strains encoded putative virulence factors such as filamentous hemagglutinin homologs, lipooligosaccharide biosynthesis proteins, and proteins involved in iron transport and utilization. The Ser83Ile substitution was identified in the DNA topoisomerase II (gyrA) in H. somni strains 532-VIEV and 551-VIEV cultured from bull semen which led to resistance to fluoroquinolones. The gene (AAC-6-Ia + APH-2'') encoding a bifunctional aminoglycoside modification enzyme was detected in strain 551-VIEV. Strains with virulence genes identified could be candidates for designing vaccines and potentially represent antigen sources. The results show that antibiotic-resistant H. somni can be spread with semen used for artificial insemination.

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage

The extensive information capacity of DNA, coupled with decreasing costs for DNA synthesis and sequencing, makes DNA an attractive alternative to traditional data storage. The processes of writing, storing, and reading DNA exhibit specific error profiles and constraints DNA sequences have to adhere to. We present DNA-Aeon, a concatenated coding scheme for DNA data storage. It supports the generation of variable-sized encoded sequences with a user-defined Guanine-Cytosine (GC) content, homopolymer length limitation, and the avoidance of undesired motifs. It further enables users to provide custom codebooks adhering to further constraints. DNA-Aeon can correct substitution errors, insertions, deletions, and the loss of whole DNA strands. Comparisons with other codes show better error-correction capabilities of DNA-Aeon at similar redundancy levels with decreased DNA synthesis costs. In-vitro tests indicate high reliability of DNA-Aeon even in the case of skewed sequencing read distributions and high read-dropout.

Draft genomes of Blastocystis subtypes from human samples of Colombia

BackgroundBlastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear.MethodsTo study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identified 10 different subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n = 3), ST2 (n = 1), ST3 (n = 2), ST6 (n = 1), ST7 (n = 1), and ST8 (n = 2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT).ResultsAnalyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scaffolds, with total genome size ranging from 12 to 13.2 Mb and N50 values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scaffolds, and an N50 of 248,997 bp.ConclusionThis work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity.Graphical

Hybrid genome assembly and annotation of multidrug-resistant Staphylococcus aureus genotype ST672-SCCmec type IVd (2B)

ObjectivesThe emergence of multidrug-resistant Staphylococcus aureus strains is mainly mediated by mobile genetic elements, such as Staphylococcal Cassette Chromosome mec (SCCmec). Currently, SCCmec elements in S. aureus are classified into 15 types, with type IV being the most common in hospital and community-associated methicillin-resistant S. aureus. Among different subtypes of SCCmec type IV strains (IVa-IVn), the complete genome sequence of the SCCmec IVd (2B) subtype is still lacking. Here, we report the complete genome sequence of multidrug-resistant S. aureus SCCmec typeIVd (2B) isolate, S. aureus S145. MethodsStaphylococcus aureus S145 was subjected to phenotypic and genotypic characterization. The whole-genome sequencing of S145 was performed using a hybrid-genome approach. The antibiotic-resistance genes were detected and compared with 112 publicly available S. aureus genomes. ResultsWe obtained a complete genome of S145 with 2.7 Mbp length, Guanine-Cytosine (GC) content of 32.8%, and 2,548 protein-coding regions with 79 virulence factors and 90 antibiotic resistance genes. The S145 has ∼17-kb SCCmec, which encodes genes such as mecA, mecR1, ccrA2B2, and SCCmec IVd (2B) subtype gene CG002. We detected a ∼30-kb multidrug-resistant plasmid with eight antibiotic-resistant genes forming three clusters. Cluster1 encoded for penicillin (blaI-blaZ-blaR1), Cluster2 for aminoglycoside-streptothricin (aph(3’)-IIIa-sat4-ΔANT(6)-Ia), and Cluster3 for macrolides (msr(A)-mph(C)) resistance genes. Comparative analysis of Cluster1-Cluster3 revealed that the genetic organization of these clusters resembles resistance genes present in plasmids of USA300 S. aureus SCCmec type IVa strains. ConclusionHere, we report the complete genome sequence of S. aureus SCCmec IVd (2B) that can be used as a reference genome for further comparative genomic analysis.

Bubble Relaxation Dynamics in Homopolymer DNA Sequences.

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.