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Abstract Background Long-term treatment with trimethoprim-sulfamethoxazole (SXT) can lead to the formation of small-colony variants (SCVs) of Staphylococcus aureus. However, the mechanism behind SCVs formation remains poorly understood. In this study, we explored the phenotype and omics-based characterization of S. aureus SCVs induced by SXT and shed light on the potential causes of SCV formation. Methods Stable SCVs were obtained by continuously treating S. aureus isolates using 12/238 µg/ml of SXT, characterized by growth kinetics, antibiotic susceptibility testing, and auxotrophism test. Subsequently, a pair of representative strains (SCV and its parental strain) were selected for genomic, transcriptomic and metabolomic analysis. Results Three stable S. aureus SCVs were successfully screened and proven to be homologous to their corresponding parental strains. Phenotypic tests showed that all SCVs were non-classical mechanisms associated with impaired utilization of menadione, heme and thymine, and exhibited slower growth and higher antibiotic minimum inhibitory concentrations (MICs), compared to their corresponding parental strains. Genomic data revealed 15 missense mutations in 13 genes in the representative SCV, which were involved in adhesion, intramolecular phosphate transfer on ribose, transport pathways, and phage-encoded proteins. The combination analysis of transcriptome and metabolome identified 35 overlapping pathways possible associated with the phenotype switching of S. aureus. These pathways mainly included changes in metabolism, such as purine metabolism, pyruvate metabolism, amino acid metabolism, and ABC transporters, which could play a crucial role in promoting SCVs development by affecting nucleic acid synthesis and energy metabolism in bacteria. Conclusion This study provides profound insights into the causes of S. aureus SCV formation induced by SXT. The findings may offer valuable clues for developing new strategies to combat S. aureus SCV infections.

The spines of Chinese red chestnut are red and the depth of their color gradually increases with maturity. To identify the anthocyanin types and synthesis pathways in red chestnut and to identify the key genes regulating the anthocyanin biosynthesis pathway, we obtained and analyzed the transcriptome and anthocyanin metabolism of red chestnut and its control variety with green spines at 3 different periods. GO and KEGG analyses revealed that photosynthesis was more highly enriched in green spines compared with red spines, while processes related to defense and metabolism regulation were more highly enriched in red spines. The analysis showed that the change in spine color promoted photoprotection in red chestnut, especially at the early growth stage, which resulted in the accumulation of differentially expressed genes involved in the defense metabolic pathway. The metabolome results revealed 6 anthocyanins in red spines. Moreover, red spines exhibited high levels of cyanidin, peonidin and pelargonidin and low levels of delphinidin, petunidin and malvidin. Compared with those in the control group, the levels of cyanidin, peonidin, pelargonidin and malvidin in red spines were significantly increased, indicating that the cyanidin and pelargonidin pathways were enriched in the synthesis of anthocyanins in red spines, whereas the delphinidin pathways were inhibited and mostly transformed into malvidin. During the process of flower pigment synthesis, the expression of the CHS, CHI, F3H, CYP75A, CYP75B1, DFR and ANS genes clearly increased, that of CYP73A decreased obviously, and that of PAL, 4CL and LAR both increased and decreased. Notably, the findings revealed that the synthesized anthocyanin can be converted into anthocyanidin or epicatechin. In red spines, the upregulation of BZ1 gene expression increases the corresponding anthocyanidin content, and the upregulation of the ANR gene also promotes the conversion of anthocyanin to epicatechin. The transcription factors involved in color formation included 4 WRKYs.

Japanese chestnut (Castanea crenata Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar ‘Tsukuba’ by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.

This study proposed an artificial intelligence (AI) approach for rapid, automatic detection of gasoline samples from different ignitable liquid samples based on their Raman spectra. The system integrated Raman spectroscopy, Raman signal transform, and transfer learning with a convolutional neural network (CNN). A hand-held Raman spectrometer was utilized to collect the learning dataset, including 180 gasoline spectra and 170 non-gasoline spectra from 17 various types of liquid samples. Continuous wavelet transform (CWT) was adopted to transform Raman spectra into image representations to facilitate transfer learning using a pre-trained CNN for image recognition. This approach streamlined AI model training, performance verification, and assessment. Experimental results showed that the CNN model could achieve 100% classification performance in precision, sensitivity, specificity, F1 score, and accuracy. The established AI model could be adopted for the Raman spectrum collected by different accessories, such as using the point-and-shoot attachment of liquid samples in glass vials. The experimental results suggested that CWT processing of Raman scattering signals enabled effective CNN transfer learning. The study demonstrated that CWT could be applied for Raman spectra processing to develop edge AI in forensic field testing of physical evidence.

AimOur previous proteomic analysis showed that small RNA SprC (one of the small pathogenicity island RNAs) of Staphylococcus aureus possesses the ability to regulate the expression of multiple bacterial proteins. In this study, our objective was to further provide insights into the regulatory role of SprC in gene transcription and metabolism of S. aureus.MethodsGene expression profiles were obtained from S. aureus N315 wild-type and its sprC deletion mutant strains by RNA-sequencing (RNA-seq), and differentially expressed genes (DEGs) were screened by R language with a |log2(fold change)| ≥1 and a false discovery rate (FDR) ≤ 0.05. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out to understand the significance of the DEGs. The quality of RNA-seq was further verified by quantitative real-time PCR (qRT-PCR), mRNA target prediction, metabolomics analysis and transcript-level expression analysis of genes of sprC complementation strain.ResultsA total of 2497 transcripts were identified, of which 60 transcripts expressions in sprC knockout strain were significantly different (37 up-regulated and 23 down-regulated DEGs). GO analysis showed that the functions of these DEGs were mainly concentrated in the biological process and molecular function related to metabolism and pathogenesis, and a higher number of genes were involved in the oxidation-reduction process, catalytic activity and binding. KEGG pathways enrichment analysis demonstrated that metabolism and pathogenesis were the most affected pathways, such as metabolic pathways, biosynthesis of secondary metabolites, purine metabolism, fructose and mannose metabolism and S. aureus infection. The qRT-PCR results of the DEGs with defined functions in the sprC deletion and complementation strains were in general agreement with those obtained by RNA-seq. Metabolomics analysis revealed 77 specific pathways involving metabolic pathways. Among them, many, such as metabolic pathways, biosynthesis of secondary metabolites and purine metabolism, were consistent with those enriched in the RNA-seq analysis.ConclusionThis study offered valuable and reliable information about the regulatory roles of SprC in S. aureus biology through transcriptomics and metabolomics analysis. These results may provide clues for new potential targets for anti-virulence adjuvant therapy on S. aureus infection.

To fully protect and utilize Acer truncatum resources, the phenotypic variation and genetic diversity of A. truncatum in different regions should be understood. In this study, leaves of A. truncatum trees from 15 provenances were used as experimental materials to analyze leaf morphological variation and genetic diversity at the molecular level. The results showed that the sizes of leaves of A. truncatum trees from different provenances were significantly different, and there was a certain correlation with the geographical environment: leaf size gradually decreased with increasing longitude, latitude and elevation. According to principal component analysis (PCA), the variation in leaf morphology among provenances concerned mainly the petioles, leaf width, and leaf length; there was no correlation between leaf morphological variation and geographic distance. From 240 pairs of sequence-related amplified polymorphism (SRAP) primer combinations, 12 pairs that met the conditions were identified, and a total of 267 bands were amplified; 252 of the bands were polymorphic, with a polymorphism percentage of 94.38%, and an average of 22.25 bands and 21 polymorphic bands were amplified from each pair of primers. Ne, H and I indicated that A. truncatum has relatively high genetic variation and a rich genetic diversity at the species level. Among the provenances, H and I were 0.1754 and 0.2707 respectively, indicating that the genetic diversity among the provenances of A. truncatum was low. There were differences in genetic diversity parameters among the various sources. Yongji, Shanxi (6) had the highest genetic diversity, and Huixian, Gansu (15) had the lowest genetic diversity. The genetic similarity coefficients among the various sources ranged from 0.8404 to 0.9558, the range of variation was 0.1154, and the average coefficient was 0.9006. The provenance of Taian, Shandong (4) and Yongji, Shanxi (6) had the closest genetic relationship, with a genetic similarity coefficient of 0.9558 and a D of 0.0824; Pingquan, Hebei (2) and Huixian, Gansu (15) were the most distantly related, with the largest D, and a genetic similarity coefficient of 0.8404. Cluster analysis based on the genetic similarity coefficient also showed that the Ds and geographic distances of A. truncatum from different provenances were not correlated. These results provide a reference for research on A. truncatum germplasm management and ecological adaptability.

Sweet chestnut (Castanea sativa) is an endemic species of genus Castanea in Europe, which is widespread in the southern part of continental Europe. The complete genome sequence of chloroplast was determined through Illumina NovaSeq platform. Totally the genome of chloroplast was 160,938 bp in length, GC rich (36.8%), comprising a pair of 25,726 bp inverted repeat sequences, separated by a 90,519 bp large and 18,967 bp small single-copy regions. There were 129 genes, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 protein-coding genes. The phylogenetic tree analysis showed that C. sativa exhibited the closest relationship with Castanea henryi.

Abstract Background The data on the prevalence of resistance to mupirocin (MUP), fusidic acid (FA) and retapamulin (RET) in methicillin-resistant Staphylococcus aureus (MRSA) from China are still limited. This study aimed to examine these three antibiotics resistance in 1206 MRSA clinical isolates from Eastern China. Phenotypic MUP, FA and RET resistance was determined by minimum inhibitory concentrations (MICs), and genotypic by PCR and DNA sequencing of the mupA/B, fusB-D, cfr, vgaA/Av/A LC /B/C/E, lsaA-C/E and salA and mutations in ileS, fusA/E, rplC, and 23S RNA V domain. The genetic characteristics of resistance isolates were conducted by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Results Overall MRSA MUP, FA and RET resistance was low (5.1, 1.0 and 0.3%, respectively). MupA was the mechanism of high-level MUP resistance. All low-level MUP resistance isolates possessed an equivocal mutation N213D in IleS; of these, 2 reported an additional V588F mutation with an impact on the Rossman fold. FusA mutations, such as L461K, H457Q, H457Y and V90I were the primary FA mechanisms among high-level resistance isolates, most of which also contained fusC; however, all low-level resistance strains carried fusB. Except lsaE gene detected in one isolate, no other resistance mechanisms tested were found among RET-resistant isolates. Additionally, sixteen PFGE types (A-P) were observed, among which type B was the most common (49/76, 64.5%), followed by types E and G (4/76, 5.3% each) and types C and M (3/76, 3.9% each). All resistant strains were divided into 15 ST types by MLST. ST764 (24/76, 31.6%), ST630 (11/76, 14.5%), ST239 (9/76, 11.8%) and ST5 (7/76, 9.2%) were the major types. PFGE type B isolates with the aforementioned STs were mainly found in mupirocin resistant isolates. Conclusions MUP, FA and RET exhibited highly activity against the MRSA isolates. Acquired genes and chromosome-borne genes mutations were responsible for MUP and FA resistance; however, the mechanism for some RET-resistant isolates remains to be further elucidated. Also, the surveillance to MUP in MRSA should be strengthened to prevent elevated resistance due to the expansion of clones.

Phytoplasmas are cell wall-less bacteria that induce abnormal plant growth and various diseases, causing severe economic loss. Phytoplasmas are highly dependent on nutrients imported from host cells because they have lost many genes involved in essential metabolic pathways during reductive evolution. However, metabolic crosstalk between phytoplasmas and host plants and the mechanisms of phytoplasma nutrient acquisition remain poorly understood. In this study, using metabolomics approach, sweet cherry virescence (SCV) phytoplasma-induced metabolite alterations in sweet cherry trees were investigated. A total of 676 metabolites were identified in SCV phytoplasma-infected and mock inoculated leaves, of which 187 metabolites were differentially expressed, with an overwhelming majority belonging to carbohydrates, fatty acids/lipids, amino acids, and flavonoids. Available omics data of interactions between plant and phytoplasma were also deciphered and integrated into the present study. The results demonstrated that phytoplasma infection promoted glycolysis and pentose phosphate pathway activities, which provide energy and nutrients, and facilitate biosynthesis of necessary low-molecular metabolites. Our findings indicated that phytoplasma can induce reprograming of plant metabolism to obtain nutrients for its own replication and infection. The findings from this study provide new insight into interactions of host plants and phytoplasmas from a nutrient acquisition perspective.

Hop stunt viroid (HSVd) is a member of the genus Hostuviroid of the family Pospiviroidae and has been found in a wide range of herbaceous and woody hosts. It causes serious dapple fruit symptoms on infected sweet cherry, notably inducing cherry tree decay. In order to better understand the molecular mechanisms of HSVd infection in sweet cherry fruit, transcriptome analysis of HSVd-infected and healthy sweet cherry fruits was carried out. A total of 1,572 differentially expressed genes (DEGs) were identified, involving 961 upregulated DEGs and 611 downregulated DEGs. Functional analysis indicated that the DEGs were mainly involved in plant hormone signal transduction, plant–pathogen interactions, secondary metabolism, and the MAPK signaling pathway. In addition, C2H2 zinc finger, MYB, bHLH, AP2/ERF, C2C2-dof, NAC and WRKY transcription factors can respond to HSVd infection. In order to confirm the high-throughput sequencing results, 16 DEGs were verified by RT-qPCR analysis. The results provided insight into the pathways and genes of sweet cherry fruit in response to HSVd infection.

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

Antibiotics have been described to modulate bacterial virulence gene expression. This study aimed to assess the changes caused by anti-Staphylococcus agents in the transcription of leucocidin ED (lukED) gene of Staphylococcus aureus strain Newman in vitro and in vivo and to determine whether the altered expression is agr dependent. The bacteria were exposed to subinhibitory concentrations [1/2, 1/4, or 1/8 minimal inhibitory concentration (MIC)] of 11 antibiotics, and the expression of lukE and agr-effector RNAIII was determined using qRT-PCR. In vivo experiments were performed to evaluate the impact exerted by six representative antibiotics on the transcription of both genes. Molecular analysis showed that in vitro lukE transcription was dramatically promoted in the Newman strain exposed to sub-MICs of vancomycin, trimethoprim–sulfamethoxazole, clindamycin, gentamicin, daptomycin, and ciprofloxacin and considerably reduced when stimulated by cefazolin, erythromycin, rifampicin, tigecycline, and linezolid. In the murine abscess model, tigecycline significantly decreased the transcription of lukE and the bacterial numbers, whereas vancomycin increased them; although cefazolin increased the lukE expression (contrary to the in vitro effect), it had a remarkable role in reducing bacterial load. The correspondence analysis shows that RNAIII expression varied under seven of 11 antibiotics in vitro, and six drugs in vivo were consistent with lukE transcripts. In conclusion, our data show that anti-Staphylococcus antibiotics exert modulatory effects on lukE expression in vitro and/or in vivo, and the changed expression caused by some drugs may be involved with agr activity, thus providing a guide to choose appropriate agents to avoid promoting bacterial virulence in lukED-positive S. aureus infections.

Abstract Background The bicomponent leukotoxins and the pyrogenic toxin superantigens (PTSAgs) are important virulence factors of Staphylococcus aureus. It is necessary to survey the prevalence and expression of these toxin-encoding genes for understanding the possible pathogenic capacity of S. aureus to cause disease. Methods Five leukotoxin genes and thirteen PTSAg determinants were detected for 177 S. aureus isolates from blood (n = 88) and wound (n = 89) infections by Polymerase Chain Reaction (PCR). The expression of leukotoxin ED (lukED) was determined by quantitative real-time PCR (qRT-PCR). The genetic backgrounds of isolates were analyzed by Staphylococcal Cassette Chromosome mec (SCCmec) typing (for methicillin-resistant S. aureus isolates), Pulsed-Field Gel Electrophoresis (PFGE), accessory gene regulator (agr) typing and Multilocus Sequence Typing (MLST, for representative isolates based on PFGE type) methods. Results 99.4% (176/177) isolates contained at least one of leukotoxin genes. Among them, 94.9% (168/177), 81.4% (144/177) and 67.8% (120/177) isolates harbored hlgBC, lukED and lukAB, respectively. Compared to leukotoxin genes, there was a relatively lower overall prevalence of PTSAg genes [99.4% versus 72.9% (129/177), P

The toxic shock syndrome toxin-1 (TSST-1), encoded by tst gene, has been proposed to cause staphylococcal toxic shock syndrome (TSS) in a susceptible host, which highlights the need to evaluate the level of tst gene expression and molecular genetic characteristics of the tst-positive isolates. A total of 916 S. aureus isolates collected from seven hospitals in China were screened for the tst gene. The tst positive isolates were characterized by spa, SCCmec, PFGE, and agr typing. Representative strains were also subjected to MLST typing. qRT-PCR was used to quantify tst and major virulence regulator genes expression. We also sequenced the regions of promoter and open reading frame (ORF) of tst to investigate whether they correlate with the variation in tst expression. We found 208 (22.7%) of surveyed isolates including 198 (29.8%) of MRSA and 10 (4.0%) of MSSA isolates harbored the tst gene. The most common clone among tst positive MRSA isolates belonged to ST5 (CC5)-agr2-t002-SCCmecII. The amount of tst mRNA varied 8.4-folds among clinical S. aureus isolates. Sequencing the tst promoter revealed a base T deletion in tst high expressed isolates. As for major virulence regulators, srrA, sarT, RNAIII, and ccpA in four tst differentially expressed strains were detected to be highly expressed, respectively. Our study revealed high prevalence of ST5 (CC5)-agr2-t002-SCCmecII clone among tst positive MRSA in hospitals from China. The levels of tst expression among clinical S. aureus isolates varied, which may be associated with tst promoter and variations in specific virulence regulators.

Aim: In this study, Staphylococcus phage JD007 bactericidal activity and induced immune responses during treatment were assessed in a dermal abscess model.Materials and Methods: Dermal abscesses in nude mice were established by injecting a clinical isolate of S. aureus SA325 isolated from the back under-dermal abscess of an in-patient.Results: Phage JD007 was able to inhibit the growth of S. aureus SA325 at MOI = 1 or 10, significantly preventing the formation of dermal abscesses. Moderate immune responses were observed in the prevention group through detection of cytokines.Conclusion: Phage JD007 inhibits the formation of dermal abscesses caused by a clinical S. aureus strain in nude mice without robust immune responses.

Prunus canescens is an endemic cherry species in China, which is distributed in Shaanxi, Gansu, Hubei, and Sichuan provinces of China. The chloroplast (cp) genome of P. canescens is 157,890 bp in size containing 125 unique genes, including 8 rRNA genes, 37 tRNA genes, and 80 protein-coding genes (PCGs). Phylogenetic analysis exhibited that P. canescens is most related to P. pseudocerasus.

Vaccinium duclouxii is an endemic species in China, which is distributed in Sichuan and Yunnan province of China. The chloroplast (cp) genome of V. duclouxii is 168,953 bp in size containing 123 unique genes, including 8 rRNA genes, 38 tRNA genes, and 77 protein-coding genes (PCGs). Phylogenetic analysis exhibited that V. duclouxii and V. macrocarpon were most related to Arbutus unedo.

Castanea seguinii is an endemic chestnut species in China, which is widely distributed over central and southeastern China. The chloroplast genome sequences were finally resolved by high-throughput sequencing platform Illumina Hiseq X Ten. Totally the genome is 160,419 bp in size, AT rich (63.3%), comprising a couple of 25,694 bp long inverted repeat regions, separated by a 90,055 bp large and 18,976 bp small single copy regions. 79 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes were identified and annotated. The results of the molecular phylogenetic analysis exhibited that C. seguinii showed the closest relationship with C. mollissima, with high bootstrap support.

Mobile watermarking robust to geometrical distortions is still a great challenge. In mobile watermarking, efficient computation is necessary because mobile devices have very limited resources due to power consumption. In this paper, we propose a low-complexity geometrically resilient watermarking approach based on the optimal tradeoff circular harmonic function (OTCHF) correlation filter and the minimum average correlation energy Mellin radial harmonic (MACE-MRH) correlation filter. By the rotation, translation and scale tolerance properties of the two kinds of filter, the proposed watermark detector can be robust to geometrical attacks. The embedded watermark is weighted by a perceptual mask which matches very well with the properties of the human visual system. Before correlation, a whitening process is utilized to improve watermark detection reliability. Experimental results demonstrate that the proposed watermarking approach is computationally efficient and robust to geometrical distortions.

Advanced Audio Coding (AAC), a standardized lossy compression scheme for digital audio, which was designed to be the successor of the MP3 format, generally achieves better sound quality than MP3 at similar bit rates. While AAC is also the default or standard audio format for many devices and AAC audio files may be presented as important digital evidences, the authentication of the audio files is highly needed but relatively missing. In this paper, we propose a scheme to expose tampered AAC audio streams that are encoded at the same encoding bit-rate. Specifically, we design a shift-recompression based method to retrieve the differential features between the re-encoded audio stream at each shifting and original audio stream, learning classifier is employed to recognize different patterns of differential features of the doctored forgery files and original (untouched) audio files. Experimental results show that our approach is very promising and effective to detect the forgery of the same encoding bit-rate on AAC audio streams. Our study also shows that shift recompression-based differential analysis is very effective for detection of the MP3 forgery at the same bit rate.

Panton-Valentine leucocidin (PVL, encoded by lukSF-PV genes), a bi-component and pore-forming toxin, is carried by different staphylococcal bacteriophages. The prevalence of PVL in Staphylococcus aureus (S. aureus) have been reported around the globe. However, the data on PVL-encoding phage types, lukSF-PV gene variation and chromosomal phage insertion sites for PVL-positive S. aureus are limited, especially in China. In order to obtain a more complete understanding of the molecular epidemiology of PVL-positive S. aureus, an integrated and modified PCR-based scheme was applied to detect the PVL-encoding phage types. Phage insertion locus and the lukSF-PV variant were determined by PCR and sequencing. Meanwhile, the genetic background was characterized by staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) gene polymorphisms typing, pulsed-field gel electrophoresis (PFGE) typing, accessory gene regulator (agr) locus typing and multilocus sequence typing (MLST). Seventy eight (78/1175, 6.6%) isolates possessed the lukSF-PV genes and 59.0% (46/78) of PVL-positive strains belonged to CC59 lineage. Eight known different PVL-encoding phage types were detected, and Φ7247PVL/ΦST5967PVL (n=13) and ΦPVL (n=12) were the most prevalent among them. While 25 (25/78, 32.1%) isolates, belonging to ST30 and ST59 clones, were unable to be typed by the modified PCR-based scheme. Single nucleotide polymorphisms (SNPs) were identified at five locations in the lukSF-PV genes, two of which were non-synonymous. Maximum-likelihood tree analysis of attachment sites sequences detected six SNP profiles for attR and eight for attL, respectively. In conclusion, the PVL-positive S. aureus mainly harbored Φ7247PVL/ΦST5967PVL and ΦPVL in the regions studied. lukSF-PV gene sequences, PVL-encoding phages and phage insertion locus generally varied with lineages. Moreover, PVL-positive clones that have emerged worldwide likely carry distinct phages.

Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.

BACKGROUND: The genus Corylus is an important woody species in Northeast China. Its products, hazelnuts, constitute one of the most important raw materials for the pastry and chocolate industry. However, limited genetic research has focused on Corylus because of the lack of genomic resources. The advent of high-throughput sequencing technologies provides a turning point for Corylus research. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive database for the Corylus heterophylla Fisch floral buds. RESULTS: The C. heterophylla Fisch floral buds transcriptome was sequenced using the Illumina paired-end sequencing technology. We produced 28,930,890 raw reads and assembled them into 82,684 contigs. A total of 40,941 unigenes were identified, among which 30,549 were annotated in the NCBI Non-redundant (Nr) protein database and 18,581 were annotated in the Swiss-Prot database. Of these annotated unigenes, 25,311 and 10,514 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. We could map 17,207 unigenes onto 128 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. Additionally, based on the transcriptome, we constructed a candidate cold tolerance gene set of C. heterophylla Fisch floral buds. The expression patterns of selected genes during four stages of cold acclimation suggested that these genes might be involved in different cold responsive stages in C. heterophylla Fisch floral buds. CONCLUSION: The transcriptome of C. heterophylla Fisch floral buds was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the C. heterophylla Fisch floral buds transcriptome. Candidate genes potentially involved in cold tolerance were identified, providing a material basis for future molecular mechanism analysis of C. heterophylla Fisch floral buds tolerant to cold stress.

The emergence and prevalence of high-level mupirocin-resistant, methicillin-resistant Staphylococcus aureus (MuH MRSA) is challenging the eradication of MRSA nasal carriage and the treatment of skin and soft tissue infections. To understand the potentially pathogenetic capacity and the genetic basis of MuH MRSA, it is important to have a detailed knowledge of the molecular traits of this organism. Fifty three MuH MRSA isolates were gathered from Shanghai (28 isolates) and Wenzhou (25 isolates) in China. These isolates, consisting of 27 different PFGE-SCCmec-spa patterns, were examined by PCR for 35 virulence genes and further typed using agr (accessory gene regulator) typing and MLST (multilocus sequence typing). All 53 strains were positive for the genes hlg/hlg variant and icaD, and negative for seb, sed, see, seh, eta, etb, hld, cap-5, and ACME-arcA. Compared with Wenzhou isolates, Shanghai isolates were more likely to carry seg (P = 0.002) and several other genes which were not found in Wenzhou strains such as sec, sei, tst (P

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods: Support Vector Machine Recursive Feature Elimination (SVMRFE), Leave-One-Out Calculation Sequential Forward Selection (LOOCSFS), Gradient based Leave-one-out Gene Selection (GLGS). To evaluate the performance of these gene selection methods, we employ several popular learning classifiers on the MicroArray Quality Control phase II on predictive modeling (MAQC-II) breast cancer dataset and the MAQC-II multiple myeloma dataset. Experimental results show that gene selection is strictly paired with learning classifier. Overall, our approach outperforms other compared methods. The biological functional analysis based on the MAQC-II breast cancer dataset convinced us to apply our method for phenotype prediction. Additionally, learning classifiers also play important roles in the classification of microarray data and our experimental results indicate that the Nearest Mean Scale Classifier (NMSC) is a good choice due to its prediction reliability and its stability across the three performance measurements: Testing accuracy, MCC values, and AUC errors.