Summary Rapidly enhancing oleoresin production in conifer stems through genomic selection and genetic engineering may increase resistance to bark beetles terpenoid yield for liquid biofuels. We integrated association prediction analyses of flow (g 24 h −1 ) using 4854 single nucleotide polymorphisms ( SNP s) expressed genes within a pedigreed population loblolly pine P inus taeda that was clonally replicated at three sites the s outheastern U nited S tates. Additive variation 2 ≈ 0.12–0.30)...

A recent genome-wide screen identified ~300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around Cas9 nuclease (Cas9Smu) encoded S. mutans UA159 genome. Using xylose-inducible dead Cas9Smu with constitutively active single-guide RNA (sgRNA), observed titratable repression of GFP fluorescence that compared favorably pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity...

Summary Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial number ( RCN ), single nucleotide polymorphisms SNP s) 4027 were tested association with two growth rings three environments a complex pedigree of 520 taeda individuals CCLONES ). The map locations associated compared quantitative trait loci QTL P. ×...

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden Clatskanie, Oregon that were previously collected across distribution range western North America. Using GEMMA mixed model analysis, tested for association of 25 phenotypic 9 multitrait combinations with 6.741 million SNPs covering entire genome. Broad-sense trait heritabilities ranged 0.117 to 0.477. Most significantly...

Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures microbes. Illumina MiSeq sequencing was provided 12 in 7 different countries as part 2018 CAMDA "MetaSUB Forensic Challenge", including also three mystery sets. We used appropriate machine learning techniques on this massive dataset to effectively identify geographical provenance "mystery" samples. Additionally, we pursued compositional analysis develop...

Health-associated biofilms in the oral cavity are composed of a diverse group microbial species that can foster an environment is less favorable for outgrowth dental caries pathogens, like Streptococcus mutans A novel bacterium, designated A12, was previously isolated from supragingival plaque caries-free individual and shown to interfere potently with growth virulence properties S. In this study, we applied functional genomics begin identify molecular mechanisms used by A12 antagonize,...

Composition of microbial communities can be location-specific, and the different abundance taxon within location could help us to unravel city-specific signature predict sample origin locations accurately. In this study, whole genome shotgun (WGS) metagenomics data from samples across 16 cities around world another 8 were provided as main mystery datasets respectively part CAMDA 2019 MetaSUB "Forensic Challenge". The feature selecting, normalization, three methods machine learning, PCoA...

Microbial communities can be location specific, and the abundance of species within locations influence our ability to determine whether a sample belongs one city or another. As part 2017 CAMDA MetaSUB Inter-City Challenge, next generation sequencing (NGS) data was generated from swipe samples collected subway stations in Boston, New York City hereafter York, Sacramento. DNA extracted Illumina sequenced. Sequencing provided for all cities as contest challenge dataset. Principal component...

Abstract The formation of dental caries is a complex process that ultimately leads to damage the tooth enamel from acids produced by microbes in attached biofilms. bacterial interactions occurring within these biofilms between cariogenic bacteria, such as mutans streptococci, and health-associated commensal are thought be critical determinants health disease. To better understand interactions, Streptococcus reporter strain actively monitors cell–cell communication via peptide signaling was...

Single seed near-infrared reflectance (NIR) spectroscopy predicts soybean (Glycine max) quality traits of moisture, oil, and protein. We tested the accuracy transferring calibrations between different single NIR analyzers same design by collecting spectra analytical trait data for globally diverse germplasm. X-ray microcomputed tomography (μCT) was used to collect density shape enhance number that can be predicted from NIR. Partial least-squares (PLS) regression gave accurate predictive...

ABSTRACT As a biological byproduct from both humans and microbes, glycerol’s contribution to microbial homeostasis in the oral cavity remains understudied. In this study, we examined glycerol metabolism by Streptococcus sanguinis, commensal associated with health. Genetic mutants of glucose-PTS enzyme II ( manL ), glp dha pathways), transcriptional regulators were characterized regard catabolism, growth, production hydrogen peroxide (H 2 O transcription, competition mutans . Biochemical...

Sphingoid base phosphates, such as s phingosine- 1 - p hosphate (S1P) and d i h ydro (dhS1P), act ligands for S1P receptors, this interaction is known to play a central role in mediating angiogenesis, vascular stability permeability, immune cell migration sites of inflammation. Studies suggest that shift ratio higher levels dhS1P relation alters downstream signaling cascades due differential binding activation the various receptor isoforms.

Neuroblastoma is the most common tumor of early childhood and notorious for its high variability in clinical presentation. Accurate prognosis has remained a challenge many patients. In this study, expression profiles from RNA-sequencing are used to predict survival times directly. Several models investigated using various annotation levels (genes, transcripts, introns), an ensemble predictor proposed as heuristic combining these different profiles.The use RNA-seq data shown improve accuracy...

A health-associated dental microbiome provides a potent defense against pathogens and diseases. Streptococcus sanguinis is an abundant member of oral flora that antagonizes by producing hydrogen peroxide. There need for better understanding the mechanisms allow bacteria to survive carbohydrate-rich acidic environments associated with development caries.

Dental caries is underpinned by a dysbiotic microbiome and increased acid production. As beneficial bacteria that can antagonize oral pathobionts, streptococci such as S. sanguinis gordonii ferment many carbohydrates, despite their relative sensitivity to low pH.

Fructose catabolism by Streptococcus mutans is initiated three PTS transporters yielding either fructose-1-phoshate (F-1-P) or fructose-6-phosphate (F-6-P). Deletion of one such F-1-P-generating PTS, fruI, has been shown to reduce the cariogenicity S. in rats fed a high-sucrose diet. Moreover, recent study linked fructose metabolism reactive electrophile species (RES) methylglyoxal. Here, we conducted comparative transcriptomic analysis exponentially grown shocked with 50 mM fructose,...

A comparative proteomic analysis was utilized to evaluate similarities and differences in membrane samples derived from the cariogenic bacterium Streptococcus mutans, including wild-type strain four mutants devoid of protein translocation machinery components, specifically ∆ffh, ∆yidC1, ∆yidC2, or ∆ffh/yidC1. The purpose this work determine extent which encoded proteins operate individually concert with one another identify potential substrates respective pathways. Ffh is principal component...

Amino sugars, particularly glucosamine (GlcN) and N-acetylglucosamine (GlcNAc), are abundant carbon nitrogen sources supplied in host secretions the diet to biofilms colonizing human oral cavity. Evidence is emerging that these amino sugars provide ecological advantages beneficial commensals over pathogens pathobionts. Here, we performed transcriptome analysis on Streptococcus mutans gordonii growing single-species or dual-species cultures with glucose, GlcN, GlcNAc as primary carbohydrate...

Integrative and conjugative elements (ICEs) are chromosomally encoded mobile genetic that can transfer DNA between bacterial strains. Recently, as part of efforts to determine hypothetical gene functions, we have discovered an important regulatory module on ICE known TnSmu1 the Streptococcus mutans chromosome. The consists a cI-like repressor with helix-turn-helix binding domain immR Smu (immunity repressor) metalloprotease immA (anti-repressor). It is not possible create in-frame deletion...

CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign by encoding CRISPR spacers help target if it re-enters cell. In this way, are type molecular tape recorder encountered host microorganism. Here, we extracted ∼8,000 from collection over three hundred Streptococcus mutans genomes. Phage major S. spacers. strains have also generated elements such as plasmids and integrative conjugative There may be...

Gingival crevicular fluid (GCF) constitutes the primary growth substrate for Porphyromonas gingivalis in vivo. The goal of this work was to evaluate different strains P. on human serum albumin (HSA), a major constituent GCF.Growth five P.gingivalis HSA medium examined and, surprisingly, three underwent autolysis within 24 h. Comparative transcriptomic analysis used identify genes involved autolysis.Two highly related reference (W50 and W83) differed dramatically their survival when grown...

Abstract The commensal bacterium Streptococcus sp. A12 has multiple properties that may promote the stability of health‐associated oral biofilms, including overt antagonism dental caries pathogen mutans . A LanFEG‐type ABC transporter, PcfFEG, confers tolerance to lantibiotic nisin and enhances ability compete against S. Here, we investigated regulation pcfFEG adjacent genes for a two‐component system, pcfRK , better understand antimicrobial peptide resistance by A12. Induction pcfFEG‐pcfRK...

The periodontal pathogen Porphyromonas gingivalis strain W83 displays at least three different surface glycans, specifically two types of lipopolysaccharides (O-LPS and A-LPS) K-antigen capsule. Despite the importance capsule to virulence P. gingivalis, little is known as how expression genes involved in synthesis this glycan regulated. required for are located a locus that encodes number transcripts, including an operon (PG0104 PG0121, generating ~19.4-kb transcript) which contains...