scholarly journals Completely dechlorinating of trichloroethene by a Dehalococcoides mccartyi-containing microbial consortium in the absence of cobalamin

2021 ◽  
Author(s):  
Haijun Li ◽  
Shanming Wei ◽  
Na Liu ◽  
Yalu Du ◽  
Guantao Ding
Keyword(s):  
Microbial Consortium ◽  
De Novo ◽  
Methanogenic Archaea ◽  
Illumina Miseq ◽  
Contaminated Site ◽  
Sequencing Analysis ◽  
Chlorinated Ethene ◽  
Dehalococcoides Mccartyi ◽  
Cobalamin Biosynthesis ◽  
Exogenous Addition

Abstract Completely dechlorinating of trichloroethene (TCE) by Dehalococcoides mccartyi (D.mccartyi) is catalyzed by reductive dehalogenases (RDases) which possess cobalamin as the crucial cofactor, whereas virtually all pure D.mccartyi strains isolated thus far are corrinoid auxotrophs. Exogenous addition of commercially available cobalamin for real TCE-contaminated site decontamination is deemed to be unrealistic. In this study, TCE reduction by a D.mccartyi-containing microbial consortium utilizing biosynthetic cobalamin generated by interior corrinoid-producing organisms within this mixed consortia was studied. The results confirmed that subcultures with exogenous cobalamin omitting from the medium apparently were impervious and enabled to successively metabolize TCE to non-chlorinated ethene. The 2-bromoethanesulfonate and ampicillin resistance tests results suggested that bacteria (particularly certain ampicillin-sensitive ones) rather than methanogenic archaea within this microbial consortium were responsible for biosynthesizing cobalamin. Moreover, relative stable Ɛ-carbon values of TCE among treatments in disregard of whether exogenous cobalamin or selective inhibitors were existed in the medium also speculated that cobalamin biosynthesized by these organisms was enable to uptake and utilize by D.mccartyi for RDases synthesis and eventually participated in TCE reduction. Finally, the Illumina MiSeq sequencing analysis indicated that Desulfitobacterium and Acetobacterium in this microbial consortium probably both were in charge of de novo cobalamin biosynthesis to fulfillment the requirements of D.mccartyi for TCE metabolism.

scholarly journals Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures

2021 ◽  
Author(s):  
Adam L. Numis ◽  
Gilberto da Gente ◽  
Elliott H. Sherr ◽  
Hannah C. Glass
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
List Type ◽  
Sequencing Analysis ◽  
Neonatal Seizures ◽  
Pathogenic Variants ◽  
Targeted Analysis ◽  
Whole Exome ◽  
Epilepsy Gene

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.

scholarly journals Co-Treatment with Single and Ternary Mixture Gas of Dimethyl Sulfide, Propanethiol, and Toluene by a Macrokinetic Analysis in a Biotrickling Filter Seeded with Alcaligenes sp. SY1 and Pseudomonas Putida S1

Fermentation ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 309
Author(s):  
Yiming Sun ◽  
Xiaowei Lin ◽  
Shaodong Zhu ◽  
Jianmeng Chen ◽  
Yi He ◽  
...  
Keyword(s):  
Ternary Mixture ◽  
Dimethyl Sulfide ◽  
Illumina Miseq ◽  
Industrial Applications ◽  
Biotrickling Filter ◽  
Sequencing Analysis ◽  
Organic Sulfur Compounds ◽  
Volatile Organic ◽  
Bacterial Groups ◽  
Maximum Removal

The biotrickling filter (BTF) treatment is an effective way of dealing with air pollution caused by volatile organic compounds (VOCs). However, this approach is typically used for single VOCs treatment but not for the mixtures of VOC and volatile organic sulfur compounds (VOSCs), even if they are often encountered in industrial applications. Therefore, we investigated the performance of BTF for single and ternary mixture gas of dimethyl sulfide (DMS), propanethiol, and toluene, respectively. Results showed that the co-treatment enhanced the removal efficiency of toluene, but not of dimethyl sulfide or propanethiol. Maximum removal rates (rmax) of DMS, propanethiol and toluene were calculated to be 256.41 g·m−3·h−1, 204.08 g·m−3·h−1 and 90.91 g·m−3·h−1, respectively. For a gas mixture of these three constituents, rmax was measured to be 114.94 g·m−3·h−1, 104.17 g·m−3·h−1 and 99.01 g·m−3·h−1, separately. Illumina MiSeq sequencing analysis further indicated that Proteobacteria and Bacteroidetes were the major bacterial groups in BTF packing materials. A shift of bacterial community structure was observed during the biodegradation process.

scholarly journals De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akifumi Azuma ◽  
Fumiya Taniguchi ◽  
Toshiya Yamamoto ◽  
Akihiko Sato ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genome Structure ◽  
Table Grape ◽  
Sequencing Analysis ◽  
Entire Genome ◽  
Table Grapes ◽  
Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

A case of Luscan-Lumish syndrome: Possible involvement of enhanced GH signaling

2020 ◽  
Author(s):  
Kentaro Suda ◽  
Hidenori Fukuoka ◽  
Genzo Iguchi ◽  
Keitaro Kanie ◽  
Yasunori Fujita ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
De Novo ◽  
Novel Mutation ◽  
Body Height ◽  
Chiari I Malformation ◽  
Oral Glucose ◽  
Tall Stature ◽  
Sequencing Analysis ◽  
Serum Growth Hormone ◽  
Chiari I

Abstract Context Luscan-Lumish syndrome (LLS) is characterized by postnatal overgrowth, obesity, Chiari I malformation, seizures, and intellectual disability. SET domain-containing protein 2 (SETD2) is a histone methyltransferase, where mutations in the gene are associated with the development of LLS. However, mechanisms underlying LLS remain unclear. Case description A 20-year-old man was referred to our hospital because of tall stature. His body height was 188.2 cm (+3.18 SD) and he showed obesity with a body mass index of 28.4 kg/m 2. He exhibited acral overgrowth, jaw malocclusion, and prognathism, but no history of seizures, intellectual disability, or speech delay. Serum growth hormone (GH), insulin-like growth factor 1 (IGF-1), and nadir GH levels after administration of 75 g oral glucose were within normal range. Pituitary magnetic resonance imaging showed no pituitary adenoma, but Chiari I malformation. Whole exome sequencing analysis of the proband revealed a de novo heterozygous germline mutation in SETD2 (c.236T>A, p.L79H). Skin fibroblasts derived from the patient grew faster than those from his father and the control subject. In addition, these cells showed enhanced tyrosine phosphorylation and transcriptional activity of signal transducer and activator of transcription 5b (STAT5b) and increased IGF-1 expression induced by GH. Conclusion This is a mild case of LLS with a novel mutation in SETD2 without neurological symptoms. LLS should be differentiated in a patient with gigantism without pituitary tumors. Although further investigation is necessary, this is the first study to suggest the involvement of aberrant GH signaling in the development of LLS.

scholarly journals Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms

2019 ◽  
Vol 7 (4) ◽  
Author(s):  
Frederique Pasquali ◽  
Federica Palma ◽  
Marcello Trevisani ◽  
Antonio Parisi ◽  
Alex Lucchi ◽  
...  
Keyword(s):  
Shiga Toxin ◽  
Iron Uptake ◽  
De Novo ◽  
Genetic Relationships ◽  
Draft Genome ◽  
Dairy Farms ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Type Assignment ◽  
Potential Biomarker

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7-loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silicousing the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.

scholarly journals Draft Genome Sequence of a New Zealand Isolate of Mycoplasma ovipneumoniae

2020 ◽  
Vol 9 (10) ◽  
Author(s):  
B. J. Bridgeman ◽  
S. K. Gupta ◽  
A. Murray ◽  
V. S. R. Dukkipati ◽  
E. Altermann ◽  
...  
Keyword(s):  
New Zealand ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Mycoplasma Ovipneumoniae

The genome of New Zealand Mycoplasma ovipneumoniae isolate 90 was sequenced and assembled using an Illumina MiSeq system and combining the built-in Geneious de novo and Velvet de novo assemblers. The 1,031,345-bp-long genome harbored 711 genes with a coding percentage of 86.6.

scholarly journals YUCCA-Mediated Biosynthesis of the Auxin IAA Is Required during the Somatic Embryogenic Induction Process in Coffea canephora

2020 ◽  
Vol 21 (13) ◽  
pp. 4751
Author(s):  
Miguel A. Uc-Chuc ◽  
Cleyre Pérez-Hernández ◽  
Rosa M. Galaz-Ávalos ◽  
Ligia Brito-Argaez ◽  
Víctor Aguilar-Hernández ◽  
...  
Keyword(s):  
De Novo ◽  
Leaf Explants ◽  
Coffea Canephora ◽  
Naphthaleneacetic Acid ◽  
Induction Process ◽  
Exogenous Addition ◽  
Pre Treatment ◽  
Process Of Se ◽  
Somatic Embryogenic ◽  
Indole 3 Acetic Acid

Despite the existence of considerable research on somatic embryogenesis (SE), the molecular mechanism that regulates the biosynthesis of auxins during the SE induction process remains unknown. Indole-3-acetic acid (IAA) is an auxin that is synthesized in plants through five pathways. The biosynthetic pathway most frequently used in this synthesis is the conversion of tryptophan to indol-3-pyruvic acid (IPA) by tryptophan aminotransferase of Arabidopsis (TAA) followed by the conversion of IPA to IAA by enzymes encoded by YUCCA (YUC) genes of the flavin monooxygenase family; however, it is unclear whether YUC-mediated IAA biosynthesis is involved in SE induction. In this study, we report that the increase of IAA observed during SE pre-treatment (plants in MS medium supplemented with 1-naphthaleneacetic acid (NAA) 0.54 µM and kinetin (Kin) 2.32 µM for 14 days) was due to its de novo biosynthesis. By qRT-PCR, we demonstrated that YUC gene expression was consistent with the free IAA signal found in the explants during the induction of SE. In addition, the use of yucasin to inhibit the activity of YUC enzymes reduced the signal of free IAA in the leaf explants and dramatically decreased the induction of SE. The exogenous addition of IAA restored the SE process in explants treated with yucasin. Our findings suggest that the biosynthesis and localization of IAA play an essential role during the induction process of SE in Coffea canephora.

scholarly journals Genomic insights into the origin, domestication and diversification of Brassica juncea

2021 ◽  
Vol 53 (9) ◽  
pp. 1392-1402
Author(s):  
Lei Kang ◽  
Lunwen Qian ◽  
Ming Zheng ◽  
Liyang Chen ◽  
Hao Chen ◽  
...  
Keyword(s):  
Brassica Juncea ◽  
De Novo ◽  
Gene Mutations ◽  
Sequencing Analysis ◽  
Genome Wide ◽  
Long Read ◽  
History Of ◽  
Crop Types ◽  
Allotetraploid Species ◽  
New Crop

AbstractDespite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000–14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.

scholarly journals Draft Genome Sequence ofComamonas thiooxydansStrain PHE2-6 (NBRC 110656), a Chlorinated-Ethene-Degrading Bacterium

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Jun Shimodaira ◽  
Kenta Yonezuka ◽  
Michiro Tabata ◽  
Shun Nagase ◽  
Daisuke Kasai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Sole Source ◽  
Draft Genome Sequence ◽  
Contaminated Site ◽  
Chlorinated Ethene ◽  
Degrading Bacterium

Comamonas thiooxydansstrain PHE2-6 (NBRC 110656), which was isolated from a trichloroethene-contaminated site in Japan, utilizes phenol as a sole source of carbon and cometabolizescis-andtrans-dichloroethenes. We report here the draft genome sequence of this strain, containing 5,309,680 bp, with 60.6% G+C content.

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