scholarly journals Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase

Genes ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 1 ◽  
Author(s):  
Ziya Liao ◽  
Mark Holtzapple ◽  
Yanchun Yan ◽  
Haisheng Wang ◽  
Jun Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Sequence ◽  
Carbon Sources ◽  
Compatible Solutes ◽  
Tween 20 ◽  
Sequence Information ◽  
Ph Homeostasis ◽  
Whole Genome Analysis ◽  
Xylanase Production ◽  
Xylan Degradation

The obligately anaerobic haloalkaliphilic bacterium Alkalitalea saponilacus can use xylan as the sole carbon source and produce propionate as the main fermentation product. Using mixed carbon sources of 0.4% (w/v) sucrose and 0.1% (w/v) birch xylan, xylanase production from A. saponilacus was 3.2-fold greater than that of individual carbon sources of 0.5% (w/v) sucrose or 0.5% (w/v) birch xylan. The xylanse is halostable and exhibits optimal activity over a broad salt concentration (2–6% NaCl). Its activity increased approximately 1.16-fold by adding 0.2% (v/v) Tween 20. To understand the potential genetic mechanisms of xylan degradation and molecular adaptation to saline-alkali extremes, the complete genome sequence of A. saponilacus was performed with the pacBio single-molecule real-time (SMRT) and Illumina Misseq platforms. The genome contained one chromosome with a total size of 4,775,573 bps, and a G+C genomic content of 39.27%. Ten genes relating to the pathway for complete xylan degradation were systematically identified. Furthermore, various genes were predicted to be involved in isosmotic cytoplasm via the “compatible-solutes strategy” and cytoplasmic pH homeostasis though the “influx of hydrogen ions”. The halostable xylanase from A. saponilacus and its genomic sequence information provide some insight for potential applications in industry under double extreme conditions.

scholarly journals Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 655
Author(s):  
Hongmei Du ◽  
Shah Zaman ◽  
Shuiqingqing Hu ◽  
Shengquan Che
Keyword(s):  
Fatty Acids ◽  
Differential Expression ◽  
Single Molecule ◽  
Unsaturated Fatty Acids ◽  
Average Length ◽  
Expression Profiles ◽  
Portulaca Oleracea ◽  
Pcr Analysis ◽  
Sequence Information ◽  
Leaves And Roots

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

scholarly journals Impact of Different Carbon Sources on the in vitro Growth and Viability of Escherichia coli (SUBE01) and Salmonella spp. (SUBS01) Cells

2016 ◽  
pp. 39-44
Author(s):  
Ifra Tun Nur ◽  
Jannatun Tahera ◽  
Md Sakil Munna ◽  
M Majibur Rahman ◽  
Rashed Noor
Keyword(s):  
Escherichia Coli ◽  
Bacterial Growth ◽  
Culture Media ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Growth Dynamics ◽  
Luria Bertani ◽  
Tween 20 ◽  
Salmonella Spp

With a previous observation of Escherichia coli growth cessation along with temperature variation within three different bacteriological culture media (nutrient agar, Luria-Bertani agar and minimal agar), current investigation further depicted on the possible growth dynamics of Escherichia coli (SUBE01) and Salmonella (SUBS01) growth and viability upon supplementation of different carbon sources (dextrose, sucrose, lactose, glycerol and tween 20) at 37°C under the aeration of 100 rpm. Viability of the tested bacterial species was assessed through the enumeration of the colony forming unit (cfu) appeared upon prescribed incubation for 12-24 hours on different agar plates consisting of the above mentioned carbon sources. Besides, to inspect the cellular phenotypic changes, morphological observations were conducted under the light microscope. Variations in bacterial growth (either growth acceleration or cessation) were further noticed through the spot tests on the agar plates. Considerable shortfalls in the culturable cells of E. coli and Salmonella spp. were noted in the minimal media separately consisting of sucrose, lactose, glycerol or tween 20 while an opposite impact of accelerated growth was noticed in the media supplied with dextrose. The data revealed a hierarchy of consequence of carbon sources as nutrient generators whereby the favourable bacterial growth and survival order of the carbon sources was estimated as dextrose > glycerol > lactose > tween 20 > sucrose.Bangladesh J Microbiol, Volume 32, Number 1-2,June-Dec 2015, pp 39-44

scholarly journals FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation

2019 ◽  
Author(s):  
Laura V. Milko ◽  
Flavia Chen ◽  
Kee Chan ◽  
Amy M. Brower ◽  
Pankaj B. Agrawal ◽  
...  
Keyword(s):  
Clinical Research ◽  
Systems Approach ◽  
Genomic Sequence ◽  
Clinical Investigation ◽  
Risk Assessments ◽  
Genomic Research ◽  
Institutional Review Boards ◽  
Sequence Information ◽  
Genomic Technologies ◽  
Challenges And Opportunities

ABSTRACTThe National Institutes of Health (NIH) funded the Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) Consortium to investigate the implications, challenges and opportunities associated with the possible use of genomic sequence information in the newborn period. Following announcement of the NSIGHT awardees in 2013, the Food and Drug Administration (FDA) contacted investigators and requested that pre-submissions to investigational device exemptions (IDE) be submitted for the use of genomic sequencing under Title 21 of the Code of Federal Regulations (21 CFR) part 812. IDE regulation permits clinical investigation of medical devices that have not been approved by the FDA. To our knowledge, this marked the first time the FDA determined that NIH-funded clinical genomic research projects are subject to IDE regulation. Here we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium’s experiences in navigating the IDE process. Overall, NSIGHT investigators found that FDA’s application of existing IDE regulations and medical device definitions aligned imprecisely with the aims of publicly funded exploratory clinical research protocols. IDE risk assessments by the FDA were similar to, but distinct from, protocol risk assessments conducted by local Institutional Review Boards (IRBs), and had the potential to reflect novel oversight of emerging genomic technologies. However, the pre-IDE and IDE process delayed the start of NSIGHT research studies by an average of 10 months, and significantly limited the scope of investigation in two of the four NIH approved projects. Based on the experience of the NSIGHT Consortium, we conclude that policies and practices governing the development and use of novel genomic technologies in clinical research urgently need clarification in order to mitigate potentially conflicting or redundant oversight by IRBs, NIH, FDA, and state authorities.

scholarly journals Comparative whole-genome analysis of a Thar desert strain Streptomyces sp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system

2021 ◽  
Author(s):  
Dharmesh Harwani ◽  
Jyotsna Begani ◽  
Jyoti Lakhani
Keyword(s):  
Genome Mining ◽  
Compatible Solutes ◽  
Gene Clusters ◽  
Flavin Mononucleotide ◽  
Thar Desert ◽  
Secretion Systems ◽  
Desert Ecosystems ◽  
Whole Genome Analysis ◽  
Genetic Traits ◽  
Metabolic Versatility

AbstractWe sequenced the genome of Streptomyces sp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including β-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol, siderophores, terpenoids, thiopeptides, and other types of hybrid compounds. Among them, ~30% BGCs displayed a high degree of novelty. The genome of JB150 was enriched for a large assortment of specialized genes coding for the production of many interesting biomolecules comprising compatible solutes, multiple stress-response regulators, transport proteins, protein secretion systems, signaling molecules, chaperones and storage reserves, etc. The presence of diverse members of CAZymes enzyme families, high numbers of riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), trehalose and aromatic compounds synthesis genes, putative orthologues to several of the classical fatty acid synthesis components, prototrophy for many essential amino acids exhibit metabolic versatility of JB150 to inhabit in the extreme desert environment. Besides, the genome of JB150 was observed to specifically encode thiazole-oxazole-modified thiazolemicrocin (TOMM) and ectoine. The comparison of the complete genomes of Streptomyces sp. JB150 and seven other actinomycete strains belonging to different desert ecosystems unveiled the presence of many previously undetected, distinctive, biological, and genomic signatures. We propose that these genetic traits endowed by these strains are essential for their adaptation in the highly underprivileged, extreme ecosystem of the Thar desert to cope with multiple abiotic stressors, oligotrophic nutrient conditions and to produce a huge repertoire of diverse secondary metabolites.

scholarly journals Morphogenesis and Production of Enzymes byPenicillium echinulatumin Response to Different Carbon Sources

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Willian Daniel Hahn Schneider ◽  
Laísa dos Reis ◽  
Marli Camassola ◽  
Aldo José Pinheiro Dillon
Keyword(s):  
Enzymatic Activity ◽  
Sugar Cane ◽  
Filter Paper ◽  
Carbon Sources ◽  
Sugar Cane Bagasse ◽  
Xylanase Production ◽  
Penicillium Echinulatum ◽  
The Media ◽  
Filter Paper Activity ◽  
Second Generation Ethanol

The effect of different carbon sources on morphology and cellulase and xylanase production ofPenicillium echinulatumwas evaluated in this work. Among the six carbon sources studied, cellulose and sugar cane bagasse were the most suitable for the production of filter paper activity, endoglucanases, xylanases, andβ-glucosidases. However, sucrose and glucose showedβ-glucosidase activities similar to those obtained with the insoluble sources. The polyacrylamide gels proved the enzymatic activity, since different standards bands were detected in the media mentioned above. Regarding morphology, it was observed that the mycelium in a dispersed form provided the greatest enzymatic activity, possibly due to greater interaction between the substrate and hyphae. These data are important in understanding the physiology of fungi and could contribute to obtaining enzyme with potential application in the technology of second generation ethanol.

Insight into cold-active xylanase production and xylan degradation pathways in psychrotrophic Acinetobacter sp. HC4 from the cold region of China

Cellulose ◽  
2020 ◽  
Vol 27 (13) ◽  
pp. 7575-7589
Author(s):  
Hailian Zang ◽  
Xiaopeng Du ◽  
Jinming Wang ◽  
Yi Cheng ◽  
Yue Wang ◽  
...  
Keyword(s):  
Degradation Pathways ◽  
Cold Region ◽  
Xylanase Production ◽  
Xylan Degradation ◽  
Cold Active ◽  
Acinetobacter Sp ◽  
Insight Into

scholarly journals Single-molecule analysis reveals widespread structural variation in multiple myeloma

2015 ◽  
Vol 112 (25) ◽  
pp. 7689-7694 ◽  
Author(s):  
Aditya Gupta ◽  
Michael Place ◽  
Steven Goldstein ◽  
Deepayan Sarkar ◽  
Shiguo Zhou ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Tumor Progression ◽  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Plasma Cells ◽  
Optical Mapping ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Whole Genome Analysis

Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation.

Feasibility of Population Scale Comprehensive Identification and Analysis of Complex Structural Variations in Cancer Genome Using Nanochannel Array

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 476-476
Author(s):  
Alex Hastie ◽  
Ernest Lam ◽  
Heng Dai ◽  
Warren Andrews ◽  
Andy Pang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Complex Traits ◽  
Genomic Dna ◽  
Genomic Sequence ◽  
Conflicts Of Interest ◽  
Large Population ◽  
Sequence Motif ◽  
Structural Variations ◽  
Hematological Cancers ◽  
Population Scale

Abstract Diseases with complex traits such as hematological cancer are known to be associated with large structural variations (SV > 1 kb). Techniques such as karyotyping, FISH and aCGH have been common tools for gross chromosomal lesion analysis. Yet population scale comprehensive SV analysis with these tools remains impractical, tedious or incomplete such as missing balanced lesions by aCGH. Recently, high throughput Next Generation Sequencing (NGS) has generated a large amount of sequencing reads that have rapidly reduced costs and are effective in detection of SNPs and small indels; however, complicated by the fact that large structural variations, often spanning tens to hundreds of thousands of base pairs or involving complex rearrangements throughout the genome, are hard for current short read sequencing technology to assemble or infer. Therefore, there is a blind spot in effectively detecting SVs within this range (1 kb ~ 1 Mb) due to insufficient tools. Here we demonstrate a technology that rapidly linearizes very long strands of genomic DNA (100 kb to Mbs) through NanoChannels to directly visualize large SVs and rearrangements preserved within intact genomic DNA at the single molecule level. Through specific sequence motif labeling, de novo genome physical maps are assembled within hours and hundreds to thousands of SV events, balanced or imbalanced, are called with no a priori knowledge of the samples. Preliminary testing data from a group of cancer samples and multiple trio families will be shown to demonstrate this highly comprehensive and cost effective approach, with results validated by direct single-molecule images and multiple orthogonal methods. We also show long spanning molecules would provide very valuable information of precise mapping of viral genomic sequence integration in human genomes that are potentially associated with malignant cell transformation. For the first time, it is now feasible to do large population-based comprehensive genome structural variation studies on a single platform. This innovations will transform the biomedical research, diagnosis and treatment of hematological cancers that result from structural variations and chromosomal lesions. Disclosures No relevant conflicts of interest to declare.

scholarly journals Reduced representation optical methylation mapping (R2OM2)

2017 ◽  
Author(s):  
Assaf Grunwald ◽  
Hila Sharim ◽  
Tslil Gabrieli ◽  
Yael Michaeli ◽  
Dmitry Torchinsky ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Mapping ◽  
Single Cells ◽  
Methylation Status ◽  
Next Generation ◽  
Whole Genome Analysis ◽  
Reduced Representation ◽  
Long Reads ◽  
Structural Aberrations ◽  
Genomic Regions

ABSTRACTReduced representation methylation profiling is a method of analysis in which a subset of CpGs is used to report the overall methylation status of the probed genomic regions. This approach has been widely adopted for genome-scale bisulfite sequencing since it requires fewer sequencing reads and uses significantly less starting material than whole-genome analysis. Consequently, this method is suitable for profiling medical samples and single cells at high throughput and reduced costs. Here, we use this concept in order to create a pattern of fluorescent optical methylation profiles along individual DNA molecules. Reduced representation optical methylation mapping (R2OM2) in combination with Bionano Genomics next generation genome mapping (NGM) technology provides a hybrid genetic/epigenetic genome map of individual chromosome segments spanning hundreds of kilobase pairs (kbp). These long reads, along with the single-molecule resolution, allow for epigenetic variation calling and methylation analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell next generation sequencing (NGS). We apply this method to facioscapulohumeral dystrophy (FSHD) showing both structural variation and hypomethylation status of a disease-associated, highly repetitive locus on chromosome 4q.

scholarly journals Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

2017 ◽  
Author(s):  
Tslil Gabrieli ◽  
Hila Sharim ◽  
Yael Michaeli ◽  
Yuval Ebenstein
Keyword(s):  
Single Molecule ◽  
Genome Mapping ◽  
Single Point ◽  
Read Length ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Whole Genome Analysis ◽  
Long Read

ABSTRACTVariations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation. Next-generation sequencing analysis is unable to reliably capture aberrations larger than the typical sequencing read length of several hundred bases. Long-read, single-molecule sequencing methods such as SMRT and nanopore sequencing can address larger variations, but require costly whole genome analysis. Here we describe a method for isolation and enrichment of a large genomic region of interest for targeted analysis based on Cas9 excision of two sites flanking the target region and isolation of the excised DNA segment by pulsed field gel electrophoresis. The isolated target remains intact and is ideally suited for optical genome mapping and long-read sequencing at high coverage. In addition, analysis is performed directly on native genomic DNA that retains genetic and epigenetic composition without amplification bias. This method enables detection of mutations and structural variants as well as detailed analysis by generation of hybrid scaffolds composed of optical maps and sequencing data at a fraction of the cost of whole genome sequencing.

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