scholarly journals Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482

2021 ◽  
Author(s):  
Warren W. Wakarchuk ◽  
Denis Brochu ◽  
Simon Foote ◽  
Anna Robotham ◽  
Hirak Saxena ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Plant Cell Wall ◽  
Genome Comparison ◽  
Genome Sequences ◽  
Carbohydrate Active Enzymes ◽  
Full Spectrum ◽  
Cellulomonas Fimi ◽  
A Genome ◽  
The Subject ◽  
New Perspective

The bacteria in the genus Cellulomonas are known for their ability to degrade plant cell wall biomass. Cellulomonas fimi ATCC 484 and C. flavigena ATCC 482 have been the subject of much research into secreted cellulases and hemicellulases. Recently the genome sequences of both C. fimi ATCC 484 and C. flavigena ATCC 482 were published, and a genome comparison has revealed their full spectrum of possible carbohydrate-active enzymes (CAZymes). Using mass spectrometry, we have compared the proteins secreted by C. fimi and C. flavigena during growth on the soluble cellulose substrate, carboxymethylcellulose (CMC), as well as a soluble xylan fraction. Many known C. fimi CAZymes were detected, which validated our analysis, as were a number of new CAZymes and other proteins that, though identified in the genome, have not previously been observed in the secretome of either organism. Our data also shows that many of these are co-expressed on growth of either CMC or xylan. This analysis provides a new perspective on Cellulomonas enzymes and provides many new CAZyme targets for characterization.

scholarly journals Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482

2021 ◽  
Author(s):  
Warren W. Wakarchuk ◽  
Denis Brochu ◽  
Simon Foote ◽  
Anna Robotham ◽  
Hirak Saxena ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Plant Cell Wall ◽  
Genome Comparison ◽  
Genome Sequences ◽  
Carbohydrate Active Enzymes ◽  
Full Spectrum ◽  
Cellulomonas Fimi ◽  
A Genome ◽  
The Subject ◽  
New Perspective

The bacteria in the genus Cellulomonas are known for their ability to degrade plant cell wall biomass. Cellulomonas fimi ATCC 484 and C. flavigena ATCC 482 have been the subject of much research into secreted cellulases and hemicellulases. Recently the genome sequences of both C. fimi ATCC 484 and C. flavigena ATCC 482 were published, and a genome comparison has revealed their full spectrum of possible carbohydrate-active enzymes (CAZymes). Using mass spectrometry, we have compared the proteins secreted by C. fimi and C. flavigena during growth on the soluble cellulose substrate, carboxymethylcellulose (CMC), as well as a soluble xylan fraction. Many known C. fimi CAZymes were detected, which validated our analysis, as were a number of new CAZymes and other proteins that, though identified in the genome, have not previously been observed in the secretome of either organism. Our data also shows that many of these are co-expressed on growth of either CMC or xylan. This analysis provides a new perspective on Cellulomonas enzymes and provides many new CAZyme targets for characterization.

Assembling Archaeology

2020 ◽  
Author(s):  
Hannah Cobb ◽  
Karina Croucher
Keyword(s):  
Resource Management ◽  
Undergraduate Student ◽  
Teaching Practice ◽  
Cultural Resource Management ◽  
First Century ◽  
Cultural Resource ◽  
Archaeological Practice ◽  
Material Turn ◽  
The Subject ◽  
New Perspective

This book provides a radical rethinking of the relationships between teaching, researching, digging, and practicing as an archaeologist in the twenty-first century. The issues addressed here are global and are applicable wherever archaeology is taught, practiced, and researched. In short, this book is applicable to everyone from academia to cultural resource management (CRM), from heritage professional to undergraduate student. At its heart, it addresses the undervaluation of teaching, demonstrating that this affects the fundamentals of contemporary archaeological practice, and is particularly connected to the lack of diversity in disciplinary demographics. It proposes a solution which is grounded in a theoretical rethinking of our teaching, training, and practice. Drawing upon the insights from archaeology’s current material turn, and particularly Deleuze and Guattari’s concept of assemblages, this volume turns the discipline of archaeology into the subject of investigation, considering the relationships between teaching, practice, and research. It offers a new perspective which prompts a rethinking of our expectations and values with regard to teaching, training, and doing archaeology, and ultimately argues that we are all constantly becoming archaeologists.

scholarly journals Integrative and Complementary Health Practices Building a New Health Paradigm

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
T Gemeli ◽  
H Silva ◽  
M Kato
Keyword(s):  
Cognitive Abilities ◽  
Universal Access ◽  
Well Being ◽  
The Elderly ◽  
Professional Service ◽  
Health It ◽  
Self Confidence ◽  
The Social ◽  
The Subject ◽  
New Perspective

Abstract This work arose from the need to broaden the therapeutic approach and offer a differentiated health intervention proposal based on the understanding that the illness process has repercussions on all integrated systems of Being. Since 2019, the Health Center for the Elderly in Blumenau (SC-Brasil), specialized multi-professional service, offering support for biopsychoenergetic transformation with the practice of Yoga and Meditation, through a holistic and comprehensive view of health. It begins with the Multidimensional Assessment of the Elderly, with a guideline in welcoming and qualified listening, which considers the subject and all subjectivity. From there, the expanded diagnosis and the Singular Therapeutic Project are built and the consultations with the team and the 'Re-Conhecer group' begin. The activity is weekly, aimed at the elderly and their family, takes place in an appropriate place and lasts two hours. Welcoming, pranayama, mantras, kriyas and meditation are made, as well as reflections on free themes. The professionals who conduct the practice are the dentist, trained in yoga, and the social worker, the welcoming process continues individually after the activity. Due to subjectivity, results are routinely collected in a qualitative way from the participants' report. There is a perception on the part of the participants, therapists and members of the multidisciplinary team that this work provides improvement in cognitive abilities, self-care, well-being, self-confidence, creativity, improved sleep, autonomy, balance, strengthening bonds, joy, vitality. Key messages This initiative builds new models of health care, transcending the traditional biomedical model, according to the operational guideline for comprehensiveness, universal access and equity. Provokes reflections and builds a new perspective of life with quality and participation of the elderly as subjects of their health.

scholarly journals Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart

2013 ◽  
Vol 79 (9) ◽  
pp. 2944-2951 ◽  
Author(s):  
Anne Holch ◽  
Kristen Webb ◽  
Oksana Lukjancenko ◽  
David Ussery ◽  
Benjamin M. Rosenthal ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Food Processing ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Genome Comparison ◽  
Physiological Factors ◽  
Content Type ◽  
Human Pathogenic Bacterium ◽  
A Genome ◽  
Genome Analyses

ABSTRACTListeria monocytogenesis a food-borne human-pathogenic bacterium that can cause infections with a high mortality rate. It has a remarkable ability to persist in food processing facilities. Here we report the genome sequences for twoL. monocytogenesstrains (N53-1 and La111) that were isolated 6 years apart from two different Danish fish processers. Both strains are of serotype 1/2a and belong to a highly persistent DNA subtype (random amplified polymorphic DNA [RAPD] type 9). We demonstrate usingin silicoanalyses that both strains belong to the multilocus sequence typing (MLST) type ST121 that has been isolated as a persistent subtype in several European countries. The purpose of this study was to use genome analyses to identify genes or proteins that could contribute to persistence. In a genome comparison, the two persistent strains were extremely similar and collectively differed from the reference lineage II strain, EGD-e. Also, they differed markedly from a lineage I strain (F2365). On the proteome level, the two strains were almost identical, with a predicted protein homology of 99.94%, differing at only 2 proteins. No single-nucleotide polymorphism (SNP) differences were seen between the two strains; in contrast, N53-1 and La111 differed from the EGD-e reference strain by 3,942 and 3,471 SNPs, respectively. We included a persistentL. monocytogenesstrain from the United States (F6854) in our comparisons. Compared to nonpersistent strains, all three persistent strains were distinguished by two genome deletions: one, of 2,472 bp, typically contains the gene forinlF, and the other, of 3,017 bp, includes three genes potentially related to bacteriocin production and transport (lmo2774,lmo2775, and the 3′-terminal part oflmo2776). Further studies of highly persistent strains are required to determine if the absence of these genes promotes persistence. While the genome comparison did not point to a clear physiological explanation of the persistent phenotype, the remarkable similarity between the two strains indicates that subtypes with specific traits are selected for in the food processing environment and that particular genetic and physiological factors are responsible for the persistent phenotype.

scholarly journals Novel Cyclic Peptides from Lethal Amanita Mushrooms through a Genome-Guided Approach

2021 ◽  
Vol 7 (3) ◽  
pp. 204
Author(s):  
Shengwen Zhou ◽  
Xincan Li ◽  
Yunjiao Lüli ◽  
Xuan Li ◽  
Zuo H. Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Amino Acid Residues ◽  
Fragment Ions ◽  
Peptide Pair ◽  
A Genome ◽  
Peptide Toxins ◽  
Poisonous Mushrooms ◽  
Large Peptide

Most species in the genus Amanita are ectomycorrhizal fungi comprising both edible and poisonous mushrooms. Some species produce potent cyclic peptide toxins, such as α-amanitin, which places them among the deadliest organisms known to mankind. These toxins and related cyclic peptides are encoded by genes of the “MSDIN” family (named after the first five amino acid residues of the precursor peptides), and it is largely unknown to what extent these genes are expressed in the basidiocarps. In the present study, Amanita rimosa and Amanita exitialis were sequenced through the PacBio and Illumina techniques. Together with our two previously sequenced genomes, Amanita subjunquillea and Amanita pallidorosea, in total, 46 previously unknown MSDIN genes were discovered. The expression of over 80% of the MSDIN genes was demonstrated in A. subjunquillea. Through a combination of genomics and mass spectrometry, 12 MSDIN genes were shown to produce novel cyclic peptides. To further confirm the results, three of the cyclic peptides were chemically synthesized. The tandem mass spectrometry (MS/MS) spectra of the natural and the synthetic peptides shared a majority of the fragment ions, demonstrating an identical structure between each peptide pair. Collectively, the results suggested that the genome-guided approach is reliable for identifying novel cyclic peptides in Amanita species and that there is a large peptide reservoir in these mushrooms.

scholarly journals Simple Emergency Triage (SET) – the new perspective on mass casualty incident triage

2020 ◽  
Vol 7 (2) ◽  
pp. 120-123
Author(s):  
Jerzy Jaskuła ◽  
Marek Siuta
Keyword(s):  
Personal Experience ◽  
Emergency Services ◽  
Statistical Data ◽  
First Aid ◽  
Mass Casualty Incident ◽  
Mass Casualty ◽  
Starting Point ◽  
Analysis And Synthesis ◽  
The Subject ◽  
New Perspective

The aim: Incidents with large number of casualties present a major challenge for the emergency services. Incident witnesses are always the first on scene. Authors aim at giving them an algorithm arranging the widely known first aid rules in such way, that the number of potential fatalities before the services’ arrival may be decreased. Material and methods: The authors’ main aim was creating an algorithm for mass casualty incident action, comprising elements not exceeding first aid skill level. Proceedings have been systematized, which led to creation of mass casualty incident algorithm. The analysis was based on the subject matter literature, legal acts and regulations, statistical data and author’s personal experience. Results: The analysis and synthesis of data from various sources allowed for the creation of Simple Emergency Triage (SET) algorithm. It has been proven – on theoretical level – that introducing an organized way of proceeding in mass casualty incident on the first aid level is justified. Conclusions: The SET algorithm presented in the article is of an implemental character. It may be a supplement to basic first aid skills. Algorithm may also be the starting point for further empirical research aimed at verifying its effectiveness.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals Analysis of the complete genome sequence of a marine-derived strainStreptomycessp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6122 ◽  
Author(s):  
Liang-Yu Chen ◽  
Hao-Tian Cui ◽  
Chun Su ◽  
Feng-Wu Bai ◽  
Xin-Qing Zhao
Keyword(s):  
Bioactive Compounds ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Dna Hybridization ◽  
Complete Genome ◽  
System Analysis ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Genome Comparison ◽  
Genome Sequences

Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomyceteStreptomycessp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed thatStreptomycessp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed thatStreptomycessp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating thatStreptomycessp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain.Streptomycessp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate thatStreptomycessp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.

scholarly journals Plant cell wall chemistry: implications for ruminant utilisation

2021 ◽  
pp. 1-26
Author(s):  
X. Li
Keyword(s):  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Current Knowledge ◽  
Plant Cell Walls ◽  
Rumen Microorganisms ◽  
Cell Wall Chemistry ◽  
Fibre Degradation ◽  
The Subject ◽  
Composition Structure

Ruminants have adapted to cope with bulky, fibrous forage diets by accommodating a large, diverse microbial population in the reticulo-rumen. Ruminants are dependent on forages as their main sources of energy and other nutrients. Forages are comprised of a complex matrix of cellulose, hemicellulose, protein, minerals and phenolic compounds (including lignin and tannins) with various linkages; many of which are poorly defined. The composition and characteristics of polysaccharides vary greatly among forages and plant cell walls. Plant cell walls are linked and packed together in tight configurations to resist degradation, and hence their nutritional value to animals varies considerably, depending on composition, structure and degradability. An understanding of the inter-relationship between the chemical composition and the degradation of plant cell walls by rumen microorganisms is of major economic importance to ruminant production. Increasing the efficiency of fibre degradation in the rumen has been the subject of extensive research for many decades. This review summarises current knowledge of forage chemistry in order to develop strategies to increase efficiency of forage utilisation by ruminants.

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