scholarly journals Microbial Extractions: Sequence-based Bioprospecting, Augmented Promises, and Elusive Politics

2021 ◽  
pp. 016224392110556
Author(s):  
Ana Delgado
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
Gene Sequencing ◽  
Life Forms ◽  
Sequencing Technologies ◽  
Policy Environments ◽  
Political Implications ◽  
Policy Frameworks ◽  
Biodiversity Governance

In view of the end of the golden years of the Norwegian oil economy, ocean genetic resources are being advertised in policy environments as holding great potential for the future of the country. Microbes have increased in popularity as promising agents of the Norwegian new bioeconomy, as advances in gene sequencing technologies and genomics have made them more accessible. This paper examines the turn toward digital sequence data in bioprospecting to inquire about its political implications. It draws on a combination of empirical materials to describe the infrastructural work that goes into extracting microbes from their in situ locations in arctic and subarctic waters to in silico collections and databases. I argue that in that infrastructural work, microbes may become both more promising and more elusive public and political matters. As biodiversity is turned into data, bioprospecting appears as less dependent on material samples, which may ultimately render policy frameworks for biodiversity governance obsolete. The shift toward big sequence data in bioprospecting entails shifts in how promise is attributed to biodiversity, which life forms appear to be more promising, and how such life forms come to appear as public good.

Engaging with the science and politics of biodiversity futures: a literature review

2021 ◽  
pp. 1-8
Author(s):  
Carina Wyborn ◽  
Elena Louder ◽  
Mike Harfoot ◽  
Samantha Hill
Keyword(s):  
Human Life ◽  
Global Environmental Change ◽  
Life Forms ◽  
Trade Offs ◽  
Global Environmental ◽  
Science And Politics ◽  
Science Community ◽  
Impact On Biodiversity ◽  
Made In

Summary Future global environmental change will have a significant impact on biodiversity through the intersecting forces of climate change, urbanization, human population growth, overexploitation, and pollution. This presents a fundamental challenge to conservation approaches, which seek to conserve past or current assemblages of species or ecosystems in situ. This review canvases diverse approaches to biodiversity futures, including social science scholarship on the Anthropocene and futures thinking alongside models and scenarios from the biophysical science community. It argues that charting biodiversity futures requires processes that must include broad sections of academia and the conservation community to ask what desirable futures look like, and for whom. These efforts confront political and philosophical questions about levels of acceptable loss, and how trade-offs can be made in ways that address the injustices in the distribution of costs and benefits across and within human and non-human life forms. As such, this review proposes that charting biodiversity futures is inherently normative and political. Drawing on diverse scholarship united under a banner of ‘futures thinking’ this review presents an array of methods, approaches and concepts that provide a foundation from which to consider research and decision-making that enables action in the context of contested and uncertain biodiversity futures.

scholarly journals In Silico Hemostasis Modeling and Prediction

2020 ◽  
Vol 40 (04) ◽  
pp. 524-535
Author(s):  
Dmitry Y. Nechipurenko ◽  
Aleksey M. Shibeko ◽  
Anastasia N. Sveshnikova ◽  
Mikhail A. Panteleev
Keyword(s):  
In Silico ◽  
Physiological Response ◽  
Platelet Adhesion ◽  
State Of The Art ◽  
Thrombus Formation ◽  
The State ◽  
Modeling And Prediction ◽  
Hemostatic System ◽  
Single Enzyme

AbstractComputational physiology, i.e., reproduction of physiological (and, by extension, pathophysiological) processes in silico, could be considered one of the major goals in computational biology. One might use computers to simulate molecular interactions, enzyme kinetics, gene expression, or whole networks of biochemical reactions, but it is (patho)physiological meaning that is usually the meaningful goal of the research even when a single enzyme is its subject. Although exponential rise in the use of computational and mathematical models in the field of hemostasis and thrombosis began in the 1980s (first for blood coagulation, then for platelet adhesion, and finally for platelet signal transduction), the majority of their successful applications are still focused on simulating the elements of the hemostatic system rather than the total (patho)physiological response in situ. Here we discuss the state of the art, the state of the progress toward the efficient “virtual thrombus formation,” and what one can already get from the existing models.

In situ and in silico evaluation of amine- and folate-terminated dendrimers as nanocarriers of anesthetics

2014 ◽  
Vol 73 ◽  
pp. 250-257 ◽  
Author(s):  
Verónica Carrasco-Sánchez ◽  
Ariela Vergara-Jaque ◽  
Matías Zuñiga ◽  
Jeffrey Comer ◽  
Amalraj John ◽  
...  
Keyword(s):  
In Silico

scholarly journals A novel theranostic activity-based probe targeting kallikrein 7 for diagnosis and treatment of skin diseases

2021 ◽  
Author(s):  
Evangelos Bisyris ◽  
Eleni Zingkou ◽  
Golfo G Kordopati ◽  
Minos-Timotheos Matsoukas ◽  
Plato A. Magriotis ◽  
...  
Keyword(s):  
In Silico ◽  
Skin Diseases ◽  
Diagnosis And Treatment ◽  
Protease Substrate

We applied a new in silico approach for fishing protease-substrate motifs to design a kallirein 7 (KLK7)-specific phosphonate activity-based probe (ABP) to quantify the active KLK7 in situ. Epidermal application...

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

scholarly journals Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

2021 ◽  
Author(s):  
Ryan O Schenck ◽  
Gabriel Brosula ◽  
Jeffrey West ◽  
Simon Leedham ◽  
Darryl Shibata ◽  
...  
Keyword(s):  
Base Pair ◽  
In Silico ◽  
Sequence Data ◽  
Agent Based Modeling ◽  
Sequence Coverage ◽  
Agent Based ◽  
Coverage Error ◽  
Somatic Evolution ◽  
User Friendly ◽  
Mutation Spectra

Gattaca provides the first base-pair resolution artificial genomes for tracking somatic mutations within agent based modeling. Through the incorporation of human reference genomes, mutational context, sequence coverage/error information Gattaca is able to realistically provide comparable sequence data for in-silico comparative evolution studies with human somatic evolution studies. This user-friendly method, incorporated into each in-silico cell, allows us to fully capture somatic mutation spectra and evolution.

scholarly journals Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data

2019 ◽  
Author(s):  
Kamela Charmaine S. Ng ◽  
Jean Claude S. Ngabonziza ◽  
Pauline Lempens ◽  
Bouke Catherine de Jong ◽  
Frank van Leth ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Data Generation ◽  
Continuous Analysis ◽  
Middle Income ◽  
Tb Control ◽  
Sequencing Technologies ◽  
Surveillance Programs ◽  
Low And Middle Income

AbstractBackgroundMycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low and middle income high TB burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance.MethodsWe developed the Python-based MTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs – Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data.ResultsThe MTBGT tool correctly transformed the SNP data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda.ConclusionOverall, the MTBGT tool allows low and middle income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the existing national connectivity platform for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation is available at https://github.com/KamelaNg/MTBGT.

scholarly journals Utilisation of 2,2DCP by Staphyloccocus aureus ZT and In Silico Analysis of Putative Dehalogenase

2021 ◽  
Vol 13 (1) ◽  
pp. 1-8
Author(s):  
Zatty Zawani Zaidi ◽  
Fahrul Huyop
Keyword(s):  
In Silico ◽  
Culture Media ◽  
Enrichment Culture ◽  
In Silico Analysis ◽  
In Situ Bioremediation ◽  
Isolation And Characterization ◽  
Halogenated Compound ◽  
Silico Analysis ◽  
Dehalogenase Gene

Halogenated compound such as 2,2-dichloropropionic acid is known for its toxicity and polluted many areas especially with agricultural activities. This study focused on the isolation and characterization of the bacterium that can utilise 2,2-dichloropropionic acid from palm oil plantation in Lenga, Johor and in silico analysis of putative dehalogenase obtained from NCBI database of the same genus and species. The bacterium was isolated using an enrichment culture media supplemented with 20 mM 2,2-dicholoropropionic acid as a carbon source.  The cells were grown at 30˚C with cells doubling time of 2.00±0.005 hours with the maximum growth at A680nm of 1.047 overnight. The partial biochemical tests and morphological examination concluded that the bacterium belongs to the genus Staphylococcus sp.. This is the first reported studies of  Staphylococcus sp. with the ability to grow on 2,2-dichloropropionic acid. The genomic DNA from NCBI database of the same species was analysed assuming the same genus and has identical genomic sequence.  The full genome of Staphylococcus sp. was screened for dehalogenase gene and  haloacid dehalogenase gene was detected in the mobile genetic element of the species revealed that the dehalogenase sequence has little identities to the previously reported dehalogenases.The main outcome of the studies suggesting an in situ bioremediation can be regarded as a natural process to detoxify the contaminated sites provided that the microorganisms contained a specialised gene sequence within its genome that served the nature for many long years. Whether microorganisms will be successful in destroying man-made contaminants entirely rely on what types of organisms play a role in in situ bioremediation and which contaminants are most susceptible to bioremediation. 

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