97 research outputs found
Editorial: The impacts of climate change and human activities on the structure and function of wetland/grassland ecosystems
Experimental investigation and mechanism analysis on rock damage by high voltage spark discharge in water : effect of electrical conductivity
High voltage spark discharge (HVSD) could generate strong pressure waves that can be combined with a rotary drill bit to improve the penetration rate in unconventional oil and gas drilling. However, there has been little investigation of the effect of electrical conductivity on rock damage and the fragmentation mechanism caused by HVSD. Therefore, we conducted experiments to destroy cement mortar, a rock-like material, in water with five conductivity levels, from 0.5 mS/cm to 20 mS/cm. We measured the discharge parameters, such as breakdown voltage, breakdown delay time, and electrical energy loss, and investigated the damage mechanism from stress waves propagation using X-ray computed tomography. Our study then analyzed the influence of conductivity on the surface damage of the sample by the pore size distribution and the cumulative pore area, as well as studied the dependence of internal damage on conductivity by through-transmission ultrasonic inspection technique. The results indicated that the increase in electrical conductivity decreased the breakdown voltage and breakdown delay time and increased the energy loss, which led to a reduction in the magnitude of the pressure wave and, ultimately, reduced the sample damage. It is worth mentioning that the relationship between the sample damage and electrical conductivity is non-linear, showing a two-stage pattern. The findings suggest that stress waves induced by the pressure waves play a significant role in sample damage where pores and two types of tensile cracks are the main failure features. Compressive stresses close horizontal cracks inside the sample and propagate vertical cracks, forming the tensile cracks-I. Tensile stresses generated at the sample-water interface due to the reflection of stress waves produce the tensile cracks-II. Our study is the first to investigate the relationship between rock damage and electrical conductivity, providing insights to guide the design of drilling tools based on HVSD
Structure and mechanism of the CMR complex for CRISPR-Mediated antiviral immunity
The prokaryotic clusters of regularly interspaced palindromic repeats (CRISPR) system utilizes genomically encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonucleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. The crystal structure of Cmr7 and low-resolution structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endo-nucleolytic reaction at UA dinucleotides. This activity is dependent on the 8 nt repeat-derived 5' sequence in the crRNA, but not on the presence of a proto-spacer-associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets.Publisher PDFPeer reviewe
Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes
The perivascular niche (PVN) plays an essential role in brain tumor stem-like cell (BTSC) fate control, tumor invasion, and therapeutic resistance. Here, a microvasculature-on-a-chip system as a PVN model is used to evaluate the ex vivo dynamics of BTSCs from ten glioblastoma patients. BTSCs are found to preferentially localize in the perivascular zone, where they exhibit either the lowest motility, as in quiescent cells, or the highest motility, as in the invasive phenotype, with migration over long distance. These results indicate that PVN is a niche for BTSCs, while the microvascular tracks may serve as a path for tumor cell migration. The degree of colocalization between tumor cells and microvessels varies significantly across patients. To validate these results, single-cell transcriptome sequencing (10 patients and 21 750 single cells in total) is performed to identify tumor cell subtypes. The colocalization coefficient is found to positively correlate with proneural (stem-like) or mesenchymal (invasive) but not classical (proliferative) tumor cells. Furthermore, a gene signature profile including PDGFRA correlates strongly with the âhomingâ of tumor cells to the PVN. These findings demonstrate that the model can recapitulate in vivo tumor cell dynamics and heterogeneity, representing a new route to study patient-specific tumor cell functions
The Global N20 Model Intercomparison Project
Nitrous oxide (N2O) is an important greenhouse gas and also an ozone-depleting substance that has both natural and anthropogenic sources. Large estimation uncertainty remains on the magnitude and spatiotemporal patterns of N2O fluxes and the key drivers of N2O production in the terrestrial biosphere. Some terrestrial biosphere models have been evolved to account for nitrogen processes and to show the capability to simulate N2O emissions from land ecosystems at the global scale, but large discrepancies exist among their estimates primarily because of inconsistent input datasets, simulation protocol, and model structure and parameterization schemes. Based on the consistent model input data and simulation protocol, the global N2O Model Intercomparison Project (NMIP) was initialized with 10 state-of-the-art terrestrial biosphere models that include nitrogen (N) cycling. Specific objectives of NMIP are to 1) unravel the major N cycling processes controlling N2O fluxes in each model and identify the uncertainty sources from model structure, input data, and parameters; 2) quantify the magnitude and spatial and temporal patterns of global and regional N2O fluxes from the preindustrial period (1860) to present and attribute the relative contributions of multiple environmental factors to N2O dynamics; and 3) provide a benchmarking estimate of N2O fluxes through synthesizing the multimodel simulation results and existing estimates from ground-based observations, inventories, and statistical and empirical extrapolations. This study provides detailed descriptions for the NMIP protocol, input data, model structure, and key parameters, along with preliminary simulation results. The global and regional N2O estimation derived from the NMIP is a key component of the global N2O budget synthesis activity jointly led by the Global Carbon Project and the International Nitrogen Initiative
Extremophiles in a changing world
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the worldâs attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.Open access funding provided by University of Pretoria.http://link.springer.com/journal/792hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-03:Good heatlh and well-beingSDG-07:Affordable and clean energySDG-09: Industry, innovation and infrastructureSDG-12:Responsible consumption and productionSDG-14:Life below waterSDG-15:Life on lan
Ammonia-oxidising archaea living at low pH: Insights from comparative genomics
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments
Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together
Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 â) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation
Characterisation of proteins involved in CRISPR-mediated antiviral defence in Sulfolobus solfataricus
One of the most surprising realisations to emerge from metagenomics studies
in the early â00s was that the population of viruses and phages in nature is about 10
times larger than the population of prokaryotic organisms. Thus, bacteria and archaea
are under constant pressure to develop resistance methods against a population of
viruses with extremely high turnover and evolution rates, in what has been described
as an evolutionary âarms raceâ. A novel, adaptive and heritable immune system
encoded by prokaryotic genomes is the CRISPR/Cas system. Arrays of clustered
regularly interspersed short palindromic repeats (CRISPR) are able to incorporate viral
or plasmid sequences which are then used to inactivate the corresponding invader
element via an RNA interference mechanism. A number of CRISPR-associated (Cas)
protein families are responsible for the maintenance, expansion and function of the
CRISPR loci. This system can be classified in a number of types and subtypes that
differ widely in their gene composition and mode of action.
This thesis describes the biochemical characteristics of CRISPR-mediated
defense in the crenarchaeon Sulfolobus solfataricus. The process of CRISPR loci
transcription and their subsequent maturation into small guide crRNA units by the
processing endonuclease of the system (Cas6) is investigated. After this step, different
pathways and effector proteins are involved in the recognition and silencing of DNA or
RNA exogenous nucleic acids. This thesis reports the identification and purification of
a native multiprotein complex from S. solfataricus P2, the Cmr complex, a homologue
of which has been found to recognise and cleave RNA targets in P. furiosus. The
recognition and silencing of DNA targets in E. coli has been shown to involve a
multiprotein complex termed CASCADE as well as Cas3, a putative helicase-HD
nuclease. S. solfataricus encodes orthologues for the core proteins of this complex,
and the formation and function of an archaeal CASCADE is investigated in this thesis
Ătude de corrĂ©lation entre la gravitĂ© clinique et la gravitĂ© scannographique chez les patients SARS-CoV-2 positifs aux urgences du CHU de Rouen du 2 mars au 30 juin 2020 : une Ă©tude de cohorte rĂ©trospective
Rechercher et quantifier la relation entre les scores de gravitĂ© NEWS2/qCSI et lâĂ©tendue de lâatteinte au scanner afin dâoptimiser la prise en charge des patients? Conception et critĂšre de jugement principal : Etude de corrĂ©lation entre la gravitĂ© clinique (NEWS2/qCSI) et la gravitĂ© scannographique (pourcentage dâatteinte parenchymateuse) sur une cohorte rĂ©trospective monocentrique aux urgences du CHU de Rouen, incluant tous les patients du 2 mars au 30 juin 2020, avec un diagnostic de SARS-COV2 par PCR ou scanner de forte probabilitĂ© et une Ă©valuation de lâatteinte parenchymateuse par scanner. Il sera attribuĂ© Ă la corrĂ©lation de Pearson entre les scores cliniques pris en variable continue et le scanner thoracique en variable ordinale, une intensitĂ© faible entre 0,3 et 0,5; moyenne entre 0,5 et 0,8 et forte au-delĂ de 0,8. RĂ©sultats/Discussion : 165 patients ont Ă©tĂ© analysĂ©s aprĂšs application des critĂšres dâexclusion et de non-inclusion. Parmi eux 48/165 (29%) sont graves (dĂ©cĂšs ou rĂ©animation durant le sĂ©jour). Les performances des scores Ă©taient moins bonnes que dans la littĂ©rature. Les corrĂ©lations sont faibles pour NEWS2 (R= 0,48) et qCSI (R= 0,39) aprĂšs imputation multiples. La distribution Ă©parse des individus en limite sa reproductibilitĂ©. Des analyses en sous-groupes ont Ă©tĂ© rĂ©alisĂ©es aprĂšs imputation simple. Les corrĂ©lations sur les sous-groupes âdĂ©but des symptĂŽmesâ âConclusion : Il existe une corrĂ©lation faible de la gravitĂ© entre le score de NEWS2/qCSI et lâatteinte parenchymateuse scannographique avec rho=0,48 et 0,39 respectivement Elle ne permet pas de sâabstenir du scanner aux urgences pour les malades modĂ©rĂ©es Ă critique lorsque celui-ci est indiquĂ©
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