scholarly journals Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea

2021 ◽  
Vol 12 ◽  
Author(s):  
Li-Jun Liu ◽  
Zhen Jiang ◽  
Pei Wang ◽  
Ya-Ling Qin ◽  
Wen Xu ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Sulfur Oxidation ◽  
Physiological Characteristic ◽  
Thermoacidophilic Archaea ◽  
Sulfite Oxidation ◽  
Code Of Nomenclature ◽  
Future Challenges ◽  
Sulfur Trafficking

The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.

scholarly journals Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

2021 ◽  
Vol 12 ◽  
Author(s):  
Nikolai V. Ravin ◽  
Tatyana S. Rudenko ◽  
Dmitry D. Smolyakov ◽  
Alexey V. Beletsky ◽  
Andrey L. Rakitin ◽  
...  
Keyword(s):  
Core Genome ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Sulfur Oxidation ◽  
Rrna Gene ◽  
Reduced Sulfur Compounds ◽  
Hybridization Data

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

scholarly journals Synthetic protocell biology: from reproduction to computation

2007 ◽  
Vol 362 (1486) ◽  
pp. 1727-1739 ◽  
Author(s):  
Ricard V Solé ◽  
Andreea Munteanu ◽  
Carlos Rodriguez-Caso ◽  
Javier Macía
Keyword(s):  
Current Knowledge ◽  
Building Blocks ◽  
Biochemical Networks ◽  
Cellular Structures ◽  
Biological Complexity ◽  
Artificial Cell ◽  
Future Challenges ◽  
Cooperative Dynamics ◽  
The Origin Of Life ◽  
Review Current

Cells are the building blocks of biological complexity. They are complex systems sustained by the coordinated cooperative dynamics of several biochemical networks. Their replication, adaptation and computational features emerge as a consequence of appropriate molecular feedbacks that somehow define what life is. As the last decades have brought the transition from the description-driven biology to the synthesis-driven biology, one great challenge shared by both the fields of bioengineering and the origin of life is to find the appropriate conditions under which living cellular structures can effectively emerge and persist. Here, we review current knowledge (both theoretical and experimental) on possible scenarios of artificial cell design and their future challenges.

scholarly journals Lung Interstitial Macrophages: Past, Present, and Future

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Joey Schyns ◽  
Fabrice Bureau ◽  
Thomas Marichal
Keyword(s):  
Dendritic Cells ◽  
Alveolar Macrophages ◽  
Historical Perspective ◽  
Current Knowledge ◽  
Allergic Airway Inflammation ◽  
Immune Functions ◽  
Immune Mediated ◽  
Future Challenges ◽  
Long Time ◽  
Review Current

For a long time, investigations about the lung myeloid compartment have been mainly limited to the macrophages located within the airways, that is, the well-known alveolar macrophages specialized in recycling of surfactant molecules and removal of debris. However, a growing number of reports have highlighted the complexity of the lung myeloid compartment, which also encompass different subsets of dendritic cells, tissue monocytes, and nonalveolar macrophages, called interstitial macrophages (IM). Recent evidence supports that, in mice, IM perform important immune functions, including the maintenance of lung homeostasis and prevention of immune-mediated allergic airway inflammation. In this article, we describe lung IM from a historical perspective and we review current knowledge on their characteristics, ontogeny, and functions, mostly in rodents. Finally, we emphasize some important future challenges for the field.

scholarly journals Biliary tract cancers: current knowledge, clinical candidates and future challenges

2019 ◽  
Vol Volume 11 ◽  
pp. 2623-2642 ◽  
Author(s):  
Noor-ul-Ain Tariq ◽  
Mairéad G McNamara ◽  
Juan W Valle
Keyword(s):  
Biliary Tract ◽  
Current Knowledge ◽  
Biliary Tract Cancers ◽  
Future Challenges

scholarly journals Ecological and Conservation Value of Small Standing-Water Ecosystems: A Systematic Review of Current Knowledge and Future Challenges

Water ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 402 ◽  
Author(s):  
Rossano Bolpagni ◽  
Sandra Poikane ◽  
Alex Laini ◽  
Simonetta Bagella ◽  
Marco Bartoli ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Structural Heterogeneity ◽  
Conservation Value ◽  
Standing Water ◽  
Management Actions ◽  
Water Ecosystem ◽  
Future Challenges ◽  
Water Ecosystems ◽  
Global Strategies ◽  
Global Water

A small standing-water ecosystem (SWE) is a shallow (<20 m) lentic water body with a surface of a few hectares (≤10 ha). Compared to larger counterparts, they exhibit wider ecotones, sometimes even equaling their whole surface, which maximizes structural heterogeneity, supporting exceptionally high biodiversity, metabolic rates, and functionality. Surprisingly, no binding regulations support global strategies for SWE conservation. This work consists of a literature review performed for the period 2004–2018 to assess the ecological and conservation value of SWEs and the contribution of the Water Framework Directive (WFD) in promoting their conservation. Outcomes from this work open new perspectives on SWEs, which emerge as valuable ecosystems, and confirm their pivotal contribution to watershed biodiversity, resilience, and functionality. Results also suggest clear narrative trends and large knowledge gaps across geographical areas, biological components, and target issues. Additionally, we note that SWEs are under-represented in the frame of WFD implementation, stressing their marginality into assessing procedures. All of this calls for further studies, especially outside Europe and with a global, multi-taxon perspective. These should be devoted to quantitatively assess the roles of SWEs in maintaining global water ecosystem quality, biodiversity, and services, and to prioritize management actions for their conservation.

scholarly journals Genomic Alterations and Their Implications on Survival in Nonmetastatic Colorectal Cancer: Status Quo and Future Perspectives

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2001 ◽  
Author(s):  
Reetu Mukherji ◽  
John Marshall ◽  
Andreas Seeber
Keyword(s):  
Colorectal Cancer ◽  
Current Knowledge ◽  
Locally Advanced ◽  
Tumor Resection ◽  
Daily Routine ◽  
Precision Oncology ◽  
Genomic Alterations ◽  
Future Challenges ◽  
The Status ◽  
Selection Of

The selection of treatment according to genomic alterations is a standard approach in metastatic colorectal cancer but is only starting to have an impact in the earlier stages of the disease. The status of genes like KRAS, BRAF, and MMR has substantial survival implications, and concerted research efforts have revolutionized treatment towards precision oncology. In contrast, a genomic-based approach has not changed the adjuvant setting after curative tumor-resection in the daily routine so far. This review focuses on the current knowledge regarding prognostic and predictive genomic biomarkers in patients with locally advanced nonmetastasized colorectal cancer. Furthermore, we provide an outlook on future challenges for a personalized adjuvant treatment approach in patients with colorectal cancer.

Ecosystem Consequences of Changing Inputs of Terrestrial Dissolved Organic Matter to Lakes: Current Knowledge and Future Challenges

Ecosystems ◽  
2015 ◽  
Vol 18 (3) ◽  
pp. 376-389 ◽  
Author(s):  
Christopher T. Solomon ◽  
Stuart E. Jones ◽  
Brian C. Weidel ◽  
Ishi Buffam ◽  
Megan L. Fork ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Current Knowledge ◽  
Future Challenges
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