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The ultimate driving force, stress, promotes adaptability/evolution in proliferating organisms, transforming tumorigenic growth. Estradiol (E2) regulates both phenomena. In this study, bioinformatics‐tools, site‐directed‐mutagenesis (human estrogen‐sulfotransferase/hSULT1E1), HepG2 cells tested with N‐acetyl‐cysteine (NAC/thiol‐inducer) or buthionine‐sulfoxamine (BSO/thiol‐depletory) were evaluated for hSULT1E1 (estradiol‐sulphating/inactivating) functions. Reciprocal redox regulation of steroid sulfatase (STS, E2‐desulfating/activating) results in the Cys‐formylglycine transition by the formylglycine‐forming enzyme (FGE). The enzyme sequences and structures were examined across the phylogeny. Motif/domain and the catalytic conserve sequences and protein‐surface‐topography (CASTp) were investigated. The E2 binding to SULT1E1 suggests that the conserved‐catalytic‐domain in this enzyme has critical Cysteine 83 at position. This is strongly supported by site‐directed mutagenesis/HepG2‐cell research. Molecular‐docking and superimposition studies of E2 with the SULT1E1 of representative species and to STS reinforce this hypothesis. SULT1E1‐STS are reciprocally activated in response to the cellular‐redox‐environment by the critical Cys of these two enzymes. The importance of E2 in organism/species proliferation and tissue tumorigenesis is highlighted. Significance statement: 1.Stress, the ultimate driving‐force promotes adaptability and evolution in proliferating‐organisms, transforming tumorigenic growth via Estradiol (E2) signaling.2.In this study, bioinformatics‐tools, site‐directed‐mutagenesis (of human estrogen sulfotransferase; hSULT1E1), HepG2 cells (treated with N‐acetyl‐cysteine; NAC, a thiol‐inducer) or buthionine‐sulfoxamine, BSO, a thiol‐depletor) were evaluated for hSULT1E1 (estradiol‐sulphating/inactivating) functions.3.Reciprocal redox‐regulation of steroid sulfatase (STs, E2‐desulfating, and activating) results Cys‐ formylglycine transition by formylglycine‐forming enzyme (FGE).4.Critical Cys83 (in SULT1E1) and the Cys‐formylglycine (in STS) transitions reciprocally activate SULT1E1‐STS in response to the cellular‐redox environment.5.The importance of E2 in organism/species proliferation and tissue tumorigenesis is highlighted. [ABSTRACT FROM AUTHOR]

Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed. [ABSTRACT FROM AUTHOR]

ABSTRACTPertussis caused by Bordetella pertussis, remains a public health problem worldwide, despite high vaccine coverage in infants and children in many countries. Iran has been using whole cell vaccine for the last 50 years with more than 95% vaccination rate since 1988 and has experienced pertussis resurgence in recent years. Here, we sequenced 55 B. pertussis isolates mostly collected from three provinces with the highest number of pertussis cases in Iran, including Tehran, Mazandaran, and Eastern-Azarbayjan from the period of 2008-2016. Most isolates carried ptxP3/prn2 alleles (42/55, 76%), the same genotype as isolates circulating in acellular vaccine-administrating countries. The second most frequent genotype was ptxP3/prn9 (8/55, 14%). Only three isolates (5%) were ptxP1. Phylogenetic analysis showed that Iranian ptxP3 isolates can be divided into eight clades (Clades 1-8) with no temporal association. Most of the isolates from Tehran grouped together as one distinctive clade (Clade 8) with six unique single nucleotide polymorphisms (SNPs). In addition, the prn9 isolates were grouped together as Clade 5 with 12 clade-supporting SNPs. No pertactin deficient isolates were found among the 55 Iranian isolates. Our findings suggest that there is an ongoing adaptation and evolution of B. pertussis regardless of the types of vaccine used.

Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application. [ABSTRACT FROM AUTHOR]

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The Qinghai-Tibet Plateau (QTP) is the highest and largest plateau in the world. It covers correspondingly wide geological, topographical, and climatic gradients, and thus hosts greater biodiversity than surrounding lowlands and other high elevation regions. Due to its extreme environmental and biological diversity, the QTP is an ideal region for studying adaptations of plant species under harsh environmental conditions at multiple evolutionary levels. Many recent ecological studies have revealed functions of distinctive morphological features of various plants in the region that improve their reproductive success. Examples include large and showy bracts, hairy inflorescences, and drooping flowers. Numerous other investigations have examined QTP plants' sexual systems, patterns of biomass allocations, and biotic interactions. This paper summarizes recent advances in understanding of morphological adaptations, plant-plant interactions, plant-pollinator interactions, floral color patterns, pollination adaptations, and resource allocation patterns of alpine plants of the QTP. The overall aim is to synthesize current knowledge of the general mechanisms of plant survival and reproduction in this fascinating region. [ABSTRACT FROM AUTHOR]

Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed., Competing Interests: Conflict of interestThe authors declare no conflict of interest., (© The Korean Society of Food Science and Technology 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Abstract: The current paper reviews strategies employed by microorganisms from the deep biosphere, especially piezophiles (from the greek piezo = to press and philo = love), to cope with high hydrostatic pressure (HHP) prevailing in these biotopes. The aim of this review is not to constitute an exhaustive report of our current knowledge on the physiology of piezophiles, as recent reviews have covered part of this subject in detail (). Rather, we illustrate here, via a few chosen examples, where we stand in our understanding of the mechanisms employed by microorganisms from the depths of our planet to cope with HHP. [ABSTRACT FROM AUTHOR]

A consultative and cooperative perspective on water management is vital in regional sustainability. However, previous approaches often failed to consider the complex trade-offs involved in water resource allocation. This study explores theoretical perspectives on regional integration as a policy goal through the process of water allocation. The main purpose is to explain new areas created by allocation and regional integration with local-scale cases. The connections between post-structuralism, fragmentation, and heterogeneity are explored with five case studies of groundwater zoning: a Xinyuan buried pipe compensation, a Ligang well closure and power shutdown, a Dachaozhou artificial lake, a Wandan hold back well, and a Meinong anti-deep-water wells. Along with the case studies, secondary literature, interviews, and a field investigation were used. The time span of water conflicts was from 1973 to 2019, and the spatial scope is the groundwater distribution area. The study found that regional integration and dynamic balance are each other's subject and object, which was empirically verified through the water conflicts in agriculture and the semiconductor industry. Regional integration comes through scaled and flexible methods of operation, and is produced through special market agents and post-structural spaces. In the process, the imbalance caused by conflict must also be adjusted and evolved through cooperation, competition, and negotiation to maintain the dynamic balance. This involves internal treatment of the local government, external integration of the central government, and technological evolution within the organization. Accordingly, several suggestions are proposed that may be helpful for sustainable water resource governance. In summary, this study makes up for the shortcomings of water management patterns constructed by simple spatial overlaying of regional integration. Our findings could effectively enhance negotiations and collaboration in water management for regional sustainability. [ABSTRACT FROM AUTHOR]

Background The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. Findings The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. Conclusions We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats. [ABSTRACT FROM AUTHOR]

Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application., (© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)