Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment

Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future.

Classification of CRISPR/Cas system and its application in tomato breeding

Remarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.

Mari of Udmurtia: Factors of Preserving Traditional Culture in Modern Conditions

The factors of preservation and intergenerational transmission of the traditional culture of the local group of Mari living in the territory of Udmurtia in a different ethnic environment is examined in the article. The source basis of the article was the field ethnographic materials collected in 2007 among the Mari of the Karakulinsky region of the Udmurt Republic and introduced into scientific circulation for the first time. The socio-economic situation of the respondents, the established mechanisms of adaptation to market relations, the preservation of traditional rituals and holidays, material and spiritual culture, the use of the native language, ethno-demographic processes, the activities of the Mari community to support ethnic culture are showed in the work. The author notes that the historically formed mechanism for ensuring the viability of the Mari society includes practices of demographic behavior, ethnic socialization of youth, reproduction of elements of spiritual and religious culture (prayers, family and calendar rituals, songs) and the material world (national costume, elements of architecture, musical instruments, national cuisine), the use of the Mari language. It has been proven that the ritual sphere of the Mari is undergoing transformations, but at the same time it continues to remain an inseparable part of the life of the people. In the course of the work, it was also revealed that the local group of Mari in modern conditions for self-preservation needs to constantly generate ethnic markers based on traditional culture. The key role in this is assigned to the village community, educational institutions and public organizations.

The Evolution of Blood Flow Restricted Exercise

The use of blood flow restricted (BFR) exercise has become an accepted alternative approach to improve skeletal muscle mass and function and improve cardiovascular function in individuals that are not able to or do not wish to use traditional exercise protocols that rely on heavy loads and high training volumes. BFR exercise involves the reduction of blood flow to working skeletal muscle by applying a flexible cuff to the most proximal portions of a person’s arms or legs that results in decreased arterial flow to the exercising muscle and occluded venous return back to the central circulation. Safety concerns, especially related to the cardiovascular system, have not been consistently reported with a few exceptions; however, most researchers agree that BFR exercise can be a relatively safe technique for most people that are free from serious cardiovascular disease, as well as those with coronary artery disease, and also for people suffering from chronic conditions, such as multiple sclerosis, Parkinson’s, and osteoarthritis. Potential mechanisms to explain the benefits of BFR exercise are still mostly speculative and may require more invasive studies or the use of animal models to fully explore mechanisms of adaptation. The setting of absolute resistive pressures has evolved, from being based on an individual’s systolic blood pressure to a relative measure that is based on various percentages of the pressures needed to totally occlude blood flow in the exercising limb. However, since several other issues remain unresolved, such as the actual external loads used in combination with BFR, the type of cuff used to induce the blood flow restriction, and whether the restriction is continuous or intermittent, this paper will attempt to address these additional concerns.

Population-specific adaptation in malaria-endemic regions of asia

Evolutionary mechanisms of adaptation to malaria are understudied in Asian endemic regions despite a high prevalence of malaria in the region. In our research, we performed a genome-wide screening for footprints of natural selection against malaria by comparing eight Asian population groups from malaria-endemic regions with two non-endemic population groups from Europe and Mongolia. We identified 285 adaptive genes showing robust selection signals across three statistical methods, iHS, XP-EHH, and PBS. Interestingly, most of the identified genes (82%) were found to be under selection in a single population group, while adaptive genes shared across populations were rare. This is likely due to the independent adaptation history in different endemic populations. The gene ontology (GO) analysis for the 285 adaptive genes highlighted their functional processes linked to neuronal organizations or nervous system development. These genes could be related to cerebral malaria and may reduce the inflammatory response and the severity of malaria symptoms. Remarkably, our novel population genomic approach identified population-specific adaptive genes potentially against malaria infection without the need for patient samples or individual medical records.

Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod

Metazoan adaptation to global change will rely on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is therefore essential to make accurate predictions for persistence in future conditions. Here, we identify the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) conditions over 25 generations. Replicate populations showed a strong and consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the genomic changes into selection, drift, and lab adaptation and found that the majority of allele frequency change in warming (56%) and OWA (63%) was driven by selection but acidification was dominated by drift (66%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%. Accounting for lab adaptation was essential for not inflating a shared response to selection between all treatments. Finally, the mechanisms of adaptation in the multiple-stressor OWA conditions were not an additive product of warming and acidification, but rather a synergistic response where 47% of the allelic responses to selection were unique. These results are among the first to disentangle how the genomic targets of selection differ between single and multiple stressors and to demonstrate the complexity that non-additive multiple stressors will contribute to attempts to predict adaptive responses to complex environments.

Lifespan Extension in Long-Lived Vertebrates Rooted in Ecological Adaptation

Contemporary studies on aging and longevity have largely overlooked the role that adaptation plays in lifespan variation across species. Emerging evidence indicates that the genetic signals of extended lifespan may be maintained by natural selection, suggesting that longevity could be a product of organismal adaptation. The mechanisms of adaptation in long-lived animals are believed to account for the modification of physiological function. Here, we first review recent progress in comparative biology of long-lived animals, together with the emergence of adaptive genetic factors that control longevity and disease resistance. We then propose that hitchhiking of adaptive genetic changes is the basis for lifespan changes and suggest ways to test this evolutionary model. As individual adaptive or adaptation-linked mutations/substitutions generate specific forms of longevity effects, the cumulative beneficial effect is largely nonrandom and is indirectly favored by natural selection. We consider this concept in light of other proposed theories of aging and integrate these disparate ideas into an adaptive evolutionary model, highlighting strategies in decoding genetic factors of lifespan control.

Digital Transformation of Small Enterprise Activities in the Context of Economic Security

Aim. The presented study aims to develop recommendations for improving the existing mechanisms of adaptation of small enterprises to the uncertain conditions of the external environment associated with digitalization processes in the economy.Tasks. The author analyzes the existing mechanisms of adaptation of small enterprises to the conditions of uncertainty; substantiates the connection between the digitalization of business processes and the economic security of enterprises; proposes an original approach to the content of the mechanism of adaptation of small enterprises to the processes of digitalization.Methods. The author uses general and special scientific methods and techniques. General scientific methods include analysis and synthesis, comparison and generalization, modeling, literature review, observation, and expert assessment. Special scientific methods include factor analysis and process analysis.Results. The author substantiates the introduction of digital tools provided by Industry 4.0 and step-by-step digitalization of small enterprises in the form of original diagrams demonstrating the content of the mechanism of adaptation of enterprises to the processes of digitalization, individual elements of this mechanism (Internet marketing and its technologies), and prospects for the development of the mechanism in the form of a diagram of its integration into a large digital ecosystem (region, cluster, etc.). The most significant elements of the proposed adaptation mechanism are the mechanism of digitalization and the mechanism of economic security of small enterprises as well as their relationship and balance of interests. The study examines practical approaches to the step-by-step digitalization of small enterprise activities by assessing the efficiency of introducing certain Internet marketing tools in the activities of a small enterprise that does not directly operate in online mode (a chain of driving schools). A relevant investment project is assessed, showing the efficiency of all proposed scenarios. The author also considers the prospects of integrating small enterprises into a single digital ecosystem of a larger structure or entity (region, cluster, etc.) for a large-scale socio-economic synergetic effect that would serve as a mutual benefit for all participants of the system.Conclusions. In spite of the lack of a clear model for the digitalization of the economy in Russia and many obstacles to the successful digital transformation of small enterprises, practical digitalization mechanisms are already being developed, offering a set of step-by-step actions for small enterprises with allowance for their limited resources and prospects for development in each market. One of the success factors of digitalization is the correlation and balance between digitalization mechanisms and the economic security of enterprises. By adopting international approaches to Internet marketing technologies, a modern small enterprise gains a significant strategic advantage in the long term.

Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.