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There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.

Short-chain fatty acids (SCFAs) are major products of intestinal microbial fermentation with beneficial effects for human health. The dynamic balance and real-time monitoring of endogenous SCFA biosynthesis are important for understanding their physiological functions. We discuss the promising future of applying CRISPRi genetic systems and biosensors for targeted SCFA improvement.

The limited availability of shared cellular resources introduces strong coupling among seemingly unrelated components. Given the fundamental role that multistable switches play in both natural and synthetic genetic systems, here we focus on how the scarcity of resources affects the behavior of these elementary building blocks. In particular, we reveal that while competition for scarce resources pushes the dynamics towards monostability, self-activation attenuates this phenomenon, as well as perturbations from the genetic context of the switch. However, this robustness comes at a price: our analysis uncovers that strong self-activation can lead to tristable dynamics that can surprisingly and misleadingly appear as if the underlying system was monostable, especially when considering cell-to-cell heterogeneity. This letter thus exposes how self-activation and competition for scarce resources establish the stability and robustness properties of genetic switches at both single cell and population levels. Due to their analytic nature, our results provide explicit guidelines for the rational and optimal design of synthetic gene circuits and facilitate the analysis of organizing principles underlying natural systems.

The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA–ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations., Synthetic riboswitches can be used as chemical gene switches in cell-free protein synthesis systems. We provide a current perspective on the state of cell-free riboswitch technologies and their future directions.

The inheritance of the height of barley plants was studied in the system of diallel crossing (66) in the conditions of the forest-steppe of the Middle Volga in contrasting hydrothermal conditions. An analysis of combinational ability according to B. Griffing and genetic analysis according to B. Hayman showed the predominance of additive effects in the control of the trait (inheritance by type of complete and incomplete dominance). The trait should be responsive to selection, which is confirmed by the heritability coefficients: in the broad sense (H2), 0.85-0.90 in the narrow sense (h2) 0.52-0.62. Dominant genes increased the height of plants. The presence of complementary epistasis increases the likelihood of negative transgressions, increasing the success of breeding to reduce plant height. None of the varieties of the diallel complex possessed all recessive alleles that reduced the trait. Varieties Anna and Omsky Golozyorny 1, with dominant alleles, will increase the height of plants in the offspring. These varieties should be used in combination with shorter parents. Varieties Condor and Margret have a higher number of recessive alleles and can be considered as donors of height reduction. Promising for selection hybrid populations have been identified., Volga Region Farmland, Выпуск 1 (5) 2020

Whole cell biosensors are genetic systems that link the presence of a chemical, or other stimulus, to a user-defined gene expression output for applications in sensing and control. However, the gene expression level of biosensor regulatory components required for optimal performance is nonintuitive, and classical iterative approaches do not efficiently explore multidimensional experimental space. To overcome these challenges, we used a design of experiments (DoE) methodology to efficiently map gene expression levels and provide biosensors with enhanced performance. This methodology was applied to two biosensors that respond to catabolic breakdown products of lignin biomass, protocatechuic acid and ferulic acid. Utilizing DoE we systematically modified biosensor dose-response behavior by increasing the maximum signal output (up to 30-fold increase), improving dynamic range (>500-fold), expanding the sensing range (4-orders of magnitude), increasing sensitivity (by >1500-fold), and modulated the slope of the curve to afford biosensors designs with both digital and analogue dose-response behavior. This DoE method shows promise for the optimization of regulatory systems and metabolic pathways constructed from novel, poorly characterized parts.

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference genomes for the widely used tomato genotype M82 along with Sweet-100, a rapid-cycling genotype that we developed to accelerate functional genomics and genome editing. This work outlines strategies to rapidly expand genetic systems and genomic resources in other plant species.

Motivation Kinship estimation is necessary for evaluating violations of assumptions or testing certain hypotheses in many population genomic studies. However, kinship estimators are usually designed for diploid systems and cannot be used in populations with mixed haploid diploid genetic systems. The only estimators for different ploidies require datasets free of population structure, limiting their usage. Results We present KIMGENS (Kinship Inference for Mixed GENetic Systems), an estimator for kinship estimation among individuals of various ploidies, that is robust to population structure. This estimator is based on the popular KING-robust estimator but uses diploid relatives of the individuals of interest as references of heterozygosity and extends its use to haploid–diploid and haploid pairs of individuals. We demonstrate that KIMGENS estimates kinship more accurately than previously developed estimators in simulated panmictic, structured and admixed populations, but has lower accuracy when the individual of interest is inbred. KIMGENS also outperforms other estimators in a honeybee dataset. Therefore, KIMGENS is a valuable addition to a population geneticist’s toolbox. Availability and implementation KIMGENS and its association simulation tool are implemented and available open-source at https://github.com/YenWenWang/HapDipKinship. Supplementary information Supplementary data are available at Bioinformatics online.

In the introduction to this special issue we consider the dynamics of language from three interrelated perspectives: ontogenesis, or the development of the language system in the individual; logogenesis, or the development of meanings across texts and discourses; and phylogenesis, or the changes to individual language systems over time. We discuss how these three methods of development are intrinsically connected, feeding into each other in such a way that they can be theorised as essentially different spatiotemporal perspectives on the same phenomenon. From there we pose three central questions for the modelling of change and contrast in Systemic Functional Linguistics (SFL), summarised briefly as: How can the theoretical and descriptive architecture of SFL be developed to account for the dynamics between these three genetic systems? How can we account for the expansion of the meaning potential of individual languages as a result of these processes? And to what extent are the fundamental categories of SFL adequate to the description of languages other than English and, hence, to the comparison of different languages? We then provide an overview of how the different papers in this special issue respond to these three questions.

The article describes a concept of epigene networks that attempts to clarify the phenomenon of heredity and presents the results of long-term studies of the control gene and epigene networks in which the authors used an integrative approach with the tools of mathematical biology, cybernetics, genetic engineering, and bioinformatics. Epigene networks are control gene networks with epigenetic properties or those containing epigenes. By epigene, we mean special hereditary units with at least two modes of functioning of the genes subordinate to them that are capable of maintaining each of the modes in a successive series of generations. Epigenes are the units of functional hereditary memory; they perform a special role in ontogeny and phylogeny. Epigenetic systems can be designed and synthesized experimentally. One such systems is a two-component, stationary epigene with specified and controlled inherited dynamic properties that functions in vivo. Artificial epigenetic constructions can serve as models of the mechanisms of differentiation and cellular memory and can be used as bacterial biosensors. The generalized threshold models of natural and synthetic molecular genetic systems for the control of gene expression have both analytical and predictive value.

The dynamics of long-term evolution in a complex genetically-structured population with a flux of random mutations is employed here to study the evolution of mutual altruism between relatives that are encountered repeatedly, where the level of altruism is measured by the risk one is willing to accept in order to save the life of one’s relative. It is shown that regardless of the number of loci involved, of the rates of recombination among them, and of the intensity of the selection forces, the long-term dynamics can phenotypically converge only to a level of altruism that maximizes the individual inclusive fitness as it has previously defined by students of the individual approach to evolution. Except for the widely studied case of weak selection, however, the convergence to such a level of altruism is not necessarily generation-to-next monotone. It is further shown that, unlike the case of the one-shot encounter, repeated encounters between relatives allow for more than one level of altruism which may maximize the inclusive fitness, in which case not all such levels of altruism are evolutionarily accessible.

The paper characterizes 52 producers of red steppe, 49 - red Danish and 169 Angler bulls of “Barnaulskoye” enterprise in terms of erythrocyte antigen occurrence. The authors used 53 antiserums in order to determine erythrocytic antigens of 9 genetic systems. The highest frequency observed was F antigen frequency equal to 0.976-1.000. This gene was not observed in one servicing red steppe bull and four servicing Angler bulls. All red Danish bulls had F allele in a homo- or heterozygous state. The concentration of antigens A2, B2, O1, Y2, G’, Q’ (system B), C1, C2, E, R2, W, X2 (system C), H’ (system S) in the red bulls was high and equal to 0.249-0.592. The frequency of erythrocytic antigens B1, I1, P2, T1, T2, Y1, I’, D’, J2’, P1’, B” (B), R1 (C), J (J), S2, U and H” (S) was the lowest at 0-0.122. All 53 blood factors were observed in Angler cattle, but no antigens B1, P2, R1, U и B1, Y1, B” were observed in the red steppe and red Danish cattle. There are no significant differences observed in genetic similarity among three red breeds; the index of genetic similarity are 0.9211-0.9307, which indicates a high relationship among them. The highest number of ejaculates and native sperm was obtained from Angler servicing bulls, the excess over other breeds was 11.9-13.9 and 15.1-42.8%. Red steppe bulls were characterized by lowest amount of ejaculate and less bioproducts for cryopreservation were received from them. The total breeding efficiency of cows with red steppe bull sperm was 85.1%, the superiority over Danish and Angler red cattle was 7.1-11.5%.

The modern stage of development of symbiogenetics, a biological discipline that addresses the formation of super-species genetic systems, is associated with the study of molecular mechanisms and environmental consequences of combining the hereditary factors of prokaryotes and eukaryotes into functionally integrated symbiogenomes, which, as partners lose their ability to autonomous existence, are transformed into structurally integrated hologenomes. The loss by intracellular symbionts of eukaryotes of their genetic individuality, determined by the ability to independently maintain and express the genome, representing a key step in symbiogenesis which results in the transformation of bacteria into cellular organelles. Genetic reconstruction of symbiogenesis provides the broad prospects for its artificial reproduction aimed at the synthesis of new organisms and biosystems possessing the predetermined sets of practically significant features.

Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non-ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.

Mitochondria are intracellular energy generators involved in various cellular processes. Therefore, mitochondrial dysfunction often leads to multiple serious diseases, including neurodegenerative and cardiovascular diseases. A better understanding of the underlying mitochondrial dysfunctions of the molecular mechanism will provide important hints on how to mitigate the symptoms of mitochondrial diseases and eventually cure them. In this review, we first summarize the key parts of the genetic processes that control the physiology and functions of mitochondria and discuss how alterations of the processes cause mitochondrial diseases. We then list up the relevant core genetic components involved in these processes and explore the mutations of the components that link to the diseases. Lastly, we discuss recent attempts to apply multiple genetic methods to alleviate and further reverse the adverse effects of the core component mutations on the physiology and functions of mitochondria.

The arms race between bacteria and phages led to the emergence of a variety of genetic systems used by bacteria to defend against viral infection, some of which were repurposed as powerful biotechnological tools. While numerous defense systems have been identified in genomic regions termed defense islands, it is believed that many more remain to be discovered. Here, we show that P2- like prophages and their P4-like satellites have genomic hotspots that represent a significant source of novel anti-phage systems. We validate the defense activity of 14 systems spanning various protein domains and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Immunity hotspots are present across prophages of distant bacterial species, highlighting their biological importance in the competition between bacteria and phages.

The relevance of the research is due to a change in the strength, frequency and direction of harmful weather stresses associated with climate change, which has an extremely negative effect on the general condition and productivity of plants, disrupts the conditions for the exit of plants from the dormant stage, while accelerating the rate of spring development. The rise of positive temperatures in the autumn period delays the entry of plants into the phase of organic dormancy, impairing their preparation for the winter. This paper provides an assessment of the adaptive response of the optimal course of growth and development of scion-rootstock combinations (SRC), taking into account changes in environmental conditions. The complexity of interaction mechanisms in the “scion-rootstock-environment” system is presented. Analysis of variance has shown that quantitative traits have complex genetic systems, which are characterized by multivariance of the reaction associated with multilevel redefinition of the genetic organization of quantitative traits of the SRC when changing the environmental limits. The value of the work is in the fact that the selected objects are perennial fruit crops, which are an interacting complex of two genotypes. The best combinations of grafts and rootstocks in the studied varieties in the specific environmental conditions and with given growing technologies were identified: Stanley / PK SK 1, Stanley / Druzhba, Renklod Donetskiy-1 / Evrika 99, Renklod Donetskiy-1 / cherry plum, Milena / Evrika 99 The highest-yielding under the changed conditions, and hence the most adaptive, were the combinations of plum variety Stanley on the rootstocks of PK SK 1 and Druzhba.

Made available in DSpace on 2020-12-12T01:28:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-01 Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation. Departamento de Química Laboratório de Pesquisas Forenses e Genômicas Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo Departamento de Genética Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Department of Anthropology University of Toronto at Mississauga Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo Department of Anthropology University of Cincinnati São Paulo State University (UNESP) Department of Pathology School of Medicine São Paulo State University (UNESP) Department of Pathology School of Medicine

DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs. ispartof: MOLECULES vol:25 issue:15 ispartof: location:Switzerland status: published

In 2015-2016, the little known Zika virus (ZIKV) caused an epidemic, in which it became recognized as a unique human pathogen associated with a range of devastating congenital abnormalities collectively categorized as congenital Zika syndrome (CZS). In adults, the virus can trigger the autoimmune disorder Guillain-Barre syndrome (GBS), characterized by ascending paralysis. In February 2016, the World Health Organization (WHO) declared ZIKV to be a Public Health Emergency of International Concern. The global public health problem prompted academia, industry, and governments worldwide to initiate development of an effective vaccine to prevent another ZIKV epidemic that would put millions at risk. The development of reverse genetic systems for the study and manipulation of RNA viral genomes has revolutionized the field of virology, providing platforms for vaccine and antiviral development. In this review, we discuss the impact of reverse genetic systems on the rapid progress of ZIKV vaccines and antiviral therapeutics.

microRNAs (miRNAs) are well-known gene regulators of various biological processes in plants. Despite the growing knowledge of the miRNAs as main players in genetic systems, their involvement in regulating plant secondary metabolite (SM) biosynthesis is still poorly understood. In plants, these metabolites provide protection against various types of stresses that arise from unfavorable conditions. These plant-derived compounds are also significantly used in pharmaceuticals, food additives, and fragrances industries. Hence, there is a pressing need to explore how their biosynthetic pathways are being regulated, especially at post-transcriptional level with the involvement of miRNAs. Here, we discuss the recent progress on the post-transcriptional regulation by miRNAs of SMs biosynthetic pathways, namely terpenoids, flavonoids and alkaloids. We also summarize the key points to utilize miRNAs for genetic engineering to manipulate SMs production in plants.

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways., This collaborative effort was supported by the Gordon and Betty Moore Foundation EMS Program of the Marine Microbiology Initiative (grant nos. GBMF4972 and 4972.01 to F.-Y.B.; GBMF4970 and 4970.01 to M.A. and A.Z.W.; GBMF3788 to A.Z.W.; GBMF 4968 and 4968.01 to H.C.; GBMF4984 to V.H.; GBMF4974 and 4974.01 to C. Brownlee; GBMF4964 to Y. Hirakawa; GBMF4961 to T. Mock; GBMF4958 to P.S.; GBMF4957 to A.T.; GBMF4960 to G.J.S.; GBMF4979 to K.C.; GBMF4982 and 4982.01 to J.L.C.; GBMF4964 to P.J.K.; GBMF4981 to P.v.D.; GBMF5006 to A.E.A.; GBMF4986 to C.M.; GBMF4962 to J.A.F.R.; GBMF4980 and 4980.01 to S.L.; GBMF 4977 and 4977.01 to R.F.W.; GBMF4962.01 to C.H.S.; GBMF4985 to J.M.; GBMF4976 and 4976.01 to C.H.; GBMF4963 and 4963.01 to V.E.; GBMF5007 to C.L.D.; GBMF4983 and 4983.01 to J.L.; GBMF4975 and 4975.01 to A.D.T.; GBMF4973 and 4973.01 to I.R.-T. and GBMF4965 to N.K.), by The Leverhulme Trust (RPG-2017-364) to T. Mock and A. Hopes, and by ERD funds (16_019/0000759) from the Czech Ministry of Education to J.L.

Исследования проводили для выявления генетического контроля показателей выхода зерна (Кхоз) в почвенноклиматических условиях лесостепи Среднего Поволжья. В системе диаллельных скрещиваний (6*6) в контрастные по гидротермическому режиму годы (2009-2010 гг.) изучали генетический контроль нескольких показателей Кхоз (индекс урожая, уборочный индекс) у ячменя: отношение массы зерна с растения к массе растения (КХР), отношение массы зерна с главного побега к массе побега (КХП), отношение массы зерна с колоса к массе главного колоса (КХК). На проявление систем генетического контроля всех изученных показателей оказывали влияние условия года исследований. Признак КХР контролируется с участием доминантных и аддитивных эффектов, в засушливый год имеет место комплементарный эпистаз и ненаправленное доминирование. Коэффициент наследуемости КХР в широком смысле - 0,70.0,82, в узком - 0,47.0,51. Наследование КХП осуществляется согласно аддитивно-доминантной модели, доминирование в F1 неполное, в F2 - полное, ненаправленное. Коэффициент наследуемости КХП в широком смысле - 0,79.0,88, в узком - 0,44.0,57. Признак КХК наследуется по аддитивнодоминантному типу с проявлением в засушливом 2010 г. эпистатических эффектов; доминирование неполное, признак увеличивают доминантные гены. Коэффициент наследуемости КХК в широком смысле - 0,88.0,95, в узком - 0,51.0,66. Селекция на увеличение признаков Кхоз может быть успешной, но отбор следует начинать в более поздних поколениях. Донорами для селекции на увеличение КХП и КХР могут быть сорта Анна (Оренбургская область) и Нутанс 553 (Саратовская область). Сорт Анна рекомендуем в качестве донора на увеличение КХР в засушливых условиях.

The characteristics of agronomic traits in the analogue lines of the Kooperatorka and Stepnyak bread wheat cultivars, in which alleles of the photoperiod sensitivity genes were identified by PCR, were studied. The level of recovery of the recurrent genetic background has been identified in the analogue lines, and the allelic state of the Rht8 dwarfing gene has been identified. The effect of the Ppd-D1a allele on the agronomic traits and growth rates of analogue lines, irrespective of other genetic systems, has been established, using the methods of dispersion and discriminant analyses. Differences in the results obtained by these two methods are explained by including intertrait correlations into the discriminant analysis. It has been shown that the most informative traits for discriminating between the lines were the date of heading and the plant height.

Massively parallel sequencing is transforming forensic work by allowing various useful forensic markers, such as STRPs and SNPs, to be multiplexed providing information on ancestry, individual and familial identification, phenotypes for eye/hair/skin pigmentation, and the deconvolution of mixtures. Microhaplotypes also become feasible with massively parallel sequencing, these are DNA segments (smaller than 300 nucleotides) that are selected to contain multiple SNPs unambiguously defining three or more haplotype alleles occurring at common frequencies. The physical extent of a microhaplotype can thus be covered by a single sequence read making these loci phase-known codominant genetic systems. Such microhaplotypes supply significantly more information than a single SNP can. Our efforts to develop useful sets of microhaplotypes have already identified 182 such loci that we have studied on a large number of human populations from around the world. We present various analyses on 83 populations in our ongoing study for a subset of the best microhaplotypes currently available illustrating their characteristics and potential utility for ancestry, identification, and mixture deconvolution.

Cellular burden limits the applications of bacterial synthetic biology. Experimental approaches for burden minimisation have recently become available. Tools to identify construct design with low footprint on the host include capacity monitors that quantify cellular capacity, high-throughput approaches and cell-free systems for construct prototyping. Orthogonal ribosomes and feedback controllers are instead useful to seek control of resource allocation and lower burden. Other approaches include genome reduction to increase the available resource pool and synthetic addiction to couple cell fitness and product accumulation. However, controlling the cellular response to exogenous expression is still a challenge, and more tools are needed in order to widen the applications of synthetic biology. Further effort that combines novel evolutionary data with burden-aware tools can set the foundation to increase the stability and robustness of future genetic systems.

Dispersal flights by the mountain pine beetle have allowed range expansion and major damage to pine stands in western Canada. We asked what the genetic and transcriptional basis of mountain pine beetle dispersal capacity is. Using flight mills, RNA-seq and a targeted association study, we compared strong-flying, weak-flying, and non-flying female beetles from the recently colonized northern end of their range. Nearly 3,000 genes were differentially expressed between strong and weak flying beetles, while weak fliers and nonfliers did not significantly differ. The differentially expressed genes were mainly associated with lipid metabolism, muscle maintenance, oxidative stress response, detoxification, endocrine function, and flight behavior. Three variant loci, two in the coding region of genes, were significantly associated with flight capacity but these genes had no known functional link to flight. Several differentially expressed gene systems may be important for sustained flight, while other systems are downregulated during dispersal and likely to conserve energy before host colonization. The candidate genes and SNPs identified here will inform further studies and management of mountain pine beetle, as well as contribute to understanding the mechanisms of insect dispersal flights.

Highlights • A model of engineered underdominance (UD) gene drive is proposed. • Numerical results suggest that UD could be an effective tool for disease control. • Success/failure of UD is affected by release strategy and fitness of mosquitoes. • A single release of only males with weakly suppressed lethals cannot succeed., Engineered underdominance is one of a number of different gene drive strategies that have been proposed for the genetic control of insect vectors of disease. Here we model a two-locus engineered underdominance based gene drive system that is based on the concept of mutually suppressing lethals. In such a system two genetic constructs are introduced, each possessing a lethal element and a suppressor of the lethal at the other locus. Specifically, we formulate and analyse a population genetics model of this system to assess when different combinations of release strategies (i.e. single or multiple releases of both sexes or males only) and genetic systems (i.e. bisex lethal or female-specific lethal elements and different strengths of suppressors) will give population replacement or fail to do so. We anticipate that results presented here will inform the future design of engineered underdominance gene drive systems as well as providing a point of reference regarding release strategies for those looking to test such a system. Our discussion is framed in the context of genetic control of insect vectors of disease. One of several serious threats in this context are Aedes aegypti mosquitoes as they are the primary vectors of dengue viruses. However, results are also applicable to Ae. aegypti as vectors of Zika, yellow fever and chikungunya viruses and also to the control of a number of other insect species and thereby of insect-vectored pathogens.

Size and shape of soybean seeds are closely related to seed yield and market value. Annual wild soybeans have the potential to improve cultivated soybeans, but their inferior seed characteristics should be excluded. To detect quantitative trait loci (QTLs)/segments of seed size and shape traits in annual wild soybean, its chromosome segment substitution lines (CSSLs) derived from NN1138-2 (recurrent parent, Glycine max) and N24852 (donor parent, Glycine soja) and then modified 2 iterations (coded SojaCSSLP3) were improved further to contain more lines (diagonal segments) and less heterozygous and missing portions. The new population (SojaCSSLP4) composed of 195 CSSLs was evaluated under four environments, and 11, 13, 7, 15 and 14 QTLs/segments were detected for seed length (SL), seed width (SW), seed roundness (SR), seed perimeter (SP) and seed cross section area (SA), respectively, with all 60 wild allele effects negative. Among them, 16 QTLs/segments were shared by 2–5 traits, respectively, but 0–3 segments for each of the 5 traits were independent. The non-shared Satt274 and shared Satt305, Satt540 and Satt239 were major segments, along with other segments composed of two different but related sets of genetic systems for SR and the other 4 traits, respectively. Compared with the literature, 7 SL, 5 SW and 2 SR QTLs/segments were also detected in cultivated soybeans; allele distinction took place between cultivated and wild soybeans, and also among cultivated parents. The present mapping is understood as macro-segment mapping, the segments may be further dissected into smaller segments as well as corresponding QTLs/genes.

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of “drift-induced selection” operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems.

Phenotypic invariance—the outcome of purifying selection—is a hallmark of biological importance. However, invariant phenotypes might be controlled by diverged genetic systems in different species. Here, we explore how an important and invariant phenotype—the development of sexually differentiated individuals—is controlled in over two dozen species in the frog family Pipidae. We uncovered evidence in different species for 1) an ancestral W chromosome that is not found in many females and is found in some males, 2) independent losses and 3) autosomal segregation of this W chromosome, 4) changes in male versus female heterogamy, and 5) substantial variation among species in recombination suppression on sex chromosomes. We further provide evidence of, and evolutionary context for, the origins of at least seven distinct systems for regulating sex determination among three closely related genera. These systems are distinct in their genomic locations, evolutionary origins, and/or male versus female heterogamy. Our findings demonstrate that the developmental control of sexual differentiation changed via loss, sidelining, and empowerment of a mechanistically influential gene, and offer insights into novel factors that impinge on the diverse evolutionary fates of sex chromosomes.

Summary: As pH is fundamental to all biological processes, pH-responsive bacterial genetic circuits enable precise sensing in any environment. Where the unintentional release of engineered bacteria poses a concern, coupling pH sensing to the expression of a toxin creates an effective bacterial containment system. Here, we present a pH-sensitive kill switch (acidic termination of replicating population [acidTRP]), based on the Escherichia coli asr promoter, with a survival ratio of

Engineered genetic systems are prone to failure when their genetic parts contain repetitive sequences. Designing many nonrepetitive genetic parts with desired functionalities remains a difficult challenge with high computational complexity. To overcome this challenge, we developed the Nonrepetitive Parts Calculator to rapidly generate thousands of highly nonrepetitive genetic parts from specified design constraints, including promoters, ribosome-binding sites and terminators. As a demonstration, we designed and experimentally characterized 4,350 nonrepetitive bacterial promoters with transcription rates that varied across a 820,000-fold range, and 1,722 highly nonrepetitive yeast promoters with transcription rates that varied across a 25,000-fold range. We applied machine learning to explain how specific interactions controlled the promoters’ transcription rates. We also show that using nonrepetitive genetic parts substantially reduces homologous recombination, resulting in greater genetic stability. An algorithm to design nonrepetitive genetic parts enables synthetic biologists to reliably engineer stable circuits.

The one-century-old theory of orthogonal genetic variance decomposition originated the field of quantitative genetics and has kept on being improved ever since. Recently, serious concerns about the possibility of attaining a satisfactory implementation of genetic variance decomposition with linkage disequilibrium (LD) and epistasis have been raised. In this paper we dissipate such doubts by completing the classical theory of variance decomposition into additive, dominance and epistasis components with LD. We apply that theory to the analysis of the genotype-to-phenotype maps of two cases of particular evolutionary interest—Bateson-Dobzhansky-Müller incompatibilities and sign epistasis. For the first case we show how negative LD and reduction of heterozygotes may contribute to maintain genetic variability after secondary contact. For the second case we show that LD transforms the set of frequencies leading to an evolutionary plateau into a ridge. Our theoretical developments reassuringly reflect the complexity LD conveys to genetic systems throughout novel properties—as compared with systems under linkage equilibrium. We argue that such particularities might have actually contributed to cause confusion about the feasibility of developing this methodology. In any case, the theory we provide in this paper enables new perspectives in both evolutionary and quantitative genetics studies Project EM2014/024 from the Autonomous Administration Xunta de Galicia to JÁ-C. Project MTM2016-76969-P from the Spanish Ministry of Economy and Competitiveness to RC SI

Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide. HuNoV infections lead to substantial societal and economic burdens. There are currently no licensed vaccines or therapeutics for the prevention or treatment of HuNoVs. A lack of well-characterized in vitro and in vivo infection models has limited the development of HuNoV countermeasures. Experimental infection of human volunteers and the use of related viruses such as murine NoV have provided helpful insights into HuNoV biology and vaccine and therapeutic development. There remains a need for robust animal models and reverse genetic systems to further HuNoV research. This review summarizes available HuNoV animal models and reverse genetic systems, while providing insight into their usefulness for vaccine and therapeutic development.