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A sugar acid dehydratase from Paraburkholderia mimosarum , potentially involved in the non-phosphorylated L-fucose pathway, was functionally characterized. A biochemical analysis revealed its unique heterodimeric structure and higher specificity toward L-fuconate than D-arabinonate, D-altronate, and L-xylonate, which differed from homomeric homologs. This unique L-fuconate dehydratase has a poor phylogenetic relationship with other functional members of the D-altronate dehydratase/galactarate dehydratase protein family. [ABSTRACT FROM AUTHOR]

As a reference mitogenome, the complete mitochondrial genome of the white-breasted hedgehog, Erinaceus concolor , was firstly presented in this study by employing Long-Range PCR and Next-Generation Sequencing. The total lengths of the mitogenomes were 17.451 bp and 17.455 bp. A total of 37 genes, namely two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a non-coding D-loop were encoded in the mitogenome, compatible with the previously reported mitogenomes belonging to representatives of the family Erinaceidae (Mammalia: Eulipotyphla). Maximum Likelihood and Bayesian Inference phylogenetic analyses of Eulipotyphla and Erinaceidae based on the complete mitogenomes revealed a conventional relationship for the relevant organism's groups. Divergence time analyses based on complete mitogenome data revealed that evolutionary divergence events within Erinaceidae began about 58.87 Myr ago corresponding to the early Eocene, and the basal split of Erinaceus dates back to approximately 11.01 Myr ago in the late Miocene. Single cytochrome b -based analyses can be considered weaker, as they produce phylogenies that are relatively inconsistent with the natural classification of Eulipotyphla and put the onset of evolutionary divergence events earlier. The genetic information obtained as a result of this study can be used as a genetic resource for conservation biology studies; it will also undoubtedly contribute to the understanding of molecular evolution of E. concolor and closely related taxa. [ABSTRACT FROM AUTHOR]

So far, the monoclonal hypothesis of tumor occurrence and development cannot be justified. The genetic diversity selection hypothesis for the occurrence and development of lung cancer links Mendelian genetics with Darwin's theory of evolution, suggesting that the genetic diversity of tumor cell populations with polyclonal origins-monoclonal selection-subclonal expansion is the result of selection pressure. Normal cells acquire mutations in oncogenic driver genes and have a selective advantage over other cells, becoming tumor initiating cells; In the interaction with the tumor microenvironment (TME), the vast majority of initiating cells are recognized and killed by the human immune system. If immune escape occurs, the incidence of malignant tumors will greatly increase, and subclonal expansion, intratumour heterogeneity, etc. will occur. This article proposed the hypothesis of genetic diversity selection and analyzed its clinical significance. [ABSTRACT FROM AUTHOR]

Avian-origin H3N2 canine influenza A viruses (CIVs) have become enzootic in China and Korea and have sporadically transmitted to North America, causing multiple epidemics. We isolated six CIVs in Korea from CIV-infected patients during 2014-2017 and conducted whole genome sequencing and phylogenetic analyses. Results revealed that CIVs have circulated and evolved in Korea since the early 2000s and then diversified into a new clade, probably contributing to multiple epidemics in China, the USA, and Canada. Our findings bridge an evolutionary gap for understanding the global transmission of CIVs, emphasizing the significance of continuous monitoring of CIVs. [ABSTRACT FROM AUTHOR]

[Display omitted] Hydrolytic degradation of polymers involves the scission of long chain molecules, leading to molecular weight reduction and mass loss. The precise degradation response however depends on the scission probability of individual bonds along the polymer backbone. In particular, bonds near the chain ends are considered to be more susceptible to hydrolysis than inner bonds. In this paper, we incorporate a discrete chain scission model that can handle arbitrary bond scission probabilities within a continuum reaction-diffusion framework. Overall hydrolysis kinetics (including autocatalysis) is described independently of the chain scission model. By decoupling the description of the chain scission mechanism from kinetics, our framework enables the identification of the chain scission mechanism from molecular weight reduction and mass loss curves commonly reported in experimental degradation studies. We further propose a reduced continuum model which is better suited for large-scale simulations while retaining the predictive capability of the full discrete-continuum model. The model capability is illustrated in representative case studies based on experimental data from the literature for different materials and geometries. Many models have been proposed to predict the evolution of molecular weight and mass loss in biodegradable polymers undergoing hydrolytic degradation. However, existing models remain limited in their ability to describe the degradation mechanism, autocatalytic kinetics and short chains diffusion simultaneously. Moreover, existing models often rely on empirical relations and a large number of fitting parameters. Here, we propose a conceptually simple discrete-continuum mathematical framework with a small number of parameters which all have a clear physical meaning. Model calibration against experimental data is simplified, and further provides insights into the degradation mechanisms at play, namely random scission, chain-end scission, or a combination of both. The framework can serve as a basis for future generalisations, including a description of evolving crystallinity, or other degradation mechanisms, such as thermal oxidation or photo-degradation. [ABSTRACT FROM AUTHOR]

[Display omitted] • First report whole genome wide comparative analysis of drought tolerant wild barley vs cultivated barley. • Drought tolerance in Tibetan wild barley attributes to candidate genes with unique genetic variants and expression patterns. • Wild barley employs effective regulators to activate various responsive pathways to adapted to water deficit conditions. • Novel functional genes HvZIFL2 and HvPOD11 positively regulate drought tolerance. Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops. [ABSTRACT FROM AUTHOR]

Paepalanthus, in its current sense, is the most diverse genus of Eriocaulaceae in the Neotropics, comprising about 400 species. Previous studies have consistently found that the genus is not monophyletic, also being morphologically heterogeneous and diagnosable by a set of homoplasies; thus, the current circumscription needs to be revised. The new classification proposed here uses a comprehensive phylogeny of Paepalanthus and closely related genera as a framework and an evaluation of a set of morphological characters using ancestral state reconstruction, which allowed the recognition of strongly supported clades with morphological diagnosability. We propose the recognition of 12 genera in the clade encompassing Paepalanthus and allied groups, including six new genera (Coracoralina, Floralia, Giuliettia, Gnomus, Hydriade, Nisius), two new statuses (Cryptanthella, Monosperma), the reestablishment of Actinocephalus, Lachnocaulon, and Tonina, and a recircumscription of Paepalanthus. In this new circumscription, Paepalanthus comprises 257 species, most of them restricted to the Brazilian campos rupestres. Among the proposed genera, nine have potential morphological synapomorphies, one has a restricted geographical distribution, and the other two can be recognized by a combination of characters. Newly generated seed morphology data is consistent within the different genera and plays an important role in their recognition. A total of 136 new combinations are hereby proposed. We provide a genus‐level identification key, as well as generic descriptions, diagnostic features, photos illustrating their morphological diversity, maps and notes on distribution, and lists of species by genus. [ABSTRACT FROM AUTHOR]

The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus. In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence. In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes. All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366 bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1 , were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth. The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships. [Display omitted] [ABSTRACT FROM AUTHOR]

Nucleic acid-based programmable devices connect the fields of computation and biology. The synthesis, stability, and molecular hybridization are paramount data storage capabilities of DNA. This potential could lead to the development of biological devices. The integration of environment-sensitive logic circuits could resemble the systematic molecular evolution within living systems. The living cells inherently respond to environmental stimuli, with proteins playing a central role by acting as extracellular entity receptors. Although semiconductors have led unparalleled advances in logic devices, they exhibit limitations when assessing living cell parameters. Novel approaches are emerging to counter these limitations, such as using chemical molecules as micro-environment sensing computational agents. The intersection of biology and computation is marked by rapid molecular evolution. A plethora of devices, ranging from sensors and diagnostic tools to therapeutic agents, is now available, each hinting at the vast possibilities in smart biotechnology. This review offers an extensive summary of the most recent progress in biomolecular logic devices, intending to give researchers an insight into the current state of the field as well as mapping out directions for future logic device research. The emphasis on the promise and potential of nanomaterials interface with DNA, nucleic acid and protein to shape the future of computational logic devices underscores the importance of ongoing exploration and innovation in the field of bio-computing systems. [Display omitted] • Synthesis of biomolecular computational circuits. • Biomolecular logic devices are exceptionally sensitive to cellular and environmental phenomena. • DNA logic devices offer a low-cost and highly customizable medium for the development of complex circuits. • Toehold-mediated strand displacement, split G-quadruplex, and other strategies facilitates designing of DNA devices. [ABSTRACT FROM AUTHOR]

Copyright of Avian Diseases is the property of American Association of Avian Pathologists, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: In the present study, adaptive laboratory evolution was used to stimulate antibiotic production in a Streptomyces strain JB140 (wild-type) exhibiting very little antimicrobial activity against bacterial pathogens. The seven different competition experiments utilized three serial passages (3 cycles of adaptation-selection of 15 days each) in which Streptomyces strain (wild-type) was challenged repeatedly to one (bi-culture) or two (tri-culture) or three (quadri-culture) target pathogens. The study demonstrates a simple laboratory model to study the adaptive potential of evolved phenotypes and genotypes in Streptomyces to induce antibiotic production. Results: Competition experiments resulted in the evolution of the wild-type Streptomyces strain JB140 into the seven unique mutant phenotypes that acquired the ability to constitutively exhibit increased antimicrobial activity against three bacterial pathogens Salmonella Typhi (NCIM 2051), Staphylococcus aureus (NCIM 2079), and Proteus vulgaris (NCIM 2027). The mutant phenotypes not only effectively inhibited the growth of the tested pathogens but were also observed to exhibit improved antimicrobial responses against one clinical multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC 1021) isolate. In contrast to the adaptively evolved mutants, only a weak antimicrobial activity was detected in the wild-type parental strain. To get molecular evidence of evolution, RAPD profiles of the wild-type Streptomyces and its evolved mutants were compared which revealed significant polymorphism among them. Conclusion: The competition-based adaptive laboratory evolution method can constitute a platform for evolutionary engineering to select improved phenotypes (mutants) with increased antibacterial profiles against targeted pathogens. [ABSTRACT FROM AUTHOR]

The histone variant H2A.Z is deposited into chromatin by specific machinery and is required for genome functions. Using a linker-mediated complex strategy combined with yeast genetic complementation, we demonstrate evolutionary conservation of H2A.Z together with its chromatin incorporation and functions. This approach is applicable to the evolutionary analyses of proteins that form complexes with interactors. [ABSTRACT FROM AUTHOR]

Copyright of Avian Diseases is the property of American Association of Avian Pathologists, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Bovine parvovirus 1 (BPV1) is a causative agent of respiratory, gastrointestinal, and reproductive cattle diseases. We collected 149 yak diarrhea fecal samples from 9 farms in the Qinghai-Tibet Plateau. The samples were screened for BPV1 by PCR, and 2 samples were positive for BPV1. The complete genomes of these BPV1 isolates were sequenced successfully. The sequences of these 2 variants were both 5,515 bp in length and shared 96.5–96.8% identity with 2 previously reported BPV1 genomes (GenBank DQ335247, NC_001540). Twenty-six identical amino acid mutations were found in the 2 yak variants, including 7 amino acid substitutions in receptor-binding regions of the VP2 protein, and 5 amino acid substitutions in the NS1 protein C-terminal region that functions to activate transcription. The new genome sequences contribute to better understanding of the evolution and molecular characteristics of BPV1. [ABSTRACT FROM AUTHOR]

• Understanding of how genotypes map onto molecular phenotypes and organismal functions is partial. • The networked organization of genotype-phenotype (GP) maps conditions evolution and adaptation. • Several topological properties of genotype spaces are universal. • The evolution of GP maps (not on GP maps) drives the emergence of phenotypes at the species level. • Technical advances permit the exhaustive empirical characterization of small GP maps. Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics—cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis. [ABSTRACT FROM AUTHOR]

Copyright of Revista Electrónica de Enseñanza de las Ciencias is the property of Revista Electronica de Ensenanza de las Ciencias and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Hypothalamic–Pituitary–Somatotropic (HPS) axis is the essential endocrine system playing important roles in animal growth. Here, the HPS axis were characterized in golden pompano (Trachinotus ovatus) and humpback grouper (Cromileptes altivelis), two marine cultured tropical teleosts representing fast and slow growth patterns, respectively. Through genomic and transcriptomic survey, 32 and 35 HPS genes were characterized in T. ovatus and C. altivelis. Functional domain and phylogeny revealed their conserved function among teleost lineages, with more sst s and igfbp s identified and actively expressed in C. altivelis than in T. ovatus. The regulation of HPS genes responding to external stimuli revealed that T. ovatus HPS genes, including gh , igf1 / 2 , igfbp1a / b , igfbp2b and igfbp5b , were differentially expressed under temperature or starvation challenges, while C. altivelis HPS genes were sensitive to salinity change with sst1.2 , ghrhrb , igf1 , igf2r , igfbp1a and igfbp5a regulated in brains. Strong interactive connectivity of igfbp s was found in both T. ovatus and C. altivelis. Moreover, HPS genes evolved differently between T. ovatus and C. altivelis , and positively selected sites were detected in more C. altivelis HPS genes, like in functional domains of igf1ra and igf1rb. The igf1ra evolved faster than igf1rb in teleosts, which may contribute to their functional divergence. In conclusion, this study represented different regulatory and evolutionary patterns of HPS axis between T. ovatus and C. altivelis , which are vital in regulating their growth and will provide comprehensive insights into the cultivation of T. ovatus and C. altivelis in aquaculture. [Display omitted] • HPS axis genes are generally conserved between T. ovatus and C. altivelis. • More igfbp s were highly expressed in C. altivelis peripheral tissues. • Igf s and igfbp s play key interactive roles in HPS axis regulation. • HPS genes evolve differently between T. ovatus and C. altivelis. • The duplicated igf1ra / b genes may have functional divergence in C. altivelis. [ABSTRACT FROM AUTHOR]

Background: Arctic-like (AL) lineages of rabies viruses (RABVs) remains endemic in some Arctic and Asia countries. However, their evolutionary dynamics are largely unappreciated. Objectives: We attempted to estimate the evolutionary history, geographic origin and spread of the Arctic-related RABVs. Methods: Full length or partial sequences of the N and G genes were used to infer the evolutionary aspects of AL RABVs by Bayesian evolutionary analysis. Results: The most recent common ancestor (tMRCA) of the current Arctic and AL RABVs emerged in the 1830s and evolved independently after diversification. Population demographic analysis indicated that the viruses experienced gradual growth followed by a sudden decrease in its population size from the mid-1980s to approximately 2000. Genetic flow patterns among the regions reveal a high geographic correlation in AL RABVs transmission. Discrete phylogeography suggests that the geographic origin of the AL RABVs was in east Russia in approximately the 1830s. The ancestral AL RABV then diversified and immigrated to the countries in Northeast Asia, while the viruses in South Asia were dispersed to the neighboring regions from India. The N and G genes of RABVs in both clades sustained high levels of purifying selection, and the positive selection sites were mainly found on the C-terminus of the G gene. Conclusions: The current AL RABVs circulating in South and North Asia evolved and dispersed independently. [ABSTRACT FROM AUTHOR]

NDP-forming type acyl-CoA synthetase superfamily proteins are known to have six essential subdomains (1, 2, 3, a, b, c) of which partition and order are varied, suggesting yet-to-be-defined subdomain rearrangement happened in its evolution. Comparison in physicochemical and biochemical characteristics between the recombinant proteins which we made from fragmented subdomains and wild-type protein, acetate-CoA ligase in a hyperthermophilic archaeon, consisting of two distinct subunits (α1-2-3 and βa-b-c) provided a clue to the mystery of its molecular evolutionary passage. Although solubility and thermostability of each fragmented subdomain turned out to be lower than that of wild-type, mixture of the three synthetic subunits of α1-2, α3, and βa-b-c had quaternary structure, thermostability, and enzymatic activity comparable to those of the wild-type. This suggests that substantial independence and mobility of subdomain 3 have enabled rearrangement of the subdomains; and thermostability of the subdomains has constrained the composition of the subunits. A mixture of fragmented subdomains α1-2, α3, and βa-b-c show enzyme activity comparable to those of the wild-type (α1-2-3 and βa-b-c) while that of α1-2-3, βa-c, and βb does not. [ABSTRACT FROM AUTHOR]