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Evolutionary traps occur when populations deviate from local adaptation and become maladapted under rapid climate change. Alpine plants, with genetically distinct ecotypes in sky islands, are susceptible to being trapped by rapid climate change. We employed landscape genomics to test a local adaptation-induced evolutionary trap in the alpine perennial plant Roscoea tibetica (Zingiberaceae) with three distinct ecotypes along altitudinal gradients in the Hengduan Mountains. Strong local adaptation to alpine environments was observed through isolation-by-environment and rapid decreases in effective population size following interglacial niche contraction. Genomic offset increased with climate warming and was positively correlated with the intensification of local adaptation. Instead of high-elevation ecotypes, an evolutionary trap was indicated in the low-elevation forest ecotype, which showed the strongest local adaptation and niche loss, requiring the greatest shift in allele frequencies to keep pace with future climate change, and will likely experience the largest population decline. Therefore, stronger local adaptation induces evolutionary traps more easily and aggravates the harm to alpine plants facing rapid climate warming. Our study provides the first empirical case of local adaptation-induced evolutionary traps for alpine plants and highlights that it is crucial for alpine biota conservation to consider and disarm evolutionary traps under climate change.

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog, Nanorana parkeri . We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. We also reveal genes related to UV defense and a corresponding temporal expression pattern in N. parkeri . Genomic and metabolomic analysis along with large-scale transcriptomic profiling revealed a time-dependent coordinated defense mechanism in N. parkeri . We also identified several microRNAs that play important regulatory roles, especially in decreasing the expression levels of cell cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Thus, both expression shifts and gene mutations contribute to UV adaptation in N. parkeri . Our work demonstrates a genetic framework for evolution of UV defense in a natural environment.

Understanding the roles of phenotypic plasticity in adaptive evolution has gained recognition for decades. Studies involving multiple taxa have shown that gene expression plasticity serves as “long-term memory” to facilitate re-adaptations to ancestral environments. Nevertheless, the general pattern and the underlying genetic basis of expression plasticity remain unclear. The transposable elements (TEs) play crucial roles in gene expression regulation and are widely distributed within the genome. Given this, we re-analyzed the transcriptomic data of chicken (Gallus gallus) generated from a reciprocal transplant experiment to examine whether expression shifts of TEs are involved in the re-adaptation process. Similar to the protein-coding genes, the plastic changes of TEs overwhelmingly exceed the genetic changes in the re-adaptation process. Further, the associated TEs co-expressed with diverse genes to perform a regulatory activity. Thus, our study supports the general function of phenotypic plasticity in adaptive evolution, and suggests a regulatory functions of TEs in this process.

Defense against increasing ultraviolet radiation (UV) exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV-defense mechanisms remains largely unexplored. Herein, we analyzed UV responses in the highest-elevation frog, Nanorana parkeri, using integrated approaches. We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. Our study revealed new UV-defense systems. Genomic and metabolomic analysis along with large-scale transcriptomic and microRNA profiling revealed a time-dependent coordinated defense mechanism in N. parkeri. Both gene mutations and expression shifts contribute to such UV adaptation. We found that microRNAs play important regulatory roles, especially in decreasing the expression levels of cell-cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Our work demonstrates a genetic framework for evolution of UV-defense in a natural environment.

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.

Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding, making it difficult for scientists to reveal the genetic regulatory mechanisms. Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions. It can identify interactions among target loci and all other loci in a genome with low cost and high resolution. Here, we developed CaptureProbe, a user-friendly, graphical Java tool for the design of capture probes across a range of target sites or regions. Numerous parameters helped to achieve and optimize the designed probes. Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity. Hence, this program will help scientists conduct genome spatial interaction research. CaptureProbe and source code are available at https://sourceforge.net/projects/captureprobe/.

Viviparous (live-bearing) vertebrates have evolved repeatedly within otherwise oviparous (egg-laying) clades. Over two-thirds of these changes in vertebrate reproductive parity mode happened in squamate reptiles, where the transition has happened between 98 and 129 times. The transition from oviparity to viviparity requires numerous physiological, morphological, and immunological changes to the female reproductive tract, including eggshell reduction, delayed oviposition, placental development for supply of water and nutrition to the embryo by the mother, enhanced gas exchange, and suppression of maternal immune rejection of the embryo. We performed genomic and transcriptomic analyses of a closely related oviparous–viviparous pair of lizards ( Phrynocephalus przewalskii and Phrynocephalus vlangalii ) to examine these transitions. Expression patterns of maternal oviduct through reproductive development of the egg and embryo differ markedly between the two species. We found changes in expression patterns of appropriate genes that account for each of the major aspects of the oviparity to viviparity transition. In addition, we compared the gene sequences in transcriptomes of four oviparous–viviparous pairs of lizards in different genera ( Phrynocephalus , Eremias , Scincella , and Sphenomorphus ) to look for possible gene convergence at the sequence level. We discovered low levels of convergence in both amino acid replacement and evolutionary rate shift. This suggests that most of the changes that produce the oviparity–viviparity transition are changes in gene expression, so occasional reversals to oviparity from viviparity may not be as difficult to achieve as has been previously suggested.

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With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan (in the LaserGene package) is an excellent program with an easy-to-use graphical user interface (GUI) employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the 'autoSeqMan' software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, 'Classification' and 'Assembly'. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https://github.com/ Sun-Yanbo/autoSeqMan.

The equilibrium structures, stability and magnetic properties of Sc(BO2)n−/0 (n = 1–4) clusters were investigated on the basis of density functional theory calculations. The BO2 ligands prefer to stretch out in the most stable Sc(BO2)n− anions but tend to come together in the lowest-lying Sc(BO2)4 structure. According to the MP2 results, the Sc(BO2)4− species could be classified as hyperhalogen anions since they have larger vertical electron detachment energies (VDEs, 5.44–8.85 eV) than that of the superhalogen anion BO2−. With titanium and vanadium playing the role of central atom, the Ti(BO2)n−/0 (n = 1–5) and V(BO2)n−/0 (n = 1–6) clusters were studied in a similar manner. In these cases, the central transition metal atoms are inclined to keep their intrinsic spin. In addition, the hyperhalogen identity of the Ti(BO2)n− (n = 4, 5) and V(BO2)n− (n = 3–6) species were also confirmed by the calculated VDE values.

Although many cases of genetic adaptations to high elevations have been reported, the processes driving these modifications and the pace of their evolution remain unclear. Many high-elevation adaptations (HEAs) are thought to have arisen in situ as populations rose with growing mountains. In contrast, most high-elevation lineages of the Qinghai-Tibetan Plateau appear to have colonized from low-elevation areas. These lineages provide an opportunity for studying recent HEAs and comparing them with ancestral low-elevation alternatives. Herein, we compare four frogs (three species of Nanorana and a close lowland relative) and four lizards ( Phrynocephalus ) that inhabit a range of elevations on or along the slopes of the Qinghai-Tibetan Plateau. The sequential cladogenesis of these species across an elevational gradient allows us to examine the gradual accumulation of HEA at increasing elevations. Many adaptations to high elevations appear to arise gradually and evolve continuously with increasing elevational distributions. Numerous related functions, especially DNA repair and energy metabolism pathways, exhibit rapid change and continuous positive selection with increasing elevations. Although the two studied genera are distantly related, they exhibit numerous convergent evolutionary changes, especially at the functional level. This functional convergence appears to be more extensive than convergence at the individual gene level, although we found 32 homologous genes undergoing positive selection for change in both high-elevation groups. We argue that species groups distributed along a broad elevational gradient provide a more powerful system for testing adaptations to high-elevation environments compared with studies that compare only pairs of high-elevation versus low-elevation species.

The structural features, properties and stability of two kinds of representative superhalogen compounds, namely hydrogenated superhalogens and lithiated superhalogens, are theoretically studied in detail, providing further insight into the behavior of superhalogens. According to topological analysis of the electron localization function, most of superhalogen clusters as a whole combine with Li atom through ionic bond(s). In contrast, the H atom tends to bind with superhalogen by covalent bond although a portion of superhalogens are broken upon hydrogenation. In addition, the electric properties of these superhalogen compounds are also obtained and compared with those of traditional acid and salt molecules.

A computer software package called 'FasParser' was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.

Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

BACKGROUNDDirect application of insect cadavers infected with entomopathogenic nematodes (EPN) can successfully control target pest insects. Little is known about the effects of environmental factors (desiccation and temperature) on the production process for infective juveniles (IJ) in insects. RESULTSWe examined the effects of desiccation time and cold storage (6.7 degrees C) on IJ production of the nematode Steinernemacarpocapsae in Galleriamellonella cadavers at 30.8 and 57% humidity. Under desiccation, the IJ yield in cadavers increased gradually and reached a maximum on day5. IJ yield gradually declined from day6 onwards and was almost zero by day15. In general, cold storage at 6.7 degrees C caused negative effects on IJ production in desiccated cadavers. Approximately 56h post infection was the time at which nematodes were most sensitive to low temperatures during development in cadavers. Five-day desiccated cadavers generated higher mortality and more rapid death of Galleriamellonella larvae than using newly (day0) desiccated cadavers. CONCLUSIONThis study describe methods of optimizing rearing techniques such as desiccation and cold storage to promote the mass production and application of EPN- infected host cadavers for the field control of insect pests. (c) 2013 Society of Chemical Industry

The paper focuses on the design of an onboard track fault diagnosis device for advanced railway condition monitoring which can be mounted on in-service vehicle. Track faults are diagnosed from the vertical and lateral acceleration of axle-box, bogie and car-body with different characteristics. As vibration signal in time-domain will not represent the condition of the track obviously, the signal is transformed into frequency-domain first. Then PCA and SVM are used to calculate probabilities of fault tracks. At last, The D-S evidence theory is employed in the track fault diagnosis to fuse multi-source information. When fault is detected, alarm message will be sent to the monitoring center of the system to ensure the safety of the following vehicles. Experiments which use three accelerometer signals in different positions as mentioned above from the inspection vehicle were carried out to show that the detection algorithm is effective to estimate the rail irregularities and diagnose track faults.

The multilayered materials with different combinations of Ti, Al and Ti-Al intermetallics were prepared by heat treatment and hot pressing (HP) with elemental foils. The microstructures and phase formation of the obtained samples were detected by scanning electron microscopy (SEM), electron probe microanalysis (EPMA), energy dispersive spectroscopy (EDS) and X-ray diffractometer (XRD). When the HP is applied under the melt point of aluminum, aluminum is the only diffusive element across the oxide films on the surface of the initial foils; however, some unusual TiAl3 particles are found in the multilayered structure due to the broken of oxide films; after hot pressing for 4 hours, all the aluminum was consumed; many voids exist at the centerline of TiAl3 layers, which are mainly caused by Kirkendall effect and the difference of molar volumes between reactants and products; before the aluminum is completely consumed, TiAl3 is the only product in the solid reaction under the melting temperature of aluminum; however, other Ti-Al intermetallics like Ti3Al and TiAl are formed in the updated temperature diffusion after aluminum is consumed.

Quantum-chemistry study was explored to investigate the electronic structures, absorption and phospho- rescence mechanism, as well as electroluminescence (EL) properties of three red-emitting Ir(III) complexes, (fpmqx)2Ir(L) {fpmqx=2-(4-fluorophenyl)-3-methyl-quinoxaline; L=triazolylpyridine (trz) (1); L=picolinate (pic) (2) and L=acetylacetonate (acac) (3)}. The calculated results show that the HOMO distribution for 1 is mainly localized on trz moiety due to its stronger π-electron acceptor ability, and HOMO for 2 and 3 is the combination of Ir d- and phenyl ring π-orbital. The higher phos- phorescence yields and differences among 1-3 are investigated in this paper. In addition, the reasons of higher EL efficiency of 2 than 1 and 3 have been rationalized.

A detailed doublet potential energy surface for the reaction of CH with CH(3)CCH is investigated at the B3LYP/6-311G(d,p) and G3B3 (single-point) levels. Various possible reaction pathways are probed. It is shown that the reaction is initiated by the addition of CH to the terminal C atom of CH(3)CCH, forming CH(3)CCHCH 1 (1a,1b). Starting from 1 (1a,1b), the most feasible pathway is the ring closure of 1a to CH(3)-cCCHCH 2 followed by dissociation to P ( 3 )(CH(3)-cCCCH+H), or a 2,3 H shift in 1a to form CH(3)CHCCH 3 followed by C-H bond cleavage to form P ( 5 )(CH(2)CHCCH+H), or a 1,2 H-shift in 1 (1a, 1b) to form CH(3)CCCH(2) 4 followed by C-H bond fission to form P ( 6 )(CH(2)CCCH(2)+H). Much less competitively, 1 (1a,1b) can undergo 3,4 H shift to form CH(2)CHCHCH 5. Subsequently, 5 can undergo either C-H bond cleavage to form P ( 5 ) (CH(2)CHCCH+H) or C-C bond cleavage to generate P ( 7 ) (C(2)H(2)+C(2)H(3)). Our calculated results may represent the first mechanistic study of the CH + CH(3)CCH reaction, and may thus lead to a deeper understanding of the title reaction.

The doublet potential energy surface (PES) for the reaction of CHCl− with CSO is explored at the B3LYP/6-311++G(d,p), B3LYP/6-311++G(3df,2p) and CCSD(T)/6-311++G(3df,2p) (single-point) levels. Various possible reaction pathways are probed. It is shown that the most favorable association between CHCl− and CSO is found to be middle-C attack forming CHClC(O)S− 1 with no barrier. Starting from 1, the most feasible pathway is the concerted S-shift along with Cl-extrusion of 1 to form product P2(Cl− + SCHCO). The minor product channel is the concerted O-shift along with Cl-extrusion of 1 to generate product P1(Cl− + OCHCS). Further conversions of P1 may form P6(SCHCl− + CO). Because the isomers and transition states involved in the feasible pathways all lie below the reactant, the title reaction is expected to proceed very fast which is consistent with the measured large rate constant in experiment. Our calculated results may be helpful for understanding the mechanism of the title reaction.

The mechanisms of the reaction of ozone with cis - and trans -1,3-butadiene are investigated at the B3LYP/6–311G(d,p) and CCSD(T)/6–311G(d,p) (single-point) computational levels. Both reactions are associated with the cycloaddition – elimination mechanism. In the O 3 + cis -1,3-butadiene reaction, the initial cycloaddition product 3 will eventually lead to four most favorable products P 1 ( cis – trans -CH 2 CHCHOO + H 2 CO), P 2 ( cis -CH 2 CHCHO + H 2 CO 2 ), P 3 ( trans -CH 2 CHCHO + H 2 CO 2 ) and P 4 ( trans – trans -CH 2 CHCHOO + H 2 CO) which have the same calculated barrier 3.0 kcal/mol with respect to the reactant (O 3 + cis -1,3-butadiene). In the O 3 + trans -1,3-butadiene reaction, there are two initial cycloaddition products 4 and 8 , which will lead to six favorable products P 1 ( cis – trans -CH 2 CHCHOO + H 2 CO), P 2 ( cis -CH 2 CHCHO + H 2 CO 2 ), P 3 ( trans -CH 2 CHCHO + H 2 CO 2 ), P 4 ( trans – trans -CH 2 CHCHOO + H 2 CO), P 7 ( trans – cis -CH 2 CHCHOO + H 2 CO) and P 8 ( cis – cis -CH 2 CHCHOO + H 2 CO) with similar calculated barriers ranging from 4.7 to 5.4 kcal/mol. The present paper will enrich our understanding of the chemistry of ozone towards other unsaturated hydrocarbons.

A detailed theoretical study is carried out at the B3LYP/6-311G(d,p) and CCSD(T)/6-311++G(3df,2pd) (single-point) levels as an attempt to investigate the mechanism of the little understand ion–molecule reaction between HCN+ and NH3. Various possible reaction pathways are considered. It is shown that six dissociation products P 1 (NH3 + + HCN), P 2 (NH4 + + CN), P 3 (NH3 + + HNC), P 9 (HCNH+ + NH2) P 10 (NCNH3 + + H), and P 12 (HNCNH2 + + H) are both thermodynamically and kinetically feasible. Among these products, P 1 is the most competitive product with predominant abundance. P 3 and P 9 may be the second feasible products with comparable yields. P 12 may be the least possible product followed by the almost negligible P 2 and P 10 . Because the isomers and transition states involved in the HCN+ + NH3 reaction all lie below the reactant, the title reaction is expected to be rapid, which is consistent with the measured large rate constant in experiment. The title reaction may have a potential relevance in Titan’s atmosphere, where the temperature is very low. Furthermore, our calculated results are compared with the previous experimental findings.

The complex triplet potential energy surface for the reaction of ground-state atomic carbon C(3P) with propylene C3H6 is explored at the B3LYP/6-311G(d,p), QCISD/6-311G(d,p), and G3B3 (single-point) levels. Various possible reaction pathways are probed. It is shown that the reaction is initiated by the addition of C(3P) to the C=C bond of C3H6 to generate barrierlessly the three-membered ring isomer 1 CH3-cCHCCH2, followed by the ring-opening process to form 2a trans-CH3CHCCH2, which can easily interconvert to 2b cis-CH3CHCCH2. Starting from 2 (2a, 2b), the most feasible pathway is the internal C-H bond rupture of 2a leading to P4(2CH3CCCH2 + 2H), terminal C-H bond cleavage of 2 (2a,2b) to form P5(2CH3CHCCH + 2H), or direct C-C bond fission of 2b to form P7(2CH2CCH + 2CH3), all of which may have comparable contributions to the title reaction. Much less competitively, 2a takes a 1,2-H-shift to form 5a trans-cis-CH3CHCHCH, followed by a C-C bond rupture leading to P6(1C2H2 + 3CH3CH). Because the intermediates and transition states involved in the feasible pathways all lie below the reactant, the title reaction is expected to be rapid, which is consistent with the measured large rate constant. The present article may provide some useful information for future experimental investigation of the title reaction.

A laboratory testing of simultaneous removal of ammonium and sulfate (SRAS) was studied from an anammox process in an anaerobic bioreactor filled with granular activated carbon. Two different phases of experiment were investigated to start up the SRAS process, and final batch tests were performed to analyze the SRAS process. The experiment included an anammox process and an SRAS process. During the anammox process, the highest removal efficiency of ammonium and nitrite was up to 97 and 98%, respectively. After 160 days in the stationary phase of anammox process, the ratio of ammonium to nitrite consumption was approximately 1:1.15, which is much higher than 1:1.32 in the traditional anammox process. The extra electron acceptor, such as sulfate, was thought to react with ammonium by bacteria. Synthetic wastewater containing ammonium chlorine and sodium sulfate was used as the feed for the bioreactor in the second phase of experiment. During the SRAS process, the influent concentrations of ammonium and sulfate were controlled to be 50–60 and 210–240 mg L−1 respectively. After start-up and acclimatization of this process for 60 days, the average effluent concentrations of ammonium and sulfate were 30 and 160 mg L−1, respectively. The simultaneous ammonium and sulfate removal was detected in the reactor. In order to further validate the biochemical interaction between ammonium and sulfate, batch tests was carried out. Abiotic tests were carried out to demonstrate that the pure chemical action between ammonium and sulfate without microorganism was not possible. Biotic assays with different ammonium and sulfate concentrations were further investigated that high concentrations of ammonium and sulfate could promote simultaneous removal of ammonium and sulfate. And elemental sulfur and nitrogen gas as the products measured in the SRAS process helped to demonstrate the occurrence of new interaction between nitrogen and sulfur. The new process of SRAS in the inorganic condition, including simultaneous removal of ammonium and sulfate, and the appearance of elemental sulfur and nitrogen gas as the terminal products, widened the cycle approach between nitrogen and sulfur.

The evolution of flight is the most important feature of birds, and this ability has helped them become one of the most successful groups of vertebrates. However, some species have independently lost their ability to fly. The degeneration of flight ability is a long process, and some species remain transitional locomotive models. Most of the energy required for locomotion is supplied by mitochondria via oxidative phosphorylation. Thus, rapidly flying birds should require a more energy efficient metabolism than weakly flying or flightless species. Therefore, we speculated that evolutionary constraints acted on the mtDNA of birds with different locomotive abilities. To test this hypothesis, we compared 76 complete avian mitochondrial genomes. Weakly flying and flightless birds, compared to rapidly flying birds, accumulated more nonsynonymous nucleotide substitutions relative to synonymous substitutions. Even after controlling for mutation rate, this trend remained significant. This finding was further tested for its generality by examining 214 complete mammalian mitochondrial genomes. The same as birds, a negative correlation was also found for the Ka/Ks ratio and locomotive speed. Our results demonstrated that, in addition to the previously described role for effective population size, functional constraints due to locomotion play an important role in the evolution of mtDNA.

The complex triplet potential energy surface for the reaction of HCNO with NH is investigated at the G3B3 level using the B3LYP/6-311++G(d,p), and QCISD/6-311++G(d,p) geometries. Various possible isomerization and dissociation pathways are probed. The initial association between HCNO and NH is found to be carbon to nitrogen attack leading to HNCHNO 2a, which can convert to 2b, 2c, and 2d. Subsequently, 1,4-H-shift of 2a to form NCHNOH 3a followed by dissociation to P 2 (1HCN + 3HON) is the most feasible pathway. Much less competitively, 2d undergoes successive 1,3-H-shift and C-N cleavage to form HNCNOH 8b, and then to product P 3 (1HNC + 3HON), the second feasible pathway. 8b can alternatively isomerize to 8c followed by N–O bond rupture to generate P 6 (2OH + 2HNCN), the lesser followed feasible pathway. In addition, 2b takes continuously 1,3- and 1,2-H-shift to form NC(H)NHO 6a, then to ONHCNH 7a which can convert to 7b. Eventually, 7b may take C-N bond fission to produce P 5 (1HNC + 3HNO), the least feasible pathway. The present paper may be helpful for future experimental identification of the product distributions for the title reaction, and may be helpful to deeply understand the mechanism of the title reaction.

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

Taxonomical analysis of two genetically distinguished Lactobacillus strains isolated from traditional Chinese fermented vegetables 'Suan cai' was performed. They formed L-lactate from glucose, were facultatively heterofermentative, and had a DNA G+C content of 53-54mol%. They fermented D- and L-arabinose. They produced lactate, ethanol and acetate from gluconate at a molar ratio of 1.1:0.4:0.7. Phylogenetic analysis of 16S rDNA revealed that the two strains were closely related to L. perolens. DNA-DNA hybridization analysis revealed that the two strains were different from L. perolens type strain DSM 12744 and formed a separate cluster with L. perolens DSM 12745. G + C molar content of DNA of the former is 51%, whereas those of the latter strains were in the range of 53-54%. Based on the results, we propose that the new species be named L. harbinensis sp. nov. and that L. perolens DSM 12745 be reclassified as L. harbinensis DSM 12745. The type strain of L. harbinensis DSM 16991T (= AHU 1762T = SBT 10908T).

The doublet potential energy surface for the reactions 3NCN+NO, 3CNN+NO, 1NNO+CN and 2N3+CO is studied at the B3LYP/6-311G(d) and G2M(cc3) (single-point) levels of theory. For the reaction 3NCN+NO, the pathways 3NCN+NO⇌1 trans-ONNCN→2 cis-ONNCN→1NNO+CN and 3NCN+NO⇌2 cis-ONNCN→1NNO+CN are the major pathways. For the reaction 3CNN+NO, the pathway 3CNN+NO⇌3 trans-ONCNN→N2+2CNO is the major pathway. For the reaction 1NNO+CN, the pathways 1NNO+CN⇌2 cis-ONNCN→3NCN+NO and 1NNO+CN⇌2 cis-ONNCN→1 trans-ONNCN→3NCN+NO are the major pathways. For the reaction 2N3+CO, the pathways 2N3+CO⇌7 trans-OCNNN→N2+2NCO and 2N3+CO⇌7 trans-OCNNN→8 cis-OCNNN→N2+2NCO are the major pathways. In addition, the quartet potential energy surface for these reactions is also considered, but no favorable pathways can be found on it.

The potential energy surface of complex doublet for the HCCCOOO system is investigated in this paper at the hybrid density functional B3LYP and CCSD(T) (single-point) levels with 6-311G(d,p) basis set in order to find out the reaction mechanism of the radical HCCCO with oxygen. Nineteen minimum isomers and 22 transition states are located and a variety of possible reaction pathways are probed. In this article, we discussed five products P 1 HCCO + CO 2 , P 2 HCO + 2CO, P 3 HCO 2 + C 2 O, P 4 H + 3CO and P 5 H + CO 2 + C 2 O. The reaction pathway leading to the major HCCO + CO 2 product is as following: HCCCO + O 2 → a 3 → TSa 3 /b 3 → b 3 → TSb 3 /b 4 → b 4 → TSb 4 /p 1 , in which the rate-determining step is isomer a 3 overcomes the barrier (27 kcal/mol) to form the isomer b 3 . It is an interesting process for it keeps the Cs symmetry in the reaction. Another important pathway leading to HCO + 2CO product is the formation of d 1 isomer. Once the structure of d 1 is formed, it will directly dissociate to g + CO. Calculation on these would be useful for our understanding about the reactions of HCCCO + O 2 .

For approaching the new silaborate sandwich anions [(η 5 -C 5 Me 5 )M(MeSiB 10 H 10 )] −1 (M=Co, Rh and Ir), the reduced model anions [(η 5 -C 5 H 5 )M(MeSiB 10 H 10 )] −1 with (η 5 -C 5 H 5 ) −1 instead of (η 5 -C 5 Me 5 ) −1 are investigated using the DFT/B3LYP method. The optimized geometries and the electron structures of the ground states are obtained. It is shown that the silaborate ligand, as the (MeSiB 10 H 10 ) −3 trianion, is coordinated to the transition metal M which adopts 18-electron configuration in all the three sandwich complexes. The metal–silicon distances are shorter than both the sum of the corresponding atomic radii and the sum of the corresponding covalence radii, indicating the strong attraction between the silicon and metal atoms. The vibrational spectrum is calculated on the basis of the ground state geometry and wave-functions, which reveals that in each of these sandwich complexes, strong interaction exists between the transition metal and the ligands (η 5 -C 5 H 5 ) −1 and (MeSiB 10 H 10 ) −3 .

In the present study, the reaction mechanism of NCS+NO2 on the singlet potential energy surface is studied using the MP2/6-311G(d,p) level of theory. It is shown that the pathway (1) NCS + NO 2 ⇌ O ( O ) NNCS → O ( NNC ( S ) O ) → N 2 O + OCS is the major pathway, and the pathways (2) NCS + NO 2 ⇌ O ( O ) NSCN → ONS + OCN and (3) NCS + NO 2 ⇌ cis ‐ cis ‐ ONONCS → NO + SCNO are the minor pathways in the singlet potential energy surface. The major pathway (1), involving the barrierless entrance to the first adduct isomer O(O)NNCS and tight transition states to the products N2O and OCS, is in good agreement with the experimentally observed negative temperature dependence of rate constants. The energies of the stationary points are refined using a multi-level method.

The reaction of 3 C 2 radical with NO molecule is studied at the B3LYP/6-311G(d) level of theory. Both doublet and quartet potential energy surfaces (PES) are considered. On the doublet potential energy surface, we obtainfour major pathways in which the pathways 3 C 2 + NO ⇄ 1 CCNO → 2 (NC)CO → 3 CNCO → P 1 CN + CO and 3 C 2 + NO ⇄ 1 → 4 CC(NO) → 2 → 3 → P 1 CN + CO have lower energetics than the other two pathways that form the 3 O atom, namely 3 C 2 + NO ⇄ 1 CCNO → P 2 3 O + 2 CCN and 3 C 2 + NO ⇄ 1 CCNO → 5 ON(CC) → P 3 3 O + 2 CCN r i n g . However, the latter two pathways may compete with the former two pathways. The calculated energetics of the four pathways may account for the experimental results that CN is the primary product at low temperatures and 3 O is the main product at higher temperatures. The barrierless entrance to the first adduct isomer 1 and the tight transition states to the products P 1 , can provide a reasonable explanation for the experimentally observed negative temperature dependence of rate constants at low temperatures. The pathways on the quartet potential energy surface are less competitive than those on the doublet potential energy surface. Thus, they are negligible.

The singlet potential energy surface of the NCO+NO2 reaction system, including four isomers and four transition states, has been studied theoretically at the Gaussian-3 level of theory in order to explore the possible mechanism of the reaction. By means of the ab initio MO calculations, we found that the pathway (1), NCO+NO2⇌O(O)NNCO→ON(NC(O)O)→NNO+CO2, is the major pathway, while the pathway (2), NCO+NO2 ⇌cis-trans-ONONCO→cis-cis-ONONCO→CO+2NO, is the minor pathway on the singlet potential energy surface. The pathways on the triplet potential energy surface are less competitive than those on the singlet potential energy surface. Thus, they are negligible. Both pathways (1) and (2), involving the barrierless entrances to the first adduct isomers and the tight transition states to the products, can give a reasonable explanation for the experimentally observed negative temperature dependence of rate constants.

The reaction of 3C2 radical with NO molecule is studied at the B3LYP/6-311G(d) level of theory. Both doublet and quartet potential energy surfaces (PES) are considered. On the doublet potential energy surface, we obtain four major pathways in which the pathways 3C2 + NO ⇌ 1 CCNO → 2 (NC)CO → 3 CNCO → P1 CN + CO and 3C2 + NO ⇌ 1 → 4 CC(NO) → 2 → 3 → P1 CN + CO have lower energetics than the other two pathways that form the 3O atom, namely 3C2 + NO ⇌ 1 CCNO → P2 3O + 2CCN and 3C2 + NO ⇌ 1 CCNO → 5 ON(CC) → P3 3O + 2CCNring. However, the latter two pathways may compete with the former two pathways. The calculated energetics of the four pathways may account for the experimental results that CN is the primary product at low temperatures and 3O is the main product at higher temperatures. The barrierless entrance to the first adduct isomer 1 and the tight transition states to the products P1, can provide a reasonable explanation for the experimentally observed negative temperature dependence of rate constants at...

A theoretical research on the low-energy structures, binding energies, and Raman spectra of the (N 2 ) n ( n =3–6) complexes has been systematically explored. Similar to the water trimer, the energetically lowest-lying structure of the nitrogen molecule trimer is a C 3h -symmetric cyclic structure. However, different from the water tetramer and pentamer being simple ring structures, the lowest-lying structures of the tetramer and the pentamer are pyramidal structures with C 3 and C 4 symmetry. Additionally, the hexamer prefers the C i -symmetric bipyramidal structure rather than the prism structure that is the most stable of the water hexamer. Moreover, the binding energy and the Raman spectrum for each complex are also predicted.

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.

Direct application of insect cadavers infected with entomopathogenic nematodes (EPN) can successfully control target pest insects. Little is known about the effects of environmental factors (desiccation and temperature) on the production process for infective juveniles (IJ) in insects.We examined the effects of desiccation time and cold storage (6.7 °C) on IJ production of the nematode Steinernema carpocapsae in Galleria mellonella cadavers at 30.8 and 57% humidity. Under desiccation, the IJ yield in cadavers increased gradually and reached a maximum on day 5. IJ yield gradually declined from day 6 onwards and was almost zero by day 15. In general, cold storage at 6.7 °C caused negative effects on IJ production in desiccated cadavers. Approximately 56 h post infection was the time at which nematodes were most sensitive to low temperatures during development in cadavers. Five-day desiccated cadavers generated higher mortality and more rapid death of Galleria mellonella larvae than using newly (day 0) desiccated cadavers.This study describe methods of optimizing rearing techniques such as desiccation and cold storage to promote the mass production and application of EPN- infected host cadavers for the field control of insect pests.

To investigate the association between fibroblast growth factor 3 (FGF3) gene rs4980700 and rs4631909 polymorphism and non-syndromic oral clefting (NSOC).Blood samples from 186 NSOC patients, patients' parents and 200 controls were collected. DNA was extracted and PCR-restriction fragment length polymorphism (PCR-RFLP) was used to identify genotypes of the samples. Case-control analyses and transmission disequilibrium test (TDT) and family based association test (FBAT) analyses were also carried out.In case-control analysis, there were significant differences in rs4980700 genotype and allele among NSOC patients compared with the control group (P0.05) and there were significant differences in rs4631909 genotype and allele among NSOC patients compared with the control group (P0.05), but no difference in cleft palate only (P = 0.49). In TDT, the G allele of rs4980700 had an overtransmission (P0.05) and the C allele of rs4631909 had an overtransmission (P0.05) in NSOC. FBAT analysis also showed a significant association between FGF3 gene rs4980700, rs4631909 polymorphism and NSOC.FGF3 gene rs4980700 and rs4631909 polymorphism were associated with NSOC.