Driver Intent Prediction and Collision Avoidance With Barrier Functions

For autonomous vehicles and driver assist systems,path planning and collision avoidance algorithms benefit from accurate predictions of future location of other vehicles and intent of their drivers.In the literature,the algorithms that provide driver intent belong to two categories:those that use physics based models with some type of filtering,and machine learning based approaches.In this paper we employ barrier functions(BF)to decide driver intent.BFs are typically used to prove safety by establishing forward invariance of an admissible set.Here,we decide if the“target”vehicle is violating one or more possibly fictitious(i.e.,non-physical)barrier constraints determined based on the context provided by the road geometry.The algorithm has a very small computational footprint and better false positive and negative rates than some of the alternatives.The predicted intent is then used by a control barrier function(CBF)based collision avoidance system to prevent unnecessary interventions,for either an autonomous or human-driven vehicle.

Partial function prediction of sulfate-reducing bacterial community from the rhizospheres of two typical coastal wetland plants in China

Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.

Effect of Bacillus amyloliquefaciens and Bacillus subtilis on fermentation, dynamics of bacterial community and their functional shifts of whole-plant corn silage

Background:Bacillus amyloliquefaciens(BA)and Bacillus subtilis(BS)are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals.However,few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling.If the BA and BS inoculants have positive effects on silages,then they could not only improve fermentation characteristics,but also deliver BA or BS viable cells to ruminants,which would play its probiotic effect.Therefore,the objectives of this study were to investigate the effects of BA and BS on the fermentation,chemical characteristics,bacterial community and their metabolic pathway of whole-plant corn silage.Results:Freshly chopped whole-plant corn was inoculated without or with BA and BS,respectively,and ensiled for1,3,7,14 and 60 d.Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control,and BA inoculation decreased acetic acid concentrations,whereas BS inoculation decreased fiber contents and increased crude protein(CP)content.Higher water-soluble carbohydrate contents and lower starch contents were observed in BA-and BS-inoculated silages compared with that in control.The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage,which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage.In addition,it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins,and decreased the relative abundances of drug resistance:antimicrobial pathways.We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study.There were no significant differences in bacterial community compositions among the three groups during ensiling.However,BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter.Conclusion:Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.

Incremental multivariable predictive functional control and its application in a gas fractionation unit

The control of gas fractionation unit(GFU) in petroleum industry is very difficult due to multivariable characteristics and a large time delay.PID controllers are still applied in most industry processes.However,the traditional PID control has been proven not sufficient and capable for this particular petro-chemical process.In this work,an incremental multivariable predictive functional control(IMPFC) algorithm was proposed with less online computation,great precision and fast response.An incremental transfer function matrix model was set up through the step-response data,and predictive outputs were deduced with the theory of single-value optimization.The results show that the method can optimize the incremental control variable and reject the constraint of the incremental control variable with the positional predictive functional control algorithm,and thereby making the control variable smoother.The predictive output error and future set-point were approximated by a polynomial,which can overcome the problem under the model mismatch and make the predictive outputs track the reference trajectory.Then,the design of incremental multivariable predictive functional control was studied.Simulation and application results show that the proposed control strategy is effective and feasible to improve control performance and robustness of process.

Time function of surface subsidence based on Harris model in mined-out area

The surface subsidence is a common environmental hazard in mined-out area. Based on careful analysis of the regularity of surface subsidence in mined-out area, we proposed a new time function based on Harris curve model in consideration of the shortage of current surface subsidence time functions. By analyzing the characteristics of the new time function, we found that it could meet the dynamic process, the velocity change process and the acceleration change process during surface subsidence. Then its rationality had been verified through project cases. The results show that the proposed time function model can give a good reflection of the regularity of surface subsidence in mined-out area and can accurately predict surface subsidence. And the prediction data of the model are a little greater than measured data on condition of proper measured data quantity, which is safety in the engineering. This model provides a new method for the analysis of surface subsidence in mined-out area and reference for future prediction, and it is valuable to engineering application.

Rheological Behaviour for Polymer Melts and Concentrated Solutions Part Ⅲ: A New Multiple Entanglement Model to Predict the Dependence of Linear Viscoelastic Function (η_0, Ψ_(10)~0,η_(ext)~0) on the Ranges of Primary Molecular Weights and th

It is shown theoretically that the viscoelasticity of polymer melts is determined by three combining factorst they are the primary molecular weight and its distribution, the number of entanglement sites on polymer chain and the sequence distribution of constituent chains in entanglement spacings. A unified quantity for the three combing factors is the average constrained dimensional number of constituent chains in the long entanglement spacings (v). A new relation of v to the primary molecular weight and the number of testing polymers were derived from the multiple entanglement and reptation model, and a new method for determining v was proposed. The dependences of linear viscoelastic functions on the primary molecular weight and its distribution were derived by the statistical method. When Mn=6Me to 18 Me, the values of (v) can range from 3.33 to 3.70. Their values are in a good agreement with the experiment data, and it can slightjy vary with the different species of polymers and the different ranges of molecular weight of

Additive predictions of aboveground stand biomass in commercial logs and harvest residues for rotation age Pinus radiata plantations in New South Wales,Australia

Two systems of additive equations were developed to predict aboveground stand level biomass in log products and harvest residue from routinely measured or predicted stand variables for Pinus radiata plantations in New South Wales,Australia.These plantations were managed under three thinning regimes or stand types before clear-felling at rotation age by cut-to-length harvesters to produce sawlogs and pulpwood.The residue material following a clear-fell operation mainly consisted of stumps,branches and treetops,short off-cut and waste sections due to stem deformity,defects,damage and breakage.One system of equations did not include dummy variables for stand types in the model specification and was intended for more general use in plantations where stand density management regimes were not the same as the stand types in our study.The other system that incorporated dummy variables was for stand type-specific applications.Both systems of equations were estimated using 61 plot-based estimates of biomass in commercial logs and residue components that were derived from systems of equations developed in situ for predicting the product and residue biomass of individual trees.To cater for all practical applications,two sets of parameters were estimated for each system of equations for predicting component and total aboveground stand biomass in fresh and dry weight respectively.The two sets of parameters for the system of equations without dummy variables were jointly estimated to improve statistical efficiency in parameter estimation.The predictive performances of the two systems of equations were benchmarked through a leave-one-plot-out cross validation procedure.They were generally superior to the performance of an alternative two-stage approach that combined an additive system for major components with an allocative system for sub-components.As using forest harvest residue biomass for bioenergy has increasingly become an integrated part of forestry,reliable estimates of product and residue biomass will assist harvest and management planning for clear-fell operations that integrate cut-to-length log production with residue harvesting.

Estimation of the unfrozen water content of saturated sandstones by ultrasonic velocity

The unfrozen water content(UWC)of rocks at low temperature is an important index for evaluating the stability of the rock engineering in cold regions and artificial freezing engineering.This study addresses a new method to estimate the UWC of saturated sandstones at low temperature by using the ultrasonic velocity.Ultrasonic velocity variations can be divided into the normal temperature stage(20 to 0℃),quick phase transition stage(0 to-5℃)and slow phase transition stage(-5 to-25℃).Most increment of ultrasonic velocity is completed in the quick phase transition stage and then turns to be almost a constant in the slow phase transition stage.In addition,the UWC is also measured by using nuclear magnetic resonance(NMR)technology.It is validated that the ultrasonic velocity and UWC have a similar change law against freezing and thawing temperatures.The WE(weighted equation)model is appropriate to estimate the UWC of saturated sandstones,in which the parameters have been accurately determined rather than by data fitting.In addition,a linear relationship between UWC and ultrasonic velocity is built based on pore ice crystallization theory.It is evidenced that this linear function can be adopted to estimate the UWC at any freezing temperature by using P-wave velocity,which is simple,practical,and accurate enough compared with the WE model.

Structure elucidation and in vitro rat intestinal fermentation properties of a novel sulfated glucogalactan from Porphyra haitanensis

This study was to investigate the structure and rat fecal microbial fermentation properties of a polysaccharide fraction(PHP2)isolated from the red marine alga Porphyra haitanensis.PHP2 was characterized as a sulfated glucogalactan,with a hypothetical backbone structure of→4)Gα(1→6)G4 Sβ(1→4)Glc(1→and a side chain of Man(1→6)Glc.PHP2 had an irregular spherical chain conformation.The 16 S r RNA sequence analysis revealed that PHP2 modulated the rat fecal micro-flora composition,with a similar effect to inulin,changing the dominant genus(Lactobacillus and Escherichia-Shigella)and promoting the growth of organisms that degrade sulfur-containing polysaccharides,such as Desulfovibrio,Ruminococcaceae_UCG-005,and Ruminococcus_2.PHP2 can promote production of acetic,propionic and butyric acid by rat fecal micro-flora.Prediction of metabolic function suggested that PHP2 could modulate cholesterol metabolism.The sulfated glucogalactan fermentation behavior may be associated with its monosaccharide composition,chain branching and chain conformation.PHP2 appeared to have considerable potential as functional food,and was associated with sulfur-containing polysaccharides in general.

Benthic bacterial communities indicate anthropogenic activity footprints in coastal area under long-term marine spatial planning practice

Marine spatial planning(MSP)is designed to divide the sea area into different types of functional zones,to implement corresponding development activities.However,the long-term impacts of anthropogenic activities associated with MSP practice on the marine microbial biosphere are still unclear.Yalu River Estuary,a coastal region in northeast of China,has been divided into fishery&agricultural(F&A)zone,shipping&port(S&P)zone and marine protected area(MPA)zone by a local MSP guideline that has been run for decades.To examine the effects of long-term executed MSP,benthic bacterial communities from different MSP zones were obtained and compared in this study.The results revealed significant differences in the bacterial community structure and predict functions among different zones.Bacterial genera enriched in different zones were identified,including SBR1031 in MPA,Woeseia and Sva0996 in S&P,and Halioglobus in F&A.In addition,correlations between some bacterial genera and sediment pollutants were uncovered.Furthermore,bacteria related to sulphide production were more abundant in the F&A zone,which was according to the accumulation of sulphides in this area.Moreover,bacteria associated with chemoheterotrophy and fermentation were more predominant in the S&P zone,consistent with high levels of organic matter and petroleum caused by shipping.Our findings indicated benthic bacterial communities could bring to light the anthropogenic activity footprints by different activities induced by long-term MSP practice.

iORbase:A database for the prediction of the structures andfunctions of insect olfactory receptors

Insect olfactory receptors(iORs)with atypical 7-transmembrane domains,unlike Chordata olfactory receptors,are not in the GPCR protein family.iORs selectively bind to volatile ligands in the environment and affect essential insect behaviors.In this study,we constructed a new platform(iORbase,https://www.iorbase.com)for the structural and functional analysis of iORs based on a combined algorithm for gene annotation and protein structure prediction.Moreover,it provides the option to calculate the binding affinities and binding residues between iORs and pheromone molecules by virtual screening of docking.Furthermore,iORbase supports the automatic structural and functional prediction of user-submitted iORs or pheromones.iORbase contains the well-analyzed results of approximately 6000 iORs and their 3D protein structures identified from 59 insect species and 2077 insect pheromones from the literature,as well as approximately 12 million pairs of simulated interactions between functional iORs and pheromones.We also built 4 online modules,iORPDB,iInteraction,iModelTM,and iOdorTool to easily retrieve and visualize the 3D structures and interactions.iORbase can help greatly improve the experimental efficiency and success rate,identify new insecticide targets,or develop electronic nose technology.This study will shed light on the olfactory recognition mechanism and evolutionary characteristics from the perspectives of omics and macroevolution.

Spatial-temporal dynamics of bacterioplankton communities in the breeding area of large yellow croaker Larimichthys crocea in Sansha Bay,China

As an important spawning ground for large yellow croaker Larimichthys crocea,Sansha Bay,South China Sea has been a research hotspot.However,studies on the influence of the bacterioplankton community and assessments of its seasonal succession of bacterioplankton in different sea areas in Sansha Bay are still limited.To address the issue,we use 16S rRNA gene amplicon sequencing and functional prediction to investigate the spatial-temporal dynamics of the bacterioplankton community in three distinct areas,i.e.,Breeding Area(BA),Yantian Harbor(YH),and Bay Margin(BM)of Sansha Bay.Results show that the structure of the bacterioplankton community in Sansha Bay had a significant seasonal succession.Moreover,the representative zero-radius Operation Taxon Units in different seasons were significantly different among the three selected sea areas.Specifically,during the breeding season,bacterioplankton communities in BA were characterized by compound-degrading bacteria,such as Rhodococcus and Owenweeksia,while in YH and BM,animal parasites or symbionts such as Vibrio and Arcobacter were dominant.Furthermore,the redundancy analysis and Spearman correlation analysis further explained that water temperature,dissolved oxygen,and ammonia nitrogen were the main environmental factors responsible for the difference.In addition,the bioindicator functions screened by Functional Annotation of Prokaryotic Taxa and random forest machine learning mainly relied on compound degradation,nitrite oxidation,and photoheterotrophy.The compound-degradationcorresponded bacterioplankton genera such as Rhodococcus had relatively higher abundance in BM,while Nitrospina corresponding to nitrite oxidation tended to be abundant in YH and BA.Based on the spatial and temporal variation in the composition and function of bacterioplankton,our findings provide a basis for understanding the theory of bacterioplankton community structure in the inner-bay habitat of the large yellow croaker in Sansha Bay.

Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants

Non-coding variants in the human genome significantly influence human traits and complex diseases via their regulation and modification effects.Hence,an increasing number of computational methods are developed to predict the effects of variants in human non-coding sequences.However,it is difficult for inexperienced users to select appropriate computational methods from dozens of available methods.To solve this issue,we assessed 12 performance metrics of 24 methods on four independent non-coding variant benchmark datasets:(1)rare germline variants from clinical relevant sequence variants(ClinVar),(2)rare somatic variants from Catalogue Of Somatic Mutations In Cancer(COSMIC),(3)common regulatory variants from curated expression quantitative trait locus(eQTL)data,and(4)disease-associated common variants from curated genomewide association studies(GWAS).All 24 tested methods performed differently under various conditions,indicating varying strengths and weaknesses under different scenarios.Importantly,the performance of existing methods was acceptable for rare germline variants from ClinVar with the area under the receiver operating characteristic curve(AUROC)of 0.4481–0.8033 and poor for rare somatic variants from COSMIC(AUROC=0.4984–0.7131),common regulatory variants from curated eQTL data(AUROC=0.4837–0.6472),and disease-associated common variants from curated GWAS(AUROC=0.4766–0.5188).We also compared the prediction performance of 24 methods for non-coding de novo mutations in autism spectrum disorder,and found that the combined annotation-dependent depletion(CADD)and context-dependent tolerance score(CDTS)methods showed better performance.Summarily,we assessed the performance of 24 computational methods under diverse scenarios,providing preliminary advice for proper tool selection and guiding the development of new techniques in interpreting non-coding variants.

Response of fungal communities to afforestation and its indication for forest restoration

Soil fungi in forest ecosystems have great potential to enhance host plant growth and systemic ecological functions and services.Reforestation at Saihanba Mechanized Forest Farm,the world's largest artificial plantation,has been integral to global forest ecosystem preservation since the 1950s.To better assess the ecological effects of soil microbiology after afforestation,fungal diversity and community structure(using Illumina sequencing)from forests dominated by Larix gmelinii var.principis-rupprechtii,Pinus sylvestris var.mongolica and Picea asperata,and from grassland were surveyed.In total,4,540 operational taxonomic units(OTUs)were identified,with Mortierella and Solicoccozyma being the dominant genera of grassland soil and Inocybe,Cortinarius,Piloderma,Tomentella,Sebacina,Hygrophorus and Saitozyma dominating the plantation soil.Principle coordinate analysis(PCoA)and co-occurrence networks revealed differences in fungal structure after afforestation.Significantly,more symbiotroph guilds were dominated by ectomycorrhizal fungi in plantations under the prediction of FUNGuild.The community composition and diversity of soil fungi were significantly influenced by pH via redundancy analysis(RDA)and the Mantel test(p<0.01).This finding emphasizes that soil pH has a strong effect on the transition of fungal communities and functional taxa from grassland to plantation,providing a novel indicator for forest restoration.

Rhizosphere bacterial communities and soil nutrient conditions reveal sexual dimorphism of Populus deltoides

Sexual dimorphism of plants shapes the diff erent morphology and physiology between males and females.However,it is still unclear whether it infl uences belowground ecological processes.In this study,rhizosphere soil of male and female Populus deltoides and bulk soil were collected from an 18-year plantation(male and female trees mix-planted)and grouped into three soil compartments.Soil carbon(C),nitrogen(N)and phosphorus(P)levels were determined,and soil bacterial communities were analyzed by high-throughput sequencing.The results showed the less total carbon and total organic carbon,the more nutrients(available phosphorus,nitrate nitrogen and ammonium nitrogen)available in the rhizosphere soils of female poplars than soils of males.However,α-diversity indices of the rhizosphere bacterial communities under male plants were signifi-cantly higher.Principal component analysis showed that the bacterial communities were signifi cantly diff erent between the male and female soil compartments.Further,the bacterial co-occurrence network in soil under male trees had more nodes and edges than under females.BugBase analysis showed the more functional bacteria taxa related to biofi lm formation and antioxidation under males.The results indicate that soils under male poplars had more diverse and more complex co-occurrence networks of the rhizosphere bacterial community than soils under female trees,implying that male poplars might have better environmental adaptability.The study provides insight into the diff erent soil-microbe interactions of dioecious plants.More details about the infl uencing mechanism of sexual dimorphism on rhizosphere soil bacterial communities need to be further studied.

Effect of Herb-Partitioned Moxibustion on Structure and Functional Prediction of Gut Microbiota in Rats with Irritable Bowel Syndrome with Diarrhea

Objective:The objective of this study was to observe the effect of herb-partitioned moxibustion(HPM)on the gut microbiota of rats with diarrhea-predominant irritable bowel syndrome(IBS-D).Materials and Methods:A total of 48 male rats were randomly divided into a normal control group and an irritable bowel syndrome(IBS)model group.Using acetic acid irrigation and constraint stress,an IBS-D rat model was developed.After the model was made,the IBS rats were divided into IBS,HPM group,and pinaverium bromide(PB)group.The HPM received HPM for 20 min every day,while the PB was given gastric perfusion once a day for 14 days.After modeling and treatment,the abdominal withdrawal reflex,fecal character score,and fecal water content of rats were scored,and a 16S rRNA sequencing analysis was performed on the gut microbiota.Results:After treatment,the fecal character score and fecal water content in the HPM increased significantly,while visceral sensitivity decreased.Investigation of 16S rDNA sequencing revealed that α-diversity was reduced in the IBS,and HPM could increase the diversity of flora.The flora structure of IBS-D rats changed.HPM can increase the abundance of probiotics such as Akkermansia and reduce the abundance of opportunistic pathogens such as Bacteroides and Prevotella.Functional prediction analysis showed that the HPM was mainly related to the bacillary secret system,tricarboxylic acid cycle,and other pathways.Conclusion:HPM can regulate the gut microbiota of rats with IBS-D.

In silico protein function prediction:the rise of machine learning-based approaches

Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.

Transcriptome-based identification and expression analysis of the glutathione S-transferase(GST)family in tree peony reveals a likely role in anthocyanin transport

For red-flowered cultivars of tree peony(Paeonia suffruticosa),anthocyanin content is a critical factor determining the different petal pigmentations.Glutathione S-transferases(GSTs)are ubiquitous and multifunctional conjugating proteins that may be responsible for the transport of anthocyanin pigments from the cytoplasm to vacuole.The underlying function of the GST family in tree peony,however,remains unclear.In this study,we systematically isolated and identified a total of 54 putative full-length Ps GST genes through a combination of bioinformatics approaches from transcriptome databases.Intraspecific phylogenetic analyses revealed extensive differentiation in their coding sequences and divided them into 10 of the 14 known classes of plant GSTs.The phylogenetic relationships,evolutionary characteristics,protein domain,and motif organization were clearly conserved among the different phylogenetic subclasses.The results of the RNA-seq and quantitative real-time polymerase chain reaction experiments exhibited extensive variation in gene expression profiles among different developmental stages and varieties.Furthermore,the phylogenetic relationships,expression profiles,protein interactions,weighted gene co-expression network analysis,and correlation analysis results suggested that PsGSTF3(Unigene 0064200)is a candidate participant in anthocyanin transport and the promotion of pigment accumulation,exhibiting a strong positive correlation with anthocyanin content among different tissues(r=0.908**)and an increasing rate of anthocyanin content during the flower developmental process(r=0.961*).These results furthered our understanding of the transport and accumulation functions of the GST family as well as the enhancement of tree peony breeding through molecular biology techniques.

Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

In pig-to-human xenotransplantation,the transmission risk of porcine endogenous retroviruses(PERVs)is of great concern.However,the distribution of PERVs in pig genomes,their genetic variation among Eurasian pigs,and their evolutionary history remain unclear.We scanned PERVs in the current pig reference genome(assembly Build 11.1),and identified 36 long complete or near-complete PERVs(lc PERVs)and 23 short incomplete PERVs(si PERVs).Besides three known PERVs(PERV-A,-B,and-C),four novel types(PERV-JX1,-JX2,-JX3,and-JX4)were detected in this study.According to evolutionary analyses,the newly discovered PERVs were more ancient,and PERV-Bs probably experienced a bottleneck~0.5 million years ago(Ma).By analyzing63 high-quality porcine whole-genome resequencing data,we found that the PERV copy numbers in Chinese pigs were lower(32.0±4.0)than in Western pigs(49.1±6.5).Additionally,the PERV sequence diversity was lower in Chinese pigs than in Western pigs.Regarding the lc PERV copy numbers,PERV-A and-JX2 in Western pigs were higher than in Chinese pigs.Notably,Bama Xiang(BMX)pigs had the lowest PERV copy number(27.8±5.1),and a BMX individual had no PERV-C and the lowest PERV copy number(23),suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors.Furthermore,we identified 451 PERV transposon insertion polymorphisms(TIPs),of which 86 were shared by all 10 Chinese and Western pig breeds.Our findings provide systematic insights into the genomic distribution,variation,evolution,and possible biological function of PERVs.

Genome-wide identification and characterization of the bHLH gene family in an ornamental woody plant Prunus mume

The basic helix-loop-helix(bHLH)transcription factor family is the second-largest family in plants,where it plays essential roles in development,and the responses to multiple abiotic and biotic stressors.However,little information is available about this gene family in Prunus mume,which is widely cultivated in East Asia as an ornamental fruit tree.Here,100 PmbHLH genes were identified,and their evolution and functions were explored in P.mume for the first time.The PmbHLH genes were classified into 21 subfamilies.The chromosomal distribution,physicochemical properties,bHLH domain,conserved motif,and intron/exon compositions were also analyzed.Furthermore,the evolutionary pattern,divergence time of the PmbHLH family,and genetic relationships among P.mume,Arabidopsis thaliana,and Prunus persica and Fragaria vesca of Rosaceae were explored.The functional prediction analysis of these PmbHLHs indicated that their functions varied,and included participating in the formation of organs and tissues,responding to stress,and the biosynthesis and metabolism of hormones and other secondary metabolites.Interestingly,expression analyses of PmbHLHs also revealed diverse expression patterns.Most of the PmbHLH genes were highly expressed in roots and stems,and a few were highly expressed in leaves,buds,and fruits,indicating tissue expression specificity.Eight PmbHLH genes,which were upregulated during low-temperature stress,may have critical roles in the response to cold stress.Ten PmbHLHs were differentially expressed between weeping and upright branches in a P.mume F_(1) population.These results shed light on the structure and evolution of the PmbHLH gene family,and lay a foundation for further functional studies of the bHLH genes.