Applications of single-cell RNA sequencing in spermatogenesis and molecular evolution

Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation.However,effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and differentiation via traditional methods is difficult.Advances in technology have led to the emergence of many single-cell transcriptome sequencing protocols,which have partially addressed these challenges.In this review,we detail the principles of 10x Genomics technology and summarize the methods for downstream analysis of single-cell transcriptome sequencing data.Furthermore,we explore the role of single-cell transcriptome sequencing in revealing the heterogeneity of testicular ecological niche cells,delineating the establishment and disruption of testicular immune homeostasis during human spermatogenesis,investigating abnormal spermatogenesis in humans,and,ultimately,elucidating the molecular evolution of mammalian spermatogenesis.

Evolution of molecular structure of TATB under shock loading from transient Raman spectroscopic technique

By combination of the transient Raman spectroscopic measurement and the density functional theoretical calculations,the structural evolution and stability of TATB under shock compression was investigated.Due to the improvement in synchronization control between two-stage light gas gun and the transient Raman spectra acquisition,as well as the sample preparation,the Raman peak of the N-O mode of TATB was firstly observed under shock pressure up to 13.6 GPa,noticeably higher than the upper limit of 8.5 GPa reported in available literatures.By taking into account of the continuous shift of the main peak and other observed Raman peaks,we did not distinguish any structural transition or any new species.Moreover,both the present Raman spectra and the time-resolved radiation of TATB during shock loading showed that TATB exhibits higher chemical stability than previous declaration.To reveal the detailed structural response and evolution of TATB under compression,the density functional theoretical calculations were conducted,and it was found that the pressure make N-O bond lengths shorter,nitro bond angles larger,and intermolecular and intra-molecular hydrogen bond interactions enhanced.The observed red shift of Raman peak was ascribed to the abnormal enhancement of H-bound effect on the scissor vibration mode of the nitro group.

Molecular simulation study on the evolution process of hydrate residual structures into hydrate

The clathrate hydrate memory effect is a fascinating phenomenon with potential applications in carbon capture,utilization and storage(CCUS),gas separation,and gas storage as it can accelerate the secondary formation of clathrate hydrate.However,the underlying mechanism of this effect remains unclear.To gain a better understanding of the mechanism,we conducted molecular dynamic simulations to simulate the initial formation and reformation processes of methane hydrate.In this work,we showed the evolution process of hydrate residual structures into hydrate cages.The simulation results indicate that the residual structures are closely related to the existence of hydrate memory effect,and the higher the contribution of hydrate dissociated water to the hydrate nucleation process,the faster the hydrate nucleation.After hydrate dissociation,the locally ordered structures still exist after hydrate dissociation and can promote the formation of cluster structures,thus accelerating hydrate nucleation.Additionally,the nucleation process of hydrate and the formation process of clusters are inseparable.The size of clusters composed of cup-cage structures is critical for hydrate nucleation.The residence time at high temperature after hydrate decomposition will affect the strength of the hydrate memory effect.Our simulation results provide microscopic insights into the occurrence of the hydrate memory effect and shed light on the hydrate reformation process at the molecular scale.

Molecular-level proton acceptor boosts oxygen evolution catalysis to enable efficient industrial-scale water splitting

Industrial water splitting has long been suppressed by the sluggish kinetics of the oxygen evolution reaction(OER),which requires a catalyst to be efficient.Herein,we propose a molecular-level proton acceptor strategy to produce an efficient OER catalyst that can boost industrial-scale water splitting.Molecular-level phosphate(-PO_(4))group is introduced to modify the surface of PrBa_(0.5)Ca_(0.5)Co_(2)O_(5)+δ(PBCC).The achieved catalyst(PO_(4)-PBCC)exhibits significantly enhanced catalytic performance in alkaline media.Based on the X-ray absorption spectroscopy results and density functional theory(DFT)calculations,the PO_(4)on the surface,which is regarded as the Lewis base,is the key factor to overcome the kinetic limitation of the proton transfer process during the OER.The use of the catalyst in a membrane electrode assembly(MEA)is further evaluated for industrial-scale water splitting,and it only needs a low voltage of 1.66 V to achieve a large current density of 1 A cm^(-2).This work provides a new molecular-level strategy to develop highly efficient OER electrocatalysts for industrial applications.

Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals(Octocorallia:Alcyonacea):Insights into slow evolution and adaptation to extreme deep-sea environments

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental pressures.Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

Morphological Evolution of Self-Assembled Sodium Dodecyl Sulfate/Dodecyltrimethylammonium Bromide@Epoxy-β-Cyclodextrin Supramolecular Aggregates Induced by Temperature

Bio-based cyclodextrins(CDs)are a common research object in supramolecular chemistry.The special cavity structure of CDs can form supramolecular self-assemblies such as vesicles and microcrystals through weak interaction with guest molecules.The different forms of supramolecular self-assemblies can be transformed into each other under certain conditions.The regulation of supramolecular self-assembly is not only helpful to understand the self-assembly principle,but also beneficial to its application.In the present study,the self-assembly behavior of epoxy-β-cyclodextrin(EP-β-CD)and mixed anionic and cationic surfactant system(sodium dodecyl sulfate/dodecyltrimethylammonium bromide,SDS/DTAB)in aqueous solution was studied.Morphological and particle size characterization found that the SDS/DTAB@EP-β-CD complex,as the basic building unit,self-assembled into worm-like micelles at lower temperatures and vesicles at higher temperatures.Nuclear magnetic resonance(NMR)and Fourier transform infrared spectroscopy(FT-IR)analysis revealed that the driving force for the formation of vesicles and worm-like micelles was the hydrogen bonds between EP-β-CD molecules,while water molecules played an important role in promoting vesicle formation between SDS/DTAB@EP-β-CD units.Herein,the mechanism of the morphologic transformation of SDS/DTAB@EP-β-CD supramolecular aggregates induced by temperature was elucidated by exploring the self-assembly process,which may provide an excellent basis for the development of delivery carriers.

Subpicosecond laser ablation behavior of a magnesium target and crater evolution:Molecular dynamics study and experimental validation

The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly.

Phylogeny,molecular evolution,and dating of divergences in Lagerstroemia using plastome sequences

Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.

Molecular phylogeny and inflorescence evolution of Prunus(Rosaceae)based on RAD-seq and genome skimming analyses

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.

Multiscale evolution mechanism of sandstone under wet-dry cycles of deionized water:From molecular scale to macroscopic scale

Water is the most abundant molecule found on the earth’s surface and is a key factor in multiscale rock destruction.However,given the fine-grained nature of rock and the complexity of its internal structure,the microstructural evolution of rock under the action of water has not yet been elucidated in detail,and little is understood about the relationship between the rock structure and solideliquid unit.A variety of techniques were used in this study to track the mechanical properties,pore and crack characteristics,and mineral structure degradation characteristics of sandstone at different stages under the action of deionized water,and the evolution mechanisms of the microstructure were analyzed at the molecular scale.The results showed that during the watererock interaction process,water was adsorbed onto the surface of dolomite minerals and the hydrophilic surface of clay minerals,forming a high-density hydrogen bond network.However,different mineral surface structures had different water adsorption structures,resulting in the strain of the dense clay mineral aggregates under expansion action.Stress concentrated at crack tips under the capillary force of dolomite minerals(very weak dolomite dissolution).These effects resulted in a substantial increase in the number of small pores and enhancements in poreecrack connectivity,and the rock strength exhibited varying degrees of decline at different stages of wet-dry cycles.In general,the results of this paper will help to further elucidate the internal connections between molecular-scale and macroscale processes in rock science.

Molecular Composition and Evolution of the Chalcone Synthase (CHS) Gene Family in Five Species of Camellia (Theaceae)

The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.

Molecular evolution of hepatitis A virus in a human diploid cell line

AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the fulllength genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS： Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-l, other than its progenitor H2w.CONCLUSION： Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.

Sequence and Molecular Evolution Analysis of Ubiquitin Proteins Encoded by Baculoviruses

[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysis,and neighbor-joining method（NJ）and maximum parsimony method（MP）were used for the construction of phylogenetic tree.[Results]The baculoviral ubiquitins showed 73%-86% sequence identity to eukaryotic ubiquitin.Two heterogeneous regions of baculoviral ubiquitins were observed：one was the residues from 15-32,the other was located from residues 53 to 60.The else parts were conserved,where many functional amino acids were also observed.Phylogenetic analysis indicated that baculoviral ubiquitins could be divided into three sub-families,including sub-family GV,sub-family I and sub-family II.The molecular evolution of baculoviral ubiquitins might be under negative selection to maintain their functional and structural stability.[Conclusion]The analysis had provided reference for the researches on functional characterization of baculoviral ubiquitins.

Molecular Evolutionary Rate Calculation of Hemoglobin α Chain and γ Chain at Different Stages in Vertebrate Evolution Process

Pseudogene and fibrin peptide which has rapid evolve speed and good stability are used in this study to determine the divergence date among groups.Through calculating the evolutionary rate of hemoglobin α chain,γ chain in vertebrate（including birds and mammals）,it is concluded that the evolutionary rate of hemoglobin α chain,γ chain is not invariable.It shows different evolutionary rates in different periods,that is,faster in early evolution stage and relatively slow in later stage.

Sequence Variation and Molecular Evolution of Hormone-Sensitive Lipase Genes in Species of Bovidae

The partial sequences of exon Ⅰ of hormone-sensitive lipase （HSL） genes in yak （Bos grunniens）, cattle （Bos taurus）, zebu （Bos indicus）, and buffalo （Bubalus bubalis） were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig （Sus scrofa）, human （Homo sapiens）, mouse （Mus musculus）, and rat （Rattus sp.） retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of the HSL genes in all species. The results showed that the homologies of the partial exon Ⅰ sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs： 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon Ⅰ of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.

O-O bond formation mechanisms during the oxygen evolution reaction over synthetic molecular catalysts

Water oxidation is one of the most important reactions in natural and artificial energy conversion schemes.In nature,solar energy is converted to chemical energy via water oxidation at the oxygen-evolving center of photosystem II to generate dioxygen,protons,and electrons.In artificial energy schemes,water oxidation is one of the half reactions of water splitting,which is an appealing strategy for energy conversion via photocatalytic,electrocatalytic,or photoelectrocatalytic processes.Because it is thermodynamically unfavorable and kinetically slow,water oxidation is the bottleneck for achieving large-scale water splitting.Thus,developing highly efficient water oxidation catalysts has attracted the interests of researchers in the past decades.The formation of O-O bonds is typically the rate-determining step of the water oxidation catalytic cycle.Therefore,better understanding this key step is critical for the rational design of more efficient catalysts.This review focuses on elucidating the evolution of metal-oxygen species during transition metal-catalyzed water oxidation,and more importantly,on discussing the feasible O-O bond formation mechanisms during the oxygen evolution reaction over synthetic molecular catalysts.

Molecular Biomarker Characteristics of the Linxi Formation Source Rocks in the Middle-Western Region of Inner Mongolia:New evidence for late-stage tectonic evolution of the Paleo-Asian Ocean

Objective Two important geological issues have long been controversial in the Xing-Meng area of North China. The first concerns the final closure of Paleo-Asian Ocean in Xing-Meng area, and the other concerns the folding and lifting of the Xing-Meng Trough. The focus of thses issues is the Late Permian sedimentary environment, which is generally considered to be either an exclusively continental environment or from the closed inland sea environment in the Early to Middle stage to continental lacustrine environment in the late stage. In recent years, we have successively discovered abundant typical marine fossils （e.g., bryozoans and calcareous algae） in the Upper Permian thick limestone layer from Linxi County and Ar Horqin Banner in eastern region of Inner Mongolia and Jiutain County in Jilin Province. These significant findings have attracted the attention from fellow academics.

Massive Molecular Parallel Evolution of the HSP90AA1 Gene between High-elevation Anurans

HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HSP90 AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N. parkeri and R. kukunoris. We generated both model based（Zhang and Kumar＇s test） and empirical data based（parallel/divergence plotting） null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90 AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported clade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.

Detecting Variation in the Rate of Molecular Evolution in Different Lineages of Mammals

A major research topic within molecular evolution studies is to understand more about the causes of the molecular evolutionary patterns that are recorded within and between taxa. The amount of germ cell divisions in females and males causes the majority of mutations, during DNA replication, that impact molecular evolution. In an XX female and an XY male system of diploid animals, the autosomes come in duplicates, with one copy from the male and female parent. Because of this, the idea that evolution is driven by male mutations has become increasingly more likely. This paper looks at the different male-mutation rates and determines that the male-mutation rate is much higher than female-mutation rates. Ry/a to be approximately 2.2, which means that Ry is approximately -24.2. From software analysis, x was approximated to be about 0.5. And since x and Ry are known, Ry/x was determined to be -49. The results for this paper show the calculated Rx/a and Ry/a are similar to the results of another study, but they are unique in that they produced a relatively high negative number for the Ry/a, which was about -49. This provides evidence that the male-mutation rate is higher than the female-mutation rate. This is interesting because this suggests that, from the data, the mutation rate in males is the defining force in molecular evolution. And because the rate goes beyond the prescribed model, future models of molecular systems will need to consider the rate of male mutations, as well as clarifying this male-mutation rate and calculating the rate of mutation in other sex-determinant systems.

Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos

Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.