Improved mammalian family phylogeny using gap-rare multiple sequence alignment:A timetree of extant placentals and marsupials

The timing of mammalian diversification in relation to the Cretaceous-Paleogene(KPg)mass extinction continues to be a subject of substantial debate.Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples.In the present study,we improved an existing dataset from the landmark study of Meredith et al.(2011)by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers.Using these two datasets,we then constructed phylogenies for extant mammalian families,providing improved resolution of many conflicting relationships.Moreover,the timetrees generated,which were calibrated using appropriate molecular clock models and multiple fossil records,indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period.Additionally,intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary,supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification.Thus,our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.

A potential distribution map of wintering Swan Goose(Anser cygnoides)in the middle and lower Yangtze River floodplain,China

Background: Reliable information on the distribution of target species and influencing environmental factors is essential for effective conservation management. However, ecologists have often derived data from costly field surveys. The Swan Goose(Anser cygnoides), a vulnerable Anatidae species, winters almost exclusively in China's Yangtze River floodplain, but wintering numbers have been steadily decreasing. To better safeguard this unique species, modern modeling approaches can be used to quantify and predict its suitable wintering habitat. Specifically, a potential wintering distribution map of this species is critically important.Methods: This study used the maximum entropy approach to model a distribution map of this species. In total, data from 97 up-to-date sites were extracted from 1263 survey sites(excluding duplicate data). After eliminating spatial autocorrelation, 11 environmental variables, including factors related to climate, land structure, vegetation, and anthropogenic activities, were used for model prediction.Results: The prediction distribution map shows that the population has concentrated mainly in the boundary area of Anhui, Hubei, and Jiangxi provinces, especially along the Yangtze River. Modeling results suggest that areas within the middle and lower Yangtze River floodplain, such as those in Hunan and Hubei provinces and the eastern coastal area of Zhejiang Province, demonstrate a potential level of "medium" suitability for this species to winter.Conclusions: Results from this study provide fundamental information for the restoration and management of the Swan Goose. Our "visualized" potential distribution map can assist in planning optimal conservation strategies, and consequently may help to increase the number of wintering populations in China.

Identification and genetic mapping of four novel genes that regulate leaf development in Arabidopsis

Molecular and genetic characterizations of mutants have led to a better understanding of many developmental processes in the model system Arabidopsis thaliana. However, the leaf development that is specific to plants has been little studied. With the aim of contributing to the genetic dissection of leaf development, we have performed a large-scare screening for mutants with abnormal leaves. Among a great number of leaf mutants we have generated by T-DNA and transposon tagging and ethylmethae sulfonate (EMS) mutagenesis, four independent mutant lines have been identified and studied genetically. Phenotypes of these mutant lines represent the defects of four novel nuclear genes designated LL1 (LOTUS LEAF 1), LL2 (LOTUS LEAF 2), URO (UPRIGHT ROSETTE), and EIL (ENVIRONT CONDITION INDUCED LESION). The phenotypic analysis indicates that these genes play important roles during leaf development. FOr the further genetic analysis of these genes and the map-based cloning of LL1 and LL2, we have mapped these genes to chromosome regions with an efficient and rapid mapping method.

Construction of HBV-specific ribozyme and its recombinant with HDV and their cleavage activity in vitro

AIM To construct the recombinant of HDVcDNA and HBV-specific ribozyme gene byrecombinant PCR in order to use HDV as atransporting vector carrying HBV-specificribozyme into liver cells for inhibiting thereplication of HBV.METHODS We separately cloned the ribozyme（RZ）gene and recombinant DVRZ（comprisingHDV cDNA and HBV-specific ribozyme gene）intothe downstream of T7 promoter of pTAdv-Tvector and studied the in vitro cleavage activityof their transcripts（rRZ,rDVRZ）on target RNA（rBVCF）from in vitro transcription of HBV Cgene fragment（BVCF）.RESULTS Both the simple（rRZ）and therecombinant ribozyme rDVRZ could efficientlycatalyze the cleavage of target RNA（rBVCF）under different temperatures（37℃,42℃ and55℃）and Mg2+concentrations（10 mmol/L,15 mmol/L and 20 mmol/L）and their catalyticactivity tended to increase as the temperaturewas rising.But the activity of rRZ was evidentlyhigher than that of rDVRZ.CONCLUSION The recombinant of HDV cDNAand ribozyme gene had the potential of beingfurther explored and used in gene therapy of HBVinfection.

Effects of Chronic Administration of Melatonin on Spatial Learning Ability and Long-term Potentiation in Lead-exposed and Control Rats

Objective To explore the changes in spatial learning performance and long-term potentiation （LTP） which is recognized as a component of the cellular basis of learning and memory in normal and lead-exposed rats after administration of melatonin （MT） for two months. Methods Experiment was performed in adult male Wistar rats （12 controls, 12 exposed to melatonin treatment, 10 exposed to lead and 10 exposed to lead and melatonin treatment）. The lead-exposed rats received 0.2% lead acetate solution from their birth day while the control rats drank tap water. Melatonin （3 mg/kg） or vehicle was administered to the control and lead-exposed rats from the time of their weaning by gastric gavage each day for 60 days, depending on their groups. At the age of 81-90 days, all the animals were subjected to Morris water maze test and then used for extracellular recording of LTP in the dentate gyrus （DG） area of the hippocampus in vivo. Results Low dose of melatonin given from weaning for two months impaired LTP in the DG area of hippocampus and induced learning and memory deficit in the control rats. When melatonin was administered over a prolonged period to the lead-exposed rats, it exacerbated LTP impairment, learning and memory deficit induced by lead. Conclusion Melatonin is not suitable for normal and lead-exposed children.

Longitudinal analysis reveals characteristically high proportions of bacterial vaginosis-associated bacteria and temporal variability of vaginal microbiota in northern pig-tailed macaques （Macaca leonina）

The complex and dynamic vaginal microbial ecosystem is critical to both health and disease of the host. Studies focusing on how vaginal microbiota influences HIV-1 infection may face limitations in selecting proper animal models. Given that northern pig-tailed macaques （Macaca leonina） are susceptible to HIV-1 infection, they may be an optimal animal model for elucidating the mechanisms by which vaginal microbiota contributes to resistance and susceptibility to HIV-1 infection. However, little is known about the composition and temporal variability of vaginal microbiota of the northern pig-tailed macaque. Here, we present a comprehensive catalog of the composition and temporal dynamics of vaginal microbiota of two healthy northern pig-tailed macaques over 19 weeks using 454-pyrosequencing of 16S rRNA genes. We found remarkably high proportions of a diverse array of anaerobic bacteria associated with bacterial vaginosis. Atopobium and Sneathia were dominant genera, and interestingly, we demonstrated the presence of Lactobacillus-dominated vaginal microbiota. Moreover, longitudinal analysis demonstrated that the temporal dynamics of the vaginal microbiota were considerably individualized. Finally, network analysis revealed that vaginal pH may influence the temporal dynamics of the vaginal microbiota, suggesting that inter-subject variability of vaginal bacterial communities could be mirrored in inter-subject variation in correlation profiles of species with each other and with vaginal pH over time. Our results suggest that the northern pig-tailed macaque could be an ideal animal model for prospective investigation of the mechanisms by which vaginal microbiota influence susceptibility and resistance to HIV-1 infection in the context of highly polymicrobial and Lactobacillus-dominated states.

Migration routes,population status and important sites used by the globally threatened Black-faced Spoonbill(Platalea minor):a synthesis of surveys and tracking studies

Background:The Black-faced Spoonbill(Platalea minor)is a globally threatened species,nesting mainly in western Korea with smaller numbers breeding in Liaoning Province,China,and Far East Russia.Recent winter field surveys to estimate the species'population size were almost totally conducted in coastal areas,but tracking studies showed that some individuals now winter inland.To ensure its long-term survival,we need a more comprehensive assessment of the current distribution and abundance of the species.Methods:We combined the most recent count data and satellite tracking information to update existing informa-tion about the population abundance and distribution of the Black-faced Spoonbill at all stages of its annual life cycle,and how these have changed during 2004-2020.Results:Black-faced Spoonbills mainly breed on the west coast of the Korean peninsula,while immature birds show a wider summer distribution throughout Yellow Sea coastal areas,when a few remain on wintering sites in the south.Combined tracking results and mid-winter counts confirmed known wintering sites on the east and south coasts of China,but showed that the species also winters on wetlands in the Yangtze River floodplain and in Southeast Asia.During 2004-2020,counts of wintering birds in coastal habitats increased from 1198 to 4864,with numbers wintering on the island of Taiwan contributing most to the overall increase.Latest counts found 5222 in 2021.We also identify key wintering and stopover sites as well as their current conservation status.Conclusions:This study revised the known summering and wintering ranges of the Black-faced Spoonbill and assessed the conservation status of key sites based on a combination of field survey and satellite tracking data.We recommend prioritisation of further field research to identify and survey inland wintering areas in the Yangtze River floodplain and summering areas of immature birds.More tracking of adult individuals and birds during spring migration is necessary to fill these information gaps.We also suggest establishing a Black-faced Spoonbill monitoring platform to store,share and show real-time distribution range and population abundance data.

Development of a new atmospheric pressure cold plasma jet generator and application in sterilization

This paper reports that a new plasma generator at atmospheric pressure, which is composed of two homocentric cylindrical all-metal tubes, successfully generates a cold plasma jet. The inside tube electrode is connected to ground, the outside tube electrode is connected to a high-voltage power supply, and a dielectric layer is covered on the outside tube electrode. When the reactor is operated by low-frequency （6 kHz-20 kHz） AC supply in atmospheric pressure and argon is steadily fed as a discharge gas through inside tube electrode, a cold plasma jet is blown out into air and the plasma gas temperature is only 25-30℃. The electric character of the discharge is studied by using digital real-time oscilloscope （TDS 200-Series）, and the discharge is capacitive. Preliminary results are presented on the decontamination of E.colis bacteria and Bacillus subtilis bacteria by this plasma jet, and an optical emission analysis of the plasma jet is presented in this paper. The ozone concentration generated by the plasma jet is 1.0× 10^16cm^-3 which is acquired by using the ultraviolet absorption spectroscopy.

Successful implementation of intestinal resection and anastomosis in non-human primates suggests the possibility of longitudinal intestinal research

DEAR EDITOR,Intestinal biopsy is a basic experimental method for studying pathological changes in the intestinal tract during human immunodeficiency virus(HIV)infection.In this study,jejunal resection and anastomosis were successfully performed in 12 Chinese rhesus macaques(Macaca mulatta).

Effects of Nitric Oxide on the Growth and Development of Porcine Preantral Follicles Cultured in Vitro

In order to investigate the effects of nitric oxide(NO) on the growth and development of porcine preantral follicles,we treated the follicles with different concentrations of sodium nitroprusside(SNP,0, 0.001,0.01,0.1 and 1 mmol/L),a NO donor.The results showed that the follicle diameter increased during in vitro culture,but there were no significant differences between the treatments(P】0.05);the survival rate in the 1 mmol/L SNP group was significantly lower than that in the 1μmol/L SNP group(61.61% vs 81.52%,P【0.05),but no significant differences were found between other treatments(P】0.05);the rate of antrum formation in the 1μmol/L SNP group peaked at 50%on day 4,and the rate in the 1μmol/L SNP group on day 6 was higher than that in the 0.01 mmol/L SNP group;in addition,the rate of antrum formation in the 1μmol/L SNP group was significantly higher than that in the 0.1 and 1 mmol/L SNP groups (Day 6:73.07%vs 50%,47.62%,P【0.05).After 6 days of culture,the proportion of normal oocytes in the1 mmol/L SNP group was significantly lower than that in the 1μmol/L SNP group(71.21%vs 48.18%, P【0.05),with no significant differences between other treatments(P】0.05).The recovery rate of cumulus cells oocyte complexes(COCs) in the 1μmol/L SNP group was significantly higher than that in the controls and all other treatments(37.27%vs 22.88%,25.59%,20.74%and 19.39%,P【0.05).The results indicate that during the in vitro culture of porcine preantral follicles,low concentration of NO released from SNP improves growth and development of oocytes and follicular antrum formation while high levels of NO are toxic to follicular survival.

Minicistron from a gene of prawn white spot bacilliform virus(WSBV)and its expression

By the sequencing and analysis of genomic DNA and cDNA of WSBV, it was found that there existed a minicistron in the leading sequence of p204 gene. The minicistron utilized rare codons of genes from prawn and WSBV. The p204 gene could be expressed in Escherichia coli whether a miniciston exited in its leading sequence or not, but the amounts of the expressed products of them were different. The minicistron might be related to the expression of p204 gene.

Author Correction: Successful implementation of intestinal resection and anastomosis in non-human primates suggests the possibility of longitudinal intestinal research

After the publication of Wang et al.(2020),we realized that there were some inappropriate statements in the content.Hereby,we correct them and apologize for any confusion this may have caused.

Identification of novel nuclear localization signal within the ErbB-2 protein

ErbB2, a member of the receptor tyrosine kinase family, is frequently over-expressed in breast cancer. Proteolysis ofthe extracellular domain of ErbB2 results in constitutive activation of ErbB2 kinase. Recent study reported that ErbB2is found in the nucleus. Here, we showed that ErbB2 is imported into the nucleus through a nuclear localization signal(NLS)-mediated mechanism. The NLS sequence KRRQQKIRKYTMRR (aa655-668) contains three clusters of basicamino acids and it is sufficient to target GFP into the nucleus. However, mutation in any basic amino acid cluster of thisNLS sequence significantly affects its nuclear localization. Furthermore, it was found that this NLS is essential for thenuclear localization of ErbB2 since the intracellular domain of Erb2 lacking NLS completely abrogates its nucleartranslocation. Taken together, our study identified a novel nuclear localization signal and reveals a novel mechanismunderlying ErbB2 nuclear trafficking and localization.

Prevalent false positives of azoospermia factor a （AZFa） microdeletions caused by single-nucleotide polymorphism rs72609647 in the sY84 screening of male infertility

Multiplex polymerase chain reaction （PCR） has been widely used to detect Y-chromosome micredeletions, which is one of the major causes of male infertility. Both the European Academy of Andrology （EAA） and the European Molecular Genetics Quality Network （EMQN） have recommended the use of sY84 and sY86 markers for the detection of azoospermia factor a （AZFa） microdeletion during DNA testing for male infertility. In this study, a large-scale analysis of AZF microdeletion in a total of 630 Chinese males, including healthy semen donors （n=200）, infertile males with normal sperm count （n=226） and patients with either nonobstructive azoospermia or severe oligozoospermia （n=204）, was performed. A series of nine sequence-tagged site （STS） markers from the AZF region of the Y chromosome was used to detect microdeletions. All primers were designed based on the recommendations of the National Center for Biotechnology Information. An unusually high incidence （73/630, 11.6%） of sY84-absent but sY86-present genotypes was observed in the AZFa microdeletion screening. Sequencing the sY84-flanking region revealed a total of 73 patients with sY84-absent but sY86-present genotypes have a T-to-G transversion at the fifth base from the 5＇ end of the reverse sY84 primer. These prevalent false positives, which were not only observed in infertile men, but also observed in donors, resulted from a single-nucleotide polymorphism （SNP） named rs72609647 in the targeting sequence of the reverse sY84 primer. Our study suggests that a pre-screening of existence of rs72609647 polymorphism can prevent the frequent false positive results of AZFa microdeletions detection in the infertile Chinese males. Given the SNP rs72609647 was recently found in a deep sequencing of a Chinese individual, the current EAA and EMQN standards may need to be scrutinized among different populations to avoid the potential genetic variations in the primer binding sequences.

Analysis of 17β-Estadiol from Sewage in Coastal Marine Environment by Surface Plasmon Resonance Technique

In this study, surface plasmon resonance （SPR） for monitoring 17β-eatradiol （E2） was developed. The small molecule E2 was immobilized on a CM5 sensor chip for an indirect competitive immunoassay to detect E2. The SPR response bahed on the antigen-antibody reaction was measured by injecting the sample solution into the flow system. The limitation of detection was 0.445 μg/L. The developed SPE-SPR system was applied to analyze the seawater samples. Recovery of E2 was 91.6%-93. 1%. Relative standard deviations（RSD） for the E2 assay were between 10.9%-15.1% （n = 3）. The range of determination of E2 samples from the sewage in the coastal marine environ-ment was between ND（lower than detection limit） and ca. 11.78 ng/L.

Flow cytometric characterizations of leukocyte subpopulations in the peripheral blood of northern pig-tailed macaques （Macaca leonina）

Pig-tailed macaques(Macaca nemistrina group) have been extensively used as non-human primate animal models for various human diseases in recent years, notably for AIDS research due to their sensitivity to HIV-1. Northern pig-tailed macaques(M. leonina) are distributed in China and other surrounding Southeast Asia countries. Although northern pig-tailed macaques have been bred on a large scale as experimental animals since 2012, the reference value of normal levels of leukocytes is not available. To obtain such information, 62 blood samples from male and female healthy northern pig-tailed macaques at different ages were collected. The normal range of major leukocyte subpopulations, such as T lymphocytes, B lymphocytes, natural killer(NK) cells, monocytes, and the expression levels of activation or differentiation related molecules(CD38, HLA-DR, CCR5, CD21, IgD, CD80 and CD86) on lymphocytes were analyzed by flow cytometry. The counts of B cells decreased with age, but those of CD8+ T cells and NK cells and the frequency of CD38+HLA-DR+CD4+ T cells were positively correlated with age. The counts of leukocyte subpopulations were higher in males than those in females except for CD4+ T cells. Males also showed higher expression levels of Ig D and CD21 within B cells. This study provides basic data about the leukocyte subpopulations of northern pig-tailed macaques and compares this species with commonly used Chinese rhesus macaques(M. mulatta), which is meaningful for the biomedical application of northern pig-tailed macaques.

Spring migration duration exceeds that of autumn migration in Far East Asian Greater White-fronted Geese (Anser albifrons)

Background:Migration theory suggests,and some empirical studies show, that in order to compete for the best breeding sites and increase reproductive success,long-distance avian migrants tend to adopt a time minimization strategy during spring migration, resulting in shorter duration spring migration compared to that in autumn.Methods:Using GPS/GSM transmitters,we tracked the full migrations of 11 Greater White-fronted Geese (Anser albifrons) between southeast China and the Russian Arctic,to reveal the migration timing and routes of the East Asian population, and compare the difference in duration between spring and autumn migration of this population.Results:We found that migration in spring (79 ± 12 days) took more than twice as long to cover the same distance as in autumn (35 ±7 days).This difference in migration duration was mainly determined by significantly more time spent in spring (59±16 days) than in autumn (23± 6days) at significantly more stopover sites. Conclusions:We suggest that these geese, thought to be partial capital breeders, spent almost three quarters of total migration time at spring stopover sites to acquire energy stores for ultimate investment in reproduction, although we cannot reject the hypothesis that timing of the spring thaw also contributed to stopover duration.In autumn,they acquired necessary energy stores on the breeding grounds sufficient to reach Northeast China staging areas almost without stop, which reduced stopover times in autumn and resulted in the faster autumn migration than spring.

Amelioration of metabolic disorders by a mushroom-derived polyphenols correlates with the reduction of Ruminococcaceae in gut of DIO mice

A polyphenolic alkaloid-enriched extract(PAE)was prepared from the fruiting bodies of a wild edible mushroom Sarcodon leucopus.Oral administration of PAE reduced hyperglycemia,hyperlipidemia,hepatic steatosis,and LPS-related infl ammation in high fat diet-induced obese(DIO)mice.Furthermore,we show that PAE produces taxonomic and predicted functional changes in the gut microbiome of DIO mice.A signifi cant decrease in the family of Ruminococcaceae,especially the secondary bile acid-producing bacteria of Intestinimonas and Anaerotruncus,is detected in the gut microbiome of PAE-treate mice.Accordingly,reductions of deoxycholic acid and lithocholic acid are found in the feces of PAE-treated DIO mice,which benefi ts for the intestinal integrity and the reduction of infl ammation.A gut microbiota related mechanism for the anti-metabolic syndrome effects of the PAE is proposed.We suppose the polyphenolic alkaloid extract from S.leucopus be a new and benefi cial prebiotic regulating glucose and lipid metabolisms.

Effect of Aspect Ratio Distribution on Localized Surface Plasmon Resonance Extinction Spectrum of Gold Nanorods

Gold nanorods with different aspect ratios are prepared in micells using a seeded growth method. Their extinction spectra are observed with an UV-visible spectrophotometer and analysed theoretically. It is known that there are two plasmon resonance peaks for gold nanorod corresponding to transverse and longitudinal plasmon resonance respectively. Moreover, the longitudinal plasmon resonance peak shifts to long wavelength when we increase the aspect ratio determined from TEM. Especially, we model the extinction spectrum using Gans＇ theory and compare it with our experimental result. Considering the aspect radios distribution of gold nanorods, it is found that longitudinal plasmon resonance peak will be wider than the nanorods with single aspect ratio, which is consistent with our experimental result. In addition, the effect of dielectric constant of surrounding medium is considered.

Identification of a potential tumor suppressor gene, UBL3, in non-small cell lung cancer

Objective: Oncogenes have been shown to be drivers of non-small cell lung cancer(NSCLC), yet the tumor suppressing genes involved in lung carcinogenesis remain to be systematically investigated. This study aimed to identify tumor suppressing ubiquitin pathway genes(UPGs) that were critical to lung tumorigenesis.Methods: The 696 UPGs were silenced by an siRNA screening in NSCLC cells;the potential tumor suppressing UPGs were analyzed, and their clinical significance was investigated.Results: We reported that silencing of 11 UPGs resulted in enhanced proliferation of NSCLC cells, and four UPGs(UBL3, TRIM22, UBE2 G2, and MARCH1) were significantly downregulated in tumor samples compared to that in normal lung tissues and their expression levels were positively associated with overall survival(OS) of NSCLC patients. Among these genes, UBL3 was the most significant one. UBL3 expression was decreased in tumor samples compared to that in paired normal lung tissues in 59/86(68.6%) NSCLCs, was correlated with TNM stage and sex of NSCLC patients, and was significantly higher in non-smoking patients than in smoking patients. Silencing UBL3 accelerated cell proliferation and ectopic expression of UBL3 suppressed NSCLC in vitro and in vivo.Conclusions: These results showed that UBL3 represented a tumor suppressor in NSCLC and may have potential for use in therapeutics and for the prediction of clinical outcome of patients.