Isolation and rapid genetic characterization of a novel T4-like bacteriophage

Ubiquitous on earth,bacteriophages are the most abundant entities in every ecosystem,but human knowledge about them is still limited compared with that about other forms of organisms.To enrich human knowledge and promote the utilization of bacteriophages,it is necessary to isolate and characterize as many as possible different bacteriophages.Here we describe the isolation of a T4-like bacteriophage IME08 and a rapid method for its genetic characterization.With this method we easily cloned a few random fragments of the bacteriophage genome.Sequence analysis of these random clones showed that bacteriophage IME08 shared the highest sequence similarity with T4-like Enterobacteria phage T4（94%identity）,JS98（95% identity）,JS10（95%identity） and RB14（94%identity） respectively,which suggested that IME08 belonged to T4-like bacteriophage genus.

Phenotypic and genetic characterization of a novel strain of Acidithiobacillus ferrooxidans(AF2)

A comparative study on the phenotypic and genetic characteristics among Acidithiobacillus ferrooxidans （AF2）, a typic strain ATCC23270 and a previously isolated strain AF3 was performed. AF2 can use ferrous ion （Fe^2＋） or elemental sulfur （S^0） as sole energy source, but oxidizes So more effectively than Fe^2＋, which is different from ATCC23270 and AF3. The G＋C content of AF2 is 51.8% （molar fraction）, however, ATCC23270 and AF3 strains have G＋C content of 63.7% and 64.8% （molar fraction）, respectively. The DNA-DNA hybridization results show that AF2 has 41.53% and 52.38% genome similarity to ATCC 23270 and AF3, respectively, but AF3 has a high genome similarity of 89.86% to ATCC 23270 strain. Rusticyanin （rus） and subunit III of aa3-type cytochrome oxidase （coxC） genes are not detected in AF2, but Fe^2＋ oxidase （iro） gene can be detected. To understand the genomic organization of iro gene, a cosmid library of AF2 genome was constructed and iro gene-containing clone was screened. The sequencing result shows that although the nucleotide sequence of iro gene in AF2 is completely identical to that of ATCC 23270 strain, its genomic organization is different from that of ATCC 23270. In AF2, iro is located at downstream ofpurA gene, while it is located at downstream ofpetC-2 gene in ATCC 23270 strain. These results indicate that AF2 is a novel strain ofA. ferrooxidans, and that phenotypic differences among the strains ofA. ferrooxidans are closely correlated with their genetic polymorphisms.

Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.

Enumeration,Genetic Characterization and Antimicrobial Susceptibility of Lactobacillus and Streptococcus Isolates from Retail Yoghurt in Beijing,China

Lactic acid bacteria （LAB） are widely used in food industries. Correct identification and safety evaluation of these bacteria at the species even strain level should take considerations into account. In this study, the LAB were recovered from yoghurt and characterized phenotypically and genetically. Fifty-two isolates of LAB from 31 yoghurt samples were cultured and grouped into 6 species including Luctobucillus bulguricus （24 isolates）, Streptococcus thermophilus （15 isolates）, L. ucidophilus （7 isolates）, L. porucusei/cusei （3 isolates）, L. delbrueckii （2 isolates）, and L. fermentum （1 isolate）, based on their Gram-staining, colony morphology and biochemical properties.

Genetic Analysis of Two Novel GPI Variants Disrupting H Bonds and Localization Characteristics of 55 Gene Variants Associated with Glucose-6-phosphate Isomerase Deficiency

Objective:Glucose-6-phosphate isomerase(GPI)deficiency is a rare hereditary nonspherocytic hemolytic anemia caused by GPI gene variants.This disorder exhibits wide heterogeneity in its clinical manifestations and molecular characteristics,often posing challenges for precise diagnoses using conventional methods.To this end,this study aimed to identify the novel variants responsible for GPI deficiency in a Chinese family.Methods:The clinical manifestations of the patient were summarized and analyzed for GPI deficiency phenotype diagnosis.Novel compound heterozygous variants of the GPI gene,c.174C>A(p.Asn58Lys)and c.1538G>T(p.Trp513Leu),were identified using whole-exome and Sanger sequencing.The AlphaFold program and Chimera software were used to analyze the effects of compound heterozygous variants on GPI structure.Results:By characterizing 53 GPI missense/nonsense variants from previous literature and two novel missense variants identified in this study,we found that most variants were located in exons 3,4,12,and 18,with a few localized in exons 8,9,and 14.This study identified novel compound heterozygous variants associated with GPI deficiency.These pathogenic variants disrupt hydrogen bonds formed by highly conserved GPI amino acids.Conclusion:Early family-based sequencing analyses,especially for patients with congenital anemia,can help increase diagnostic accuracy for GPI deficiency,improve child healthcare,and enable genetic counseling.

Phylogenetic and genetic characterization of a 2017 clinical isolate of H7N9 virus in Guangzhou,China during the fifth epidemic wave

Pathogenic H7N9 influenza viruses continue to pose a public health concern. The H7N9 virus has caused five outbreak waves of human infections in China since 2013. In the present study, a novel H7N9 strain(A/Guangdong/8 H324/2017) was isolated from a female patient with severe respiratory illness during the fifth wave of the 2017 H7N9 epidemic. Phylogenetic analysis showed that the H7N9 viruses collected during the fifth wave belong to two different lineages: the Pearl River Delta lineage and the Yangtze River Delta lineage. The novel isolate is closely related to the Pearl River Delta H7N9 viruses, which were isolated from patients in Guangdong Province. The novel H7N9 isolate has an insertion of three basic amino acids in the cleavage site of hemagglutinin(HA), which may enhance virulence in poultry. The 2017 isolate also possesses an R292 K substitution in the neuraminidase(NA)protein, which confers oseltamivir resistance. This study highlights the pandemic potential of the novel H7N9 virus in mammals;thus, future characterization and surveillance is warranted.

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

Melon(C.melo L.)is an economically important vegetable crop cultivated worldwide.The melon collection in the U.S.National Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding.Here we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist.Population structure and genetic diversity analyses suggested that C.melo ssp.melo was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and Americas.C.melo ssp.melo from East Asia was likely derived from C.melo ssp.agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp.melo accessions from other geographic regions.We developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of melon.Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection.Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits.This study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Epidemiological survey and genetic characterization of type 3 vaccine-derived poliovirus isolated from a patient with four doses of inactivated polio vaccine in Henan Province,China

Background:Vaccine-derived poliovirus(VDPV)is a potential threat to polio eradication because they can reintroduce into the general population and cause paralytic polio outbreaks,a phenomenon that has recently emerged as a prominent public health concern at the end of global polio eradication.This study aimed to describe the epidemiology and genetic characteristics of the frst VDPV identifed from a patient with acute faccid paralysis(AFP),with four doses of inactivated polio vaccine immunization in Henan Province,China in 2017.Methods:The patient was diagnosed with type 3 VDPV.Subsequently,a series of epidemiological approaches was implemented,including a retrospective search of AFP cases,rate of vaccination assessment,study of contacts,and supplementary immunization activities.Fecal samples were collected,viral isolation was performed,and the viral isolates were characterized using full-length genomic sequencing and bioinformatic analysis.Results:Phylogenetic analysis showed that the viral isolates from the patient were diferent from other reported genetic clusters of type 3 VDPV worldwide.They were identifed as a Sabin 3/Sabin 1 recombinant VDPV with a crossover site in the P2 region.Nucleotide substitutions,including U→C(472)and C→U(2493),have been identifed,both of which are frequently observed as reversion mutations in neurovirulent type 3 poliovirus.A unique aspect of this case is that the patient had been vaccinated with four doses of inactive polio vaccine,and the serum neutralizing antibody for Sabin types 1 and 3 were 1∶16 and 1∶512,respectively.Thus,the patient was speculated to have been infected with type 3 VDPV,and the virus continued to replicate and be excreted for at least 41 d.Conclusions:The existence of this kind of virus in human population is a serious risk and poses a severe challenge in maintaining a polio-free status in China.To the best of our knowledge,this is the frst report of VDPV identifed in the Henan province of China.Our results highlight the importance of maintaining a high-level vaccination rate and highly sensitive AFP case surveillance system in intercepting VDPV transmission.

Genome-Wide Analysis of Gene Expression in Stationary Phase and Genetic Characterization of Stationary-Phase-Dependent Halocin Gene Expression in the Haloarchaeon Haloferax mediterranei

The stationary phase of microbial growth is a very complex state regulated by various environmental and physiological factors. An intensive study of stationary phase could promote a comprehensive understanding of the complete life cycle of microorganisms, and may provide important insights into their adaptation to harsh and nutrient-depleted conditions. Although the underlying mechanisms have been weU-studied in bacteria and yeasts （Herman, 2002; Navarro Llorens et al., 2010）, less is known about this growth phase in archaea yet. The haloarchaeon Haloferax mediterranei has served as a good model for studying haloarchaeal physiology and metabolism for several decades because of its accelerated growth, remarkable metabolic ability and genomic stability （Han et al., 2012）. During stationary phase, H. mediterranei can produce halocin H4 （Cheung et al.,

Gene frequency of five genetic characteristics in six nationalities in Southern Guizhou Province,China

Five characteristics(hair forms,nasal profile,nostril forms,mongoloid fold and upper eyelid fold)were respectively investigated in six nationalities,including the Buyi,Miao,Shui,Maonan,Dong,and Han nationalities in Southern Guizhou,China.The gene frequencies of five characteristics in the six nationalities were estimated and compared.The results indicated that:(1)for hair forms and nasal profile,the frequency of the dominant gene was lower than that of their recessive gene,but the opposite was true for nostril forms.(2)Among different nationalities,the difference of gene frequency of the mongoloid fold,nasal profile,hair forms and upper eyelid fold was quite significant,which was followed by that of nostril forms.

Evaluation of Growth Performance of a Genetically Characterized F1 Rainbow Trout,Oncorhynchus mykiss in a Recirculating Aquaculture System

The growth performance of a selected F1 rainbow trout genetically characterized as polymorphic with locus Omy207UoG (NA = 13, PIC = 0.891, HE = 0.9003) was evaluated in a recirculating aquaculture system (RAS). A set of 157 rainbow trout of 37.8 g of mean body weight and 14.6 cm mean total length per tank, were introduced in each of six fish tank of 5 m3 connected to a recirculating aquaculture system (RAS). The trout was rearing during 317 days. Growth performance indicators and water quality were evaluated during the experiment. The genetically selected F1 rainbow trout showed a tendency towards homogeneity in growth performance along the culture period, reaching a mean total weight of 552.2 g. The length-weight relationship indicated an isometric growth (>3.0). This study presents the basis to establish a long-term marker-assisted selection program for rainbow trout culture in a subtropical region.

Analysis of seed and maternal genetic effects on cooking quality characters in indica hybrid rice

We analysed seed and maternal genetic effects on characters of cooking quality in indica hybrid rice by using the model for quantitative characters of seeds of cereal crops. Incomplete diallel crosses were made by using six male sterile lines (Zhenshan 97A, Erjiuqing A, Erjiunan 1A, V20A, Zhe’nan 1A and Zhe’nan 3A)as females and three restorer lines(Cezao 2-2, T49 and 26715)as males. Sampled seeds were used to measure the cooking quality characters, including amylose content(%), gelatinization temperature(alkali spreading score)and gel consistency(mm). Results indicated that some rice cooking quality characters were controlled by both seed genes and maternal genes (see table). Gel consistency was mainly controlled by maternal effects, but also

Study on Genetic Diversity among Soybean in Heilongjiang Province

Genetic characters of 10 soybean breeds in Heilongjiang Province were studied using RAPD technique. We calculated the genetic similarity and genetic distance, made the cluster analysis, and also studied the genetic relationship among the 10 breeds. We found 93 amplification segments by RAPE） analysis, in which there were 70 polymorphism segments, 75.26% of amplification segments, using 13 random primers, 11, 12, 5, 4, 7, 8, 3, 7, 2, 5, 10, 10, 9 amplificated bands were found. There were 7.15 bands per primer in average, The genetic similarity among the breeds ranged from 0.6848 to 0.9019, and the genetic distance ranged from 0.0981 to 0.3152. Genetic relationship between 90035 and 9674 was the closest, and between Heifeng 27 and 90035 was the farthest. Protein analysis revealed that the closest genetic relationship was between 90035 and 90024, and the farthest was between 1330 and Sui 4, and between 1330 and Heinong 39.

First detection of cutavirus DNA in stools of patients with rheumatic diseases in Guangzhou,China

Cutavirus(CuV)is a novel protoparvovirus possibly associated with diarrhea and cutaneous T-cell lymphomas.Patients with rheumatic disease are immunosuppressed and may be more vulnerable to pathogenic viruses.A descriptive study was conducted among hospitalized patients with rheumatic diseases and individuals undergoing medical health check-ups between June 2019 and June 2022 in Guangzhou,China.Stool samples of subjects were tested for CuV DNA.Demographic and fecal examination data of patients were obtained from electronic medical records.A total of 505 patients with rheumatic diseases and 244 individuals who underwent medical health check-ups were included in the study.Of the patients with rheumatic disease,5.74%[95%confidence interval(CI):4.03%–8.12%]were positive for CuV DNA,while no individual in the medical health check-up group was positive,indicating a close correlation between CuV and rheumatic disease.Men and patients with rheumatoid arthritis or ankylosing spondylitis,according to the disease classification,were more susceptible to being infected with CuV(P<0.01).After adjustments,being male remained the only significant factor,with an adjusted odd ratio(OR)of 4.4(95%CI:1.7–11.4,P=0.002).Phylogenetic analysis of the CuV VP2 sequences showed three diverse clades,one of which was segregated to be a single branching independent of previously known sequences,which is possible a new genotype.

Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China

Background:Avian influenza viruses have caused human infection and posed the pandemic potential.Live poultry markets are considered as a source of human infection with avian influenza viruses.Avian influenza routine surveillance of live poultry markets is taken annually in China.We isolated the 2 H11N9 influenza virus from the surveillance program.To better understand the risk caused by these new viruses,we characterize the genetic and pathogenicity of the two viruses.Methods:Viral isolation was conducted with specific pathogen-free(SPF)embryonated chicken eggs.Whole genome was sequenced,and phylogenetic analysis was conducted.Results:Two H11N9 viruses were identified,with all 8 segments belonging to the Eurasian lineage.The HA,NA,M,NS and PA genes were similar to virus isolates from ducks,and the NP,PB2 and PB1 gene segments were most similar to those viruses from wild birds,indicating that the H11N9 viruses might represent reassortant viruses from poultry and wild birds.The HA receptor binding preference was avian-like,and the cleavage site sequence of HA showed low pathogenic.The NA gene showed 94.6%identity with the novel H7N9 virus that emerged in 2013.There was no drug resistance mutation in the M2 protein.The Asn30Asp and Thr215Ala substitutions in the M1 protein implied a potentially increased pathogenicity in mice.Both viruses were low-pathogenic strains,as assessed by the standards of intravenous pathogenicity index(IVPI)tests.Conclusion:Two reassortant H11N9 avian influenza viruses were detected.These viruses showed low pathogenicity to chickens in the IVPI test.Public health concern caused by the reassortant H11N9 viruses should be emphasized during the future surveillance.