Persistence of the Recombinant Genomes of Woodchuck Hepatitis Virus in the Mouse Model

Hydrodynamic injection (HI) with a replication competent hepatitis B virus (HBV) genome may lead to transient or prolonged HBV replication in mice. However, the prolonged HBV persistence after HI depends on the specific backbone of the vector carrying HBV genome and the genetic background of the mouse strain. We asked whether a genetically closely related hepadnavirus, woodchuck hepatitis virus (WHV), may maintain the gene expression and replication in the mouse liver after HI. Interestingly, we found that HI of pBS-WHV1.3 containing a 1.3 fold overlength WHV genome in BALB/c mouse led to the long presence of WHV DNA and WHV proteins expression in the mouse liver. Thus, we asked whether WHV genome carrying foreign DNA sequences could maintain the long term gene expression and persistence. For this purpose, the coding region of HBV surface antigen (HBsAg) was inserted into the WHV genome to replace the corresponding region. Three recombinant WHV-HBV genomes were constructed with the replacement with HBsAg a-determinant, major HBsAg, and middle HBsAg. Serum HBsAg, viral DNA, hepatic WHV protein expression, and viral replication intermediates were detected in mice after HI with recombinant genomes. Similarly, the recombinant genomes could persist for a prolonged period of time up to 45 weeks in mice. WHV and recombinant WHV-HBV genomes did not trigger effective antibody and T-cell responses to viral proteins. The ability of recombinant WHV constructs to persist in mice is an interesting aspect for the future investigation and may be explored for in vivo gene transfer.     

非洲猪瘟病毒跨膜蛋白CD2v的结构与功能研究进展

非洲猪瘟(African swine fever,ASF)是由非洲猪瘟病毒(African swine fever virus,ASF V)感染家猪和野猪,引起的高度传染性和致死性动物传染病,不同品种和年龄阶段的猪均易感,发病率和死亡率可高达100％.ASFV是全球生猪产业的重点疫病之一,目前无商品化疫苗.ASFV是一种大而复杂的双链DNA双层囊膜病毒.ASFV主要跨膜蛋白CD2v是介导血细胞吸附(Hemadsorption,HAD)和鉴定病毒血清型的关键蛋白,它参与ASFV宿主免疫应答、免疫逃逸和病毒复制等生理生化过程,且是ASFV疫苗和抗病毒分子研发的潜在重要靶点.探究CD2v在ASFV感染中的作用及机制渐成热点.因此,本文对ASFV CD2v的结构及其生物学功能研究报道进行分析综述,将为阐明ASFV致病机理和疫苗研发等提供重要参考.     

LTR retrotransposons from the <Emphasis Type="Italic">Citrus x clementina</Emphasis> genome: characterization and application

Long terminal repeat retrotransposons (LTR-RTs) are a large portion of most plant genomes, and can be used as a powerful molecular marker system. The first citrus reference genome (Citrus x clementina) has been publicly available since 2011; however, previous studies in citrus have not utilized the whole genome for LTR-RT marker development. In this study, 3959 full-length LTR-RTs were identified in the C. x clementina genome using structure-based (LTR_FINDER) and homology-based (RepeatMasker) methods. LTR-RTs were first classified by protein domain into Gypsy and Copia superfamilies, and then clustered into 1074 families based on LTR sequence similarity. Three hundred fifty Copia families were grouped into four lineages: Retrofit, Tork, Sire, and Oryco. One hundred seventy-eight Gypsy families were sorted into six lineages: Athila, Tat, Renia, CRM, Galadriel, and Del. Most LTR-RTs (3218 or 81.3%) were anchored to the nine Clementine mandarin linkage groups, accounting for 9.74% of chromosomes currently assembled. Accessions of 25 Rutaceae species were genotyped using 17 inter-retrotransposon amplified polymorphism (IRAP) markers developed from conserved LTR regions. Sequence-specific amplified polymorphism (SSAP) makers were used to distinguish ‘Valencia’ and ‘Pineapple’ sweet oranges (C. x sinensis), and 24 sweet orange clones. LTR-RT markers developed from the Clementine genome can be transferred within the Rutaceae family demonstrating that they are an excellent tool for citrus and Rutaceae genetic analysis.     

Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China

Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we determined the structure of an SCC composite island (CI_SH32) found in the clinical Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CI_SH32 was 48 kb in length and mainly composed of two imperfect SCC elements, namely (i) a ΨSCCmec(SH32) part containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCC_SH32 part with a ccrA5B3 gene complex but lacking mec genes. In addition, CI_SH32 contained a type III restriction-modification system and several resistance loci, for example genes conferring resistance to cadmium and arsenic. ΨSCCmec(SH32) is almost entirely identical to a pseudo SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a ΨSCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S. haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCC_SH32 that are more similar to SCC_SH32 than those elements found in S. haemolyticus, suggesting that CI_SH32 of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite structure of CI_SH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has remained questionable.     

围栏封育对天山北坡草甸草原土壤呼吸的影响

对新疆天山北坡草甸草原围封9a的样地和围栏外的放牧样地进行比较,采用LI-8100土壤呼吸监测系统对草甸草原围栏内外土壤呼吸进行监测,分析围栏内外土壤呼吸的日变化、季节变化及其与环境因子的关系。结果表明:围栏内外土壤呼吸速率存在明显的日变化和月变化规律,均呈单峰曲线,且在植物生长季峰形比较明显,围栏内和围栏外土壤呼吸速率最高值出现在6月份17:00,分别为5.87、4.41μmol m~(-2)s~(-1),围栏内土壤呼吸速率比围栏外高出33.1%。最低值出现在10月份8:00,分别是0.26、0.29μmol m~(-2)s~(-1)。土壤CO_2日排放量与日均气温和地温的变化特征一致,与日均土壤含水量的变化特征相反,围栏内的土壤呼吸明显高于围栏外。土壤呼吸速率与气温和5 cm地温呈显著正相关,与其它深度的地温相关性不显著;与土壤湿度相关性不显著。     

From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits

Computational circuit design with desired functions in a living cell is a challenging task in synthetic biology. To achieve this task, numerous methods that either focus on small scale networks or use evolutionary algorithms have been developed. Here, we propose a two-step approach to facilitate the design of functional circuits. In the first step, the search space of possible topologies for target functions is reduced by reverse engineering using a Boolean network model. In the second step, continuous simulation is applied to evaluate the performance of these topologies. We demonstrate the usefulness of this method by designing an example biological function: the SOS response of E. coli. Our numerical results show that the desired function can be faithfully reproduced by candidate networks with different parameters and initial conditions. Possible circuits are ranked according to their robustness against perturbations in parameter and gene expressions. The biological network is among the candidate networks, yet novel designs can be generated. Our method provides a scalable way to design robust circuits that can achieve complex functions, and makes it possible to uncover design principles of biological networks.     

Prevalence and Associated Factors of Unprotected Anal Intercourse with Regular Male Sex Partners among HIV Negative Men Who Have Sex with Men in China: A Cross-Sectional Survey

The HIV prevalence and incidence among men who have sex with men (MSM) in China are high. Unprotected anal intercourse (UAI) with a regular male sex partner (RP), a significant predictor of HIV sero-conversion, was high yet under-emphasized among MSM having RP (MSMRP). The present cross-sectional survey interviewed 307 HIV negative MSMRP recruited through convenient sampling from multiple sources, including venue-based outreaching, online recruitment, and referrals made by peers, in Beijing and Chengdu, China. Among MSMRP, the prevalence of UAI with RP in the last three months was 52.4%. The results of the multivariate analysis showed that trust and intimacy within the relationship with RP and presence of clinical depression symptoms were positively associated with UAI with RP in the last three months. Other associated scalar factors derived from the Theory of Planned Behavior were related to perceptions on condom use, including positive attitudes toward condom use (a negative association), subjective norm of the perception that MSM do not usually use condoms during anal intercourse with RP (a positive association), perceived behavioral control over condom use with RP (a negative association), and behavioral intention to use condoms with RP in the coming three months (a negative association). It is seen that MSMRP were at high risk of HIV/STD transmission. The associated factors hence involved those related to perceptions about condom use, mental health, and interpersonal relationship. Future interventions should take these multi-dimensional factors into account. In particular, future research to test the efficacy of couple-based interventions that include mental health elements needs to be conducted, as trust and intimacy within the relationship were associated with UAI among MSMRP, and mental health problems may exist for both the MSMRP and their RP.     

民勤绿洲荒漠过渡带植物白刺和梭梭光合特性

研究了民勤绿洲荒漠过渡带两种优势植物白刺(Nitrariatangutorum)和梭梭(Haloxylonammodendron)气体交换特征参数和叶绿素荧光参数的日变化,结果表明:梭梭同化枝日均净光合速率(Pn)、蒸腾速率(E)、水分利用效率(WUE)和早晨PSII最大光化学效率(Fv/Fm)明显低于白刺叶片;同时它们在中午都呈现明显的光合“午休”现象。通过气孔限制值(Ls)、胞间二氧化碳浓度(Ci)和叶绿素荧光参数(Fv/Fm)变化趋势分析表明:梭梭同化枝净光合速率的下降在9:00~12:00主要是由于气孔关闭引起的,而在12:00~15:00主要是非气孔因素光抑制的影响;而白刺叶片光合速率的下降主要是气孔关闭引起的。同时,梭梭在一天中其同化枝的温度(Tleaf)高于大气温度尤其在中午差值更大,而白刺叶片的温度却低于大气温度,因此说明梭梭同化枝在中午不仅遭受着干旱和强光的胁迫而且面临严酷的高温胁迫。总之,在绿洲荒漠过渡带生境中白刺比梭梭具有更好的适应性,这可能是民勤绿洲荒漠过渡带人工梭梭林衰退的重要原因之一。     

Histidine kinase two-component response regulator proteins regulate reproductive development, virulence, and stress responses of the fungal cereal pathogens Cochliobolus heterostrophus and Gibberella zeae

Histidine kinase (HK) phosphorelay signaling is a major mechanism by which fungi sense their environment. The maize pathogen Cochliobolus heterostrophus has 21 HK genes, 4 candidate response regulator (RR) genes (SSK1, SKN7, RIM15, REC1), and 1 gene (HPT1) encoding a histidine phosphotransfer domain protein. Because most HKs are expected to signal through RRs, these were chosen for deletion. Except for pigment and slight growth alterations for rim15 mutants, no measurable altered phenotypes were detected in rim15 or rec1 mutants. Ssk1p is required for virulence and affects fertility and proper timing of sexual development of heterothallic C. heterostrophus. Pseudothecia from crosses involving ssk1 mutants ooze masses of single ascospores, and tetrads cannot be found. Wild-type pseudothecia do not ooze. Ssk1p represses asexual spore proliferation during the sexual phase, and lack of it dampens asexual spore proliferation during vegetative growth, compared to that of the wild type. ssk1 mutants are heavily pigmented. Mutants lacking Skn7p do not display any of the above phenotypes; however, both ssk1 and skn7 mutants are hypersensitive to oxidative and osmotic stresses and ssk1 skn7 mutants are more exaggerated in their spore-type balance phenotype and more sensitive to stress than single mutants. ssk1 mutant phenotypes largely overlap hog1 mutant phenotypes, and in both types of mutant, the Hog1 target gene, MST1, is not induced. ssk1 and hog1 mutants were examined in the homothallic cereal pathogen Gibberella zeae, and pathogenic and reproductive phases of development regulated by Ssk1 and Hog1 were found to mirror, but also vary from, those of C. heterostrophus.     

Synthesis of carbamate-linked lipids for gene delivery

Series of lipids 1a-d and 2a,b, with carbamate linkages between hydrocarbon chains and ammonium or tertiary amine head, which were pH sensitive, were synthesized for liposome-mediated gene delivery. The variable length of carbon chains and quaternary ammonium or neutral tertiary amine heads allowed to find the structure-function relationship of how these factors affect cationic lipids on gene delivery performance.