Paenibacillus hordei sp. nov., isolated from naked barley in Korea

A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24^T, was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24^T was observed at 4–40 °C (optimum: 35–37 °C) and at pH 5.0–9.0 (optimum: pH 6.0–7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G + C content: 53.5 mol %; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB_15:0 and CB_16:0B) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24^T belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24^T was most closely related to Paenibacillus hunanensis FeL05^T and Paenibacillus illinoisensis NRRL NRS-1356^T with similarities of 94.64 and 94.54 %, respectively. On the basis of phenotypic and molecular properties, strain RH-N24^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24^T (=KACC 15511^T = JCM 17570^T).     

Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles

DNA barcoding facilitates the identification of species and the estimation of biodiversity by using nucleotide sequences, usually from the mitochondrial genome. Most studies accomplish this task by using the gene encoding cytochrome oxidase subunit I (COI; Entrez COX1). Within this barcoding framework, many taxonomic initiatives exist, such as those specializing in fishes, birds, mammals, and fungi. Other efforts center on regions, such as the Arctic, or on other topics, such as health. DNA barcoding initiatives exist for all groups of vertebrates except for amphibians and nonavian reptiles. We announce the formation of Cold Code, the international initiative to DNA barcode all species of these ‘cold‐blooded’ vertebrates. The project has a Steering Committee, Coordinators, and a home page. To facilitate Cold Code, the Kunming Institute of Zoology, Chinese Academy of Sciences will sequence COI for the first 10 specimens of a species at no cost to the steward of the tissues.     

基因组分析揭示拟茎点霉XP-8产松脂醇及其糖苷等多种次级代谢产物的合成途径

【目的】通过解析拟茎点霉属XP-8的基因组序列信息,揭示该菌株潜在的代谢途径,并分析松脂醇及其糖苷化合物等次级代谢产物生物合成相关的关键基因。【方法】使用Illumina Hi Seq 2500高通量测序平台对拟茎点霉XP-8菌株进行全基因组测序,并通过不同软件对测序数据进行序列拼接,基因预测与功能注释。【结果】组装后的拟茎点霉XP-8基因组大小为55.2 Mb,GC含量53.5%,含有17094个蛋白编码基因和310个非编码基因。获得了松脂醇及其糖苷化合物等次级代谢产物生物合成相关的基因。系统发育分析揭示出拟茎点霉XP-8与5种子囊菌共有12635个同源基因和5626个基因家族。【结论】拟茎点霉XP-8具有用于合成松脂醇及其糖苷化合物等多种次级代谢物的基因组基础,为下一步的代谢工程改造提供依据。     

动物病原大肠杆菌K88的绿色荧光蛋白基因标记及其稳定性研究

成功地将gfp/luxAB双标记基因整合到K88染色体上,得到绿色荧光蛋白基因标记的大肠杆菌K88∶gfp/lux,其菌体和菌落形态与原始菌株K88完全一致,引入的新质粒不影响菌株的基本形态。从含gfp基因的质粒DNA和K88∶gfp/lux基因组DNA上均可扩增出大小约700 bp的gfp基因片段。大肠杆菌特异性基因检测结果表明,从大肠杆菌K88和K88∶gfp/lux基因组DNA上均扩增出大小约260 bp的大肠杆菌特异性基因片段,说明gfp基因标记后的菌株均为大肠杆菌。在相同的培养条件下,K88∶gfp/lux和K88的生长曲线的变化趋势基本相同。通过检测肠毒性基因(estA)发现,从大肠杆菌K88和K88∶gfp/lux基因组DNA上均扩增出大小约158 bp的肠毒性基因片段,说明gfp基因标记后的菌株在肠毒性方面未发生变化。在无选择压力条件下将K88∶gfp/lux菌株每隔12 h连续转接10次后,所有菌落均保持着均匀并且强烈的绿色荧光,说明标记基因在K88∶gfp/lux中的表达稳定性很高。K88∶gfp/lux和K88在中性偏酸性的环境中生长较好,当初始pH值偏碱性时,生长较差。     

Vaccine design of hemagglutinin glycoprotein against influenza

Influenza viruses continue to cause annual epidemics and pose the threat of a deadly global pandemic. Vaccination has remained the best approach for prevention and control of influenza infection. However, current influenza vaccines are only effective against closely-matched circulating strains, and therefore must be updated and administered every year. In this review, we discuss recent developments in the search for better influenza vaccines, especially using the major virus surface glycoprotein hemagglutinins (HAs). Understanding how glycans on HAs affect the immune response and knowledge of how broadly neutralizing antibodies are induced will pave the way for a cross-protective influenza vaccine that does not require frequent updates or annual immunizations.     

沈阳市大气微生物的研究Ⅲ．大气真菌粒子浓度及其分布

本研究用ＡＮＤＥＲＳＥＮ生物粒子采样器在沈阳市对大气真菌粒子浓度及其分布进行了一年的观测。结果表明,沈阳市大气真菌粒子年平均浓度为１７９７个／ｍ￣３。四季中,秋季大气真菌粒子浓度高,为２８５８个／ｍ３;春季低,为１０９４个／ｍ￣３。在不同地点中,造纸厂大气真菌粒子浓度明显高,为５７８０个／ｍ￣３。一天中的７：００,１９：００为大气真菌粒子浓度的高峰时,１３：００为低谷时。大气真菌粒子的浓度分布是单峰型,高峰在第３、４级,峰值为５３５个／ｍ￣３。造纸厂大气真菌粒子浓度分布的高峰在第５级,小粒子浓度比其余地点明显高。     

Identification and characterization of in vitro expanded hematopoietic stem cells

Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved > 200‐fold expansion of functional HSCs, but their molecular characterization has not been possible since the majority of cells are non‐HSCs and single cell‐initiated cultures have substantial clone‐to‐clone variability. Using the Fgd5 reporter mouse in combination with the EPCR surface marker, we report exclusive identification of HSCs from non‐HSCs in expansion cultures. By directly linking single‐clone functional transplantation data with single‐clone gene expression profiling, we show that the molecular profile of expanded HSCs is similar to proliferating fetal HSCs and reveals a gene expression signature, including Esam, Prdm16, Fstl1, and Palld, that can identify functional HSCs from multiple cellular states. This “repopulation signature” (RepopSig) also enriches for HSCs in human datasets. Together, these findings demonstrate the power of integrating functional and molecular datasets to better derive meaningful gene signatures and opens the opportunity for a wide range of functional screening and molecular experiments previously not possible due to limited HSC numbers.     

Intracellular antibody targeting HBx suppresses invasion and metastasis in hepatitis B virus‐related hepatocarcinogenesis via protein phosphatase 2A‐B56γ‐mediated dephosphorylation of protein kinase B

ObjectivesHepatitis B virus X (HBx) is closely associated with HBV‐related hepatocarcinogenesis via the inactivation of tumour suppressors. Protein phosphatase 2A (PP2A) regulatory subunit B56 gamma (B56γ), as a tumour suppressor, plays a critical role in regulating cellular phosphorylation signals via dephosphorylation of signalling proteins. However, the underlying mechanism that B56γ involved in regulating HBx‐associated hepatocarcinogenesis phenotypes and mediating anti‐HBx antibody‐mediated tumour suppression remains unknown.Materials and MethodsWe used bioinformatics analysis, paired HCC patient specimens, HBx transgenic (HBx‐Tg) mice, xenograft nude mice, HBV stable replication in the HepG2.2.15 cells, and anti‐HBx antibody intervention to systematically evaluate the biological function of protein kinase B (AKT) dephosphorylation through B56γ in HBx‐associated hepatocarcinogenesis.ResultsBioinformatics analysis revealed that AKT, matrix metalloproteinase 2 (MMP2), and MMP9 were markedly upregulated, while cell migration and viral carcinogenesis pathways were activated in HBV‐infected liver tissues and HBV‐associated HCC tissues. Our results demonstrated that HBx‐expression promotes AKT phosphorylation (p‐AKT^{Thr308/Ser473}), mediating the migration and invasion phenotypes in vivo and in vitro. Importantly, in clinical samples, HBx and B56γ were downregulated in HBV‐associated HCC tumour tissues compared with peritumor tissues. Moreover, intervention with site‐directed mutagenesis (AKT^T308A, AKT^S473A) of p‐AKT^{Thr308/Ser473} mimics dephosphorylation, genetics‐based B56γ overexpression, and intracellular anti‐HBx antibody inhibited cell growth, migration, and invasion in HBx‐expressing HCC cells.ConclusionsOur results demonstrated that B56γ inhibited HBV/HBx‐dependent hepatocarcinogenesis by regulating the dephosphorylation of p‐AKT^{Thr308/Ser473} in HCC cells. The intracellular anti‐HBx antibody and the activator of B56γ may provide a multipattern chemopreventive strategy against HBV‐related HCC.

Schematic diagram of PP2A‐B56γ mediated the dephosphorylation of p‐AKT^{Thr308/Ser473} in HBx‐expressing HCC cells to regulate the migration and invasion phenotypes of HBV/HBx‐related hepatocarcinogenesis. In current study, HBx‐expression induced the phosphorylation of specific AKT sites (p‐AKT^{Thr308/Ser473}) involved in mediating the migration and invasion phenotypes of HCC cells. The inducible upregulation of B56γ mediated the dephosphorylation of p‐AKT^{Thr308/Ser473} in HBx‐expressing HCC cells. Specific blockade of HBx‐expression via pTT5‐anti‐HBx plasmid‐mediated targeting intracellular anti‐HBx mAb production and genetic activation of B56γ would help to target the p‐AKT^{Thr308/Ser473}‐MMP2/9 signalling axis to mediate the multipattern chemoprevention and intervention in HBV/HBx‐related hepatocarcinogenesis.     

Integrated pathological analysis to develop a Gal-9 based immune survival stratification to predict the outcome of lung large cell neuroendocrine carcinoma and its usefulness in immunotherapy

This study aimed to integrate the cell spatial organization to develop a Gal-9-based immune survival stratification in the lung large cell neuroendocrine carcinoma (LCNEC) and investigate its potentials to immunotherapy.The expression of Gal-9 and other twelve immune markers were evaluated in 122 cases of surgical LCNEC samples from our center using immunohistochemistry. The Gal-9-based immune survival stratification risk score was constructed and its predictive performance was evaluated. Then, we thoroughly explored the effects of Gal-9 and immune risk score on LCNEC immune pathways, immune micro-environment and immunotherapy sensitivity in different cohort and platform, and made a validation in pathology images using Histology-based Digital-Staining (HDS).In 122 LCNEC samples, 43 cases were positive Gal-9 expression on tumor cells (Gal-9 TC). Increased Gal-9 TC predicted worse overall survival. Gal-9''s interaction with other immune markers added to the immune suppression and immune tolerance in LCNEC. Immune protein marker-based risk score consisting of Gal-9, CD3, CD4, PD-L1, and PD-1 was developed and validated to robustly discriminate survival high-risk or low-risk in LCNEC patients. The high-risk group characterized by immune-desert tumor had less various T cells. The low-risk group featuring immune-inflamed tumor was more likely to respond to anti-PD1 immunotherapy. HDS in 122 LCNEC samples'' 108,369 cells validated that the high-risk group had more tumor cells, less stromal cells, less lymphocytes, higher tumor cell nucleic solidity and lower stromal cells nucleic solidity.An integrated pathological analysis confirms the Gal-9 based immune survival stratification is distinctively related to micro-environment status involved in immune suppression and immune tolerance and could act as a combinatorial biomarker to predict the outcome of LCNEC. These findings may help effectively stratify LCNEC patients sensitive to immunotherapy.     

Morris water maze: a versatile and pertinent tool for assessing spatial learning and memory

Since its development about 40 years ago (1981–2021), Morris water maze has turned into a very popular tool for assessing spatial learning and memory. Its many advantages have ensured its pertinence to date. These include its effectiveness in evaluating hippocampal-dependent learning and memory, exemption from motivational differences across diverse experimental manipulations, reliability in various cross-species studies, and adaptability to many experimental conditions with various test protocols. Nonetheless, throughout its establishment, several experimental and analysis loopholes have galvanized researchers to assess ways in which it could be improved and adapted to fill this gap. Therefore, in this review, we briefly summarize these developments since the early years of its establishment through to the most recent advancements in computerized analysis, offering more comprehensive analysis paradigms. In addition, we discuss the adaptability of the Morris water maze across different test versions and analysis paradigms, providing suggestions with regard to the best paradigms for particular experimental conditions. Hence, the proper selection of the experimental protocols, analysis paradigms, and consideration of the assay’s limitations should be carefully considered. Given that appropriate measures are taken, with various adaptations made, the Morris water maze will likely remain a relevant tool to assess the mechanisms of spatial learning and memory.