Genome‐wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1‐AIPP1‐EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin‐containing genes. However, the genome‐wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome‐wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin‐containing genes, including not only intronic heterochromatin‐containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin‐overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin‐containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.     

The Crystal Structure of L-Leucine Dehydrogenase from Pseudomonas aeruginosa

Leucine dehydrogenase (LDH, EC 1.4.1.9) catalyzes the reversible deamination of branched-chain L-amino acids to their corresponding keto acids using NAD⁺ as a cofactor. LDH generally adopts an octameric structure with D4 symmetry, generating a molecular mass of approximately 400 kDa. Here, the crystal structure of the LDH from Pseudomonas aeruginosa (Pa-LDH) was determined at 2.5 _Å resolution. Interestingly, the crystal structure shows that the enzyme exists as a dimer with C2 symmetry in a crystal lattice. The dimeric structure was also observed in solution using multiangle light scattering coupled with size-exclusion chromatography. The enzyme assay revealed that the specific activity was maximal at 60°C and pH 8.5. The kinetic parameters for three different amino acid and the cofactor (NAD⁺) were determined. The crystal structure represents that the subunit has more compact structure than homologs’ structure. In addition, the crystal structure along with sequence alignments indicates a set of non-conserved arginine residues which are important in stability. Subsequent mutation analysis for those residues revealed that the enzyme activity reduced to one third of the wild type. These results provide structural and biochemical insights for its future studies on its application for industrial purposes.     

Pericyte-derived extracellular vesicle-mimetic nanovesicles ameliorate erectile dysfunction via lipocalin 2 in diabetic mice

Diabetes mellitus is one of the main causes of erectile dysfunction (ED). Men with diabetic ED do not respond well to oral phosphodiesterase-5 inhibitors owing to neurovascular dysfunction. Pericyte-derived extracellular vesicle-mimetic nanovesicles (PC-NVs) are known to promote nerve regeneration in a mouse model of cavernous nerve injury. Here, we report that administration of PC-NVs effectively promoted penile angiogenesis and neural regeneration under diabetic conditions, thereby improving erectile function. Specifically, PC-NVs induced endothelial proliferation and migration and reduced cell apoptosis under diabetic conditions. In addition, PC-NVs induced neural regeneration in STZ-induced diabetic mice in dorsal root ganglion and major pelvic ganglion explants in vivo and ex vivo under high-glucose conditions. We found that lipocalin 2 (Lcn2) is a new target of PC-NVs in this process, demonstrating that PC-NVs exert their angiogenic and nerve-regeneration effects by activating MAP kinase and PI3K/Akt and suppressing P53 signaling pathway in an Lcn2-dependent manner. Our findings provide new conclusive evidence that PC-NVs can promote neurovascular regeneration and recovery of erectile function under diabetic conditions via an Lcn2-dependent mechanism. Thus, local administration of PC-NVs may be a promising treatment strategy for the treatment of diabetic ED.     

邻苯二甲酸对萝卜种子萌发、幼苗叶片膜脂过氧化及渗透调节物质的影响

华北地区是我国玉米的主产区,玉米秸秆还田不仅可有效改善土壤理化性状、提高土壤生物有效性,还会在腐解过程中释放出目前公认的化感物质——酚酸类物质,邻苯二甲酸是玉米秸秆腐解液中的主要酚酸类物质。从玉米秸秆还田过程中主要腐解产物(邻苯二甲酸)对蔬菜作物的化感效应角度进行了研究,为量化秸秆还田量及构建粮-菜轮作制度探寻化感效应依据。试验以萝卜为蔬菜材料,通过配置4个浓度(0.05、0.5、1.0、2.0 mmol/L)的邻苯二甲酸溶液,模拟玉米秸秆还田条件,以清水为对照,研究主要腐解产物邻苯二甲酸对萝卜种子萌发、幼苗生长、膜脂过氧化作用及渗透调节物质的影响。结果表明:(1)萝卜不同生育期对邻苯二甲酸化感效应的响应程度不同。在0.05-1 mmol/L浓度范围内,邻苯二甲酸处理促进了萝卜种子萌发,但随着处理浓度的增大,促进作用减弱;浓度达到2 mmol/L时对萝卜种子萌发具有抑制效果。(2)邻苯二甲酸0.05mmol/L处理,促进了萝卜幼苗干鲜物质积累,幼苗根系生长,其中根系长度和根系表面积分别比对照提高42.03%、38.36%,显著高于清水对照;植株体内超氧化物歧化酶(Superoxide dismutase, SOD)活性增大,过氧化物酶(Peroxidase, POD)、过氧化氢酶(Catalase, CAT)活性降低,膜脂过氧化产物丙二醛(Malonaldehyde, MDA)含量与对照无显著差异。(3)当邻苯二甲酸浓度超过0.5 mmol/L时,萝卜幼苗脂质过氧化伤害加剧,体内MDA含量急剧增加,代谢与生理功能出现紊乱,正常生长及干鲜物质积累受到显著抑制。邻苯二甲酸浓度达到2 mmol/L时,叶片数较对照降低了36.51%;根系长度、根系表面积及根尖数降幅分别为64.46%、40.20%、41.28%。(4)对于渗透调节物质的影响,邻苯二甲酸处理促进了萝卜幼苗叶片可溶性糖含量的增加,但随着处理浓度的升高其促进作用逐渐减弱;可溶性蛋白含量随着邻苯二甲酸处理浓度的升高表现出逐渐减少的趋势,分别较对照降低了12.82%、14.88%、21.58%、24.73%。因此,华北地区实施玉米-萝卜轮作模式,从化感效应角度研究玉米秸秆量化还田,应将土壤中邻苯二甲酸浓度控制在0.5 mmol/L范围以内,以防止邻苯二甲酸浓度过高对萝卜幼苗生长的抑制作用。     

Comparing Protein Expression in Erwinia amylovora Strain TS3128 Cultured under Three Sets of Environmental Conditions

Erwinia amylovora, the causal agent of fire-blight disease in apple and pear trees, was first isolated in South Korea in 2015. Although numerous studies, including omics analyses, have been conducted on other strains of E. amylovora, studies on South Korean isolates remain limited. In this study, we conducted a comparative proteomic analysis of the strain TS3128, cultured in three media representing different growth conditions. Proteins related to virulence, type III secretion system, and amylovoran production, were more abundant under minimal conditions than in rich conditions. Additionally, various proteins associated with energy production, carbohydrate metabolism, cell wall/membrane/envelope biogenesis, and ion uptake were identified under minimal conditions. The strain TS3128 expresses these proteins to survive in harsh environments. These findings contribute to understanding the cellular mechanisms driving its adaptations to different environmental conditions and provide proteome profiles as reference for future studies on the virulence and adaptation mechanisms of South Korean strains.     

Role of PCK2 in the proliferation of vascular smooth muscle cells in neointimal hyperplasia

Vascular smooth muscle cell (VSMC) proliferation is a hallmark of neointimal hyperplasia (NIH) in atherosclerosis and restenosis post-balloon angioplasty and stent insertion. Although numerous cytotoxic and cytostatic therapeutics have been developed to reduce NIH, it is improbable that a multifactorial disease can be successfully treated by focusing on a preconceived hypothesis. We, therefore, aimed to identify key molecules involved in NIH via a hypothesis-free approach. We analyzed four datasets ({"type":"entrez-geo","attrs":{"text":"GSE28829","term_id":"28829"}}GSE28829, {"type":"entrez-geo","attrs":{"text":"GSE43292","term_id":"43292"}}GSE43292, {"type":"entrez-geo","attrs":{"text":"GSE100927","term_id":"100927"}}GSE100927, and {"type":"entrez-geo","attrs":{"text":"GSE120521","term_id":"120521"}}GSE120521), evaluated differentially expressed genes (DEGs) in wire-injured femoral arteries of mice, and determined their association with VSMC proliferation in vitro. Moreover, we performed RNA sequencing on platelet-derived growth factor (PDGF)-stimulated human VSMCs (hVSMCs) post-phosphoenolpyruvate carboxykinase 2 (PCK2) knockdown and investigated pathways associated with PCK2. Finally, we assessed NIH formation in Pck2 knockout (KO) mice by wire injury and identified PCK2 expression in human femoral artery atheroma. Among six DEGs, only PCK2 and RGS1 showed identical expression patterns between wire-injured femoral arteries of mice and gene expression datasets. PDGF-induced VSMC proliferation was attenuated when hVSMCs were transfected with PCK2 siRNA. RNA sequencing of PCK2 siRNA-treated hVSMCs revealed the involvement of the Akt-FoxO-PCK2 pathway in VSMC proliferation via Akt2, Akt3, FoxO1, and FoxO3. Additionally, NIH was attenuated in the wire-injured femoral artery of Pck2-KO mice and PCK2 was expressed in human femoral atheroma. PCK2 regulates VSMC proliferation in response to vascular injury via the Akt-FoxO-PCK2 pathway. Targeting PCK2, a downstream signaling mediator of VSMC proliferation, may be a novel therapeutic approach to modulate VSMC proliferation in atherosclerosis.     

The small nonstructural protein NP1 of human bocavirus 1 directly interacts with Ku70 and RPA70 and facilitates viral DNA replication

Human bocavirus 1 (HBoV1), a member of the genus Bocaparvovirus of the family Parvoviridae, causes acute respiratory tract infections in young children. Well-differentiated pseudostratified human airway epithelium cultured at an air-liquid interface (HAE-ALI) is an ideal in vitro culture model to study HBoV1 infection. Unique to other parvoviruses, bocaparvoviruses express a small nonstructured protein NP1 of ~25 kDa from an open reading frame (ORF) in the center of the viral genome. NP1 plays an important role in viral DNA replication and pre-mRNA processing. In this study, we performed an affinity purification assay to identify HBoV1 NP1-inteacting proteins. We identified that Ku70 and RPA70 directly interact with the NP1 at a high binding affinity, characterized with an equilibrium dissociation constant (K_D) of 95 nM and 122 nM, respectively. Furthermore, we mapped the key NP1-interacting domains of Ku70 at aa266-439 and of RPA70 at aa181-422. Following a dominant negative strategy, we revealed that the interactions of Ku70 and RPA70 with NP1 play a significant role in HBoV1 DNA replication not only in an in vitro viral DNA replication assay but also in HBoV1-infected HAE-ALI cultures. Collectively, our study revealed a novel mechanism by which HBoV1 NP1 enhances viral DNA replication through its direct interactions with Ku70 and RPA70.     

三峡库区不同水文类型支流大型底栖动物对蓄水的响应

为探究三峡水库修建对库区不同水文类型支流大型底栖动物的影响,于2015年7月和2016年1月对三峡水库四条支流的大型底栖动物进行调研,分别对周期性受蓄水影响支流的非回水区与回水区和长期受蓄水影响支流的非回水区与回水区大型底栖动物群落结构进行比较研究,结果表明:⑴7月份三峡水库145米低水位时期共采集到底栖动物655头计59种(属),在受蓄水影响河段采集到底栖动物4种共40头,优势种为日本沼虾(占受蓄水影响区域的57.5%); 1月份三峡水库175米蓄水时期共采集到底栖动物1123头计69种(属),在受蓄水影响河段采集到16种238头,优势种为锯齿新米虾(占受蓄水影响区域的14.2%)。⑵周期性受蓄水影响支流的非回水区与回水区底栖动物密度、生物量和多样性指数无显著差异(P0.05);长期受蓄水影响支流的非回水区与回水区之间底栖动物密度和Pielou均匀度指数无显著差异(P0.05),但非回水区底栖动物生物量显著高于回水区(P0.05),底栖动物多样性和丰富度极显著高于回水区(P0.01)。⑶7月份影响底栖动物分布的主要环境因子共6个,分别是水深、流速、硝态氮、溶解氧、水温和电导率; 1月份影响底栖动物分布的主要环境因子共7个,分别是水温、溶解氧、总磷、流速、深度、电导率和透明度。     

基于mtDNA D-loop分析高原鳅群体遗传多样性和系统发育

本研究以高原鳅属6个群体共82尾个体的线粒体DNA D-loop高变区为标记,采用分子生物信息学方法分析其遗传多样性及系统发育关系.结果表明,在570 bp的mtDNA D-loop中共检测到149个多态位点,由此界定了 39个单倍型.在6个群体中,单倍型多样度(Hd)由高到低依次为细尾高原鳅(T.stenura)(0...