放射敏感性启动子调控CD基因/5-FC自杀系统慢病毒载体的构建及125I诱导表达的研究

合成了含8个CArG元件的放射敏感性启动子E8,将其连接于胞嘧啶脱氨酶（Cytosine Deaminase, CD）基因及GFP报告基因上游,构建了重组慢病毒载体pGC-FU-E8-codA-GFP。与慢病毒包装系统共转染293T细胞包装重组慢病毒颗粒E8-codA-GFP LV,研究重组慢病毒感染EJ细胞在不同剂量¹²⁵I的电离辐射下绿色荧光表达情况及其将5-FC转化为5-FU的能力。结果显示：构建的含有E8启动子及CD基因的重组慢病毒载体,包装的重组慢病毒滴度为2×10⁸TU/mL;经¹²⁵I照射的重组慢病毒感染EJ细胞均可观察到绿色荧光,其细胞上清液均可检测到5-FC转化成的5-FU紫外峰,其中55.5 kBq及74.0 kBq ¹²⁵I照射的细胞组绿色荧光明显,148 kBq ¹²⁵I照射的细胞组,其5-FU紫外峰最为明显。以上结果表明：本工作所构建的放射敏感性启动子调控CD基因/5-FC自杀系统重组慢病毒载体具有电离辐射调控作用,可在¹²⁵I的电离辐射作用下诱导下游基因表达,为放射性核素¹²⁵I联合CD基因/5-FC自杀系统对肿瘤细胞的治疗作用研究提供了实验基础。     

腺病毒载体携带HSV1-TK报告基因感染BMSCs后摄取~(131)I-FIAU的实验研究

用内部核糖体进入序列(IRES)将报告基因单纯疱疹I型病毒胸苷激酶(HSV1-TK)和治疗基因脑源性神经营养因子(BDNF)连接,双启动子法将TK-IRES-BDNF与增强绿色荧光蛋白(EGFP)包装到重组腺病毒载体中,得到Ad5-TK-IRES-BDNF-EGFP,扩增、纯化、测定病毒滴度;以感染复数(MOI)为0、50、100、150、200、250感染体外培养的骨髓间充质干细胞(BMSCs),以重组腺病毒Ad5-EGFP为无效对照病毒。荧光显微镜下观察感染细胞的绿色荧光细胞阳性率。四甲基偶氮唑蓝(MTT)比色法检测感染细胞增殖能力。碱性成纤维细胞生长因子(bFGF)和表皮生长因子(EGF)诱导感染细胞向神经元细胞分化,显微镜下观察细胞形态变化。实时定量聚合酶链反应(RQ-PCR)和2-△△CT法分析两目的基因的相对表达量(CT)。观察感染细胞对131I-FIAU的摄取情况。重组腺病毒Ad5-TK-IRES-BDNF-EGFP在MOI为150可高效感染BMSCs,感染细胞存活率98%,且保持良好的神经元细胞诱导分化能力。RQ-PCR检测两目的基因随着腺病毒MOI增加表达增强,且TK和BNDF两基因的表达有良好的线性相关(r=0.973,P0.05,n=3)。在前3h可见感染目的基因组细胞对131I-FIAU的摄取程度与时间呈正相关,3h感染目的基因组对131I-FIAU摄取率可达(31.42±0.46)%(n=3),随后增加不明显。各点感染目的基因组摄取率均显著高于对照组(t=23.06–173.83,P0.05,n=3)。重组腺病毒载体能高效、低毒感染BMSCs,IRES介导两目的基因表达有良好的线性相关。本研究表明感染目的基因细胞可有效介导HSV1-TK摄取131I-FIAU,为后续放射性核素报告基因活体显像示踪转基因BMSCs治疗脑梗死提供了细胞水平依据。     

天山北坡绿洲乡村聚落空间基因解析及 影响机制研究

空间基因蕴含着聚落与环境互动形成的空间信息, 在空间特色传承上有着重要作用。由于新疆天山北坡地区聚落 在独特的自然环境中形成了互动演化的聚落空间形态,因此以 其为研究对象,通过卫星影像图和三维数据采集其中的12个 典型聚落样本,在从自然环境、空间片段形态、聚落形态、路 网形态和拓扑连接五方面提取空间基因的基础上,构建聚落 空间基因图谱,运用因子分析与聚类分析方法,对聚落进行分 类,阐释其背后蕴含的环境-空间互动影响模式,并提出保护 与改造建议,以期为不同地区乡村聚落空间基因研究提供借 鉴,为聚落类型划分、乡村特色保护与发展提供研究思路。     

内蒙古典型草原区传统村落景观基因 解析与特征研究

立足于“十四五”全面推进乡村振兴的时代背景,聚焦内蒙古典型草原区传统村落景观,以文化地理学“景观-基因”理论为基础,基于内蒙古典型草原区传统村落景观具有人工营建与草原环境相协调的核心价值,提出了“时间-空间-文化”三维耦合的景观基因识别、提取方法,解译出“逐水草居、农牧结合、聚散有致、内生植入、崇尚自然、天人合一、共融开放、热情豪迈”八大景观基因。从景观空间格局、景观过程、景观感知3个维度总结出内蒙古典型草原区传统村落的景观特征：景观空间格局的地域系统性、景观过程的历史演化性、景观感知的民族融合性。拓展了内蒙古典型草原区传统村落景观类型辨析和传承保护的理论视野,为内蒙古人居环境的可持续发展和乡村振兴提供科学的方法指导。     

Identification of a Maturation Plasma Cell Index through a Highly Sensitive Droplet Digital PCR Assay Gene Expression Signature Validation in Newly Diagnosed Multiple Myeloma Patients

DNA microarrays and RNA-based sequencing approaches are considered important discovery tools in clinical medicine. However, cross-platform reproducibility studies undertaken so far have highlighted that microarrays are not able to accurately measure gene expression, particularly when they are expressed at low levels. Here, we consider the employment of a digital PCR assay (ddPCR) to validate a gene signature previously identified by gene expression profile. This signature included ten Hedgehog (HH) pathways’ genes able to stratify multiple myeloma (MM) patients according to their self-renewal status. Results show that the designed assay is able to validate gene expression data, both in a retrospective as well as in a prospective cohort. In addition, the plasma cells’ differentiation status determined by ddPCR was further confirmed by other techniques, such as flow cytometry, allowing the identification of patients with immature plasma cells’ phenotype (i.e., expressing CD19+/CD81+ markers) upregulating HH genes, as compared to others, whose plasma cells lose the expression of these markers and were more differentiated. To our knowledge, this is the first technical report of gene expression data validation by ddPCR instead of classical qPCR. This approach permitted the identification of a Maturation Index through the integration of molecular and phenotypic data, able to possibly define upfront the differentiation status of MM patients that would be clinically relevant in the future.     

Systematic Review of Clinical and Pathophysiological Features of Genetic Creutzfeldt–Jakob Disease Caused by a Val-to-Ile Mutation at Codon 180 in the Prion Protein Gene

Genetic Creutzfeldt–Jakob disease (gCJD) is a subtype of genetic prion diseases (gPrDs) caused by the accumulation of mutated pathological prion proteins (PrP^Sc). gCJD has a phenotypic similarity with sporadic CJD (sCJD). In Japan, gCJD with a Val to Ile substitution at codon 180 (V180I-gCJD) is the most frequent gPrD, while the mutation is extremely rare in countries other than Japan and Korea. In this article, we aim to review previously elucidated clinical and biochemical features of V180I-gCJD, expecting to advance the understanding of this unique subtype in gCJD. Compared to classical sCJD, specific clinical features of V180I-gCJD include older age at onset, a relatively slow progression of dementia, and a lower positivity for developing myoclonus, cerebellar, pyramidal signs, and visual disturbance. Diffuse edematous ribboning hyperintensity of the cerebral cortex, without occipital lobes in diffusion-weighted magnetic resonance imaging, is also specific. Laboratory data reveal the low positivity of PrP^Sc in the cerebrospinal fluid and periodic sharp wave complexes on an electroencephalogram. Most patients with V180I-gCJD have been reported to have no family history, probably due to the older age at onset, and clinical and biochemical features indicate the specific phenotype associated with the prion protein gene mutation.     

hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer

Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.     

Genome-Wide Identification and Expression Analysis of Fatty Acid Desaturase (FAD) Genes in Camelina sativa (L.) Crantz

Camelina sativa (L.) Crantz is an indispensable oilseed crop, and its seeds contain many unsaturated fatty acids. FAD (fatty acid desaturase) regulates the synthesis of unsaturated fatty acids. In this research, we performed CsFAD gene family analysis and identified 24 CsFAD genes in Camelina, which were unevenly distributed on 14 of the 19 total chromosomes. Phylogenetic analysis showed that CsFAD includes four subfamilies, supported by the conserved structures and motifs of CsFAD genes. In addition, we investigated the expression patterns of the FAD family in the different tissues of Camelina. We found that CsFAD family genes were all expressed in the stem, and CsFAD2-2 was highly expressed in the early stage of seed development. Moreover, during low temperature (4 °C) stress, we identified that the expression level of CsFAD2-2 significantly changed. By observing the transient expression of CsFAD2-2 in Arabidopsis protoplasts, we found that CsFAD2-2 was located on the nucleus. Through the detection and analysis of fatty acids, we prove that CsFAD2-2 is involved in the synthesis of linolenic acid (C18:3). In conclusion, we identified CsFAD2-2 through the phylogenetic analysis of the CsFAD gene family and further determined the fatty acid content to find that CsFAD2-2 is involved in fatty acid synthesis in Camelina.     

Direct Cardiac Epigenetic Reprogramming through Codelivery of 5′Azacytidine and miR-133a Nanoformulation

Direct reprogramming of cardiac fibroblasts to induced cardiomyocytes (iCMs) is a promising approach to cardiac regeneration. However, the low yield of reprogrammed cells and the underlying epigenetic barriers limit its potential. Epigenetic control of gene regulation is a primary factor in maintaining cellular identities. For instance, DNA methylation controls cell differentiation in adults, establishing that epigenetic factors are crucial for sustaining altered gene expression patterns with subsequent rounds of cell division. This study attempts to demonstrate that 5′AZA and miR-133a encapsulated in PLGA-PEI nanocarriers induce direct epigenetic reprogramming of cardiac fibroblasts to cardiomyocyte-like cells. The results present a cardiomyocyte-like phenotype following seven days of the co-delivery of 5′AZA and miR-133a nanoformulation into human cardiac fibroblasts. Further evaluation of the global DNA methylation showed a decreased global 5-methylcytosine (5-medCyd) levels in the 5′AZA and 5′AZA/miR-133a treatment group compared to the untreated group and cells with void nanocarriers. These results suggest that the co-delivery of 5′AZA and miR-133a nanoformulation can induce the direct reprogramming of cardiac fibroblasts to cardiomyocyte-like cells in-vitro, in addition to demonstrating the influence of miR-133a and 5′AZA as epigenetic regulators in dictating cell fate.