动物中microRNA 的保守性和进化历程

microRNA 是一类长度约为22 个核苷酸的内源性非编码单链RNA, 在后生动物中普遍存在, 在转录后过程调控基因表达. miRNA 在个体发育过程中发挥着各种功能, 如发育时序调控和细胞分化、神经发育等. miRNA 在各种后生动物中具有保守性, 而且多个关键类群的出现皆伴随着大量新miRNA 的产生, 这些现象都表明miRNA 与动物的系统发生密切相关. 本文从miRNA 的产生和作用机制、在后生动物中的分布格局及其在个体发育中的调控功能3 个方面论述了miRNA 的保守性, 并结合miRNA 的发生和发展历程, 探讨了miRNA 在动物进化中起到的重要作用.     

Heparanase as a potential player in SARS-CoV-2 infection and induced coagulopathy

During the current formidable COVID-19 pandemic, it is appealing to address ideas that may invoke therapeutic interventions. Clotting disorders are well recognized in patients infected with severe acute respiratory syndrome (SARS) caused by a novel coronavirus (SARS-CoV-2), which lead to severe complications that worsen the prognosis in these subjects.Increasing evidence implicate Heparan sulfate proteoglycans (HSPGs) and Heparanase in various diseases and pathologies, including hypercoagulability states. Moreover, HSPGs and Heparanase are involved in several viral infections, in which they enhance cell entry and release of the viruses.Herein we discuss the molecular involvement of HSPGs and heparanase in SARS-CoV-2 infection, namely cell entry and release, and the accompanied coagulopathy complications, which assumedly could be blocked by heparanase inhibitors such as Heparin and Pixatimod.     

Conservation of miR-15a/16-1 and miR-15b/16-2 clusters

MiR-15a/16-1 and miR-15b/16-2 clusters have been shown to play very important roles in regulating cell proliferation and apoptosis by targeting cell cycle proteins and the antiapoptotic Bcl-2 gene. However, the physiological implications of those two clusters are largely elusive. By aligning the primary miR-15a/16-1 sequence among 44 vertebrates, we found that there was a gap in the homologous region of the rat genome. To verify that there was a similar miR-15a/16-1 cluster in rats, we amplified this region from rat genomic DNA using PCR and found that a 697-bp sequence was missing in the current rat genome database, which covers the miR-15a/16-1 cluster. Subsequently, we also investigated the expression pattern of individual miRNAs spliced from miR-15a/16-1 and miR-15b/16-2 clusters, including miR-15a, miR-15a*, miR-15b, miR-15b*, miR-16-1/2, and miR-16-1/2* from various rat tissues, and found that all of those miRNAs were expressed in the investigated tissues. MiR-16 was most expressed in the heart, followed by the brain, lung, kidney, and small intestine, which indicates tissue specificity for individual miRNA expression from both clusters. Our results demonstrated that both miR-15a/16-1 and miR-15b/16-2 clusters are highly conserved among mammalian species. The investigation of the biological functions of those two clusters using transgenic or knockout/knockdown models will provide new clues to understanding their implications in human diseases and finding a new approach for miRNA-based therapy.     

The Structural Conservation of S100 Protein During Evolution: Analysis by Reactivity with a Monoclonal Antibody

A hybridoma cell line producing a monoclonal antibody (A4) against bovine S100 protein has been produced by fusing mouse myeloma P3X63/Ag8 cells with spleen cells from a BALB/c mouse immunized with bovine S100 protein. A4 is of the IgG2b subclass and was purified by affinity chromatography on a protein A-Sepharose column. Brain extracts from several mammalian and one avian species reacted both with polyclonal rabbit anti-S100 protein antiserum and with A4 in a radioimmunoassay. Brain extract from dog was a notable exception. It reacted with the rabbit antiserum but not with A4. Therefore A4 reacts with a common epitope that is present on S100 proteins from different vertebrate species but is absent on dog S100 protein.     

冠状病毒的糖基化研究进展

冠状病毒(coronavirus)为一类具有囊膜结构、单股正链RNA病毒,可感染哺乳动物或禽类等.目前已知7种冠状病毒可造成人际间传播,其中以新型冠状病毒(Severe acute respiratory syndrome coronavirus-2,SARS-CoV-2)为代表,可引起严重的呼吸系统疾病,并感染全球数...     

猪2型圆环病毒ORF1与ORF2基因和伪狂犬病毒基因的重组与表达的研究

根据GenBank发布的猪2型圆环病毒(PCV2 )序列(AY0 35 82 0 ) ,设计两对特异性引物,采用PCR方法,分别扩增了猪2型圆环病毒ORF1和ORF2基因。将ORF1和ORF2基因的PCR产物回收并酶切后,依次插入到伪狂犬病毒gE gI双缺失通用转移载体pIECMV中,构建了猪2型圆环病毒_伪狂犬病毒重组中间转移质粒pIEORF1-ORF2。采用脂质体介导法,将重组中间转移质粒pIEORF1_ORF2与伪狂犬病毒TK^- gE^- LacZ⁺ 基因组共转染IBRS_2细胞,待发生细胞病变后收集病毒液进行空斑纯化,利用检测PCV2ORF1基因和ORF2基因的PCR方法筛选重组病毒TK^- gE^- gI^- ORF1-ORF2⁺ ,用Southernblotting鉴定重组病毒,并用Westernblotting检测ORF1_ORF2融合蛋白的表达情况,在此基础上也测定了重组病毒在不同细胞上的增殖滴度。结果表明,外源基因ORF1和ORF2已成功插入到TK^- gE^- LacZ⁺ 亲本株的基因组中,并获得了表达,表达的蛋白可与PCV2阳性血清发生反应。同时发现ORF1和ORF2基因的插入不影响重组病毒的增殖特性,其毒力与亲本株相当。     

The Human–Macaque Interface: Conservation Implications of Current and Future Overlap and Conflict in Lore Lindu National Park, Sulawesi, Indonesia

Here, I examine overlapping resource use of forest and cultivated resources by villagers and tonkean macaques (Macaca tonkeana) in Lore Lindu National Park, Sulawesi, Indonesia. An integrative research design was employed, using methods from primatology and cultural anthropology, in conjunction with quantitative measurements of cacao crop loss. The results indicate that the current patterns of overlapping resource use may not be severely affecting the tonkean macaques or villagers in Lindu. The research does, however, point to possible future difficulty if cacao crop raiding by macaques increases, and as changing socioeconomic trends and loss of traditional folklore result in further modification of macaque habitat. Successful strategies to ameliorate human–macaque conflict may require efforts aimed at the adoption of alternative buffer zone crops that use shade-management systems, the deliberate protection of important macaque food species, and increasing local tolerance to crop raiding by exploring the role of macaques in forest regeneration.     

Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions1

ABSTRACT. The field studying unusual mitochondria in microbial eukaryotes has come full circle. Some 10–15 years ago it had the evangelical task of informing the wider scientific community that not all eukaryotes had mitochondria. Advances in the field indicated that although some protists might not have mitochondria, the presence of genes of mitochondrial ancestry suggested their lineage once had. The subsequent discovery of mitochondrial compartments in all supposedly amitochondriate protists studied so far indicates that all eukaryotes do have mitochondria indeed. This assertion has fuelled novel eukaryotic origin theories and weakened others. But what do we know about these unusual mitochondria from anaerobic protists? Have they all converged onto similar roles? Iron–sulphur cluster assembly is often hailed as the unifying feature of these organelles. However, the iron–sulphur protein that is so important that a complete organelle is being maintained has not been identified. Is it to be expected that all unusual mitochondria perform the same physiological role? These organelles have been found in numerous protists occupying different ecological niches. Different selection pressures operate on different organisms so there is no reason to suspect that their mitochondria should all be the same.     

Conservation genetics of insular Podarcis lizards using partial cytochrome b sequences

Sequence data derived from a 306 bp fragment of mitochondrial cytochrome b and molecular variance estimates were used to investigate the genetic population structure of the endangered and endemic lizard Podarcis atrata of the Columbretes archipelago (Mediterranean, Spain). Our results show a very high and significant among-population genetic differentiation. F _ST values and phylogenetic analyses confirm the evolutionary distinctiveness of P. atrata populations, suggesting that the populations of these islands deserve special protection measures. The populations of the two islands Columbrete Grande and Mancolibre are less differentiated than those of Foradada and Lobo, and seem to have retained mainland haplotypes. This situation needs further attention as the origin of the mainland haplotypes is still unclear. If they are a result of recent introductions from mainland specimens, then they may represent a threat to the endemic lizards of the Columbretes islands.     

Conservation, Rearrangement, and Deletion of Gene Pairs During the Evolution of Four Grass Genomes

Gene order and content differ among homologous regions of closely related genomes. Similarities in the expression profiles of physically adjacent genes suggest that the proper functioning of these genes depends on maintaining a specific position relative to each other. To better understand the results of the interaction of these two genomic forces, convergent, divergent, and tandem gene pairs in rice and sorghum, as well as their homologs in rice, sorghum, maize, and Brachypodium were analyzed. The status of each pair in all four species: whether it was conserved, inverted, rearranged, or missing homologs was determined. We observed that divergent gene pairs had lower rates of conservation than convergent or tandem pairs, but higher rates of rearranged pairs and missing homologs in maize than in any other species. We also discovered species-specific gene pairs in rice and sorghum. In rice, gene pairs with strongly correlated expression levels were conserved significantly more often than those with little or no correlation. We assigned three types of gene pair to one of 14 possible evolutionary history categories to uncover their evolutionary dynamics during the evolution of grass genomes.     

保护行为学: 正在兴起的保护生物学分支学科

过去的30年里, 人们利用动物行为的进化生物学方法来解决保护实践中遇到的问题, 行为学、行为生态学与保护生物学相结合, 产生了保护生物学的一个新分支学科--保护行为学。保护行为学的研究目的是: 从物种保护实践中发现环境对动物行为的影响以及行为的生态适应性, 并把动物行为学和行为生态学理论应用到物种保护实践中, 从而促进物种保护工作。目前全球有10%的物种濒临灭绝, 生物多样性保护日趋紧迫, 保护行为学的诞生为行为学和保护生物学研究带来了新的机遇, 也表明行为学家和保护生物学家正在担负起挽救濒危物种的使命。不久的将来, 保护行为学及其相关学科将更加繁荣。     

HCV 1a／1b型嵌合体能在HepG2细胞内复制与表达

采用HCV 1a／1b嵌合体cDNA构建表达质粒转染HepG2细胞,以免疫组化和Westem blotting检测HCV蛋白表达,RT-PCR检测HCV正、负链RNA,研究丙型肝炎病毒(HCV) 1a和1b型嵌合体全长cDNA在HepG2细胞中的复制和表达。结果证明,转染细胞中检测到分子量约70kDa的HCV NS3蛋白,转染细胞连续传20代,仍能检测到HCV正、负链RNA。表明该HCV嵌合体可以在细胞中复制和表达,HCV1b型的RNA依赖的RNA聚合酶(RdRp)可以起始含1a型非编码区的病毒复制。HCV5′端非翻译区第11、12、13、34和35位核苷酸改变可不影响其与核糖体结合。3′非翻译区9400,9403和9407位核苷酸改变,9435位缺失“A”,9409,9410位及9495,9496,9497位分别插入“TT”和“AAT”可不影响RdRp的生物活性。本研究对阐明HCV复制和翻译机制有重要意义。     

Conservation and amyloid formation: a study of the gelsolin-like family

The mechanism through which globular proteins transform into amyloid fibrils is still not understood. Here we analyze the structure and sequence conservation to assess the differential stability of segments from two structurally related protein families: the amyloidogenic gelsolin-like and its structurally related cofilin-like. The two families belong to the actin depolymerizing proteins, with a central beta-sheet stacked between 2 and 4 alpha-helices. Although sequentially remote, the two families share regions of high and low conservation and stability. Our results show a highly conserved hydrophobic and aromatic cluster, located at a central buried beta-hairpin. The geometry of the aromatic residues with respect to each other is strictly conserved, suggesting involvement in strand registering and beta-sheet stabilization. Consistent with experiment, we find a region of weak conservation and stability at one of the exposed beta-strands (strand B in the gelsolin-like family). This region was recently found to be affected by a point mutation-mediated destabilization of the human gelsolin domain 2, which facilitates the first proteolytic event in the formation of the amyloidogenic fragment. Thus, both experimental and computational conservation analyses suggest that this unstable region may constitute a first step in amyloid formation. Our analysis uses a recently developed multiple-structure comparison algorithm in which molecules are aligned simultaneously.     

Selection of peptides interfering with a ribosomal frameshift in the human immunodeficiency virus type 1

The human immunodeficiency virus of type 1 (HIV-1) uses a programmed -1 ribosomal frameshift to produce the precursor of its enzymes, and changes in frameshift efficiency reduce replicative fitness of the virus. We used a fluorescent two-reporter system to screen for peptides that reduce HIV-1 frameshift in bacteria, knowing that the frameshift can be reproduced in Escherichia coli. Expression of one reporter, the green fluorescent protein (GFP), requires the HIV-1 frameshift, whereas the second reporter, the red fluorescent protein (RFP), is used to assess normal translation. A peptide library biased for RNA binding was inserted into the sequence of the protein thioredoxin and expressed in reporter-containing bacteria, which were then screened by fluorescence-activated cell sorting (FACS). We identified peptide sequences that reduce frameshift efficiency by over 50% without altering normal translation. The identified sequences are also active against different frameshift stimulatory signals, suggesting that they bind a target important for frameshifting in general, probably the ribosome. Successful transfer of active sequences to a different scaffold in a eukaryotic test system demonstrates that the anti-frameshift activity of the peptides is neither due to scaffold-dependent conformation nor effects of the scaffold protein itself on frameshifting. The method we describe identifies peptides that will provide useful tools to further study the mechanism of frameshift and may permit the development of lead compounds of therapeutic interest.     

人乳头瘤病毒6b型晚期蛋白L_2免疫反应表位的确定

人乳头瘤病毒（ＨＰＶ）含有２个晚期开放读码框（ＯＲＦ）,Ｌ＿２ＯＲＦ编码的蛋白具有型特异性。本研究用能表达产生完整ＨＰＶ６ｂＬ＿２蛋白的质粒ｐ６ｂＬ＿２ＮＸ,采取核酸外切酶Ⅲ定向连续次级克隆的方法,制备了一系列一端逐渐删切的ＤＮＡ片段,诱生一组从Ｃ端至Ｎ瑞依次减少的Ｌ＿２蛋白与相应血清作免疫印迹实验,最小的仍保持阳性反应的多肽即含有抗原表位,实验结果ＨＰＶ６ｂＬ＿２蛋白的核酸编码区位于５４８１－５５０６之间,其相应氨基酸序列是ＥＰＧＩＮＰＴＱ。     

Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential

ORF7a is an accessory protein common to SARS-CoV1 and the recently discovered SARS-CoV2, which is causing the COVID-19 pandemic. The ORF7a protein has a structural homology with ICAM-1 which binds to the T lymphocyte integrin receptor LFA-1. As COVID-19 has a strong immune component as part of the disease, we sought to determine whether SARS-CoV2 would have a similar structural interaction with LFA-1. Using molecular docking simulations, we found that SARS-CoV2 ORF7a has the key structural determinants required to bind LFA-1 but also the related leukocyte integrin Mac-1, which is also known to be expressed by macrophages. Our study shows that SARS-CoV2 ORF7a protein has a conserved Ig immunoglobulin-like fold containing an integrin binding site that provides a mechanistic hypothesis for SARS-CoV2’s interaction with the human immune system. This suggests that experimental investigation of ORF7a-mediated effects on immune cells such as T lymphocytes and macrophages (leukocytes) could help understand the disease further and develop effective treatments.     

The Evolutionary Rates of HCV Estimated with Subtype 1a and 1b Sequences over the ORF Length and in Different Genomic Regions

Background

Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance.

Methods/Results

176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10⁻³ substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure.

Conclusion

Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.     

Knowledge, Learning and the Evolution of Conservation Practice for Social-Ecological System Resilience

There are two broadly conceptualized ways in which conservation knowledge may evolve: the depletion crisis model and the ecological understanding model. The first one argues that developing conservation thought and practice depends on learning that resources are depletable. Such learning typically follows a resource crisis. The second mechanism emphasizes the development of conservation practices following the incremental elaboration of environmental knowledge by a group of people. These mechanisms may work together. Following a perturbation, a society can self-organize, learn and adapt. The self-organizing process, facilitated by knowledge development and learning, has the potential to increase the resilience (capability to absorb disturbance and reorganize while undergoing change) of resource use systems. Hence, conservation knowledge can develop through a combination of long-term ecological understanding and learning from crises and mistakes. It has survival value, as it increases the resilience of integrated social--ecological systems to deal with change in ways that continue to sustain both peoples and their environments.