A story: unpaired adenosine bases in ribosomal RNAs

In 1985 an analysis of the Escherichia coli 16 S rRNA covariation-based structure model revealed a strong bias for unpaired adenosines. The same analysis revealed that the majority of the G, C, and U bases were paired. These biases are (now) consistent with the high percentage of unpaired adenosine nucleotides in several structure motifs.An analysis of a larger set of bacterial comparative 16 S and 23 S rRNA structure models has substantiated this initial finding and revealed new biases in the distribution of adenosine nucleotides in loop regions. The majority of the adenosine nucleotides are unpaired, while the majority of the G, C, and U bases are paired in the covariation-based structure model. The unpaired adenosine nucleotides predominate in the middle and at the 3' end of loops, and are the second most frequent nucleotide type at the 5' end of loops (G is the most common nucleotide). There are additional biases for unpaired adenosine nucleotides at the 3' end of loops and adjacent to a G at the 5' end of the helix. The most prevalent consecutive nucleotides are GG, GA, AG, and AA. A total of 70 % of the GG sequences are within helices, while more than 70 % of the AA sequences are unpaired. Nearly 50 % of the GA sequences are unpaired, and approximately one-third of the AG sequences are within helices while another third are at the 3' loop.5' helix junction. Unpaired positions with an adenosine nucleotide in more than 50 % of the sequences at the 3' end of 16 S and 23 S rRNA loops were identified and arranged into the A-motif categories XAZ, AAZ, XAG, AAG, and AAG:U, where G or Z is paired, G:U is a base-pair, and X is not an A and Z is not a G in more than 50 % of the sequences. These sequence motifs were associated with several structural motifs, such as adenosine platforms, E and E-like loops, A:A and A:G pairings at the end of helices, G:A tandem base-pairs, GNRA tetraloop hairpins, and U-turns.     

肾细胞癌CD15和BCL—2的表达及临床意义

为了探讨评估肾细胞癌（RCC）预后指标,应用免疫组化法研究60例RCC中细胞粘附分子CD15和Bcl-2蛋白表达及其相关关系。结果表明,在RCC中CD15和Bcl-2表达阳性率分别为70.0%和61.7%。CD15高表达与RCC分级、分期和淋巴结转移有关。Bcl-2低表达与RCC分级有关,与其分期和淋巴结转移无关。CD15表达与Bcl-2表达呈负相关。结果提示,CD15表达是RCC发生、发展和转移的指标,Bcl-2是RCC发生的早期事件。     

Interleukin 4 and 13 participation in mycobacterial (type-1) and schistosomal (type-2) antigen-elicited pulmonary granuloma formation: multiparameter analysis of cellular recruitment, chemokine expression and cytokine networks

The contribution of IL-4 and IL-13 to inflammation and cytokine responses was compared in mice with types-1 or -2 pulmonary granulomas (GR) elicited by beads bound to antigens of Mycobacteria bovis (PPD) or Schistosoma mansoni eggs (SEA). Type-2 SEA-GR produced the most IL-4 and IL-13. Type-1 PPD-GR produced detectable IL-13, but not IL-4. Mice were treated with anti-IL4 or anti-IL-13 Abs, then lesion size/composition, cytokine/chemokine mRNA and lymph node cytokines were measured. Type-1 GRs resisted individual Abs, but combined Abs augmented lesions by 20%. In contrast, anti-IL-4 abrogated type-2 GR by 30-40% and eosinophil recruitment by 60%. Anti-IL-13 abrogated type-2 GR by 20-30% with no effect on eosinophils. Combined depletion reduced lesion area by 60% and eosinophils by more than 80%. In type-1 GR lungs, anti-IL-4 and anti-IL-13 augmented IFNgamma and TNFalpha mRNA. In type 2 lungs, anti-IL-13 did likewise, but anti-IL-4 decreased TNFalpha without affecting IFNgamma mRNA. In both responses, IL-4 promoted MCP-1 and MCP-5 mRNA, but IL-13 inhibited chemokines in type-1 GR. In lymph nodes, anti-IL-4, but not anti-IL-13, abrogated type-2 cytokines. In fact, IL-13 down-regulated itself and other type-2 cytokines. In summary, IL-4 and IL-13 have common and disparate regulatory functions in types 1 and 2 responses.     

桑萎缩病的类菌原体病原物及其超微病变特征

对感染桑萎缩病的桑叶及嫩梢进行超薄切片的电镜观察发现,其韧皮部组织,筛管及伴胞内有多型性类菌原体。菌体为圆形及椭圆形,大小约为50～160nm,双层膜,厚度约为8～10nm,内含物中具有核质样的纤维状物质,而在健株叶梢中未观察到任何病原体．随着病害的发展,可观察到细胞成份的降解。第一,在感病植株叶肉细胞内存在部分细胞核的降解、核膜破裂或核质流失甚至核仁分散消失。第二,叶绿体内有不同程度的淀粉粒和嗜锇颗粒累积,部分叶绿体外膜破裂,基质流失,基粒降解。第三,线粒体及粗面内质网在数量上有所增加,部分线粒体嵴已降解。     

棉田蜘蛛群落的组成及生态位分析

1997年对山西太谷棉田的蜘蛛群落进行了调查研究,共发现蜘蛛7科、17种、群落主要成分是星豹蛛和草间小黑蛛;对7种棉田主要蜘蛛的时间、空间及时空二维生态位进行了分析,结果表明星豹蛛和草间小黑蛛的时空二维生态位宽度值和重叠值均较大,说明这2种蜘蛛不但发生时间长,而且分布范围广,是棉田蜘蛛的优势种;根据生态位重叠值,利用模糊聚类法将7种棉田主要蜘蛛划分为4个类群。     

Analysis of expressed sequence tags from Chaetomium cupreum grown under conditions associated with mycoparasitism

Aims:  To elucidate the molecular mechanisms associated with mycoparasitism from Chaetomium cupreum , an effective biocontrol agent with ability against plant pathogenic fungi.
Methods and Results:  One cDNA library was constructed from conditions predicted to resemble mycoparasitic process. A total of 1876 ESTs were generated and assembled into 1035 unigenes. B last X search revealed that 585 unigenes had similarities with sequences available from public databases. Based on the ESTs abundance, MFS monosaccharide transporter was found as the gene expressed at the highest level. A KEGG analysis allowed mapping of 60 metabolic pathways well represented by the glycolysis/gluconeogenesis, d -arginine and ornithine metabolism, and tryptophan metabolism. The genes related to mycoparasitism were detected.
Conclusions:  The results revealed that the cell walls of the fungal pathogen can simulate some aspects of the mycoparasitic interaction between C. cupreum and its targets.
Significance and Impact of the Study:  This is the first report to study genes expression under conditions associated with the mycoparasitic process. The findings contribute to elucidate the molecular mechanisms involved in mycoparasitism and will help to advance our efforts in developing novel strategies for biocontrol of plant fungal diseases.     

Light inhibition of the conversion of 1-aminocyclopropane-1-carboxylic acid to ethylene in leaves is mediated through carbon dioxide

The mechanism of light-inhibited ethylene production in excised rice (Oryza sativa L.) and tobacco (Nicotiana tabacum L.) leaves was examined. In segments of rice leaves light substantially inhibited the endogenous ethylene production, but when CO₂ was added into the incubation flask, the rate of endogenous ethylene production in the light increased markedly, to a level which was even higher than that produced in the dark. Carbon dioxide, however, had no appreciable effect of leaf segments incubated in the dark. The endogenous level of 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, was not significantly affected by lightdark or CO₂ treatment, indicating that dark treatment or CO₂exerted its effect by promoting the conversion of ACC to ethylene. This conclusion was supported by the observations that the rate of conversion of exogenously applied ACC to ethylene was similarly inhibited by light, and this inhibition was relieved in the presence of CO₂. Similar results were obtained with tobacco leaf discs. The concentrations of CO₂ giving half-maximal activity was about 0.06%, which was only slightly above the ambient level of 0.03%. The modulation of ACC conversion to ethylene by CO₂ or light in detached leaves of both rice and tobacco was rapid and fully reversible, indicating that CO₂ regulates the activity, but not the synthesis, of the enzyme converting ACC to ethylene. Our results indicate that light inhibition of ethylene production in detached leaves is mediated through the internal level of CO₂, which directly modulates the activity of the enzyme converting ACC to ethylene.Abbreviation ACC 1-aminocyclopropane-1-carboxylic acid Recipient of a Republic of China National Science Council Fellowship     

Metabolism of α-aminoisobutyric acid in mungbean hypocotyls in relation to metabolism of 1-aminocyclopropane-1-carboxylic acid

1-Aminocyclopropane-1-carboxylic acid (ACC) is known to be converted to ethylene and conjugated into N-malonyl-ACC in plant tissues. When -amino[1-¹⁴C]isobutyric acid (AIB), a structural analog of ACC, was administered to mungbean (Vigna radiata L.) hypocotyl segments, it was metabolized to ¹⁴CO₂ and conjugated to N-malonyl-AIB (MAIB). -Aminoisobutyric acid inhibited the conversion of ACC to ethylene and also inhibited, to a lesser extent, N-malonylation of ACC and d-amino acids. Although the malonylation of AIB was strongly inhibited by ACC as well as by d-amino acids, the metabolism of AIB to CO₂ was inhibited only by ACC but not by d-amino acids. Inhibitors of ACC conversion to ethylene such as anaerobiosis, 2,4-dinitrophenol and Co²⁺, similarly inhibited the conversion of AIB to CO₂. These results indicate that the malonyalation of AIB to MAIB is intimately related to the malonylation of ACC and d-amino acids, whereas oxidative decarboxylation of AIB is related to the oxidative degradation of ACC to ethylene.Abbreviations ACC 1-aminocyclopropane-1-carboxylic acid - AIB -aminoisobutyric acid - MACC 1-(malonylamino)-cyclopropane-1-carboxylic acid - MAIB -(malonylamino)-isobutyric acid - Mes 2-(N-morpholino)ethanesulfonic acid     

Repressible Transgenic Sterilization in Channel Catfish, <Emphasis Type="Italic">Ictalurus punctatus</Emphasis>, by Knockdown of Primordial Germ Cell Genes with Copper-Sensitive Constructs

Repressible knockdown approaches were investigated to manipulate for transgenic sterilization in channel catfish, Ictalurus punctatus. Two primordial germ cell (PGC) marker genes, nanos and dead end, were targeted for knockdown and an off-target gene, vasa, was monitored. Two potentially copper-sensitive repressible promoters, yeast ctr3 (M) and ctr3-reduced (Mctr), were coupled with four knockdown strategies separately including: ds-sh RNA targeting the 5′ end (N1) or 3′ end (N2) of channel catfish nanos, full-length cDNA sequence of channel catfish nanos for overexpression (cDNA), and ds-sh RNA-targeting channel catfish dead end (DND). Each construct had an untreated group and treated group with copper sulfate as the repressor compound. Spawning rates of full-sibling P₁ fish exposed or not exposed to the constructs as treated and untreated embryos were 85 and 54%, respectively, indicating potential sterilization of fish and repression of the constructs. In F₁ fish, mRNA expressions of PGC marker genes for most constructs were downregulated in the untreated group and the knockdown was repressed in the treated group. Gonad development in transgenic, untreated F₁ channel catfish was reduced compared to non-transgenic fish for MctrN2, MN1, MN2, and MDND. For 3-year-old adults, gonad size in the transgenic untreated group was 93.4% smaller than the non-transgenic group for females and 92.3% for males. However, mean body weight of transgenic females (781.8 g) and males (883.8 g) was smaller than of non-transgenic counterparts (984.2 and 1254.3 g) at 3 years of age, a 25.8 and 41.9% difference for females and males, respectively. The results indicate that repressible transgenic sterilization is feasible for reproductive control of fish, but negative pleiotropic effects can result.