Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea

Archeal proteomes can be clustered into two groups based on their cysteine content. One group of proteomes displays a low cysteine content ( approximately 0.7% of the entire proteome), whereas the second group contains twice as many cysteines as the first ( approximately 1.3%). All cysteine-rich organisms belong to the methanogenic Archaea, which generates special cysteine clusters associated with primitive metabolic reactions. Our findings suggest that cysteine plays an important role in early forms of life.     

Distance-Decay and Taxa-Area Relationships for Bacteria,Archaea and Methanogenic Archaea in a Tropical Lake Sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.     

河西走廊植物群落特征及其与气候的关系初探

对河西走廊荒漠植物的群落类型、盖度、密度、重要值、地上生物量等进行了调查,收集整理各区域的气候资料,对它们的关系进行了初步研究。结果显示:(1)物种种类组成、总密度与海拔、经度呈正相关,与纬度呈负相关,在走廊的东南→西北方向上呈递减趋势。(2)在活动积温(>10℃)>3 200℃的荒漠地区,灌木(包括半灌木)在群落中占有绝对优势,其重要值可达到100;当活动积温在3 000℃左右时,群落往往是一些过渡类型,或以草本为优势种、以半灌木或灌木为伴生种,或以半灌木为优势种、以多年生草本为伴生种。(3)在年降水量110 mm以上的荒漠地区,植物群落生活型主要为半灌木或多年生草本;在年降水量110 mm以下的地区,生活型主要为小灌木或一年生草本;在年降水量小于50 mm的极端干旱地区,只有在雨季时有一年生草本生长。表明荒漠生态系统植被稀疏,生物量小,对气候因子,特别是降水变化敏感,对其保育显得尤为重要。     

Presence of Rhapidosomes in Various Species of Bacteria and Their Morphological Characteristics

Rod-shaped structures have been observed in cells of Pseudomonas, Photobacterium, Proteus, and Saprospira by use of the negative-contrast stain. These structures, referred to as rhapidosomes, appear to be normal components of these cells. Other bacteria including Escherichia, Salmonella, Shigella, Klebsiella, Micrococcus, Bacillus, Mycobacterium, Rhodospirillum, and Hydrogenomonas genera failed to reveal these structures. The rhapidosomes of Saprospira were found to consist of two rods, one encasing a narrower, longer structure. In contrast, the rhapidosomes of Pseudomonas, Proteus, and Photobacterium were without the rigid inner structure, but were occasionally seen filled with a homogeneous material as observed by the negative stain. Ultrathin sections of Pseudomonas cells indicate that these rhapidosomes are embedded within or are in close association with the nucleoplasm.     

环状RNA的结构和功能特性及其与胃癌发生的关系

环状RNA是一类新发现以共价键形成环状结构的RNA分子,没有5'帽和3'尾,具有高度的序列保守性和稳定性,不易被核酸外切酶降解,在转录或转录后水平发挥基因表达调控的作用。近年来,已发现环状RNA与许多肿瘤包括胃癌发生密切相关。首先介绍环状RNA形成、分类、分子特征和功能,然后从环状RNA与胃癌发生、环状RNA与胃癌诊断、以及环状RNA在胃癌治疗中的作用等三个方面阐述环状RNA与胃癌的关系。     

水稻剑叶部分形态生理特性QTL分析以及它们与产量、产量性状的关系

光合产物是水稻产量的主要来源,因此对水稻后期功能叶片尤其是剑叶形态生理性状的遗传分析对水稻高产育种很重要。利用来源于籼／粳交后代的重组自交系群体为材料对水稻剑叶形态（叶片长、宽、面积）和生理性状（叶绿度、持绿性）进行了QTL定位,并对这些性状与产量、产量性状的相关性进行了分析。两年分别定位了17、6和14个与剑叶形态性状、叶绿度和持绿性有关的QTL,其中10个QTL在两年中共同检测到。相关分析表明,较大的剑叶可以增加穗粒数并显著增加产量,然而叶绿度和持绿性与产量、产量性状无关或呈显著负相关。叶绿度与剑叶大小呈显著负相关以及籼／粳交群体后代半不育是叶绿度和持绿性与产量、产量性状无关或呈显著负相关的可能原因。染色体4上的RM255-RM349区域同时控制3个剑叶形态性状并且解释的变异也较大,该区域可用于遗传改良以提高水稻产量。染色体3上的RM422-RM565区域重叠了3个与持绿性有关的QTL,它们对产量的贡献有待于通过构建近等基因系进行深入研究。     

QTL Analysis for Flag Leaf Characteristics and Their Relationships with Yield and Yield Traits in Rice

Photosynthesis of carbohydrate is the primary source of grain yield in rice (Oryza sativa L.). It is important to genetically analyze the morphological and the physiological characteristics of functional leaves, especially flag leaf, in rice improvement. In this study, a recombinant inbred population derived from a cross between an indica (O. sativa L. ssp. indica) cultivar and a japonica (O. sativa L. ssp. japonica) cultivar was employed to map quantitative traits loci (QTLs) for the morphological (i.e., leaf length, width, and area) and physiological (i.e., leaf color rating and stay-green) characteristics of flag leaf and their relationships with yield and yield traits in 2003 and 2004. A total of 17 QTLs for morphological traits (flag leaf length, width, and area), 6 QTLs for degree of greenness and 14 QTLs for stay-green-related traits (retention-degrees of greenness, relative retention of greenness, and retention of the green area) were resolved, and 10 QTLs were commonly detected in both the years. Correlation analysis revealed that flag leaf area increased grain yield by increasing spikelet number per panicle. However, the physiological traits including degree of greenness and stay-green traits were not or negatively correlated to grain yield and yield traits, which may arise from the negative relation between degree of greenness and flag leaf size and the partial sterility occurred in a fraction of the lines in this population. The region RM255-RM349 on chromosome 4 controlled the three leaf morphological traits simultaneously and explained a large part of variation, which was very useful for genetic improvement of grain yield. The region RM422-RM565 on chromosome 3 was associated with the three stay-green traits simultaneously, and the use of this region in genetic improvement of grain yield needs to be assessed by constructing near-isogenic lines.     

Soil Infiltration Characteristics in Agroforestry Systems and Their Relationships with the Temporal Distribution of Rainfall on the Loess Plateau in China

Many previous studies have shown that land use patterns are the main factors influencing soil infiltration. Thus, increasing soil infiltration and reducing runoff are crucial for soil and water conservation, especially in semi-arid environments. To explore the effects of agroforestry systems on soil infiltration and associated properties in a semi-arid area of the Loess Plateau in China, we compared three plant systems: a walnut (Juglans regia) monoculture system (JRMS), a wheat (Triticum aestivum) monoculture system (TAMS), and a walnut-wheat alley cropping system (JTACS) over a period of 11 years. Our results showed that the JTACS facilitated infiltration, and its infiltration rate temporal distribution showed a stronger relationship coupled with the rainfall temporal distribution compared with the two monoculture systems during the growing season. However, the effect of JTACS on the infiltration capacity was only significant in shallow soil layer, i.e., the 0–40 cm soil depth. Within JTACS, the speed of the wetting front’s downward movement was significantly faster than that in the two monoculture systems when the amount of rainfall and its intensity were higher. The soil infiltration rate was improved, and the two peaks of soil infiltration rate temporal distribution and the rainfall temporal distribution coupled in rainy season in the alley cropping system, which has an important significance in soil and water conservation. The results of this empirical study provide new insights into the sustainability of agroforestry, which may help farmers select rational planting patterns in this region, as well as other regions with similar climatic and environmental characteristics throughout the world.     

The Spermatozoon in Tardigrades: Evolution and Relationships with the Environment

The spermatozoon ultrastructure of seven species of tardigrades, one heterotardigrade echiniscid and six eutardigrades, was analysed and described. Tardigrade species were collected from freshwater sediments, moss and leaf litter. Aphylogenetic evaluation was made and relationships of spermatozoon shape and habitat were discussed. The spermatozoon morphology of the moss-dwelling echiniscid(heterotardigrade) was very similar to that found in marine species of the same order. This indicates that in Echiniscoididae change of habitat had little influence on sperm structural organisation. In contrast, eutardigrade spermatozoa have developed several different structural organisations that may be related to family and/or habitat.     

国产画眉草亚族叶表皮微形态特征及其在属间关系上的意义

通过国产画眉草亚族叶片表皮的解剖观察,结合外部形态,对该亚族内6个属的属间关系进行了分析。结果表明：羽穗草属应是国产画眉草亚族中最原始的类群,最高级的类群仍数细画眉草属,而其余4属即画眉草属、弯穗草属、尖稃草属和镰稃草属的演化水平居于两者之间;画眉草属和弯穗草属可能直接起源于原始的羽穗草属,而较高级的尖稃草属和镰稃草属又可能直接起源于较原始的画眉草属,并在镰稃草属的基础上进而派生了最进化的细画眉草属。整个研究结果既弥补了前人演化理论的不足,又为今后族进化的全面探讨提供了参考。     

Toxic-Metabolite-Producing Bacteria and Fungus in an Indoor Environment

Toxic-metabolite-emitting microbes were isolated from the indoor environment of a building where the occupant was suffering serious building-related ill-health symptoms. Toxic substances soluble in methanol and inhibitory to spermatozoa at <10 μg (dry weight) ml⁻¹ were found from six bacterial isolates and one fungus. The substances from isolates of Bacillus simplex and from isolates belonging to the actinobacterial genera Streptomyces and Nocardiopsis were mitochondriotoxic. These substances dissipated the mitochondrial membrane potential (Δψ) of boar spermatozoa. The substances from the Streptomyces isolates also swelled the mitochondria. The substances from isolates of Trichoderma harzianum Rifai and Bacillus pumilus damaged the cell membrane barrier function of sperm cells.     

裸盖菇属的真菌鉴定及分子系统学初探

裸盖菇属(Psilocybe)的许多真菌含有神经致幻型毒素,这些毒素被中国卫生部列为A类管制药品。在药检时,这些真菌样品通常是粉末。因此,仅依靠形态分类鉴定该类真菌非常困难。研究采用ITS序列分析的方法鉴定该类真菌并初步探讨了该属种间的系统发育关系。由系统发育树推断Psilocybe属可能是多源进化的。通过序列分析可以鉴定真菌样品为Psilocybe属。     

古核生物ABC转运体系的重构及其基因组比较

代谢途径和调控网络的重建和比较研究是基因组功能预测的高级内容。运用多种生物信息学工具在基因组水平上重构了古核生物深海热球菌（Ｐｙｒｃｏｃｃｕｓ ａｂｙｓｓｉ）的ＡＢＣ（ＡＴＰ－ｂｉｎｄｉｎｇ ｃａｓｓｅｔｔｅ）转运体系,预测了它们的功能特性;并与另一古核生物詹氏甲烷球菌（Ｍ．ｊａｎｎａｓｃｈｉｉ）的对应体系作了进化比较,发现Ｍ．ｊａｎｎａｓｃｈｉｉ缺少负责短肽摄入的ＡＢＣ转运体系,推测与二者分属不     

Prevalence and Impact of Bacteriophages on the Presence of Escherichia coli O157:H7 in Feedlot Cattle and Their Environment

The relationship between endemic bacteriophages infecting E. coli O157:H7 (referred to as “phage”) and levels of shedding of E. coli O157:H7 by cattle was investigated in two commercial feedlots in southern Alberta, Canada. Between May and November 2007, 10 pens of cattle were monitored by collection of pooled fecal pats, water with sediment from troughs, manure slurry from the pen floor, and rectal fecal samples from individual animals (20 per pen) at two separate times. Bacteriophages infecting E. coli O157:H7 were detected more frequently (P < 0.001) after 18 to 20 h enrichment than by initial screening and were recovered in 239 of 855 samples (26.5% of 411 pooled fecal pats, 23.8% of 320 fecal grab samples, 21.8% of 87 water trough samples, and 94.6% of 37 pen floor slurry samples). Overall, prevalence of phage was highest (P < 0.001) in slurry. Recovery of phage from pooled fecal pats was highest (P < 0.05) in May. Overall recovery did not differ (P > 0.10) between fecal grab samples and pooled fecal pats. A higher prevalence of phage in fecal pats or water trough samples was associated (P < 0.01) with reduced prevalence of E. coli O157:H7 in rectal fecal samples. There was a weak but significant negative correlation between isolation of phage and E. coli O157:H7 in fecal grab samples (r = −0.11; P < 0.05). These data demonstrate that the prevalence of phage fluctuates in a manner similar to that described for E. coli O157:H7. Phage were more prevalent in manure slurry than other environmental sources. The likelihood of fecal shedding of E. coli O157:H7 was reduced if cattle in the pen harbored phage.Bacteriophages are the most abundant biological entities on earth. An estimated 10³⁰ marine bacteriophages are harbored in the ocean, and they significantly influence microbial communities and function (27). As resistance is an increasing challenge in antimicrobial therapy, the antimicrobial nature of bacteriophages is being more intensively studied (13, 15). Bacteriophages naturally inhabit the mammalian gastrointestinal tract (1, 8), and Escherichia coli-infecting bacteriophages are commonly isolated from sewage, hospital wastewater, and fecal samples from humans and animals (3). Ruminants have been shown to shed up to 10⁷ bacteriophage per gram of feces (6), and in humans multiple types of bacteriophage exhibiting activity against E. coli have been isolated from a single fecal sample (7).E. coli O157:H7 is an important zoonotic bacterium carried asymptomatically by cattle and readily isolated from manure, manure slurry, and drinking water in dairies and feedlots (11, 24, 30). Additionally, E. coli O157:H7 shedding by cattle has a seasonal pattern, peaking in the summer months (2, 25). Bacteriophage strains that infect E. coli O157:H7 have also been isolated from animal feces and have shown lytic activity against this bacterium in vivo and in vitro (5, 23, 28, 31). In recent studies, such phages were shown to be widely distributed in cattle and in feces on the pen floor within feedlots (4, 18). However, the relationships between the presence of E. coli O157:H7-infecting bacteriophage in cattle and their environment and the shedding of this bacterium by cattle are largely undefined. Consequently, the aims of the present study were (i) to determine the prevalence of endemic E. coli O157:H7-infecting bacteriophage (referred to as “phage”) in feedlots over a 7-month period and (ii) to compare the presence of phage to the occurrence of E. coli O157:H7 in cattle and their environment.     

叶际微生物及其与外界互作的研究进展

叶际微生物及其生存环境共同形成了一个复杂的生态系统。建立在纯种分离和纯培养技术基础之上的传统研究方法只能了解其中部分叶际微生物,但对物种组成、种群结构和生态学作用等方面的认识都比较片面。近年来随着分子生物学和生物信息学的进步,人们对叶际微生物总群落的分析逐渐揭示了叶际微生物组成的多样性及其特点,以及与外界互相作用的复杂性。研究表明,植物种类、地理位置和季节差异等都不同程度地影响着叶际微生物群落的构成。本文综述了近年来国内外叶际微生物群落结构组成及其与外界互作方面的研究进展,有利于加深对叶际微生物的了解,也有助于深入理解叶际微生物与植物生长和植物病虫害防治的关联关系。     

上海农耕区鸟类群落特征及与几种生境因子的关系

2000-2002年冬季和夏季,采用固定样带法在上海郊区所有区县选择了17条样带,对农耕区鸟类做了4次抽样调查。记录了鸟类的组成、数量、出现频率及生境因子特征。根据调查数据,计算鸟类密度、多样性、均匀度、优势度、生物量、相对重要值等群落特征参数。调查共记录到鸟类76种,隶属13目26科。平均密度为5．19只／hm^2,多样性指数为1．8742。优势种为麻雀、家燕、白头鹎、棕背伯劳和白鹊鸰。鸟类组成中水鸟(夜鹭、白鹭等)较多,占了总数的1／3;与上海其他区域相比,鸟类密度较高,但种类相对较少,数量集中在少数几个物种(麻雀、家燕、白头鹎、棕背伯劳等)。鸟类物种丰富度与荒地面积呈显著正相关,与环境污染程度呈显著负相关,与林地面积、人口密度、水体面积等相关不显著。提示荒地对鸟类多样性非常重要。     

Root Pressure of Tropical Lianas and Their Relationships with Phylogeny and Environments

Lianas usually possess large vessels, which are vulnerable to cavitation. Root pressure may play an important role in embolism repair of vessels. However, little is known about the generality of root pressure in tropical lianas. To characterize root pressure of lianas in tropical rainforests, we used pressure transducers to measure root pressure in the rainy and dry seasons for a total of 32 lianas from 14 families common in Xishuangbanna. We further analyzed the associations of maximum root pressure with phylogeny and of transient root pressure with environmental factors. We found that all lianas we selected had root pressure, with maximum root pressure ranging from 2-138kPa. In the dry season, about 72% (23 species) of the lianas had relatively low root pressure (<15kPa) and maintained positive throughout the day. This may be important for water balance for roots and basal stems of lianas. There were three types of diurnal changes in liana root pressure. In Type I, root pressure had obvious diurnal variation in the dry and rainy seasons. In Type II, root pressure did not show obvious diurnal variation in the dry and rainy seasons. In Type III, either in the dry or in the rainy season, root pressure showed obvious diurnal variation. Root pressure varied substantially among lianas, with lianas from two families, Fabaceae and Vitaceae, usually having relatively higher root pressure, suggesting that phylogeny may influence root pressure. Transient root pressure closely responded to photosynthetically active radiation. In most cases, however, it was not related to rainfall and vapour pressure deficit. These results suggest that the associations of liana root pressure with environments need further investigation.     

Hemocyanins Relationships in Their Structure, Function and Assembly

Hemocyanins are high molecular weight oxygen-carrying proteinsthat occur in the molluscs and arthropods. The oxygen-bindingsite in these proteins is a pair of copper atoms bound directlyto ammo acid side chains. The biscopper sites of these proteinsbind single molecules of dioxygen or carbon monoxide. In arthropodsthere are two copper atoms per approximately 70 000 daltonsof protein. This corresponds to the molecular weight of theminimum polypeptide chain. In molluscs however there are twocopper atoms per 50,000 daltons of protein. This does not correspondto the minimum polypeptide chain although it does correspondto the minimal functional unit. The minimal polypeptide chainin molluscan hemocyanins is approximately 400,000 daltons andappears to be composed of eight or more 50 000 dalton unitslinked together like a string of pearls. In the molluscs, thenative hemocyanins found in the hemolymph generally occur asgiant cylindrical molecules 350 Å in diameter, 380 Ålong, with molecular weights of 9 000,000. These large moleculesare composed of approximately 20 polypeptide chains. In thehemolymph of the arthropods depending upon the species, hemocyaminsoccur as hexamers dodecamers 24-mers and 48-mers. The molecularweight of the 48-mers is about 3 600,000. The respiratory functionsof hemocyamns show a wide range of allosteric properties. Thelarge molecules commonly show cooperativity in oxygen binding.The number of interacting subunits is in some cases dependentupon external conditions of pH and ionic composition. The oxygenaffinity is usually sensitive to pH and to low molecular weightcofactors like chloride, calcium and magnesium ions. The intrinsicoxygen binding properties of an organism s hemocyanin and itsallosteric control by modulators allow organisms possessingthese giant molecules to adapt to their environmental conditions.     

DNA Replication in the Archaea

The archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus. In recent years, considerable advances have been made in understanding the biochemistry of the archaeal replication proteins. Furthermore, a number of structures have now been obtained for individual components and higher-order assemblies of archaeal replication factors, yielding important insights into the mechanisms of DNA replication in both archaea and eukaryotes.