Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

新生儿首次呼吸前后脐带动静脉血液氧和二氧化碳变化探索呼吸调控机制的初步报告II—同一个新生儿同一时间的脐带动静脉血液氧和二氧化碳分压差值个体化分析*

目的: 为探讨新生儿自主呼吸产生机制,前文已对新生儿出生后自主呼吸开始前脐带动静脉氧气和二氧化碳差值进行了人群组间分析;而本部分则对相关信息进行个体化分析。方法: 在产前经所有胎儿父母签署知情同意书,新生儿出生后还没有呼吸之前在脐带动脉和脐带静脉分别连续逐搏取血,仅有3例同时采集到Pua和Puv血液样本进行血气分析测定,计算分析脐带静脉和脐带动脉的异同和动态变化。结果: 虽然准备了数十产妇,但仅有3例同时采集到Pua和Puv血液样本,同一时间的PuvO₂显著高于PuaO₂（P均<0.01）,平均相差（24.17±7.09） mmHg;而PuvCO₂显著低于PuaCO₂（P均<0.01）,平均相差（-7.67±3.70） mmHg。在同一时间的Puv-uaO₂显著高于Puv-uaCO₂（P<0.05）。结论: 新生儿出生后自主呼吸前,全部氧气供应由脐带静脉运输,只要胎盘开始剥离则新生儿的PuaO₂随时间（心跳次数）逐渐降低,当PuaO₂达到触发呼吸阈值（最低值）诱发第一次吸气开始其自主呼吸。     

Current Status of Cereal Root Diseases in Western Australia Under Intensive Cereal Production and Their Comparison with the Historical Survey Conducted During 1976–1982

Two separate surveys of root diseases of cereals in the Western Australian (WA) cereal belt were conducted: the first conducted annually for wheat and barley during 1976–1982 and the second for wheat during 2005–2007. For the 1976–1982 survey, the cereal belt was divided into 15 zones based on the location and rainfall. Sampling was representative of the actual cropping area, with both wheat and barley sampling sites selected by zone as a percentage of total sites. Over 31 000 plants were assessed from a total of 996 fields. Average take‐all incidence ranged from 3% in the northern low rainfall zone to 57% in the southern high rainfall zone. Other root diseases assessed included rhizoctonia root rot, fusarium crown rot and subcrown internode discolouration. During the 2005–2007 survey, around 20 000 plants from a total of 210 fields being intensively cropped with cereals were surveyed for take‐all, rhizoctonia root rot, fusarium crown rot, common root rot, root lesion nematode and cereal cyst nematode. The 2005–2007 survey results indicated that root and crown diseases prevailed in paddocks frequently cropped with cereals and occurred at damaging levels across all WA cropping districts surveyed. The more recent root disease survey identified that the fungal diseases rhizoctonia root rot and fusarium crown rot and the root lesion nematode were the most serious impediments to intensive cereal production, particularly in the southern region of WA. Comparing the 2005–2007 results with the previous survey of 1976–1982, the relative importance of take‐all appears to have declined over the past 30 years.     

Monitoring population‐level responses of marine mammals to human activities

We provide guidance for monitoring whether human activities affect the physiology or behavior of marine mammals and, if so, whether those effects may lead to changes in survival and reproduction at the population level. We suggest that four elements be included in designing and implementing such a monitoring program. The first is development of a theory of change: a set of mechanistic hypotheses that outline why a given activity might be expected to have one or more measurable effects on individuals and populations, and ideally the magnitude, timing, and duration of the effects. The second element, definition of biologically meaningful effect sizes, ultimately facilitates the development of a monitoring program that can detect those magnitudes of effect with the desired levels of precision. The third element, selection of response variables for monitoring, allows inference to whether observed changes in the status of individuals or populations are attributable to a given activity. Visual observations, passive acoustic and tagging instruments, and direct physical measurements all can provide data that facilitate quantitative hypothesis testing. The fourth element is specification of the temporal sequence of monitoring. These elements also can be used to inform monitoring of the responses of other taxonomic groups to human activities.     

<Emphasis Type="Italic">Heteroepichloë</Emphasis>, gen. nov. (Clavicipitaceae; Ascomycotina) on bamboo plants in East Asia

The causal agents of witches' broom of bamboo plants in East Asia, Epichloë bambusae and E. sasae, were morphologically and phylogenetically examined. The phylogenetic studies were conducted using ITS 1, 2, and 5.8 S rDNA regions. Both Epichloë species produce Ephelis-type conidia in artificial medium and are phylogenetically situated in different clades from Epichloë and Parepichloë. Here, we propose a new genus Heteroepichloë for these two bambsicolous Epichloë species.     

Allowable level of lifetime cadmium intake calculated from the individuals in the Jinzu River basin of Japan

We investigated a dose-response relationship between renal dysfunction and liftime cadmium intake in individual subjects using logistic regression analysis and calculated the allowable level of lifetime cadmium intake among the inhabitants of the Jinzu River basin. From the participants of 1967 and 1968 health examinations, target subjects in whose hamlet the cadmium concentration in rice was known and whose history of residence was also known were selected. Cadmium concentrations in rice from data analyzed by the Toyama Prefecture from 1971 to 1976 were used. The urinary examination was done by semiquantitative determination of protein and glucose. All odds ratios for lifetime cadmium intake obtained from logistic regression analysis were more than 1 in both males and females who had resided in their current hamlet since birth with and without subjects who moved from nonpolluted areas and with or without the control group. The allowable levels of lifetime cadmium intake were calculated by substituting the abnormality rates of urinary findings of the controls 40, 50, 60, and 70 yr old into the logistic regression formula. The allowable levels of lifetime cadmium intake were less than 1.58 g for both sexes and each age group using proteinuria with glucosuria measurements.     

The Israel National Skin Bank: Quality Assurance and Graft Performance of Stored Tissues

The Israel National Skin Bank (INSB) was founded jointly by the Israel Defense Forces (IDF) Medical Corps and the Ministry of Health in 1986. The prime purpose of the Skin Bank is to treat burn victims incurred at war or during mass casualty incidences. The INSB Protocol is comprised of international skin bank protocols and our previous and present research results. They provide the framework for selecting optimal guidelines for procurement, processing, preservation, storage and evaluation of transplantation performance of viable skin grafts. For evaluation and direct comparison of graft performance of glycerolized or cryopreserved skin stored for long periods, we have applied a mouse recipient model developed by us. This model assesses graft performance before the rejection process takes place. The in vivo design has inherent clinical relevance, which is especially appealing. Cryopreserved skin performed better than glycerolized skin (p > 0.027), but fresh skin performed significantly better than cryopreserved skin (p > 0.003), as analyzed by the Mann–Whitney non-parametric test. Then graft performance of skin specimens were cryopreserved by programmed or stepwise freezing and stored at -80°C or in liquid nitrogen for 1 and 6–10 months was evaluated. The average score of skin preserved by programmed freezing and stored in liquid nitrogen is the highest for both storage periods. This method has a highly significant advantage (p < 0.007) over the others for 6–10 months storage, evaluated by graft adherence. Several interaction factors determine the quality of cryopreserved skin. Highly significant is the interaction factor/'combined effect' of sample variability with the method of cryopreservation or with the storage period. Finally, the results of paired comparison of selected histology criteria of cryopreserved to fresh skin indicated that storage of skin for up to 5 years did not impair significantly its performance compared to fresh skin, whereas, after six years of storage, there was a highly significant (p < 0.001) impairment in skin quality. We offer a simplified in vivo model and analysis for cryopreserved skin graft performance, suggesting that the evaluation procedures, which are issues of great interest in skin banking, may help future skin banks to make informed choices and decisions regarding quality issues.     

Large‐scale,multidirectional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no‐take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of larval connectivity across larger seascapes remain unknown. Here, we apply genetic parentage analysis to investigate larval dispersal patterns for two exploited coral reef groupers (Plectropomus maculatus and Plectropomus leopardus) within and among three clusters of reefs separated by 60–220 km within the Great Barrier Reef Marine Park, Australia. A total of 69 juvenile P. maculatus and 17 juvenile P. leopardus (representing 6% and 9% of the total juveniles sampled, respectively) were genetically assigned to parent individuals on reefs within the study area. We identified both short‐distance larval dispersal within regions (200 m to 50 km) and long‐distance, multidirectional dispersal of up to ~250 km among regions. Dispersal strength declined significantly with distance, with best‐fit dispersal kernels estimating median dispersal distances of ~110 km for P. maculatus and ~190 km for P. leopardus. Larval exchange among reefs demonstrates that established reserves form a highly connected network and contribute larvae for the replenishment of fished reefs at multiple spatial scales. Our findings highlight the potential for long‐distance dispersal in an important group of reef fishes, and provide further evidence that effectively protected reserves can yield recruitment and sustainability benefits for exploited fish populations.     

虹鳟生长激素cDNA在酵母中的表达

采用聚合酶链式反应（ Ｐ Ｃ Ｒ） 技术对虹鳟生长激素ｃ Ｄ Ｎ Ａ 进行改造。将改造后的基因克隆到含酵母 Ｐ Ｇ Ｋ 启动子的大肠杆菌酵母穿梭质粒ｐ Ｍ Ａ９１ ,转化酿酒酵母 Ｙ３３ ,构建表达鱼生长激素的酵母工程菌 Ｙ３３（ｐ Ｍ Ａｒ Ｇ Ｈ１６） ,并在酵母中获得表达,表达量约占细胞可溶性蛋白总量的３ ％ 。表达产物作为饲料添加剂投喂罗非鱼,具有明显的促进生长作用     

popharvest: An R package to assess the sustainability of harvesting regimes of bird populations

Bird harvest for recreational purposes or as a source for food is an important activity worldwide. Assessing or mitigating the impact of these additional sources of mortality on bird populations is therefore crucial issue. The sustainability of harvest levels is however rarely documented, because knowledge of their population dynamics remains rudimentary for many bird species. Some helpful approaches using limited demographic data can be used to provide initial assessment of the sustainable use of harvested bird populations, and help adjusting harvest levels accordingly. The Demographic Invariant Method (DIM) is used to detect overharvesting. In complement, the Potential Take Level (PTL) approach may allow setting a level of take with regard to management objectives and/or to assess whether current harvest levels meet these objectives. Here, we present the R package popharvest that implements these two approaches in a simple and straightforward way. The package provides users with a set of flexible functions whose arguments can be adapted to existing knowledge about population dynamics. Also, popharvest enables users to test scenarios or propagate uncertainty in demographic parameters to the assessment of sustainability through easily programming Monte Carlo simulations. The simplicity of the package makes it a useful toolbox for wildlife managers or policymakers. This paper provides them with backgrounds about the DIM and PTL approaches and illustrates the use of popharvest''s functionalities in this context.