Distribution and Evolution of Pseudogenes, Gene Losses, and a Gene Rearrangement in the Plastid Genome of the Nonphotosynthetic Liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida)

The plastid genome sequence of the parasitic liverwort Aneura mirabilis revealed the loss of five chlororespiration (ndh) genes. Additionally, six ndh genes, subunits of photosystem I, photosystem II, and the cytochrome b6f complex were inferred to be pseudogenes. Pseudogenes of cysA, cyst, ccsA, and ycf3, an inversion of psbE and petL, were also detected. The designation of pseudogenes was made using comparisons with the distantly related liverwort Marchantia polymorpha. We sampled several populations of A. mirabilis and its photosynthetic sister groups to correlate functional gene losses with the evolution of a achlorophylly. The gene losses, pseudogenes, or the psbE-petL inversion were never detected in a photosynthetic Aneura but were detected in every population of A. mirabilis. One population of A. mirabilis revealed a unique deletion of 541 bp in the psbE-petL region; another is characterized by a unique deletion of 471 bp in the trnV(UAC)-ndhC region. The ratio of synonymous-to-nonsynonymous substitution rates (omega) was estimated for eight pseudogenes and six ORFs to detect relaxed purifying selection. A significant increase in omega for the nonphotosynthetic liverwort was detected in six pseudogenes. Relaxation purifying selection, determined by a significant increase in omega, was detected for three intact ORFs: psbA, psbM, and rbcL.     

Assessing the Threatened Status of Bumble Bee Species (Hymenoptera: Apidae) in Hungary,Central Europe

Decline in the populations of bumble bees and other pollinators stress the need for more knowledge about their conservation status. Only one of the 25 bumble bee species present in Hungary is included in the Hungarian Red List. We estimated the endangerment of the Hungarian bumble bee (Bombus Latr.) species using the available occurrence data from the last 50 years of the 20th century. Four of the 25 species were data deficient or extinct from Hungary. About 60% of species were considered rare or moderately rare. Changes in distribution and occurrence frequency indicated that 10 of the 21 native species showed a declining trend, while only three species increased in frequency of occurrence. According to the IUCN Red List categories, seven species (33% of the native fauna) should be labelled as critically endangered (CR) and 3 (14%) as endangered (EN). Our results stress an urgent need of protection plans for bumble bees in Hungary, and further underlines the validity of concern over bumble bees all over Europe.     

Protective Status,Ecology and Strategies for Improving Conservation of <Emphasis Type="Italic">Cercocebus sanjei</Emphasis> in the Udzungwa Mountains,Tanzania

Sanje mangabeys (Cercocebus sanjei), first described in 1981, are among the most endangered primates in the world. They are endemic to the Udzungwa Mountains of Tanzania, in a biogeographic region designated one of the world’s biodiversity hotspots. Conservation research since 1997 has documented the presence of the mangabey in only 3 of the relict montane forest blocks of the Udzungwas. The total population, possibly < 1,500 animals, is fragmented and not adequately protected. A substantial proportion (perhaps 40%) live in forest reserves outside the protective confines of the Udzungwa Mountains National Park, and they are affected by habitat loss and hunting. Efforts to improve their conservation status include assessment of distribution, relative abundance, and habitat quality, and initiation of observational research with habituated individuals to acquire critically important data on their habitat requirements, diet, movement patterns, socioecology, and community ecology. These interrelated research activities should contribute to effective management for conservation, provide baseline information to support current efforts to expand the boundaries of the national park, and guide potential future establishment of corridors between the major forests known to support mangabey groups.     

A spatially explicit model for integrating species assessments into landscape planning as exemplified by the Corn Bunting (Emberiza calandra)

The integration of spatial information concerning animal species into static, rule-based spatially explicit non-probabilistic models for decision-making regarding the planning of landscapes and regions provides generalised habitat-described landscape-structural parameters. As a basis for an individually developed model, a discussion is first of all presented which involves general data and parametric requirements, necessary for the development of a species-referenced, spatially explicit model for analysis and evaluation. The parameters necessary for an assessment of habitat characteristics of birds in Central Europe will be discussed on the basis of landscape and structural information, using the Corn Bunting (Emberiza calandra) as an example. A spatial analysis and assessment procedure supported by geographical information system (GIS) for this species has been developed for the definition of regulations and assessment categories and subsequently applied to the example of an open agricultural landscape in Saxony-Anhalt. Within the area of examination of approximately 42.4 km², 56 songbird perches were located (density of 1.34 territories/km²). A comparison with the 45 mapped territories from the year 2004 indicated a good correlation with the model assumptions. Indeed, 16 of these 45 territories were only briefly occupied and the establishment of breeding pairs was ascertained in only 17 territories. The analysis and assessment model as presented yielded reality-based results after the utilisation of relatively little landscape-structural entry data, and is well suited for support of the decision-making process for spatial planning. The model framework presented in this paper can be modified and transferred to other species.     

The Distribution of an Introduced Mollusc and its Role in the Long-term Demise of a Native Confamilial Species

The estuarine mud snail, Batillaria attramentaria, was transported to the Pacific coast of North America with the Pacific oyster, Crassostrea gigas (C. gigas), imported from Japan in the early part of this century, and has proliferated in several bays where the oyster was introduced. Since the arrival of Batillaria there have been declines in populations of its native ecological equivalent, Cerithidea californica. This study documents the distribution of the exotic Batillaria throughout its entire introduced range, concentrating on the few bays in northern California where both snails exist sympatrically. Using dates of initial importation of C. gigas and dates of first documentation of Batillaria within a bay, I established the earliest possible date for the introduction of Batillaria in a particular area. In cases where Cerithidea also was, or had been, present within a bay, I calculated a range of time for either the continued coexistence of the two species or the time until local exclusion of the native. Density measurements of Cerithidea within these bays where the species co-occurred allowed comparison of present Cerithidea numbers to historical accounts. Results indicated that Batillaria is replacing Cerithidea in the northern marshes of California. This replacement of the northernmost Cerithidea populations is not only reducing Cerithidea's overall range, but also eliminating a race recently shown to be a genetically distinct from southern Cerithidea populations. Other studies that have demonstrated superior exploitative competitive ability by Batillaria provide a potential mechanism for this displacement pattern. Regardless, the results presented here indicate that the displacement process is slow, taking on average >50 years to complete. This study illustrates a gradual, but predictable process of exotic replacement of native species, and argues strongly against complacency toward invaders that may currently seem innocuous. This revised version was published online in July 2006 with corrections to the Cover Date.     

Developing landscape habitat models for rare amphibians with small geographic ranges: a case study of Siskiyou Mountains salamanders in the western USA

To advance the development of conservation planning for rare species with small geographic ranges, we determined habitat associations of Siskiyou Mountains salamanders (Plethodon stormi) and developed habitat suitability models at fine (10 ha), medium (40 ha), and broad (202 ha) spatial scales using available Geographic Information Systems data and logistic regression analysis with an information theoretic approach. Across spatial scales, there was very little support for models with structural habitat features, such as tree canopy cover and conifer diameter. Model-averaged 95% confidence intervals for regression coefficients and associated odds ratios indicated that the occurrence of Siskiyou Mountains salamanders was positively associated with rocky soils and Pacific madrone (Abutus menziesii) and negatively associated with elevation and white fir (Abies concolor); these associations were consistent across 3 spatial scales. The occurrence of this species also was positively associated with hardwood density at the medium spatial scale. Odds ratios projected that a 10% decrease in white fir abundance would increase the odds of salamander occurrence 3.02–4.47 times, depending on spatial scale. We selected the model with rocky soils, white fir, and Oregon white oak (Quercus garryana) as the best model across 3 spatial scales and created habitat suitability maps for Siskiyou Mountains salamanders by projecting habitat suitability scores across the landscape. Our habitat suitability models and maps are applicable to selection of priority conservation areas for Siskiyou Mountains salamanders, and our approach can be easily adapted to conservation of other rare species in any geographical location.     

Ontogenetic Variation in the Diurnal Food and Habitat Associations of an Endemic and an Exotic Fish in Floodplain Ponds: Consequences for Niche Partitioning

In floodplain ponds with low piscivore abundance, both endemic Midgley's gudgeons, Hypseleotris sp. 5, and exotic mosquitofish, Gambusia holbrooki, showed significant ontogenetic variation in the use of food and space. Small gudgeons were generally associated with surface and benthic habitats, then restricted their distribution to benthic habitats at a size of approximately 24mm (standard length). The ontogenetic variation in mosquitofish habitat use was less discrete, and could be described as a tendency for larger individuals to be associated with the bottom of the littoral macrophyte beds than with the surface of the macrophyte beds or surface of the limnetic zone. Small gudgeons exhibited high spatial overlap with mosquitofish within the surface habitats of the ponds. All size-class/species comparisons showed significant partitioning of food resources, however, the diets of small gudgeons and mosquitofish were very similar. Therefore, juvenile gudgeons may have to pass through a similar spatial and trophic niche to introduced mosquitofish before recruiting to the adult stage. Possible mechanisms driving the ontogenetic variation in gudgeon and mosquitofish habitat use are discussed. This paper demonstrates that ontogenetic niche shifts at fine spatial scales can affect our interpretation of interactions between native and introduced fishes.     

A review on the impacts of feral cats (Felis silvestris catus) in the Canary Islands: implications for the conservation of its endangered fauna

Feral cats have been directly responsible for the extinction of numerous species on islands worldwide, including endemic species of mammals, birds and reptiles. The diet of feral cats in the main habitats of the Canary Islands, as generally occurred on oceanic islands, is mainly composed of introduced mammals, and native species of birds, reptiles and insects. The impact of feral cat upon the endangered species was assessed by evaluating their relative abundance in the cats’ diet and by considering their current conservation status. A total of 68 different preys were identified at species level in all studies carried out in the Canary Islands (5 mammals, 16 birds, 15 reptiles and 32 invertebrates). From all the species preyed by feral cats in the Canary Islands, only four of them are considered threatened by the IUCN Red List of Threatened Species: one endemic bird Saxicola dacotiae and three endemic giant lizards, Gallotia simonyi, Gallotia intermedia, and Gallotia gomerana. Although some efforts on management control have been carried out, it is necessary to enforce these conservation activities on those areas of Tenerife, La Gomera and El Hierro where giant lizards are still present. Furthermore some local areas where endangered bird species are highly predated should be protected. Nevertheless, it is important to take into account the presence of other introduced species such as rats, mice or rabbits in order to avoid problems derived from the hyperpredation process and mesopredator release effect.     

Hairy Root Cultures of <Emphasis Type="Italic">Gynostemma pentaphyllum</Emphasis> (Thunb.) Makino: A Promising Approach for the Production of Gypenosides as an Alternative of Ginseng Saponins

Hairy root cultures of Gynostemma pentaphyllum were established by infecting leaf discs with Agrobacterium rhizogenes. The dry biomass of hairy roots grown in MS medium for 49 days was 7.3 g l⁻¹ with a gypenoside content of 38 mg g⁻¹ dry wt.     

A two-stage refinement approach for the enhancement of excretory production of an exoglucanase from Escherichia coli

Hyper-expression of a secretory exoglucanase, Exg, encoded by the cex gene of Cellulomonas fimi was previously shown to saturate the SecYEG pathway and result in dramatic cell death of recombinant Escherichia coli (Z.B. Fu, K.L. Ng, T.L. Lam, W.K.R. Wong, Cell death caused by hyper-expression of a secretory exoglucanase in Esherichia coli, Protein Expr. Purif. 42 (2005) 67-77). We propose here that the cell lysate ratio (Pre/Mat RQ) of the unprocessed precursor Exg protein (Pre-Exg) and its processed mature product (Mat-Exg) reflects the capacity of E. coli to secrete Exg. A Pre/Mat RQ of 20/80, designated the "Critical Value," was an important threshold measurement. A rise in the Pre/Mat RQ triggered a mass killing effect. The use of various secretion signal peptides did not improve the viability of cells expressing high levels of Pre-Exg under strong tac promoter control. However, use of the weaker vegG promoter in conjunction with a change in start codon of the spa leader sequence from ATG to TTG in a pM1vegGcexL plasmid construct resulted in a high level (0.9 U ml(-1)) of excreted Exg in shake-flask cultures. This was 50% higher than the best result obtained from plasmid construct lacUV5par8cex, using the lacUV5 promoter and the ompA leader sequence. Variations in the excreted Exg activities were attributable to differences in the Pre/Mat RQ values of the induced cultures harboring pM1vegGcexL and lacUV5par8cex. These values were 18/82 and 10/90, respectively. Employing fed-batch cultivation in two-liter fermentors, an induced JM101(pM1vegGcexL) culture yielded 4.5 U ml(-1) of excreted Exg, which was over six fold greater that previously reported. Our results illustrate the successful application of the Pre/Mat RQ ratio as a guide to the attainment of a maximum level of secreted/excreted Exg.     

A new approach to the solution of the linear mixing model for a single isotope: application to the case of an opportunistic predator

Mixing models are used to determine diets where the number of prey items are greater than one, however, the limitation of the linear mixing method is the lack of a unique solution when the number of potential sources is greater than the number (n) of isotopic signatures +1. Using the IsoSource program all possible combinations of each source contribution (0–100%) in preselected small increments can be examined and a range of values produced for each sample analysed. We propose the use of a Moore Penrose (M-P) pseudoinverse, which involves the inverse of a 2×2 matrix. This is easily generalized to the case of a single isotope with (p) prey sources and produces a specific solution. The Antarctic leopard seal (Hydrurga leptonyx) was used as a model species to test this method. This seal is an opportunistic predator, which preys on a wide range of species including seals, penguins, fish and krill. The M-P method was used to determine the contribution to diet from each of the four prey types based on blood and fur samples collected over three consecutive austral summers. The advantage of the M-P method was the production of a vector of fractions f for each predator isotopic value, allowing us to identify the relative variation in dietary proportions. Comparison of the calculated fractions from this method with means from IsoSource allowed confidence in the new approach for the case of a single isotope, N.     

基于UAV低空遥感的荒漠林大沙鼠洞群覆盖率及分布特征研究——以新疆古尔班通古特沙漠南缘局部为例

草原鼠害是影响草原生态平衡的重要因素,草原鼠害监测是鼠害防治工作的重要环节。无人机低空遥感是一种新的鼠害监测方法,其具备高空间分辨率、高时效、低成本、低损耗等特点,在新疆鼠害监测防治方法中完成了示范工作。于2015年10月与2016年5月对新疆古尔班通古特沙漠南缘的荒漠林大沙鼠典型鼠害区进行两次无人机低空航拍,分别获取分辨率0.02m与0.024m的实验区超高分辨率影像,对两片实验区整幅影像进行目视解译,获得鼠洞分布情况;在鼠洞分布图基础上进行缓冲区分析并添加趋势线,获取鼠洞空间分布趋势,与研究区山体阴影图叠加分析鼠洞分布与地形间的相互关系。通过GIS格网与GIS叠加分析,获取鼠洞洞群覆盖率。得出如下结论:无人机低空遥感可以为大沙鼠鼠害调查提供准确度甚高的解译结果;古尔班通古特沙漠南缘局部研究区的荒漠林大沙鼠鼠害区洞群覆盖率分别为19.4%、18.8%,已为高密度发生区;研究区大沙鼠鼠洞表现出明显的聚集特征和带状分布特征;聚集特征说明鼠洞是以洞群的形式存在;研究区鼠洞带状分布特征与地形有着密不可分的关系;根据其空间分布特征可以科学规划鼠害治理方案;此研究表明无人机低空遥感在鼠害监测防治方面具有广阔的应用前景。     

A direct immunoassay for detecting diatoms in groundwater as an indicator of the direct influence of surface water

Groundwater under the direct influence of surface water (GWUDISW) is of concern in communities where growing public demand on groundwater resources has resulted in increased withdrawals and hydraulic stress near surface water bodies. Under these conditions, contaminants such as methyl-tert butyl ether (MTBE) and biological materials have been detected in domestic wells. Other contaminants and pathogens associated with surface water are not routinely tested for in groundwater-supplied systems. To address the need for methods to easily identify potentially vulnerable supplies, a direct immunoassay for the quantitative detection of diatoms in raw water samples was developed as a measure of surface water influence on groundwater. Cell wall preparations from Nitzschia palea Kützing, a freshwater diatom found throughout North America, were used to produce a polyclonal antibody that was applied in a direct enzyme-linked immunosorbent assay (ELISA) developed to detect the presence of N. palea cell wall components. The direct immunoassay allows detection at 500 cells L⁻¹, a level similar to diatom concentrations observed in samples of groundwater collected near the test site. This investigation was the first attempt to utilize an ELISA as an indicator of surface water influence on groundwater. Further research is needed to develop more specific diatom-based monoclonal antibodies, determine cross-reactivity, and optimize sample processing and ELISA procedures for development of a standardized method.     

DNA sequence analysis of spontaneous and γ-radiation (anoxic)-induced lacI mutations in Escherichia coliumuC122::Tn5: differential requirement for umuC at G · C vs. A · T sites and for the production of transversions vs. transitions

Escherihica coliumC122::Tn5 cells were γ-radiated (¹³⁷Cs, 750 Gy, under N₂), and lac-constitutive mutants were produced at 36% of the wild-type level (the umC strain was not deficient in spontaneous mutagenesis, and the mutational spectrum determined by sequencing 263 spontaneous lacI^d mutations was very similar to that for the wild-type strain). The specific nature of the umC strain's partial radiation was determined by sequencing 325 radiation-induced lacI^d mutations. The yields of radiation-induced mutation classes in the umC strain (as a percentage of the wild-type yield) were: 80% for A · T → G · C transitions, 70% for multi-base additions, 60% for single-base deletions, 53% for A · T → C · G transversions, 36% for G · C → A · T transitions, 25% for multi-base deletions, 21% for A · T → T · A transversions, 11% for G · C → C · G transversions, 9% for G · C → T · A transversions and 0% for multiple mutations. Based on these deficiencies and other factors, it is concluded that the umC strain is near-normal for A · T → G · C transitions, single-base deletions and possibly A · T → C · G transversions; is generally deficient for mutagenesis at G · C sites fro transversions, and is grossly deficient in multiple mutations. Damage at G · C sites seems more difficult for translesion DNA synthesis to bypass than damage at A · T sites, and especially when trying to produced a transversion. The yield of G · C → A · T transitions in the umC strain *36% of the wild-type level) argues that a basic sites are involved in no more than 64% of γ-radiation-induced base substitutions in the wild-type strain. Altogether, these data suggest that the UmuC and UmuD′ proteins facilitate, rather than being absolutely required for, translesion DNA synthesis; with the degree of facilitation being dependent both on the nature of the noncoding DNA damage, i.e., at G · C vs A · T sites, and on the nature of the misincorporated base, i.e., whether it induces transversions or transitions.     

A method for the analysis of temporal changes in vegetation pattern at the landscape level

A new approach to study temporary changes in small landscape units is proposed, based on vegetation-complex relevés (sigma relevés). The method is introduced using extensively grazed or abandoned heathland and Nardus-sward landscapes in the Black Forest as examples. Thirty-six sigma relevés of the years 1979–80 are compared with those of 1989–90. Each of the compared plot areas covers on the average 2–4 hectares, and has a diversity of about 20 different vegetation types. The vegetation complex relevés can be ordered to 3 different types which characterize landscape ecological zones dependant on former rural management.As a result of the comparison 2 main developments which have a spatial differentiation in the Black Forest are confirmed and documentated:

A method for the regulation of microbial population density during continuous culture at high growth rates

A method for the continuous culture of microorganisms is described which employs growth-dependent pH changes to control the rate of addition of fresh medium to a culture vessel. The apparatus (the phauxostat) supports, at constant pH, longterm continuous culture at rates near or at the maximum of which the organisms are capable. The buffering capacity of the inflowing medium determines the steady-state population density of the culture, but the rate of growth is independent of the buffering capacity. The fundamental theory of operation is tested and some basic parameters of growth are estimated using Escherichia coli B growing continuously in media containing glucose, glycerol or DL-lactate.Joseph C. Wilson Scholar.