Red List of amphibians and reptiles of the Wadden Sea area

In the Wadden Sea, in total, 8 species of amphibians and 4 species of reptiles are threatened in at least one subregion. Of these, 7 species of amphibians and all 4 species of reptiles are threatened in the entire area and are therefore placed on the trilateral Red List. 1 species of the listed reptiles is (probably) extinct in the entire Wadden Sea area. The status of 1 species of amphibians is endangered, the status of (probably) 4 species of amphibians and 3 species of reptiles are vulnerable and of 2 species of amphibians susceptible. This list forms part of the Report on the RED LISTS OF BIOTOPES, FLORA AND FAUNA OF THE TRILATERAL WADDEN SEA AREA. For basic information concerning, for example, function of these lists, species taken into account, structure of the lists and abbreviations used, see also the general introduction to the Red Lists.     

Isolation and characterization of new facultatively alkalophilic strains of Bacillus species.

Four facultatively alkalophilic isolates were purified from enrichment cultures initiated with lime-treated garden soil. Four isolates, OF1, OF3, OF4, and OF6, were obligately aerobic, spore-forming, gram-positive, motile rods which were capable of growth at both pH 7.5 and pH 10.5. Strains OF1 and OF6 grew best at the lower pH value; and whereas growth of these strains at pH 10.5 was completely dependent on added Na+, growth at pH 7.5 was only partially dependent on added Na+. Strains OF3 and OF4 grew better at pH 10.5 than at pH 7.5, with strain OF3 growing modestly over its entire pH range, while OF4 grew well. Growth of OF3 and OF4 was completely dependent on added Na+ at both pH 7.5 and pH 10.5. DNA-DNA hybridization studies indicated that OF1 and OF6 are closely related strains but are not related to the other isolates, Bacillus subtilis, or two previously studied obligately alkalophilic bacilli. OF3 was unrelated to any of the other organisms examined in the study, whereas OF4 showed complete homology with obligately alkalophilic Bacillus firmus RAB. All four isolates maintained a cytoplasmic pH that was considerably lower than the external pH when the latter was 10.5. Although substantial transmembrane electrical potentials were observed, the total electrochemical proton gradient (delta mu H+) was low at pH 10.5 in all the strains. By contrast, delta mu H+ was substantial at pH 7.5 and at that pH was composed entirely of an electrical potential. These results are in contrast to previous findings that obligately alkalophilic bacilli generate only small electrical potentials at near neutral pH. All the isolates exhibited substantial rates of respiration as measured by oxygen consumption. Neither respiration nor NADH oxidation by everted membrane vesicles was significantly stimulated by Na+. Analyses of reduced versus oxidized difference spectra of membranes from OF4 showed that the total membrane cytochrome content was considerably higher in cells grown at pH 10.5 than at pH 7.5, with the levels of c- and a-type cytochromes exhibiting the largest pH-dependent differences. Initial examination of membrane protein profiles on gel electrophoresis also indicated a number of changes in pattern in each isolate, depending on the growth pH.     

A comparative analysis of global, national, and state red lists for threatened amphibians in Brazil

The knowledge about the conservation status of species is an important data for conservation biology. Therefore, threatened species lists are a powerful tool for conservation planning and prioritization. Our objective is to compare the global, the national and state red lists of amphibians in Brazil. Threatened species were categorized according to their listing in one or several of these lists. We analyzed for true inconsistencies across lists in order to evaluate practical consequences of such incongruences on amphibian conservation in Brazil. We recorded a total of 61 threatened amphibian species in Brazil (across all red lists). Only one species, Phrynomedusa fimbriata, was listed as Extinct (both in IUCN, Brazil and S?o Paulo lists). A total of eleven endemic species are listed as threatened by the global red list, but do not appear in Brazil’s national red list, which represent an inconsistence among these lists. Besides that, the threat category of Thoropa lutzi and Thoropa petropolitana, two endemic species, differ among both lists, which also represents a problem between both lists. These mismatches may be due to several reasons such as different interpretation of the criteria; different methodologies used; different data availability on species; differences in the dates of assessments processes; the assessors’ attitudes to uncertainty; outdated red lists. Harmonization among red lists permits a better picture of threatened amphibian diversity across scales and to develop global, national and state plans to complement conservation actions in order to maximize the chance of success of these initiatives.     

人MEPE/OF45基因的克隆及序列分析

目的：克隆人MEPE/OF45全长基因,为进一步研究MEPE/OF45在DNA损伤应答中的作用及特异的信号通路奠定基础。方法：选取人宫颈癌细胞HeLa为靶细胞,从中提取总RNA,设计扩增人MEPE/OF45基因片段的特异引物,进行RT-PCR分析;用蛋白质合成抑制剂亚胺环己酮（CHX）对细胞进行处理,观察处理前后MEPE/OF45基因的表达情况。结果：在经CHX处理的HeLa细胞中扩增到了MEPE/OF45基因片段,随后利用重叠PCR方法获得了人MEPE/OF45全长基因,并经序列分析确证。结论：获得了人MEPE/OF45基因片段及全长基因,为阐明MEPE/OF45在细胞中复杂的功能提供了线索。     

Chemical Characterization of Organisms Isolated from Leprosy Patients

CHEMICAL ANALYSES OF THE CELL WALLS OF ORGANISMS ISOLATED IN VARIOUS PARTS OF THE WORLD FROM CASES OF LEPROMATOUS AND TUBERCULOID LEPROSY MAKE POSSIBLE THEIR ASSIGNMENT TO ONE OF THE THREE GENERA: Corynebacterium, Mycobacterium, or Propionibacterium. One, bacterium 22M, remains unassigned. The combined chemical and enzymatic properties attributed to leprosy bacilli freshly harvested from lepromata are found collectively, but not individually, in these three genera.     

Are species lists derived from modeled species range maps appropriate for macroecological studies? A case study on data from BIEN

Because survey-based species lists for fine-scale areas are generally lacking, ecologists have been using species lists derived from modeled range maps in macroecological studies. Here I evaluate whether it is appropriate to use species lists derived from modeled range maps in macroecological studies. I compared species lists derived from about 90,000 range maps in the Botanical Information and Ecology Network (BIEN) for over 180 geographic regions (12 broad regions covering the whole of the New World; 172 smaller regions, i.e. Taxonomic Databases Working Group units) with those representing complete or nearly complete species lists obtained from the literature for the regions. I determined the completeness of native species composition and proportion of false presences and exotic (non-native) species in species lists derived from range maps in BIEN. I determined whether errors in species lists derived from modeled range maps affect macroecological inferences by comparing the relationships of α- and β-diversity with geographic and climatic variables between different datasets (i.e. species lists derived from range maps versus complete or nearly complete species lists derived from the literature). The completeness for native species lists derived from range maps was 60–74%, depending on spatial scale. On average, 65% of the species in a species list derived from BIEN for a geographic area are false presences or non-native species to the area. The relationships of α- and β-diversity derived from the BIEN dataset with geographic and climatic variables differ significantly from those derived from complete species lists. This study shows that the results of a macroecological study based on species lists derived from modeled range maps may be substantially incorrect due to high percentages of missing native species, and high numbers of non-native species and false presences. Thus, it may not be appropriate to use species lists derived from modeled range maps in the macroecological studies that require complete or nearly complete species lists.     

Temporal stability of novelty exploration in mice exposed to different open field tests

We investigated behavioural activity and temporal distribution (patterning) of mouse exploration in different open field (OF) arenas. Mice of 129S1 (S1) strain were subjected in parallel to three different OF arenas (Experiment 1), two different OF arenas in two trials (Experiment 2) or two trials of the same OF test (Experiment 3). Overall, mice demonstrated a high degree of similarity in the temporal profile of novelty-induced horizontal and vertical exploration (regardless of the size, colour and shape of the OF), which remained stable in subsequent OF exposures. In Experiments 4 and 5, we tested F1 hybrid mice (BALB/c-S1; NMRI-S1), and Vitamin D receptor knockout mice (generated on S1 genetic background), again showing strikingly similar temporal patterns of their OF exploration, despite marked behavioural strain differences in anxiety and activity. These results suggest that mice are characterised by stability of temporal organization of their exploration in different OF novelty situations.     

The future prospects of electronic seed lists

For many botanic gardens worldwide, seed lists have provided a cost-effective means to replace plant losses in their collections for many decades, if not centuries. In seed lists, seeds are offered on the basis of what each garden can manage to collect and considers ‘of interest’ to other botanic gardens, some offering relatively few, while others offer many, or only wild collected seeds. Seed lists have always been printed on paper. With the use of printed seed lists, the amount of information per accession has always been quite limited to keep printing costs low. Over the past few years, electronic seed lists have been rapidly replacing printed seed lists. Since distribution is electronic, there is no longer a direct link between the amount of information provided and the cost per seed list sent out. This now offers new opportunities to share information that is linked to the plant material that botanic gardens exchange. Information is not limited to text, as images can also be included. This situation is beneficial if seed-raised plants are to be used for in situ conservation. Electronic seed lists have other advantages, but there are also some disadvantages. e.g., electronic information offered via websites is quite ephemeral in nature. Some suggestions are made to overcome the several drawbacks.     

Characterization of a highly glycosylated biosynthetic intermediate of ovalbumin

Ovalbumin extracted from oviduct slices incubated with [35S]methionine or [2-3]mannose contained two biosynthetic intermediates, OE and OF (Y. Kato, H. Iwase, and K. Hotta, 1984, J. Biochem. (Tokyo) 95, 455-463). In the present study, these intermediates are further characterized. The 3H dpm/35S dpm ratio of OF labeled with both [35S]methionine and [3H]mannose was twice that or greater than that of OE. The tritium-labeled OF migrated more slowly than OE on sodium dodecyl sulfate-gel electrophoresis and had a molecular weight exceeding that of OE by about 1500. These findings, along with the fact that [3H]OF had sugar chains similar to those of [3H]OE, suggest that OF may possibly have two sugar chains in one molecule. For confirmation of this, the glycosylation sites of OF were examined. Peptic and tryptic glycopeptides were prepared from [2-3H]mannose-labeled OF and the other ovalbumin subfractions--OA, OC, OD, and OE--and then analyzed by high-performance liquid chromatography. The peptic glycopeptides prepared from [3H]OF contained glycopeptides in addition to those derived from the other subfractions although tryptic glycopeptides obtained from [3H]OF were similar to those from the other subfractions. This shows that the above hypothesis is valid.     

Anti-ulcerogenic action of a combination of a psychostimulator of the phenylalkylsydnone imine series and arginine]

It has been revealed that OF 743, one of the psychostimulators belonging to phenylalkylsydnonimine derivatives, exerts anti-ulcerogenic action in case of stress- and ethanol-induced damage of gastric mucosa in rats. However OF 743 was not effective in case of indomethacin-induced gastric mucosal damage. Complex administration of OF 743 and arginine was accompanied by a considerable decrease of indomethacin-induced gastric mucosal damage. That combination was more effective than OF 743 alone in case of ethanol-induced gastric mucosal damage.     

Algebraic comparison of partial lists in bioinformatics

The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or to a meta-analysis comparison, it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained, instead of just one list. Here we introduce a method, based on permutations, for studying the variability between lists ("list stability") in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated by finding and comparing gene profiles on a large prostate cancer dataset, consisting of two cohorts of patients from different countries, for a total of 455 samples.     

Automatic term list generation for entity tagging

MOTIVATION: Many entity taggers and information extraction systems make use of lists of terms of entities such as people, places, genes or chemicals. These lists have traditionally been constructed manually. We show that distributional clustering methods which group words based on the contexts that they appear in, including neighboring words and syntactic relations extracted using a shallow parser, can be used to aid in the construction of term lists. RESULTS: Experiments on learning lists of terms and using them as part of a gene tagger on a corpus of abstracts from the scientific literature show that our automatically generated term lists significantly boost the precision of a state-of-the-art CRF-based gene tagger to a degree that is competitive with using hand curated lists and boosts recall to a degree that surpasses that of the hand-curated lists. Our results also show that these distributional clustering methods do not generate lists as helpful as those generated by supervised techniques, but that they can be used to complement supervised techniques so as to obtain better performance. AVAILABILITY: The code used in this paper is available from http://www.cis.upenn.edu/datamining/software_dist/autoterm/     

Opacity factor from group A streptococci is an apoproteinase

Opacity factor (OF) is an enzyme, elaborated by certain serotypes of group A streptococci, which produces opalescence in mammalian sera. OF has been designated a lipoproteinase. Lipoproteins are complex structures and many enzymes are involved in their catalysis. We therefore set out to establish which of the many enzymes OF could be. Results showed that OF rendered high density lipoprotein (HDL) insoluble, accounting for the opalescence in serum, and altered its electrophoretic mobility. Electron microscopy revealed that OF caused an aggregation of HDL and an alteration in molecule shape. OF specifically split apoprotein AI of HDL into two fragments demonstrable by SDS-PAGE. We therefore designate OF as an apoproteinase.     

BOOK REVIEWS

Books reviewed in this article:
MAMMALS OF THE SEA. BIOLOGY AND MEDICINE, edited by Sam. H. Ridgway
METHODS FOR THE ESTIMATION OF PRODUCTION OF AQUATIC ANIMALS, edited by G.G. Winberg
WATER TREATMENT by G. V. James
SEVENTY YEARS AGROWING—A HISTORY OF THE INTERNATIONAL COUNCIL FOR THE EXPLORATION OF THE SEA 1902–1972 by A. E. J. Went
FUNCTIONAL ANATOMY OF MARINE MAMMALS, edited by R. J. Harrison
FISH FARMING INTERNATIONAL, No. 1, 1973.     

丙氨酸消旋酶C-端结构域重组体的构建及其功能初探

[目的]将嗜碱芽孢杆菌丙氨酸消旋酶OF4DadX的N-端结构域分别与多个不同种属的丙氨酸消旋酶C-端结构域重组,探究丙氨酸消旋酶C-端结构域功能.[方法]利用基因拼接构建丙氨酸消旋酶重组基因,通过镍亲和层析纯化酶蛋白,采用D-氨基酸氧化酶偶联法检测重组酶蛋白的酶学特性,借助分子筛和HPLC液相色谱分析其聚合状态及动力学...     

Targeted disruption of the osteoblast/osteocyte factor 45 gene (OF45) results in increased bone formation and bone mass

We have previously described osteoblast/osteocyte factor 45 (OF45), a novel bone-specific extracellular matrix protein, and demonstrated that its expression is tightly linked to mineralization and bone formation. In this report, we have cloned and characterized the mouse OF45 cDNA and genomic region. Mouse OF45 (also called MEPE) was similar to its rat orthologue in that its expression was increased during mineralization in osteoblast cultures and the protein was highly expressed within the osteocytes that are imbedded within bone. To further determine the role of OF45 in bone metabolism, we generated a targeted mouse line deficient in this protein. Ablation of OF45 resulted in increased bone mass. In fact, disruption of only a single allele of OF45 caused significantly increased bone mass. In addition, knockout mice were resistant to aging-associated trabecular bone loss. Cancellous bone histomorphometry revealed that the increased bone mass was the result of increased osteoblast number and osteoblast activity with unaltered osteoclast number and osteoclast surface in knockout animals. Consistent with the bone histomorphometric results, we also determined that OF45 knockout osteoblasts produced significantly more mineralized nodules in ex vivo cell cultures than did wild type osteoblasts. Osteoclastogenesis and bone resorption in ex vivo cultures was unaffected by OF45 mutation. We conclude that OF45 plays an inhibitory role in bone formation in mouse.     

Peakmatch: a simple and robust method for peak list matching

Peak lists are commonly used in NMR as input data for various software tools such as automatic assignment and structure calculation programs. Inconsistencies of chemical shift referencing among different peak lists or between peak and chemical shift lists can cause severe problems during peak assignment. Here we present a simple and robust tool to achieve self-consistency of the chemical shift referencing among a set of peak lists. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned. The chemical shift referencing offset between two peak lists is determined by optimizing an assignment-free match score function using either a complete grid search or downhill simplex optimization. It is shown that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. Using a simulated peak list, the Peakmatch algorithm can also be used to obtain the optimal agreement between a chemical shift list and experimental peak lists. Combining these features makes Peakmatch a useful tool that can be applied routinely before automatic assignment or structure calculation in order to obtain an optimized input data set.     

BOOK REVIEWS

Books reviewed in this article.
SHARKS AND RAYS OF AUSTRALIA. By P. R. Last and J. D. Stevens
PARASITIC WORMS OF FISH. By Harford Williams and Arlene Jones
NUTRIENT REQUIREMENTS OF FISH. By the Committee on Animal Nutrition, Board on Agriculture, National Research Council
WATER QUALITY AND THE EARLY LIFE STAGES OF FISHES. Edited by L A. Fuiman
GENETICS AND EVOLUTION OF AQUATIC ORGANISMS. Edited by A. R. Beaumont
FISH BIOENERGETICS. By Malcolm Jobling
TRANSGENIC ANIMAL TECHNOLOGY, A LABORATORY HANDBOOK. Edited by Carl A. Pinkert
ECOLOGY OF MARINE PARASITES, 2nd edn. By K. Rohde
FRESHWATER FISHES OF VIRGINIA. By R. E. Jenkins and N. M. Burkhead     

Books Reviews

Book review in this article
INTERNATIONAL REGULATION OF WHALING: FROM CONSERVATION OF WHALING TO CONSERVATION OF WHALES AND REGULATION OF WHALE WATCHING . Patricia Birnie
BEHAVIOUR OF WHALES IN RELATION TO MANAGEMENT . G. P. Donovan (ed.).
A HANDBOOK FORTHEIDENTIFICATIONOFCEPHALOPODBEAKS . Malcolm R. Clarke(ed.).
THE WAR AGAINST THE SEALS: A HISTORY OF THE NORTH AMERICAN SEAL FISHERY . Briton Cooper Busch.
THE HARBOR SEAL . Doug Bertran Productions, Box 10340, Olympia, Washington 98502.