Tetrataxis: a loosely attached limpet-like foraminifer from the Upper Palaeozoic

Associations of Tetrataxis preserved in situ and attached to a varicty of biogenic substrates are described from the Carboniferous of northern and central England. Environmental changes considered unsuitable for foraminiferal activity initially caused the tetrataxids to cling to their substrates of attachment in a similar way that limpets do when disturbed. Before conditions conducive to foraminiferal activity returned, the development of encapsulating fabrics (of either organic. cement or sediment origin) effected their preservation in life position. Comparisons made with Recent foraminifera. together with an appreciation of distributional data and the development of hard and soft tissue morphologies. provides strong evidence to suggest that Tetrataxis was primarily a loosely adherent, but mobile, phytal form which grazed upon benthic algae and a variety of marine invertebrates in search of food and shelter. *** Tetrataxis, Carboniferous, foraminifera, mode of life.     

PALYNOLOGY AND SYSTEMATICS OF THE LYTHRACEAE. III. GENERA PHYSOCALYMMA THROUGH WOODFORDIA,ADDENDA, AND CONCLUSIONS

Pollen of the 27 genera presently recognized as comprising the family Lythraceae have been surveyed with light microscopy and scanning and transmission electron microscopy. Results for five genera (Physocalymma, Pleurophora, Rotala, Tetrataxis, Woodfordia), in addition to Duabanga, Sonneratia, and Punica (assigned to the Lythraceae in some classifications), are presented here; the remaining genera were treated previously in the series. The family is revealed as the most diverse palynologically of the order Myrtales. The most simple pollen type and the one common to the largest number of genera is prolate-spheroidal to prolate; tricolporate, without pseudocolpi; psilate, scabrate or finely verrucate; and 16–28 μm or less in length. Specializations include oblate grains, development of pseudocolpi (three or six in number), diversification of exine sculpturing, broadening of the colpal and pseudocolpal areas, and reduction in the conspicuousness of the colpi. Pollen evidence provides qualified support for inclusion of Punica in the Lythraceae, the generalized nature of the pollen tempering the conclusion, and little support for inclusion of Sonneratia and Duabanga in the family. Completion of the survey provides a data base of pollen characters that will be integrated in future studies with other evidence into an overall phenetic and cladistic assessment of the family leading to production of a more natural classification.     

Estimating the probability of illegal desert tortoise collection in the Sonoran Desert

The expansion of road networks in desert tortoise (Gopherus agassizii) habitat in the Sonoran Desert has raised questions concerning appropriate mitigation to reduce impacts at the population level. Although some effects, namely road-kill and habitat loss, have been well documented, illegal tortoise collection has been insufficiently addressed. It has become increasingly important for wildlife and land-use managers to understand the cumulative impacts of roads on tortoises and the effect that those impacts have on population persistence. We estimated the probability of desert tortoise detection and collection along 2-lane paved, maintained gravel, and non-maintained gravel roads to evaluate whether collection probabilities were related to road type. Although collection probability did not vary by road type, the probability of desert tortoise detection by passing motorists was greatest on maintained gravel roads and fewest on non-maintained gravel and paved roads. These results have implications for effectively mitigating the impacts of roads on desert tortoises. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.     

Small molecule interactions were central to the origin of life

Many scientists believe life began with the spontaneous formation of a replicator. This idea has been supported by "prebiotic" syntheses carried out by chemists using modern apparatus and purified reagents. The probability that such reactions would take place spontaneously on the early Earth is minute. These points are illustrated here by considering the often cited oligomerization of activated RNA components by clay minerals. A more likely alternative for the origin of life is one in which a collection of small organic molecules multiply their numbers through catalyzed reaction cycles, driven by a flow of available free energy. Although a number of possible systems of this type have been discussed, no experimental demonstration has been made. The inclusion of a "driver" reaction, directly coupled to the energy source, may lead to a solution.     

植物模式标本数据整合新的机遇与挑战

命名模式是分类群名称永久依附的成分,在分类学研究中有不可替代的价值。中国复杂的植物采集历史以及对中国植物标本开展研究的单位各异,导致我国植物模式标本零散分布于全球各大标本馆,给分类工作的开展带来了极大的困难。标本数字化的开展为模式标本数据整合提供了新的机遇,同时也给我们带来了人名和地名标准化以及模式类型确认等方面的挑战。我国于2006年开始对模式标本数据进行收集和整理,迄今已完成国内外20余家标本馆9万余条标本数据的收集。模式考证和模式类型清理是我们下一步亟须开展的工作,同时我们应将地名变更资料、人名考证资料进行整合并建立相应的数据库以推动模式标本数据的标准化。这将在很大程度上有助于我们摸清中国模式标本的家底。     

Automated crystal mounting and data collection for protein crystallography

To increase the efficiency of diffraction data collection for protein crystallographic studies, an automated system designed to store frozen protein crystals, mount them sequentially, align them to the X-ray beam, collect complete data sets, and return the crystals to storage has been developed. Advances in X-ray data collection technology including more brilliant X-ray sources, improved focusing optics, and faster-readout detectors have reduced diffraction data acquisition times from days to hours at a typical protein crystallography laboratory [1,2]. In addition, the number of high-brilliance synchrotron X-ray beam lines dedicated to macromolecular crystallography has increased significantly, and data collection times at these facilities can be routinely less than an hour per crystal. Because the number of protein crystals that may be collected in a 24 hr period has substantially increased, unattended X-ray data acquisition, including automated crystal mounting and alignment, is a desirable goal for protein crystallography. The ability to complete X-ray data collection more efficiently should impact a number of fields, including the emerging structural genomics field [3], structure-directed drug design, and the newly developed screening by X-ray crystallography [4], as well as small molecule applications.     

MolMovDB: analysis and visualization of conformational change and structural flexibility

The Database of Macromolecular Movements (http://MolMovDB.org) is a collection of data and software pertaining to flexibility in protein and RNA structures. The database is organized into two parts. Firstly, a collection of 'morphs' of solved structures representing different states of a molecule provides quantitative data for flexibility and a number of graphical representations. Secondly, a classification of known motions according to type of conformational change (e.g. 'hinged domain' or 'allosteric') incorporates textual annotation and information from the literature relating to the motion, linking together many of the morphs. A variety of subsets of the morphs are being developed for use in statistical analyses. In particular, for each subset it is possible to derive distributions of various motional quantities (e.g. maximum rotation) that can be used to place a specific motion in context as being typical or atypical for a given population. Over the past year, the database has been greatly expanded and enhanced to incorporate new structures and to improve the quality of data. The 'morph server', which enables users of the database to add new morphs either from their own research or the PDB, has also been enhanced to handle nucleic acid structures and multi-chain complexes.     

西藏普兰县姜叶玛地区中二叠统西兰塔组中的有孔虫及其地质意义

西藏雅鲁藏布江缝合带蛇绿混杂岩中混杂着大小不一的二叠纪灰岩块体,它的来源一直颇有争议,这些灰岩块体中动物群的古生物地理面貌是判断其来源的重要手段。姜叶玛灰岩体是位于西藏普兰县境内混杂在中生代蛇绿混杂岩中的一个大型二叠纪灰岩块体。其中,中二叠世西兰塔组中含有丰富的非?有孔虫化石,它们主要由Neodiscus,Climacammina,Pachyphloia和Lysites组成,伴生有Dagmarita,Deckerella,Globivalvulina,Neoendothyra,Lasiodiscus,Lasiotrochus,Tetrataxis,Geinitzina,Ichthyofrondina,Nodosaria,Nodosinelloides,Agathammina,Septoagathammina和Shanita,时代相当于中二叠世Capitanian期。古生物地理上,Lysites和Shanita的出现表明这个动物群属于基墨里生物区,它们从古生物地理上以及生物多样性上和印度板块北缘的巴基斯坦盐岭地区以及藏南喜马拉雅区的同时代动物群有显著差别。结合前期?类动物群古生物地理的研究,姜叶玛灰岩块体很可能位于拉萨地块与喜马拉雅之间的新特提斯洋海山上,与两个地块之间都有一定的隔离。这也说明新特提斯打开的时间早于中二叠世。     

Identification of Enterococcus spp. with a biochemical key.

A six-step biochemical key is presented for the identification of all recognized Enterococcus spp. The key consists of 12 tests, but no more than 6 are needed for the most complicated identification. The reliability of the key has been evaluated with collection type strains and clinical and environmental isolates. This key has fewer tests than those reported in previous studies. There is no commercial kit that includes the whole set of tests. However, some of the tests are included in enzyme activity-based kits that could be used with the proposed key. The key is designed for use in routine applications, especially in environmental and clinical studies with a high number of isolates.     

Assessment of sexual behavior and effect of semen collection pen design and sexual stimulation of boars on behavior and sperm output--a review

The importance of sexual behavior and factors influencing sexual behavior of AI boars has received minimal study. The majority of studies reviewed used a very small number of boars. A sexual behavior index (SBI) has been developed for naturally mating boars but not for AI boars. Some studies have reported significant correlations between sexual behavior traits and semen characteristics; while other studies did not find significant correlations. A new semen collection pen design (Reicks Design) has reduced the duration of time a boar requires to mount a dummy sow after entering the collection pen and the duration of time needed to exit the collection pen after ejaculation. In general, the observation of another boar mounted on the dummy sow prior to collection, releasing the penis after extension, exposing boars to non-estrous gilts for 2 days before collecting semen, placing a non-estrous gilt underneath a dummy, and removing the boar for 2 min after first mount did not enhance the number of sperm cells collected. Treatment of boars with PGF2alpha has facilitated the training of sexually experienced boars to mount a dummy sow but not that of sexually inexperienced boars. In general, the treatment of boars with PGF2alpha did not increase the total number of spermatozoa ejaculated.     

Methods of collection for salivary cortisol measurement in dogs

Salivary cortisol has been increasingly used as a measure of stress response in studies of welfare, reaction to stress and human-animal interactions in dogs and other species. While it can be a very useful measure, there are a number of saliva collection issues made evident through studies in the human and animal fields which have not been investigated in the canine species. Collection materials and the volume of saliva that is collected; the use of salivary stimulants; and the effect of food contamination can all dramatically impact cortisol measurement, leading to spurious results. In order to further examine the limitations of the collection method and the effects of collection material and salivary stimulant on salivary cortisol levels, a series of clinical, in vitro and in vivo studies were performed. It was found that there is a large amount of inter- and intra-individual variation in salivary cortisol measurement. Beef flavoring of collection materials leads to unpredictable variability in salivary cortisol concentration. Using salivary stimulants such as citric acid also has the potential to affect cortisol concentration measurement in saliva. Hydrocellulose appears to be a useful collection material for salivary cortisol determination. Recommendations for collection materials and use of salivary stimulants are presented.     

Identification of Enterococcus spp. with a Biochemical Key

A six-step biochemical key is presented for the identification of all recognized Enterococcus spp. The key consists of 12 tests, but no more than 6 are needed for the most complicated identification. The reliability of the key has been evaluated with collection type strains and clinical and environmental isolates. This key has fewer tests than those reported in previous studies. There is no commercial kit that includes the whole set of tests. However, some of the tests are included in enzyme activity-based kits that could be used with the proposed key. The key is designed for use in routine applications, especially in environmental and clinical studies with a high number of isolates.     

Multiple Locus Variable number of tandem repeat Analysis: A molecular genotyping tool for Paenibacillus larvae

American Foulbrood, caused by Paenibacillus larvae, is the most severe bacterial disease of honey bees (Apis mellifera). To perform genotyping of P. larvae in an epidemiological context, there is a need of a fast and cheap method with a high resolution. Here, we propose Multiple Locus Variable number of tandem repeat Analysis (MLVA). MLVA has been used for typing a collection of 209 P. larvae strains from which 23 different MLVA types could be identified. Moreover, the developed methodology not only permits the identification of the four Enterobacterial Repetitive Intergenic Consensus (ERIC) genotypes, but allows also a discriminatory subdivision of the most dominant ERIC type I and ERIC type II genotypes. A biogeographical study has been conducted showing a significant correlation between MLVA genotype and the geographical region where it was isolated.     

The rediscovery of Biebersteinia orphanidis Boiss. (Geraniaceae) in Greece

Biebersteinia orphanidis was considered extinct from Greece and Europe as it had not been collected since Orphanides' type collection of 1851. Its rediscovery is reported here from a mountain close to the classical locality. The species serves as a distinct phytogeographical link between the floras of Greece and Anatolia. In Greece, at least, it grows in a critically low number of individuals. Data on the species habitat and population status are given, and potential threats to its survival are discussed.     

Quantification of Goods Purchases and Waste Generation at the Level of Individual Households

Quantifying differences in resource use and waste generation between individual households and exploring the reasons for the variations observed implies the need for disaggregated data on household activities and related physical flows. The collection of disaggregated data for water use, gas use, electricity use, and mobility has been reported in the literature and is normally achieved through sensors and computational algorithms. This study focuses on collecting disaggregated data for goods consumption and related waste generation at the level of individual households. To this end, two data collection approaches were devised and evaluated: (1) triangulating shopping receipt analysis and waste component analysis and (2) tracking goods consumption and waste generation using a smartphone. A case study on two households demonstrated that it is possible to collect quantitative data on goods consumption and related waste generation on a per unit basis for individual households. The study suggested that the type of data collected can be relevant in a number of different research contexts: eco‐feedback; user‐centered research; living‐lab research; and life cycle impacts of household consumption. The approaches presented in this study are most applicable in the context of user‐centered or living‐lab research. For the other contexts, alternative data sources (e.g., retailers and producers) may be better suited to data collection on larger samples, though at a lesser level of detail, compared with the two data collection approaches devised and evaluated in this study.     

The type material of Mantodea (praying mantises) deposited in the National Museum of Natural History,Smithsonian Institution,USA

The collection of Mantodea of the National Museum of Natural History, Smithsonian Institution, includes 26 holotypes, 7 allotypes, 4 lectotypes, 23 paratypes, and 1 paralectotype. Four type specimens were designated as lectotypes within this work. Highly accurate measurement data, high resolution images of specimens and labels, verbatim label data, georeferenced coordinates, original and newly assigned database codes, and bibliographic data are presented for all primary types. Label data for all paratype specimens in the collection are provide in tabular form. The location of the USNM collection has been moved to the Cleveland Museum of Natural History as a loan under the Off-site Enhancement Program.     

Index to the vascular plant types collected by H. H. Smith near Santa Marta,Colombia

An index to 360 names based on specimens collected from 1898 to 1901 by H. H. Smith in Santa Marta, Colombia is provided. Each citation includes the plant name, author, place of publication, exact locality and date of collection, and, when possible, the location of the holotype and isotypes. Additional comments are provided to clarify the type status of specimens representing a single taxon and given a single collection number but collected on several different dates or from several different localities, and for truly mixed collections where two or more taxa were given the same number.     

微生物气溶胶采集技术的特点及应用

微生物气溶胶是悬浮于空气中粒径差异显著的生物粒子。污水处理、垃圾填埋等污水和固体废弃物的处理过程会产生大量的微生物气溶胶。近年来,随着对微生物气溶胶的不断认识,对其产生、逸散以及危害环境和人体的研究越来越多。在过去的150年,研究者们研发了多种微生物气溶胶采集技术和仪器设备,每种采集技术各有特点和适用条件。本文阐述沉降法、惯性采样法和过滤法3种典型微生物气溶胶采集技术的特点和原理,分析各种采样设备的适用性,为微生物气溶胶的采集和研究提供参考。     

Distribution and Abundance of Insertion Sequences among Natural Isolates of Escherichia coli

A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS1, IS2, IS3, IS4, IS5 and IS30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS4 and IS30.