Analysis of sampling strategies for collecting genetic material1

A study was made using the data obtained during a 1973 expedition to collect wheat in Sicily in order to determine possible sampling strategies for collecting genetic resource material. Based on these analyses tables have been developed for selecting optimum sample sizes depending on relative cost and variance component considerations. It is almost impossible to make a general recommendation for optimum sampling strategy. Variation may be (andprobably is) different in diverse areas, thus what is true in Sicily may not be true for Ethiopia, etc. Also sampling strategy should be different for characters which are inherited quantitatively from those which are controlled by one or two genes. Visual selection will reduce quantitative genetic variation and thus will defeat the primary purpose of collecting geneticresource material, which is to preserve as much genetic variation as possible. On the other hand, all collectors intuitively collect forms which seem new or unusual to them. Certainly when collecting for specific characters, such as disease resistance, dwarf growth type, stem strength, etc., collectors will not resort to random sampling. Many of the traits are rare and only large samples will ensure that genes responsible for these traits will be represented in the collection.     

The Ladew expedition to Bolivia and Peru: George Tate’s Botanical Collections

In 1926 George Tate participated in a collecting expedition to the Cordillera Real of Bolivia and Peru under the auspices of H. S. Ladew and The American Museum of Natural History. Although the emphasis of the expedition was zoological, Tate managed to collect 1215 plant numbers from which over 50 new species were later described, primarily by H. H. Rusby. These specimens, including most types, were deposited at The New York Botanical Garden. Tate retained 632 duplicate sheets at the Museum to form the core of the “Ecological Herbarium of Dept. of Mammals.” The 24 collecting stations worked by Tate in Bolivia are described and mapped from data obtained from a transcribed copy of Tate’s field notes deposited in the archives of The New York Botanical Garden.     

Benthic isopods (Crustacea,Malacostraca) from the Ross Sea,Antarctica: species checklist and their zoogeography in the Southern Ocean

In this study isopod species of the Ross Sea were investigated. Literature until May 2008 was checked to provide an overview of all known and described species in the Ross Sea. This species checklist was then enlarged through material of the 19th Italica expedition in 2004. During this expedition for the first time a small mesh net (500 μm) was used. Nine thousand four hundred and eighty one isopod specimens were collected during this expedition. Through this material the number of isopod species in the Ross Sea increased from 42 to 117 species, which belong to 20 families and 49 genera. Fifty-six percentage of the isopods species collected during the Italica expedition are new to science. The zoogeography of the 117 species was investigated. A non-transformed binary presence-absence data matrix was constructed using the Bray–Curtis coefficient. The results were displayed in a cluster analysis and by nonmetric multidimensional scaling (MDS). This paper gives a first insight into the occurrence and distribution of the isopod species of the Ross Sea.     

New liverwort records for Vietnam

A short collecting expedition to Vietnam in 2016 yielded 700 specimens of 170 liverwort species of which 79 were new to the flora of Vietnam, including 43 species new to Indochina. Many of the newly recorded species have meta-Himalayan distributions (that predicts occurrence of these taxa in the areas of north-west Vietnam situated in the south-easternmost spurs of the Himalaya). Some species were recorded based on the study of living material, permitting the examination of oil body characteristics for Riccardia and Calypogeia. The known taxonomic liverwort diversity of Vietnam is currently 379 taxa, estimated to represent ca 80% of the actual taxonomic diversity in the country.     

关于植物DNA条形码研究技术规范

DNA条形码是利用标准的基因片段对物种进行快速鉴定的技术,已经成功用于生物物种分类和鉴定、生态学调查和生物多样性评估等研究领域。尽管生命条形码数据（BOLD）系统提供了主要针对动物类群DNA条形码研究的技术规范,但由于植物本身的生物学特性与所使用的条形码不同,因此已有技术规范并不完全适用于植物DNA条形码的研究。本文根据植物DNA条形码研究的特点与我国的实际情况,编写了植物DNA条形码研究技术标准和规范指南,具体包括十个方面的内容,即植物DNA条形码研究的样品采集策略;植物标本和野外数据的采集规范;植物标本图像信息的采集规范;植物DNA材料的采集规范;植物DNA材料的干燥与保存规范;植物总DNA的质量标准及保存规范;植物标准DNA条形码的选择与通用引物;DNA条形码的扩增与测序;DNA条形码数据的命名、编辑和提交规范;以及DNA条形码数据分析。我们期望通过这些标准规范的实施和在实践中的不断修订和完善,能为我国学者开展植物DNA条形码和iFlora研究提供参考和借鉴。
关键词：植物DNA条形码;技术规范;物种鉴定;标准;新一代植物志     

Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes

Aerobic anoxygenic photosynthetic bacteria (AAnP) were recently proposed to be significant contributors to global oceanic carbon and energy cycles. However, AAnP abundance, spatial distribution, diversity and potential ecological importance remain poorly understood. Here we present metagenomic data from the Global Ocean Sampling expedition indicating that AAnP diversity and abundance vary in different oceanic regions. Furthermore, we show for the first time that the composition of AAnP assemblages change between different oceanic regions, with specific bacterial assemblages adapted to open ocean or coastal areas respectively. Our results support the notion that marine AAnP populations are complex and dynamic, and compose an important fraction of bacterioplankton assemblages in certain oceanic areas.     

图位克隆技术在农作物基因分离中的应用与评价

图位克隆(Map-based cloning)作为分离基因的有效方法, 已在小基因组作物的基因分离中得到了广泛应用和发展, 而在具有大量重复DNA序列的大基因组作物中的应用仍存在挑战。基于图位克隆在基因分离中的重要性, 文章就图位克隆技术的基本内容及发展做简要概述, 着重对图位克隆技术在大基因组作物中的应用进行分析和评价, 同时对它今后可能的发展方向进行了讨论, 以期为大基因组作物基因的分离提供借鉴。     

Collecting,processing, and storing avian blood: a review

ABSTRACT With recent advances in molecular techniques, collecting blood from birds has become a common practice among field ornithologists. There are a variety of techniques for collecting blood samples and numerous caveats for how samples should be processed, depending on the research question being asked. Currently, few resources are available for individuals learning how to collect blood from birds or needing more information about how to process blood samples. Here, I describe commonly used methods for collecting, processing, and storing blood for particular research objectives, and provide answers to frequently asked questions about blood collection. The information provided is intended primarily for investigators working with passerines, but many techniques and suggestions are applicable to other avian taxa.     

Evidence of mutualistic synzoochory between cryptogams and hummingbirds

Endozoochory is usually involved in seed dispersal mutualisms, whereas ectozoochory is non‐rewarding, and therefore neutral (or even negative) for the animal vector. Synzoochory is an intermediate dispersal type between endo and ectozoochory in which propagules are deliberately transported (usually in the mouth) but with no ingestion or gut passage involved. We present empirical evidence of synzoochoric mutualism between the hummingbird Sephanoides sephaniodes and cryptogams (one fern and seven moss species). Two species (Lophosoria quadripinnata and Ancistrodes genuflexa) constituted the bulk of nest biomass, and another six moss species were present in lesser quantity. The hummingbird was selective when collecting nest material so that the nests contained a higher density of reproductive structures (that could be dispersed further) than natural patches of the cryptogam species. Even after one year, the nests maintained half of the original reproductive structures (sporangia, sporophytes) and biomass, constituting an important dispersal source. These results show a new type of mutualism in which mosses could be dispersed throughout longer distances (several km) by hummingbirds and to higher positions (particularly for ground‐living species, promoting dispersal potential). The hummingbird benefits from collecting cryptogam material for nest building, and cryptogams benefit from the concentration and relocation of diaspore sources into more effective recruiting sites. Similar mutualistic relationships could be a general phenomenon, of importance in many ecosystems.     

A new bird-flea Peru

A new species of bird-flea of the genusb Ceratophyllus is described from material collected from a nest of a cormorant during the 1937 Percy Sladen Trust expedition to Lake Titicaca, Peru.     

Identification of new genes by systematic analysis of cdnas and database construction

The large-scale collection of partial cDNA sequences is becoming a powerful tool in biology. Similarity or motif searches in DNA databases using these partial cDNA sequences have facilitated the discovery of new genes of interest. By collecting and registering large numbers of partial sequences with a well designed non-biased cDNA library, an expression profile of active genes in a particular tissue can be obtained. Tissue-specific or stage-specific genes can be discovered by comparing the profiles from different tissues or from a tissue at different stages of development, respectively. The compilation of such expression profiles enables genes to be mapped to the tissue(s) where they are actively transcribed. The large-scale collation of gene sequences actively expressed in the body into databases complements efforts directed towards the structural analysis of the genome, with the ultimate aim of decoding all the genetic information carried in the human genome. This cDNA strategy is also being widely applied to organisms other than man.     

On the Spiders Collected during the Swedish Expeditions to Novaya Zemlya and Yenisey in 1875 and 1876

The material collected in 1875 and determined by L. Koch has been revised. The material from 1876 has been determined and a list of 197 species from Russia, Novaya Zemlya and Siberia represented in the two collections is given and in addition 14 species collected by the 1875 expedition in Northern Norway. Hybauchenidium gen.n. of the fam. Erigonidae is established with Erigone aquilonaris L. Koch, 1879, as type species. Eboria sibirica sp.n. (Erigonidae), and Diplocephalus cristatus angustieeps subsp.n. (Erigonidae) are described. A list of the species described and recorded by L. Koch in 1879 with the actual names is given.     

Cardio-respiratory adaptation to physical exercise and hypoxia after a high-altitude expedition.

Seven young, male subjects were tested before and immediately after 6 weeks high-mountain expedition. Cardio-respiratory measurements were performed at rest and during standard physical excercise (10 min, 100 W) when breathing atmospheric air or hypoxic mixture (14% O2 in N2). After the expedition an increased V o2 max (16% an average) and diminished heart rate response to submaximal exercise were found. This was observed during air and hypoxic mixture breathing. There was significant increase in stroke volume and cardiac output during the exercise. No significant differences in ventilatory parameters were found nor at rest or during exercise under condition of breathing atmospheric air or hypoxic mixture. No changes in erythrocyte count or haemoglobin concentration in the blood were found. The physiological changes which developed during high-mountain expedition were more dependent on physical that hypoxic training.     

White lupin in cultivation in Iberia

This article arises from a recent expedition to collect seed samples of the white lupin (Lupinus albus) in Iberia. Observations on the distribution, uses, agronomy and status of the grain legume are presented. The cultivation of white lupin is more common in Portugal than in Spain where decreasing interest in the crop is leading to a gradual disappearance of potentially valuable genetic material.     

An Osteologic Study of Twenty-Nine Human Skulls from the Guajira Peninsula Region of Colombia-Venezuela

Abstract

Craniometric data is presented for two series of skulls.

In the year 193 5 a joint anthropological survey undertaken by Columbia University and the University Museum of the University of Pennsylvania uncovered 29 human skulls on the Guajira Peninsula of Colombia-Venezuela (Fig. 1) during research sponsored by the Latin-American Institute. The members of the expedition included: Dr. Vincenzo Petrullo, field director, and Mr. Lewis Korn, archeologist. Other members were Dr. Paul Kirchoff, Mrs. Hanna Kirchoff, Mrs. Gwyneth Browne Harrington, and Miss Lydia duPont. The skeletal material obtained by this expedition has been measured by Agogino, 1 and the results are presented in this paper.

The skeletal material for this study was divided into two major groups; the 35-30 series from Valera, Venezuela, and the 35-32 series from Cuzi, Venezuela. With the exception of three skulls, these two series were used for our calculations of means and for comparisons with other South American skull series.     

Collection and preliminary evaluation of sweet-stalk pearl millet (Pennisetum)

During a germplasm collecting expedition to Tamil Nadu, India, sweet-stalk types of pearl millet, Pennisetum americanum, were collected around Coimbatore (11°N) and Madurai (10°′N). The local farmers cut the crop before flowering for fodder and the ratoon crop provides some grain and straw. When planted at the International Crops Research Institute for the Semi-Arid Tropics Center, Patancheru (17°30N), these types flowered later and grew relatively tall in the rainy season in comparison with their growth during postrainy season. The sweet-stalk types are characterized by long narrow leaf blades, profuse nodal tillering with asynchronous maturity, short thin spikes, and very small grains as compared with the normal types. The sweet-stalk types could be easily identified by chewing them at the dough stage. At maturity they contained more than twice the amount of soluble sugars than the normal types.     

Mass spectrometry based approach for identification and characterisation of fluorescent proteins from marine organisms

We present here a new analytical strategy for identification and characterisation of fluorescent proteins from marine organisms. By applying basic proteomics tools it is possible to screen large sample collections for fluorescent proteins of desired characteristics prior to gene cloning. Our methodology which includes isolation, spectral characterisation, stability testing, gel-based separation and mass spectrometric identification was optimised on samples collected during the Danish Galathea 3 expedition. Four corals of the Fungia, Sarcophyton and Acropora species emitting green fluorescence were tested. Each of the fluorescent extracts behaves differently under denaturing conditions but complete fluorescence loss was not observed. Optimised electrophoretic conditions yielded effective separation of active fluorescent proteins in both 1DE and 2DE. Mass spectrometric analysis of the proteins in the fluorescent spots excised directly from unstained 2DE gels provides sequence information that might be sufficient to design degenerate primers for gene cloning. Identified fluorescent proteins are in agreement with the coral species determined by visual examination of the samples. The presented methodology is a viable alternative to direct gene cloning for the discovery of novel fluorescent proteins and will be further validated on other samples collected during the Galathea 3 expedition.     

Gut wash,body soak,blender and heat-fixation: approaches to the effective collection,fixation and preservation of trematodes of fishes

Advice is offered on some effective methods for collecting and preserving trematodes from fishes for taxonomy and systematics. Emphasis is placed on obtaining high-quality specimens that have reliable data and that are amenable to study by both morphological and molecular approaches. We emphasise the importance of the freshness of the host specimen, the reliability of its provenance and the labelling of the specimens. For the collecting itself, we recommend a ‘gut-wash’ approach for gastro-intestinal species and specific searches for atypical taxa such as didymozoids, aporocotylids, Saturnius Manter, 1969 and transversotrematids. For metacercariae, we recommend a ‘blender’ approach to release parasites from host tissues. For fixation, we argue in favour of heat-killing in fluid at close to boiling temperature. We recommend against flattening as a routine procedure for collecting specimens for morphology. Preservation for morphological study is best in formalin or alcohol, and alcohol works well for molecular samples. The importance of reliable labelling and the deposition of specimens in museums is emphasised.     

Functionally-stabilized proteins--a review

The maintenance or stabilization of protein or enzyme function is of vital importance in Biotechnology. Investigations of thermophilic organisms, studies of denaturation and the use of enzymes in organic solvents have each contributed to an understanding of protein stability. Enzymes can reliably and reproducibly be stabilized by variety of means including immobilization, use of additives, chemical modification in solution and protein engineering. Examples of each of these are discussed. With these recent advances it appears that a rational strategy for achieving a particular stabilized enzyme or protein may be within reach.