Yeast culture collections of the world: meeting the needs of industrial researchers

The importance of selecting optimal yeast strains for research or industrial applications is often underestimated. For example, utilizing a strain background that already provides the desired stress tolerance or nutrient utilization profile can eliminate costly strain optimization. Yeast culture collections can provide not only the yeast strains but also data and curator expertise to help narrow the search for the optimal strain. While some collections are known for a broad range of cultures and services, other "boutique" collections can provide a broader selection of strains of certain categories, a surprising amount of characterization data, and assistance in selecting strains. This article provides information on dozens of yeast collections of the world, profiles of selected yeast culture collections, and the services that they provide: e.g., strain preservation for patent or safe deposit purposes, species identification service, training workshops, and consulting on yeast identification and physiology. Utilization of these services can save industrial researchers valuable time and resources.     

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction

Expression arrays facilitate the monitoring of changes in the expression patterns of large collections of genes. The analysis of expression array data has become a computationally-intensive task that requires the development of bioinformatics technology for a number of key stages in the process, such as image analysis, database storage, gene clustering and information extraction. Here, we review the current trends in each of these areas, with particular emphasis on the development of the related technology being carried out within our groups.     

On the scientific,medical, dental and educational value of collections of human skeletons

Having been approached from time to time by various museum, university and governmental authorities in Australia, California and Scotland, I have set down some brief notes on the scientific, medical, dental and educational importance and value of collections of recent human skeletons drawn from populations in all parts of the world. This article does not pretend to completeness. It has been set down in the hope that it may be of assistance to those officiers in charge of such collections and who may be pondering upon the worthwhileness of such collections being retained and maintained.     

Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains

A major challenge in the post-genomic era is the development of experimental approaches to monitor the properties of proteins on a proteome-wide level. It would be particularly useful to systematically assay protein subcellular localization, post-translational modifications and protein-protein interactions, both at steady state and in response to environmental stimuli. Development of new reagents and methods will enhance our ability to do so efficiently and systematically. Here we describe the construction of two collections of budding yeast strains that facilitate proteome-wide measurements of protein properties. These collections consist of strains with an epitope tag integrated at the C-terminus of essentially every open reading frame (ORF), one with the tandem affinity purification (TAP) tag, and one with the green fluorescent protein (GFP) tag. We show that in both of these collections we have accurately tagged a high proportion of all ORFs (approximately 75% of the proteome) by confirming expression of the fusion proteins. Furthermore, we demonstrate the use of the TAP collection in performing high-throughput immunoprecipitation experiments. Building on these collections and the methods described in this paper, we hope that the yeast community will expand both the quantity and type of proteome level data available.     

Effects of the spatial repellent metofluthrin on landing rates of outdoor biting anophelines in Cambodia,Southeast Asia

The emergence of artemisinin‐resistant malaria in Southeast Asia is a major problem. The fact that many people become infected with malaria when they are outside has prompted the development of ‘spatial’ rather than topical repellents. The respective effects of one or four slow‐release emanators of metofluthrin, a pyrethroid, were tested in Pailin, Pursat and Koh Kong, Cambodia. Numbers of mosquitoes counted in outdoor landing catches when one or four emanators were suspended close to the collector were compared with control collections. In Pailin, the effects of emanators on catches in Furvela tent traps and Centers for Disease Control (CDC) light traps suspended underneath houses were also investigated. Rate ratios were used to determine differences. A total of 29 255 mosquitoes were collected over 2934 h of landing collections, 87 nights of tent trapping and 81 nights of light trap capture. In Pailin, landing rates were reduced by 48% by a single emanator and by 67% by four emanators (P < 0.001). Similar reductions were observed in the number of mosquitoes collected in tent traps and the number of anophelines only collected in light traps. Results were similar in Pursat, but, for unknown reasons, those in Koh Kong showed no difference between control and metofluthrin collections (P > 0.05). These findings suggest that although the product can produce a significant effect, it requires further improvement.     

CAFTAN: a tool for fast mapping, and quality assessment of cDNAs

Background  

The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics.     

Do living ex situ collections capture the genetic variation of wild populations? A molecular analysis of two relict tree species,Zelkova abelica and Zelkova carpinifolia

Botanic gardens and arboreta, particularly in regions where iconic relict trees naturally occur, play a vital role in the conservation of these species. Maintaining well-managed living ex situ collections of rare and threatened relict tree species provides an immediate insurance policy for the future species conservation. The aim of this research was to investigate the origin, representativeness and genetic diversity of relict trees kept in botanic gardens and arboreta. We used as a model two ecologically and biogeographically distinct members of the prominent relict genus Zelkova (Ulmaceae), which survived the last glaciation in disjunct and isolated refugial regions: Z. carpinifolia in Transcaucasia and Z. abelicea endemic to Crete (Greece) in the Mediterranean. Our study revealed substantial differences in the genetic diversity and the origin of living ex situ collections of the two investigated taxa. The living ex situ collections of Z. carpinifolia have relatively high representativeness compared with the global genetic variability of natural stands identified in a previous study. In contrast, Z. abelicea, which possesses an extraordinarily high genetic variability in natural populations, is clearly underrepresented in botanic garden collections. Moreover, all Z. abelicea trees investigated in this study most probably originated from a single region, the Levka Ori in western Crete. Thus, the ex situ conservation of Z. abelicea requires major planning and coordination efforts, including the establishment of well-documented collections in botanic gardens in Greece and especially on Crete. New living ex situ collections should be created using plant material collected from all of the mountain regions where Z. abelicea still occurs. Our study highlights the need for re-evaluating the existing living ex situ collections of trees and the development of new strategies for future conservation efforts in botanic gardens and arboreta. The coordination of conservation efforts between gardens must be enhanced to prioritize actions for the most threatened relict tree species.     

Securing a future for China's plant biodiversity through an integrated conservation approach

The severely threatened Chinese flora urgently needs a new, well adapted to China and properly formulated conservation strategy. The present review provides a detailed conservation methodology that complements previously described guidelines for preservation of plant species with extremely small populations (PSESP) in China. This review adds to the above concept in several aspects, making it relevant to all threatened Chinese plant species. The proposed integral conservation strategy has the following crucial components: -ecoregional basis for conservation planning and implementation; -a unified scoring system that is used in regional systematic planning for reserve design, monitoring and assessment of efficiency of a reserve network, and creation of seed banks and living collections; -a focus on population demography and the presence of naturally occurring regeneration as the key criteria for defining the conservation status of a species and the appropriate major focus of the species recovery plan; -creation of multi-species living collections that preserve species genetic variation and provide material for in situ actions; -experimental translocation of threatened species into multiple locations within and outside their known range. Adopting and implementing these strategies successfully and more fully in China requires that the country changes PA legislation and improves PA management, the National Science Foundation of China (NSFC) re-prioritizes the type of research that receives research funds, and local scientists improve their approach toward information sharing.     

Large‐scale molecular genetic analysis in plant‐pathogenic fungi: a decade of genome‐wide functional analysis

Plant‐pathogenic fungi cause diseases to all major crop plants world‐wide and threaten global food security. Underpinning fungal diseases are virulence genes facilitating plant host colonization that often marks pathogenesis and crop failures, as well as an increase in staple food prices. Fungal molecular genetics is therefore the cornerstone to the sustainable prevention of disease outbreaks. Pathogenicity studies using mutant collections provide immense function‐based information regarding virulence genes of economically relevant fungi. These collections are rich in potential targets for existing and new biological control agents. They contribute to host resistance breeding against fungal pathogens and are instrumental in searching for novel resistance genes through the identification of fungal effectors. Therefore, functional analyses of mutant collections propel gene discovery and characterization, and may be incorporated into disease management strategies. In the light of these attributes, mutant collections enhance the development of practical solutions to confront modern agricultural constraints. Here, a critical review of mutant collections constructed by various laboratories during the past decade is provided. We used Magnaporthe oryzae and Fusarium graminearum studies to show how mutant screens contribute to bridge existing knowledge gaps in pathogenicity and fungal–host interactions.     

Adaptational assistance in clusters of bacterial chemoreceptors

Sensory adaptation of low-abundance chemoreceptors in Escherichia coli requires assistance from high-abundance receptors, because only high-abundance receptors carry the carboxyl-terminal pentapeptide sequence NWETF that enhances adaptational covalent modification. Using membrane vesicles containing both high-abundance receptor Tar and low-abundance receptor Trg, we observed effective assistance in vitro for all three adaptational modifications: methylation, demethylation and deamidation. These results demonstrated that adaptational assistance involves not only the previously documented assistance for methylation but also assistance for the two CheB-catalysed reactions. We determined rates of assisted methylation and demethylation at many ratios of assisting to assisted receptor. Analysis by a model of assistance indicated one Tar dimer could assist seven Trg dimers in methylation or five in demethylation, defining assistance neighbourhoods. These neighbourhoods were larger than a trimer of homodimers, required only receptors and were minimally affected by formation of signalling complexes. Time courses of assisted Trg methylation in membranes with low amounts of Tar showed that assisting receptors did not diffuse beyond initial neighbourhoods for at least two hours. Taken together, these observations indicate that chemoreceptors can form stable neighbourhoods larger than trimers in the absence of other chemotaxis proteins. Such interactions are likely to occur in natural receptor clusters in vivo.     

Collecting collections: building the library of The New York Botanical Garden

The history of the collections in the Library of The New York Botanical Garden includes the acquisition of previously accumulated collections as well as individual items acquired in the normal course of collection development. Particularly during the first 50 years of the institution, collections of library materials were acquired along with herbaria specimens, and, occasionally, collections of living plants, assembled by an individual as part of his or her personal research interests. While curatorial practice dictates that such an assemblage of research materials be separated when shifted from individual to institutional curatorship, the knowledge of the whole of the collection as received may fill in the background pattern of institutional collection development. A chronological table of these collections is appended, including reference to any extended discussion or listing.     

微藻种质资源库——藻类科学研究和产业发展的重要平台

微藻是指一类形态微小, 能够进行光合作用, 以单细胞或简单多细胞形式存在的藻类。作为一类重要的生物资源, 活体微藻的保藏和共享服务是开展藻类科学研究和藻类产业发展的必要平台和基础。坐落于中国科学院水生生物研究所的淡水藻种库(FACHB-Collection)正式成立于1973年, 1996年作为创会成员加入中国科学院典型培养物保藏委员会; 2019年成为国家水生生物种质资源库的核心成员。该库保藏逾3400株微藻, 隶属于9门169属。年均为国内外用户提供2500株藻株, 并提供藻种鉴定、分离纯化和培养技术等方面的服务和咨询。文章回顾了国际微藻种质资源库的发展历史和现状, 介绍了国内微藻种质资源保藏情况, 着重介绍国家水生生物种质资源库——淡水藻种库在库藏藻株多样性、共享服务、藻株无菌化、超低温保藏技术及优良品种选育与应用等方面的进展, 瞄准提升我国在藻类学研究和藻类产业研发的竞争力, 提出了藻种资源库未来发展的建议。     

Successful treatment of 19 consecutive groin lymphoceles with the assistance of intraoperative lymphatic mapping

Postoperative groin lymphoceles that fail to resolve spontaneously or with interventional therapy present a formidable problem that is associated with a high degree of morbidity. Numerous interventional methods and operative techniques have been described to treat these fluid collections, yet recurrence rates remain high. The use of lymphatic mapping has gained widespread use in the treatment of cutaneous malignancies and breast cancer and has been proven effective in delineating the course of lymphatic channels. We present here a series of 17 consecutive patients with 19 problematic groin lymphoceles who were treated with the assistance of intraoperative lymphatic mapping using isosulfan blue dye. To date there have been no recurrences and minimal morbidity associated with the technique and prescribed postoperative treatment regimen.     

Brain collections at the National Museum of Health and Medicine

Owing in large part to the foresight and efforts of Wally Welker, the National Museum of Health and Medicine has become a major repository for collections of brain specimens vital to the study of neurobehavioral evolution. From its origins in the Armed Forces Institute of Pathology, with the collection of largely pathological specimens assembled by Paul Yakovlev, the museum has added to its resources four additional extensive collections, largely consisting of specimens acquired specifically for comparative and evolutionary studies: Welker's collection from the University of Wisconsin-Madison, John I. Johnson's collection from Michigan State University, the Adolf Meyer Collection from the Johns Hopkins University, and the Elizabeth Crosby collections from the University of Michigan. We describe here the history and contents of each of these five collections, to inform the scientific field of the extent and details of these remarkable resources.     

The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis

Patterns of genetic diversity within populations of human pathogens, shaped by the ecology of host-microbe interactions, contain important information about the epidemiological history of infectious disease. Exploiting this information, however, requires a systematic approach that distinguishes the genetic signal generated by epidemiological processes from the effects of other forces, such as recombination, mutation, and population history. Here, a variety of quantitative techniques were employed to investigate multilocus sequence information from isolate collections of Neisseria meningitidis, a major cause of meningitis and septicemia world wide. This allowed quantitative evaluation of alternative explanations for the observed population structure. A coalescent-based approach was employed to estimate the rate of mutation, the rate of recombination, and the size distribution of recombination fragments from samples from disease-associated and carried meningococci obtained in the Czech Republic in 1993 and a global collection of disease-associated isolates collected globally from 1937 to 1996. The parameter estimates were used to reject a model in which genetic structure arose by chance in small populations, and analysis of molecular variation showed that geographically restricted gene flow was unlikely to be the cause of the genetic structure. The genetic differentiation between disease and carriage isolate collections indicated that, whereas certain genotypes were overrepresented among the disease-isolate collections (the "hyperinvasive" lineages), disease-associated and carried meningococci exhibited remarkably little differentiation at the level of individual nucleotide polymorphisms. In combination, these results indicated the repeated action of natural selection on meningococcal populations, possibly arising from the coevolutionary dynamic of host-pathogen interactions.     

Cryopreserved storage of clonal germplasm in the USDA National Plant Germplasm System

The US Department of Agriculture-Agricultural Research Service (USDA-ARS), National Plant Germplasm System (NPGS) plant collections are a critical source of genetic diversity for breeding and selection of improved crops, including vegetatively propagated plants. Information on these collections is readily accessible to breeders and researchers on the internet from the Germplasm Resources Information Network (GRIN). The clonal collections are at risk for loss due in part to their genetic diversity that makes growing them in one location a challenge, but also because it is difficult to have duplicate collections without incurring great expense. The development of cryopreservation techniques during the last two decades provides a low maintenance form of security backup for these collections. National plant collections for vegetatively propagated crop plants and their wild relatives are maintained by the USDA-ARS, NPGS at 15 sites across the country. These sites include various combinations of field, greenhouse, screenhouse, and in vitro collections. Cryopreserved backup collections in liquid nitrogen storage were instituted in the 1990s, increased greatly in the 2000s with the advent of new techniques, and are continuing today. Collections of dormant buds of temperate trees, shoot tips of in vitro cultures of many crops, and embryonic axes of some large seeded or recalcitrant seeded plants are all part of the clonal backup storage system.     

Assembling the archaeal ribosome: roles for translation-factor-related GTPases

The assembly of ribosomal subunits from their individual components (rRNA and ribosomal proteins) requires the assistance of a multitude of factors in order to control and increase the efficiency of the assembly process. GTPases of the TRAFAC (translation-factor-related) class constitute a major type of ribosome-assembly factor in Eukaryota and Bacteria. They are thought to aid the stepwise assembly of ribosomal subunits through a 'molecular switch' mechanism that involves conformational changes in response to GTP hydrolysis. Most conserved TRAFAC GTPases are involved in ribosome assembly or other translation-associated processes. They typically interact with ribosomal subunits, but in many cases, the exact role that these GTPases play remains unclear. Previous studies almost exclusively focused on the systems of Bacteria and Eukaryota. Archaea possess several conserved TRAFAC GTPases as well, with some GTPase families being present only in the archaeo-eukaryotic lineage. In the present paper, we review the occurrence of TRAFAC GTPases with translation-associated functions in Archaea.     

High‐throughput species identification: from DNA isolation to bioinformatics

Ichthyoplankton collections provide a valuable means to study fish life histories. However, these collections are greatly underutilized, as larval fishes are frequently not identified to species due to their small size and limited morphological development. Currently, there is an effort underway to make species identification more readily available across a broad range of taxa through the sequencing of a standard gene. This effort requires the development of new methodologies to both rapidly produce and analyse large numbers of sequences. The methodology presented in this paper addresses these issues with a focus on the larvae of large pelagic fish species. All steps of the methodology are targeted towards high‐throughput identification using small amounts of tissue. To accomplish this, DNA isolation was automated on a liquid‐handling robot using magnetic bead technologies. Polymerase chain reaction and a unidirectional sequencing reaction followed standard protocols with all template cleanup and transferring also automated. Manual pipetting was thus reduced to a minimum. A character‐based bioinformatics program was developed to handle the large sequence output. This program incorporates base‐call quality scores in two types of sample to voucher sequence comparisons and provides suggested identifications and sequence information in an easily interpreted spreadsheet format. This technique when applied to tuna and billfish larvae collected in the Straits of Florida had an 89% success rate. A single species (Thunnus atlanticus) was found to dominate the catch of tuna larvae, while billfish larvae were more evenly divided between two species (Makaira nigricans and Istiophorus platypterus).     

Open versus laparoscopic radical prostatectomy

Expert laparoscopic surgeons have demonstrated that laparoscopic radical prostatectomy with or without robotic assistance can be performed with excellent results. There is no evidence that laparoscopic radical prostatectomy with or without robotic assistance offers any clinically relevant advantage over open radical prostatectomy. Laparoscopic radical prostatectomy with or without robotic assistance requires a significant learning curve, is a longer surgical procedure, carries greater costs, and requires an expanded operating room team. The literature suggests that laparoscopic radical prostatectomy is associated with more intraoperative complications and higher positive surgical margins. The lesser amount of postoperative bleeding associated with laparoscopic radical prostatectomy is not clinically relevant. Laparoscopic radical prostatectomy is not associated with less pain and does not facilitate earlier urinary catheter removal. The best way to improve overall outcomes after radical prostatectomy is to direct patients to expert open or laparoscopic surgeons.