Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies

Plant specimens stored in herbaria are being used as never before to document the impacts of global change on humans and nature. However, published statistics on the use of biological collections are rare, and ecologists lack quantitative data demonstrating the relevance to science of herbarium specimens. I found 382 studies with original data that used herbarium specimens to document biogeographical patterns or environmental changes. Most studies are less than 10 years old, and only 1.4% of the herbarium specimens worldwide have been used to answer biogeographical or environmental questions. The vast majority (82%) of papers dealt with vascular plants, but some studies also used bryophytes, lichens, seaweeds and fungi. The herbarium specimens were collected from all continents, but most of the studies used specimens from North America (40% of studies) or Europe (28%). Many types of researches (conservation, plant disease, plant invasion, pollution, etc.) can be conducted using herbarium specimens. Climate change, and especially phenological reconstructions, are clearly emerging research topics. By group, small herbaria (<100,000 specimens) are consulted as often as very large herbaria (>1,000,000 specimens) for biogeographical and environmental research, but in most cases, only large facilities provide specimens collected worldwide. The median number of specimens per study in papers using computerized collections (15,295) was much higher than for papers that did not include electronic data (226). The use of molecular analyses to investigate herbarium specimens is still relatively unexplored, at least from biogeographical and environmental points of view. Combined with recently developed procedures to correct biases, herbarium specimens might provide in the near future exciting additional spatio-temporal insights that are currently unimaginable.     

Preventive action of organosilicon treatments against disfigurement of wood under laboratory and outdoor conditions

Organosilicons and biocides with known effectiveness against fungal disfigurement were used for dipping or impregnating Scots pine sapwood specimens. All specimens were artificially or naturally weathered and the colour of all specimens was determined with a spectrophotometer at fixed times. After artificial weathering the specimens were used in blue stain tests according to EN 152 or according to the EN 152 reverse method. The naturally exposed specimens were inspected for fungal disfigurement on their back side. Although the results learn that the coating approach is far better than the wood preservatives approach for evaluating blue stain attack of organosilicon-treated wood, organosilicons fail to protect wood under laboratory conditions. Outdoor exposure, however, revealed that organosilicon impregnated specimens were better protected against fungal disfigurement. The addition of a biocide improves the performance. Artificially aged specimens did not show significant colour differences compared to untreated Scots pine sapwood, while naturally aged specimens did, depending on the treatment conditions and presence of biocides. Organosilicons are able to reduce leaching of (degraded) wood constituents, leading to fewer colour changes compared to untreated scots pine and to decreased availability of nutrients for superficial fungal growth.     

CT imaging of wet specimens from a pathology museum: How to build a "virtual museum" for radiopathological correlation teaching.

X-rays and CT have been used to examine specimens such as human remains, mummies and formalin-fixed specimens. However, CT has not been used to study formalin-fixed wet specimens within their containers. The purpose of our study is firstly to demonstrate the role of CT as a non-destructive imaging method for the study of wet pathological specimens and secondly to use the CT data as a method for teaching pathological and radiological correlation. CT scanning of 31 musculoskeletal specimens from a pathology museum was carried out. Images were reconstructed using both soft-tissue and bone algorithms. Further processing of the data produced coronal and sagittal reformats of each specimen. The container and storage solution were manually removed using Volume Viewer Voxtool software to produce a 3D reconstruction of each specimen. Photographs of each specimen (container and close-up) were displayed alongside selected coronal, sagittal, 3D reconstructions and cine sequences in a specially designed computer program. CT is a non-destructive imaging modality for building didactic materials from wet specimens in a Pathology Museum, for teaching radiological and pathological correlation.     

PCR Amplification and Species Determination of Microsporidia in Formalin-Fixed Feces after Immunomagnetic Separation

The term microsporidia is used to describe several species of opportunistic protozoan parasites. Encephalitozoon intestinalis and Enterocytozoon bieneusi have been found in stools of more than 40% of AIDS patients with diarrhea. Diagnosis of infection with these small protozoans has been difficult, and until recently their occurrence has not been well documented. Formalin is widely used to preserve clinical specimens, but due to the nature of the fixation process, subsequent analysis, especially analysis by the PCR, is difficult. This study evaluated methods used to prepare formalin-fixed fecal specimens for PCR amplification of microsporidial DNA. Two methods were devised to allow PCR detection and subsequent identification of microsporidia in formalin-fixed fecal specimens to the species level. One method involved immunomagnetic separation to concentrate microsporidial spores from fecal specimens. In the second method Chelex resin (Bio-Rad, Hercules, Calif.) was used to remove inhibitory substances, followed by a DNA concentration step. Both methods resulted in reproducible, confirmed detection of microsporidia in formalinized fecal specimens and subsequent species determination by PCR sequencing. The detection sensitivity was two in vitro culture-derived spores (Encephalitozoon intestinalis) for the direct PCR. The reproducible detection sensitivity for DNA amplification from formalin-fixed fecal samples was 200 spores for either the Chelex method or the immunomagnetic bead separation method. Thus, we developed two methods for rapid, inexpensive detection of microsporidial spores in formalin-fixed fecal specimens.     

Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

Specimen collection is time consuming and expensive, yet few laboratories test preservation methods before setting out on field expeditions. The most common preservation buffer used for coral specimens is >70% EtOH. However, alternatives exist that are less flammable, easier to ship, and are widely used in other taxa. Here, we compare the effects of salt-saturated DMSO (SSD) and EtOH preservation buffers on post-extraction DNA quantity and quality. We found that soft tissue integrity was better maintained and higher quantities of DNA were extracted from EtOH-preserved specimens; however, by all other measures, SSD was a superior preservative to EtOH. Extractions of SSD-preserved specimens resulted in higher molecular weight DNA, higher PCR success, and more efficient amplification than specimens preserved in EtOH. Our results show that SSD is generally a superior preservative to EtOH for specimens destined for PCR studies, but species-specific differences indicate that preservation comparisons should be undertaken before collection and storage of samples.     

Museum collections, species distributions, and rarefaction

Biological specimens in museums and herbaria are sometimes used to compare the geographical distribution of different species. In doing so, it is necessary to account for differences in the numbers of specimens. We show how rarefaction can be used for this purpose. Rarefaction is a simple mathematical method originally designed to compare species richness in communities that differed in the number of sampled individuals. We present an example involving two Phragmipedium orchid species. In this case, rarefaction suggests that the apparent difference in range can be explained by the difference in the numbers of specimens.     

成人腹泻轮状病毒ELISA方法的建立和应用

本文通过特异性试验、阻断试验、交叉试验、敏感度试验和重复性试验,建立了成人腹泻轮状病毒一酶联免疫吸附试验法(ADRV—ELISA)。应用此法检测了全国20多个省区202份病人腹泻标本,检出率为91％。采用本ELISA、核酸电泳、电镜三种方法对48份病人腹泻标本进行了双盲法检测比较,结果三种方法的阳性检出率分别为100％、85.4％、56.25％(P<0.05)。实验结果表明,本ELISA应用于检测成人腹泻轮状病毒(ADRV),具有敏感度高。特异性强等优点。     

Molecular and Immunohistochemical Characterization of Historical Long-Term Preserved Fixed Tissues from Different Human Organs

University and museum collections are very important sources of biological samples that can be used to asses the past and present genetic diversity of many species. Modern genetic and immunohistochemical techniques can be used on long-term preserved fixed tissues from museum specimens to answer epidemiological questions. A proof of principle was established to apply modern molecular genetics and immunohistochemical methods to these old specimens and to verify the original diagnosis. We analysed 19 specimens from our university collection including human organs that had been in fixative for more than 80 years. The tissues originated from lung, colon, brain, heart, adrenal gland, uterus and skin. We isolated amplifiable DNA from these wet preparations and performed mutational analysis of BRAF, KRAS and EGFR. The tissues were also embedded in paraffin and used for modern histology and immunohistochemistry. Our data show that amplifiable DNA is extractable and ranged from 0.25 to 22.77 μg of total DNA. In three specimens BRAF^V600E or KRAS^G12D mutations were found. Additionally, expression of different proteins like vimentin and GFAP was detected immunohistochemical in six investigated specimens. On the basis of our results the original diagnosis was altered in three specimens. Our work showed that it is possible to extract amplifiable DNA suitable for sequence analysis from long-term fixed tissue. Furthermore, histology and immunohistochemistry is feasible in specimens fixed long time ago. We conclude that these old preparations are suitable for further epidemiological research and that our methods open up new opportunities for future studies.     

A procedure for differential staining of cartilage and bone in whole formalin-fixed vertebrates.

This paper describes a modification of the Simons and Van Horn (1971) procedure for rendering cartilage blue, bone red, and soft tissue translucent or transparent in whole vertebrate specimens. Alcian blue and alizarin red S are used to stain cartilage and bone respectively. In our procedure formalin is used as a fixative. This is a significant modification because formalin is the common fixative for museum specimens. This clearing and staining procedure is thus readily applicable to comparative studies in anatomy, embryology and systematic zoology.     

应用DNA条形码对植物标本的核查

DNA条形码主要目的是物种鉴定和新物种或隐存种的发现,而DNA条形码参考数据库是物种快速鉴定的重要基础。目前中国维管植物DNA条形码参考数据库正在建设之中,借助于公共数据库（NCBI）和初步建立的中国植物DNA条形码参考数据库,运用DNA条形码数据开展了植物标本鉴定的核查工作：（1）比较DNA序列信息与标本鉴定信息,从科、属、种级水平查找鉴定错误的标本;（2）基于有较好研究基础的DNA条形码参考数据库,开展未知标本的鉴定;（3）通过对标本核查的总结,提出DNA条形码参考数据库建设过程中的几点建议。     

Detection of Candida antigen in bronchoalveolar lavage fluid

While bronchoalveolar lavage is frequently performed to evaluate immunocompromised hosts for infection, the significance of rare yeasts found on the cytologic examination of lavage fluid is unclear. This study used the latex agglutination method to test lavage fluids for Candida antigen to assess its usefulness in distinguishing Candida pneumonia from Candida colonization of the respiratory tract or oral contamination of the lavage specimen. Ninety-seven specimens from 87 patients were categorized on the basis of historical, microbiologic, cytologic and serologic data. Bronchoalveolar lavage fluids were positive for Candida antigen in 0 of 20 specimens from normal controls, 0 of 14 specimens from patient controls, 5 (36%) of 14 specimens from patients with Pneumocystis carinii pneumonia, 0 of 5 specimens from patients with gastrointestinal candidiasis, 0 of 9 specimens contaminated by oral-derived yeasts, 2 (10%) of 19 specimens from patients with probable Candida colonization and 15 (94%) of 16 specimens from patients with clinical and laboratory evidence of Candida pneumonia. We conclude that this test assists in the differentiation of Candida pneumonia from other situations in which yeasts are recovered by bronchoalveolar lavage.     

PCR for the detection of Campylobacter spp. in clinical specimens

The suitability of PCR (based on the amplification of the 16S rRNA gene) for use as a diagnostic test for the detection of Campylobacter spp. in human faecal specimens was assessed. A total of 493 faecal specimens from patients with symptoms of enteritis were tested for the presence of campylobacters using PCR. Results were compared with those obtained from the analyses of the same specimens by culture techniques, using chi 2 square with Fisher's exact test. PCR was found to detect significantly more positive specimens than culture (chi 2 = 200.086; P < 0.0001). The sensitivity and specificity of PCR when compared with the culture technique were found to be 91 and 97%, respectively. It is proposed that the PCR is a reliable and sensitive method which may be used as a routine diagnostic technique for the detection of campylobacters in clinical specimens.     

一种用于显微观察的蓟马标本的制片新方法

蓟马（昆虫纲：缨翅目）是昆虫纲中有重要经济意义的目之一,由于个体微小,因此需要制作成高质量的玻片在高倍显微镜下观察和研究。如果玻片标本质量欠佳,常常导致无法鉴定其种类。不同的研究中处理蓟马标本的技术和方法各异。本文介绍一种新的制片方法,这一方法需要更少的化学药品,且适合处理深颜色的标本。而且,用这个方法处理的标本清晰,保持其自然体色,这些特征在鉴定种类时是十分必要的。本方法处理标本包括4个步骤：氢氧化钾透明（一般5％一10％KOH溶液中,常温放置1～2d或者100℃水浴加热1～2h,处置时间随材料大小和颜色的深浅有所变化）、纯酒精脱水（材料透明后转移到纯酒精中浸泡4—5min）、Hoyer＇s介质装片（滴一滴Hoyer＇s介质于载玻片中央,而后将脱水后的材料转移至介质中,用细拨针小心整翅、足以及触角的姿态,盖上盖玻片）和干燥贴标签（装片后放置在35～45℃烘箱中2～3d或者室温下放置1星期,然后将采集信息、寄主信息以及鉴定表格制成标签,贴于玻片两侧）,与其它制片方法相比,此法最简洁。文末对不同的制片方法作了比较和讨论。     

基因重组抗原检测梅毒螺旋体抗体研究

梅毒是一种传染性很强的性传播疾病,早期诊断是防止其传播及治疗的关键。采用基因重组的梅毒螺旋体P47和P15抗原对289份临床标本进行梅毒螺旋体抗体的检测,并与常规方法进行了比较,结果表明：重组抗原ELISA法具有较高的敏感性和特异性,并能对梅毒进行早期诊断,可以代替常规方法检测梅毒螺旋体抗体。186份现患和已治愈梅毒患者标本,重组抗原ELISA法、TPHA法和RPR法均为阳性;60份健康献血员标本,重组抗原ELISA法和TPHA法、RPR法均为阴性;17份与梅毒患者有性接触者的标本,重组抗原ELISA法有2份阳性,而TPHA法、RPR法均为阴性,1个月后复查这2份血清TPHA和RPR均为阳性;6份RPR和类风湿因子均为阳性的血清,重组抗原ELISA法和TPHA法均为阴性,;20份肝硬化患者血清,3种方法检测均为阴性。     

激光显微切割技术用于子宫内膜异位组织DNA的提取及其完整性分析

目的：探索一套激光显微切割（LCM）分离子宫内膜异位症腺体细胞后提取微量DNA并进行完整性分析的操作流程。方法：分别对20例石蜡标本及20例冰冻标本进行LCM,收集切割后的腺体细胞;2组标本各取10例提取微量DNA,检测DNA浓度并通过PCR扩增进行验证;余20例标本分别进行全基因组扩增,检测产物浓度并利用8种常见管家基因作为引物通过PCR扩增进行验证,对比分析其结果。结果：石蜡标本与冰冻标本在LCM获取腺体细胞及提取微量DNA两个环节中均可获得满意效果;但经全基因组扩增后,石蜡标本无法保留完整DNA信息。结论：LCM获取子宫内膜异位症腺体细胞提取微量DNA是一种操作简单、结果稳定的方法,可作为日后子宫内膜异位症基因组研究的常规方法;冰冻切片相对石蜡切片,更能保留完整的DNA信息。     

Simulation model for gynecologic specimen classification in a high-resolution prescreening system

Presentation is made of the design of a statistical model for the generation of "artificial specimens" to be used in the development and testing of a high-resolution prescreening system for gynecologic specimen classification. The model is based on two considerations: (1) the nature of the biologic material to be examined and (2) the system to be studied, which in this case is the FAZYTAN cervical prescreening system. Since gynecologic specimens that belong to the same clinical class (Papanicolaou group) have similar compositions of the different cytologic cell types, the simulation model presented is based on the close relationship between the degree of cancer suspiciousness expressed in the clinical diagnostic group and the composition of the cellular samples on a specimen. Statistically, the model considered here is based on an analysis of the single-cell classification (SCC) output process, taking the inherent system properties into account. The statistical information obtained by evaluating large sets of labelled cells is then used to produce artificially generated point distributions in the SCC decision space ("artificial specimens"), which can be used for examination of system reactions under controlled conditions. False-positive and false-negative error rates and system operation characteristics can be measured, and the effects of varying cell compositions as well as the relative performance of different specimen classifiers can be investigated. Although the "artificial specimens" thus created allow the investigation of system reactions with respect to a great variety of input processes, they cannot replace experiments on thousands of original specimens in order to measure system quality under realistic conditions.     

Preparatory methods for DNA hydrolysis, cytochemistry, immunocytochemistry and ploidy analysis. Their application to automated and routine diagnostic cytopathology

A review is presented of some methods used to prepare cytologic specimens for analytical and/or automated studies, with the steps of the procedures detailed in appendices. The preparation of the cell monolayers required for optimal automated cell image analysis and classification, e.g., by the Cytoscan 110, is discussed, as is the preparation of poly-L-lysine-coated slides used in the production of monolayered specimens. These monolayers, which can be prepared from a variety of specimens, are also useful for cytochemical and immunocytochemical studies and DNA ploidy analysis. For DNA analysis, a modified gallocyanin chrome alum staining procedure is described as a stoichiometric alternative to the time-consuming Feulgen reaction. The hydrolysis technique required by the latter method is also detailed. The freeze-fracturing technique for the enhancement of monoclonal antibody immunocytochemical staining of detectable antigens is described, along with an indirect immunoalkaline phosphatase staining method. The use of enzyme cytochemical reactions for glucose 6 phosphate dehydrogenase and lysosomal naphthylamidase is also presented.     

Thamniscus King, 1849 (Fenestellida: Bryozoa): William King’s original specimens and their bearing on the genus concept

Reassessment of the suite of specimens used by William King when he erected the fenestrate bryozoan genus Thamniscus in 1849 has shown that they belong to two genera. However, King’s original generic concept only allows for some of these specimens to be included within Thamniscus. These specimens are illustrated. A recent generic treatment is consistent with King’s original generic concept.     

The chick embryo chorioallantoic membrane as an in vivo experimental model to study human neuroblastoma

The chick embryo chorioallantoic membrane (CAM) has long been a favored system for the study of tumor angiogenesis because at the stage of development when generally tumor grafts are placed (6–10 days of incubation), the chick’s immunocompetent system is not fully developed and the conditions for rejection have not yet been established. All studies for mammalian neoplasms, including neuroblastoma, have used tumor cell lines, tumor bioptic specimens, cell suspensions derived from tumors, and mouse tumor xenografts bioptic specimens. CAM can also be used to study the effects of antiangiogenic molecules on tumor cell suspensions of tumor bioptic specimens. This review article summarizes and discusses the literature data on the use of the CAM as an in vivo experimental model to study human neuroblastoma.