Bulk Handling Racks for Free-Floating Serial Sections, Especially Suitable for Nauta Staining

Staining racks, each containing 20 shallow compartments, were constructed by drilling 1.5 cm holes in 8 × 11 cm sheets of 1 mm thick Darvic, an unplasticised polyvinyl-chloride compound, and cementing fibre-glass gauze of 1.3 mm mesh size to one surface. Sections were placed serially—one to each compartment—in the racks, and stacks of up to 9 racks were clamped by Perspex (methyl methacrylate) nuts and bolts, and side clamps. Thus, sections could be handled easily and kept in strict serial order, even in bulk. For Nauta staining, brains had to be gelatin embedded before sectioning. By storing sections in groups of 4 in ice-cube trays, evenly spaced series could be selected for placement in the racks. As many as 160 sections were taken together through all stages of the Nauta method, the timing of critical stages being controlled by taking 4 to 6 free-floating sections, together with the racks, through the various solutions.     

Apparatus for the Simultaneous Handling of Numerous Histological Specimens

An apparatus has been devised consisting of a series of bakelite plates 2 3/4 inches in diameter which can be clamped together one on top of the other. Each contains 37 depressions 1/4 inch in diameter, with a 1/16 inch hole at the bottom of each passing completely thru the plate. Each depression can contain its own specimen, its identity established by the number of the plate and the position of the depression. Several plates can be clamped together and run simultaneously thru the necessary reagents, thus handling large numbers of specimens without losing the identity of any of them.     

利用简易测量板估测白三叶群落地上生物量

地上生物量是草地群落的一个重要指标,而直接收割法对生态系统较脆弱的地区有极大的破坏.为了更有效地估测白三叶群落地上生物量而又不破坏草地,采用自制测量板对陕西省杨凌区大寨镇杜寨村的白三叶群落高度和地上生物量进行了研究.采用铝塑板和高分子板不同规格的17种测量板,将各测量板分别置于白三叶群落上方,记录测量板下方到地面的植物群落高度,重复20次,然后将测量板下方对应面积内的植物齐地面刈割,烘干后,称量得到地上生物量,最后进行数学模型建立、相关性分析,并对模型进行验证.结果表明: 以测量板下方群落高度为自变量,对应面积内群落地上生物量为因变量,建立多种回归方程,群落高度和地上生物量之间呈正相关,R²为0.37～0.76;铝塑板与高分子板相比,其测量得到的生物量变异系数和建立的回归方程决定系数均表现较好,精度较高;最佳测量板为直径35 cm的圆形铝塑板,其最优估测模型为: y=1.6460x-3.3462 (R²=0.76),预测精度达到92.1%.     

A STAINING TECHNIQUE FOR AUTORADIOGRAPHS OF NONDIFFUSIBLE ISOTOPES

Nondeparaffinized radioactive tissue sections are stained with hematoxylin and eosin by being floated on aqueous solutions for 1 hr each. The sections are then thoroughly washed, dried and exposed to autoradiographic plates or emulsions for predetermined periods of time. When desirable, both stained and unstained adjacent tissue sections can be mounted on a single slide of autoradiographic plate for exposure. Kodak DK-19 and 30% Na₂S₂O₃.5H₂O solutions are used for subsequent developing and fixing. The finished autoradiographs show excellent resolution and cytologic detail, since the gelatin remains unstained while the tissue retains its stain. Stains other than hematoxylin and eosin can be applied to this technique, provided they withstand the developmental and fixation processes.     

A Tribasic Stain for Thin Sections of Plastic-Embedded, OsO4-Fixed Tissues

Thin (0.5-1 μ) sections of plastic-embedded, OsO₄-fixed tissues were attached to glass slides by heating to 70 C for 1 min. A saturated solution combining toluidine blue and malachite green was prepared in ethanol (8% of each dye) or water (4% of each dye). Methacrylate or epoxy sections were stained in the ethanol solution for 2-5 min. The water solution was more effective for some epoxy sections (10-80 min). Epoxy sections could be mordanted by 2% KMnO₄, in acetone (1 min) before use of the aqueous dye, reducing staining time to 5-10 min and improving contrast. Aqueous basic fuchsin (4%) was used as the counter-stain in all cases; staining time varied from 1-30 min depending upon the embedding medium and desired effects, methacrylate sections requiring the least time. In the completed stain, nuclei were blue to violet; erythrocytes and mitochondria, green; collagen and elastic tissue, magenta; and much and cartilage, bright cherry red. Sections were coated with an acrylic resin spray and examined or photographed with an oil-immersion lens.     

Hematoxylin-Eosin Staining of OsO4-Fixed Epon- Embedded Tissue; Prestaining Oxidation by Acidified H2O2

Successful application of hematoxylin-eosin staining to 0.5-1 μ sections of OsO₄-fixed Epon-embedded mammalian tissue is made possible by first treating the sections for approximately 1 min at 25-30 C with 10% H₂O₂ acidified with 0.1 or 0.01 N H₂SO₄ to pH 3.2. Subsequent steps are: washing; drying; Hams hematoxylin at 50 C, 1-2 min; washing; drying; 0.2-0.3% NH₄OH in 70% ethanol, 3-5 sec, drying at 50 C; 5% aqueous eosin for 3 & 45 sec at 25-30 C, washing; drying; clearing in xylene and mounting in resin. The use of acidified H₂O₂ prevents the staining of Epon and permits the characteristic staining picture to be obtained. Sections were attached to glass slides without adhesive and processed horizontally on a rack. Slides should be well drained and blotted before each drying step, to prevent formation of precipitate on the section.     

Improved method of obtaining micro-core paraffin sections in dendroecological research

树轮气候学及树轮生态学研究在国内外取得了长足进展, 但对树轮与气候的响应机制缺乏深入的了解, 迫切需要进行以微树芯石蜡切片为基础的树轮生态学研究。形成层活动监测从生理生态学角度出发, 广泛用于树轮对气候变化响应的机制探讨研究中, 然而目前还没有对微树芯石蜡切片制作的方法作详细的论述和探讨。该文通过对祁连圆柏(Sabina przewalskii)等5个不同树种微树芯石蜡切片的制作实践, 对已有的植物石蜡切片技术进行改进, 增加组织软化的步骤, 并对其他步骤作了相应的调整, 详细介绍了微树芯石蜡切片制作的方法, 为树轮生态学、解剖学, 以及木材解剖学关于木质化材料石蜡切片的制作方法提供参考。     

Application of the Periodic Acid-Schiff Technique to Whole Chick Embryos

The practicability of applying histochemical reactions to bulk staining has been explored by subjecting whole chick embryos at early stages to the periodic acid-Schiff (PAS) reaction. A comparison of the microscopic distribution of PAS positive substances revealed by this procedure with that obtained by the standard routine, i.e., staining of deparaffinized sections on slides, has shown similar localizations of PAS positive material and, in addition, finer morphological detail and more intensive reactions by staining the specimens in toto. The following method is recommended for chick embryos between stages 11-17 (Hamburger and Hamilton): Fixation in Gendre's fluid at 4°C; oxidation with alcoholic buffered periodic acid, 15 min; rinsing in distilled water, 10 min; Schift's reagent, 30 min; 3 sulfite rinses, 5 min each; running tap water, 10 min; dehydration, clearing and double-embedding in celloidin and paraffin.     

Localization of tubulin in the mitotic apparatus of mammalian cells by immunofluorescence and immunoelectron microscopy

Antitubulin antibody was used as an immunofluorescent and immunoelectron microscopic probe to localize tubulin in components of the mitotic apparatus of rat kangaroo (strain PtK₁) cells in vitro. In addition to the detection of tubulin in the spindle microtubules and centrioles, other structures were found to display specific staining including kinetochores, amorphous pericentriolar material and small virus-like particles associated with the centrioles. The kinetochores consisted of a densely stained outer layer about 400 Å thick which is separated from an inner layer of the same dimension by a lightly staining middle layer. Microtubules were primarily associated with the outermost plate of the kinetochore but tubulin was uniformly distributed in both outer and inner plates. Colcemid treatment prevented the assembly of spindle microtubules and resulted in specific alterations of the kinetochore but failed to diminish the staining of the kinetochores. These observations suggest that tubulin molecules may comprise an important structural component of the kinetochore.     

Flat, Adherent, Well-Contrasted Semithin Plastic Sections for Light Microscopy

Semithin (0.5-2.0 μm) sections of plastic embedded specimens have long been used for identifying and orienting structures destined for electron microscopic observation. Improved staining methods and the development of more versatile plastics have increased the use of semithin plastic sections for histochemical and autoradiographic studies. The principal advantage of plastic over paraffin sections is the possibility of increased resolution. This advantage is often compromised, however, by problems arising during processing and staining. Wrinkles are common in sections containing tissues of different consistencies or when the hardness of the tissue does not match that of the surrounding plastic (Millonig 1980). Unfortunately, many of the methods designed to eliminate wrinkles (e.g., Alsop 1974, Sommer et al. 1979) require prolonged staining or repeated handling of the sections. Section adhesion problems usually arise during staining, particularly if the protocol requires alkaline or oxidizing reagents. Adhesives such as Mayer's albumen or chrome alum-gelatin (Hayat 1981) work well but may contribute to undesirable background staining or trapping of debris. A more complicated problem, inadequate stain contrast for photomicrography, usually can be traced to inability of the stain to penetrate the plastic, staining of the plastic, or nonspecific staining of the tissue. Alkaline staining solutions and chemicals which etch plastic can increase penetration, but may also cause section loss or staining of the plastic. The following is a simple method to eliminate these processing problems. It exploits the solvent properties and low surface tension of glycerol to aid in softening, flattening, and adhering semithin plastic sections to microscope slides.     

Silver Protein Staining of Nerve Fibers in Celloidin Sections

Celloidin sections from formalin-fixed brain and spinal cord of primates are stored in 70% alcohol after cutting, soaked in 2% pyridine in 50% alcohol for 6-8 hr at 37 C, and transferred to 1% concentrated NH₄OH in 50% alcohol 15-18 hr at 20-25 C. After washing and flattening, the sections are transferred to 1% silver protein solution containing 30 ml of 0.2 M H₃BO₃/100 ml. Impregnation is accomplished in 50 ml screw-top jars, 50 mm in diameter, which are filled to a depth of 35 mm, and have 1 gm of copper foil, 0.002 inch thick added. The foil is folded in loose accordion-fashion, pierced and threaded, cleaned in 5% HNO₃, rinsed in distilled water, and suspended in the solution just above the sections by fastening the thread to the jar lid. The sections are impregnated for 24 hr at 37 C, rinsed in distilled water, reduced in a solution of 5% Na₂SO₃ and 1% hydroquinone for 10 min, washed in distilled water and toned in 0.2% gold chloride for 5 min. After rinsing in distilled water, the sections are transferred to 1% oxalic acid for 45-60 sec, washed in distilled water and placed in 5% Na₂S₂O₃ for 5 min. Sections are then washed, dehydrated to 95% alcohol, cleared in terpineol, followed by 3 changes in xylene, and mounted.     

刺芹侧耳交配型基因敲入单核体后锁状联合和核相的表征观察

刺芹侧耳是一种典型的具四极性交配型系统的担子菌,通常需要一对可亲和的单核菌丝体才能够形成稳定的双核菌丝体。本研究将刺芹侧耳单核菌株181（A1B1）中A和B交配型基因HD1和HD2以及信息素前体基因PEphb3.1和PEphb3.3克隆后,通过PEG介导的方式敲入到可亲和的单核菌株183（A2B2）中,获得了22个阳性转化子。运用荧光显微镜对其中11个具有锁状联合的转化子进行了详细观察,描述了锁状联合和细胞核相。研究结果为进一步开展交配型基因的遗传操作研究提供了方法学上的借鉴和参考。本文还探讨了同核双核体的概念和应用价值。     

Enumeration of heterotrophs, fecal coliforms and Escherichia coli in water: comparison of 3M Petrifilm plates with standard plating procedures

A total of 177 naturally contaminated water samples were analyzed by membrane filtration according to the Standard Methods for the Examination of Water and Wastewater published by the American Public Health Association. Filters were incubated in parallel on mHPC-agar and 3M™ Petrifilm™ Aerobic Count Plates (Petrifilm™ AC plates) for heterotrophic counts. Fecal coliforms and Escherichia coli were enumerated on mFC-agar and 3M™ Petrifilm™ E. coli/Coliform Count Plates (Petrifilm™ EC plates). Typical colonies on each media type were confirmed following standard procedures. Heterotrophic counts were between 10³ and 10⁴ CFU/mL and the average log₁₀ counts obtained on Petrifilm™ AC plates were about two-fold lower than on mHPC-agar. Counts for fecal coliforms and E. coli were between 10² and 10³ CFU/mL. Average log₁₀ counts for confirmed fecal coliforms obtained on Petrifilm™ EC plates were slightly lower than on mFC agar with a correlation coefficient of 0.949. The average log₁₀ counts for confirmed E. coli on Petrifilm™ EC plates and on mFC agar were statistically not different (P=0.126) with a correlation coefficient of 0.879. Specificity of Petrifilm™ EC plates and mFC agar was evaluated by comparing typical colony counts with confirmed counts. On mFC agar, counts for typical colonies were by 2 log₁₀ CFU higher than the actual confirmed counts. In contrast, on Petrifilm™ EC plates typical colony counts were almost identical to confirmed colony counts for both fecal coliforms and E. coli. This comparison illustrates the high specificity of Petrifilm™ EC plates for enumeration of both fecal coliforms and E. coli in water.     

Current challenges and solutions of de novo assembly

Background: Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings.Results: In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks (overlap graph-based, de Bruijn graph-based and string graph-based), and introduce the characteristics of each assembly tool and their adaptation scene. Next, we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data, single-cell sequencing data and single molecule sequencing data. At last, we discuss the application of SMS long reads in solving problems encountered in NGS assembly.Conclusions: This review not only gives an overview of the latest methods and developments in assembly algorithms, but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type.     

An appraisal of methods used in coral recruitment studies

 A new method for attaching individual artificial settlement plates directly to the reef surface using small stainless steel base plates is described. Recruitment of corals to settlement plates attached to the reef substratum and to steel mesh racks is compared. The effects of differences in depth, settlement plate angle, and local topography on recruitment of corals were also investigated. No significant difference in mean recruit density was found between settlement plates deployed using the two attachment methods. Small differences in depth and plate angle among replicate plates explained less than 6% of the variability in coral recruitment on replicate settlement plates. The direct-attachment method is less obtrusive, more cost and time efficient, and settlement plates can be deployed at precise locations. Additionally, because settlement plates are deployed individually rather than grouped on racks or frames, the direct-attachment method avoids complications associated with assumptions of independence implicit in most statistical procedures. Accepted: 24 November 1999     

斑马鱼hoxa1a基因调控颅面骨骼发育的功能研究*

hox基因编码一类高度保守的转录因子家族,人类HOXA1的突变会导致阿萨巴斯卡发育不良综合征 (Athabascan brainstem dysgenesis syndrome, ABDS),使人出现因颅骨异常导致的面部畸形和面部麻痹等症状。利用模式生物斑马鱼研究其同源基因hoxa1a的功能机制。首先利用CRISPR/Cas9技术对斑马鱼hoxa1a进行基因编辑,获得了hoxa1a基因突变,T7E1酶切结果显示F₀酶切效率平均为70%。F₁进一步筛选到两种突变类型,分别是插入了8 bp和删除了7 bp的杂合突变体。杂合子自交得到hoxa1a F₂纯合突变体,并且测序验证hoxa1a基因突变成功。5 dpf时,hoxa1a纯合突变体出现颅面发育异常。阿尔新蓝软骨染色和茜素红硬骨染色结果表明,hoxa1a突变体中颅骨发育异常、筛骨板断裂,鳃弓发育出现缺损。成功在斑马鱼中构建ABDS疾病模型,表明hoxa1a突变会造成斑马鱼颅面骨骼发育异常,为其功能机制研究奠定了基础,为人类ABDS疾病的致病机制研究提供了新的思路。     

The structure of the wall plate in chthamalus depressus (poli)

The structure of the calcitic shell of extreme hypobiotic Chthamalus depressus (Poli) using untreated, treated, and polished material has been investigated by scanning electron microscopy, and supplemented by observations on normal forms and C. Stellatus (Poli). The laterale has been largely used. The plate is made up of prisms consisting of stacks of units ≈ 5 μm high; the prisms are separated by matrix and intraprismatic organic matter may also be present. The inner side of the plate is penetrated by holes. The structure of the wall plate is reflected in that of the sheath. Epicuticular lamina run across the wall plates separating the stacks of prisms. Attention is drawn to the possible implications with respect to the recent controversy regarding the form of chitin in crustacean endocuticle.

The various structures give the surface a ‘banded’ appearance. From the available data on growth rate, shape, and moulting frequency, estimates are made of the expected size of these bands; the results agree reasonably well with the observations.

The frequency of the smaller bands would seem to be endogenously determined by processes taking place within an intermoult period.     

Wrinkle-Free Plastic Sections for Light Microscopy

Plastic sections 0.5 to 2 μm thick are routinely used for light microscopy. Although plastic sections have several advantages over paraffin or celloidin sections, a problem that is often encountered with plastic sections is wrinkling (Fig. 1). Wrinkling occurs during staining when sections dried on glass slides are covered with stain and heated to hasten the penetration of the stain. Mounted sections heated on glass slides, but not stained, ordinarily lack wrinkles, even when examined with phase contrast optics. Similarly, mounted sections covered with stain, but not heated, lack wrinkles; unfortunately, such sections fail to stain adequately. Unmounted sections floated on heated drops of stain also lack wrinkles (Millonig 1980). Thus, it is clear that wrinkling occurs only when mounted sections are covered with stain and heated.     

Colorimetry for the Stain Technologist. III. The Specification of Color Difference

This paper illustrates the calculation of color differences, involving luminance as well as chromaticity components. Color differences have been calculated for a large number of stained histological objects. Four different color difference formulae have been used, namely, those associated with the FMC 2, U*V*W*, L*u*v* and L^*a^*b^* systems. Comparison has first been made between various hematological substrates after staining with two different azure B-eosin Y stains. Next, comparison is made for the same substrates after staining with one of the azure B stains and a methylene blue-eosin Y stain. Pairwise comparison is also made of various substrates from the epithelium of the uterine cervix after Papanicolaou staining. Finally, pairwise comparison documents color differences accompanying maturation for the erythroid and myeloid cell lines in azure B-eosin Y stained bone marrow. The limitations of current color difference formulae are discussed.