Cytology of lumpectomy specimens.

Residual microscopic disease after lumpectomy may cause significant local recurrence. This study evaluated the use of touch preparation cytology to assess lumpectomy margins. For 90 specimens, the findings on Diff-Quik-stained touch preparations (rendered intraoperatively within 15 minutes after the lumpectomy) were correlated with the gross findings, frozen-section results and, later, the findings in the permanent histologic sections. Three specimens were cytologically unsatisfactory, 68 yielded benign findings, and 19 were suspicious or diagnostic for malignancy. The margins showed tumor involvement in 5 lumpectomy samples by gross examination, in 13 by frozen-section evaluation and in 17 by the study of permanent sections. Touch preparation cytology was putatively falsely positive in two cases while frozen-section evaluation was falsely negative in four cases. Cytology had a sensitivity of 100%, a specificity of 97.1% and a diagnostic accuracy of 97.7%. These results demonstrate that touch preparation cytology rapidly and reliably evaluates lumpectomy margins and can overcome some sampling errors and artifacts related to frozen-section analysis. Touch preparation cytology is now being used to complement frozen-section evaluation of lumpectomy margins as part of a protocol aimed at reducing the local recurrence rate.     

Genomics and museum specimens

Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990 ). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. ( 1990 ) spawned dozens of studies in which museum specimens were used to compare historical and present‐day genetic diversity (reviewed in Wandeler et al. 2007 ). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. ( 2013 ) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next‐generation (Illumina) sequencing to compare patterns of genetic variation in historic and present‐day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years.     

Infectious disease screening of blood specimens collected post-mortem provides comparable results to pre-mortem specimens

Serology assays for standard screening are optimised for use with sera collected from living adults and children. Because of potential changes in the vascular compartments after death, methods used for screening sera from cadaveric organ donors need to be validated before testing these specimens. Serum was separated from blood collected from cadaveric donors within 24?h of death and biochemical parameters measured to detect dilution of protein and haemolysis. In order to demonstrate if any inhibitors that might interfere with the assays were present, pre and post-mortem specimens were spiked with aliquots of human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human T-cell Lymphotropic Virus (HTLV) and T. pallidum-positive sera. Comparison of serum from living subjects with serum obtained post-mortem showed that while the concentration of total protein decreased, concentrations of albumin, immunoglobulin G (IgG) and immunoglobulin M (IgM) remained unchanged. The degree of haemolysis, as measured by free haemoglobin, was within the limits accepted for the Architect analyser. Spiking of pre- and post-mortem specimens with aliquots of HIV, HCV, HBV, HTLV and T. pallidum-positive sera showed no statistical difference in the signal between pre-mortem and post-mortem results when tested on the Abbott Architect analyser. Positive results were obtained in each of a further nine subjects who had tested positive for HIV (n?=?1), HCV (n?=?8), HBV (n?=?1) on pre-mortem serological testing. These findings suggest that the sensitivity of the Abbott Architect serological screening tests is not significantly affected in specimens collected within 24?h of the cessation of life.     

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

Despite advances that allow DNA sequencing of old museum specimens, sequencing small‐bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small‐bodied (3–6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58–159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1–10 ng). We also explored low‐cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low‐input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.     

Montage electron tomography of vitrified specimens

Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 Å were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.     

Ultrasound-facilitated formalin fixation of biological specimens

Abstract

In a previous study, we showed that ultrasound can dramatically reduce the time required for tissue fixation in formalin. It generally is believed that ultrasound increases the speed of tissue fixation in two possible ways: 1) increasing the speed of penetration of fixative molecules into tissue samples and 2) increasing the speed of cross-linking reactions. We addressed here the second possible way by using protein solutions and cultured cells, which minimized the effects of the penetration factor. Proteins or cultured cells in solution were fixed with formalin with or without ultrasound irradiation. Fixed proteins and cell lysates then were separated by SDS-poly acrylamide gel electrophoresis and subjected to Western blotting to examine cross-linking formation in certain proteins. Unexpectedly, irradiation with ultrasound did not produce an observable difference in the rate of cross-linking in protein solutions. In similar experiments using cultured cells, however, we observed a significant reduction in recovery of certain proteins from cells fixed by formalin under the influence of ultrasound, which indicated that the ultrasound fixation procedure accelerated cross-linking formation within cells. Studies on protein and cell fixation without ultrasound showed that cross-linking formation was closely related to incubation temperature, which indicates that the heating function, which is inherently associated with ultrasound is another major factor in the ability of ultrasound to accelerate cross-linking.     

Stiffness behaviour of trabecular bone specimens

Trabecular bone specimens were tested by non-destructive technique with the purpose of investigating stiffness behaviour and optimizing stiffness determination. Cylindrical specimens (n = 25) were loaded repetitively (0.1 Hz, 30 cycles) by axial compression to 50% of predicted ultimate strength and finally compressed to failure. Analyses of single compression curves showed increasing stiffness (E') until a stress level about 50% of ultimate stress followed by decreasing stiffness. Curve fit analysis of the elastic part of the compression curve showed the best fit, when a second order polynomial was used (r = 0.94, p less than 0.001). The stiffness determined non-destructively at the 25% level of ultimate strength increased significantly to the tenth loading cycle followed by a steady state. The precision of stiffness determination as an average of five consecutive measurements at steady state was E' +/- less than 5% (95% confidence limits). A reproducibility test by repetition of the test sequence after 3 h rest showed qualitatively the same stiffness behaviour. The variation of stiffness determination between the two test sequences was +/- 27% at the first loading cycle falling to +/- 12% at steady state.     

植物腊叶标本的消毒方法

植物腊叶标本消毒是腊叶标本制作的关键技术之一,是腊叶标本发挥其应有作用和长久保存的保障。对腊叶标本的消毒方法进行了总结．将目前所采用的方法分为物理方法和化学方法两大类,并对各种消毒方法的优缺点及注意事项进行了分析,以期对提高植物腊叶标本的制作质量提供技术支持。