A microcomputer program for establishing and maintaining a database for laboratory culture collections

A computer program that facilitates the creation of a culture collection database has been written for a microcomputer (Apple He with a Z-80 card) using dBASE II® (Ashton-Tate). The Culture Collection Program accommodates up to 250 individual strain records on one 5 1/4" floppy disk. For each strain, information that can be stored includes the name of the micro-organism, culture collection number, antibiotic resistance markers, plasmids, genetic markers, references, growth medium, growth temperature and additional comments. The last date of subculturing can be ascertained and information about the status of the preserved cultures can also be noted. With a menu-driven format which requires no computer programming expertise, the user can readily create new entries, update old ones and search the database for strains with certain common properties.     

On the stability of salivary progesterone under various conditions of storage

The concentrations of progesterone in saliva of women exhibited significant decreases when the fluid was stored in plastic vials for 3 days at room temperature or 37 C. The addition of antibiotics or a variety of metabolic poisons to the saliva prior to storage did not prevent the progesterone decrement. However, the addition of albumin (2 g/dl) was protective, suggesting that the protein impeded adsorption of salivary progesterone by the plastic container. Saliva could be maintained at 37 C for 3 days in glass vials or at -20 C in plastic containers for indefinite periods without loss of progesterone titers. These data indicate that a patient under luteal function assessment may collect saliva samples in glass vials at regular intervals during the latter half of her cycle and store them in the freezer compartment of the refrigerator until shipment by mail to the laboratory for progesterone assay. With special care, plastic vials charged with albumin may also be used.     

Laboratory voice data entry system

We have assembled a system using a personal computer workstation equipped with standard office software, an audio system, speech recognition software and an inexpensive radio-based wireless microphone that permits laboratory workers to enter or modify data while performing other work. Speech recognition permits users to enter data while their hands are holding equipment or they are otherwise unable to operate a keyboard. The wireless microphone allows unencumbered movement around the laboratory without a "tether" that might interfere with equipment or experimental procedures. To evaluate the potential of voice data entry in a laboratory environment, we developed a prototype relational database that records the disposal of radionuclides and/or hazardous chemicals. Current regulations in our laboratory require that each such item being discarded must be inventoried and documents must be prepared that summarize the contents of each container used for disposal. Using voice commands, the user enters items into the database as each is discarded. Subsequently, the program prepares the required documentation.     

Do-It-Yourself device for recovery of cryopreserved samples accidentally dropped into cryogenic storage tanks

Liquid nitrogen is colorless, odorless, extremely cold (-196 °C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term storage of biological materials such as blood, cells and tissues (1,2). The cryogenic nature of liquid nitrogen, while ideal for sample preservation, can cause rapid freezing of live tissues on contact - known as 'cryogenic burn' (2), which may lead to severe frostbite in persons closely involved in storage and retrieval of samples from Dewars. Additionally, as liquid nitrogen evaporates it reduces the oxygen concentration in the air and might cause asphyxia, especially in confined spaces (2). In laboratories, biological samples are often stored in cryovials or cryoboxes stacked in stainless steel racks within the Dewar tanks (1). These storage racks are provided with a long shaft to prevent boxes from slipping out from the racks and into the bottom of Dewars during routine handling. All too often, however, boxes or vials with precious samples slip out and sink to the bottom of liquid nitrogen filled tank. In such cases, samples could be tediously retrieved after transferring the liquid nitrogen into a spare container or discarding it. The boxes and vials can then be relatively safely recovered from emptied Dewar. However, the cryogenic nature of liquid nitrogen and its expansion rate makes sunken sample retrieval hazardous. It is commonly recommended by Safety Offices that sample retrieval be never carried out by a single person. Another alternative is to use commercially available cool grabbers or tongs to pull out the vials (3). However, limited visibility within the dark liquid filled Dewars poses a major limitation in their use. In this article, we describe the construction of a Cryotolerant DIY retrieval device, which makes sample retrieval from Dewar containing cryogenic fluids both safe and easy.     

An economical system for liquid scintillation counting

Small glass shell vials (12 × 35 mm minivials), containing 2.0 ml of a dioxane-based scintillation solution plus a ¹⁴C-labeled sample, were placed in a conventional glass, 20-ml count vial and assayed in a scintillation spectrometer. Statistical comparison of counts recorded from ¹⁴C samples prepared both in the minivial system and conventional 20-ml count vials indicated that the two systems were equivalent with sample volumes of 10 and 100 μliters (1600-cpm solution) and 10 μliters (60-cpm solution). Conventional 20-ml glass or plastic count vials were both acceptable as containers for the minivials.There were no significant differences in the counts from samples in minivials placed on-center and off-center in the container vial. Cost per sample was reduced from 24.8 cents (conventional glass vials) to 4.7 cents (minivial system).     

Protection of histones isolated from elastase-treated mouse epidermis

Small glass shell vials (12 × 35 mm minivials), containing 2.0 ml of a dioxane-based scintillation solution plus a ¹⁴C-labeled sample, were placed in a conventional glass, 20-ml count vial and assayed in a scintillation spectrometer. Statistical comparison of counts recorded from ¹⁴C samples prepared both in the minivial system and conventional 20-ml count vials indicated that the two systems were equivalent with sample volumes of 10 and 100 μliters (1600-cpm solution) and 10 μliters (60-cpm solution). Conventional 20-ml glass or plastic count vials were both acceptable as containers for the minivials.There were no significant differences in the counts from samples in minivials placed on-center and off-center in the container vial. Cost per sample was reduced from 24.8 cents (conventional glass vials) to 4.7 cents (minivial system).     

Stability of containerized urban street trees

Trees are usually grown in containers in the nursery until they reach a certain size, whereupon they are transplanted to a permanent location. Infrastructure development has often led to the removal of large trees. To maintain lush foliage and trees of a size that benefit urban ecology, trees can be grown in containers. Containerized trees can be moved from one location to another, and this relocation does not require root pruning or crown-size reduction. The drawback to having trees in containers is the small and confined volume of the container, which limits tree root development and thus affects containerized tree stability. The objective of this study was to understand the failure mechanisms for and the effect of the root dimensions on the stability of containerized trees. Therefore, small-scale stability model tests were conducted which were verified using numerical and analytical models. The results identified two failure modes that were likely to occur: tree overturning and container overturning. The mode of failure was dependent on the root dimensions. When the trees had extended their roots deep into the container, the whole container would overturn in the event of failure due to increased root confinement and shear resistance of the soil. On the other hand, the main failure mechanism when there was shallow root development was the uplifting of the tree from the container while the container remained upright. The results from numerical and analytical models were consistent with those obtained during the small-scale model stability tests.     

Determining replication for discrimination among microbial communities in environmental samples using community-level physiological profiles

A statistical approach was employed to assess microbial community variability within a single 4-l water sample and among 10 independent 4-l water samples from a single location using community-level physiological profiles. Power calculations demonstrated that duplicate analyses could distinguish between two different locations at two times during the year. Variability associated with replicates from a single container or from different containers was nearly the same for the two sites examined. Duplicate assays (one from each of two independent samples) were sufficient to resolve the between-site differences at alpha=0.05 with power exceeding 0.95 at both times of the year. Similar methods are recommended to determine the appropriate number of replicates for environments of interest.     

Impact of Natural Variations in Freeze-Drying Parameters on Product Temperature History: Application of Quasi Steady-State Heat and Mass Transfer and Simple Statistics

Inter- and intra-batch variability in heat and mass transfer during the drying phase of lyophilization is well recognized. Heat transfer variability between individual vials in the same batch arise from both different positions in the vial array and from variations in the bottom contour of the vials, both effects contributing roughly equally to variations in the effective heat transfer coefficient of the vials, K_v. Both effects can be measured in the laboratory, and variations in average K_v values as a function of vial position in the array for lab and production can be calculated by use of the simple steady-state heat and mass transfer theory. Typically, in the laboratory dryer, vials on the edge of the array, “edge vials,” run 2–4°C warmer than “center vials,” but differences between laboratory and manufacturing temperatures are modest. The variability in mass transfer can be assigned to major variations in ice nucleation temperature (both intra-batch and inter-batch), including major differences between laboratory and manufacturing. The net effect of all random variations, for each class of vial, can be evaluated by a simple statistical model-propagation of error, which then allows prediction of the distribution in product temperatures and drying times, and therefore prediction of percent of vials dry and percent of vials collapsed and proximity to the edge of failure for a given process. Good agreement between theoretical and experimentally determined maximum temperatures in primary drying and percent collapsed product demonstrates the calculations have useful accuracy.     

Evaluation of cultivar-testing locations in sugarcane

Summary Selection of test locations, representative of conditions and practices of an area can be a challenging process in a breeding program. Data from two groups of sugarcane (trispecies hybrids of Saccharum sp.) cultivar experiments in Florida were analyzed to determine if relative cultivar response at any two of six current locations was sufficiently similar so that at least one location could be replaced by a location with a different environment. The parameter analyzed was metric tons per ha of sugar (THS). To determine similarity between location pairs for all cultivars within each group of cultivars, an unbiased stability-variance parameter ( ) developed by Shukla was used. After identified similar location pairs, single degree of freedom interactions were calculated for important cultivars to determine which of the location pairs identified by contained the two most similar locations. Use of the above procedure can assist in making optimum location assignments in a breeding program.Cooperative investigation of the U.S. Sugarcane Field Stn., Canal Point, FL; and University of Florida, Everglades. Res. and Educ. Ctr., Belle Glade, FL, USA     

A comparison of double vial to serum bottle radiorespirometry to measure microbial mineralization in soils

Two methods of measuring mineralization rates were compared for their ability to quantify the microbiol mineralization of organic compounds in soils. In each of three soils used, the serum bottles gave higher yields for the mineralization of both [¹⁴C]glucose and [¹⁴C]cellulose (lignocellulose) than the double vials. In two of the soils, the serum bottles also showed less variation between replicates than the double vials. Furthermore, the mineralization of glucose in the serum bottles fit a first order rate model, whereas the mineralization of glucose in the double vials showed best fit to a linear model. Results using different amounts of soils indicated that container geometry may have placed unfavorable restrictions upon the double vial system, lowering the yield of ¹⁴CO₂ from the soils. Therefore, the serum bottle method was found to be the better method for measuring mineralization rates in soils.     

Post-licensure evaluation of vaccine safety: current status and future directions. Symposium organised by the International Alliance for Biological Standardization (IABS) in Barcelona, Spain, 27-28 April 2011

Adverse events following immunization, while rare, unfortunately do occur. And when they do, the public's faith in vaccines waves. It's a known fact, for example, that vaccine safety concerns are among the most important factors contributing to parents refusing vaccination for their children. How best, then, to tackle these concerns and increase public confidence in the vaccine safety system? In an effort to contribute to identifying the right mechanisms, the International Alliance for Biological Standardization organized an international symposium on "Post-Licensure Evaluation of Vaccine Safety" in Barcelona in early Spring. Delegates from 24 countries took a close look at the current status of this challenging problem and identified several practical measures which could help address the situation. They suggested an integrated vaccine safety program to be in place in all countries and standardized so that information and data can be exchanged on a routine basis. Another proposal was to put in place simple measures such as the use of bar codes on vaccine vials.     

Utilization Trends and Positive Biopsy Rates for Prostate Biopsies in the United States: 2005 to 2011

This article assesses the positive biopsy rate and core sampling pattern in patients undergoing needle biopsy of the prostate in the United States at a national reference laboratory (NRL) and anatomic pathology laboratories integrated into urology group practices, and analyzes the relationship between positive biopsy rates and the number of specimen vials per biopsy. For the years 2005 to 2011 we collected pathology data from an NRL, including number of urologists and urology practices referring samples, total specimen vials submitted for prostate biopsies, and final pathologic diagnosis for each case. The diagnoses were categorized as benign, malignant, prostatic intraepithelial neoplasia, or atypical small acinar proliferation. Over the same period, similar data were gathered from urology practices with in-house laboratories performing global pathology services (urology practice laboratories; UPLs) as identified by a survey of members of the Large Urology Group Practice Association. For each year studied, positive biopsy rate and number of specimen vials per biopsy were calculated in aggregate and separately for each site of service. From 2005 to 2011, 437,937 biopsies were submitted in > 4.23 million vials (9.4 specimen vials/biopsy); overall positive biopsy rate was 40.3%-this was identical at both the NRL and UPL (P = .97). Nationally, the number of specimen vials per biopsy increased sharply from a mean of 8.8 during 2005 to 2008 to a mean of 10.3 from 2009 to 2011 (difference, 1.5 specimen vials/biopsy; P = .03). For the most recent 3-year period (2009–2011), the difference of 0.6 specimen vials per biopsy between the NRL (10.0) and UPL (10.6) was not significant (P = 0.08). Positive biopsy rate correlated strongly (P < .01) with number of specimen vials per biopsy. The positive prostate biopsy rate is 40.3% and is identical across sites of service. Although there was a national trend toward increased specimen vials per biopsy from 2005 to 2011, from 2009 to 2011 there was no significant difference in specimen vials per biopsy across sites of service. Increased cancer detection rate correlated significantly with increased number of specimens examined. Segregation of prostate biopsy cores into 10 to 12 unique specimen vials has been widely adopted by urologists across sites of service.Key Words: Prostate cancer, Prostate biopsy, Utilization trends, National reference laboratory, Urology practice laboratoriesPublished data over the past decade suggesting that prostate cancer detection rates are enhanced with additional sampling of the prostate have resulted in modifications to the traditional 6-core (sextant) biopsy regimen^1,2 such that recent clinical guidelines recommend that extended biopsy schemes with 10 to 12 specimens be obtained.^3–5 There are also data that suggest that segregation of prostate biopsy tissue specimens into individual vials improves specimen handling, enhances tissue representation, and improves diagnostic accuracy.^6–8 Furthermore, focal prostate cancer treatment strategies gaining recent popularity are dependent on more precise tumor mapping, requiring even greater tissue sampling.⁹Over approximately the same time frame, there has been an increase in consolidation of medical practices into larger single- or multispecialty group practices. By incorporating efficiencies of scale, these groups afford physicians the opportunity to retain the characteristics of traditional medical practices while improving their ability to adapt to changing health care circumstances.¹⁰ These groups often integrate additional capabilities beyond professional services, including anatomic and clinical pathology, diagnostic imaging, and radiation therapy. Proponents of these arrangements argue that integration of medical services facilitates the development of coordinated clinical pathways, improves communication between specialists, offers better quality control of ancillary services, and enhances data collection—all of which can improve patient care and lead to lower costs.^11–13 Specifically with regard to anatomic pathology, recent data suggest that certain specimen handling errors are significantly lower (P = .018) at urology practices with integrated in-house pathology laboratories (urology practice laboratories [UPLs]) than at other sites of service¹⁴; however, some contend that group practice integration creates conflicts of interest and self-referral issues, which ultimately leads to increased utilization of services.^15–19 A recent study based on analysis of Medicare claims data purported that positive prostate biopsy rates and the number of samples submitted per biopsy are significantly different across sites of service²⁰; however, this study has been criticized as both methodologically flawed and scientifically inaccurate.²¹ Also problematic is the fact that calculation of prostate cancer incidence has been identified as particularly susceptible to error when determined by analysis of outpatient claims data alone.²²We sought to determine positive biopsy rates and utilization trends in the United States via direct analysis of laboratory records from both a national reference laboratory (NRL) and UPLs, and to determine if there was a correlation between positive biopsy rates and number of specimen vials submitted.     

Characterization of the B cell epitopes associated with a truncated form of Pseudomonas exotoxin (PE38) used to make immunotoxins for the treatment of cancer patients

Recombinant immunotoxins composed of an Ab Fv fragment joined to a truncated portion of Pseudomonas exotoxin A (termed PE38) have been evaluated in clinical trials for the treatment of various human cancers. Immunotoxin therapy is very effective in hairy cell leukemia and also has activity in other hemological malignancies; however, a neutralizing Ab response to PE38 in patients with solid tumors prevents repeated treatments to maximize the benefit. In this study, we analyze the murine Ab response as a model to study the B cell epitopes associated with PE38. Sixty distinct mAbs to PE38 were characterized. Mutual competitive binding of the mAbs indicated the presence of 7 major epitope groups and 13 subgroups. The competition pattern indicated that the epitopes are discrete and could not be reproduced using a computer simulation program that created epitopes out of random surface residues on PE38. Using sera from immunotoxin-treated patients, the formation of human Abs to each of the topographical epitopes was demonstrated. One epitope subgroup, E1a, was identified as the principal neutralizing epitope. The location of each epitope on PE38 was determined by preparing 41 mutants of PE38 in which bulky surface residues were mutated to either alanine or glycine. All 7 major epitope groups and 9 of 13 epitope subgroups were identified by 14 different mutants and these retained high cytotoxic activity. Our results indicate that a relatively small number of discrete immunogenic sites are associated with PE38, most of which can be eliminated by point mutations.     

Non-compliance with growth hormone treatment in children is common and impairs linear growth

Background

GH therapy requires daily injections over many years and compliance can be difficult to sustain. As growth hormone (GH) is expensive, non-compliance is likely to lead to suboptimal growth, at considerable cost. Thus, we aimed to assess the compliance rate of children and adolescents with GH treatment in New Zealand.

Methods

This was a national survey of GH compliance, in which all children receiving government-funded GH for a four-month interval were included. Compliance was defined as ≥85% adherence (no more than one missed dose a week on average) to prescribed treatment. Compliance was determined based on two parameters: either the number of GH vials requested (GHreq) by the family or the number of empty GH vials returned (GHret). Data are presented as mean ± SEM.

Findings

177 patients were receiving GH in the study period, aged 12.1±0.6 years. The rate of returned vials, but not number of vials requested, was positively associated with HVSDS (p<0.05), such that patients with good compliance had significantly greater linear growth over the study period (p<0.05). GHret was therefore used for subsequent analyses. 66% of patients were non-compliant, and this outcome was not affected by sex, age or clinical diagnosis. However, Maori ethnicity was associated with a lower rate of compliance.

Interpretation

An objective assessment of compliance such as returned vials is much more reliable than compliance based on parental or patient based information. Non-compliance with GH treatment is common, and associated with reduced linear growth. Non-compliance should be considered in all patients with apparently suboptimal response to GH treatment.     

Structural damages in adsorbed vaccines affected by freezing

This study was planned to evaluate structural damages in adsorbed vaccines affected by freezing using scanning electron microscopy and X-ray analysis of the elements. Randomly selected 42 vials of eight different types of WHO pre-qualified adsorbed freeze-sensitive vaccines from 10 manufacturers were included in the study. Vaccines were kept at 5 °C. Selected numbers of vials from each type were then exposed to ?25 °C for 24 h periods. All samples were evaluated for their structure using scanning electron microscopy, X-ray analysis of the elements and precipitation time. Scanning electron microscopy of vaccines affected by freezing showed either smooth or rough surfaced conglomerates associated with phosphate content of the precipitate. These vaccines precipitated 2–15 times faster compared to non-frozen samples. Non-frozen samples showed uniform flocculent structure either dense or dispersed. X-ray analysis of precipitates in frozen samples confirmed that the precipitate is mainly aluminium clutters. Scanning electron microscopy confirmed that the lattice structure of bonds between adsorbent and the antigen is broken and aluminium forms conglomerates that grow in size and weight. The precipitation time of vaccines affected by freezing is 4.5 times faster on average compared to non-frozen samples. These facts form the basis of the "shake test".     

BIOLAB, EPU and EMCS for cell culture experiments on the ISS

Two ESA facilities are under development for biological research on the International Space Station: BIOLAB as part of the European "Columbus" Laboratory and the European Modular Cultivation System (EMCS), foreseen for accommodation in the US Lab "Destiny". Both facilities have an incubator (18-40 degrees C) and use standard Experiment Containers, mounted on two centrifuge rotors providing either microgravity or variable g-levels from 0.001 x g to 2.0 x g. Standard interface plates supply each container with power and data lines, with gas (controlled CO2, O2 and water vapour concentration; trace gas removal), and--for EMCS only--with water. The degree of automation is higher in BIOLAB: it contains a robotic Handling Mechanism for automatic sampling and handling of liquids, which can be stored at cool or cold temperatures or injected for automatic on-board analysis into a microscope or a spectrophotometer. For analyses on the running centrifuge, small automatic microscopes can be installed in the Experiment Containers. Several designs for supporting cell culture experiments have been studied for BIOLAB and EMCS. BIOLAB has in addition a Bio-Glovebox, which can be sterilised and where new cell cultures may be prepared under 1 x g conditions from deep-frozen samples in the Experiment Preparation Unit (EPU): the cryo-protectant will be removed by automatic washing cycles. Both facilities, EMCS and BIOLAB (with EPU), have also provisions for telescience operations through video, data and command lines, either operated by the crew or by the experimenter on ground.     

乙酸乙酯对果蝇(Drosophila melanogaster)的麻醉效应研究

麻醉是果蝇实验中最基本的操作,乙醚是最常用的麻醉剂。但因为乙醚是二类易制毒化学品而被国家控制使用。报道一种容易获得的试剂——乙酸乙酯对果蝇的麻醉效果。实验采用的麻醉室大小为125cm3,每处理20~30只果蝇,乙酸乙酯剂量为40、80、120μL,以同等剂量的乙醚为对照,每个实验重复4次,用所有果蝇完全麻醉后20min及120min时的未苏醒率为指标评估麻醉效果及安全性。结果表明:乙酸乙酯对果蝇具有麻醉作用;麻醉时乙酸乙酯开始起效应的时间略晚于同等剂量的乙醚,但使果蝇完全麻醉的时间却比同等剂量的乙醚略短或相接近;麻醉持续的时间则长于同等剂量的乙醚。乙酸乙酯麻醉的果蝇,90%以上的果蝇均在120min内苏醒,表明在这些剂量范围内是安全的。乙酸乙酯完全可以替代乙醚用于果蝇的麻醉。     

Counting emissions from potassium-42 in plant tissue with a liquid scintillation spectrometer

Summary A method has been devised to count emissions from K⁴² in plant tissue by liquid scintillation spectrometer with low quenching. The plant samples were ashed in aluminium dishes, folded into aluminium wafers and suspended in the liquid scintillator of counting vials. The samples were counted in a scintillation spectrometer at one to five minute intervals seven or more times and until the total exceeded 1000 counts. The efficiency of counting was approximately 70%.A computer program was written to calculate decay corrections for the short half-life isotope K⁴². The program computed the weighted mean of the counts, standard deviation of the mean, percentage standard deviation of the mean and Chi-square value for each sample. The measurements were precise enough for K-uptake studies.