A moorable,automated plankton sampler

A moorable, automated plankton sampler is described, designed to obtain series of plankton samples over extended time periods in the absence of a surface vessel. The sampler consists of one or more net-containing boxes, a unit for generating as well as measuring water flow through the net boxes, a programmeable control unit, and a frame. Each net box contains several nets on a vinyl strip, used to move the nets from the storage chamber into the fishing position and then into the preservative chamber. Preservation of samples is in a formalin-brine mixture.Net boxes can be added and the number of nets per box changed; the prototype is described with 1 net box with 10 nets. Volume of water to be filtered, time between sample collections, number of net boxes and the number of nets in each box is programmed into the control unit before sampler deployment. Collections made with the sampler are compared with those made with a SCOR net and a pump.     

Evaluation of a pumping system for sampling zooplankton

This study describes the sampling efficiency of a plankton pumpdesigned to operate from a moving research vessel. The samplingefficiency of the pump was evaluated by comparing the catchper unit volume of several planktonic taxa sampled simultaneouslywith the pump and with a modified Gulf V plankton sampler ora tube sampler. The estimates of plankton density obtained withthe pump sampler corresponded well with those obtained withthe modified plankton net and tube sampler. We conclude thatthe use of a plankton pump in zooplankton sampling gives resultscomparable to those found with traditional sampling, exceptthat the results were biased for the sampling of rotifers andcopepod eggs.     

An automated front-end monitor for anthrax surveillance systems based on the rapid detection of airborne endospores

A fully automated anthrax smoke detector (ASD) has been developed and tested. The ASD is intended to serve as a cost effective front-end monitor for anthrax surveillance systems. The principle of operation is based on measuring airborne endospore concentrations, where a sharp concentration increase signals an anthrax attack. The ASD features an air sampler, a thermal lysis unit, a syringe pump, a time-gated spectrometer, and endospore detection chemistry comprised of dipicolinic acid (DPA)-triggered terbium ion (Tb(3+)) luminescence. Anthrax attacks were simulated using aerosolized Bacillus atrophaeus spores in fumed silica, and corresponding Tb-DPA intensities were monitored as a function of time and correlated to the number of airborne endospores collected. A concentration dependence of 10(2)-10(6) spores/mg of fumed silica yielded a dynamic range of 4 orders of magnitude and a limit of detection of 16 spores/L when 250 L of air were sampled. Simulated attacks were detected in less than 15 min.     

A method for the rapid,automated filtration of protein hydrolyzates

A method for the automated filtration of protein hydrolyzates prior to amino acid analysis is described. Minor modification of a Technicon Sampler II enables it to function simultaneously as a sampler and a filtrate collector. Samples are drawn from cups in the sampler tray and are forced through a Teflon filter (pore size, 0.2 μm) in a Millipore Swinnex filter holder by a variable-speed Technicon proportioning pump. The filtrates are collected in cups in the sampler tray opposite those containing unfiltered hydrolyzates. Using this technique, 12 hydrolyzates can be filtered in 25 min compared to the approximately 2 h of technician time required for their manual filtration. Aliquots from each of 48 samples representing different proteins and hydrolysis conditions are filtered manually and by the automated technique. Analysis of variance of the resulting recoveries of each amino acid indicate little likelihood of effects due to filtration method.     

Semiautomated Method for Microbiological Vitamin Assays

A semiautomated method for microbiological vitamin assays is described, which includes separate automated systems for the preparation of the cultures and for the measurement of turbidity. In the dilution and dosage unit based on the continuous-flow principle, vitamin samples were diluted to two different dose levels at a rate of 40 per hr, mixed with the inoculated test broth, and dispensed into culture tubes. After incubation, racks with culture tubes were placed on the sampler of an automatic turbidimeter. This unit, based on the discrete-sample system, measured the turbidity and printed the extinction values at a rate of 300 per hr. Calculations were computerized and the results, including statistical data, are presented in an easily readable form. The automated method is in routine use for the assays of thiamine, riboflavine, pyridoxine, cyanocobalamin, calcium pantothenate, nicotinic acid, pantothenol, and folic acid. Identical vitamin solutions assayed on different days gave variation coefficients for the various vitamin assays of less than 10%.     

The Bottom Sampler – a new technique for sampling bed sediments in streams and lakes

New, easy to use, liquid nitrogen-cooled equipment is described for sampling the upper layer (80–160 mm) of water sediment and associated benthic organisms in streams and lakes up to 1.2 m deep. The sediment sample has an area of 0.0531 m² and retains its natural composition and spatial structure. The two sampler components weigh 15 kg in total, which enables sampler use by hand, even in rural areas that are not readily accessible. A successful 2-year testing period in several first and second order streams demonstrated the suitability of the apparatus for sampling sediment textures ranging from fine clay to cobbles and current velocities up to 1 m s^?1.     

The efficiency of a new lightweight suction sampler for sampling aphids and their predators in arable land

A petrol driven machine, normally used to collect leaf litter, was modified to be used as a suction sampler for polyphagous predators in cereals and grassy habitats and aphids in cereals. Recovery efficiency of Araneae, Carabidae and Staphylinidae did not differ significantly between winter sampling from Agrostis stolonifera, Dactylis glomerata, Festuca rubra, Holcus lanatus or Lolium perenne although the structure of these grasses was very different. Summer sampling of aphids and their predators in winter wheat showed that the new sampler captured significantly more target organisms per unit area than did a traditional suction sampler. The machine was also lighter, cheaper and much easier to use than a traditional machine.     

A quantitative sampler for collecting invertebrates associated with deep submerged vegetation

Only few of the numerous samplers for collecting invertebrate fauna associated with vegetation permit sampling at depths of more than approximately 0.5 m. This paper describes a sampler allowing collection of epifauna from submerged plants at a depth of up to approximately 2 m, growing in varied densities. The sampler is composed of two panels made of duralumin, connected on one side by means of piano-hinges. One of the panels has an opening covered with mesh, and the other is equipped with a cone-shaped net and detachable sample concentrator at its end. The sampler is coupled with a manipulator with a several meter extension for lowering the sampler under water, as well as for its opening, and closing. The initial assessment of the sampler efficiency, verified in beds of Potamogeton perfoliatus, provided similar results as two other, older and commonly used samplers. In comparison with the older devices, the sampler has the advantage of permitting collecting samples from greater depths. It also enables studying both the vertical and horizontal distribution of invertebrates within a plant patch.     

A simple and inexpensive trap-tube sampler for zooplankton collection in shallow waters

The paper describes a new type of zooplankton sampler, which combines the concepts of the Pennak core sampler and the Schindler-Patalas plankton trap. The new sampler, called Trap Tube Sampler, consists of a PVC water pipe (1.5–2.0 m, long; 10 cm diameter) provided, at the bottom end, of a filtering unit and closing mechanism which alternatively closes the mouth of the tube and the mouth of the filtering unit. The new device is particularly suitable for collecting samples from the entire water column in shallow vegetated water bodies, fish ponds and mesocosm tanks.     

Comparison of bacterial recovery by Reuter centrifugal air sampler and slit-to-agar sampler.

Bacterial recovery by a portable Reuter centrifugal air sampler and a standard Mattson-Garvin slit-to-agar air sampler was compared in a series of experiments. Microbial air quality was monitored in seven typical laboratory locations. Tests showed that the Reuter centrifugal air sampler yielded significantly higher recoveries than did the slit-to-agar unit.     

The MacVuti sampler: a new and inexpensive volume sampler for plankton and water

SUMMARY. Details are presented for the construction and operation of a cheap simple volume sampler for Zooplankton and water. This sampler has been used in waters up to 45 m deep over a number of years and proved to be reliable and effective.     

Automated assay of glycosidases

The Technicon Basic AutoAnalyzer sampler system was modified for simultaneous sampling of glycosidase(s) and substrate-buffer solutions. The inexpensive modification allows performance of automated enzyme analyses and enzyme kinetic studies with minimal consumption of substrate and/or enzyme.     

Successful completion of a semi-automated enzyme-free cloning method

Nowadays, in scientific fields such as Structural Biology or Vaccinology, there is an increasing need of fast, effective and reproducible gene cloning and expression processes. Consequently, the implementation of robotic platforms enabling the automation of protocols is becoming a pressing demand. The main goal of our study was to set up a robotic platform devoted to the high-throughput automation of the polymerase incomplete primer extension cloning method, and to evaluate its efficiency compared to that achieved manually, by selecting a set of bacterial genes that were processed either in the automated platform (330) or manually (94). Here we show that we successfully set up a platform able to complete, with high efficiency, a wide range of molecular biology and biochemical steps. 329 gene targets (99 %) were effectively amplified using the automated procedure and 286 (87 %) of these PCR products were successfully cloned in expression vectors, with cloning success rates being higher for the automated protocols respect to the manual procedure (93.6 and 74.5 %, respectively).     

Seabird image identification in natural scenes using Grabcut and combined features

This paper proposes an automated seabird segmentation and identification method that applies to seabird images taken in natural scenes with a non-uniform and complex background. A variety of different bird postures appeared in natural scenes present different features from different points of view, even for the same posture. At first, the Grabcut method is introduced to segment seabird unit from a complicated background. Then, global features, namely the colour, shape and texture characteristics, and local features are integrated to describe the birds regarding various postures. Later, a combined recognition model, which is built using the k-Nearest Neighbor, Logistic Boost and Random Forest models by a voting mechanism that is designed for seabird identification. Finally, the efficiency and effectiveness of the proposed method in recognising seabirds were experimentally demonstrated. The experimental results on 900 field samples (6 seabird species, and 150 samples of each species) achieved a recognition accuracy of 88.1%, which indicates that the proposed method is effective for automated seabird identification.     

A comparison of vacuum sampling versus sweep-netting for arthropod biodiversity measurements in California coastal sage scrub

The recent growth of conservation biology has demanded that faster and more effective measures of biodiversity be utilized. Arthropods, due to high levels of diversity and their relative ease of capture, are often the subject of such surveys. The vacuum sampler, used quite often in the context of agricultural arthropod surveys, has never been adequately evaluated or compared to more traditional collection techniques in relatively complex ecosystems. The purpose of this study was to determine whether the vacuum sampler was more or less effective than a sweep-net in measuring arthropod biodiversity in California coastal sage scrub. The results show that significantly more individuals were collected by the vacuum sampler per unit effort for three out of six orders of arthropods examined. In addition, the vacuum sampler collected a significantly greater number of arthropod species than the sweep-net technique for two out of the six orders sampled. There were no significant differences in the number of species collected for the remaining four orders. We feel these findings are important for arthropod biodiversity studies utilized for conservation efforts as the vacuum sampler can attain a level of efficiency and sensitivity (with regard to species detection) that sweep-net techniques cannot. © Rapid Science Ltd. 1998     

A new sampler for stream benthos, epiphytic macrofauna and aquatic macrophytes

SUMMARY. A new sampler is described combining the advantages of both box and Surber samplers. The sample area is 200 × 250 mm (0.05 m²) and the device has been used to sample the benthos of rivers to a depth of c . 60 mm where the substratum consists of particles with diameters of 50 mm or less. The basic design may be used in water up to 0.5 m in depth, but with an optional top unit this depth may be increased to 1 m. Aquatic macrophytes can also be sampled either on their own or together with the underlying substratum. Results from sampling programmes designed to estimate macrophyte biomass, the biomass of the macroinvertebrate community and the density of Gammarus pulex are given as examples of the flexibility of the sampler on a variety of biotopes.     

A moorable,automated plankton sampler: comments on Lewis & Heckl (1991)

Comments on a recently described moorable, automated plankton sampler are given, mainly because it was designed to capture large zooplankton. However, the need for automatic devices for sampling phyto- and zooplankton is stressed. A new design for such a device is presented. A preliminary test was made using standard continuous-flow (auto-analyser) equipment, a cultured flagellate and formalin as a fixative.     

The Sea Core Sampler: a simple water sampler that allows direct observations of undisturbed plankton

A simple water sampler that brings undisturbed water samplesto the deck-laboratory and that allows video recording of planktonand small-scale plankton phenomena directly in the sampler isdescribed. Using the sampler, it is possible to follow individualplankton organisms and marine snow aggregates for longer periodsof time in an environment where the original three-dimensionalorganization of particles and chemical gradients have been retained.The sampler has been used to film sinking marine snow, the microbiallife on a snow flake, and the behaviour of delicate zooplanktersthat are otherwise difficult to collect live. Video clips demonstratingthe utility of the sampler are available online.     

A new quantitative air-lift sampler for collecting macroinvertebrates on stony bottoms in deep rivers

SUMMARY. 1. As three previous comparative studies of deep-water samplers for benthic macroinvertebrates in rivers highlighted the need for a quantitative sampler for use on stony substrata, a new air-lift sampler was developed. It can be operated from a small boat by two people, weighs 13.5–20.0 kg, depending on the length of riser used, and extends the maximum range of substrata that may be sampled quantitatively from 16–32 mm to 128—256 mm. The sampling area is isolated by forcing a collecting cylinder into the substratum, and rapid evacuation of the contents is assisted by a vibrator.
2. All the major specifications of the sampler were determined experimentally in a large tank using three sizes of substrata and plastic pellets to represent invertebrates. The sampler performed accurately to a depth of at least 8 cm on substrata ranging from gravel (2–4 mm) to large stones (32–36 mm long).
3. The performance of the sampler was compared with that of a Ponar grab and Pearson el at. air-lift sampler at two sites on a large river and also with a Naturalist's dredge and a diver-operated Hess-Waters sampler at one of the sites where there were large stones up to 280 mm long. In terms of both mean taxa per sample and mean numbers m⁻², samples taken using the new air-lift sampler provided estimates comparable to or belter than those obtained with the other samplers.     

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

MOTIVATION: Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates novel features optimized for the task of recognizing the binding motif of MHC classes I and II. The method locates the binding motif in a set of sequences and characterizes the motif in terms of a weight-matrix. Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design. RESULTS: We apply the motif sampler method to the complex problem of MHC class II binding. The input to the method is amino acid peptide sequences extracted from the public databases of SYFPEITHI and MHCPEP and known to bind to the MHC class II complex HLA-DR4(B1*0401). Prior identification of information-rich (anchor) positions in the binding motif is shown to improve the predictive performance of the Gibbs sampler. Similarly, a consensus solution obtained from an ensemble average over suboptimal solutions is shown to outperform the use of a single optimal solution. In a large-scale benchmark calculation, the performance is quantified using relative operating characteristics curve (ROC) plots and we make a detailed comparison of the performance with that of both the TEPITOPE method and a weight-matrix derived using the conventional alignment algorithm of ClustalW. The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method.