An improved chamber for direct visualisation of chemotaxis

There has been a growing appreciation over the last decade that chemotaxis plays an important role in cancer migration, invasion and metastasis. Research into the field of cancer cell chemotaxis is still in its infancy and traditional investigative tools have been developed with other cell types and purposes in mind. Direct visualisation chambers are considered the gold standard for investigating the behaviour of cells migrating in a chemotactic gradient. We therefore drew up a list of key attributes that a chemotaxis chamber should have for investigating cancer cell chemotaxis. These include (1) compatibility with thin cover slips for optimal optical properties and to allow use of high numerical aperture (NA) oil immersion objectives; (2) gradients that are relatively stable for at least 24 hours due to the slow migration of cancer cells; (3) gradients of different steepnesses in a single experiment, with defined, consistent directions to avoid the need for complicated analysis; and (4) simple handling and disposability for use with medical samples. Here we describe and characterise the Insall chamber, a novel direct visualisation chamber. We use it to show GFP-lifeact transfected MV3 melanoma cells chemotaxing using a 60x high NA oil immersion objective, which cannot usually be done with other chemotaxis chambers. Linear gradients gave very efficient chemotaxis, contradicting earlier results suggesting that only polynomial gradients were effective. In conclusion, the chamber satisfies our design criteria, most importantly allowing high NA oil immersion microscopy to track chemotaxing cancer cells in detail over 24 hours.     

An improved version of the DNA Methylation database (MethDB)

Cytosine methylation is a characteristic property of prokaryotic and eukaryotic genomes. In the latter, it is indispensable for a healthy development of the organism and uncontrolled changes in the distribution of 5-methylcytosine (5mC) have been linked to severe disorders, in particular cancer. The growing scientific interest in DNA methylation has led to a considerable amount of data about this epigenetic phenomenon. In order to make these data readily available, we have established a dedicated database. The DNA Methylation database (MethDB) is currently the only public database for DNA methylation (http://www.methdb.net). This constantly growing database has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of September 4, 2002). About 14% of the data have not been published elsewhere. These data can be conveniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter new data into MethDB.     

An improved diffusion chamber (DC) for culture of hematopoietic cells.

A DC with Nuclepore filter wall has been described. Recovery of in vitro incubated human nucleated peripheral blood cells and in vivo growth of mouse bone marrow cells in intraperitoneally implanted DCs were improved when compared to the growth obtained in the more commonly used Millipore filter chambers.     

An evaluation of the metabolism of sestonic and epilithic communities in running waters using an improved chamber technique

SUMMARY. 1. A chamber technique is described which allows the uptake of nutrients in a lotic system to be assessed during a brief experimental period. Sensitive radioisotope techniques were used to determine the metabolism of the planktonic and epilithic communities simultaneously in a pristine boreal forest stream in N.E. Quebec, Canada.
2. Abiotic adsorption of bicarbonate, glucose, methylammonium and phosphate was unimportant in the riffle investigated. Among the biological components, the epilithon was responsible for more than 87% of the uptake of bicarbonate, glucose and methylammonium.
3. The uptake of orthophosphate was predominantly (80%) by organisms in the overlying water. Phosphorus, the nutrient most limiting the system, may be conserved by the epilithon through internal cycling. Uptake rates are within the range reported for other oligotrophic systems.     

CSI 2.0: a significantly improved version of the Chemical Shift Index

Protein chemical shifts have long been used by NMR spectroscopists to assist with secondary structure assignment and to provide useful distance and torsion angle constraint data for structure determination. One of the most widely used methods for secondary structure identification is called the Chemical Shift Index (CSI). The CSI method uses a simple digital chemical shift filter to locate secondary structures along the protein chain using backbone ¹³C and ¹H chemical shifts. While the CSI method is simple to use and easy to implement, it is only about 75–80 % accurate. Here we describe a significantly improved version of the CSI (2.0) that uses machine-learning techniques to combine all six backbone chemical shifts (¹³C_α, ¹³C_β, ¹³C, ¹⁵N, ¹HN, ¹H_α) with sequence-derived features to perform far more accurate secondary structure identification. Our tests indicate that CSI 2.0 achieved an average identification accuracy (Q3) of 90.56 % for a training set of 181 proteins in a repeated tenfold cross-validation and 89.35 % for a test set of 59 proteins. This represents a significant improvement over other state-of-the-art chemical shift-based methods. In particular, the level of performance of CSI 2.0 is equal to that of standard methods, such as DSSP and STRIDE, used to identify secondary structures via 3D coordinate data. This suggests that CSI 2.0 could be used both in providing accurate NMR constraint data in the early stages of protein structure determination as well as in defining secondary structure locations in the final protein model(s). A CSI 2.0 web server (http://csi.wishartlab.com) is available for submitting the input queries for secondary structure identification.     

用于研究大气二氧化碳浓度升高对农田有害生物影响的田间试验装置--改良的开顶式气室

开顶式气室可精准控制大气CO2(或其它气体成分)的浓度,使之稳定在一个特定的水平,为研究未来大气CO2浓度升高(或其它气体成分变化)对植物一害虫一天敌之间相互关系的影响提供了条件。该装置由CO2气源、CO2浓度测控系统和气室3部分组成。气室又包括无色透明玻璃(2．5mm厚)室壁,正八边形的铁框架和中空底座,以及换气扇组成的通风系统4部分。能实现气室内CO2浓度的自动控制。经试验检测,气室内CO2浓度、温度、相对湿度等环境条件的水平分布和垂直分布都很均匀,与自然环境十分接近。该气室设计的结构合理,使用性能稳定,可广泛应用于大气特定成分变化对生态系统影响的研究。     

Initial psychometric characterization for the Portuguese version of the Morningness-Eveningness-Stability-Scale improved (MESSi)

ABSTRACT

This work reports the initial psychometric characterization of the Morningness-Eveningness-Stability-Scale improved (MESSi) for Portuguese young-adults (N = 466). A confirmatory factor analysis confirmed a three-factor model (i.e. Morning Affect, Eveningness and Distinctness) in our data, as originally proposed. Furthermore, construct validity evidence in relation to external variables (i.e. morningness/eveningness and satisfaction with life), as well as adequate reliability (i.e. internal consistency and test-retest reliability), were found. Finally, sex-based invariance and between-sex differences were investigated for the three subscales, as were correlations with age. Results point to the suitability of the MESSi for multi-cultural research on relevant and multiple aspects of chronotype.     

An integrating sphere leaf chamber

Abstract. A combination of an optical integrating sphere and leaf chamber is described, and some principles of its design are given. It is shown that the number of quanta absorbed by the leaf inside the sphere can be found from measurements of the quantum flux density inside the sphere with and without the leaf present, when certain constant parameters of the sphere are known. Methods for finding these are given. It is not necessary to know leaf area or absorptivity for the quantum yield for photosynthesis to be derived from additional measurement of CO₂, fixation.     

The hot IVGTT two-compartment minimal model: an improved version

The two-compartment minimal model (2CMM) interpretation of a labeled intravenous glucose tolerance test (IVGTT) is a powerful tool to assess glucose metabolism in a single individual. It has been reported that a derived 2CMM parameter describing the proportional effect of glucose on insulin-independent glucose disposal can take physiologically unplausible negative values. In addition, precision of 2CMM parameter estimates is sometimes not satisfactory. Here we resolve the above issues by presenting an improved version of 2CMM that relies on a new assumption on the constant component R(d0) of insulin-independent glucose disposal. Here R(d0) is not fixed to 1 mg x kg(-1) x min(-1) but instead is expressed as a fraction of steady-state glucose disposal. The new 2CMM is identified on the same stable labeled IVGTT data base on which the original 2CMM was formulated. A more reliable insulin-independent glucose disposal portrait is obtained while that of insulin action remains unchanged. The new 2CMM also improves the precision with which model parameters and metabolic indexes are estimated.     

A twin Gliwicz--Haney in situ zooplankton grazing chamber: design, operation and potential applications

The design and operation of a twin-chambered modification ofthe Gliwicz — Haney in situ grazing vessel is described.Grazing rates are determined in one chamber, while the secondfunctions as a self-draining plankton trap.     

An update on the nutrition of dairy sheep grazing Mediterranean pastures

In the light of recent findings in sheep nutrition and feeding behaviour, the diets of grazing dairy sheep should be based on forages encompassing a variety of complementary nutritional values and containing moderate levels of diverse plant secondary metabolites, until recently regarded as “anti-nutritional”. In lactating sheep, pastures of tannin-containing legumes like sulla (Hedysarum coronarium) and chicory (Cichorium intybus) can be integrated with annual grasses for establishing artificial pastures under rainfed conditions. Diets based on these forages, while ensuring high milking performance, can mitigate the unbalance of CP to energy ratio of grazing sheep. By grazing sulla and Italian ryegrass (50:50 by area) as spatially adjacent monocultures or in timely sequence (complementary grazing) sheep eat more and perform better than by grazing the ryegrass pasture only. Concentrate supplementation of lactating sheep should be preferably based on sources rich in digestible plant fiber (soyhulls or beet pulps), particularly from mid-lactation onwards and when supplementation levels are high. Milk urea concentration is confirmed as a useful monitoring tool to balance protein nutrition and curb the waste of N at animal and system level. Finally, challenging tasks for future research on dairy sheep grazing management and nutrition are on-farm application of recent technological advances, such as image-based estimation of pasture biomass and quality, evaluation of sheep dietary quality by faecal Near Infrared Reflectance Spectrometry, and establishment of remote control systems.     

An improved hexagon open‐top chamber system for stable diurnal and nocturnal warming and atmospheric carbon dioxide enrichment

The use of solar passive hexagonal open‐top chambers (POTCs) is a viable method for experimentally manipulating daytime air temperatures in low‐stature plant communities at high latitudes. Here we describe a new hexagon POTC‐based system that uses thermal inertia to increase overnight temperatures and variable chamber height to reduce overheating in summer. Field data collected in tall temperate grasslands show that the presence of thermal mass raised minimum and mean nighttime air temperatures by up to 1.5 °C while lowering chamber height, along with thermal mass, limited the development of extreme daytime chamber temperatures in summer. We also demonstrate that, by using a simple, inexpensive twin carbon dioxide (CO₂) injection system regulated by an infrared gas monitor, it is possible to generate targeted and stable atmospheric CO₂ enrichment within these chambers. These innovations significantly improve the conventional hexagon POTC design and represent a low‐cost method for assessing the effects of warming and CO₂ enrichment on low‐stature vegetation in low latitude environments.