The ‘Densitometric Image Analysis Software’ and Its Application to Determine Stepwise Equilibrium Constants from Electrophoretic Mobility Shift Assays

Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the ‘Densitometric Image Analysis Software’ has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.     

Do climatic conditions affect host and parasite phenotypes differentially? A case study of magpies and great spotted cuckoos

Climatic conditions, through their effects on resource availability, may affect important life history strategies and trade-offs in animals, as well as their interactions with other organisms such as parasites. This impact may depend on species-specific pathways of development that differ even among species with similar resource requirements (e.g., avian brood parasites and their hosts). Here we explore the degree of covariation between environmental-climatic conditions and nestling phenotypes (i.e., tarsus length, body mass, immune response to phytohemagglutinin injection) and ectoparasite loads of great spotted cuckoos (Clamator glandarius) and those of their magpie (Pica pica) hosts, both within and among 11 study years (1997–2011). Our main results were that (1) nestling phenotypes differed among years, but differently for great spotted cuckoos and magpies; (2) nestling phenotypes showed significant among-year covariation with breeding climatic conditions (temperature and precipitation); and (3) these associations differed for cuckoos and magpies for some phenotypic traits. As the average temperature at the beginning of the breeding season (April) increased, body mass and tarsus length increased only for cuckoos, but not for magpie hosts, while immune response decreased in both species. Finally, (4) the strength of the within-year relationships between the probability of ectoparasitism by Carnus hemapterus flies and laying date (used as an estimate of the within-year variation in climatic conditions) was negatively affected by the annual accumulated precipitation in April. These results strongly suggest that variation in climatic conditions would result in asymmetric effects on different species with respect to the probability of ectoparasitism, immunity and body size. Such asymmetric effects may affect animal interactions in general and those of brood parasites and their hosts in particular.     

Recombinant Antigens Expressed in Pichia pastoris for the Diagnosis of Sleeping Sickness Caused by Trypanosoma brucei gambiense

Background

Screening tests for gambiense sleeping sickness, such as the CATT/T. b. gambiense and a recently developed lateral flow tests, are hitherto based on native variant surface glycoproteins (VSGs), namely LiTat 1.3 and LiTat 1.5, purified from highly virulent trypanosome strains grown in rodents.

Methodology/Principal Findings

We have expressed SUMO (small ubiquitin-like modifier) fusion proteins of the immunogenic N-terminal part of these antigens in the yeast Pichia pastoris. The secreted recombinant proteins were affinity purified with yields up to 10 mg per liter cell culture.

Conclusions/Significance

The diagnostic potential of each separate antigen and a mixture of both antigens was confirmed in ELISA on sera from 88 HAT patients and 74 endemic non-HAT controls. Replacement of native antigens in the screening tests for sleeping sickness by recombinant proteins will eliminate both the infection risk for the laboratory staff during antigen production and the need for laboratory animals. Upscaling production of recombinant antigens, e.g. in biofermentors, is straightforward thus leading to improved standardisation of antigen production and reduced production costs, which on their turn will increase the availability and affordability of the diagnostic tests needed for the elimination of gambiense HAT.     

Expression of a Heterologous Glutamate Dehydrogenase Gene in Lactococcus lactis Highly Improves the Conversion of Amino Acids to Aroma Compounds

The first step of amino acid degradation in lactococci is a transamination, which requires an α-keto acid as the amino group acceptor. We have previously shown that the level of available α-keto acid in semihard cheese is the first limiting factor for conversion of amino acids to aroma compounds, since aroma formation is greatly enhanced by adding α-ketoglutarate to cheese curd. In this study we introduced a heterologous catabolic glutamate dehydrogenase (GDH) gene into Lactococcus lactis so that this organism could produce α-ketoglutarate from glutamate, which is present at high levels in cheese. Then we evaluated the impact of GDH activity on amino acid conversion in in vitro tests and in a cheese model by using radiolabeled amino acids as tracers. The GDH-producing lactococcal strain degraded amino acids without added α-ketoglutarate to the same extent that the wild-type strain degraded amino acids with added α-ketoglutarate. Interestingly, the GDH-producing lactococcal strain produced a higher proportion of carboxylic acids, which are major aroma compounds. Our results demonstrated that a GDH-producing lactococcal strain could be used instead of adding α-ketoglutarate to improve aroma development in cheese.     

The evaluation of the transport medium for extracted premolars prior to cryopreservation: a systematic literature review

Prior to cryopreservation, a tooth is transported from a contaminated oral environment to the tooth bank. Our objective was to identify all studies reporting or investigating a transport protocol prior to the cryopreservation of teeth, in terms of decontamination of the subjects. The systematic literature search (1970–2017) was based on MEDLINE via PubMed, Web of Science and the Cochrane Library. The reference lists of the included studies and the Science Citation Index were used for hand searching (snowballing). Only studies reporting the transport conditions of the transplant were included. Language restrictions for English, Dutch or French were applied. The search led to 14 eligible studies. Almost all studies were laboratory studies, so the methodological quality of evidence was low. The majority of the included studies was performed by only five different research groups and the number of subjects varied between 1 and 120 teeth. In general, the teeth were stored in a tissue culture medium supplemented with fetal calf serum and/or different combinations of antibiotics and/or antimycotics. The teeth were transported cooled (4 °C) or at room temperature, for a period of time not exceeding 24 h. Only three studies reported the irrigation of the teeth with phosphate buffered saline prior to the transport. The optimisation of the decontamination during transport was investigated in three studies (from 1971, 1980 and 1982). It was concluded that the literature on this topic is scarce, and the decontamination protocol for teeth, prior to cryopreservation has not been validated recently.     

Ecophysiological and morphological parameters related to survival in grass species exposed to an extreme climatic event

An experiment was performed to elucidate interspecific differences in survival time of grass species subjected to an extreme climatic event. We exposed eight grass species to a simulated heat wave in the field ('free air' temperature increase at 11°C above ambient) combined with drought. We determined whether interspecific differences in survival time were related to the responses of the species to the imposed stress or could be explained by their ecophysiological or morphological characteristics in unstressed conditions. Surprisingly, there was no effect of specific leaf area, but species with a higher total leaf area survived longer. This may arise from a greater water reserve in the plant as a whole, which could delay the desiccation of the meristem, or from reduced evaporation due to a higher leaf area index. Species in which the decrease in light-saturated stomatal conductance ( g _s ) and photosynthetic CO₂ uptake rate ( A _max ) was strongly related to the decrease in soil water availability (measured as soil relative water content and stress duration) survived longer than species in which g _s and A _max likewise declined but responded more to daily fluctuations in irradiance, temperature, and vapor pressure deficit during the heat wave. We, therefore, hypothesize that interspecific differences in stress survival time might be related to the extent to which stomata react to changes in soil water conditions relatively to changes in other environmental and physiological factors. The results suggest that resistance to extremes is governed by other mechanisms than resistance to moderate drought.     

Long Term Outcomes of a Geriatric Liaison Intervention in Frail Elderly Cancer Patients

Background

The aim of this study was to evaluate the long term effects after discharge of a hospital-based geriatric liaison intervention to prevent postoperative delirium in frail elderly cancer patients treated with an elective surgical procedure for a solid tumour. In addition, the effect of a postoperative delirium on long term outcomes was examined.

Methods

A three month follow-up was performed in participants of the Liaison Intervention in Frail Elderly study, a multicentre, prospective, randomized, controlled trial. Patients were randomized to standard treatment or a geriatric liaison intervention. The intervention consisted of a preoperative geriatric consultation, an individual treatment plan targeted at risk factors for delirium and daily visits by a geriatric nurse during the hospital stay. The long term outcomes included: mortality, rehospitalisation, Activities of Daily Living (ADL) functioning, return to the independent pre-operative living situation, use of supportive care, cognitive functioning and health related quality of life.

Results

Data of 260 patients (intervention n = 127, Control n = 133) were analysed. There were no differences between the intervention group and usual-care group for any of the outcomes three months after discharge. The presence of postoperative delirium was associated with: an increased risk of decline in ADL functioning (OR: 2.65, 95% CI: 1.02–6.88), an increased use of supportive assistance (OR: 2.45, 95% CI: 1.02–5.87) and a decreased chance to return to the independent preoperative living situation (OR: 0.18, 95% CI: 0.07–0.49).

Conclusions

A hospital-based geriatric liaison intervention for the prevention of postoperative delirium in frail elderly cancer patients undergoing elective surgery for a solid tumour did not improve outcomes 3 months after discharge from hospital. The negative effect of a postoperative delirium on late outcome was confirmed.

Trial Registration

Nederlands Trial Register, Trial ID NTR 823.     

Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH)

While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions.