iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

Background  

In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques.     

The role of the spectral domain ocular coherence tomography in detection of age-related macular degeneration

Age-related macular degeneration (ARMD) is one of the most common causes of the vision loss and blindness in developed countries. Among other harmful effects, exposure to the UV radiation is the most prominent factor for the development of the disorder. Using the method of SD OCT (Spectral Domain Ocular Coherence Tomography) we performed measurement of the neurosensory retinal thickness of 19 eyes of low vision patients from the population of Primorsko-Goranska County of Republic of Croatia, with dry form of the terminal macular degeneration. These results we compared with control measurements performed on 28 eyes of healthy, normal vision subjects from same County. We determined following parameters: central foveal thickness (CFT), macular volume (MV) and mean foveal thickness (MFT) in the both groups. Results showed statistically significant reduction of CFT in the group of normal vision female patients when compared to males, while any significant difference of CFT between total groups of normal vision individuals and low vision patients was not detected. Furthermore, we noticed statistically significant (p < 0.000001) decrease of the MV in the group of the low vision patients in comparison to healthy subjects and statistically significant (p < 0.000001) reduction of the MFT of the low vision patients when compared to normal vision individuals. In our study we detected the absence of any significant difference of the CFT between healthy and low vision population, what looks like controversial finding, because neurosensory retina in the ARMD is thin and atrophic, but on the other side it is known that fixation point in low vision patients is translocated from the damaged fovea to extrafoveal region, usually above the fovea, where neurosensory retina is of the normal thickness, but with the less sensitivity. Furthermore, our results suggest possible connection of higher incidence of ARMD with lower CFT in females. Owing to the thicker neurosensory retina in males and better protection, damaging effect of the UV irradiation, which is the proven factor of ARMD development, is smaller. From the evolutionary point of view it is possible that males in all vertebrates have more resistant macula because during the evolutionary process they have spent much more time outside in the sunlight than females.     

The effect of temperature on midgut and brain protein profiles in Morimus funereus larvae (Coleoptera: Cerambycidae)

The 7-days shift of M. funereus larvae, from nature to a constant temperature of 23 degrees C led to changes in midgut and brain protein quality and quantity. The changes in midgut protein profiles are characterized by an intensified protein band Mr of 29 kD, the absence of protein Mr of 22 kD and less intense bands Mr of 8.5-2.5 kD. Electrophoretic patterns of brain proteins showed less intense Mr of 66-2.5 kD protein bands.     

The effects of the level of physical activity on calcaneal ultrasound measurements: bone properties of medical and physical education students

The aim of the study was to compare bone properties of two groups of students which strongly differ in the level of their everyday physical activity; the School of Medicine (SM) students and the Faculty of Physical Education (FPE) students, University of Zagreb. Quantitative ultrasound parameters--broadband ultrasound attenuation (BUA) and speed of sound (SOS) were measured. Quantitative ultrasound index (QUI) and estimated bone mineral density (BMD) were calculated by the device software. The final study sample consisted of 165 students from SM (94 males and 71 females) and 215 students from the FPE (164 males, 51 females). Sixty eight percent of FPE students and 21% of SM students reported a high level of everyday physical activity (P < 0.001). All ultrasound parameters were significantly higher in FPE students than in SM students (at the P < 0.001 level). The multiple regression model of the QUI confirmed that the school students attended was the single significant predictor variable for both genders. Our data indirectly showed the beneficial role of physical activity on bone properties.     

Nitrogen Utilization Efficiency in Canola Cultivars at Grain Harvest

Canola (Brassica napus L.) cultivars with improved nitrogen utilization efficiency (NUE) at grain harvest are of interest to growers to reduce fertilizer inputs. Our objective was to determine whether cultivar-specific responses in NUE (seed yield per N accumulated in the whole plant) could be related to the differences in dry matter and N partitioning among various plant parts. Four spring canola cultivars were grown in a glasshouse under the conditions of low and high N supply. When compared to high-N treatment, deficient N conditions resulted in a similar decrease in dry weight for all cultivars, averaging 46% for shoot, 47% for root, and 45% for dropped leaves. The reductions in N concentrations at low-N compared to high-N treatment were much smaller and averaged 15% for shoot, 16% for root and 10% for dropped leaves. Although significant variations occurred for dry weight, N concentration and N uptake in various plant sections, all cultivars accumulated a similar amount of N in total plant biomass at harvest. However, significant differences in plant biomass, seed yield and consequently, NUE existed because more N-efficient cultivars Eyre and Charlton produced larger seed yields than less N-efficient cultivars Pinnacle and Rainbow. No consistent variations in N concentration in various plant parts could be established among tested cultivars. Thus, cultivar-specific responses in NUE were mainly attributed to the differences in the root-to-shoot ratio and harvest index. N-efficient Eyre produced seed yield similar to the highest yielding Charlton, though it had the smallest plant dry weight of all cultivars. In contrast, N-inefficient Rainbow had the largest plant biomass, but produced the smallest seed yield because of its lowest harvest index and the highest root-to-shoot ratio. The absence of cultivar×N treatment interactions indicated that cultivars performed similarly for plant biomass, N uptake and seed yield across two contrasting N supplies. Canola cultivars significantly differed in NUE despite a similar amount of absorbed N in plant biomass; more N-efficient cultivars outyielded less N-efficient ones primarily because of cultivar-specific variations in the root-to-shoot ratio and harvest index.     

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

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Activating immunity in the liver. II. IFN-beta attenuates NK cell-dependent liver injury triggered by liver NKT cell activation

Dendritic cell (DC)-dependent activation of liver NKT cells triggered by a single i.v. injection of a low dose (10-100 ng/mouse) of alpha-galactosyl ceramide (alphaGalCer) into mice induces liver injury. This response is particularly evident in HBs-tg B6 mice that express a transgene-encoded hepatitis B surface Ag in the liver. Liver injury following alphaGalCer injection is suppressed in mice depleted of NK cells, indicating that NK cells play a role in NK T cell-initiated liver injury. In vitro, liver NKT cells provide a CD80/86-dependent signal to alphaGalCer-pulsed liver DC to release IL-12 p70 that stimulates the IFN-gamma response of NKT and NK cells. Adoptive transfer of NKT cell-activated liver DC into the liver of nontreated, normal (immunocompetent), or immunodeficient (RAG(-/-) or HBs-tg/RAG(-/-)) hosts via the portal vein elicited IFN-gamma responses of liver NK cells in situ. IFN-beta down-regulates the pathogenic IL-12/IFN-gamma cytokine cascade triggered by NKT cell/DC/NK cell interactions in the liver. Pretreating liver DC in vitro with IFN-beta suppressed their IL-12 (but not IL-10) release in response to CD40 ligation or specific (alphaGalCer-dependent) interaction with liver NKT cells and down-regulated the IFN-gamma response of the specifically activated liver NKT cells. In vivo, IFN-beta attenuated the NKT cell-triggered induction of liver immunopathology. This study identifies interacting subsets of the hepatic innate immune system (and cytokines that up- and down-regulate these interactions) activated early in immune-mediated liver pathology.     

Determination of standard zinc values in the intact tissues of mice by ICP spectrometry

The most commonly encountered difficulties for the quantitative measurement of zinc in biological samples are the limited sample amount, total and effective digestion of connective and fatty residues, and low zinc concentrations. These problems often lead to the determination of lower zinc values than actually present, so that the sample preparation, digestion, and analytical procedure deserve careful attention. In this short communication, a new method for microwave tissue disintegration is described. The authors have obtained consistent and reproducible results with tissue samples of 0.5 g or less.     

Effect of olive oil- and corn oil-enriched diets on the tissue mineral content in mice

The mineral content (zinc, iron, magnesium, and calcium) in the liver, spleen, and thymus of male Balb/C mice was analyzed. Animals were fed, over 21 d, diets enriched with corn oil (FCO diet) or olive oil (FOO diet) (5% addition to standard pellet, w/w). Olive oil with predominant oleic acid (C18:1, n-9) had a quite different composition than corn oil, in which linoleic acid (C18:2, n-6) prevails. The zinc and magnesium tissue concentrations were not changed in either group. The calcium concentration in liver as well as the calcium concentration in spleen increased in mice fed both the FCO and FOO diets. Furthermore, mice fed both the FOO and FCO diets had increased spleen iron concentration. Mice fed the FCO diet had increased thymus calcium concentration compared to controls. The results show the effect of diets with unsaturated, particularly polyunsaturated fatty acids, on the calcium and iron concentration in some organs.