Metabolomics method to comprehensively analyze amino acids in different domains

Amino acids play essential roles in both metabolism and the proteome. Many studies have profiled free amino acids (FAAs) or proteins; however, few have connected the measurement of FAA with individual amino acids in the proteome. In this study, we developed a metabolomics method to comprehensively analyze amino acids in different domains, using two examples of different sample types and disease models. We first examined the responses of FAAs and insoluble-proteome amino acids (IPAAs) to the Myc oncogene in Tet21N human neuroblastoma cells. The metabolic and proteomic amino acid profiles were quite different, even under the same Myc condition, and their combination provided a better understanding of the biological status. In addition, amino acids were measured in 3 domains (FAAs, free and soluble-proteome amino acids (FSPAAs), and IPAAs) to study changes in serum amino acid profiles related to colon cancer. A penalized logistic regression model based on the amino acids from the three domains had better sensitivity and specificity than that from each individual domain. To the best of our knowledge, this is the first study to perform a combined analysis of amino acids in different domains, and indicates the useful biological information available from a metabolomics analysis of the protein pellet. This study lays the foundation for further quantitative tracking of the distribution of amino acids in different domains, with opportunities for better diagnosis and mechanistic studies of various diseases.

Dynamic analysis for different finite element models of beams with viscoelastic damping layer

Many new viscoelastic materials have been developed recently to help improve noise and vibration levels in mechanical structures for applications in automobile and aeronautical industry. The viscoelastic layer treatment applied to solid metal structures modifies two main properties which are related to the mass distribution and the damping mechanism. The other property controlling the dynamics of a mechanical system is the stiffness that does not change much with the viscoelastic material. The model of such system is usually complex, because the viscoelastic material can exhibit nonlinear behavior, in contrast with the many available tools for linear dynamics. In this work, the dynamic behavior of sandwich beam is modeled by finite element method using different element types which are then compared with experimental results developed in the laboratory for various beams with different viscoelastic layer materials. The finite element model is them updated to help understand the effects in the damping for various natural frequencies and the trade-off between attenuation and the mass add to the structure.

Twelve chromatically opponent ganglion cell types in turtle retina

The turtle retina has been extensively used for the study of chromatic processing mechanisms. Color opponency has been previously investigated with trichromatic paradigms, but behavioral studies show that the turtle has ail ultraviolet (UV) channel and a tetrachromatic visual system. Our laboratory has been working ill the characterization of neuronal responses in the retina of vertebrates using stimuli in the UV-visible range of the electromagnetic spectrum. In the present investigation, we recorded color-opponent responses from turtle amacrine and ganglion cells to UV and visible stimuli and extended our previous results that UV color-opponency is present at the level of the inner nuclear layer. We recorded from 181 neurons, 36 of which were spectrally opponent. Among these, there were 10 amacrine (5%), and 26 ganglion cells (15%). Morphological identification of color-opponent neurons was possible for two ganglion cell classes (G17 and G22) and two amacrine cell classes (A22 and A23b). There was a variety of cell response types and a potential for complex processing of chromatic stimuli, with intensity- and wavelength-dependent response components. Ten types of color opponency were found in ganglion cells and by adding previous results from our laboratory, 12 types of opponent responses have been found. The majority of the ganglion cells were R+UVBG- and RG+UVB-color-opponents but there were other less frequent types of chromatic opponency. This study confirms the participation of a UV channel in the processing of color opponency in the turtle inner retina and shows that the turtle visual system has the retinal mechanisms to allow many possible chromatic combinations.

HPV type infection in different anogenital sites among HIV-positive Brazilian women

Abstract Objectives To evaluate the prevalence of human papillomavirus (HPV) types, and risk factors for HPV positivity across cervix, vagina and anus, we conducted a study among 138 women with human immunodeficiency virus (HIV). Goal Compare the prevalence of different HPV types and the risk factors for HPV positivity in three sites. Results The most frequently detected HPV types in all sites were, in decreasing order, HPV16, 53, 18, 61 and 81. Agreement between the cervix and vagina was good (kappa 0.60 – 0.80) for HPV16 and 53 and excellent (Kappa > 0.80) for HPV18 and 61. HPV positivity was inversely associated with age for all combinations including the anal site. Conclusion In HIV positive women, HPV18 is the most spread HPV type found in combinations of anal and genital sites. The relationship of anal to genital infection has implications for the development of anal malignancies. Thus, the efficacy of the current HPV vaccine may be considered not only for the cervix, but also for prevention of HPV18 anal infection among immunossuppressed individuals.

Context-dependent interpretation of the conjunction 'und' in different age-groups

In contrast to formal semantics, the conjunction and is nonsymmetrical in pragmatics. The events in Marc went to bed and fell asleep seem to have occurred chronologically although no explicit time reference is given. As the temporal interpretation appears to be weaker in Mia ate chocolate and drank milk, it seems that the kind and nature of events presented in a context influences the interpretation of the conjunction. This work focuses on contextual influences on the interpretation of the German conjunction und (‘and’). A variety of theoretic approaches are concerned with whether and contributes to the establishment of discourse coherence via pragmatic processes or whether the conjunction has complex semantic meaning. These approaches are discussed with respect to how they explain the temporal and additive interpretation of the conjunction and the role of context in the interpre-tation process. It turned out that most theoretic approaches do not consider the importance of different kinds of context in the interpretation process.rnIn experimental pragmatics there are currently only very few studies that investigate the inter-pretation of the conjunction. As there are no studies that investigate contextual influences on the interpretation of und systematically or investigate preschoolers interpretation of the con-junction, research questions such as How do (preschool) children interpret ‘und’? and Does the kind of events conjoined influence children’s and adults’ interpretation? are yet to be answered. Therefore, this dissertation systematically investigates how different types of context influence children’s interpretation of und. Three auditory comprehension studies were conducted in German. Of special interest was whether and how the order of events introduced in a context contributes to the temporal read-ing of the conjunction und. Results indicate that the interpretation of und is – at least in Ger-man – context-dependent: The conjunction is interpreted temporally more often when events that typical occur in a certain order are connected (typical contexts) compared to events with-out typical event order (neutral contexts). This suggests that the type of events conjoined in-fluences the interpretation process. Moreover, older children and adults interpret the conjunc-tion temporally more often than the younger cohorts if the conjoined events typically occur in a certain order. In neutral contexts, additive interpretations increase with age. 5-year-olds reject reversed order statements more often in typical contexts compared to neutral contexts. However, they have more difficulties with reversed order statements in typical contexts where they perform at chance level. This suggests that not only the type of event but also other age-dependent factors such as knowledge about scripts influence children’s performance. The type of event conjoined influences children’s and adults’ interpretation of the conjunction. There-fore, the influence of different event types and script knowledge on the interpretation process does not only have to be considered in future experimental studies on language acquisition and pragmatics but also in experimental pragmatics in general. In linguistic theories, context has to be given a central role and a commonly agreed definition of context that considers the consequences arising from different event types has to be agreed upon.

Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging

In clinical diagnostics, it is of outmost importance to correctly identify the source of a metastatic tumor, especially if no apparent primary tumor is present. Tissue-based proteomics might allow correct tumor classification. As a result, we performed MALDI imaging to generate proteomic signatures for different tumors. These signatures were used to classify common cancer types. At first, a cohort comprised of tissue samples from six adenocarcinoma entities located at different organ sites (esophagus, breast, colon, liver, stomach, thyroid gland, n = 171) was classified using two algorithms for a training and test set. For the test set, Support Vector Machine and Random Forest yielded overall accuracies of 82.74 and 81.18%, respectively. Then, colon cancer liver metastasis samples (n = 19) were introduced into the classification. The liver metastasis samples could be discriminated with high accuracy from primary tumors of colon cancer and hepatocellular carcinoma. Additionally, colon cancer liver metastasis samples could be successfully classified by using colon cancer primary tumor samples for the training of the classifier. These findings demonstrate that MALDI imaging-derived proteomic classifiers can discriminate between different tumor types at different organ sites and in the same site.

Comparison of Fluid Types for Resuscitation in Acute Hemorrhagic Shock and Evaluation of Gastric Luminal and Transcutaneous P co 2 in Leghorn Chickens

The objective of this study was to compare the effects of 3 different fluid types for resuscitation after experimentally induced hemorrhagic shock in anesthetized chickens and to evaluate partial pressures of carbon dioxide measured in arterial blood (Paco2), with a transcutaneous monitor (TcPco2), with a gastric intraluminal monitor (GiPco2), and by end tidal measurements (Etco2) under stable conditions and after induced hemorrhagic shock. Hemorrhagic shock was induced in 40 white leghorn chickens by removing 50% of blood volume by phlebotomy under general anesthesia. Birds were divided into 4 groups: untreated (control group) and treated with intravenous hetastarch (haes group), with a hemoglobin-based oxygen carrier (hemospan group), or by autotransfusion (blood group). Respiratory rates, heart rates, and systolic arterial blood pressure (SAP) were compared at 8 time points (baseline [T0]; at the loss of 10% [T10%], 20% [T20%], 30% [T30%], 40% [T40%], and 50% [T50%] of blood volume; at the end of resuscitation [RES]; and at the end of anesthesia [END]). Packed cell volume (PCV) and blood hemoglobin content were compared at 6 time points (T0, T50%, RES, and 1, 3, and 7 days after induced hemorrhagic shock). Measurements of Paco2, TcPco2, GiPco2, and Etco2 were evaluated at 2 time points (T0 and T50%), and venous lactic acid concentrations were evaluated at 3 time points (T0, T50%, and END). No significant differences were found in mortality, respiratory rate, heart rate, PCV, or hemoglobin values among the 4 groups. Birds given fluid resuscitation had significantly higher SAPs after fluid administration than did birds in the control group. In all groups, PCV and hemoglobin concentrations began to rise by day 3 after phlebotomy, and baseline values were reached 7 days after blood removal. At T0, TcPco2 did not differ significantly from Paco2, but GiPco2 and Etco2 differed significantly from Paco2. After hemorrhagic shock, GiPco2 and TcPco2 differed significantly from Paco2. The TcPco2 or GiPco2 values did not differ significantly at any time point in birds that survived or died in any of the groups and across all groups. These results showed no difference in mortality in leghorn chickens treated with fluid resuscitation after hemorrhagic shock and that the PCV and hemoglobin concentrations increased by 3 days after acute hemorrhage with or without treatment. The different CO2 measurements document changes in CO2-values consistent with poor perfusion and may prove useful for serial evaluation of responses to shock and shock treatment.

Natural Tracers in recent groundwaters from different Alpine aquifers

Groundwater with underground residence times between days and a few years have been investigated over more than 20 years from 487 remote sites located in different aquifer types in the Alpine belt. Analysis of the data reveals that groundwaters evolved in crystalline, evaporite, carbonate, molasse, and flysch aquifers can be clearly distinguished based on their major and trace element composition and degree of mineralisation. A further subdivision can be made even within one aquifer type based on the trace element compositions, which are characteristic for the lithologic environment. Major and trace element concentrations can be quantitatively described by interaction of the groundwater with the aquifer- specific mineralogy along the flow path. Because all investigated sites show minimal anthropogenic influences, the observed concentration ranges represent the natural background concentrations and can thus serve as a “geo-reference” for recent groundwaters from these five aquifer types. This “geo-reference” is particularly useful for the identification of groundwater contamination. It further shows that drinking water standards can be grossly exceeded for critical elements by purely natural processes

Benthic oxygen and nitrogen fluxes at different time series sites in the southern North Sea, 2012 to 2014

Benthic oxygen and nitrogen fluxes were quantified within the years 2012 to 2014 at different time series sites in the southern North Sea with the benthic lander NuSObs (Nutrient and Suspension Observatory). In situ incubations of sediments, in situ bromide tracer studies, sampling of macrofauna and pore water investigations revealed considerable seasonal and spatial variations of oxygen and nitrogen fluxes. Seasonal and spatial variations of oxygen fluxes were observed between two different time series sites, covering different sediment types and/or different benthic macrofaunal communities. On a sediment type with a high content of fine grained particles (<63 µm) oxygen fluxes of -15.5 to -25.1 mmol/m**2/d (June 2012), -2.0 to -8.2 mmol/m**2/d (March 2013), -16.8 to -21.5 mmol/m**2/d (November 2013) and -6.1 mmol/m**2/d (March 2014) were measured. At the same site a highly diverse community of small species of benthic macrofauna was observed. On a sediment type with a low content of fine grained particles (<63 µm) high oxygen fluxes (-33.2 mmol/m**2/d August 2012; -47.2 to -55.1 mmol/m**2/d November 2013; -16.6 mmol/m**2/d March 2014) were observed. On this sediment type a less diverse benthic macrofaunal community, which was dominated by the large bodied suspension feeder Ensis directus, was observed. Average annual rain rates of organic carbon and organic nitrogen to the seafloor of 7.44 mol C/m**2/y and 1.34 mol N/m**2/y were estimated. On average 79% of the organic bound carbon and 95% of the organic bound nitrogen reaching the seafloor are recycled at the sediment-water interface.

A human protein containing multiple types of protease-inhibitory modules

By using sensitive homology-search and gene-finding programs, we have found that a genomic region from the tip of the short arm of human chromosome 16 (16p13.3) encodes a putative secreted protein consisting of a domain related to the whey acidic protein (WAP) domain, a domain homologous with follistatin modules of the Kazal-domain family (FS module), an immunoglobulin-related domain (Ig domain), two tandem domains related to Kunitz-type protease inhibitor modules (KU domains), and a domain belonging to the recently defined NTR-module family (NTR domain). The gene encoding these WAP, FS, Ig, KU, and NTR modules (hereafter referred to as the WFIKKN gene) is intron-depleted—its single 1,157-bp intron splits the WAP module. The validity of our gene prediction was confirmed by sequencing a WFIKKN cDNA cloned from a lung cDNA library. Studies on the tissue-expression pattern of the WFIKKN gene have shown that the gene is expressed primarily in pancreas, kidney, liver, placenta, and lung. As to the function of the WFIKKN protein, it is noteworthy that it contains FS, WAP, and KU modules, i.e., three different module types homologous with domains frequently involved in inhibition of serine proteases. The protein also contains an NTR module, a domain type implicated in inhibition of zinc metalloproteinases of the metzincin family. On the basis of its intriguing homologies, we suggest that the WFIKKN protein is a multivalent protease inhibitor that may control the action of multiple types of serine proteases as well as metalloproteinase(s).

Immortalization of distinct human mammary epithelial cell types by human papilloma virus 16 E6 or E7.

Multiple mammary epithelial cell (MEC) types are observed both in mammary ducts in vivo and in primary cultures in vitro; however, the oncogenic potential of different cell types remains unknown. Here, we used human papilloma virus 16 E6 and E7 oncogenes, which target p53 and Rb tumor suppressor proteins, respectively, to immortalize MECs present in early or late passages of human mammary tissue-derived cultures or in milk. One MEC subtype was exclusively immortalized by E6; such cells predominated in late-passage cultures but were rare at early passages and apparently absent in milk. Surprisingly, a second cell type, present only in early-passage tissue-derived cultures, was fully immortalized by E7 alone. A third cell type, observed in tissue-derived cultures and in milk, showed a substantial extension of life span with E7 but eventually senesced. Finally, both E6 and E7 were required to fully immortalize milk-derived MECs and a large proportion of MECs in early-passage tissue-derived cultures, suggesting the presence of another discrete subpopulation. Identification of MECs with distinct susceptibilities to p53- and Rb-targeting human papillomavirus oncogenes raises the possibility that these cells may serve as precursors for different forms of breast cancer.

Changes in morphology and physiology of an East Mediterranean sponge in different habitats

The sponge Tetilla sp. (Tetractinomorpha: Tetillidae) is a common species in the eastern Mediterranean. This sponge inhabits four different habitat types differing in wave impact and irradiance levels. Two of these habitats (a shallow cave and deep water) are characterized by relatively calm water, whereas the other two (shallow exposed site and tide pools) are in turbulent water with high energy flow. The present study examined the influence of physical (depth, illumination and water motion) and biotic factors on morphology, skeletal plasticity and reproductive traits among the four spatially separated populations. Sponges from tidal pools had significantly larger body volume than sponges from deep water and from shallow caves (ANOVA: tidal-deep P< 0.0001; tidal-shallow caves P< 0.05). Sponges from exposed habitats were significantly larger than deep-water sponges (ANOVA: P=0.01). In addition, individuals from tide pools and from the exposed habitat had a significantly higher proportion of structural silica than sponges from the calmer deep water and from the cave sites. Oxea spicules in sponges from the calm habitats were significantly shorter than in those from the tidal pools and the exposed habitats. The percentage of spicules out of a sponge's dry weight in individuals transplanted from deep (calm) to shallow (turbulent) water significantly increased by 21.9&PLUSMN; 12.9%. The new spicule percentage did not differ significantly from that of sponges originally from shallow water. Oocyte diameter differed significantly between habitats. The maximal size of mature eggs was found in deep-water sponges in June (97&PLUSMN; 5 μ m). In the shallow habitats, a smaller maximal oocyte diameter was found in the cave, in May (56.5&PLUSMN; 3 μ m). Furthermore, oocyte density in shallow-water sponges was highest in May and decreased in June (with 88.2&PLUSMN; 9 and 19.3&PLUSMN; 9 oocytes mm(-2), respectively). At the same time (June), oocyte density of deep-water sponges had just reached its maximum (155&PLUSMN; 33.7 oocytes mm(-2)). The difference in oocyte size and density between deep- and shallow-water individuals indicates an earlier gamete release in the shallow sponge population. The results suggest that plasticity in skeletal design of this sponge indicates a trade off between spicule production and investment in reproduction.

Behavior of trace elements in quartz from plutons of different geochemical signature: a case study from the Bohemian Massif, Czech Republic

Trace-element content in igneous quartz from granitoids of different geochemical types from Bohemian Massif (Central Evrope) was investigated using the laser ablation ICP-MS technique. Two laboratories (Geological Survey of Norway, Trondheim, and Institute of Geology of the Academy of Science of Czech Republic, Praha) were involved in the trace-element (Li, Be, B, Mn, Ge, Rb, Ba, Pb, Mg, Al, P, Ca, Ti, Fe, and Sn) analyses of quartz (altogether, ~300 analyses of 17 rock samples). About 200 representative analyses of quartz are given in Tables 1 and 2.

The effect of chaperone compounds on glucocerebrosidase stability and activity in fibroblasts from Gaucher Disease patients with different genotypes

Dissertação de mestrado, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2014

Modeling The Effects Of Temperature And Ph On The Resistance Of Alicyclobacillus Acidoterrestris In Conventional Heat-treated Fruit Beverages Through A Meta-analysis Approach.

In this work, all publicly-accessible published findings on Alicyclobacillus acidoterrestris heat resistance in fruit beverages as affected by temperature and pH were compiled. Then, study characteristics (protocols, fruit and variety, °Brix, pH, temperature, heating medium, culture medium, inactivation method, strains, etc.) were extracted from the primary studies, and some of them incorporated to a meta-analysis mixed-effects linear model based on the basic Bigelow equation describing the heat resistance parameters of this bacterium. The model estimated mean D* values (time needed for one log reduction at a temperature of 95 °C and a pH of 3.5) of Alicyclobacillus in beverages of different fruits, two different concentration types, with and without bacteriocins, and with and without clarification. The zT (temperature change needed to cause one log reduction in D-values) estimated by the meta-analysis model were compared to those ('observed' zT values) reported in the primary studies, and in all cases they were within the confidence intervals of the model. The model was capable of predicting the heat resistance parameters of Alicyclobacillus in fruit beverages beyond the types available in the meta-analytical data. It is expected that the compilation of the thermal resistance of Alicyclobacillus in fruit beverages, carried out in this study, will be of utility to food quality managers in the determination or validation of the lethality of their current heat treatment processes.