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

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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.     

A field investigation of the relationship between zinc and acid volatile sulfide concentrations in freshwater sediments

Understanding relationships between cationic metals such as cadmium, copper, nickel, lead and zinc, and amorphous iron sulfides, measured as acid volatile sulfide (AVS), is key to predicting metal bioavailability and toxicity insediments. The objective of the present study was to assess seasonal and spatial variations of AVS in freshwater sediments contaminated with zinc. Sediments were sampled from three streams with varying levels of zinc contamination at two different times, March and June of 1995, representing cold- and warm-weather situations. Interstitial (pore) water concentrations of zinc, and solid phase concentrations of AVS and zinc were measured in surficial and deep sediment horizons. Toxicity tests (10-d) with the amphipodHyalella azteca were conducted using intact cores. Sediment zinc concentrations from six sites within the primary test stream differed by about five-fold, and also varied seasonally. Acid volatile sulfide concentrations were generally lower than those of zinc, and pore water zinc concentrations typically were elevated. There was a positive correlation between solid-phase AVS and zinc concentrations, suggesting that the system was dominated by zinc, as opposed to iron sulfides. In contrast to expectations arising from some studies of seasonal variations of AVS in iron-dominated systems, AVS concentrations were smaller in June than in March. However, this was likely due to a major storm event and associated sediment scouring before the June sampling, rather than to seasonal processes related to variations in temperature and dissolved oxygen. Based upon an indirect analysis of depth variations in AVS, there was some indication that zinc sulfide might be less prone to oxidation than iron sulfide. There was a strong correlation between toxicity of the sediment samples toH. azteca and interstitial water concentrations of zinc; however, the possible contribution of other contaminants to sediment toxicity cannot be dismissed.     

Interaction of Staphylococcal Alpha Toxin and the Estrogenic Hormone Diethylstilbestrol

Previous work in this laboratory showed that diethylstilbestrol was capable of suppressing induced furunculosis in rabbits. The present study indicates that the synthetic estrogenic hormone diethylstilbestrol which is used for acne, estrogen deficiency, cancer, and other disorders, can reduce the cytolytic action of staphylococcal alpha toxin. The cytotoxic action of purified alpha toxin for tissue cultures was evaluated by use of such parameters as total and viable cell counts, glucose, and protein determination, and cytopathic effects (CPE) in the presence and absence of steroids. To 3-day-old primary rabbit baby kidney tissue cultures, 1 to 5 μg of diethylstilbestrol per ml was added; growth of tissue cultures in Eagles medium was continued till the 6th day, and then one tissue cytopathic dose per milliliter of alpha toxin was added, and the subsequent fate of tissue cultures was assayed. Such cultures yielded higher total and viable cell counts, utilized more glucose, and contained more protein than the control cultures. In control cultures, CPE was observed on the 3rd hr after the addition of alpha toxin, and it was complete in 24 hr, whereas in tissue cultures treated with diethylstilbestrol, the CPE was significantly reduced. The data presented in this study made possible the availability of a suppressor of the cytolytic action of alpha toxin and might be useful in assaying the action of alpha toxin in an in vitro inexpensive test system.     

Chemotype Diversity of Indigenous Dalmatian Sage (Salvia officinalis L.) Populations in Montenegro

To identify how many chemotypes of Salvia officinalis exist in Montenegro, the chemical composition of the essential oils of 12 wild‐growing populations was determined by GC‐FID and GC/MS analyses. Among the 40 identified constituents, the most abundant were cis‐thujone (16.98–40.35%), camphor (12.75–35.37%), 1,8‐cineol (6.40–12.06%), trans‐thujone (1.5–10.35%), camphene (2.26–9.97%), borneol (0.97–8.81%), viridiflorol (3.46–7.8%), limonene (1.8–6.47%), α‐pinene (1.59–5.46%), and α‐humulene (1.77–5.02%). The composition of the essential oils under study did not meet the ISO 9909 requirements, while the oils of populations P02–P04, P09, and P10 complied with the German Drug Codex. A few of the main essential‐oil constituents appeared to be highly intercorrelated. Strong positive correlations were observed between α‐pinene and camphene, camphene and camphor, as well as between cis‐thujone and trans‐thujone. Strong negative correlations were evidenced between cis‐thujone and α‐pinene, cis‐thujone and champhene, cis‐thujone and camphor, as well as between trans‐thujone and camphene. Multivariate analyses allowed the grouping of the populations into three distinct chemotypes, i.e., Chemotype A, rich in total thujones, Chemotype B, with intermediate contents of thujones, α‐pinene, camphene, and camphor and high borneol contents, and Chemotype C, rich in camphor, camphene, and α‐pinene. The chemotypes did not significantly differ in the total essential‐oil content and the cis/trans‐thujone ratio.     

Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays

Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods high-resolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6–3.0 Mb in single cells.     

Effect of porcine brain growth factor on primary cell cultures and BHK-21 [C-13] cell line

Growth factors from neural tissues have been described as potent mitogens for a wide variety of mesoderm- and ectoderm-derived cells in vitro. We used porcine brain extract for in vitro testing of proliferation properties on primary ovarian cells, uterine cells, and cardiomyocytes in culture as well as for BHK-21 [C-13] cell line. The addition of this extract accelerates proliferation in all examined cultures. It also lowers serum requirement and shortens the cultivation period for BHK-21 [C-13] cells. Fibroblast growth factors from brain of different species, but not porcine, are already characterized and their proliferative effect proved. Therefore, we purified, determined, and confirmed the presence of basic fibroblast growth factor in porcine brain extract by Western blot analysis and showed its biological activity on BHK-21 [C-13] cells.     

QPCR: Application for real-time PCR data management and analysis

Background  

Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and multiple methods covering the complete analysis pipeline.     

Unstructured Hydrophilic Sequences in Prokaryotic Proteomes Correlate with Dehydration Tolerance and Host Association

Water loss or desiccation is among the most life-threatening stresses. It leads to DNA double-strand breakage, protein aggregation, cell shrinkage, and low water activity precluding all biological functions. Yet, in all kingdoms of life, rare organisms are resistant to desiccation through prevention or reversibility of such damage. Here, we explore possible hallmarks of prokaryotic desiccation tolerance in their proteomes. The content of unstructured, low complexity (LC) regions was analyzed in a total of 460 bacterial and archaeal proteomes.It appears that species endowed with proteomes abundant in unstructured hydrophilic LC regions are desiccation-tolerant or sporulating bacteria, halophilic archaea and bacteria, or host-associated species. In the desiccation- and radiation-resistant bacterium Deinococcus radiodurans, most proteins that contain large hydrophilic LC regions have unassigned function, but those with known function are mostly involved in diverse cellular recovery processes. Such LC regions are typically absent in orthologous proteins in desiccation-sensitive species. D. radiodurans encodes also special LC proteins, akin to those associated with desiccation resistance of plant seeds and some plants and animals. Therefore, we postulate that large unstructured hydrophilic LC regions and proteins provide for cellular resistance to dehydration and we discuss mechanisms of their protective activity.