Impact of post-surgical freezing delay on brain tumor metabolomics

Metabolomics - The identification of frequent acquired mutations shows that patients with oligodendrogliomas have divergent biology with differing prognoses regardless of histological...     

Effect of freezing on cord blood serum proteins

The effect of freezing regimes and storage temperatures on protein conformation and the spectrum of cord blood serum was investigated. Changes in the parameters of EPR spectra of spin probes in cord blood serum after slow freezing and subsequent thawing were established, indicating protein conformational changes characterized by loosening. This fact was confirmed by an earlier, first stage of albumin heat denaturation, as indicated by calorimetric data. It was shown that slow cooling resulted in aggregation of serum protein in which serum albumin and immunoglobulins played an important role. It was concluded that, for retaining the properties of cord blood serum proteins, it is preferable to perform cooling at a rate not lower than 100°C/min and a storage temperature of ?80°C and lower.     

Impact of climate variation on mosquito abundance in California

Temporal variation in the abundance of the encephalitis virus vector mosquito, Culex tarsalis Coquillet, was linked significantly with coincident and antecedent measures of regional climate, including temperature, precipitation, snow pack, and the El Ni?o/Southern Oscillation anomaly. Although variable among traps, historical records that spanned two to five decades revealed climate influences on spring and summer mosquito abundance as early as the previous fall through early summer. Correlations between winter and spring precipitation and snow pack and spring Cx. tarsalis abundance were stronger than correlations with summer abundance. Spring abundance was also correlated positively with winter and spring temperature, whereas summer abundance correlated negatively with spring temperature and not significantly with summer temperature. Correlations with antecedent climate provide the opportunity to forecast vector abundance and therefore encephalitis virus risk, a capability useful in intervention decision support systems at local and state levels.     

Effects of delayed freezing on content of phosphagens in human skeletal muscle biopsy samples

The concentrations of ATP, phosphocreatine (PCr), creatine, and lactate were determined in muscle biopsy samples frozen immediately or after a delay of 1-6 min. During the delay the samples were exposed to normal air or a gas mixture of 6.5% CO2-93.5% O2. The ATP content was unchanged, but PCr increased significantly from 72 mmol after rapid freezing to 85 mmol X kg dry muscle-1 during the 1st min in air. The lactate concentration increased (2.8 to 5.2 mmol X kg-1). If muscles were made anoxic by circulatory occlusion for 4-6 min before sampling, no increase in PCr was observed. Direct homogenization of fresh tissue in perchloric acid gave the same ATP, PCr, and lactate contents as frozen samples. It is concluded that the ATP and PCr contents in muscle are unaffected by freezing but that the biopsy procedure activates the energy utilization processes resulting in PCr decrease. It is suggested that the muscle PCr content after a 1-min delay in tissue freezing corresponds to the level in resting fresh muscle.     

Chronic coffee consumption in the diet-induced obese rat: impact on gut microbiota and serum metabolomics

Epidemiological data confirms a strong negative association between regular coffee consumption and the prevalence of type 2 diabetes. Coffee is initially absorbed in the stomach and small intestine but is further fermented in the colon by gut microbiota. The bioavailability, production and biological activity of coffee polyphenols is modulated, in part, by gut microbiota. The purpose of this study was to determine if chronic coffee consumption could mitigate negative gut microbiota and metabolomic profile changes induced by a high-fat diet. Male Sprague–Dawley rats were randomized to chow (12% kcal fat) or high-fat (60% kcal fat) diet. Each group was further divided into water or caffeinated coffee for 10 weeks. Coffee consumption in high-fat-fed rats was associated with decreased body weight, adiposity, liver triglycerides and energy intake. Despite a more favorable body composition, rats displayed profound systemic insulin resistance, likely due to caffeine. Coffee consumption attenuated the increase in Firmicutes (F)-to-Bacteroidetes (B) ratio and Clostridium Cluster XI normally associated with high-fat feeding but also resulted in augmented levels of Enterobacteria. In the serum metabolome, coffee had a distinct impact, increasing levels of aromatic and circulating short-chain fatty acids while lowering levels of branched-chain amino acids. In summary, coffee consumption is able to alter gut microbiota in high-fat-fed rats although the role of these changes in reducing diabetes risk is unclear given the increased insulin resistance observed with coffee in this study.     

Impact of time between repeated sperm freezing cycles on sperm quality

Refreezing of sperm samples would provide the possibility of performing more cycles of fertility treatments. Although the effect of repeated cycles of freezing on sperm quality was studied, the effect of the length of the time interval between each freeze-thaw cycle has not been reported. Hence, we assessed the effect of incubation time on the sperm quality of thawed sperm after repeated freezing.One-hundred samples of potential sperm donations with normal sperm quality were evaluated. The fresh semen samples were analyzed and cryopreserved in liquid nitrogen until use. After thawing, the samples were divided randomly to two groups and reanalyzed for motility, vitality, and DNA fragmentation. They were incubated at room temperature and reanalyzed after either 90 min (group A) or 180 min (group B) of incubation, and once again after a repeated cycle of freezing and thawing.Our results showed that the sperm parameters of fresh samples of both groups were similar. After one freeze-thaw cycle, both groups still had comparable values. At the end of their respective incubation time periods, however, there was a significant difference in the mean values of the assessed parameters between the two groups (p < 0.01). An additional freeze-thaw cycle further exacerbated those differences, with group B undergoing an even more substantial decline (p < 0.001).Our data suggest that thawed human spermatozoa sustain a significant decline in sperm parameters in association with longer incubation time, which is further exacerbated by an additional freeze-thaw cycle.     

Effect of pregnancy on serum cytokines in SLE patients

Introduction

The aim of this study was to evaluate an extensive panel of cytokines involved in immune regulation during pregnancy in patients with systemic lupus erythematosus (SLE) and in healthy women.

Methods

A total of 47 consecutive successful pregnancies in 46 SLE patients and 56 pregnancies in 56 matched healthy subjects, as controls, were prospectively studied. Serum interleukin (IL)-1-α, IL-1-β, IL-2, IL-6, IL-8, IL-10, IL-12p70, interferon (INF)-γ and tumor necrosis factor (TNF)-α were detected in sera obtained at the first and third trimester of pregnancy by a highly sensitive, multiplexed sandwich ELISA.

Results

Medians (pg/ml) of serum levels of most helper T (Th)1-type cytokines were significantly lower in the third trimester compared with those observed in the first trimester of pregnancy in healthy women: INF-γ 2.0 vs 3.4, TNF-α 10.2 vs 11.5, IL-1-α 0.9 vs 1.1, IL-1-β 0.6 vs 1.0, IL-2 3.0 vs 3.5, and IL-12p70 4.9 vs 5.6 (P-values < 0.02 for all). By contrast, only the IL-1-α serum levels were lower in the third trimester compared with the first trimester in SLE patients (P = 0.006). IFN-γ/IL-6 and IFN-γ/IL-10 ratios were higher in controls than in SLE (P = 0.002, and P = 0.001, respectively); moreover, they were significantly reduced in the third compared to the first trimester of pregnancy in healthy women, but not in SLE.

Conclusions

In SLE patients, Th1/Th2 cytokine serum level ratio does not decrease during pregnancy progression as much as in healthy pregnant women. This could account for the observation of a low frequency of disease flares in the third trimester of gestation.     

Distribution of silicoflagellates in plankton and core top samples from the Gulf of California

Plankton and surface sediment samples from the Gulf of California were examined to determine the present geographic distribution of silicoflagellate species in this area. Variations in the species composition of the silicoflagellate assemblage were found to be related to water mass distributions. Eight species were identified in these samples. Octactis pulchra is associated with high levels of primary productivity in the surface waters and is found in greatest abundance in the central Gulf of California. Dictyocha messanensis dominates the silicoflagellate assemblage in stations outside the Gulf of California and increases in relative abundance with decreasing amounts of Octactis pulchra. Dictyocha calida, Dictyocha sp. A, and Dictyocha sp. B are associated with equatorial waters and have the highest relative abundance near the mouth of the Gulf. Dictyocha epiodon and Distephanus speculum are associated with cold California Current Water, and Dictyocha epiodon is present in minor abundance in Gulf samples. Dictyocha sp. 2 has a patchy distribution with low relative abundance.     

Impact of sudden oak death on tree mortality in the Big Sur ecoregion of California

The Big Sur ecoregion in coastal California is a botanically and ecologically diverse area that has recently experienced substantial mortality of oak (Quercus spp.) and tanoak (Lithocarpus densiflorus) trees due to the emerging forest disease sudden oak death, caused by the invasive pathogen Phytophthora ramorum. In response to the urgent need to examine environmental impacts and create management response strategies, we quantified the impact of P. ramorum invasion on tree mortality across the Big Sur ecoregion using high-resolution aircraft imagery and field data. Using the imagery, we mapped all detectable oak and tanoak trees possibly killed by P. ramorum infection within redwood-tanoak forests and mixed oak woodlands. To validate and improve our remote assessment, we quantified the number, size, and infection status of host trees in 77 field plots (0.25 ha). The field data showed that our remote assessment underestimated mortality due to the occurrence of dead trees in the forest understory. For each forest type, we developed regression models that adjusted our remote assessments of tree mortality in relation to field observations of mortality and local habitat variables. The models significantly improved remote assessment of oak mortality, but relationships were stronger for mixed oak woodlands (r ² = 0.77) than redwood-tanoak forests (r ² = 0.66). Using the field data, we also modeled the amount of dead tree basal area (m²) in relation to the density of mapped dead trees in mixed oak woodlands (r ² = 0.73) and redwood-tanoak forests (r ² = 0.54). Application of the regression models in a GIS estimated 235,678 standing dead trees in 2005 and 12,650 m² of tree basal area removed from the ecoregion, with 63% of mortality occurring in redwood-tanoak forests and 37% in mixed oak woodlands. Integration of the remote assessment with population estimates of host abundance, obtained from an independent network of 175 field plots (0.05 ha each), indicated similar prevalence of mortality in redwood-tanoak forests (20.0%) and mixed oak woodlands (20.5%) at this time. This is the first study to quantify a realistic number of dead trees impacted by P. ramorum over a defined ecological region. Ecosystem impacts of such widespread mortality will likely be significant.

Influence of common preanalytical variations on the metabolic profile of serum samples in biobanks

A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4°C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4°C. Five or ten serum freeze–thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of human serum.     

Systems biology in unruptured intracranial aneurysm: a metabolomics study in serum for the detection of biomarkers

Intracranial aneurysm (IA) is a common devastating condition occurs in up to 6 % of the population. It is asymptomatic but potentially fatal because of the progressive enlargement and rupturing leads to subarachnoid hemorrhage. Early diagnosis of IA is more valuable before it ruptures and hemorrhage. The diagnosis of IA is usually carried out using computerized tomography or magnetic resonance imaging. However, there is no biochemical test or a marker available for diagnosis. Serum metabolites were analyzed from normal and unruptured intracranial aneurysms patients (UIA) by NMR spectroscopy to identify the presence of serum markers, which could provide a clue for diagnosis and altered metabolic pathways in UIA condition. Analysis of proton spectra revealed significant perturbations in 20 serum metabolites in UIA. Multivariate analysis showed a distinct separation of normal from UIA based on 17 most contributing metabolites, and the scoring algorithm determines the perturbed metabolic pathways in UIA (urea cycle, citric acid cycle and ammonia recycling). Also, the gene expression analysis shows the significant (p ≤ 0.05) change in ARG, CPS1 and OTC genes leading to dysregulation in the urea cycle. Further, estimation of urea showed a significant increase in serum urea, which provides the prospect of rapid diagnosis. Overall, this study demonstrates the promise of developing biomarkers for the diagnosis of UIA from serum. In addition, the implementation of systems biological approach in metabolomic context gained an understanding about UIA that reflects the numerous metabolic pathways identified to be affected in disease condition.     

Long-term storage of blood samples at freezing temperatures in the presence of a cryoprotectant for hemiglobin assay

Changes in Hi levels in experimentally prepared blood samples during storage at various temperatures were studied. When whole blood in which Hi levels were elevated by sodium nitrite was stored unfrozen, rapid reduction of Hi was observed within 24 hr even at 0 degrees C. When whole blood or a diluted hemolysate was stored frozen for a week or longer, considerable formation of Hi by autoxidation was observed, the formation at -20 degrees C being much more significant than that at -30 degrees C. On the other hand, addition of an equal volume of the cryoprotectant solution of Rowe et al. to blood almost completely inhibited this Hi formation during freezing storage until at least 30 days. Thus, a new method for long-term storage of blood samples for Hi assay was devised.     

On the reliability of Ponar grab samples for the quantitative study of benthic invertebrates in ponds

We present observations on the variability of sediment penetration depth by the Ponar grab sampler, which lead us to question the reliability of grab samples in the quantitative study of freshwater benthos. Penetration depth of the Petite Ponar grab depends on substrate type, and correlates with the amount of organic carbon, the water content and the granulometry of the sediment. Since these factors can also influence faunal composition and vertical distribution in the sediment, it is important to study the performance of the sampler before a biological explanation for the observed pattern is given. At the site studied, a case study was performed, in which variable grab penetration did not influence biological interpretation because the penetration depth of the grab followed that of the organisms under study.Research Assistant of the Belgian National Fund for Scientific Research (N.F.W.O.)Research Assistant of the Belgian National Fund for Scientific Research (N.F.W.O.)     

Impact of freezing/thawing procedures on the post-thaw viability of cryopreserved human saphenous vein conduits

BACKGROUND: Cryopreserved human blood vessels are important tools in reconstructive surgery. However, patency of frozen/thawed conduits depends largely on the freezing/thawing procedures employed. METHODS: Changes in tone were recorded on rings from human saphenous vein (SV) and used to quantify the degree of cryoinjury after different periods of exposure at room temperature to the cryomedium (Krebs-Henseleit solution containing 1.8M dimethyl sulfoxide and 0.1M sucrose) and after different cooling speeds and thawing rates following storage at -196 degrees C. RESULTS: Without freezing, exposure of SV to the cryomedium for up to 240 min did not modify contractile responses to noradrenaline (NA). Pre-freezing exposure to the cryomedium for 10-120 min attenuated significantly post-thaw maximal contractile responses to NA, endothelin-1 (ET-1) and potassium chloride (KCl) by 30-44%. Exposure for 240 min attenuated post-thaw contractile responses to all tested agents markedly by 62-67%. Optimal post-thaw contractile activity was obtained with SV frozen at about -1.2 degrees C/min and thawed slowly at about 15 degrees C/min. In these SV maximal contractile responses to NA, ET-1 and KCl amounted to 66%, 70% and 60% of that produced by unfrozen controls. Following cryostorage of veins for up to 10 years the responsiveness of vascular smooth muscle to NA was well maintained. CONCLUSION: Cryopreservation allows long-term banking of viable human SV with only minor loss in contractility.     

Impact of methodological choices on assessments of the reliability of fossil primate phylogenetic hypotheses

It has been argued in several recent studies that conventional craniodental characters cannot be assumed to be reliable for the purposes of reconstructing primate phylogenetic relationships and that as a consequence little confidence can be invested in published fossil primate phylogenies. Here, we evaluate this claim by revisiting the analyses reported in one of these studies [Collard and Wood, 2000]. Specifically, we investigate whether the use of alternative methodological procedures would have altered their findings. We focus on three key issues: (1) size correction, (2) outgroup composition and (3) non-phylogenetic correlation among characters. Our analyses suggest that the results of Collard and Wood [2000] were not affected by the size correction method they used or by the outgroup they employed. Our analyses also suggest that their results were not affected by their decision to ignore developmental, functional and other non-phylogenetic correlations among the characters in their data sets. Accordingly, our study supports the assertion that conventional craniodental characters cannot be assumed to be reliable for reconstructing primate phylogenetic relationships. This in turn suggests that many published fossil primate phylogenies may be unreliable.     

Follistatin-like protein 1: a serum biochemical marker reflecting the severity of joint damage in patients with osteoarthritis

Introduction  

Follistatin-like protein 1 (FSTL1) is a secreted glycoprotein that has been implicated in arthritis pathogenesis in a mouse model. The aim of this study is to detect FSTL1 expression and to further assess its potential utility as a biomarker of joint damage in osteoarthritis (OA) patients.     

Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates

Background

Genome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in cattle. However, the very small quantity of genomic DNA in biopsy material from early embryos poses daunting technical challenges. A reliable whole-genome amplification (WGA) procedure would greatly facilitate the procedure.

Results

Several PCR-based and non-PCR based WGA technologies, namely multiple displacement amplification, quasi-random primed library synthesis followed by PCR, ligation-mediated PCR, and single-primer isothermal amplification were tested in combination with different DNA extractions protocols for various quantities of genomic DNA inputs. The efficiency of each method was evaluated by comparing the genotypes obtained from 15 cultured cells (representative of an embryonic biopsy) to unamplified reference gDNA. The gDNA input, gDNA extraction method and amplification technology were all found to be critical for successful genome-wide genotyping. The selected WGA platform was then tested on embryo biopsies (n = 226), comparing their results to that of biopsies collected after birth. Although WGA inevitably leads to a random loss of information and to the introduction of erroneous genotypes, following genomic imputation the resulting genetic index of both sources of DNA were highly correlated (r = 0.99, P<0.001).

Conclusion

It is possible to generate high-quality DNA in sufficient quantities for successful genome-wide genotyping starting from an early embryo biopsy. However, imputation from parental and population genotypes is a requirement for completing and correcting genotypic data. Judicious selection of the WGA platform, careful handling of the samples and genomic imputation together, make it possible to perform extremely reliable genomic evaluations for pre-transfer embryos.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-889) contains supplementary material, which is available to authorized users.     

Effect of the inflammatory response on serum indices of iron status in late pregnancy

Background and aimsA systemic inflammatory response complicates the evaluation of iron status during pregnancy. We investigated the magnitude of this effect on indices of iron status in late pregnancy.MethodsWe retrospectively interrogated laboratory data and hospitalisation records from April 2016 to March 2017 and obtained results from pregnant women in which serum high-sensitivity C-reactive protein (hsCRP) or albumin had been examined together with indicators of iron status (serum ferritin [SF] and serum transferrin [ST], n = 11,571). We assessed the association of the inflammatory response, as evidenced by hsCRP and albumin, with iron status indicators by general linear regression analysis.ResultCompared to women with an hsCRP of ≤ 5 mg/L, the median SF level in those with an hsCRP of 6–10, 11–20, and > 20 mg/L significantly increased by 2.24 μg/L (95 % confidence interval [CI]: 1.22, 3.26), 4.04 μg/L (95 % CI: 2.05, 6.04), and 13.49 μg/L (95 % CI: 10.44, 16.53); while the ST level decreased by 0.10 g/L (95 % CI: 0.13, 0.06), 0.16 g/L (95 % CI: 0.23, 0.09), and 0.21 g/L (95 % CI: 0.32, 0.11), respectively (all P < 0.001). With regard to the association of inflammation with SF and ST, no significant interaction between albumin (< 35 and ≥ 35 g/L) and hsCRP was observed (SF: P for interaction = 0.426; ST: P for interaction = 0.872).ConclusionsMeasurement of hsCRP in late pregnancy is necessary to correct the levels of SF and ST. The impact of the inflammatory response on indices of iron status in late pregnancy could not be adjusted by albumin.