Primary production in lakes Huron and Michigan: in vitro and in situ comparisons

Oxygen- and carbon-14-based primary production estimates from9–16 h in vitro incubations were compared in lakes Huronand Michigan. For surface mixing layer compansons, gross O₂/¹⁴Cphotosynthetic quotients (gross PQ) averaged 2.2, and net O₂/¹⁴Cphotosynthetic quotients (net PQ) averaged 1.4. The mean grossPQ is consistent with a theoretical P0 based on the CO₂ andNO₃ assimilation ratio. However, within the deep chlorophylllayer, gross PQ and net PQ averaged 4.9 and 2.8 respectively.These higher values were likely due to excess NO₃ reductionat the expense of CO₂ uptake. Thus, during short experimentsunder low light conditions, oxygen evolution and CO₂ uptakemay not be tightly coupled. In vitro and in situ O₂ productionestimates were compared in four diurnal (dawn to dusk) experimentsin Lake Huron. In situ production estimates were determinedby measuring water-mass oxygen changes and oxygen transfer acrossthe air-water interface. In situ production estimates were approximatelytwice in vitro production estimates for both surface mixinglayer and deep chlorophyll layer comparisons. The differencebetween estimates was attributable to containment effects manifestin 13–16 h bottle incubations. Short-term (1–2 h)in vitro production was also compared to diurnal in vitro production.Rates of short-term production were {small tilde}1.6 times higherthan rates of diurnal production, suggesting that short-termin vitro production experiments may provide reasonable estimatesof in situ primary production.     

Interactions of cadmium and selenium in rat plasma in vivo and in vitro

⁷⁵Se and ¹⁰⁹Cd tracers were used to study the binding of Se and Cd to plasma proteins at various SeO₃^2? doses and times up to 24 h after the simultaneous subcutaneous administration of SeO₃^2? and CdCl₂ to adult male rats. The simultaneous injection of CdCl₂ and SeO₃^2? markedly increased both Se and Cd plasma levels over that in control animals. Gel permeation chromatography of plasma indicated that at all times up to 24 h Cd and Se were bound in an atomic ratio of approx. 1 : 1 in 330 000 and 130 000 dalton fractions. From 4 to 24 h, Cd and Se appeared in the 420 000 dalton fraction, also with an atomic ratio of approx. 1 : 1. The 330 000 dalton molecules appeared to have a maximal binding capacity for the Cd-Se complex at a concentration of approx. 30 μmol/ml of plasma, while the 130 000 and 420 000 dalton molecules show a higher binding capacity. Studies in vitro revealed that SeO₃^2? does not interact directly with Cd and plasma proteins. It is metabolized by erythrocytes to a form that interacts in an atomic ratio of 1 : 1 with Cd to form a protein-bound complex of 130 000 daltons.     

Chemo- and baroresponses differ in African-Americans and Caucasians in sleep

To determine sleep effects on baro- andventilatory responses to transient chemo- and barostimulation inAfrican-Americans and Caucasians, 26 nonobese normotensive youngsubjects (13 African-Americans and 13 Caucasians) were studied awakeand in non-rapid-eye movement (NREM) and rapid-eye-movement sleepduring induced transient hypoxemia (N₂), hypertension(phenylephrine, PE), and concomitant hypoxemia and hypertension(N₂ + PE). Arterial blood pressurewas recorded by plethysmographic volume clamp, minute ventilation bypneumotachograph, and arterial O₂saturation by pulse oximeter. For all subjects, chronotropicbaroresponse (pulse interval/systolic blood pressure, where  is change) increased with NREM sleep(P = 0.007). Baroresponse slope wasgreater in Caucasians than in African-Americans (ANOVA, P = 0.02). Hypoxemic ventilatoryresponse (minute ventilation/arterial O₂ saturation) was greater inAfrican-Americans than in Caucasians in NREM sleep(P = 0.01), as was hypoxemicattenuation of baroresponse (N₂ + PE, P = 0.03). These data suggestsleep-related differences in arterial chemo- and baroreceptor responsesin normal young African-Americans and Caucasians, which may haveimplications concerning development of systemic hypertension.

     

Update in research and methods in proteomics and bioinformatics

The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013)

Philadelphia, PA, USA, 15–17 July 2013

The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.     

Training intensity-dependent and tissue-specific increases in lactate uptake and MCT-1 in heart and muscle

We investigatedthe effects of 3 wk of moderate- (21 m/min, 8% grade) andhighintensity treadmill training (31 m/min, 15% grade) on1) monocarboxylate transporter 1 (MCT-1) content in rat hindlimb muscles and the heart and2) lactate uptake in isolated soleus(Sol) muscles and perfused hearts. In the moderately trained groupMCT-1 was not increased in any of the muscles [Sol, extensor digitorum longus (EDL), and red (RG) and white gastrocnemius(WG)] (P > 0.05). Similarly,lactate uptake in Sol strips was also not increased(P > 0.05). In contrast, in theheart, MCT-1 (+36%, P < 0.05) andlactate uptake (+72%, P < 0.05)were increased with moderate training. In the highly trained group,MCT-1 (+70%, P < 0.05) and lactateuptake (+79%, P < 0.05) wereincreased in Sol. MCT-1 was also increased in RG (+94%,P < 0.05) but not in WG and EDL(P > 0.05). In the highly trainedgroup, heart MCT-1 (+44%, P < 0.05)and lactate uptake (+173%, P < 0.05) were increased. In conclusion, it has been shown that1) in both heart and skeletal musclelactate uptake is increased only when MCT-1 is increased; 2) training-induced increases inMCT-1 occurred at a lower training intensity in the heart than inskeletal muscle; 3) in the heart, lactate uptake was increased much more after high-intensity training than after moderate-intensity training, despite similar increases inheart MCT-1 with these two training intensities; and4) the increases in MCT-1 occurredindependently of any changes in the heart's oxidative capacity (asmeasured by citrate synthase activity).

     

Hypotransferrinemia and changes in plasma lipid and metabolic patterns in sepsis

This study was performed to obtain a characterization of the changes in plasma transferrin (Tf, g/L) in sepsis. More than four hundred determinations of Tf, and of a large series of simultaneously collected blood and hemodynamic variables, were obtained in 17 patients with post-traumatic sepsis. Tf during sepsis was consistently low (mean ± SD = 1.46 ± 0.46) however fluctuated markedly according to changes in metabolic and hemodynamic patterns. Regression analysis showed that decreases in Tf were simultaneously correlated with the plasma lipid pattern (in particular with decreasing cholesterol and increasing triglycerides), with decreases in albumin and peripheral O₂ extraction, and with increasing cardiac index (p < 0.001 for all). Decreases in Tf were moderated by increasing the parenteral amino acid dose (p < 0.001). Combinations of these variables in multiple regressions explained nearly 80% of the variability of Tf. There were no similar correlations for other acute phase proteins except ceruloplasmin, which showed opposite changes compared to those of Tf. These results show that within the hypotransferrinemia which characterizes sepsis, Tf may oscillate remaining strongly correlated with changes in metabolic and hemodynamic patterns, which may account for nearly 80% of the variability of Tf.     

Quantitative changes in in vitro and in vivo protein synthesis in aging and rejuvenated soybean cotyledons

Cotyledons of light-grown soybean (Glycine max L. var Wayne) seedlings were used as a model system to study the possibility that aging requires qualitative changes in protein synthesis. Cotyledons reached a final stage of senescence and then abscised about 22 days after imbibition. Cotyledon senescence was reversed at 20 days after germination by epicotyl removal. Thereafter, the cotyledons regained much of the chlorophyll, RNA, protein, and polyribosomes lost during aging.

Total poly(A)mRNA was extracted from 4-, 12-, 20-day-old, and rejuvenated cotyledons and translated in a wheat germ system. Comparison of translation products on two-dimensional O'Farrell gels showed that many translation products increased in quantity during aging, while roughly half as many decreased. Rejuvenation returned the translation products to approximately 4-day-old levels in roughly half of those products which were diminished with age. Conversely, almost one-third of the products which had increased with age decreased with rejuvenation. None of the translation products were totally lost nor were newly synthesized products detected during aging. Therefore, aging in this system probably does not involve complete gene repression or depression. The observation that epicotyl removal causes a reversal in the levels of various proteins synthesized in vitro was corroborated by similar observations following in vivo labeling of cotyledon sections and analysis by SDS-polyacrylamide gel electrophoresis and fluorography. Densitometric scans of fluorograms revealed a gradual shift in profiles of both in vitro and in vivo translation products during aging. Rejuvenated cotyledon proteins had a profile resembling that of 4-day-old cotyledons. The overall level of [³⁵S]methionine incorporation into protein in vivo declined gradually during aging but was restored to 4-day-old levels within 2 days after epicotyl removal.

     

Mycotoxins in organic and conventional cereals and cereal products grown and marketed in Croatia

In this study, the levels of aflatoxin B₁ (AFB₁), ochratoxin A (OTA), zearalenone (ZEN), deoxynivalenol (DON) and fumonisins (FUM) in unprocessed cereals (n = 189) and cereal-based products (n = 61) were determined using validated ELISA methods. All samples originated from either conventional or organic production corresponded to the 2015 harvest in Croatia. Based on the mean mycotoxin concentrations, the risk for the consumer to exceed the tolerable daily intake (TDI) for these toxins by the consumption of both types of cereals and cereal-based products was assessed. Mycotoxin contamination of organic cereals and organic cereal-based products was not significantly different (p > 0.05). Given that the exposure assessment resulted in a small fraction of the TDI (maximum: DON, 12% of TDI), the levels of the investigated mycotoxins in both types of cereals and cereal-based products from the 2015 harvest did not pose a human health hazard.     

Drought and warming induced changes in P and K concentration and accumulation in plant biomass and soil in a Mediterranean shrubland

A field experiment involving drought and warming manipulation was conducted over a 6-year period in a Mediterranean shrubland to simulate the climate conditions projected by IPCC models for the coming decades (20% decreased soil moisture and 1°C warming). We investigated P and K concentration and accumulation in the leaves and stems of the dominant species, and in soil. Drought decreased P concentration in Globularia alypum leaves (21%) and in Erica multiflora stems (30%) and decreased K concentration in the leaves of both species (20% and 29%, respectively). The general decrease of P and K concentration in drought plots was due to the reduction of soil water content, soil and root phosphatase activity and photosynthetic capacity that decreased plant uptake capacity. Warming increased P concentration in Erica multiflora leaves (42%), but decreased it in the stems and leaf litter of Erica multiflora and the leaf litter (33%) of Globularia alypum, thereby demonstrating that warming improved the P retranslocation and allocation from stem to leaves. These results correlate with the increase in photosynthetic capacity and growth of these two dominant shrub species in warming plots. Drought and warming had no significant effects on biomass P accumulation in the period 1999–2005, but drought increased K accumulation in aboveground biomass (10 kg ha⁻¹) in Globularia alypum due to the increase in K concentration in stems. The stoichiometric changes produced by the different responses of the nutrients led to changes in the P/K concentration ratio in Erica multiflora leaves, stems and litter, and in Globularia alypum stems and litter. This may have implications for the nutritional value of these plant species and plant–herbivore relationships. The effects of climate change on P and K concentrations and contents in Mediterranean ecosystems will differ depending on whether the main component of change is drought or warming.     

Contrasts in energy intake and expenditure in sit-and-wait and widely foraging lizards

Summary Daily energy metabolism and water flux were measured with doubly labeled water in the free-living insectivorous lizards Cnemidophorus tigris (mean body mass 15.7 g) and Callisaurus draconoides (8.6 g) in June 1979 in the Colorado Desert of California. C. tigris was an active forager; it spent 91% of its 5-h daily activity period in movement. C. draconoides was a sit-and-wait predator; it spent less than 2% of its 10-h activity period in movement. C. tigris had significantly higher rates of field energy metabolism and water influx (210 Jg^-1 day^-1, 36.8 ul H₂O g^-1 day^-1, N=19) than C. draconoides (136, 17.1, N=18). There were no significant differences between the sexes within either species.The extra costs of free existence were calculated from differences between field metabolic rates and maintenance costs estimated from laboratory respirometry. Rates of energy metabolism during the field activity period were about 1.5x resting levels at 40° C (field active body temperature) for C. draconoides and 3.3 x resting levels at 40° C (field active body temperature) for the more active C. tigris. Feeding rates calculated from water influx data were 13.3 mg g^-1 day^-1 for C. tigris and 5.8 mg g^-1 day^-1 for C. draconoides. Though C. tigris had a high rate of energy expenditure, its foraging efficiency was higher than C. draconoides'.     

Cannabinoids stimulate and inhibit testosterone production in vitro and in vivo

The major psychoactive Δ⁹-tetrahydrocannabinol (THC) and the non-psychoactive cannabinol (CBN) of cannabidiol (CBD) can both stimulate and inhibit testicular testosterone (T) production $\text{in vitro}$ and $\text{in vivo}$. At nanomolar concentrations, these cannabinoids stimulate T production by decapsulated mouse testes while, in micromolar amounts, the effects are markedly inhibitory.     

Socio-Demographic and Geographical Factors in Esophageal and Gastric Cancer Mortality in Sweden

Background

Socio-demographic factors and area of residence might influence the development of esophageal and gastric cancer. Large-scale population-based research can determine the role of such factors.

Methods

This population-based cohort study included all Swedish residents aged 30–84 years in 1990–2007. Educational level, marital status, place of birth, and place of residence were evaluated with regard to mortality from esophageal or gastric cancer. Cox regression yielded hazard ratios (HR) with 95% confidence intervals (CI), adjusted for potential confounding.

Results

Among 84 920 565 person-years, 5125 and 12 230 deaths occurred from esophageal cancer and gastric cancer, respectively. Higher educational level decreased the HR of esophageal cancer (HR = 0.61, 95%CI 0.42–0.90 in women, HR = 0.71, 95%CI 0.60–0.84 in men) and gastric cancer (HR = 0.80, 95%CI 0.63–1.03 in women, HR = 0.73, 95%CI 0.64–0.83 in men). Being unmarried increased HR of esophageal cancer (HR = 1.64, 95%CI 1.35–1.99 in women, HR = 1.64, 95%CI 1.50–1.80 in men), but not of gastric cancer. Being born in low density populated areas increased HR of gastric cancer (HR = 1.23, 95%CI 1.10–1.38 in women, HR = 1.37, 95%CI 1.25–1.50 in men), while no strong association was found with esophageal cancer. Living in densely populated areas increased HR of esophageal cancer (HR = 1.31, 95%CI 1.14–1.50 in women, HR = 1.40, 95%CI 1.29–1.51 in men), but not of gastric cancer.

Conclusion

These socio-demographic inequalities in cancer mortality warrant efforts to investigate possible preventable mechanisms and to promote and support healthier lifestyles among deprived groups.     

Tools for probing and perturbing O-GlcNAc in cells and in vivo

1. Download : Download high-res image (330KB)
2. Download : Download full-size image

     

MPD and DNA Bending in Crystals and in Solution

Bending of 15 to 24° is observed within crystal structures ofB-DNA duplexes, is strongly sequence-dependent, and exhibits no correlation with the concentration of MPD (2-methyl-2,4-pentanediol) in the crystallizing solution. Two types of bends are observed: facultative bends or flexible hinges at junctions between regions of G·C and A·T base-pairs, and a persistent and almost obligatory bend at the center of the sequence R-G-C-Y. Only A-tracts are characteristically straight and unbent in every crystal structure examined to date. A detailed examination of normal vector plots for individual strands of a double helix provides an explanation, in terms of the stacking properties of guanine and adenine bases. The effect of high MPD concentrations, in both solution and crystal, is to decrease local bending somewhat without removing it altogether. MPD gel retardation experiments provide no basis for choosing among the three models that seek to explain macroscopic curvature of DNA by means of microscopic bending: junction bending, bent A-tracts, or bent general- sequence DNA. Crystallographic data on the straightness of A-tracts, the bendability of non-A sequences, and the identity of inclination angles in A-tract and non-A-tractB-DNA support only the general-sequence bending model. The pre-melting transition observed in A-tract DNA probably represents a relaxation of stiff adenine stacks to a flexible conformation more typical of general-sequence DNA.     

Fish eating and variations in selenium and mercury levels in plasma and erythrocytes in free-living healthy Japanese men

The levels and its interindividual and intraindividual variations of selenium (Se) and mercury (Hg) in erythrocytes and plasma were investigated in seven healthy young men during a period of 10 wk, with emphasis on the relationship to the dietary intake of several defined food items. The intraindividual variation, estimated by coefficients of variation (CVs), was 9.9% for plasma Se (PSe), 9.5% for erythrocyte Se (ESe), 42.4% for PHg, and 11.7% for EHg on the average. Significant correlations were found for mean ESe levels in each subject and his fish-eating frequency during this study (r=0.752, p<0.01). Weekly PHg levels were also correlated with average fish-eating frequency in the corresponding week of blood collection (r=0.367, p<0.05). Fish intake within 24 h before blood collection influenced PHg levels significantly.     

Growth and DNA synthesis in embryonic chick heart cells, in vivo and in vitro

On the basis of cell shape, refractility under phase optics, spontaneous beating and nucleolar number, two cell types have been distinguished in embryonic heart cell cultures: M cells (myoblastlike) and F cells (fibroblast-like). However, by different criteria, more than two cell types have been found in the heart in vivo. In the present study, heart cell types are redefined by properties which can be used for identifying cells both in vitro and in vivo. Trypsin-dissociated cells from 7-day chick hearts were cultured for 24 h. PAS staining indicated that all M (thick, refractile) cells contain glycogen (gly⁺), while most F (spread) cells do not (gly⁻). Under the electronmicroscope, only gly⁺ cells contain myofibrils; most of these cells beat spontaneously in culture. Gly⁻ cells do not beat. Gly⁺ cells with myofibrils as well as gly⁻ cells are found in the inoculum and in the heart in vivo. The ultrastructure of gly⁺ cells in vitro and of muscle cells in the myocardium in vivo is similar. Therefore, it is concluded that gly⁺ cells in culture are derived from the myocardium (muscle) of the heart. Gly⁻ cells are apparently derived from the epicardium, the endocardium and the endothelial lining of blood vessels.     

Synthesis and degradation of termination and premature-termination fragments of beta-galactosidase in vitro and in vivo.

A number of abnormal polypeptides which are products of the lacZ gene in Escherichia coli have been characterized. A variety of experiments indicates that one class of at least nine different fragments arises from premature termination of protein synthesis. They have been detected as products of protein synthesis both in vitro and in vivo, although the percentage of fragments made in vitro is greater than that in vivo. The percentage of total Z gene-encoded protein which is found as fragments is estimated to be roughly 23% in vivo. This means that about 31% of the total number of β-galactosidase monomers synthesized are prematurely terminated molecules. The average molecular weight of the polypeptides produced is 91,000. This corresponds to a termination event occurring on the average once every 3200 codons. The sites at which termination occurs appear to be specific and are located primarily near the 3′-end of the gene.Polypeptides synthesized in vitro and in vivo from templates containing mutations in the Z gene have also been compared. Most of the mutationally generated fragments synthesized in vitro are stable, unlike their in vivo counterparts, which are often rapidly degraded. One fragment, however, generated by an early amber mutation in the Z gene, is degraded in the in vitro system. The mechanism of degradation appears to be specific for small abnormal polypeptides. Internal reinitiation polypeptides generated by nonsense mutations, which have been found in vivo, are not detected in the in vitro protein synthesis system under the conditions used here.     

Seasonal and Diel Variability in Dissolved DNA and in Microbial Biomass and Activity in a Subtropical Estuary

Dissolved DNA and microbial biomass and activity parameters were measured over a 15-month period at three stations along a salinity gradient in Tampa Bay, Fla. Dissolved DNA showed seasonal variation, with minimal values in December and January and maximal values in summer months (July and August). This pattern of seasonal variation followed that of particulate DNA and water temperature and did not correlate with bacterioplankton (direct counts and [³H]thymidine incorporation) or phytoplankton (chlorophyll a and ¹⁴CO₂ fixation) biomass and activity. Microautotrophic populations showed maxima in the spring and fall, whereas microheterotrophic activity was greatest in late summer (September). Both autotrophic and heterotrophic microbial activity was greatest at the high estuarine (low salinity) station and lowest at the mouth of the bay (high salinity station), irrespective of season. Dissolved DNA carbon and phosphorus constituted 0.11 ± 0.05% of the dissolved organic carbon and 6.6 ± 6.5% of the dissolved organic phosphorus, respectively. Strong diel periodicity was noted in dissolved DNA and in microbial activity in Bayboro Harbor during the dry season. A noon maximum in primary productivity was followed by an 8 p.m. maximum in heterotrophic activity and a midnight maximum in dissolved DNA. This diel periodicity was less pronounced in the wet season, when microbial parameters were strongly influenced by episodic inputs of freshwater. These results suggest that seasonal and diel production of dissolved DNA is driven by primary production, either through direct DNA release by phytoplankton, or more likely, through growth of bacterioplankton on phytoplankton exudates, followed by excretion and lysis.     

Differences in uptake kinetics of ammonium and nitrate in legumes and cereals

Influx isotherms were obtained for nitrate and ammonium from three legumes, Cajanus cajan (L.) Millsp., Cicer arietinum L. and Arachis hypogaea L. and three cereals, Sorghum bicolor (L.) Moench., Pennisetum glaucum L. and Zea mays L. The transition in influx isotherms for both nitrogen sources was found to be within the concentration range (0.05–2.5 mM) tested. There were significant differences in Km and Vmax for ammonium between legumes and cereals. The difference in the kinetic properties for nitrate uptake between the two groups of plants only became apparent at the higher concentration tested. Legumes translocated absorbed nitrate and ammonium to shoots more rapidly than cereals. Results show that there are significant differences in uptake and translocation of ammonium and nitrate between legumes and cereals.