Nitrogen inputs accelerate phosphorus cycling rates across a wide variety of terrestrial ecosystems

? Biologically essential elements--especially nitrogen (N) and phosphorus (P)--constrain plant growth and microbial functioning; however, human activities are drastically altering the magnitude and pattern of such nutrient limitations on land. Here we examine interactions between N and P cycles of P mineralizing enzyme activities (phosphatase enzymes) across a wide variety of terrestrial biomes. ? We synthesized results from 34 separate studies and used meta-analysis to evaluate phosphatase activity with N, P, or N×P fertilization. ? Our results show that N fertilization enhances phosphatase activity, from the tropics to the extra-tropics, both on plant roots and in bulk soils. By contrast, P fertilization strongly suppresses rates of phosphatase activity. ? These results imply that phosphatase enzymes are strongly responsive to changes in local nutrient cycle conditions. We also show that plant phosphatases respond more strongly to fertilization than soil phosphatases. The tight coupling between N and P provides a mechanism for recent observations of N and P co-limitation on land. Moreover, our results suggest that terrestrial plants and microbes can allocate excess N to phosphatase enzymes, thus delaying the onset of single P limitation to plant productivity as can occur via human modifications to the global N cycle.     

Fermentability of eastern gamagrass, big bluestem and sand bluestem grown across a wide variety of environments

Plant biomass has attracted interest as a feedstock for biofuels production, but much of this work has been focused on relatively few plant species. In this study, three relatively-unstudied species of warm-season perennial grasses, grown at multiple locations in the eastern and central US and harvested over a three year period, were examined for fermentability via in vitro ruminal gas production and dry matter digestibility assays, and near-infrared reflectance calibrations were developed for these fermentation parameters. Big bluestem (Andropogon gerardii Vitman) displayed greater fermentability than did sand bluestem (Andropogon hallii Hack) or eastern gamagrass [Tripsacum dactyloides (L.) L.], but displayed lower biomass yields. The bluestems also displayed lower N contents and less variation in fermentability over different growth environments (geographic locations and harvest years), suggesting a more consistent biomass quality than for eastern gamagrass. Thus, in addition to their use as forage for ruminant animals, bluestems may be of particular interest as feedstocks for bioconversion to ethanol and other products via direct microbial fermentation (consolidated bioprocessing) schemes, and thus merit additional efforts to enhance biomass yield potential.     

Screening and assessment of performance and molecule quality attributes of industrial cell lines across different fed‐batch systems

The major challenge in the selection process of recombinant cell lines for the production of biologics is the choice, early in development, of a clonal cell line presenting a high productivity and optimal cell growth. Most importantly, the selected candidate needs to generate a product quality profile which is adequate with respect to safety and efficacy and which is preserved across cell culture scales. We developed a high‐throughput screening and selection strategy of recombinant cell lines, based on their productivity in shaking 96‐deepwell plates operated in fed‐batch mode, which enables the identification of cell lines maintaining their high productivity at larger scales. Twelve recombinant cell lines expressing the same antibody with different productivities were selected out of 470 clonal cell lines in 96‐deepwell plate fed‐batch culture. They were tested under the same conditions in 50 mL vented shake tubes, microscale and lab‐scale bioreactors in order to confirm the maintenance of their performance at larger scales. The use of a feeding protocol and culture conditions which are essentially the same across the different scales was essential to maintain productivity and product quality profiles across scales. Compared to currently used approaches, this strategy has the advantage of speeding up the selection process and increases the number of screened clones for getting high‐producing recombinant cell lines at manufacturing scale with the desired performance and quality. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:160–170, 2016     

Cryopreservation of porcine articular cartilage: MRI and biochemical results after different freezing protocols

The objective of this study was to investigate the effects of cryopreservation on the components of articular cartilage (AC) matrix by utilizing magnetic resonance imaging (MRI) and biochemical assessments. Porcine AC (10mm osteochondral dowels) was collected into four groups - (1) phosphate buffered saline (PBS) control, (2) PBS snap frozen in liquid nitrogen, (3) slow-cooled in dimethyl sulfoxide (DMSO), and (4) slow cooled in PBS (in absence of DMSO). MRI results demonstrated three distinct zones in the cartilage. After exposure to ice formation during cryopreservation procedures, alterations in MRI determined matrix fixed charged density and magnetization transfer rate were noted. In addition, biochemical assays demonstrated significant alterations in chondroitin sulfate and hydroxyproline content over time without differences in hydration or DNA content. In conclusion, MRI was able to detect some changes in the intact cartilage matrix structure consistent with biochemical assessments after ice formation during cryopreservation of intact porcine AC. Furthermore, biochemical assessments supported some of these findings and changed significantly after incubating the cartilage matrix for 36-72 h in PBS in terms of chondroitin sulfate and hydroxyproline content.     

Multicellular behaviour and production of a wide variety of toxic substances support usage of Bacillus subtilis as a powerful biocontrol agent

Intensive cultivation of plants in the monoculture field system in order to feed the continuously growing human population creates a need for their protection from the variety of natural competitors such as: bacteria, fungi, insects as well as other plants. The increase in the use of chemical substances in the 20th century has brought many effective solutions for the agriculture. However, it was extremely difficult to obtain a substance, which would be directed solely against a specific plant pathogen and would not be harmful for the environment. In the late 1900's scientists began trying to use natural antagonisms between resident soil organism to protect plants. This phenomenon was named biocontrol. Biological control of plants by microorganisms is a very promising alternative to an extended use of pesticides, which are often expensive and accumulate in plants or soil, having adverse effects on humans. Nonpathogenic soil bacteria living in association with roots of higher plants enhance their adaptive potential and, moreover, they can be beneficial for their growth. Here, we present the current status of the use of Bacillus subtilis in biocontrol. This prevalent inhabitant of soil is widely recognized as a powerful biocontrol agent. Naturally present in the immediate vicinity of plant roots, B. subtilis is able to maintain stable contact with higher plants and promote their growth. In addition, due to its broad host range, its ability to form endospores and produce different biologically active compounds with a broad spectrum of activity, B. subtilis as well as other Bacilli are potentially useful as biocontrol agents.     

Sorafenib fails to trigger ferroptosis across a wide range of cancer cell lines

Sorafenib, a protein kinase inhibitor approved for the treatment of hepatocellular carcinoma and advanced renal cell carcinoma, has been repeatedly reported to induce ferroptosis by possibly involving inhibition of the cystine/glutamate antiporter, known as system x_c⁻. Using a combination of well-defined genetically engineered tumor cell lines and canonical small molecule ferroptosis inhibitors, we now provide unequivocal evidence that sorafenib does not induce ferroptosis in a series of tumor cell lines unlike the cognate system x_c⁻ inhibitors sulfasalazine and erastin. We further show that only a subset of tumor cells dies by ferroptosis upon sulfasalazine and erastin treatment, implying that certain cell lines appear to be resistant to system x_c⁻ inhibition, while others undergo ferroptosis-independent cell death. From these findings, we conclude that sorafenib does not qualify as a bona fide ferroptosis inducer and that ferroptosis induced by system x_c⁻ inhibitors can only be achieved in a fraction of tumor cell lines despite robust expression of SLC7A11, the substrate-specific subunit of system x_c⁻.Subject terms: Cell death, Small molecules     

Method for generation of homogeneous multicellular tumor spheroids applicable to a wide variety of cell types

Multicellular tumor spheroids (MCTS) are used as organotypic models of normal and solid tumor tissue. Traditional techniques for generating MCTS, such as growth on nonadherent surfaces, in suspension, or on scaffolds, have a number of drawbacks, including the need for manual selection to achieve a homogeneous population and the use of nonphysiological matrix compounds. In this study we describe a mild method for the generation of MCTS, in which individual spheroids form in hanging drops suspended from a microtiter plate. The method has been successfully applied to a broad range of cell lines and shows nearly 100% efficiency (i.e., one spheroid per drop). Using the hepatoma cell line, HepG2, the hanging drop method generated well-rounded MCTS with a narrow size distribution (coefficient of variation [CV] 10% to 15%, compared with 40% to 60% for growth on nonadherent surfaces). Structural analysis of HepG2 and a mammary gland adenocarcinoma cell line, MCF-7, composed spheroids, revealed highly organized, three-dimensional, tissue-like structures with an extensive extracellular matrix. The hanging drop method represents an attractive alternative for MCTS production, because it is mild, can be applied to a wide variety of cell lines, and can produce spheroids of a homogeneous size without the need for sieving or manual selection. The method has applications for basic studies of physiology and metabolism, tumor biology, toxicology, cellular organization, and the development of bioartificial tissue.     

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Background

Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.

Principal Findings

We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).

Conclusions

Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.     

Syk expression and novel function in a wide variety of tissues.

Syk protein-tyrosine kinase has been implicated in a variety of hematopoietic cell responses, in particular immunoreceptor signaling events that mediate diverse cellular responses including proliferation, differentiation, and phagocytosis. On the other hand, Syk exhibits a more widespread expression pattern in nonhematopoietic cells like fibroblasts, epithelial cells, breast tissue, hepatocytes, neuronal cells, and vascular endothelial cells and has been shown to be functionally important on these cell types. Thus, Syk appears to play a general physiological function in a wide variety of cells. In this article, we briefly review the current literature regarding the expression and novel function of Syk in various cells and tissues.     

Effect of different protocols of caffeine intake on metabolism and endurance performance.

Competitive athletes completed two studies of 2-h steady-state (SS) cycling at 70% peak O(2) uptake followed by 7 kJ/kg time trial (TT) with carbohydrate (CHO) intake before (2 g/kg) and during (6% CHO drink) exercise. In Study A, 12 subjects received either 6 mg/kg caffeine 1 h preexercise (Precaf), 6 x 1 mg/kg caffeine every 20 min throughout SS (Durcaf), 2 x 5 ml/kg Coca-Cola between 100 and 120 min SS and during TT (Coke), or placebo. Improvements in TT were as follows: Precaf, 3.4% (0.2-6.5%, 95% confidence interval); Durcaf, 3.1% (-0.1-6.5%); and Coke, 3.1% (-0.2-6.2%). In Study B, eight subjects received 3 x 5 ml/kg of different cola drinks during the last 40 min of SS and TT: decaffeinated, 6% CHO (control); caffeinated, 6% CHO; decaffeinated, 11% CHO; and caffeinated, 11% CHO (Coke). Coke enhanced TT by 3.3% (0.8-5.9%), with all trials showing 2.2% TT enhancement (0.5-3.8%; P < 0.05) due to caffeine. Overall, 1) 6 mg/kg caffeine enhanced TT performance independent of timing of intake and 2) replacing sports drink with Coca-Cola during the latter stages of exercise was equally effective in enhancing endurance performance, primarily due to low intake of caffeine (approximately 1.5 mg/kg).     

Sensing and modulation of invadopodia across a wide range of rigidities

Recent studies have suggested that extracellular matrix rigidity regulates cancer invasiveness, including the formation of cellular invadopodial protrusions; however, the relevant mechanical range is unclear. Here, we used a combined analysis of tissue-derived model basement membrane (BM) and stromal matrices and synthetic materials to understand how substrate rigidity regulates invadopodia. Urinary bladder matrix-BM (UBM-BM) was found to be a rigid material with elastic moduli of 3-8 MPa, as measured by atomic force microscopy and low-strain tensile testing. Stromal elastic moduli were ∼6-fold lower, indicating a more compliant material. Using synthetic substrates that span kPa–GPa moduli, we found a peak of invadopodia-associated extracellular matrix degradation centered around 30 kPa, which also corresponded to a peak in invadopodia/cell. Surprisingly, we observed another peak in invadopodia numbers at 2 GPa as well as gene expression changes that indicate cellular sensing of very high moduli. Based on the measured elastic moduli of model stroma and BM, we expected to find more invadopodia formation on the stroma, and this was verified on the stromal versus BM side of UBM-BM. These data suggest that cells can sense a wide range of rigidities, up into the GPa range. Furthermore, there is an optimal rigidity range for invadopodia activity that may be limited by BM rigidity.     

Inhibitory effect of cocoa powder on the growth of a variety of bacteria in different media.

The inhibitory effect of cocoa powder on 102 organisms belonging to 13 genera was determined. All organisms tested were inhibited by 5% cocoa. Shigella, Staphylococcus, Micrococcus, and Bacillus were the most sensitive. The degree of inhibition depended on the organism, temperature of incubation, and the medium in which the cocoa powder was suspended. Of six media tested, lactose broth and nutrient broth were the most inhibitory, while non-fat dry milk was the least inhibitory. Supplementing NB with tryptone or casein reduced the toxicity of cocoa.     

Comparison of assay technologies for a tyrosine kinase assay generates different results in high throughput screening

In today's high-throughput screening (HTS) environment, an increasing number of assay detection technologies are routinely utilized in lead finding programs. Because of the relatively broad applicability of several of these technologies, one is often faced with a choice of which technology to utilize for a specific assay. The aim of this study was to address the question of whether the same compounds would be identified from screening a set of samples in three different versions of an HTS assay. Here, three different versions of a tyrosine kinase assay were established using scintillation proximity assay (SPA), homogeneous time-resolved fluorescence resonance energy transfer (HTR-FRET), and fluorescence polarization (FP) technologies. In this study, 30,000 compounds were evaluated in each version of the kinase assay in primary screening, deconvolution, and dose-response experiments. From this effort, there was only a small degree of overlap of active compounds identified subsequent to the deconvolution experiment. When all active compounds were then profiled in all three assays, 100 and 101 active compounds were identified in the HTR-FRET and FP assays, respectively. In contrast, 40 compounds were identified in the SPA version of the kinase assay, whereas all of these compounds were detected in the HTR-FRET assay only 35 were active in the FP assay. Although there was good correlation between the IC(50) values obtained in the HTR-FRET and FP assays, poor correlations were obtained with the IC(50) values obtained in the SPA assay. These findings suggest that significant differences can be observed from HTS depending on the assay technology that is utilized, particularly in assays with high hit rates.     

Development of a high throughput Pseudomonas aeruginosa epithelial cell adhesion assay

Pseudomonas aeruginosa colonizes the lungs of cystic fibrosis and mechanically ventilated patients by binding to specific carbohydrate residues on the surface of lung epithelial cells. Studies have shown that blocking this interaction may have therapeutic effects in vivo. To test compounds that may have an effect on the binding of P. aeruginosa to epithelial cells, we have developed a pseudomonal adhesion assay that is compatible with high throughput technology. This assay utilizes a 96-well culture plate assay and P. aeruginosa strains that have been modified to bioluminesce. This method has proven to be a rapid, sensitive and reproducible system for screening agents that inhibit bacterial adhesion.     

Two-step accelerating freezing protocol yields a better motility,membranes and DNA integrities of thawed ram sperm than three-steps freezing protocols

The present study compares a protocol that mimics freezing of ram semen in static nitrogen vapor with two protocols with an initial low cooling rate in the first step, followed by higher cooling rates where ice nucleation occurs. Semen ejaculates, obtained from twelve adults rams, were diluted with TEST-based extender and frozen with either Protocol 1 (three-step decelerating cooling): from +5 °C to −35 °C (40 °C/min), from −35 °C to −65 °C (17 °C/min), and then from −65 °C to −85 °C (3 °C/min); or Protocol 2 (three-step accelerating cooling): from +5 °C to −5 °C (4 °C/min), from −5 °C to −110 °C (25 °C/min), and then from −110 °C to −140 °C (35 °C/min); or Protocol 3 (two-step accelerating cooling), from +5 °C to −10 °C (5 °C/min), and then from −10 °C to −130 °C (60 °C/min). Post-thaw sperm quality was reduced for all protocols (p < .05) compared with fresh semen. Post-thaw percentages of sperm motility characteristics and sperm with intact plasma membrane, intact acrosome, and intact mitochondrial membrane were greater using Protocol 3 than Protocol 2 (p < .05) and Protocol 1 (p < .01). In addition, the post-thaw percentage of sperm with fragmented DNA was lower (p < .05) using Protocol 3 compared with Protocol 1. The present results indicate that a cooling rate of 60 °C/min around and after the time point of ice nucleation provided better post thaw survival and function of ram sperm than lower (and/or decelerating) cooling rates.     

Generation and application of a monoclonal antibody that detects a wide variety of protein tyrosine kinases

To investigate expression profiles of the entire family of protein tyrosine kinases (PTKs), we attempted to generate an antibody that detects a variety of PTKs. For production of the antibody, antigenic peptides corresponding to amino acid sequences of a highly conserved region (subdomain VIB) of PTKs were synthesized and immunized to BALB/c mice. Among various antigens, a peptide with 11 amino acids, CYVHRDLRAAN, efficiently produced a polyclonal antibody with a broad cross-reactivity to PTKs. We established a hybridoma cell line producing a monoclonal antibody, YK34, which appeared to cross-react with at least 68 PTKs in the human genome, as evidenced by its reactivity with the recombinant Src tyrosine kinases whose subdomain VIB had been replaced by those of the other PTKs. When differentiation of HL-60 cells was induced by 12-O-tetradecanoylphorbol-13-acetate, on Western blotting we observed significant changes in immunoreactive bands with YK34 in HL-60 cell extracts along with changes in the morphology of the cells. These results suggest that the YK34 antibody will be a powerful tool for analysis of a variety of cellular PTKs.     

Acute effects of different warm-up protocols with and without a weighted vest on jumping performance in athletic women

The purpose of this study was to examine the acute effects of 3 different warm-up protocols with and without a weighted vest on vertical jump (VJ) and long jump (LJ) performance in athletic women. Sixteen subjects (19.7 +/- 1.4 years, 67.0 +/- 10.7 kg, 165.7 +/- 11.4 cm) participated in 3 testing sessions in random order on 3 nonconsecutive days. Prior to the testing of the VJ and LJ, the subjects performed 1 of the following 10-minute warm-up protocols: (a) low- to moderate-intensity stationary cycling followed by 4 lower-body static stretches (SS) (3 x 20 seconds); (b) 12 moderate- to high-intensity dynamic exercises (DY); and (c) the same 12 dynamic exercises with a weighted vest (10% of body mass) worn for the last 4 exercises (DYV). Analysis of the data revealed that VJ performance was significantly greater (p < 0.05) following DYV (43.9 +/- 6.7 cm) and DY (43.6 +/- 6.5 cm) as compared to SS (41.7 +/- 6.0 cm). Long jump performance was significantly greater (p < 0.05) following DYV (186.8 +/- 19.5 cm) as compared to DY (182.2 +/- 19.1 cm), which in turn was significantly greater (p < 0.05) than performance following SS (177.2 +/- 18.8 cm). Warm-up protocols that include dynamic exercise may be a viable method of enhancing jumping performance in athletic women as compared to stationary cycling and static stretching. In addition, these data suggest that it may be desirable for athletic women to perform dynamic exercises with a weighted vest on some movements prior to the performance of the long jump.