Seasonal nutrient co-limitation in a temperate shelf sea: A modelling approach

Nutrient limitation on phytoplankton growth plays a critical role in ocean productivity, the functioning of marine ecosystems, and the ocean carbon cycle. In the Celtic Sea, a temperate shelf sea, many studies have shown the importance of nitrate on phytoplankton growth focusing on the seasonal cycle of nitrate and feedbacks with the physical environment; but only recently has it been demonstrated, through discrete measurements, that dissolved iron also plays an important role in the ecosystem of the region. A well-established one-dimensional model has been developed to analyse the nutrient co-limitation between dissolved iron and dissolved inorganic nitrogen in the Celtic Sea. This model allows us to study the full seasonal cycle and inter-annual variability of these two nutrients. Simulations show that dissolved iron is an important nutrient for the development of the spring bloom, while nitrate plays a more important role during the summer season. Sensitivity analyses show that these results are robust when varying the nutrient-related parameters; the largest variability observed for primary production was observed when varying the nutrient sediment flux rates for dissolved iron and nitrate while less impact on phytoplankton production occurs when changing the half saturation constants. Here, we demonstrate that dissolved iron is an important nutrient for the development of the spring bloom and it should not be neglected as a state variable when modelling the Celtic Sea or other temperate shelf seas

Non-commutative desingularization of determinantal varieties, I

We show that determinantal varieties defined by maximal minors of a generic matrix have a non-commutative desingularization, in that we construct a maximal Cohen-Macaulay module over such a variety whose endomorphism ring is Cohen-Macaulay and has finite global dimension. In the case of the determinant of a square matrix, this gives a non-commutative crepant resolution.Comment: 52 pages, 3 figures, all comments welcom

Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell–cell approach

Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell–cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 μm. Moreover, the motile response displays spatial sensitivity with greater cell–cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation

Graded decomposition numbers for cyclotomic Hecke algebras

In recent joint work with Wang, we have constructed graded Specht modules for cyclotomic Hecke algebras. In this article, we prove a graded version of the Lascoux-Leclerc-Thibon conjecture, describing the decomposition numbers of graded Specht modules over a field of characteristic zero.Comment: 57 pages; final versio

A self-consistent, multi-variate method for the determination of gas phase rate coefficients, applied to reactions of atmospheric VOCs and the hydroxyl radical

Gas-phase rate coefficients are fundamental to understanding atmospheric chemistry, yet experimental data are not available for the oxidation reactions of many of the thousands of volatile organic compounds (VOCs) observed in the troposphere. Here a new experimental method is reported for the simultaneous study of reactions between multiple different VOCs and OH, the most important daytime atmospheric radical oxidant. This technique is based upon established relative rate concepts but has the advantage of a much higher throughput of target VOCs. By evaluating multiple VOCs in each experiment, and through measurement of the depletion in each VOC after reaction with OH, the OH + VOC reaction rate coefficients can be derived. Results from experiments conducted under controlled laboratory conditions were in good agreement with the available literature for the reaction of nineteen VOCs, prepared in synthetic gas mixtures, with OH. This approach was used to determine a rate coefficient for the reaction of OH with 2,3-dimethylpent-1-ene for the first time; k = 5.7 (±0.3) × 10–11–cm3 molecule−1 s−1. In addition, a further seven VOCs had only two, or fewer, individual OH rate coefficient measurements available in the literature. The results from this work were in good agreement with those measurements. A similar dataset, at an elevated temperature of 323 (±10) K, was used to determine new OH rate coefficients for twelve aromatic, five alkane, five alkene and three monoterpene VOC + OH reactions. In OH relative reactivity experiments that used ambient air at the University of York, a large number of different VOCs were observed, of which 23 were positively identified. 19 OH rate coefficients were derived from these ambient air samples, including ten reactions for which data was previously unavailable at the elevated reaction temperature of T = 323 (±10) K

On central idempotents in the Brauer algebra

We provide a method for constructing central idempotents in the Brauer algebra (using the splitting of short exact sequences of bimodules). From this we determine certain primitive central idempotents. By working over a suitable integral ring we hence demonstrate an efficient method of constructing pieces of the representation theory of the Brauer algebra over Artinian rings from the integral case

Degradation, Bioactivity, and Osteogenic Potential of Composites Made of PLGA and Two Different Sol–Gel Bioactive Glasses

We have developed poly(l-lactide-co-glycolide) (PLGA) based composites using sol–gel derived bioactive glasses (S-BG), previously described by our group, as composite components. Two different composite types were manufactured that contained either S2—high content silica S-BG, or A2—high content lime S-BG. The composites were evaluated in the form of sheets and 3D scaffolds. Sheets containing 12, 21, and 33 vol.% of each bioactive glass were characterized for mechanical properties, wettability, hydrolytic degradation, and surface bioactivity. Sheets containing A2 S-BG rapidly formed a hydroxyapatite surface layer after incubation in simulated body fluid. The incorporation of either S-BG increased the tensile strength and Young’s modulus of the composites and tailored their degradation rates compared to starting compounds. Sheets and 3D scaffolds were evaluated for their ability to support growth of human bone marrow cells (BMC) and MG-63 cells, respectively. Cells were grown in non-differentiating, osteogenic or osteoclast-inducing conditions. Osteogenesis was induced with either recombinant human BMP-2 or dexamethasone, and osteoclast formation with M-CSF. BMC viability was lower at higher S-BG content, though specific ALP/cell was significantly higher on PLGA/A2-33 composites. Composites containing S2 S-BG enhanced calcification of extracellular matrix by BMC, whereas incorporation of A2 S-BG in the composites promoted osteoclast formation from BMC. MG-63 osteoblast-like cells seeded in porous scaffolds containing S2 maintained viability and secreted collagen and calcium throughout the scaffolds. Overall, the presented data show functional versatility of the composites studied and indicate their potential to design a wide variety of implant materials differing in physico-chemical properties and biological applications. We propose these sol–gel derived bioactive glass–PLGA composites may prove excellent potential orthopedic and dental biomaterials supporting bone formation and remodeling

BRITER: A BMP Responsive Osteoblast Reporter Cell Line

BACKGROUND: BMP signaling pathway is critical for vertebrate development and tissue homeostasis. High-throughput molecular genetic screening may reveal novel players regulating BMP signaling response while chemical genetic screening of BMP signaling modifiers may have clinical significance. It is therefore important to generate a cell-based tool to execute such screens. METHODOLOGY/PRINCIPAL FINDINGS: We have established a BMP responsive reporter cell line by stably integrating a BMP responsive dual luciferase reporter construct in the immortalized calvarial osteoblast cells isolated from tamoxifen inducible Bmp2; Bmp4 double conditional knockout mouse strain. This cell line, named BRITER (BMP Responsive Immortalized Reporter cell line), responds robustly, promptly and specifically to exogenously added BMP2 protein. The sensitivity to added BMP may be further increased by depleting the endogenous BMP2 and BMP4 proteins. CONCLUSION: As the dynamic range of the assay (for BMP responsiveness) is very high for BRITER and as it responds specifically and promptly to exogenously added BMP2 protein, BRITER may be used effectively for chemical or molecular genetic screening for BMP signaling modifiers. Identification of novel molecular players capable of influencing BMP signaling pathway may have clinical significance

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

Key role of NO3 radicals in the production of isoprene nitrates and nitrooxyorganosulfates in Beijing

The formation of isoprene nitrates (IsN) can lead to significant secondary organic aerosol (SOA) production and they can act as reservoirs of atmospheric nitrogen oxides. In this work, we estimate the rate of production of IsN from the reactions of isoprene with OH and NO3 radicals during the summertime in Beijing. While OH dominates the loss of isoprene during the day, NO3 plays an increasingly important role in the production of IsN from the early afternoon onwards. Unusually low NO concentrations during the afternoon resulted in NO3 mixing ratios of ca. 2 pptv at approximately 15:00, which we estimate to account for around a third of the total IsN production in the gas phase. Heterogeneous uptake of IsN produces nitrooxyorganosulfates (NOS). Two mono-nitrated NOS were correlated with particulate sulfate concentrations and appear to be formed from sequential NO3 and OH oxidation. Di- and tri-nitrated isoprene-related NOS, formed from multiple NO3 oxidation steps, peaked during the night. This work highlights that NO3 chemistry can play a key role in driving biogenic–anthropogenic interactive chemistry in Beijing with respect to the formation of IsN during both the day and night