The impact of influent nutrient ratios and biochemical reactions on oxygen transfer in an EBPR process--a theoretical explanation

In this investigation, a laboratory-scale enhanced biological phosphorus removal (EBPR) process was operated under controlled conditions to study the impact of varying the influent ratio of chemical oxygen demand (COD), total Kjeldahl nitrogen (TKN) and total phosphorus (TP), and the consequential biochemical reactions on oxygen transfer parameters. The data showed that the experiment with high influent phosphorus relative to nitrogen (COD/TP = 51 and TKN/TP = 3.1) achieved higher alpha and oxygen transfer efficiency (OTE(f)). On the other hand, the experiment with high influent nitrogen relative to phosphorus (TKN/TP = 14.7 and COD/TP = 129) resulted in approximately 50% reduction in alpha and OTE(f) under similar organic loading. This suggested that the intracellular carbon storage and the enhanced biological P removal phenomenon associated with the phosphorus-accumulating organisms (PAOs) had a positive influence on OTE(f) in the high phosphorus experiment compared to an active population of nitrifying and denitrifying organisms in the high nitrogen experiment. The intracellular carbon storage by the glycogen-accumulating organisms also appeared to have had a positive effect on oxygen transfer efficiency, although to a lesser extent in comparison to the PAOs. It was also found that oxygen uptake rate (OUR) was not a good indicator of the measured alpha and OTE(f), because it was a combined effect of several biochemical reactions, each having a varying degree of influence. It is difficult to underestimate the crucial role of flocs in mass transfer of oxygen, because microorganisms associated with flocs carry out the biochemical reactions. It seems that the combination of influent characteristics and biochemical reactions in each experiment produced a unique biomass quality (determined by the biomass N to P ratio), ultimately affecting the mass transfer of oxygen. A theoretical explanation for the observed oxygen transfer efficiency under the process conditions is also proposed in this article.     

MetaboLights: towards a new COSMOS of metabolomics data management

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6?C8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.     

Intracellular calcium dysregulation in autism spectrum disorder: An analysis of converging organelle signaling pathways

Autism spectrum disorder (ASD) is a group of complex, neurological disorders that affect early cognitive, social, and verbal development. Our understanding of ASD has vastly improved with advances in genomic sequencing technology and genetic models that have identified >800 loci with variants that increase susceptibility to ASD. Although these findings have confirmed its high heritability, the underlying mechanisms by which these genes produce the ASD phenotypes have not been defined. Current efforts have begun to “functionalize” many of these variants and envisage how these susceptibility factors converge at key biochemical and biophysical pathways. In this review, we discuss recent work on intracellular calcium signaling in ASD, including our own work, which begins to suggest it as a compelling candidate mechanism in the pathophysiology of autism and a potential therapeutic target. We consider how known variants in the calcium signaling genomic architecture of ASD may exert their deleterious effects along pathways particularly involving organelle dysfunction including the endoplasmic reticulum (ER), a major calcium store, and the mitochondria, a major calcium ion buffer, and theorize how many of these pathways intersect.     

A simple method to estimate the contribution of biological floc and reactor-solution to mass transfer of oxygen in activated sludge processes

In this study, the mass transfer coefficient of biological floc (K(L)a(bf)) was estimated from the mass transfer coefficient of the mixed-liquor (K(L)a(f)) and the reactor-solution (K(L)a(e)). The biological floc resistance (BFR) and reactor-solution resistance (SR) were defined as the reciprocal of K(L)a(bf) and K(L)a(e), respectively, by applying the concept of serial-resistance originally presented in two-film theory (Lewis and Whitman (1924) Ind Eng Chem 16:1215-1220). The specific biological floc resistance (SBFR) was defined as biological floc resistance per unit biomass concentration. The data indicated that an activated sludge process yielding low BFR/MLR and BFR/SR tended to produce higher oxygen transfer efficiency. Surprisingly, the reactor-solution posed the same level of resistance as clean water in all experiments, except in a 5-day SRT, non-nitrifying, completely mixed activated sludge (CMAS) process run. Furthermore, SBFR successfully represented biological floc and showed a positive correlation to sludge volume index (SVI). In addition, SBFR/SR and oxygen transfer efficiency (OTE(f)) followed an exponential relationship for the complete data set. The method of separating the mixed-liquor into biological floc and reactor-solution improved the understanding of oxygen transfer under process conditions, without resorting to intrusive techniques or direct handling of fragile biological floc.     

Opposite roles of Kindlin orthologs in cell survival and proliferation

ObjectiveIt is unclear why adhesion‐dependent cells such as epithelium undergo anoikis without anchorage, while adhesion‐independent blood cells thrive in suspension. The adhesive machinery of these cells is similar, with the exception of Kindlin orthologs, Kindlin 2 (K2) and Kindlin 3 (K3). Here we address how Kindlins control cell survival and proliferation in anchorage‐dependent and independent cells.Material and MethodsTo demonstrate the opposite roles of Kindlin''s in cell survival we utilized in vivo and in vitro models and K3 and K2 knockdown and knockin cells. We used human lymphocytes from the K3 deficient patients in tumour model, K3 knockout and knockin macrophages and K2 knockout and knockin MEF cells for experiments in under conditions of adhesion and in suspension.ResultsDepletion of K3 promotes cell proliferation and survival of anchorage‐independent cells regardless of cell attachment. In contrast, the absence of K2 in anchorage‐dependent cells accelerates apoptosis and limits proliferation. K3 deficiency promotes human lymphoma growth and survival in vivo. Kindlins'' interaction with paxillin, is critical for their differential roles in cell anchorage. While disruption of K2‐paxillin binding leads to increased apoptosis, the lack of K3‐paxillin binding has an opposite effect in adhesion‐independent cells.ConclusionKindlin ortologs and their interaction to cytoskeletal protein paxillin define the mechanisms of anchorage dependence. Our study identifies the key elements of the cell adhesion machinery in cell survival and tumour metastasis, proposing possible targets for tumour treatment.

Cell anchorage is critical for tissue morphogenesis and protection against dysplasia and cancer metastasis. Only transformed and circulating haematopoietic cells thrive without anchorage. The adhesive machinery of anchorage‐dependent and ‐independent cells is similar, with the exception of Kindlin orthologs, Kindlin 2 (K2) and Kindlin 3 (K3). Our study reveals paradoxically opposite roles of K2 and K3 in cell survival despite their identical functions in cell adhesion. K3 deficiency promotes human lymphoma growth and survival. K3 deficiency protects anchorage‐independent cells from apoptosis and promotes their proliferation, while K2 deficiency triggers apoptosis and diminishes proliferation in anchorage‐dependent cells. We further demonstrate that Kindlins'' effects on proliferation rely upon the interaction between Kindlin and paxillin in both, anchorage‐dependent and ‐independent cells.     

Fine Mapping Major Histocompatibility Complex Associations in Psoriasis and Its Clinical Subtypes

Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C^∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10⁻³⁶⁴). Stepwise analysis revealed multiple HLA-C^∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C^∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10⁻⁸), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (p_omnibus = 2.2 × 10⁻¹¹), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC.     

Changes in Carboxy Methylation and Tyrosine Phosphorylation of Protein Phosphatase PP2A Are Associated with Epididymal Sperm Maturation and Motility

Mammalian sperm contain the serine/threonine phosphatases PP1γ2 and PP2A. The role of sperm PP1γ2 is relatively well studied. Here we confirm the presence of PP2A in sperm and show that it undergoes marked changes in methylation (leucine 309), tyrosine phosphorylation (tyrosine 307) and catalytic activity during epididymal sperm maturation. Spermatozoa isolated from proximal caput, distal caput and caudal regions of the epididymis contain equal immuno-reactive amounts of PP2A. Using demethyl sensitive antibodies we show that PP2A is methylated at its carboxy terminus in sperm from the distal caput and caudal regions but not in sperm from the proximal caput region of the epididymis. The methylation status of PP2A was confirmed by isolation of PP2A with microcystin agarose followed by alkali treatment, which causes hydrolysis of protein carboxy methyl esters. Tyrosine phosphorylation of sperm PP2A varied inversely with methylation. That is, PP2A was tyrosine phosphorylated when it was demethylated but not when methylated. PP2A demethylation and its reciprocal tyrosine phosphorylation were also affected by treatment of sperm with L-homocysteine and adenosine, which are known to elevate intracellular S-adenosylhomocysteine, a feedback inhibitor of methyltransferases. Catalytic activity of PP2A declined during epididymal sperm maturation. Inhibition of PP2A by okadaic acid or by incubation of caudal epididymal spermatozoa with L-homocysteine and adenosine resulted in increase of sperm motility parameters including percent motility, velocity, and lateral head amplitude. Demethylation or pharmacological inhibition of PP2A also leads to an increase in phosphorylation of glycogen synthase kinase-3 (GSK3). Our results show for the first time that changes in PP2A activity due to methylation and tyrosine phosphorylation occur in sperm and that these changes may play an important role in the regulation of sperm function.