Numerical modelling of surface aeration and N2O emission in biological water resource recovery

Biokinetic modelling of N2O production and emission has been extensively studied in the past fifteen years. In contrast, the physical-chemical hydrodynamics of activated sludge reactor design and operation, and their impact on N2O emission, is less well understood. This study addresses knowledge gaps related to the systematic identification and calibration of computational fluid dynamic (CFD) simulation models. Additionally, factors influencing reliable prediction of aeration and N2O emission in surface aerated oxidation ditch-type reactor types are evaluated. The calibrated model accurately predicts liquid sensor measurements obtained in the Lynetten Water Resource Recovery Facility (WRRF), Denmark. Results highlight the equal importance of design and operational boundary conditions, alongside biokinetic parameters, in predicting N2O emission. Insights into the limitations of calibrating gas mass-transfer processes in two-phase CFD models of surface aeration systems are evaluated.

Modeling of wastewater treatment processes with hydrosludge

The pressure for Water Resource Recovery Facilities (WRRF) operators to efficiently treat wastewater is greater than ever because of the water crisis, produced by the climate change effects and more restrictive regulations. Technicians and researchers need to evaluate WRRF performance to ensure maximum efficiency. For this purpose, numerical techniques, such as CFD, have been widely applied to the wastewater sector to model biological reactors and secondary settling tanks with high spatial and temporal accuracy. However, limitations such as complexity and learning curve prevent extending CFD usage among wastewater modeling experts. This paper presents HydroSludge, a framework that provides a series of tools that simplify the implementation of the processes and workflows in a WRRF. This work leverages HydroSludge to preprocess existing data, aid the meshing process, and perform CFD simulations. Its intuitive interface proves itself as an effective tool to increase the efficiency of wastewater treatment. PRACTITIONER POINTS: This paper introduces a software platform specifically oriented to WRRF, named HydroSludge, which provides easy access to the most widespread and leading CFD simulation software, OpenFOAM. Hydrosludge is intended to be used by WRRF operators, bringing a more wizard-like, automatic, and intuitive usage. Meshing assistance, submersible mixers, biological models, and distributed parallel computing are the most remarkable features included in HydroSludge. With the provided study cases, HydroSludge has proven to be a crucial tool for operators, managers, and researchers in WRRF.

Experimental and CFD evaluation of ozone efficacy against coronavirus and enteric virus contamination on public transport surfaces

The limited information about the routes of the transmission of SARS-CoV-2 within the ongoing pandemic scenario mobilized the administration, industry and academy to develop sanitation and disinfection systems for public and private spaces. Ozone has been proposed as an effective disinfection method against enveloped and non-enveloped viruses, including viruses with similar morphology to SARS-CoV-2. Due to this efficacy, numerous gaseous and aqueous phase ozone applications have emerged potentially to inhibit virus persistence in aerosols, surfaces, and water. In this work, a numerical model, a RANS CFD model for ozone dispersion inside tram and underground coach has been developed including the chemical self-decomposition and surface reactions of the ozone. The CFD model has been developed for a real tram coach of 28.6 × 2.4 × 2.2 m (L × W × H) using 1.76 million nodes and the Menter's shear stress transport turbulence model. The model predicts the O₃ concentration needed to meet disinfection criteria and the fluid dynamics inside the public transport coach. The effectiveness of the system has been validated with laboratory and field tests in real full-scale coach using porcine epidemic diarrhea virus (PEDV) and murine norovirus (MNV-1) as SARS-CoV-2 and human norovirus surrogates, respectively. Lab-scale experiments on plastic surfaces demonstrated O₃ disinfection (100 ppm, 95% RH, 25 min) inactivate > 99.8% MNV-1 and PEDV. Additionally, field tests in real full-scale coach demostrate the efficacy of the system as > 98.6% of infectious MNV-1 and > 96.3% PEDV were inactivated.

Do cone age and heating mode determine the opening of serotinous cones during wildfires? A new bench scale approach applied to Pinus halepensis Mill

Serotiny is a well-known fire adaptive trait in some species, as the Mediterranean conifer Pinus halepensis. However, information about cone opening mechanisms during wildfires and consequences on post fire dispersal is scarce. In addition, standardized methods allowing a realistic simulation of heating modes at bench-scale are not available. In this study, we address for the first time the interacting effects of radiation, convection and direct flame on the opening and seed release of serotinous cones, following a novel repeatable methodology. Using a Mass Loss Calorimeter (MLC) device and a wide range of heat exposures (between 5 and 75 kW m^-2) with or without ignition, we intended to simulate realistic cone heating during surface and crown fires in laboratory conditions. Additionally, we included the effect of contrasting serotinous cone ages interacting with heating mode and considering the random individual variation. The proposed methodology has shown a high potential to simulate the complex process of crown fires in relation to cone opening under controlled conditions, detecting a threshold of heat exposure (25-30 kW m^-2) for cone opening. We confirmed that heating mode had a highly significant effect in cone opening, interacting with cone age, while cone age effect on its own was marginal. Particularly, ignition significantly increased the efficacy of cone opening and seed release. Moreover, young and old cones behave differently in seed release, both in surface and crown fire simulations. Implementing and adjusting this methodology in other species will allow more realistic and reliable quantitative comparisons than previously attained.

Hindered and compression solid settling functions - Sensor data collection, practical model identification and validation

Secondary settling tanks (SSTs) are the most hydraulically sensitive unit operations in activated sludge water resource recovery facilities (WRRF). Mathematical models for predicting activated sludge solids settling velocity include parameters that show irreducible epistemic uncertainty. Therefore, reliable and periodic calibration of the settling velocity model is key for predicting activated sludge process capacity, thus averting possible failures under wet-weather flow- and filamentous bulking conditions. The two main knowledge gaps addressed here are: (1) Do constitutive functions for hindered and compression settling exist, for which all velocity parameters can be uniquely estimated? (2) What is the optimum sensor data requirement of developing reliable settling velocity functions? Innovative settling column sensor and full-scale data were used to identify and validate amended Vesilind function for hindered settling and a new exponential function for compression settling velocity using one-dimensional and computational fluid dynamics simulations. Results indicate practical model identifiability under well-settling and filamentous bulking conditions.

Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch)

Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster

BACKGROUND AND AIMS

The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted across a broad geographical range of the Mediterranean conifer species Pinus pinaster. In particular, the study investigates whether this monoecious species varies genetically among populations in terms of whether individuals start to reproduce through their male function, their female function or both sexual functions simultaneously. Whether differences among populations could be attributed to local adaptation across a climatic gradient is then considered.

METHODS

Male and female reproduction and growth were measured during early stages of sexual maturity of a P. pinaster common garden comprising 23 populations sampled across the species range. Generalized linear mixed models were used to assess genetic variability of early reproductive life-history traits. Environmental correlations with reproductive life-history traits were tested after controlling for neutral genetic structure provided by 12 nuclear simple sequence repeat markers.

KEY RESULTS

Trees tended to reproduce first through their male function, at a size (height) that varied little among source populations. The transition to female reproduction was slower, showed higher levels of variability and was negatively correlated with vegetative growth traits. Several female reproductive traits were correlated with a gradient of growth conditions, even after accounting for neutral genetic structure, with populations from more unfavourable sites tending to commence female reproduction at a lower individual size.

CONCLUSIONS

The study represents the first report of genetic variability among populations for differences in the threshold size for first reproduction between male and female sexual functions in a tree species. The relatively uniform size at which individuals begin reproducing through their male function probably represents the fact that pollen dispersal is also relatively invariant among sites. However, the genetic variability in the timing of female reproduction probably reflects environment-dependent costs of cone production. The results also suggest that early sex allocation in this species might evolve under constraints that do not apply to other conifers.

Hipk2 cooperates with p53 to suppress γ-ray radiation-induced mouse thymic lymphoma

A genome-wide screen for genetic alterations in radiation-induced thymic lymphomas generated from p53+/- and p53-/- mice showed frequent loss of heterozygosity (LOH) on chromosome 6. Fine mapping of these LOH regions revealed three non-overlapping regions, one of which was refined to a 0.2 Mb interval that contained only the gene encoding homeobox-interacting protein kinase 2 (Hipk2). More than 30% of radiation-induced tumors from both p53+/- and p53-/- mice showed heterozygous loss of one Hipk2 allele. Mice carrying a single inactive allele of Hipk2 in the germline were susceptible to induction of tumors by γ-radiation, but most tumors retained and expressed the wild-type allele, suggesting that Hipk2 is a haploinsufficient tumor suppressor gene for mouse lymphoma development. Heterozygous loss of both Hipk2 and p53 confers strong sensitization to radiation-induced lymphoma. We conclude that Hipk2 is a haploinsufficient lymphoma suppressor gene.

Characterization of breast cancer by array comparative genomic hybridization

Cancer progression is due to the accumulation of recurrent genomic alterations that induce growth advantage and clonal expansion. Most of these genomic changes can be detected using the array comparative genomic hybridization (CGH) technique. The accurate classification of these genomic alterations is expected to have an important impact on translational and basic research. Here we review recent advances in CGH technology used in the characterization of different features of breast cancer. First, we present bioinformatics methods that have been developed for the analysis of CGH arrays; next, we discuss the use of array CGH technology to classify tumor stages and to identify and stratify subgroups of patients with different prognoses and clinical behaviors. We finish our review with a discussion of how CGH arrays are being used to identify oncogenes, tumor suppressor genes, and breast cancer susceptibility genes.

RNA-binding properties and membrane insertion of Melon necrotic spot virus (MNSV) double gene block movement proteins

Advances in structural and biochemical properties of carmovirus movement proteins (MPs) have only been obtained in p7 and p9 from Carnation mottle virus (CarMV). Alignment of carmovirus MPs revealed a low conservation of amino acid identity but interestingly, similarity was elevated in regions associated with the functional secondary structure elements reported for CarMV which were conserved in all studied proteins. Nevertheless, some differential features in relation with CarMV MPs were identified in those from Melon necrotic virus (MNSV) (p7A and p7B). p7A was a soluble non-sequence specific RNA-binding protein, but unlike CarMV p7, its central region alone could not account for the RNA-binding properties of the entire protein. In fact, a 22-amino acid synthetic peptide whose sequence corresponds to this central region rendered an apparent dissociation constant (K(d)) significantly higher than that of the corresponding entire protein (9 mM vs. 0.83-25.7 microM). This p7A-derived peptide could be induced to fold into an alpha-helical structure as demonstrated for other carmovirus p7-like proteins. Additionally, in vitro fractionation of p7B transcription/translation mixtures in the presence of ER-derived microsomal membranes strongly suggested that p7B is an integral membrane protein. Both characteristics of these two small MPs forming the double gene block (DGB) of MNSV are discussed in the context of the intra- and intercellular movement of carmovirus.

Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers

The Canary archipelago, located on the northwestern Atlantic coast of Africa, is comprised of seven islands aligned from east to west, plus seven minor islets. All the islands were formed by volcanic eruptions and their geological history is well documented providing a historical framework to study colonization events. The Canary Island pine ( Pinus canariensis C. Sm.), nowadays restricted to the westernmost Canary Islands (Gran Canaria, Tenerife, La Gomera, La Palma and El Hierro), is considered an old (Lower Cretaceous) relic from an ancient Mediterranean evolutionary centre. Twenty seven chloroplast haplotypes were found in Canary Island pine but only one of them was common to all populations. The distribution of haplotypic variation in P. canariensis suggested the colonization of western Canary Islands from a single continental source located close to the Mediterranean Basin. Present-day populations of Canary Island pine retain levels of genetic diversity equivalent to those found in Mediterranean continental pine species, Pinus pinaster and Pinus halepensis. A hierarchical analysis of variance (AMOVA) showed high differentiation among populations within islands (approximately 19%) but no differentiation among islands. Simple differentiation models such as isolation by distance or stepping-stone colonization from older to younger islands were rejected based on product-moment correlations between pairwise genetic distances and both geographic distances and population-age divergences. However, the distribution of cpSSR diversity within the islands of Tenerife and Gran Canaria pointed towards the importance of the role played by regional Pliocene and Quaternary volcanic activity and long-distance gene flow in shaping the population genetic structure of the Canary Island pine. Therefore, conservation strategies at the population level are strongly recommended for this species.

Loss of a novel tumor suppressor gene locus at chromosome 8p is associated with leukemic mantle cell lymphoma

Patients with mantle cell lymphoma (MCL) may present with either nodal or leukemic disease. The molecular determinants underlying this different biologic behavior are not known. This study compared the pattern of genetic abnormalities in patients with nodal and leukemic phases of MCL using comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) for specific gene loci. Although both leukemic and nodal MCL showed similar genomic patterns of losses (involving 6q, 11q22-q23, 13q14, and 17p13) and gains (affecting 3q and 8q), genomic loss of chromosome 8p occurred more frequently in patients with leukemic disease (79% versus 11%, P <.001). Subsequent CGH analysis confirmed the genomic loss of 8p21-p23 in 6 of 8 MCL cell lines. Interestingly, MYC gene amplification was restricted to cases with 8p deletion. These data indicate the presence of a novel tumor suppressor gene locus on 8p, whose deletion may be associated with leukemic dissemination and poor prognosis in patients with MCL.

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.

Analysis of the CDKN2A and CDK4 genes and HLA-DR and HLA-DQ alleles in two Spanish familial melanoma kindreds

Some confusion exists in the literature about which criteria should be used to define familial melanoma. This could explain the different reported frequencies of mutations in predisposing genes, mostly CDKN2A, in these patients. This study evaluated the human leucocyte antigen (HLA) class II genotype and the presence of mutations in CDKN2A and CDK4 genes in 2 families with very different clinical features. The family with a germinal mutation in exon 2 of CDKN2A (Gly101Try) presented the following clinical features: 3 first-degree affected members, 1 of whom had 2 melanomas, and all the melanomas appearing before 35 years of age. In contrast, the second family did not present any mutation in the studied genes and included 2 first-degree affected members diagnosed at over 45 years of age. Neither family showed an association with HLA genotype. Other genes are also involved in familial melanoma but, when the CDKN2A gene is affected, some clinical features seem to be uniform.

Diffuse large B-cell lymphoma: is morphologic subdivision useful in clinical management?

The diffuse large B-cell lymphoma category of the REAL classification encompasses different morphologic lymphoma subtypes in a single entity. The aim of this study is to determine the influence of the morphologic subdivision within this category with respect to clinical features and response to treatment. From January 1993 to October 1996, 132 patients were diagnosed de novo with diffuse large B-cell lymphoma in our institution. All cases were classified according to the REAL and the Updated Kiel classifications, and immunohistochemical study was performed in all of them. Sixty-three per cent of patients received chemotherapy with a curative approach. Of the 105 assessable patients, 80 cases (74%) were classified as centroblastic (CB) and 25 cases (26%) as immunoblastic (IB), according to the updated Kiel classification. These 2 subsets of lymphomas did not differ with respect to major clinical features and laboratory parameters. Both groups had a similar complete response rate with a uniform therapeutic approach and the overall 2-yr survival did not show statistical differences (49% in CB vs. 45% in IB). In conclusion, for clinicians, morphologic subdivision of the diffuse large B-cell lymphoma category into CB and IB subtypes has little clinical and prognostic significance.