Characterization of ash derived from combustion of paper mill waste sludge: Comparison with municipal solid waste incinerator ash

Fly ash derived from incineration of Malaysian paper mill waste sludge (PMWS) was physically and chemically characterized in order to determine its potential toxicity as well as its application as cement replacement material. The results were compared with results obtained from similar characterization on Malaysian municipal solid waste incineration (MSWI) bottom ash. Principal analyses conducted include particle size distribution, elemental analysis, toxicity characteristic leaching procedure (TCLP) as well as thermogravimetric, x-ray diffractometry and FTIR analyses. TCLP result indicated that both the PMWS and MSWI ashes should not be classified as hazardous wastes in terms of heavy metal leachability, since leachable copper, cadmium, lead and nickel concentrations were detected below the stipulated leachability limits. Both ashes could be reused as cement replacement materials since both contained SiO2 which is one of the main building components in cement and concrete utilizations. Nonetheless, PMWS ash could be more suitable as a cement replacement material as compared to MSWI ash, as the former had significantly smaller particle size distribution and lower organic content

Magnetic Quantum Wire as a Spin Filter: An Exact Study

We propose that a magnetic quantum wire composed of magnetic and non-magnetic atomic sites can be used as a spin filter for a wide range of applied bias voltage. We adopt a simple tight-binding Hamiltonian to describe the model where the quantum wire is attached to two semi-infinite one-dimensional non-magnetic electrodes. Based on single particle Green's function formalism all the calculations are performed numerically which describe two-terminal conductance and current through the wire. Our exact results may be helpful in fabricating mesoscopic or nano-scale spin filter.Comment: 6 pages, 5 figure

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

DATA AVAILABILITY : Data will be made available on request.Please read abstract in the article.https://www.elsevier.com/locate/syapmhj2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

A Systematic Study on Energy Dependence of Quasi-Periodic Oscillation Frequency in GRS 1915+105

Systematically studying all the RXTE/PCA observations for GRS 1915+105 before November 2010, we have discovered three additional patterns in the relation between Quasi-Periodic Oscillation (QPO) frequency and photon energy, extending earlier outcomes reported by Qu et al. (2010). We have confirmed that as QPO frequency increases, the relation evolves from the negative correlation to positive one. The newly discovered patterns provide new constraints on the QPO models

Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts

BACKGROUND: Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms. RESULTS: The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors. CONCLUSIONS: P. ananatis has an ‘open’ pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts.This study was partially supported by the University of Pretoria Postdoctoral Fellowship Program, National Research Foundation (NRF), the Tree Protection Co-operative Programme (TPCP), the NRF/Dept. of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), and the THRIP support program of the Department of Trade and Industry, South Africa. IKT and PRJB were supported by a grant from the Scottish Government’s Rural and Environmental Science and Analytical Services (RESAS) division.http://www.biomedcentral.com/1471-2164/15/404am201

Mixta gen. nov., a new genus in the Erwiniaceae

The Erwiniaceae contain many species of agricultural and clinical importance. Although relationships among most of the genera in this family are relatively well resolved, the phylogenetic placement of several taxa remains ambiguous. In this study, we aimed to address these uncertainties by using a combination of phylogenetic and genomic approaches. Our multilocus sequence analysis and genome-based maximum-likelihood phylogenies revealed that the arsenate-reducing strain IMH and plant-associated strain ATCC 700886, both previously presumptively identified as members of Pantoea , represent novel species of Erwinia . Our data also showed that the taxonomy of Erwinia teleogrylli requires revision as it is clearly excluded from Erwinia and the other genera of the family. Most strikingly, however, five species of Pantoea formed a distinct clade within the Erwiniaceae , where it had a sister group relationship with the Pantoea + Tatumella  clade. By making use of gene content comparisons, this new clade is further predicted to encode a range of characters that it shares with or distinguishes it from related genera. We thus propose recognition of this clade as a distinct genus and suggest the name Mixta in reference to the diverse habitats from which its species were obtained, including plants, humans and food products. Accordingly, a description for Mixta gen. nov. is provided to accommodate the four species Mixta calida comb. nov., M. gaviniae comb. nov., M. intestinalis comb. nov. and M. theicola comb. nov., with M. calida as the type species for the genus.The DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) at the University of Pretoria for student funding.http://ijs.sgmjournals.org2019-04-01hj2018Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Practically delineating bacterial species with genealogical concordance

Bacterial species are commonly defined by applying a set of predetermined criteria, including DNA–DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation. However, we believe that these complexities and limitations can be easily circumvented by recognizing that bacterial species represent unique and exclusive assemblages of diversity. Within such a framework, methods that account for the population processes involved in species evolution are used to infer species boundaries. A method such as genealogical concordance analysis is well suited to delineate a putative species. The existence of the new taxon is then interrogated using an array of traditional and genome-based characters. By making use of taxa in the genera Pantoea, Paraburkholderia and Escherichia we demonstrate in a step-wise process how genealogical concordance can be used to delimit a bacterial species. Genetic, phenotypic and biological criteria were used to provide independent lines of evidence for the existence of that taxon. Our six-step approach to species recognition is straightforward and applicable to bacterial species especially in the post-genomic era, with increased availability of whole genome sequences. In fact, our results indicated that a combined genome-based comparative and evolutionary approach would be the preferred alternative for delineating coherent bacterial taxa.The South African National Research Foundation (NRF) and the Department of Science and Technology for funding through their Center of Excellence programme.http://link.springer.com/journal/104822018-10-30hj2017Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant Patholog

Os sistemas agroflorestais como alternativa de sustentabilidade em ecossistemas de várzea no Amazonas.

Os sistemas agroflorestais (SAFs) representam uma alternativa agroecológica de produção, sob regime sustentável, para os agricultores familiares na várzea dos Rios Solimões/Amazonas, principalmente no que se refere ao manejo florestal, à diversidade de produtos e à geração de renda. Diante disso, o objetivo deste trabalho foi compreender as diferentes formas de apropriação e de manejo dos recursos naturais através dos SAFs, nos subsistemas roça, sítio e lagos, como componente para a sustentabilidade dos agricultores familiares da localidade Costa da Terra Nova, município do Careiro da Várzea, Amazonas. O método empregado foi o Estudo de Caso com aplicação de questionários, entrevistas e observação participante. A produção familiar na Costa da Terra Nova é representada pelos SAFs, constituído pelos os subsistemas: roça quintal e lago, que proporcionam produtos tanto para subsistência quanto para comercialização local, e estabelecendo a agricultura como fundamental atividade na localidade. O principal produto para comercialização é obtido das hortaliças cultivadas na época da vazante no subsistema roça nas comunidades São Francisco e Nossa Senhora da Conceição; e do extrativismo pesqueiro no subsistema lago, na época da cheia, principalmente na comunidade São José. A criação de animal se dá no subsistema sítio e é apenas para subsistência, sendo as aves e os suínos os principais animais domésticos criados nas três comunidades. Portanto os SAFs tradicionais, constituídos pelos subsistemas, roça, sitio e lago, são responsáveis pela sustentabilidade socioeconômica da localidade pesquisada, servindo, como alternativa agrícola melhor adaptada às condições locais das áreas de várzea na Amazônia

Draft genome sequences of the onion center rot Pathogen Pantoea ananatis PA4 and maize brown stalk rot Pathogen P. ananatis BD442

Pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts. Here, we present the genomes of two South African isolates, P. ananatis PA4, which causes center rot of onion, and BD442, isolated from brown stalk rot of maize.The University of Pretoria, the National Research Foundation (NRF), the Forestry and Agricultural Biotechnology Institute (FABI), the Tree Protection Cooperative Programme (TPCP), the NRF/Department of Science and Technology Centre of Excellence in tree Health Biotechnology (CTHB), and the THRIP support program of the Department of Trade and Industry, South Africa.http://genomea.asm.orgam201

Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis

Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.This study was partially supported by the University of Pretoria Postdoctoral Fellowship Fund, National Research Foundation (NRF), the Tree Protection Co-operative Programme (TPCP), the NRF/Dept. of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), and the THRIP support program of the Department of Trade and Industry, South Africa, the department of Life Sciences and Facility Management of ZHAW, the Swiss Federal Office for Agriculture (BLW Fire Blight Research – Achilles), and the Swiss Secretariat for Education and Research (SBF C07.0038).http://www.frontiersin.org/Microbiologyam2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog