Evolutionary implications of microplastics for soil biota

This is the author accepted manuscript. The final version is available from CSIRO Publishing via the DOI in this recordMicroplastic pollution is increasingly considered to be a factor of global change: in addition to aquatic ecosystems, this persistent contaminant is also found in terrestrial systems and soils. Microplastics have been chiefly examined in soils in terms of the presence and potential effects on soil biota. Given the persistence and widespread distribution of microplastics, it is also important to consider potential evolutionary implications of the presence of microplastics in soil; we offer such a perspective for soil microbiota. We discuss the range of selection pressures likely to act upon soil microbes, highlight approaches for the study of evolutionary responses to microplastics, and present the obstacles to be overcome. Pondering the evolutionary consequences of microplastics in soils can yield new insights into the effects of this group of pollutants, including establishing ‘true’ baselines in soil ecology, and understanding future responses of soil microbial populations and communities.MR acknowledges support from the ERC Advanced Grant ‘Gradual Change’ (694368). UK received funding from the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 751699

From Pig Breeding Environment to Subsequently Produced Pork: Comparative Analysis of Antibiotic Resistance Genes and Bacterial Community Composition

This is the author accepted manuscriptIt is well verified that pig farms are an important reservoir and supplier of antibiotic resistance genes (ARGs). However, little is known about the transmission of ARGs between the breeding environment and subsequently produced pork. This study was conducted to investigate if ARGs and associated host bacteria spread from the breeding environment onto the meat through the food production chain. We thus analyzed the occurrence and abundance of ARGs, as well as comparing both ARG and bacterial community compositions in farm soil, pig feces and pork samples from a large-scale pig farm located in Xiamen, People’s Republic of China. Among the 26 target ARGs, genes conferring resistance to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, macrolide, florfenicol, and tetracycline were observed at high frequency in both the pig breeding environment and pork. The prevalence of ARGs in pork was surprisingly consistent with breeding environments, especially between the pork and feces. The relative abundance of 10 representative ARGs conferring resistance to six classes of antibiotics ranged from 3.01 × 10−1 to 1.55 × 10−6 copies/16S rRNA copies. The ARGs conferring resistance to sulfanilamide (sulI and sulII), aminoglycoside (aadA), and tetracycline [tet(A) and tet(M)] were most highly abundant across most samples. Samples from feces and meat possessed a higher similarity in ARG compositions than samples from the farms soil. Enterobacteriaceae found on the meat samples were further identical with previously isolated multidrug-resistant bacteria from the same pig farm. Our results strongly indicate that ARGs can be potentially spreading from pig breeding environment to meat via the pork industry chain, such as feed supply, pig feeding and pork production.Medical Research Council (MRC)European Commissio

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

This is the author accepted manuscript.Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10−1–1.20 × 10−4 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGsEuropean Union's Horizon 202

Metamagnetic phase transition in the Ising plus Dzyaloshinskii-Moriya model

We study the 1D ferromagnetic Ising (spin-1/2) model with the Dzyaloshinskii-Moriya (DM) interaction. We analyze the low energy excitation spectrum and the ground state magnetic phase diagram using the Lanczos method. The DM interaction-dependency is calculated for the low-energy excitation spectrum, spiral order parameter and spin-spin correlation functions. We show that a metamagnetic quantum phase transition occurs between the ferromagnetic and spiral phases. The existence of the metamagnetic phase transition is confirmed, using the variational matrix product states approach.Comment: 5 pages, 6 figure

Cell proliferation is related to in vitro drug resistance in childhood acute leukaemia

0.05) with sensitivity to antimetabolites (cytarabine, mercaptopurine, thioguanine), L-asparaginase, teniposide, and vincristine. Similar results were found within subgroups of initial ALL (nonhyperdiploid and common/precursor-B-lineage ALL). In relapsed ALL and AML such correlations were not found. In conclusion, cell proliferation differs between leukaemia subgroups and increased proliferation is associated with increased in vitro sensitivity to several anticancer agents in initial ALL

Tensor network techniques for the computation of dynamical observables in 1D quantum spin systems

We analyze the recently developed folding algorithm [Phys. Rev. Lett. 102, 240603 (2009)] to simulate the dynamics of infinite quantum spin chains, and relate its performance to the kind of entanglement produced under the evolution of product states. We benchmark the accomplishments of this technique with respect to alternative strategies using Ising Hamiltonians with transverse and parallel fields, as well as XY models. Additionally, we evaluate its ability to find ground and thermal equilibrium states.Comment: 33 pages, 22 figure

Diagonal Ladders: A New Class of Models for Strongly Coupled Electron Systems

We introduce a class of models defined on ladders with a diagonal structure generated by $n_p$ plaquettes. The case $n_p=1$ corresponds to the necklace ladder and has remarkable properties which are studied using DMRG and recurrent variational ansatzes. The AF Heisenberg model on this ladder is equivalent to the alternating spin-1/spin-1/2 AFH chain which is known to have a ferrimagnetic ground state (GS). For doping 1/3 the GS is a fully doped (1,1) stripe with the holes located mostly along the principal diagonal while the minor diagonals are occupied by spin singlets. This state can be seen as a Mott insulator of localized Cooper pairs on the plaquettes. A physical picture of our results is provided by a $t_p-J_p$ model of plaquettes coupled diagonally with a hopping parameter $t_d$. In the limit $t_d \to \infty$ we recover the original $t-J$ model on the necklace ladder while for weak hopping parameter the model is easily solvable. The GS in the strong hopping regime is essentially an "on link" Gutzwiller projection of the weak hopping GS. We generalize the $t_p-J_p-t_d$ model to diagonal ladders with $n_p >1$ and the 2D square lattice. We use in our construction concepts familiar in Statistical Mechanics as medial graphs and Bratelli diagrams.Comment: REVTEX file, 22 pages (twocolumn), 35 figures inserted in text. 12 Table

The human equilibrative nucleoside transporter 1 mediates in vitro cytarabine sensitivity in childhood acute myeloid leukaemia

Cytarabine (ara-C) is the most effective agent for the treatment of acute myeloid leukaemia (AML). Aberrant expression of enzymes involved in the transport/metabolism of ara-C could explain drug resistance. We determined mRNA expression of these factors using quantitative-real-time-PCR in leukemic blasts from children diagnosed with de novo AML. Expression of the inactivating enzyme pyrimidine nucleotidase-I (PN-I) was 1.8-fold lower in FAB-M5 as compared to FAB-M1/2 (P=0.007). In vitro sensitivity to deoxynucleoside analogues was determined using the MTT-assay. Human equilibrative nucleoside transporter-1 (hENT1) mRNA expression and ara-C sensitivity were significantly correlated (rp=−0.46; P=0.001), with three-fold lower hENT1 mRNA levels in resistant patients (P=0.003). hENT1 mRNA expression also seemed to correlate inversely with the LC50 values of cladribine (rp=−0.30; P=0.04), decitabine (rp=−0.29; P=0.04) and gemcitabine (rp=−0.33; P=0.02). Deoxycytidine kinase (dCK) and cytidine deaminase (CDA) mRNA expression seemed to correlate with in vitro sensitivity to gemcitabine (rp=−0.31; P=0.03) and decitabine (rp=0.33; P=0.03), respectively. The dCK/PN-I ratio correlated inversely with LC50 values for gemcitabine (rp=−0.45, P=0.001) and the dCK/CDA ratio seemed to correlate with LC50 values for decitabine (rp=−0.29; 0.04). In conclusion, decreased expression of hENT1, which transports ara-C across the cell membrane, appears to be a major factor in ara-C resistance in childhood AML

Determination of caspase-3 activation fails to predict chemosensitivity in primary acute myeloid leukemia blasts

BACKGROUND: Ex-vivo chemosensitivity tests that measure cell death induction may predict treatment outcome and, therefore, represent a powerful instrument for clinical decision making in cancer therapy. Such tests are, however, work intensive and, in the case of the DiSC-assay, require at least four days. Induction of apoptosis is the mode of action of anticancer drugs and should, therefore, result in the induction of caspase activation in cells targeted by anticancer therapy. METHODS: To determine, whether caspase activation can predict the chemosensitivity, we investigated enzyme activation of caspase-3, a key executioner caspase and correlated these data with chemosensitivity profiles of acute myeloid leukemia (AML) blasts. RESULTS: There was, however, no correlation between the ex-vivo chemosensitivity assessed by measuring the overall rates of cell death by use of the DiSC-assay and caspase-3 activation. CONCLUSION: Thus, despite a significant reduction of duration of the assay from four to one day, induction of apoptosis evaluated by capase-3 activity does not seem to be a valid surrogate marker for chemosensitivity

Authenticity and drug resistance in a panel of acute lymphoblastic leukaemia cell lines

Cell lines are important models for drug resistance in acute lymphoblastic leukaemia (ALL), but are often criticised as being unrepresentative of primary disease. There are also doubts regarding the authenticity of many lines. We have characterised a panel of ALL cell lines for growth and drug resistance and compared data with that published for primary patient specimens. In contrast to the convention that cell lines are highly proliferative, those established in our laboratory grow at rates similar to estimates of leukaemic cells in vivo (doubling time 53–442 h). Authenticity was confirmed by genetic fingerprinting, which also demonstrated the potential stability of long-term cultures. In vitro glucocorticoid resistance correlated well with that measured ex vivo, but all lines were significantly more sensitive to vincristine than primary specimens. Sensitivity to methotrexate was inversely correlated to that of glucocorticoids and L-asparaginase, indicating possible reciprocity in resistance mechanisms. A cell line identified as highly methotrexate resistant (IC50 >8000-fold higher than other lines) was derived from a patient receiving escalating doses of the drug, indicating in vivo selection of resistance as a cause of relapse. Many of these lines are suitable as models to study naturally occurring resistance phenotypes in paediatric ALL