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Abstract Adoptive T-cell immunotherapy holds great promise for the treatment of viral complications in immunocompromised patients resistant to standard anti-viral strategies. We present a retrospective analysis of 78 patients from 19 hospitals across Australia and New Zealand, treated over the last 15 years with “off-the-shelf” allogeneic T cells directed to a combination of Epstein–Barr virus (EBV), cytomegalovirus (CMV), BK polyomavirus (BKV), John Cunningham virus (JCV) and/or adenovirus (AdV) under the Australian Therapeutic Goods Administration’s Special Access Scheme. Most patients had severe post-transplant viral complications, including drug-resistant end-organ CMV disease, BKV-associated haemorrhagic cystitis and EBV-driven post-transplant lymphoproliferative disorder. Adoptive immunotherapy is well tolerated with few adverse effects. Importantly, 46/71 (65%) patients show definitive clinical improvement including reduction in viral load, clinical symptoms and complete resolution of end-organ disease. In addition, seven high-risk patients remain disease free. Based on this long-term encouraging clinical experience, we propose that a dedicated nationally funded centre for anti-viral cellular therapies should be considered to provide T cell therapies for critically ill patients for compassionate use.

Abstract Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

A simple, cheap and non-destructive technique is introduced for the collection of micro-arthropods in sensitive habitats, focussing on suspended soils (accumulations of humus and organic detritus in trees, elevated above soil level). These habitats contain distinctive communities of soil fauna, but in most European forests suspended soil volumes are so small and slow to regenerate that systematic collections can destroy much of the suspended soil resource in a woodland, requiring years to recover. Here I calibrate a non-destructive collection technique based on inserting a pad of inert material with a wide pore space, allowing the material to be colonised then removing the pad for Tullgren extraction. Standard domestic scouring pads are ideal for this purpose and extract quickly in high gradient extractors. This method has the potential to become a standard non-destructive collection technique for suspended soils as well as in other sensitive habitats such as caves. It is also a suitable platform for a wide variety of small-scale projects involving experimental manipulations.

Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs’ running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.

A 15-year-old male with a mesenteric desmoid tumor and underlying familial adenomatous polyposis presented 2 weeks after initiating sorafenib with severe abdominal pain and chills and was found to have an acute abdomen. Exploratory laparotomy revealed a necrotic, ruptured tumor with impending small bowel obstruction. The patient was later able to resume sorafenib and experienced sustained a radiographic response. It is possible that sorafenib toxicity contributed to tumor rupture yet later provided clinical benefit. Here we review the gastrointestinal complications that are associated with intra-abdominal desmoid tumors and their therapies.

miRNAs biomarkers are emerging as an essential part of clinical oncology. Their oncogenic and tumour suppressor properties playing a role in malignancy has generated interest in their potential for use in disease prognosis. While several studies on miRNA have been carried out across the globe, evaluating the clinical implications of miRNAs in cancer diagnosis and prognosis research has currently not been attempted. A study delineating the area of miRNA research, including the topics presently being focused on, the seminal papers in this field, and the direction of research interest, does not exist. This study aims to conduct a large-scale, global data analysis and bibliometric profiling analysis of studies to evaluate the research output of clinical implications of miRNAs in cancer diagnosis and prognosis listed in the SCOPUS database. A systematic search strategy was followed to identify and extract all relevant studies, subsequently analysed to generate a bibliometric map. SPSS software (version 27) was used to calculate bibliometric indicators or parameters for analysis, such as year and country of affiliation with leading authors, journals, and institutions. It is also used to analyse annual research outputs, including total citations and the number of times it has been cited with productive nations and H-index. The number of global research articles retrieved for miRNA-Cancer research over the study period 2003 to 2019 was 18,636. Between 2012 and 2019, the growth rate of global publications is six times (n = 15,959; 90.71 percent articles) that of 2003 to 2011. (2704; 9.29 per cent articles). China published the most publications in the field of miRNA in cancer (n = 7782; 41%), while the United States had the most citations (n = 327,538; 48%) during the time span. Of these journals, Oncotarget has the highest percentage of article publications. The journal Cancer Research had the most citations (n = 41,876), with 6.20 per cent (n = 41,876). This study revealed a wide variety of journals in which miRNA-Cancer research are published; these bibliometric parameters exhibit crucial clinical information on performance assessment of research productivity and quality of research output. Therefore, this study provides a helpful reference for clinical oncologists, cancer scientists, policy decision-makers and clinical data researchers.

Biosolids are the solid by-product of the wastewater treatment system. They are regularly applied to agricultural land in the UK to fertilize and increase crop yields, but they have been shown to contain high concentrations of microplastics. Here we sampled a selection of agricultural soils in the Southeast of England which had received or never received biosolid treatment. Sites were sampled on two occasions in the summer and winter. Microplastic (MP) numbers were high in both the biosolid treated fields (874 MP/kg) and the untreated fields (664 MP/kg) and a wide variety of polymers were found across sites. However, there was a lack of significant difference between treated and untreated soils. This suggests the influence of other microplastic sources e.g. agricultural plastic and general littering, and external conditions e.g. farm management and rainfall. Microplastic concentrations were higher in the summer suggesting that erosion, runoff, and wind transport may be removing microplastics from these systems. The dynamic nature of the agricultural soils may result in them becoming a vector for microplastics into the wider environment. The high variability in results seen here highlights the complexity of microplastic concentrations in heterogeneous agricultural soils. This study suggests that biosolids, whilst are likely a contributor, are not the sole source of microplastics in agricultural soils. Further research is required to determine source and sink dynamics in these systems. Understanding the sources of microplastic contamination in soils is imperative for future mitigation strategies to be effective.

Polydopamine (PDA) is a biocompatible cell-adhesive polymer with versatile applications in biomedical devices. Previous studies have shown that PDA coating could improve cell adhesion and differentiation of human mesenchymal stem cells (hMSCs). However, there is still a knowledge gap in the effect of PDA-mediated protein adsorption on the epigenetic status of MSCs. This work used gelatin-coated cell culture surfaces with and without PDA underlayer (Gel and PDA-Gel) to culture and differentiate primary human adipose-derived stem cells (hASCs). The properties of these two substrates were significantly different, which, in combination with a variation in extracellular matrix (ECM) protein bioactivity, regulated cell adhesion and migration. hASCs reduced focal adhesions by downregulating the expression of integrins such as αV, α1, α2, and β1 on the PDA-Gel compared to the Gel substrate. Interestingly, the ratio of H3K27me3 to H3K27me3+H3K4me3 was decreased, but this only occurred for upregulation of AGG and BMP4 genes during chondrogenic differentiation. This result implies that the PDA-Gel surface positively affects the chondrogenic, but not adipogenic and osteogenic, differentiation. In conclusion, for the first time, this study demonstrates the sequential effects of PDA coating on the biophysical property of adsorbed protein and then focal adhesions and differentiation of hMSCs through epigenetic regulation. This study sheds light on PDA-mediated mechanotransduction.

Angiopoietin-like proteins (ANGPTL) constitute a family of eight proteins (1–8) which play a pivotal role in the regulation of various pathophysiological processes. The current study sought to identify high-risk, “non-synonymous, single-nucleotide polymorphisms” (nsSNPs) in both ANGPTL3 and ANGPTL8 to evaluate the role that these nsSNPs play in various types of cancer. We retrieved a total of 301 nsSNPs from various databases; 79 of these candidates constitute high-risk nsSNPs. Moreover, we identified eleven high-risk nsSNPs that cause various types of cancer: seven candidates for ANGPTL3 (L57H, F295L, L309F, K329M, R332L, S348C, and G409R) and four candidates for ANGPTL8 (P23L, R85W, R138S, and E148D). Protein–protein interaction analysis revealed a strong association of ANGPTL proteins with several tumor-suppressor proteins such as ITGB3, ITGAV, and RASSF5. ‘Gene-expression profiling interactive analysis’ (GEPIA) showed that expression of ANGPTL3 is significantly downregulated in five cancers: sarcoma (SARC); cholangio carcinoma (CHOL); kidney chromophobe carcinoma (KICH); kidney renal clear cell carcinoma (KIRC); and kidney renal papillary cell carcinoma (KIRP). GEPIA also showed that expression of ANGPTL8 remains downregulated in three cancers: CHOL; glioblastoma (GBM); and breast invasive carcinoma (BRCA). Survival rate analysis indicated that both upregulation and downregulation of ANGPTL3 and ANGPTL8 leads to low survival rates in various types of cancer. Overall, the current study revealed that both ANGPTL3 and ANGPTL8 constitute potential prognostic biomarkers for cancer; moreover, nsSNPs in these proteins might lead to the progression of cancer. However, further in vivo investigation will be helpful to validate the role of these proteins in the biology of cancer.

Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.

Abstract Background Limiting treatment to those recommended by the American Academy of Orthopaedic Surgeon Clinical Practice Guidelines has been suggested to decrease costs by 45% in the year prior to total knee arthroplasty, but this only focuses on expenditures leading up to, but not including, the surgery and not the entire episode of care. We evaluated the treatment costs following knee osteoarthritis (OA) diagnosis and determined whether these are different for patients who use intra-articular hyaluronic acid (HA) and/or knee arthroplasty. Methods Claims data from a large commercial database containing de-identified data of more than 100 million patients with continuous coverage from 2012 to 2016 was used to evaluate the cumulative cost of care for over 2 million de-identified members with knee OA over a 4.5-year period between 2011 and 2015. Median cumulative costs were then stratified for patients with or without HA and/or knee arthroplasty. Results Knee OA treatment costs for 1,567,024 patients over the 4.5-year period was $6.60 billion (mean $4210/patient) as calculated by the authors. HA and knee arthroplasty accounted for 3.0 and 61.5% of the overall costs, respectively. For patients who underwent knee arthroplasty, a spike in median costs occurred sooner for patients without HA use (around the 5- to 6-month time point) compared to patients treated with HA (around the 16- to 17-month time point). Conclusions Non-arthroplasty therapies, as calculated by the authors, accounted for about one third of the costs in treating knee OA in our cohort. Although some have theorized that limiting the use of HA may reduce the costs of OA treatment, HA only comprised a small fraction (3%) of the overall costs. Among patients who underwent knee arthroplasty, those treated with HA experienced elevated costs from the surgery later than those without HA, which reflects their longer time to undergoing knee arthroplasty. The ability to delay or avoid knee arthroplasty altogether can have a substantial impact on the cost to the healthcare system.

Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.

With limited data comparing hematopoietic cell transplant outcomes between myeloablative total body irradiation (TBI) containing and non-TBI regimens in children with de novo acute myeloid leukemia, the aim of this study was to compare transplant-outcomes between these regimens. Cox regression models were used to compare transplant-outcomes after TBI and non-TBI regimens in 624 children transplanted between 2008 and 2016. Thirty two percent (n=199) received TBI regimens whereas 68% (n=425) received non-TBI regimens. Five-year non-relapse mortality was higher with TBI regimens (22% vs. 11%, p

Background: substantial increases in plastic production have resulted in plastics proliferating of in the environment, with subsequent seabed plastic deposition and ingestion by marine fauna. There is an urgent need to monitor mismanaged plastic waste from household consumption. Household expenditure survey analysis has quantified mismanaged plastic waste generated from household packaged (bottled or bagged) water consumption, but not from consumption of other products. Methods: to evaluate whether household expenditure surveys can quantify mismanaged waste from other widely consumed commodities, we quantify mismanaged plastic waste from the domestic consumption of cooking oil alongside packaged water in urban Greater Accra, Ghana, and all cities nationally in Kenya using two household expenditure surveys. Results: household survey-derived estimates indicate packaged water consumption generates considerably more plastic waste than oil packaging in Greater Accra, whereas oil packaging generates more plastic waste than packaged water in urban Kenya. Conclusion: by successfully transferring a survey analysis protocol from packaged water to cooking oil, we conclude that there is ample potential for expenditure surveys to be used internationally to quantify mismanaged plastic waste from households. However, uncertainties affecting mismanaged waste estimates need to be accounted for.

Abstract Background Intra-articular hyaluronic acid (IA-HA) is a common therapy used to treat knee pain and suppress knee inflammation in knee osteoarthritis (OA), typically prescribed in regimens ranging from a single injection to 5 weekly injections given once weekly. We conducted a systematic review to determine the efficacy of IA-HA, with subgroup analyses to explore the differences in knee pain and adverse events (AEs) across different dosing regimens. Methods We conducted a systematic search of the literature to identify studies evaluating IA-HA for the management of knee OA compared to IA-saline. Primary outcome measure was the mean knee pain score at 13 Weeks (3 months) or 26 weeks (6 months). Secondary outcome was the number of treatment-related AEs and treatment-related serious adverse events (SAEs). We evaluated differences in levels of pain and AEs/SAEs between dosing regimens compared to IA-Saline. Results Thirty articles were included. Overall, IA-HA injections were associated with less knee pain compared to IA-Saline injections for all dosing regimens. 2–4 injections of IA-HA vs. IA-Saline produced the largest effect size at both 3-months and 6-months (Standard mean difference [SMD] = −0.76; −0.98 to −0.53, 95% CI, P

In South Asia, south-west Sri Lanka alone represents the sole surviving perhumid region where Mixed Dipterocarp Forests (MDF) harbour a number of relict signature taxa providing evidence of ancient plant migration routes from Gondwana to perhumid Far Eastern Sunda land, at least partially via southern Laurasia. Palynological and phylogenetic evidence now confirm that the Malesian rain forest flora overwhelmingly immigrated from tropical Africa/Madagascar and South Asia along an ever-wet equatorial corridor sometime before the collision of the Indian Plate with the Southern Laurasian coast in middle Eocene (c. 45 Ma). This ever-wet climatic and geological history has led to the evolution of a characteristic species composition and dynamics within SW Sri Lanka’s rain forest communities, which exhibit remarkable patterns of species distribution and habitat specialization, and which parallel those of Far Eastern sister taxa. We here examine the patterns of floristic variation in each of three MDF sites using classification and ordination methods to analyse tree data collected in 62 random plots, each 0.25ha, along an altitudinal gradient. In addition, a 25 ha forest dynamics plot (FDP) was established in the Sinharaja World Heritage Site, within the CTFS-ForestGEO network that addresses issues related to community ecology and phylogenetics incorporating large-scale biogeographic patterns of major clades of both plants and animals. In the above studies, ecologically distinct floristic assemblages were revealed, i) among the three MDF sites as well as, ii) among the ridge-, slope-, and valley habitats within each forest site. In the FDP too, >80% of the 125 species, with individuals >1 cm dbh and >100 individuals per species, are significantly more associated with one or more of eight topographic habitat categories than in others. These results suggest that ecological ranges and dispersion of tree species in SW Sri Lanka is primarily mediated by soil water and nutrient levels in topographically different catenal habitats mirroring those in the Far East.Many of these species are threatened relict endemics, and their distribution patterns have important conservation implications. Their spatial distributional features provide useful criteria in site-species matching or environmental filtering in forest restoration efforts.

The majority of children undergoing Hematopoietic Stem cell Transplantation (HSCT) require conditioning therapy to make space and prevent rejection of the donor stem cells. The exception is certain children with Severe Combined immune deficiency, who have limited or no ability to reject the donor graft. Transplant conditioning is associated with significant morbidity and mortality from both direct toxic effects of chemotherapy as well as opportunistic infections associated with profound immunosuppression. The ultimate goal of transplant practice is to achieve sufficient engraftment of donor cells to correct the underlying disease with minimal short- and long-term toxicity to the recipient. Traditional combinations, such as busulfan and cyclophosphamide, achieve a high rate of full donor engraftment, but are associated with significant acute transplant-related-mortality and late effects such as infertility. Less “intensive” approaches, such as combinations of treosulfan or melphalan with fludarabine, are less toxic, but may be associated with rejection or low level chimerism requiring the need for re-transplantation. The major benefit of these novel approaches, however, which we hope will be realized in the decades to come, may be the preservation of fertility. Future approaches look to replace chemotherapy with non-toxic antibody conditioning. The lessons learnt in refining conditioning for HSCT are likely to be equally applicable to gene therapy protocols for the same diseases.

Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from six different genotypes: wheat, wheat–rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologs is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Further studies in wheat and other polyploid species will be required to reveal whether these observations are specific to wheat meiosis.

Wild relatives provide an important source of useful traits in wheat breeding. Wheat and wild relative hybrids have been widely used in breeding programs to introduce such traits into wheat. However, successful introgression is limited by the low frequency of homoeologous crossover (CO) between wheat and wild relative chromosomes. Hybrids between wheat carrying a 70 Mb deletion on chromosome 5B (ph1b) and wild relatives, have been exploited to increase the level of homoeologous CO, allowing chromosome exchange between their chromosomes. In ph1b-rye hybrids, CO number increases from a mean of 1 CO to 7 COs per cell. CO number can be further increased up to a mean of 12 COs per cell in these ph1b hybrids by treating the plants with Hoagland solution. More recently, it was shown that the major meiotic crossover gene ZIP4 on chromosome 5B (TaZIP4-B2) within the 70 Mb deletion, was responsible for the restriction of homoeologous COs in wheat-wild relative hybrids, confirming the ph1b phenotype as a complete Tazip4-B2 deletion mutant (Tazip4-B2 ph1b). In this study, we have identified the particular Hoagland solution constituent responsible for the increased chiasma frequency in Tazip4-B2 ph1b mutant-rye hybrids and extended the analysis to Tazip4-B2 TILLING and CRISPR mutant-Ae variabilis hybrids. Chiasma frequency at meiotic metaphase I, in the absence of each Hoagland solution macronutrient (NH4 H2PO4, KNO3, Ca (NO3)2·4H2O or Mg SO4·7H2O) was analyzed. A significant decrease in homoeologous CO frequency was observed when the Mg2+ ion was absent. A significant increase of homoeologous CO frequency was observed in all analyzed hybrids, when plants were irrigated with a 1 mM Mg2+ solution. These observations suggest a role for magnesium supplementation in improving the success of genetic material introgression from wild relatives into wheat.

Stress cardiomyopathy (SCM) is a unique cardiac disorder that more often occurs in women. SCM presents in a similar fashion as acute myocardial infarction (AMI), with chest pain, ECG changes, and congestive heart failure. The primary distinguishing feature is the absence of thrombotic coronary occlusion in SCM. How this reduction in cardiac function occurs in the absence of coronary occlusion remains unknown. Therefore, we tested the hypothesis that a targeted proteomic comparison of patients with acute SCM and AMI might identify relevant mechanistic differences. Blood was drawn in normal controls (n = 6), women with AMI (n = 12), or women with acute SCM (n = 15). Two-week follow-up samples were available in AMI (n = 4) and SCM patients (n = 11). Relative concentrations of 1,310 serum proteins were measured in each of the 48 samples using the SOMAscan assay. Women with AMI had greater myocyte necrosis, as reflected by a higher peak troponin I concentration (AMI 32.03 ± 29.46 vs. SCM 2.68 ± 2.6 ng/ml, p 1; q

The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

Two studies were undertaken using inert fibrous pads as a non-destructive approach to sampling microarthropod communities on the bark of broadleaved trees. In the first study, pads were suspended at heights varying from 0–5m elevation in broad leaved trees in London to determine the vertical distribution of Collembola. In the second study, pads were attached to bark with excluders restricting arthropod ingress either from above or below to check directionality of movement. Collembola were found up to 5 m up trees, with clear vertical zonation in density and species composition. Willowsia platani (Nicolet, 1841) was the most heightassociated species, but was only collected in summer. The second study suggested that Willowsia platani mainly climbed upwards, but none of the results were statistically significant.

We report early results from a project to accumulate COI barcodes from UK Collembola to confirm taxonomy and explore their status at an international level. We validated COI sequences for 48 species of Collembola, ranging from 335–670 bp. Of these, seventeen species matched public sequences of the same name, six species were identifiable but the molecular identity disagreed with the morphological identification, and twenty five species gave no reliable match. The successful matches included accurate matches to BINs from countries far from the UK, including Canada, South Africa and Russia. We suggest that, in many cases, these may have been accidentally transported with horticultural materials.

Chromatin-binding proteins play a crucial role in chromatin structure and gene expression. Direct binding of chromatin proteins both maintains and regulates transcriptional states. It is therefore important to study the binding properties of these proteins in vivo within the natural environment of the nucleus. Photobleaching, photoactivation and photoconversion (photoswitching) can provide a non-invasive experimental approach to study dynamic properties of living cells and organisms. We used photoactivation to determine exchange dynamics of histone H2B in plant stem cells of the root (Rosa et al., 2014). The stem cells of the root are located in the middle of the tissue, which made it impossible to carry out photoactivation of sufficiently small and well-defined sub-cellular regions with conventional laser illumination in the confocal microscope, mainly because scattering and refraction effects within the root tissue dispersed the focal spot and caused photoactivation of too large a region. We therefore used 2-photon activation, which has much better inherent resolution of the illuminated region. This is because the activation depends on simultaneous absorption of two or more photons, which in turns depends on the square (or higher power) of the intensity-a much sharper peak. In this protocol we will describe the experimental procedure to perform two-photon photoactivation experiments and the corresponding image analysis. This protocol can be used for nuclear proteins tagged with photoactivable GFP (PA-GFP) expressed in root tissues.

The aim of this article is to review the consequences of advances in molecular genetics for researchers of Collembola biogeography. Gene sequence data have generally confirmed existing high-level taxonomy, but complicated species-level taxonomy by uncovering extensive cryptic diversity. Several commonly recorded European Collembola ‘species’ have proved to be complexes of closely related taxa, reducing the value of many older (pre-1990) records to near-zero. It seems likely that many more cryptic species of Collembola remain to be uncovered, even in well studied areas in Europe. The inevitable proliferation of genetically defined ‘species’ will be awkward to integrate into existing databases, which are based on morphospecies. Eventually the results will transform our understanding of Collembola biodiversity, since molecular data contain greatly more information, notably estimates of divergence times. In ancient and relatively pristine ecosystems (e.g. Antarctica, oceanic islands) genetic data can be used to show both extreme isolation of endemics (pre-dating ice ages) and the arrival of European/North American invasives. Collembola from the genus Lepidocyrtus in several very different areas show patterns of intra-specific divergence dated in the millions of years, a pattern likely to be repeated in other genera. An exciting approach to speeding up these genetic studies comes from the advent of high throughput pyrosequencing technology, which already allows mass identification of mixed life forms from clustering then sequencing DNA amplicons (‘metabarcoding’), raising the possibility of automating the identification of bulked soil faunal extracts. A trial of this using soil extracts from Tenerife identified an apparent endemic Friesea species, along with mainland invasive species. These next generation techniques rely on Molecular Taxonomic units (MOTUs), identified purely by sequence analysis (usually of mtCOI), so vigilance will always be needed against the spurious identification of sequence artefacts such as nuclear copies of mitochondrial genes (NUMTS). A new risk of relying simply on high throughput sequence analysis is the possibility of inventing non-existent ‘species’ from irrelevant DNA.

Collembola are well known to occur in soils and litters, as well as inter-tidal habitats, caves and tree canopies, but are not normally thought of as members of the groundwater community. Here we report on studies of the colonisation of gravels in the hyporheic zone under the river Skirfare, a karstic river in Yorkshire. Unexpectedly, flooding during the second experimental run allowed a comparison between low- and high-flow conditions. Five species of Collembola were found in permanently saturated habitats 30 cm below a river bed. One of these species, Hymenaphorura nova, is the first record of its genus in the UK, and appears to be a groundwater specialist. The other named species (Anurida granaria and Mucrosomia (= Cryptopygus) garretti), Deuteraphorura cebennaria (= D. inermis) have wider distributions but are often associated with mines and caves; D. cebennaria is known to occur in the Scoska cave, whose waters feed into the Skirfare shortly upstream of the experimental location. There was some evidence of differences between dates (more first instars and fewer adults after the flood) and between sediments (adults found mainly in coarser materials, first instars in finer sediments), but the statistical significance was weak (0.1 > p > 0.05). The distribution of animals was not clumped (as is typical for Collembola) but followed a Poisson distribution, suggesting it to be primarily random. These results agree with previous authors who suggested that several species of Collembola may live for prolonged periods wholly submerged. The random distribution and their water-repellent cuticles suggest a model of eggs or early instars being washed underground following groundwater, surviving underwater for prolonged periods. We do not have evidence that these Collembola are able to complete their life cycle underwater.

It is often desirable to collect Collembola from remote locations where the usual extraction systems based on thermal gradients are simply impossible, e.g. for lack of adequate energy supplies. Winkler funnels are often used in such situations as zero-energy extractors of soil arthropods, but have not been calibrated for the collection of Collembola. Here we report a series of trials comparing densities and species-richness of Collembola in leaf moulds using parallel Tullgren and Winkler extractions. Each litter was tested separately with the Winkler funnel environment at low and at high humidity. Our results showed that Winkler funnels are a poor substitute for Tullgrens, under-recording species by 30% and densities by 78%, suggesting that the basic Winkler funnel method is not suitable for objective quantitative Collembola population studies.

BACKGROUND: Chromatin organizational and topological plasticity, and its functions in gene expression regulation, have been strongly revealed by the analysis of nucleolar dominance in hybrids and polyploids where one parental set of ribosomal RNA (rDNA) genes that are clustered in nucleolar organizing regions (NORs), is rendered silent by epigenetic pathways and heterochromatization. However, information on the behaviour of dominant NORs is very sparse and needed for an integrative knowledge of differential gene transcription levels and chromatin specific domain interactions. METHODOLOGY/PRINCIPAL FINDINGS: Using molecular and cytological approaches in a wheat-rye addition line (wheat genome plus the rye nucleolar chromosome pair 1R), we investigated transcriptional activity and chromatin topology of the wheat dominant NORs in a nucleolar dominance situation. Herein we report dominant NORs up-regulation in the addition line through quantitative real-time PCR and silver-staining technique. Accompanying this modification in wheat rDNA trascription level, we also disclose that perinucleolar knobs of ribosomal chromatin are almost transcriptionally silent due to the residual detection of BrUTP incorporation in these domains, contrary to the marked labelling of intranucleolar condensed rDNA. Further, by comparative confocal analysis of nuclei probed to wheat and rye NORs, we found that in the wheat-rye addition line there is a significant decrease in the number of wheat-origin perinucleolar rDNA knobs, corresponding to a diminution of the rDNA heterochromatic fraction of the dominant (wheat) NORs. CONCLUSIONS/SIGNIFICANCE: We demonstrate that inter-specific interactions leading to wheat-origin NOR dominance results not only on the silencing of rye origin NOR loci, but dominant NORs are also modified in their transcriptional activity and interphase organization. The results show a cross-talk between wheat and rye NORs, mediated by ribosomal chromatin dynamics, revealing a conceptual shift from differential amphiplasty to 'mutual amphiplasty' in the nucleolar dominance process.