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Angioimmunoblastic T‐cell lymphoma (AITL) is a neoplastic proliferation of T follicular helper cells with clinical and histological presentations suggesting a role of antigenic drive in its development. Genetically, it is characterized by a stepwise acquisition of somatic mutations, with early mutations involving epigenetic regulators (TET2, DNMT3A) and occurring in haematopoietic stem cells, with subsequent changes involving signaling molecules (RHOA, VAV1, PLCG1, CD28) critical for T‐cell biology. To search for evidence of potential oncogenic cooperation between genetic changes and intrinsic T cell receptor (TCR) signaling, we investigated somatic mutations and T‐cell receptor β (TRB) rearrangement in 119 AITL, 11 peripheral T‐cell lymphomas with T follicular helper phenotype (PTCL‐TFH), and 25 PTCL‐NOS using Fluidigm polymerase chain reaction (PCR) and Illumina MiSeq sequencing. We confirmed frequent TET2, DNMT3A, and RHOA mutations in AITL (72%, 34%, 61%) and PTCL‐TFH (73%, 36%, 45%) and showed multiple TET2 mutations (2 or 3) in 57% of the involved AITL and PTCL‐TFH. Clonal TRB rearrangement was seen in 76 cases with multiple functional rearrangements (2–4) in 18 cases (24%). In selected cases, we confirmed bi‐clonal T‐cell populations and further demonstrated that these independent T‐cell populations harboured identical TET2 mutations by using BaseScope in situ hybridization, suggesting their derivation from a common TET2 mutant progenitor cell population. Furthermore, both T‐cell populations expressed CD4. Finally, in comparison with tonsillar TFH cells, both AITL and PTCL‐TFH showed a significant overrepresentation of several TRB variable family members, particularly TRBV19*01. Our findings suggest the presence of parallel neoplastic evolutions from a common TET2 mutant haematopoietic progenitor pool in AITL and PTCL‐TFH, albeit to be confirmed in a large series of cases. The biased TRBV usage in these lymphomas suggests that antigenic stimulation may play an important role in predilection of T cells to clonal expansion and malignant transformation. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

The normal colon epithelium is transformed into its neoplastic counterpart through a series of genetic alterations in driver genes including activating mutations in PIK3CA. Treatment often involves surgery followed by 5‐fluorouracil (5‐FU) based therapy, which has limited efficiency and serious side effects. We sought to determine whether fisetin, a dietary flavonoid, alone or in combination with 5‐FU affected tumorigenesis in the mammalian intestine. We first determined the effect of fisetin, 5‐FU or their combination on PIK3CA‐mutant and PIK3CA wild‐type colon cancer cells by assessing cell viability, colony formation, apoptosis and effects on PI3K/AKT/mTOR signaling. Treatment of PIK3CA‐mutant cells with fisetin and 5‐FU reduced the expression of PI3K, phosphorylation of AKT, mTOR, its target proteins, constituents of mTOR signaling complex and this treatment increased the phosphorylation of AMPKα. We then determined whether fisetin and 5‐FU together or singly affected tumorigenesis in ApcMin/+ mice that also express constitutively active PI3K in the distal small intestine and colon. Tumor incidence was markedly lower in fisetin‐treated FC13K1ApcMin/+ mice that also express constitutively active PI3K in distal small intestine and colon, as compared to control animals, indicating that fisetin is a strong preventive agent. In addition, the combination of fisetin and 5‐FU also reduced the total number of intestinal tumors. Fisetin could be used as a preventive agent plus an adjuvant with 5‐FU for the treatment of PIK3CA‐mutant colorectal cancer. What's new? Activating mutations in PIK3CA occur in 15 to 20% of advanced colorectal cancers (CRCs) and are associated with increased CRC‐specific mortality. Hence, therapeutic inhibition of PIK3CA is a potential strategy for improving outcome in some CRC patients. Here, the dietary flavonoid fisetin, an inhibitor of the PI3K/AKT and mTOR pathways, when given in combination with 5‐fluorouracil (5‐FU), was found to significantly enhance apoptosis in PIK3CA‐mutant CRC cells. Fisetin further prevented tumor formation in mice, and together with 5‐FU reduced the total number of intestinal tumors. The data suggest that fisetin can broaden opportunities for 5‐FU use against PIK3CA‐mutant CRC. [ABSTRACT FROM AUTHOR]

The functional potential of soil ecosystems can be predicted from the activity and abundance of the microbial community in relation to key soil properties. When describing microbial community dynamics, soil physicochemical properties have traditionally been used. The extent of correlations between properties, however, differs between studies, especially across larger spatial scales. In this research we analysed soil microbial biomass and substrate‐induced respiration of 156 samples from Irish grasslands. In addition to the standard physicochemical, soil type and land management variables, soil diagnostic properties were included to identify if these important soil–landscape genesis classes affected microbial biomass and respiration dynamics in Irish soil. Apart from physicochemical properties, soil drainage class was identified as having an important effect on microbial properties. In particular, biomass‐specific basal (qCO2) and substrate‐induced respiration (SIR:CFE) were explained best by the soil drainage. Poorly drained soil had smaller values of these respiration measures than well‐drained soil. We concluded that this resulted from different groups within the microbial community that could use readily available carbon sources, which suggests a change in microbial community dynamics associated with soil texture and periods of water stress. Overall, our results indicate that soil quality assessments should include both physicochemical properties and diagnostic classes, to provide a better understanding of the behaviour of soil microbial communities. Highlights: Assessing the effect of soil diagnostic features and properties on microbial biomass and respiration A soil biological survey from 156 grassland sites in Ireland Soil drainage class has an important effect on microbial properties Soil quality assessments should include both physicochemical properties and diagnostic classes [ABSTRACT FROM AUTHOR]

Both antigenic drive and genetic change play critical roles in the development of mucosa-associated lymphoid tissue (MALT) lymphoma, but neither alone is sufficient for malignant transformation, and lymphoma development critically depends on their cooperation. However, which of these different events concur and how they cooperate in MALT lymphomagenesis is totally unknown. To explore this, we investigated somatic mutations of 17 genes and immunoglobulin heavy chain variable region (IGHV) usage in 179 MALT lymphomas from various sites. We showed that: (1) there was a significant association between the biased usage of IGHV4-34 (binds to the carbohydrate I/i antigens) and inactivating mutation of TNFAIP3 [encoding a global negative regulator of the canonical nuclear factor-κB (NF-κB) pathway] in ocular adnexal MALT lymphoma; (2) IGHV1-69 was significantly overrepresented (54%) in MALT lymphoma of the salivary gland, but was not associated with mutation in any of the 17 genes investigated; and (3) MALT lymphoma lacked mutations that are frequently seen in other B-cell lymphomas characterized by constitutive NF-κB activities, including mutations in CD79B, CARD11, MYD88, TNFRSF11A, and TRAF3. Our findings show, for the first time, a significant association between biased usage of autoreactive IGHV and somatic mutation of NF-κB regulators in MALT lymphoma, arguing for their cooperation in sustaining chronic B-cell receptor signalling and driving oncogenesis in lymphoma development. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: A proportion of MYC translocation positive diffuse large B‐cell lymphomas (DLBCL) harbour a BCL2 and/or BCL6 translocation, known as double‐hit DLBCL, and are clinically aggressive. It is unknown whether there are other genetic abnormalities that cooperate with MYC translocation and form double‐hit DLBCL, and whether there is a difference in clinical outcome between the double‐hit DLBCL and those with an isolated MYC translocation. We investigated TP53 gene mutations along with BCL2 and BCL6 translocations in a total of 234 cases of DLBCL, including 81 with MYC translocation. TP53 mutations were investigated by PCR and sequencing, while BCL2 and BCL6 translocation was studied by interphase fluorescence in situ hybridization. The majority of MYC translocation positive DLBCLs (60/81 = 74%) had at least one additional genetic hit. In MYC translocation positive DLBCL treated by R‐CHOP (n = 67), TP53 mutation and BCL2, but not BCL6 translocation had an adverse effect on patient overall survival. In comparison with DLBCL with an isolated MYC translocation, cases with MYC/TP53 double‐hits had the worst overall survival, followed by those with MYC/BCL2 double‐hits. In MYC translocation negative DLBCL treated by R‐CHOP (n = 101), TP53 mutation, BCL2 and BCL6 translocation had no impact on patient survival. The prognosis of MYC translocation positive DLBCL critically depends on the second hit, with TP53 mutations and BCL2 translocation contributing to an adverse prognosis. It is pivotal to investigate both TP53 mutations and BCL2 translocations in MYC translocation positive DLBCL, and to distinguish double‐hit DLBCLs from those with an isolated MYC translocation. [ABSTRACT FROM AUTHOR]

Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8-fold to 33-fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P-type ATPases and thioredoxin transcripts were more abundant in the phenanthrene-amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further. [ABSTRACT FROM AUTHOR]

A bivalent dynamic covalent chemistry (DCC) system has been designed to selectively target members of the homodimeric glutathione- S-transferase (GST) enzyme family. The dynamic covalent libraries (DCLs) use aniline-catalysed acylhydrazone exchange between bivalent hydrazides and glutathione-conjugated aldehydes and the bis-hydrazides act as linkers to bridge between each glutathione binding site. The resultant DCLs were found to be compatible and highly responsive to templating with different GST isozymes, with the best results coming from the M and Schistosoma japonicum (Sj) class of GSTs, targets in cancer and tropical disease, respectively. The approach yielded compounds with selective, nanomolar affinity ( Ki=61 n M for mGSTM1-1) and demonstrates that DCC can be used to simultaneously interrogate binding sites on different subunits of a dimeric protein. [ABSTRACT FROM AUTHOR]

Agricultural improvement of seminatural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming) on ammonia-oxidising bacterial (AOB) communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaris and L. perenne) were planted in microcosms, and lime, nitrogen (NH4NO3), or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP) of the amoA gene. AOB community structure was largely altered by NH4NO3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure. [ABSTRACT FROM AUTHOR]

The composition of baled silage frequently differs from that of comparable conventional silage. A factorial experiment was conducted with three wilting treatments (0, 24 or 48 h) × three ensiling systems [unchopped grass in bales, unchopped grass in laboratory silos (LS), precision-chopped grass in LS] × six stages of ensiling to (i) confirm that the fermentation of unchopped grass in LS could be used as an adequate model for baled silage fermentation, (ii) quantify the differences between baled silage and silage made from precision-chopped herbage across a range of dry-matter contents and (c) quantify the fermentation dynamics within the various treatments. The onset of fermentation as evidenced by the accumulation of fermentation products and the decline in pH were slower ( P < 0·05) in baled silage compared with silage made from precision-chopped herbage. Furthermore the pH ( P < 0·001) and overall concentration of fermentation acids ( P < 0·01) were lower while ammonia-N concentration was generally higher in baled silage, making it more conducive to the activities of Clostridia, Enterobacteria and yeast. Numbers of Enterobacteria were higher ( P < 0·001) in baled silage in the early stages of ensilage and persisted in baled silage at the end of the storage period. The implications of a slower onset of fermentation in baled herbage are greater in farm practice, as the fermentation would be further restricted by a more extensive wilting of the herbage prior to ensiling. [ABSTRACT FROM AUTHOR]

ribosort is a computer package for convenient editing of automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) data. It is designed to eliminate the labourious task of manually classifying community fingerprints in microbial ecology studies. This program automatically assigns detected fragments and their respective relative abundances to appropriate ribotypes. It permits simultaneous sorting of multiple profiles and facilitates direct workflow from TRFLP and ARISA output through to community analyses.ribosort also provides several options to merge repeat profiles of a sample into a single composite profile. By creating a ‘ribotypes by samples’ matrix ready for statistical analyses, use of the package saves time and simplifies the preparation of DNA fingerprint data sets for statistical analysis. In addition, ribosort performs exploratory analysis on the data by creating multidimensional scaling plots that compare the similarity of sample profiles using the statistical softwarer. [ABSTRACT FROM AUTHOR]

The chemical composition of baled silage frequently differs from that of comparable conventional silage. The extents of wilting, chopping, compaction and air infiltration potentially contribute to these differences in conservation characteristics. An experiment was organized in a 3 (0, 24 or 48-h wilting to influence herbage dry-matter content) × 2 (unchopped or chopped) × 2 (with or without compaction) × 2 (with or without air infiltration) factorial arrangement of treatments, to elucidate the relative effects of these factors on the conservation characteristics of ensiled grass. Dry-matter content of herbage and infiltration of air had a greater effect on silage conservation characteristics than chopping and compaction. The main interactions were between wilting and air infiltration, wilting and compaction, and compaction and air infiltration. Air infiltration stimulated a secondary fermentation in the unwilted herbage, reflected in a large increase ( P < 0·001) in clostridial activity. As wilting progressed, air infiltration facilitated yeast respiration of water-soluble carbohydrates (WSC) and resulted in an increase ( P < 0·001) in in-silo fresh-weight losses. Compaction reduced ( P < 0·05) silage pore space and, as a result, the extent to which air could penetrate the silage mass. Compaction of the wilted herbage restricted respiration and was reflected in increased ( P < 0·05) concentrations of WSC and in a reduction ( P < 0·001) in fresh-weight loss. The rapid achievement and maintenance of adequately anaerobic conditions is the primary requirement for baled silage. This study showed that failure to achieve this will lead to progressively greater losses, especially with drier herbage. [ABSTRACT FROM AUTHOR]

This laboratory study of a variably mineralized and hydrothermally altered granite outcrop investigated the influences of rock-surface chemistry and heavy metal content on resident bacterial populations. Results indicated that elevated heavy metal concentrations had a profound impact on bacterial community structure, with strong relationships found between certain ribotypes and particular chemical/heavy metal elements. Automated ribosomal intergenic sequence analysis (ARISA) was used to assess the nature and extent of bacterial diversity, and this was combined with chemical analysis and multivariate statistics to identify the main geochemical factors influencing bacterial community structure. A randomization test revealed significant changes in bacterial structure between samples, while canonical correspondence analysis (CCA) related each individual ARISA profile to linear combinations of the chemical variables (mineralogy, major element and heavy metal concentrations) revealing the geochemical factors that correlated with changes in the ARISA data. anova was performed to further explore interactions between individual ribotypes and chemical/heavy metal composition, and revealed that a high proportion of ribotypes correlated significantly with heavy metals. [ABSTRACT FROM AUTHOR]

A microcosm-based approach was used to study impacts of plant and chemical factors on the fungal community structure of an upland acidic grassland soil. Seven plant species typical of both unimproved and fertilized grasslands were either left unamended or treated with lime, nitrogen or lime plus nitrogen. Fungal community structure was assessed by a molecular approach, fungal automated ribosomal intergenic spacer analysis (FARISA), while fungal biomass was estimated by measuring soil ergosterol content. Addition of nitrogen (with or without lime) had the largest effect, decreasing soil pH, fungal biomass and fungal ribotype number, but there was little corresponding change in fungal community structure. Although different plant species were associated with some changes in fungal biomass, this did not result in significant differences in fungal community structure between plant species. Addition of lime alone caused no changes in fungal biomass, ribotype number or community structure. Overall, fungal community structure appeared to be more significantly affected through interactions between plant species and chemical treatments, as opposed to being directly affected by changes in individual improvement factors. These results were in contrast to those found for the bacterial communities of the same soils, which changed substantially in response to chemical (lime and nitrogen) additions. [ABSTRACT FROM AUTHOR]

A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved ( Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved ( Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects. [ABSTRACT FROM AUTHOR]

The Catch Up Programme is a literacy intervention designed for children who are behind with reading at the start of Year 3 (7 to 8 year-olds). This paper describes pilot research that informed the project in its early stages of development, and the findings should therefore be treated with caution. The reading progress of a sample of 74 Catch Up pupils from 15 schools in three local education authorities was measured. This showed a considerable increase in pupils’ reading ages across a 10 week period. A smaller experimental study was also carried out in nine Oxfordshire schools (48 pupils) to compare a Catch Up sub-sample with a Matched Time group and a Control group. Findings showed that the Catch Up pupils made considerably more progress during the same period than both the other groups. [ABSTRACT FROM AUTHOR]

A stereological analysis of the response of cellular characteristics of hyphae of the marine hyphomycete Dendryphiella salina to salinity is presented. Analyses of volume fractions, compartmental volumes, membrane surface densities and membrane areas have been made. A major finding has been that the wall forms 40% of the compartment volume. Total hyphal compartment volume was maximal at 200 mM NaCl at 109 μm3 with compartments increasing in width and decreasing in length with salinity. Maximal protoplasmic and cytoplasmic volumes were also found at 200 mM. Electron microscopy demonstrated three different vacuolar types differentiated by their staining characteristics. A light-staining vacuolar type increased in total volume from 4.5 to 12.2 μm3 from 0 to 1 M NaCl. Data are considered not only in terms of hyphal anatomical characteristics but also in terms of those physiological processes occuring in D. salina which allow it to grow in saline media. [ABSTRACT FROM AUTHOR]

Rates of ion transport and transpiration were measured during the day and night in whole seedlings of Suaeda maritima growing over a range of salinities, in order to calculate concentrations of sodium and potassium in the xylem during these periods. Mean sodium concentration in the xylem was maximal at 56 mol m-3 Na with an external salinity of 200 mol m-3 NaCl. The sodium concentration in the xylem was greater in the dark than in the light at all external salinities investigated. Comparison of the external sodium with that in the xylem indicated that sodium was more strongly excluded from the transpiration stream as salinity increased. The mean concentration of potassium in the xylem declined as external NaCl concentration increased, although selectivity for potassium increased at higher salinities. Results are discussed in relation to osmotic adjustment in S. maritima. [ABSTRACT FROM AUTHOR]

Phosphate uptake as a function of external medium concentration has been determined for mycelium grown in the laboratory, segments of cords collected from the field and cords in the field for a range of wood-decay basidiomycetes. Hofstee plots in all cases can be interpreted as indicating the presence of two uptake systems. Uptake of phosphate by mycelium is reduced by increasing the concentration of phosphate in the growth medium from 10 μM to 10 mM. The major portion absorbed by cords in the field remains within the segment exposed to radioactive solution, suggesting conversion of the phosphate to an immobile form unavailable for translocation. [ABSTRACT FROM AUTHOR]

Although successful new product development practices often require joint efforts of professionals from various departments, all too often these professionals are trained as specialists with little exposure to other functional viewpoints. Colin Clipson describes the results of an educational initiative designed to bring together selected technical, business and design students enrolled in classes at The University of Michigan. Members of various student teams quickly ascertained a need to overcome language and cultural barriers in order to develop product recommendations for sponsoring firms. The results of this educational experiment have implications for current educational programs as long as improved innovation management is seen as a desirable social goal. INSET: BIOGRAPHICAL SKETCHES. [ABSTRACT FROM AUTHOR]

Catalytic antibodies showing carbamatase activity have significant potential in antibody-directed prodrug therapy against tumours. The Fab fragment of an IgG1 mouse monoclonal carbamatase catalytic antibody JC1 raised against a transition-state analogue, ethyl N-(3,5-dicarboxyphenyl)-P-[N-[5'-(2",5"-dioxo-1"-pyrrolidinyl)oxy-1',5'-dioxopentyl]-4-aminophenylmethyl]phosphonamidate, was obtained by digestion of the whole antibody with papain and was purified by two-step ion-exchange chromatography. Using hanging-drop vapour-diffusion crystallization techniques, three different crystal forms of the Fab fragment were obtained in the presence and absence of the transition-state analogue. All crystals diffract X-rays to between 3.5 and 3.2 Å resolution. The two crystal forms grown in the presence of the transition-state analogue contain up to four or eight copies of the Fab in the asymmetric unit and diffract to 3.5 and 3.2 Å, respectively. The crystal of the Fab alone is most likely to contain only two copies of the Fab in the asymmetric unit and diffracts to beyond 3.5 Å. Determination of the structure will provide insights into the active-site arrangement of this antibody and will help to increase our understanding of the molecular mechanisms by which the immune system can evolve catalytic function. [ABSTRACT FROM AUTHOR]