Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A.

Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a common event in cancer. Whether chromothripsis might constitute an actionable molecular event amenable to therapeutic targeting remains an open question. We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ∼25% of patients ('chr21amp'). We report that chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. The chr21amp event is highly clonal and present throughout the hematopoietic hierarchy. DYRK1A , a serine threonine kinase and transcription factor, is the only gene in the 2.7Mb minimally amplified region which showed both increased expression and chromatin accessibility compared to non-chr21amp BP-MPN controls. We demonstrate that DYRK1A is a central node at the nexus of multiple cellular functions critical for BP-MPN development, including DNA repair, STAT signalling and BCL2 overexpression. DYRK1A is essential for BP-MPN cell proliferation in vitro and in vivo , and DYRK1A inhibition synergises with BCL2 targeting to induce BP-MPN cell apoptosis. Collectively, these findings define the chr21amp event as a prognostic biomarker in BP-MPN and link chromothripsis to a druggable target.

Insecticidal Activity of Jatropha Extracts Against the Azalea Lace Bug, Stephanitis pyrioides (Hemiptera: Tingidae).

We assessed bioactivity of ethanolic extracts from 35 species of Jatropha L. against an ornamental plant pest, the azalea lace bug, Stephanitis pyrioides (Scott). Jatropha extracts were prepared by air-drying stem, root, or whole plant material, grinding the tissue into a fine powder, adding 70% ethanol, and then vacuum filtering the contents. Emulsions included the extract diluted to the desired concentration in de-ionized water and 10% dimethyl sulfoxide (DMSO). Treatments involved pipetting 20 µl of emulsion onto three adult lace bugs in each well of a 96-well microtiter plate. Treated wells served as replicates for each of six extract concentrations and were arranged according to a RCBD. Extracts of Jatropha clavuligera Müll. Arg. and J. ribifolia (Pohl) Ballion from 0.06 to 0.50% were the most acutely bioactive with bug mortality exceeding that of the positive control - azadirachtin, a terpenoid and chief active ingredient in neem oil. At 1.00%, extracts of J. clavuligera, J. ribifolia and azadirachtin killed 100% of bugs within 3 hr. Jatropha clavuligera induced the lowest LC50 and ranked first in insecticidal potency based on ≥98% of bugs dying within 3 hr. Extracts of J. curcas L., J. gossypiifolia L., J. excisa Griseb, and azadirachtin were equally bioactive; although after 3 hr, the three Jatropha species killed bugs faster. When compared with DMSO, all extract emulsions were bioactive against adult bugs. Thus, active ingredients in a new biopesticide could be sourced from the stem, root, or whole plant extracts of at least five Jatropha species.

Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity.

Barrett's esophagus is a pre-malignant lesion that can progress to esophageal adenocarcinoma. We perform a multi-omic analysis of pre-cancer samples from 146 patients with a range of outcomes, comprising 642 person years of follow-up. Whole genome sequencing reveals complex structural variants and LINE-1 retrotransposons, as well as known copy number changes, occurring even prior to dysplasia. The structural variant burden captures the most variance across the cohort and genomic profiles do not always match consensus clinical pathology dysplasia grades. Increasing structural variant burden is associated with: high levels of chromothripsis and breakage-fusion-bridge events; increased expression of genes related to cell cycle checkpoint, DNA repair and chromosomal instability; and epigenetic silencing of Wnt signalling and cell cycle genes. Timing analysis reveals molecular events triggering genomic instability with more clonal expansion in dysplastic samples. Overall genomic complexity occurs early in the Barrett's natural history and may inform the potential for cancer beyond the clinically discernible phenotype.

Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy.

The evolutionary progression from primary to metastatic prostate cancer is largely uncharted, and the implications for liquid biopsy are unexplored. We infer detailed reconstructions of tumor phylogenies in ten prostate cancer patients with fatal disease, and investigate them in conjunction with histopathology and tumor DNA extracted from blood and cerebrospinal fluid. Substantial evolution occurs within the prostate, resulting in branching into multiple spatially intermixed lineages. One dominant lineage emerges that initiates and drives systemic metastasis, where polyclonal seeding between sites is common. Routes to metastasis differ between patients, and likely genetic drivers of metastasis distinguish the metastatic lineage from the lineage that remains confined to the prostate within each patient. Body fluids capture features of the dominant lineage, and subclonal expansions that occur in the metastatic phase are non-uniformly represented. Cerebrospinal fluid analysis reveals lineages not detected in blood-borne DNA, suggesting possible clinical utility.

Antifungal activities of cytochalasins produced by Diaporthe miriciae, an endophytic fungus associated with tropical medicinal plants.

In the present study, we evaluated the antifungal potential of cytochalasins produced by Diaporthe taxa against phytopathogenic fungi. Using molecular methods, seven endophytic fungal strains from the medicinal plants Copaifera pubiflora and Melocactus ernestii were identified as Diaporthe miriciae, while two isolates were identified to the genus level (Diaporthe sp.). All crude extracts of Diaporthe species produced via solid-state fermentation were evaluated by 1H NMR analyses. Crude extracts of the isolates D. miriciae UFMGCB 6350, 7719, 7646, 7653, 7701, 7772, and 7770 and Diaporthe sp. UFMGCB 7696 and 7720 were demonstrated to produce highly functionalized compounds. The extracts of D. miriciae UFMGCB 7719 and 6350 were selected as representative Diaporthe samples and subjected to bioassay-directed fractionation to isolate cytochalasins H and J. Cytochalasins H and J were evaluated for activities against the fungal plant pathogens Colletotrichum fragariae, Colletotrichum gloeosporioides, Colletotrichum acutatum, Botrytis cinerea, Fusarium oxysporum, Phomopsis obscurans, and Phomopsis viticola using microdilution broth assays. Cytochalasins H and J exhibited the most potent activities against the Phomopsis species tested. Our results showed that Diaporthe species were potential producers of different cytochalasins, which exhibit potential for controlling fungal diseases in planta and (or) maintaining antagonism.

Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2.

BACKGROUND: Somatic mutations in the Janus kinase 2 gene (JAK2) occur in many myeloproliferative neoplasms, but the molecular pathogenesis of myeloproliferative neoplasms with nonmutated JAK2 is obscure, and the diagnosis of these neoplasms remains a challenge. METHODS: We performed exome sequencing of samples obtained from 151 patients with myeloproliferative neoplasms. The mutation status of the gene encoding calreticulin (CALR) was assessed in an additional 1345 hematologic cancers, 1517 other cancers, and 550 controls. We established phylogenetic trees using hematopoietic colonies. We assessed calreticulin subcellular localization using immunofluorescence and flow cytometry. RESULTS: Exome sequencing identified 1498 mutations in 151 patients, with medians of 6.5, 6.5, and 13.0 mutations per patient in samples of polycythemia vera, essential thrombocythemia, and myelofibrosis, respectively. Somatic CALR mutations were found in 70 to 84% of samples of myeloproliferative neoplasms with nonmutated JAK2, in 8% of myelodysplasia samples, in occasional samples of other myeloid cancers, and in none of the other cancers. A total of 148 CALR mutations were identified with 19 distinct variants. Mutations were located in exon 9 and generated a +1 base-pair frameshift, which would result in a mutant protein with a novel C-terminal. Mutant calreticulin was observed in the endoplasmic reticulum without increased cell-surface or Golgi accumulation. Patients with myeloproliferative neoplasms carrying CALR mutations presented with higher platelet counts and lower hemoglobin levels than patients with mutated JAK2. Mutation of CALR was detected in hematopoietic stem and progenitor cells. Clonal analyses showed CALR mutations in the earliest phylogenetic node, a finding consistent with its role as an initiating mutation in some patients. CONCLUSIONS: Somatic mutations in the endoplasmic reticulum chaperone CALR were found in a majority of patients with myeloproliferative neoplasms with nonmutated JAK2. (Funded by the Kay Kendall Leukaemia Fund and others.).

Preparation and anti-bacterial properties of a temperature-sensitive gel containing silver nanoparticles.

The purpose of this study was to prepare a temperature-sensitive gel containing silver nanoparticles and to investigate its anti-bacterial properties in vitro. The aqueous gel was prepared using Pluronic F127 (18-22%) and Pluronic F68 (3-9%) in a cold method to obtain a proper gelation temperature at 37 degrees C. Viscoelastic properties of the system were measured by rheological measurements and the physicochemical properties were evaluated by MJ-22 Dial-reflex metaloscope and Zetasizer Nano ZS90. The in vitro antimicrobial activity was evaluated by a disk diffusion test, minimum inhibitory concentration, and minimum bactericidal concentration. A temperature-sensitive gel containing silver nanoparticles with 20 wt% F127 and 6 wt% F68 had suitable fluidity at 25 degrees C and was semi-solid at 37 degrees C. Silver nanoparticle size averaged 78.0 nm. The gel optimized formulation achieved a suitable viscosity. The MIC and MBC of the gel ranged from 1.0 to 2.0 mg/L against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The activity of the gel against these three species was significantly enhanced (p<0.05) compared to 400 mg/L Asimi standard. This optimized silver nanoparticle dosage form demonstrated a high potential for further development for the clinical treatment of bacterial vaginosis.

Convergent evolution to an aptamer observed in small populations on DNA microarrays.

The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.

Fabrication of planar organic nanotransistors using low temperature thermal nanoimprint lithography for chemical sensor applications.

A new fabrication process for the patterning of organic semiconductors at the nanoscale has been developed using low temperature thermal nanoimprint lithography and the details of this process are discussed. Novel planar nanotransistors have been fabricated and characterized from poly(3-hexylthiophene) (P3HT) and we demonstrate the feasibility of using such devices as highly sensitive chemical sensors.

pK(a) prediction from "Quantum Chemical Topology" descriptors.

Knowing the pK(a) of a compound gives insight into many properties relevant to many industries, in particular the pharmaceutical industry during drug development processes. In light of this, we have used the theory of Quantum Chemical Topology (QCT), to provide ab initio descriptors that are able to accurately predict pK(a) values for 228 carboxylic acids. This Quantum Topological Molecular Similarity (QTMS) study involved the comparison of 5 increasingly more expensive levels of theory to conclude that HF/6-31G(d) and B3LYP/6-311+G(2d,p) provided an accurate representation of the compounds studies. We created global and subset models for the carboxylic acids using Partial Least Square (PLS), Support Vector Machines (SVM), and Radial Basis Function Neural Networks (RBFNN). The models were extensively validated using 4-, 7-, and 10-fold cross-validation, with the validation sets selected based on systematic and random sampling. HF/6-31G(d) in conjunction with SVM provided the best statistics when taking into account the large increase in CPU time required to optimize the geometries at the B3LYP/6-311+G(2d,p) level. The SVM models provided an average q(2) value of 0.886 and an RMSE value of 0.293 for all the carboxylic acids, a q(2) of 0.825 and RMSE of 0.378 for the ortho-substituted acids, a q(2) of 0.923 and RMSE of 0.112 for the para- and meta-substituted acids, and a q(2) of 0.906 and RMSE of 0.268 for the aliphatic acids. Our method compares favorably to ACD/Laboratories, VCCLAB, SPARC, and ChemAxon's pK(a) prediction software based of the RMSE calculated by the leave-one-out method.

Isolation and identification of antifungal and antialgal alkaloids from Haplophyllum sieversii.

Bioassay-guided fractionation of the hexane/ethyl acetate/water (H/EtOAc/H2O) crude extract of the aerial parts of Haplophyllum sieversii was performed because of preliminary screening data that indicated the presence of growth inhibitory components against Colletotrichum fragariae, Colletotrichum gloeosporioides, and Colletotrichum acutatum. Fractionation was directed using bioautographical methods resulting in the isolation of the bioactive alkaloids flindersine, anhydroevoxine, haplamine, and a lignan eudesmin. These four compounds were evaluated for activity against C. fragariae, C. gloeosporioides, C. acutatum, Botrytis cinerea, Fusarium oxysporum, and Phomopsis obscurans in a dose-response growth-inhibitory bioassay at 50.0, 100.0, and 150.0 microM. Of the four compounds tested, flindersine demonstrated the highest level of antifungal activity. Additionally, flindersine, eudesmin, and haplamine were screened against the freshwater phytoplanktons Oscillatoria perornata, Oscillatoria agardhii, Selenastrum capricornutum, and Pseudanabaena sp. (strain LW397). Haplamine demonstrated selective inhibition against the odor-producing cyanobacterium O. perornata compared to the activity against the green alga S. capricornutum, with lowest observed effect concentration values of 1.0 and 10.0 microM, respectively.

Plant-derived antifungal proteins and peptides.

Plants produce potent constitutive and induced antifungal compounds to complement the structural barriers to microbial infection. Approximately 250,000-500,000 plant species exist, but only a few of these have been investigated for antimicrobial activity. Nevertheless, a wide spectrum of compound classes have been purified and found to have antifungal properties. The commercial potential of effective plant-produced antifungal compounds remains largely unexplored. This review article presents examples of these compounds and discusses their properties.

Phytotoxic and fungitoxic activities of the essential oil of kenaf (Hibiscus cannabinus L.) leaves and its composition.

The chemical composition of the essential oil of kenaf (Hibiscus cannabinus) was examined by GC-MS. Fifty-eight components were characterized from H. cannabinus with (E)-phytol (28.16%), (Z)-phytol (8.02%), n-nonanal (5.70%), benzene acetaldehyde (4.39%), (E)-2-hexenal (3.10%), and 5-methylfurfural (3.00%) as the major constituents. The oil was phytotoxic to lettuce and bentgrass and had antifungal activity against Colletotrichum fragariae, Colletotrichum gloeosporioides, and Colletotrichum accutatum but exhibited little or no algicidal activity.

Extracts of Flourensia cernua (L): volatile constituents and antifungal, antialgal, and antitermite bioactivities.

The chemical components of tarbush (Flourensia cernua) leaves were fractionated by extracting successively with hexanes, diethyl ether, and ethanol. Volatile profiles of each fraction were identified by using GC-MS. The hexanes fraction contained mostly monoterpenoids, while the ethanol fraction volatiles were primarily sesquiterpenoids. Crude fractions were tested for activity against fungi, algae, and termites. Application of as little as 1 microg of the essential oil from the hexanes fraction was sufficient to provide visible antifungal activity in bioautography assays. The diethyl ether fraction showed selective activity against the cyanobacterium responsible for the 2-methylisoborneol-induced off-flavor sometimes associated with catfish farming operations. All three fractions exhibited a high degree of antitermite activity.

A new 2D-TLC bioautography method for the discovery of novel antifungal agents To control plant pathogens.

A new bioassay has been developed combining the simplicity of direct bioautography with the improved chromatographic resolution of 2D-TLC. Mixtures of structurally diverse antifungal agents were tested to establish the validity and utility of this method in the discovery of new natural products with activity against agriculturally important fungal pathogens.

Composition and some biological activities of the essential oil of Callicarpa americana (L.).

The essential oil profile of Callicarpa americana was examined. Samples were collected from Lafayette county in north central Mississippi, and GC-MS data and retention indices were used to identify 67 oil components. Humulene epoxide II (13.9%), alpha-humulene (10.0%), 7-epi-alpha-eudesmol (9.4%), beta-pinene (8.8%), and 1-octen-3-ol (8.5%) were the major components of the steam-distilled oil. The oil was selectively toxic toward the cyanobacterium Oscillatoria perornata compared to Oscillatoria agardhii and the green alga Selenastrum capricornutum, with complete growth inhibition at 28.5 microgram/mL. The oil was only mildly phytotoxic and antifungal.

Fungicidal activity of natural and synthetic sesquiterpene lactone analogs.

Fungicidal activity of 36 natural and synthetic sesquiterpene lactones with guaianolide, trans, trans-germacranolide, cis, cis-germacranolide, melampolide, and eudesmanolide carbon skeletons was evaluated against the phytopathogenic fungi Colletotrichum acutatum, C. fragariae, C. gloeosporioides, Fusarium oxysporum, Botrytis cinerea, and Phomopsis sp. Dose-response data for the active compounds dehydrozaluzanin C, dehydrocostuslactone, 5alpha-hydroxydehydrocostuslacone, costunolide, and zaluzanin C are presented. A new 96-well microbioassay procedure for fast and easy evaluation of antifungal activity was used to compare these compounds with commercial fungicide standards. Some structure-activity conclusions are also presented.

Phytotoxicity of Discula destructiva Culture Filtrates to Cornus spp. and the Relationship to Disease Symptomology.

Discula destructiva culture filtrates and partially purified culture filtrates (PPCF) inhibited radish (Raphanus sativus) and dogwood (Cornus) species in a seedling root bioassay. Noninoculated potato-dextrose broth (PDB) extracted and separated in a similar manner also inhibited seedling growth. Reverse phase high performance liquid chromatography separated this inhibitory activity into two fractions, with one associated with the inhibitory action observed with PDB controls. The active fraction without interference with PDB, determined by bioassays, was extracted from cultures grown on Murishige-Skoog (MS) medium, which had no inhibitory activity associated with noninoculated controls. The active fraction was tested in a leaf overlay technique using 10 Cornus spp. All dogwood species were sensitive to the fraction and exhibited necrotic lesions bounded by a red margin, typical of dogwood anthracnose. The active fraction was translocated in Cornus alba to the leaf margin. C. canadensis showed minimal primary lesion formation but developed leaf curling and necrosis on leaf margins of newly emerging leaves, indicating apical translocation of the fraction from the application site. Comparison of three D. destructiva (Type 1) isolates and a Discula sp. (Type 2) isolate for production of the active fraction showed that the Type 2 isolate did not produce detectable amounts of the active component.