The complex chromosomal aberrations found in therapy related acute myeloid leukemia (t-AML) suggest that the DNA double strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor cell-intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.
therapy-related AML; DNA damage; DNA repair; Trisomy 8
Novel graphene-based tunable plasmonic metamaterials featuring single and multiple transparency windows are numerically studied in this paper. The designed structures consist of a graphene layer perforated with quadrupole slot structures and dolmen-like slot structures printed on a substrate. Specifically, the graphene-based quadrupole slot structure can realize a single transparency window, which is achieved without breaking the structure symmetry. Further investigations have shown that the single transparency window in the proposed quadrupole slot structure is more likely originated from the quantum effect of Autler-Townes splitting. Then, by introducing a dipole slot to the quadrupole slot structure to form the dolmen-like slot structure, an additional transmission dip could occur in the transmission spectrum, thus, a multiple-transparency-window system can be achieved (for the first time for graphene-based devices). More importantly, the transparency windows for both the quadrupole slot and the dolmen-like slot structures can be dynamically controlled over a broad frequency range by varying the Fermi energy levels of the graphene layer (through electrostatic gating). The proposed slot metamaterial structures with tunable single and multiple transparency windows could find potential applications in many areas such as multiple-wavelength slow-light devices, active plasmonic switching, and optical sensing.
Oil reservoirs are specific habitats for the survival and growth of microorganisms in general. Pseudomonas stutzeri which is believed to be an exogenous organism inoculated into oil reservoirs during the process of oil production was detected frequently in samples from oil reservoirs. Very little is known, however, about the distribution and genetic structure of P. stutzeri in the special environment of oil reservoirs. In this study, we collected 59 P. stutzeri 16S rRNA gene sequences that were identified in 42 samples from 25 different oil reservoirs and we isolated 11 cultured strains from two representative oil reservoirs aiming to analyze the diversity and genomovar assignment of the species in oil reservoirs. High diversity of P. stutzeri was observed, which was exemplified in the detection of sequences assigned to four known genomovars 1, 2, 3, 20 and eight unknown genomic groups of P. stutzeri. The frequent detection and predominance of strains belonging to genomovar 1 in most of the oil reservoirs under study indicated an association of genomovars of P. stutzeri with the oil field environments.
16S rRNA gene; Genomovar; oil reservoirs; Pseudomonas stutzeri
Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions—the population frequency of individual clones, their genetic composition, and their evolutionary relationships—which we set out to test by sequencing individual cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples. Single-cell mutation profiling strongly supported the clonal architecture implied by the analysis of bulk material. In addition, it resolved the clonal assignment of single nucleotide variants that had been initially ambiguous and identified areas of previously unappreciated complexity. Accordingly, we find that many of the key assumptions underlying the analysis of tumor clonality by deep sequencing of unfractionated material are valid. Furthermore, we illustrate a single-cell sequencing strategy for interrogating the clonal relationships among known variants that is cost-effective, scalable, and adaptable to the analysis of both hematopoietic and solid tumors, or any heterogeneous population of cells.
Human cancers are genetically diverse populations of cells that evolve over the course of their natural history or in response to the selective pressure of therapy. In theory, it is possible to infer how this variation is structured into related populations of cells based on the frequency of individual mutations in bulk samples, but the accuracy of these models has not been evaluated across a large number of variants in individual cells. Here, we report a strategy for analyzing hundreds of variants within a single cell, and we apply this method to assess models of tumor clonality derived from bulk samples in three cases of leukemia. The data largely support the predicted population structure, though they suggest specific refinements. This type of approach not only illustrates the biological complexity of human cancer, but it also has the potential to inform patient management. That is, precise knowledge of which variants are present in which populations of cells may allow physicians to more effectively target combinations of mutations and predict how patients will respond to therapy.
The hypoxia-inducible factors (HIFα) are the critical factors that couple angiogenesis and osteogenesis by activating transcription of VEGF in osteoblasts. Mice lacking von Hippel–Lindau gene (Vhl), thus overexpressing HIFα in osteoblasts develop extremely dense and highly vascularized long bones. Here we provide evidence that osteoblasts lacking Vhl overexpress and secrete high levels of VEGF, which subsequently promotes the proliferation and osteogenic differentiation of bone marrow stromal cells (BMSC) by promoting expression of Heme oxygenase-1 (HO-1) in BMSC. Conditioned medium from osteoblasts Vhl (CM-CRE) promoted the proliferation and osteogenic differentiation of BMSC, in comparison with conditioned medium derived from normal osteoblasts (CM-GFP). Recombinant VEGF stimulated the proliferation and osteogenic differentiation of BMSC culturing in CM-GFP. By contrast, VEGF-neutralizing antibody inhibited the proliferation and osteogenic differentiation of BMSC culturing in CM-CRE. Treatment with a HO-1 inhibitor, SnPP, significantly inhibited VEGF-induced BMSC proliferation and osteogenic differentiation. On the contrary, activation of HO-1 with CoPP reversed the suppressing of VEGF-antibody on the proliferation and osteogesis of BMSC culturing in CM-CRE. These studies suggest that osteoblasts promote the proliferation and osteogenic differentiation of BMCS by VEGF/HO-1 pathway.
Background: With the influx of rural migrants into urban areas, the spread of HIV has increased significantly in Shaanxi Province (China). Migrant workers are at high risk of HIV infection due to social conditions and hardships (isolation, separation, marginalization, barriers to services, etc.). Objective: We explored the efficacy of a HIV/AIDS prevention and control program for rural migrants in Shaanxi Province, administered at both rural and urban sites. Methods: Guidance concerning HIV/AIDS prevention was given to the experimental group (266 migrants) for 1 year by the center of disease control, community health agencies and family planning department. The intervention was conducted according to the HIV/AIDS Prevention Management Manual for Rural Migrants. A control group of migrants only received general population intervention. The impact of the intervention was evaluated by administering HIV/AIDS knowledge, attitudes and sexual behavior (KAB) questionnaires after 6 and 12 months. Results: In the experimental group; 6 months of intervention achieved improvements in HIV/AIDS related knowledge. After 12 months; HIV/AIDS-related knowledge reached near maximal scores. Attitude and most behaviors scores were significantly improved. Moreover; the experimental group showed significant differences in HIV-AIDS knowledge; attitude and most behavior compared with the control group. Conclusions: The systematic long-term cross-site HIV/AIDS prevention in both rural and urban areas is a highly effective method to improve HIV/AIDS KAB among rural migrants.
HIV/AIDS; cross-site joint prevention and control; rural migrants; China; knowledge attitude and behavior
Up to date, little is known about the repair mode of microdamage in osteonal cortical bone resulting from bone screw implantation. In this study, self-tapping titanium cortical bone screws were inserted into the tibial diaphyses of 24 adult male rabbits. The animals were sacrificed at 1 day, 2 weeks, 1 month and 2 months after surgery. Histomorphometric measurement and confocal microscopy were performed on basic fuchsin stained bone sections to examine the morphological characteristics of microdamage, bone resorption activity and spatial relationship between microdamage and bone resorption. Diffuse and linear cracks were coexisted in peri-screw bone. Intracortical bone resorption was significantly increased 2 weeks after screw installation and reach to the maximum at 1 month. There was no significant difference in bone resorption between 1-month and 2-months groups. Microdamage was significantly decreased within 1 month after surgery. Bone resorption was predisposed to occur in the region of <100 µm from the bone-screw interface, where had extensive diffuse damage mixed with linear cracks. Different patterns of resorption cavities appeared in peri-screw bone. These data suggest that 1) the complex microdamage composed of diffuse damage and linear cracks is a strong stimulator for initiating targeted bone remodeling; 2) bone resorption activities taking place on the surfaces of differently oriented Haversian and Volkmann canals work in a team for the repair of extensive microdamage; 3) targeted bone remodeling is a short-term reaction to microdamage and thereby it may not be able to remove all microdamage resulting from bone screw insertion.
AIM: To establish a Chinese esophageal squamous cell carcinoma (ESCC) cell line with high bone metastasis potency using 99mTc-methylene diphosphonate (99mTc-MDP) micro-pinhole scintigraphy, X ray and micro-positron emission tomography/computed tomography (PET/CT) for exploring the mechanism of occurrence and development in esophageal cancer.
METHODS: The cells came from a BALB/c nu/nu immunodeficient mouse, and oncogenic tumor tissue was from a surgical specimen from a 61-year-old male patient with ESCC. The cell growth curve was mapped and analysis of chromosome karyotype was performed. Approximately 1 × 106 oncogenic cells were injected into the left cardiac ventricle of immunodeficient mice. The bone metastatic lesions of tumor-bearing mice were detected by 99mTc-MDP scintigraphy, micro-PET/CT and X-ray, and were resected from the mice under deep anesthesia. The bone metastatic cells in the lesions were used for culture and for repeated intracardiac inoculation. This in vivo/in vitro experimental metastasis study was repeated for four cycles. All of the suspicious bone sites were confirmed by pathology. Real-time polymerase chain reaction was used to compare the gene expression in the parental cells and in the bone metastatic clone.
RESULTS: The surgical specimen was implanted subcutaneously in immunodeficient mice and the tumorigenesis rate was 100%. First-passage oncogenic cells were named CEK-Sq-1. The chromosome karyotype analysis of the cell line was hypotriploid. The bone metastasis rate went from 20% with the first-passage oncogenic cells via intracardiac inoculation to 90% after four cycles. The established bone metastasis clone named CEK-Sq-1BM had a high potential to metastasize in bone, including mandible, humerus, thoracic and lumbar vertebrae, scapula and femur. The bone metastasis lesions were successfully detected by micro-pinhole bone scintigraphy, micro-PET/CT, and X-ray. The sensitivity, specificity and accuracy of the micro-pinhole scintigraphy, X-ray, and micro-PET/CT imaging examinations were: 89.66%/32%/80%, 88.2%/100%/89.2%, and 88.75%/77.5%/87.5%, respectively. Some gene expression difference was found between parental and bone metastasis cells.
CONCLUSION: This newly established Chinese ESCC cell line and animal model may provide a useful tool for the study of the pathogenesis and development of esophageal carcinoma.
Esophageal squamous cell carcinoma; Cell line; Bone metastasis; Molecular imaging; Real-time polymerase chain reaction
Background. gcrR gene acts as a negative regulator related to sucrose-dependent adherence in S. mutans. It is constructive to test the potential capacity of mutans with gcrR gene deficient in bacteria replacement therapy. Methods. In this study, we constructed the mutant by homologous recombination. The morphological characteristics of biofilms were analyzed by confocal laser scanning microscopy. S. mutans UA159 and the mutant MS-gcrR-def were inoculated, respectively, or together for competitive testing in vitro and in rat model. Results. Adhesion assay showed that the adhesion ability of the mutant increased relative to the wild type, especially in the early stage. MS-gcrR-def out-competed S. mutans UA159 in vitro biofilm, and correspondingly coinfection displayed significantly fewer caries in vivo. The former possessed both a lower level of acid production and a stronger colonization potential than S. mutans UA159. Conclusion. These findings demonstrate that MS-gcrR-def appears to be a good candidate for replacement therapy.
Gracilaria eucheumoides Linn (Gracilariaceae; G. eucheumoides) is abundant in dietary fiber, which aids the clearance of excess cholesterol from the blood and maintains stable blood glucose levels. The aim of the present study was to investigate the antifatigue effect of G. eucheumoides in mice and the physiological and molecular mechanisms underlying this effect. Mice were randomly divided into four groups and three of the groups were administered different doses of G. eucheumoides extract. A loaded swimming test demonstrated that the swimming times of the low-, medium- and high-dose groups were longer than those of the control group. Examinations revealed that the liver and muscle glycogen, lactate dehydrogenase and blood glucose concentration levels of the treatment groups were higher than those of the control group (P<0.05). However, this was not the case for lactic acid concentration (P>0.05). Quantitative polymerase chain reaction showed that the gene expression levels of glucose transport protein 4 and AMP-activated protein kinase in the medium-dose group exhibited the largest increases, compared with the other treatment groups, and were 3.0- and 1.8-fold higher than those in the control group, respectively. The results of the present study indicated that G. eucheumoides exerts an antifatigue effect on mice.
seaweed; physical symptoms; glucose transport protein 4; AMP-activated protein kinase
Squamous cell carcinoma is the major pathology type of esophageal cancer in China, where adenocarcinoma is rare and adenoid cystic carcinoma (ACC) is more rare comparing to the western countries. We report the surgical and pathologic findings of two cases of primary ACC of the esophagus, and review of the Chinese literature of this tumor.
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1507582238843246
Adenoid cystic carcinoma; Esophagus; Surgery
The myelodysplastic syndromes are a group of hematologic disorders that often evolve into secondary acute myeloid leukemia (AML). The genetic changes that underlie progression from the myelodysplastic syndromes to secondary AML are not well understood.
We performed whole-genome sequencing of seven paired samples of skin and bone marrow in seven subjects with secondary AML to identify somatic mutations specific to secondary AML. We then genotyped a bone marrow sample obtained during the antecedent myelodysplastic-syndrome stage from each subject to determine the presence or absence of the specific somatic mutations. We identified recurrent mutations in coding genes and defined the clonal architecture of each pair of samples from the myelodysplastic-syndrome stage and the secondary-AML stage, using the allele burden of hundreds of mutations.
Approximately 85% of bone marrow cells were clonal in the myelodysplastic-syndrome and secondary-AML samples, regardless of the myeloblast count. The secondary-AML samples contained mutations in 11 recurrently mutated genes, including 4 genes that have not been previously implicated in the myelodysplastic syndromes or AML. In every case, progression to acute leukemia was defined by the persistence of an antecedent founding clone containing 182 to 660 somatic mutations and the outgrowth or emergence of at least one subclone, harboring dozens to hundreds of new mutations. All founding clones and subclones contained at least one mutation in a coding gene.
Nearly all the bone marrow cells in patients with myelodysplastic syndromes and secondary AML are clonally derived. Genetic evolution of secondary AML is a dynamic process shaped by multiple cycles of mutation acquisition and clonal selection. Recurrent gene mutations are found in both founding clones and daughter subclones. (Funded by the National Institutes of Health and others.)
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders that often progress to chemotherapy-resistant secondary acute myeloid leukemia (sAML). We used whole genome sequencing to perform an unbiased comprehensive screen to discover all the somatic mutations in a sAML sample and genotyped these loci in the matched MDS sample. Here we show that a missense mutation affecting the serine at codon 34 (S34) in U2AF1 was recurrently mutated in 13/150 (8.7%) de novo MDS patients, with suggestive evidence of an associated increased risk of progression to sAML. U2AF1 is a U2 auxiliary factor protein that recognizes the AG splice acceptor dinucleotide at the 3′ end of introns and mutations are located in highly conserved zinc fingers in U2AF11,2. Mutant U2AF1 promotes enhanced splicing and exon skipping in reporter assays in vitro. This novel, recurrent mutation in U2AF1 implicates altered pre-mRNA splicing as a potential mechanism for MDS pathogenesis.
Alterations in DNA methylation have been implicated in the pathogenesis of myelodysplastic syndromes (MDS), although the underlying mechanism remains largely unknown. Methylation of CpG dinucleotides is mediated by DNA methyltransferases, including DNMT1, DNMT3A, and DNMT3B. DNMT3A mutations have recently been reported in patients with de novo acute myeloid leukemia (AML), providing a rationale for examining the status of DNMT3A in MDS samples. Here, we report the frequency of DNMT3A mutations in patients with de novo MDS, and their association with secondary AML. We sequenced all coding exons of DNMT3A using DNA from bone marrow and paired normal cells from 150 patients with MDS and identified 13 heterozygous mutations with predicted translational consequences in 12/150 patients (8.0%). Amino acid R882, located in the methyltransferase domain of DNMT3A, was the most common mutation site, accounting for 4/13 mutations. DNMT3A mutations were expressed in the majority of cells in all tested mutant samples regardless of blast counts, suggesting that DNMT3A mutations occur early in the course of MDS. Patients with DNMT3A mutations had worse overall survival compared to patients without DNMT3A mutations (p=0.005) and more rapid progression to AML (p=0.007), suggesting that DNMT3A mutation status may have prognostic value in de novo MDS.
myelodysplastic syndrome; DNMT3A; mutation
Membrane tethers or nanotubes play a critical role in a variety of cellular and subcellular processes such as leukocyte rolling and intercellular mass transport. The current constitutive equations that describe the relationship between the pulling force and the tether velocity during tether extraction have serious limitations. Here we propose a new phenomenological constitutive equation that captures all known characteristics of nanotube formation, including nonlinearity, nonzero threshold force, and possible negative tether velocity. We used tether extraction from endothelial cells as a prototype to illustrate how to obtain the material constants in the constitutive equation. With the micropipette aspiration technique, we measured tether pulling forces at both positive and negative tether velocities. We also determined the threshold force of 55 pN experimentally for the first time. This new constitutive equation unites two established ones and provides us a unified platform to better understand not only the physiological role of tether extraction during leukocyte rolling and intercellular or intracellular transport, but also the physics of membrane tether growth or retraction.
Membrane nanotube; leukocyte rolling; threshold force; intercellular transport; intracellular transport; micropipette aspiration
Angiogenesis and osteogenesis are tightly coupled during bone development and regeneration. Mesenchymal cells in the developing stroma elicit angiogenic signals to recruit new blood vessels into bone. Reciprocal signals, likely emanating from the incoming vascular endothelium, stimulate mesenchymal cell specification through additional interactions with cells within the vascular stem cell niche. The hypoxia-inducible factor-1 alpha (HIF-1) pathway has been identified as a key component in this process. We demonstrated that overexpression of HIF-1 in mature osteoblasts through disruption of the von Hippel-Lindau protein profoundly increases angiogenesis and osteogenesis; these processes appear to be coupled by cell nonautonomous mechanisms involving the action of vascular endothelial growth factor (VEGF) on the endothelial cells. The same occurred in the model of injury-mediated bone regeneration (distraction osteogenesis). Surprisingly, manipulation of HIF-1 does not influence angiogenesis of the skull bones, where earlier activation of HIF-1 in the condensing mesenchyme upregulates osterix during cranial bone formation.
knockout mice; osteoblasts; hypoxia-inducible factor; angiogenesis
The micropipette aspiration technique (MAT) has been successfully applied to many studies in cell adhesion such as leukocyte-endothelium interactions. However, this technique has never been validated experimentally and it has been only employed to impose constant forces. In this study, we validated the force measurement of the MAT with the optical trap and analyzed two technical issues of the MAT, force-transducer offset and cell-micropipette gap, with finite element simulation. We also modified the MAT so that increasing or decreasing forces can be applied. With the modified MAT, we studied tether extraction from endothelial cells by pulling single tethers at increasing velocities and constant force loading rates. Before the onset of tether extraction, an apparently-linear surface protrusion of a few hundred nanometers was observed, which is likely related to membrane receptors pulling on the underlying cytoskeleton. The strength of the modified MAT lies in its capability and consistency to apply a wide range of force loading rates from several piconewtons per second up to thousands of piconewtons per second. With this modification, the MAT becomes more versatile in the study of single molecule and single cell biophysics.
cell adhesion; cellular mechanics; molecular biomechanics; optical trap; finite element analysis; tether extraction
In cellular and molecular biomechanics, extensional stiffness of rod-like structures such as leukocyte microvilli can be easily measured with many techniques, but not many techniques are available for measuring their flexural stiffness. In this paper, we report a novel technique of measuring the flexural stiffness of rod-like structures. This technique is based on image deconvolution and, as an example, it was used for determining the flexural stiffness of neutrophil microvilli. The probes we used were 40-nm-diameter fluorescent beads, which were bound to the tips of neutrophil microvilli by anti-L-selectin antibody. The fluorescent images of the bead, which was positioned at the center of the cell bottom, were acquired with high magnification and long exposure time (3 s). Using a Gaussian function as the point spread function of our imaging system, we established a convolution equation based on Boltzmann’s law, which yields an analytical expression that relates the bead image profile to the flexural stiffness of the microvillus. The flexural stiffness was then obtained by the least squares regression. On average, the flexural stiffness was determined to be 7 pN/μm for single neutrophil microvilli. With the resolution of our imaging system, this technique can be used for measuring any flexural stiffness smaller than 34 pN/μm and it has great potential in single molecule biomechanics.
biomechanics; microvillus; leukocyte; micropipette; point spread function; deconvolution
Deletions spanning chromosome 5q31.2 are among the most common recurring cytogenetic abnormalities detectable in myelodysplastic syndromes (MDS). Prior genomic studies have suggested that haploinsufficiency of multiple 5q31.2 genes may contribute to MDS pathogenesis. However, this hypothesis has never been formally tested. Therefore, we designed this study to systematically and comprehensively evaluate all 28 chromosome 5q31.2 genes and directly test whether haploinsufficiency of a single 5q31.2 gene may result from a heterozygous nucleotide mutation or microdeletion. We selected paired tumor (bone marrow) and germline (skin) DNA samples from 46 de novo MDS patients (37 without a cytogenetic 5q31.2 deletion) and performed total exonic gene resequencing (479 amplicons) and array comparative genomic hybridization (CGH). We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH. Twelve novel single nucleotide polymorphisms were discovered. The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression. Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.
The cation of the title compound, C36H34N6O2
−, lies across a crystallographic inversion centre. The imidazole and pyridine rings form dihedral angles of 82.28 (5)° and 11.87 (7)°, respectively, with the anthracene ring system. The crystal packing is stabilized by π–π interactions between the pyridine ring and the central ring of anthracene, with a ring centroid–centroid distance of 3.684 (3) Å. The PF6
− anion is disordered over three different positions with occupancies of 0.284 (6), 0.354 (8) and 0.362 (9).
The multi-billion dollar US tree nut industries rely heavily on methyl bromide fumigation for postharvest insect control and are facing a major challenge with the mandated cessation by 2005 of its use for most applications. There is an urgent need to develop effective and economically viable alternative treatments to replace current phytosanitary and quarantine practices in order to maintain the competitiveness of US agriculture in domestic and international markets. With the reliable heating block system, the thermal death kinetics for fifth-instar codling moth, Indianmeal moth, and navel orangeworm were determined at a heating rate of 18 °C/min. A practical process protocol was developed to control the most heat resistant insect pest, fifth-instar navel orangeworm, in in-shell walnuts using a 27 MHz pilot scale radio frequency (RF) system. RF heating to 55 °C and holding in hot air for at least 5 min resulted in 100% mortality of the fifth-instar navel orangeworm. Rancidity, sensory qualities and shell characteristics were not affected by the treatments. If this method can be economically integrated into the handling process, it should have excellent potential as a disinfestation method for in-shell walnuts.
Disinfestation; Heat; Nut; Postharvest; Radio frequency