Mechanisms of structure direction in zeolite synthesis

The mechanisms by which the geometries of organic structure-directing agents are translated into the product pore architectures in the synthesis of pure-silica and aluminosilicate zeolites are investigated by numerous spectroscopic techniques and variations in synthesis gel composition. For the tetrapropylammonium- and 1,6-hexanediamine-mediated syntheses of pure-silica ZSM-5 (Si-ZSM-5), 1H-29Si CP MAS NMR is performed between the protons of the organic species and the silicon atoms of the zeolite framework precursors in a deuterated synthesis medium to probe the interactions between the organic and inorganic components. The origin of structural specificity in the synthesis of pure-silica zeolites in the presence of structure-directing agents is attributed to the formation of favorable intermolecular van der Waals interactions within inorganic-organic composite species that form the key components in zeolite self-assembly. Investigation of the 1H-29Si CP MAS NMR profiles of silicate gels containing tetraalkylammonium cations that do not induce the formation of a crystalline zeolite product suggest the significance of hydrophobic hydration of the organic component in the formation of the inorganic-organic composite structures that is essential to the synthesis of pure-silica zeolites. For the syntheses of the hexagonal (EMT) and cubic (FAU) polymorphs of the aluminosilicate zeolite faujasite in the presence of 18-crown-6 and 15-crown-5, respectively, a combination of NMR and vibrational spectroscopic techniques and variations in the synthesis compositions are used to elucidate the structure-directing roles of the crown ethers. Sodium/crown ether complexes facilitate and direct the assembly of sodium-templated extended aluminosilicate structures via ion-dipole interactions to form the EMT and FAU products. Thus, for the synthesis of Si-ZSM-5 and the synthesis of EMT and FAU, two different mechanisms of structure direction and self-assembly via the formation of extended inorganic or inorganic-organic composite species are proposed

Chromosome painting in the manatee supports Afrotheria and Paenungulata

BACKGROUND: Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee. RESULTS: The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19. CONCLUSION: There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking afrotherian taxa

Active drag as a criterion for evidence-based classification in Para swimming

Paralympic classification should provide athletes with an equitable starting point for competition by minimizing the impact their impairment has on the outcome of the event. As swimming is an event conducted in water, the ability to overcome drag (active and passive) is an important performance determinant. It is plausible that the ability to do this is affected by the type and severity of the physical impairment, but the current World Para Swimming classification system does not objectively account for this component. The aim of this study was to quantify active and passive drag in Para swimmers and evaluate the strength of association between these measures and type of physical impairment, swimming performance, and sport class. Methods Seventy-two highly trained Para swimmers from sport classes S1 to S10 and 14 highly trained nondisabled swimmers were towed by a motorized winch while the towing force was recorded. Passive drag was measured with the arms held by the side; active drag was determined during freestyle swimming using an assisted towing method. Results Active and passive drag were higher in Para swimmers with central motor and neuromuscular impairments than for nondisabled swimmers and were associated with severity of swim-specific impairment (sport class) and maximal freestyle performance in these swimmers (r = −0.40 to −0.50, P ≤ 0.02). Para swimmers with anthropometric impairments showed similar active and passive drag to nondisabled swimmers, and between swimmers from different sport classes. Conclusions Para swimmers with central motor and neuromuscular impairments are predisposed to high active drag during freestyle swimming that impacts on their performance. It is recommended that drag measures be considered in revised classification for these swimmers, but not for those with anthropometric impairments

RAD51C deficiency in mice results in early prophase I arrest in males and sister chromatid separation at metaphase II in females

RAD51C is a member of the RecA/RAD51 protein family, which is known to play an important role in DNA repair by homologous recombination. In mice, it is essential for viability. Therefore, we have generated a hypomorphic allele of Rad51c in addition to a null allele. A subset of mice expressing the hypomorphic allele is infertile. This infertility is caused by sexually dimorphic defects in meiotic recombination, revealing its two distinct functions. Spermatocytes undergo a developmental arrest during the early stages of meiotic prophase I, providing evidence for the role of RAD51C in early stages of RAD51-mediated recombination. In contrast, oocytes can progress normally to metaphase I after superovulation but display precocious separation of sister chromatids, aneuploidy, and broken chromosomes at metaphase II. These defects suggest a possible late role of RAD51C in meiotic recombination. Based on the marked reduction in Holliday junction (HJ) resolution activity in Rad51c-null mouse embryonic fibroblasts, we propose that this late function may be associated with HJ resolution

Untangling the controls on bedload transport in a wood‐loaded river with RFID tracers and linear mixed modelling

Bedload transport is a fundamental process by which coarse sediment is transferred through landscapes by river networks and may be well described stochastically by distributions of grain step length and rest time obtained through tracer studies. To date, none of these published tracer studies have specifically investigated the influence of large wood in the river channel on sediment transport dynamics, limiting the applicability of stochastic sediment transport models in these settings. Large wood is a major component of many forested rivers and is increasing due to anthropogenic ‘Natural Flood Management’ (NFM) practices. This study aims to investigate and model the influence of large wood on grain-scale bedload transport. We tagged 957 cobble – pebble sized particles (D50 = 73 mm) and 28 pieces of large wood (> 1 m in length) with RFID tracers in an alpine mountain stream. We monitored the transport distance of tracers annually over three years, building distributions of tracer transport distances with which to compare with published distributions from wood free settings. We also applied linear mixed modelling (LMM), to tease out the influence of wood from other controls on likelihood of entrainment, deposition, and the transport distances of sediments. Tracer sediments accumulated both up and downstream of large wood pieces, with LMM analysis confirming a reduction in the probability of entrainment of tracers closer to wood in all three years. Upon remobilisation, tracers entrained from positions closer to large wood had shorter subsequent transport distances in each year. In 2019, large wood also had a trapping effect, significantly reducing the transport distances of tracer particles entrained from upstream, i.e. forcing premature deposition of tracers. This study demonstrates the role of large wood in influencing bedload transport in alpine stream environments, with implications for both natural and anthropogenic addition of wood debris in fluvial environments

Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response.

Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis

Mesothelioma patient derived tumor xenografts with defined BAP1 mutations that mimic the molecular characteristics of human malignant mesothelioma

Background: The development and evaluation of new therapeutic approaches for malignant mesothelioma has been sparse due, in part, to lack of suitable tumor models. Methods: We established primary mesothelioma cultures from pleural and ascitic fluids of five patients with advanced mesothelioma. Electron microscopy and immunohistochemistry (IHC) confirmed their mesothelial origin. Patient derived xenografts were generated by injecting the cells in nude or SCID mice, and malignant potential of the cells was analyzed by soft agar colony assay. Molecular profiles of the primary patient tumors, early passage cell cultures, and patient derived xenografts were assessed using mutational analysis, fluorescence in situ hybridization (FISH) analysis and IHC. Results: Primary cultures from all five tumors exhibited morphologic and IHC features consistent to those of mesothelioma cells. Mutations of BAP1 and CDKN2A were each detected in four tumors. BAP1 mutation was associated with the lack of expression of BAP1 protein. Three cell cultures, all of which were derived from BAP1 mutant primary tumors, exhibited anchorage independent growth and also formed tumors in mice, suggesting that BAP1 loss may enhance tumor growth in vivo. Both early passage cell cultures and mouse xenograft tumors harbored BAP1 mutations and CDKN2A deletions identical to those found in the corresponding primary patient tumors. Conclusions: The mesothelioma patient derived tumor xenografts with mutational alterations that mimic those observed in patient tumors which we established can be used for preclinical development of novel drug regimens and for studying the functional aspects of BAP1 biology in mesothelioma. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1362-2) contains supplementary material, which is available to authorized users

EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells

Background: Chromosomal inversions involving anaplastic lymphoma kinase (ALK) and echinoderm microtubule associated protein like 4 (EML4) generate a fusion protein EML4-ALK in non-small cell lung cancer (NSCLC). The understanding of EML4-ALK function can be improved by a functional study using normal human cells. Methods: Here we for the first time conduct such study to examine the effects of EML4-ALK on cell proliferation, cellular senescence, DNA damage, gene expression profiles and transformed phenotypes. Results: The lentiviral expression of EML4-ALK in mortal, normal human fibroblasts caused, through its constitutive ALK kinase activity, an early induction of cellular senescence with accumulated DNA damage, upregulation of p16INK4A and p21WAF1, and senescence-associated β-galactosidase (SA-β-gal) activity. In contrast, when EML4-ALK was expressed in normal human fibroblasts transduced with telomerase reverse transcriptase (hTERT), which is activated in the vast majority of NSCLC, the cells showed accelerated proliferation and acquired anchorage-independent growth ability in soft-agar medium, without accumulated DNA damage, chromosome aberration, nor p53 mutation. EML4-ALK induced the phosphorylation of STAT3 in both mortal and hTERT-transduced cells, but RNA sequencing analysis suggested that the different signaling pathways contributed to the different phenotypic outcomes in these cells. While EML4-ALK also induced anchorage-independent growth in hTERT-immortalized human bronchial epithelial cells in vitro, the expression of EML4-ALK alone did not cause detectable in vivo tumorigenicity in immunodeficient mice. Conclusions: Our data indicate that the expression of hTERT is critical for EML4-ALK to manifest its in vitro transforming activity in human cells. This study provides the isogenic pairs of human cells with and without EML4-ALK expression

Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants.

The unknown pathogenicity of a significant number of variants found in cancer-related genes is attributed to limited epidemiological data, resulting in their classification as variant of uncertain significance (VUS). To date, Breast Cancer gene-2 (BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determine their functional significance. Here we report the use of a humanized-mouse embryonic stem cell (mESC) line expressing a single copy of the human BRCA2 for a CRISPR-Cas9-based high-throughput functional assay. As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. Specifically, we used a pool of 180-mer single-stranded donor DNA to generate all possible combination of variants. Using a high throughput sequencing-based approach, we show a significant drop in the frequency of non-functional variants, whereas functional variants are enriched in the pool of the cells. We further demonstrate the response of these variants to the DNA-damaging agents, cisplatin and olaparib, allowing us to use cellular survival and drug response as parameters for variant classification. Using this approach, we have categorized 599 BRCA2 variants including 93-single nucleotide variants (SNVs) across the 11 codons, of which 28 are reported in ClinVar. We also functionally categorized 252 SNVs from exon 13 into 188 functional and 60 non-functional variants, demonstrating that saturation genome editing (SGE) coupled with drug sensitivity assays can enhance functional annotation of BRCA2 VUS

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE