Description: This paper describes devices to extract α-cellulose from small whole wood samples developed at the Lamont-Doherty Earth Observatory Tree-Ring Lab and explains the procedures for chemical extractions and for the dual analysis of carbon (δ13C) and oxygen (δ18O) stable isotopes. Here, we provide the necessary steps and guidelines for constructing a cellulose extraction system for small amounts of wood and leaves. The system allows the simultaneous extraction of cellulose from 150 samples by means of in-house filter tubes, where chemicals used for the cellulose extraction are exchanged and eliminated in batches. This new implementation diminishes the processing time, minimizes physical sample manipulation and potential errors, increases sample throughput, and reduces the amount of chemicals and analytic costs. We also describe the dual measurement of δ13C and δ18O ratios in tree-ring cellulose using high-temperature pyrolysis in a High Temperature Conversion Elemental Analyzer (TC/EA) interfaced with a Thermo Delta V plus mass spectrometer.

Description: Hard X-ray microscopy is a prominent tool suitable for nanoscale-resolution non-destructive imaging of various materials used in different areas of science and technology. With an ongoing effort to push the 2D/3D imaging resolution down to 10 nm in the hard X-ray regime, both the fabrication of nano-focusing optics and the stability of the microscope using those optics become extremely challenging. In this work a microscopy system designed and constructed to accommodate multilayer Laue lenses as nanofocusing optics is presented. The developed apparatus has been thoroughly characterized in terms of resolution and stability followed by imaging experiments at a synchrotron facility. Drift rates of ∼2 nm h −1 accompanied by 13 nm × 33 nm imaging resolution at 11.8 keV are reported.

Description: We present MethHC ( http://MethHC.mbc.nctu.edu.tw ), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.

Description: Some patients with soft-tissue sarcoma (STS) report a history of injury at the site of their tumor. Although this phenomenon is widely reported, there are relatively few experimental systems that have directly assessed the role of injury in sarcoma formation. We recently described a mouse model of STS whereby p53 is deleted and oncogenic Kras is activated in muscle satellite cells via a Pax7CreER driver following intraperitoneal injection with tamoxifen. Here, we report that after systemic injection of tamoxifen, the vast majority of Pax7-expressing cells remain quiescent despite mutation of p53 and Kras. The fate of these muscle progenitors is dramatically altered by tissue injury, which leads to faster kinetics of sarcoma formation. In adult muscle, quiescent satellite cells will transition into an active state in response to hepatocyte growth factor (HGF). We show that modulating satellite cell quiescence via intramuscular injection of HGF increases the penetrance of sarcoma formation at the site of injection, which is dependent on its cognate receptor c-MET. Unexpectedly, the tumor-promoting effect of tissue injury also requires c-Met. These results reveal a mechanism by which HGF/c-MET signaling promotes tumor formation after tissue injury in a mouse model of primary STS, and they may explain why some patients develop a STS at the site of injury. Cancer Res; 75(3); 605–14. ©2014 AACR.

Description: Dolutegravir (DTG) is the latest antiretroviral (ARV) approved for the treatment of human immunodeficiency virus (HIV) infection. The G118R substitution, previously identified with MK-2048 and raltegravir, may represent the initial substitution in a dolutegravir resistance pathway. We have found that subtype C integrase proteins have a low enzymatic cost associated with the G118R substitution, mostly at the strand transfer step of integration, compared to either subtype B or recombinant CRF02_AG proteins. Subtype B and circulating recombinant form AG (CRF02_AG) clonal viruses encoding G118R-bearing integrases were severely restricted in their viral replication capacity, and G118R/E138K-bearing viruses had various levels of resistance to dolutegravir, raltegravir, and elvitegravir. In cell-free experiments, the impacts of the H51Y and E138K substitutions on resistance and enzyme efficiency, when present with G118R, were highly dependent on viral subtype. Sequence alignment and homology modeling showed that the subtype-specific effects of these mutations were likely due to differential amino acid residue networks in the different integrase proteins, caused by polymorphic residues, which significantly affect native protein activity, structure, or function and are important for drug-mediated inhibition of enzyme activity. This preemptive study will aid in the interpretation of resistance patterns in dolutegravir-treated patients. IMPORTANCE Recognized drug resistance mutations have never been reported for naive patients treated with dolutegravir. Additionally, in integrase inhibitor-experienced patients, only R263K and other previously known integrase resistance substitutions have been reported. Here we suggest that alternate resistance pathways may develop in non-B HIV-1 subtypes and explain how "minor" polymorphisms and substitutions in HIV integrase that are associated with these subtypes can influence resistance against dolutegravir. This work also highlights the importance of phenotyping versus genotyping when a strong inhibitor such as dolutegravir is being used. By characterizing the G118R substitution, this work also preemptively defines parameters for a potentially important pathway in some non-B HIV subtype viruses treated with dolutegravir and will aid in the inhibition of such a virus, if detected. The general inability of strand transfer-related substitutions to diminish 3' processing indicates the importance of the 3' processing step and highlights a therapeutic angle that needs to be better exploited.

Description: Photoresponse of bimetallic Au-Ag nanoparticle embedded soda glass (Au-Ag@SG) substrate is reported for surface plasmon assisted optical switching using 808 nm excitation. Au-Ag@SG system is made by an ion beam technique where Ag + is introduced first in the soda glass matrix by ion exchange technique. Subsequently, 400 keV Au + is implanted in the sample for different fluences, which is followed by an ion beam annealing process using 1 MeV Si + at a fixed fluence of 2 × 10 16 ions·cm −2 . Characteristic surface plasmon resonance (SPR) peaks around 400 and 550 nm provided evidence for the presence of Au and Ag nanoparticles. An optical switching in the Au-Ag@SG system with 808 nm, which is away from the characteristic SPR peaks of Ag and Au nanoparticles, suggests the possible role of two photon absorption (TPA) owing to the presence of interacting electric dipole in these systems. The role of surface plasmon polariton is emphasized for the propagation of electronic carrier belonging to the conduction electron of Au-Ag system in understanding the observed photoresponse. Unique excitation dependent photoresponse measurements confirm the possible role of TPA process. A competitive interband and intraband transitions in the bimetallic system of Au and Ag, which may be primarily responsible for the observation, are validated qualitatively using finite difference time domain calculations where inter-particle separation of Au and Ag plays an important role. Thus, a smart way of optical switching can be envisaged in noble bimetallic nanocluster system where long wavelength with higher skin depth can be used for communication purpose.

Description: We present a wideband low-jitter LC-VCO phase-locked loop in 130 nm CMOS technology for high speed serial link applications. The PLL covers a 5.6 GHz to 13.4 GHz frequency range by using two LC-VCO cores with an RMS jitter of 370 fs. The single event effects testing is performed with a neutron beam at Los Alamos National Laboratory and no frequency disturbance is found over the test period. The PLL consumes 50.88 mW of power under a 1.2 V power supply.

Description: Transcription factors (TFs) containing the basic leucine zipper (bZIP) domain are widely distributed in eukaryotes and display an array of distinct functions. In this study, a bZIP-type TF gene (MBZ1) was deleted and functionally characterized in the insect pathogenic fungus Metarhizium robertsii. The deletion mutant (ΔMBZ1) showed defects in cell wall integrity, adhesion to hydrophobic surfaces, and topical infection of insects. Relative to the WT, ΔMBZ1 was also impaired in growth and conidiogenesis. Examination of putative target gene expression indicated that the genes involved in chitin biosynthesis were differentially transcribed in ΔMBZ1 compared with the WT, which led to the accumulation of a higher level of chitin in mutant cell walls. MBZ1 exhibited negative regulation of subtilisin proteases, but positive control of an adhesin gene, which is consistent with the observation of effects on cell autolysis and a reduction in spore adherence to hydrophobic surfaces in ΔMBZ1. Promoter binding assays indicated that MBZ1 can bind to different target genes and suggested the possibility of heterodimer formation to increase the diversity of the MBZ1 regulatory network. The results of this study advance our understanding of the divergence of bZIP-type TFs at both intra- and interspecific levels.