A spectroscopic study of the cycling transition 4s[3/2]_2-4p[5/2]_3 at 811.8 nm in Ar-39: Hyperfine structure and isotope shift

Doppler-free saturated absorption spectroscopy is performed on an enriched radioactive Ar-39 sample. The spectrum of the 3s^2 3p^5 4s [3/2]_2 - 3s^2 3p^5 4p [5/2]_3 cycling transition at 811.8 nm is recorded, and its isotope shift between Ar-39 and Ar-40 is derived. The hyperfine coupling constants A and B for both the 4s [3/2]_2 and 4p [5/2]_3 energy levels in Ar-39 are also determined. The results partially disagree with a recently published measurement of the same transition. Based on earlier measurements as well as the current work, the isotope shift and hyperfine structure of the corresponding transition in Ar-37 are also calculated. These spectroscopic data are essential for the realization of laser trapping and cooling of Ar-37 and Ar-39

Spectroscopic study of the cycling transition 4s[3/2]2-4p[5/2] 3 at 811.8 nm in Ar39: Hyperfine structure and isotope shift

Doppler-free saturated absorption spectroscopy is performed on an enriched radioactive Ar39 sample. The spectrum of the 3s23p54s[3/2]2- 3s23p54p[5/2]3 cycling transition at 811.8 nm is recorded, and its isotope shift between Ar39 and Ar40 is derived. The hyperfine coupling constants A and B for both the 4s[3/2]2 and 4p[5/2]3 energy levels in Ar39 are also determined. The results partially disagree with a recently published measurement of the same transition. Based on earlier measurements as well as the current work, the isotope shift and hyperfine structure of the corresponding transition in Ar37 are also calculated. These spectroscopic data are essential for the realization of laser trapping and cooling of Ar37,39. © 2011 American Physical Society

Tracer Applications of Noble Gas Radionuclides in the Geosciences

The noble gas radionuclides, including 81Kr (half-life = 229,000 yr), 85Kr (11 yr), and 39Ar (269 yr), possess nearly ideal chemical and physical properties for studies of earth and environmental processes. Recent advances in Atom Trap Trace Analysis (ATTA), a laser-based atom counting method, have enabled routine measurements of the radiokrypton isotopes, as well as the demonstration of the ability to measure 39Ar in environmental samples. Here we provide an overview of the ATTA technique, and a survey of recent progress made in several laboratories worldwide. We review the application of noble gas radionuclides in the geosciences and discuss how ATTA can help advance these fields, specifically determination of groundwater residence times using 81Kr, 85Kr, and 39Ar; dating old glacial ice using 81Kr; and an 39Ar survey of the main water masses of the oceans, to study circulation pathways and estimate mean residence times. Other scientific questions involving deeper circulation of fluids in the Earth's crust and mantle also are within the scope of future applications. We conclude that the geoscience community would greatly benefit from an ATTA facility dedicated to this field, with instrumentation for routine measurements, as well as for research on further development of ATTA methods

Diabetes Alters Contraction-Induced Mitogen Activated Protein Kinase Activation in the Rat Soleus and Plantaris

The prescription of anaerobic exercise has recently been advocated for the management of diabetes; however exercise-induced signaling in diabetic muscle remains largely unexplored. Evidence from exercise studies in nondiabetics suggests that the extracellular-signal-regulated kinases (Erk1/2), p38, and c-JUN NH2-terminal kinase (Jnk) mitogen-activated protein kinases (MAPKs) are important regulators of muscle adaptation. Here, we compare the basal and the in situ contraction-induced phosphorylation of Erk1/2- p38- and Jnk-MAPK and their downstream targets (p90rsk and MAPKAP-K2) in the plantaris and soleus muscles of normal and obese (fa/fa) Zucker rats. Compared to lean animals, the time course and magnitude of Erk1/2, p90rsk and p38 phosphorylation to a single bout of contractile stimuli were greater in the plantaris of obese animals. Jnk phosphorylation in response to contractile stimuli was muscle-type dependent with greater increases in the plantaris than the soleus. These results suggest that diabetes alters intramuscular signaling processes in response to a contractile stimulus

Diabetes Alters Contraction-Induced Mitogen Activated Protein Kinase Activation in the Rat Soleus and Plantaris

The prescription of anaerobic exercise has recently been advocated for the management of diabetes; however exercise-induced signaling in diabetic muscle remains largely unexplored. Evidence from exercise studies in nondiabetics suggests that the extracellular-signal-regulated kinases (Erk1/2), p38, and c-JUN NH2-terminal kinase (Jnk) mitogen-activated protein kinases (MAPKs) are important regulators of muscle adaptation. Here, we compare the basal and the in situ contraction-induced phosphorylation of Erk1/2- p38- and Jnk-MAPK and their downstream targets (p90rsk and MAPKAP-K2) in the plantaris and soleus muscles of normal and obese (fa/fa) Zucker rats. Compared to lean animals, the time course and magnitude of Erk1/2, p90rsk and p38 phosphorylation to a single bout of contractile stimuli were greater in the plantaris of obese animals. Jnk phosphorylation in response to contractile stimuli was muscle-type dependent with greater increases in the plantaris than the soleus. These results suggest that diabetes alters intramuscular signaling processes in response to a contractile stimulus

An evaluation tool for FKBP12-dependent and -independent mTOR inhibitors using a combination of FKBP-mTOR fusion protein, DSC and NMR

Mammalian target of rapamycin (mTOR), a large multidomain protein kinase, regulates cell growth and metabolism in response to environmental signals. The FKBP rapamycin-binding (FRB) domain of mTOR is a validated therapeutic target for the development of immunosuppressant and anticancer drugs but is labile and insoluble. Here we designed a fusion protein between FKBP12 and the FRB domain of mTOR. The fusion protein was successfully expressed in Escherichia coli as a soluble form, and was purified by a simple two-step chromatographic procedure. The fusion protein exhibited increased solubility and stability compared with the isolated FRB domain, and facilitated the analysis of rapamycin and FK506 binding using differential scanning calorimetry (DSC) and solution nuclear magnetic resonance (NMR). DSC enabled the rapid observation of protein–drug interactions at the domain level, while NMR gave insights into the protein–drug interactions at the residue level. The use of the FKBP12–FRB fusion protein combined with DSC and NMR provides a useful tool for the efficient screening of FKBP12-dependent as well as -independent inhibitors of the mTOR FRB domain

Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages

Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as “Pfa synthases”. In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of “secondary lipids” to describe these biosynthetic pathways and products, a proposition consistent with the “secondary metabolite” vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages

Rapid processing of ⁸⁵5 Kr/Kr ratios using Atom Trap Trace Analysis

We report a methodology for measuring ⁸⁵ Kr/Kr isotopic abundances using Atom Trap Trace Analysis (ATTA) that increases sample measurement throughput by over an order of magnitude to six samples per 24 h. The noble gas isotope ⁸⁵ Kr (half-life 510.7 years) is a useful tracer for young groundwater in the age range of 5–50 years. ATTA, an efficient and selective laser-based atom counting method, has recently been applied to ⁸⁵ Kr/Kr isotopic abundance measurements, requiring 5–10 μL of krypton gas at STP extracted from 50 to 100 L of water. Previously, a single such measurement required 48 h. Our new method demonstrates that we can measure 85Kr/Kr ratios with 3–5% relative uncertainty every 4 h, on average, with the same sample requirements

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

Many types of epigenetic profiling have been used to classify stem cells, stages of cellular differentiation, and cancer subtypes. Existing methods focus on local chromatin features such as DNA methylation and histone modifications that require extensive analysis for genome-wide coverage. Replication timing has emerged as a highly stable cell type-specific epigenetic feature that is regulated at the megabase-level and is easily and comprehensively analyzed genome-wide. Here, we describe a cell classification method using 67 individual replication profiles from 34 mouse and human cell lines and stem cell-derived tissues, including new data for mesendoderm, definitive endoderm, mesoderm and smooth muscle. Using a Monte-Carlo approach for selecting features of replication profiles conserved in each cell type, we identify “replication timing fingerprints” unique to each cell type and apply a k nearest neighbor approach to predict known and unknown cell types. Our method correctly classifies 67/67 independent replication-timing profiles, including those derived from closely related intermediate stages. We also apply this method to derive fingerprints for pluripotency in human and mouse cells. Interestingly, the mouse pluripotency fingerprint overlaps almost completely with previously identified genomic segments that switch from early to late replication as pluripotency is lost. Thereafter, replication timing and transcription within these regions become difficult to reprogram back to pluripotency, suggesting these regions highlight an epigenetic barrier to reprogramming. In addition, the major histone cluster Hist1 consistently becomes later replicating in committed cell types, and several histone H1 genes in this cluster are downregulated during differentiation, suggesting a possible instrument for the chromatin compaction observed during differentiation. Finally, we demonstrate that unknown samples can be classified independently using site-specific PCR against fingerprint regions. In sum, replication fingerprints provide a comprehensive means for cell characterization and are a promising tool for identifying regions with cell type-specific organization