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

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

<p>Abstract</p> <p>Background</p> <p>Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types.</p> <p>Results</p> <p>We have developed ReplicationDomain <url>http://www.replicationdomain.org</url> as a web-based database for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data) via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1) view their data sets privately without sharing; (2) share with other registered users; or (3) make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing.</p> <p>Conclusion</p> <p>ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the scientific community.</p

Determination of Rare Earth Element Isotopic Compositions Using Sample-Standard Bracketing and Double-Spike Approaches

Rare earth elements (REEs) have been found to have numerous uses to trace geological and cosmochemical processes through analyses of elemental patterns, radioactive decay, nucleosynthetic anomalies, and cosmogenic effects. Stable isotopic fractionation is one aspect of REE geochemistry that has been seldom studied, with most publications focusing on the development of analytical methodologies for individual REEs, and most applications concerning terrestrial igneous rocks. In this study, we present a method to systematically analyze stable isotopic fractionations of 8 REEs, including Ce, Nd, Sm, Eu, Gd, Dy, Er, and Yb, using sample-standard bracketing (SSB) and double-spike (DS) approaches. All REEs are separated and purified using a fluoropolymer pneumatic liquid chromatography (FPLC) system. We introduce procedures for identifying and correcting some isobaric interferences in double-spike data reduction. Several geostandards, including igneous rocks and sediments, are analyzed using SSB and DS methods. The results indicate that REE isotopic fractionation in igneous processes is limited, except for Eu. Other REEs can still be isotopically fractionated by low-temperature processes and kinetic effects at a high temperature

Investigating the enigma of an irregular groundwater age pattern in a confined, presumed “fossil” complex aquifer through mixing cell flow modeling

Significant fluctuations in the groundwater (GW) age along the eastern flow path of the Nubian Sandstone Aquifer's (NSA), as derived from Krypton-81 groundwater dating, have suggested that this aquifer, located in Israel's Negev Desert and previously presumed to be a fossil, is not entirely isolated but mixes with younger and even recent water. The intermittent rejuvenation and drastic increases in the GW age across short distances most likely imply hydraulic connectivity with the surrounding aquifers, which contribute both younger and more ancient water to the NSA. The current study aims at modeling the GW flow system to locate and quantify its water sources despite the aquifer's hydrogeological complexity and the scarcity of hydrological data. We implemented the Mixing Cell Modeling (MCM) approach, understanding that the alternating rejuvenations and increases in the GW age downstream of the NSA's eastern flow trajectory reflect the mixing of the NSA's groundwater with young and old GW bodies, respectively. Thus, prompted by the 81Kr water age distribution, yet independent of the Kr radioisotope data, a multi-tracer mixing cell flow model was adopted based on a set of balance equations of water, dissolved minerals, and stable environmental isotopes. The findings indicate that (1) there is a small, yet substantial, intrusion of old brackish GW from a deep-seated, highly pressurized aquifer into the NSA in the northeastern Negev; (2) the rejuvenation of GW in the NSA is due to significant mixing with water from nearby overlying carbonate and chert aquifers, and (3) the NSA is substantially replenished through the Nubian Sandstone (NS) outcrops along the Negev Desert anticlines. Most GW intrusions into the NSA occur near the intersections of the eastern flow path with some of the Negev's major faults and synclines, such as the Paran and Ramon Fault zones and the Zin Syncline. In light of the relatively young GW age at the end of the NSA's western flow path in the northern Negev, and based on the similarities in the hydrogeological structures in the Negev and northern Sinai Deserts, we propose that similar mixing processes with GW from the overlying carbonate aquifers and direct GW recharge through the NS outcrops also occur in the northern Sinai Peninsula. The approach presented in this study might apply to examining recharge processes and hydraulic connectivity in other aquifers that were formerly classified as “fossil,” such as the immense NSA found in the Arabian (Jordan & Saudi Arabia) and the Western (Egypt) Deserts

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

Potential role of monkey inferior parietal neurons coding action semantic equivalences as precursors of parts of speech

The anterior portion of the inferior parietal cortex possesses comprehensive representations of actions embedded in behavioural contexts. Mirror neurons, which respond to both self-executed and observed actions, exist in this brain region in addition to those originally found in the premotor cortex. We found that parietal mirror neurons responded differentially to identical actions embedded in different contexts. Another type of parietal mirror neuron represents an inverse and complementary property of responding equally to dissimilar actions made by itself and others for an identical purpose. Here, we propose a hypothesis that these sets of inferior parietal neurons constitute a neural basis for encoding the semantic equivalence of various actions across different agents and contexts. The neurons have mirror neuron properties, and they encoded generalization of agents, differentiation of outcomes, and categorization of actions that led to common functions. By integrating the activities of these mirror neurons with various codings, we further suggest that in the ancestral primates' brains, these various representations of meaningful action led to the gradual establishment of equivalence relations among the different types of actions, by sharing common action semantics. Such differential codings of the components of actions might represent precursors to the parts of protolanguage, such as gestural communication, which are shared among various members of a society. Finally, we suggest that the inferior parietal cortex serves as an interface between this action semantics system and other higher semantic systems, through common structures of action representation that mimic language syntax

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