bluuebunny/crossref_metadata_2025 huggingface dataset:
The prediction of soil carbon fractions using mid-infrared-partial least square analysis
Authors: Janik L. J. , Skjemstad J. O. , Shepherd K. D. , Spouncer L. R.
Published: March 2007

This paper describes the application of mid-infrared (MIR) spectroscopy and partial least-squares (PLS) analysis to predict the concentration of organic carbon fractions present in soil. The PLS calibrations were derived from a standard set of soils that had been analysed for total organic carbon (TOC), particulate organic carbon (POC), and charcoal carbon (char-C) using physical and chemical means. PLS calibration models from this standard set of soils allowed the prediction of TOC, POC, and char-C fractions with a coefficient of determination (R2) of measured v. predicted data ranging between 0.97 and 0.73. For the POC fraction, the coefficient of determination could be improved (R2 = 0.94) through the use of local calibration sets. The capacity to estimate soil fractions such as char-C rapidly and inexpensively makes this approach highly attractive for studies where large numbers of analyses are required. Inclusion of a set of soils from Kenya demonstrated the robustness of the method for total organic carbon and charcoal carbon prediction.
An analytical tool for understanding the properties and behaviour of variable charge soils
Authors: Gillman G. P.
Published: March 2007

Routine analyses for soil cation exchange properties usually give only limited insight into the properties and management of soils containing significant amounts of variable charge. In this paper a procedure for determining a soil Charge Fingerprint is fully described, a model developed from simplified theory to underpin the methodology is discussed, and examples of the usefulness of the approach are given. Operationally defined cation and anion exchange capacities (CEC and AEC) are determined over an appropriate pH range (pH 4 to pH 6 is suggested) using Ca and Cl as the index cations. At low pH, Ca does not always fully saturate the CEC, so that it is necessary to distinguish a Basic CEC (Ca ads.) from the Total CEC (Ca + Al ads.). The graphical representation of CECT, CECB, and AEC v. pH constitutes the Charge Fingerprint. Though not intended as a routine instrument, its determination on key samples in a characterisation exercise places routinely determined basic and acidic cations in context.
Examples are given of large scale characterisation studies that link soils from different continents having similar surface charge characteristics; of the assessment of the success or otherwise of producing permanent positive charge in synthetically prepared Ti-substituted goethites; and of the evaluation of the effect of adding crushed basic rock amendment on the surface charge properties of a variable charge soil. The formulation of a Depreciation Index, which classifies soils in terms of their departure in basic cation content from an arbitrarily defined ‘ideal’ condition, is suggested for use in soil resource assessment.
Denitrification capacity in the vadose zone at three sites in the Lake Taupo catchment, New Zealand
Authors: Barkle Greg , Clough Tim , Stenger Roland
Published: March 2007

Land use in the Lake Taupo catchment is under scrutiny, as early signs of deteriorating water quality in Lake Taupo have been observed. Although the fate of contaminants in soil and groundwater are comparatively well studied, the transformations in the lower vadose zone, i.e. the zone between the soil and the groundwater, are less well understood. The capacity for NO3-N removal via biological denitrification, based on utilising the resident C substrate, in the vadose zone of the Lake Taupo catchment is quantified in this work. Complete vadose zone profiles were sampled at 3 sites (Rangiatea, Waihora, and Kinloch), from the soil surface down to the watertable in approximately 0.5-m depth increments. Texture, allophane content, pH, and concentrations of extractable NO3-N, NH4-N, and dissolved organic carbon were determined. Incubations were undertaken to determine the denitrification capacity of the vadose zone materials amended with NO3-15N, but no added carbon substrate, and maintained under anaerobic conditions at 28°C. Gas samples were taken from the headspace after 48 h and analysed for N2 and N2O. In soil depths down to about 1.2 m, the denitrification capacity ranged from 0.03 to 9.18 kg N/ha.day, and below this depth it ranged from <0.01 to 0.09 kg N/ha.day. A palaeosol layer in the Waihora profile had an enhanced denitrification capacity compared with the other samples in deeper zones of the profiles. In the surface sampling, at least 99.9% of the gas recovered from the 15N applied was in the form of N2. In contrast, no N2 gas production could be detected in any sample from below the second sampling depth, with only N2O detected. Denitrification capacities of all vadose zone materials were low when compared with other studies. Thus, careful land management is required to avoid groundwater contamination by nitrate leaching from the root-zone of the pasture.
Jagged-mediated Notch signaling maintains proliferating neural progenitors and regulates cell diversity in the ventral spinal cord
Authors: Yeo Sang-Yeob , Chitnis Ajay B.
Published: March 2007

Previous studies have shown that Delta-mediated Notch signaling regulates the number of early differentiating neurons. However, the role of Notch activation and Jagged-mediated signaling during late neurogenesis remains poorly defined. In the developing spinal cord of zebrafish, GABAergic Kolmer–Agduhr (KA′′) cells and motor neurons (MN) emerge sequentially from their progenitors in the p3 domain. Jagged2 is expressed uniformly in the pMN domain during late neurogenesis where Olig2 is required for its expression. We suggest that Jagged2 interacts ventrally with progenitors in the adjacent p3 domain, where it has a critical role in the maintenance of proliferating neural progenitors and in preventing differentiation of these progenitors as GABAergic KA′′ cells or secondary MN. This study identifies a critical role for Jagged–Notch signaling in the maintenance of proliferating neural precursors in a discrete compartment of the neural tube during the continuing growth and development of the vertebrate nervous system.
Germ-line chimerism and paternal care in marmosets (
Callithrix kuhlii
)
Authors: Ross C. N. , French J. A. , Ortí G.
Published: March 2007

The formation of viable genetic chimeras in mammals through the transfer of cells between siblings
in utero
is rare. Using microsatellite DNA markers, we show here that chimerism in marmoset (
Callithrix kuhlii
) twins is not limited to blood-derived hematopoietic tissues as was previously described. All somatic tissue types sampled were found to be chimeric. Notably, chimerism was demonstrated to be present in germ-line tissues, an event never before documented as naturally occurring in a primate. In fact, we found that chimeric marmosets often transmit sibling alleles acquired
in utero
to their own offspring. Thus, an individual that contributes gametes to an offspring is not necessarily the genetic parent of that offspring. The presence of somatic and germ-line chimerism may have influenced the evolution of the extensive paternal and alloparental care system of this taxon. Although the exact mechanisms of sociobiological change associated with chimerism have not been fully explored, we show here that chimerism alters relatedness between twins and may alter the perceived relatedness between family members, thus influencing the allocation of parental care. Consistent with this prediction, we found a significant correlation between paternal care effort and the presence of epithelial chimerism, with males carrying chimeric infants more often than nonchimeric infants. Therefore, we propose that the presence of placental chorionic fusion and the exchange of cell lines between embryos may represent a unique adaptation affecting the evolution of cooperative care in this group of primates.
20th-Century doubling in dust archived in an Antarctic Peninsula ice core parallels climate change and desertification in South America
Authors: McConnell Joseph R. , Aristarain Alberto J. , Banta J. Ryan , Edwards P. Ross , Simões Jefferson C.
Published: March 2007

Crustal dust in the atmosphere impacts Earth's radiative forcing directly by modifying the radiation budget and affecting cloud nucleation and optical properties, and indirectly through ocean fertilization, which alters carbon sequestration. Increased dust in the atmosphere has been linked to decreased global air temperature in past ice core studies of glacial to interglacial transitions. We present a continuous ice core record of aluminum deposition during recent centuries in the northern Antarctic Peninsula, the most rapidly warming region of the Southern Hemisphere; such a record has not been reported previously. This record shows that aluminosilicate dust deposition more than doubled during the 20th century, coincident with the ≈1°C Southern Hemisphere warming: a pattern in parallel with increasing air temperatures, decreasing relative humidity, and widespread desertification in Patagonia and northern Argentina. These results have far-reaching implications for understanding the forces driving dust generation and impacts of changing dust levels on climate both in the recent past and future.
Correction of prototypic ATM splicing mutations and aberrant ATM function with antisense morpholino oligonucleotides
Authors: Du Liutao , Pollard Julianne M. , Gatti Richard A.
Published: March 2007

We used antisense morpholino oligonucleotides (AMOs) to redirect and restore normal splicing of three prototypic splicing mutations in the
ataxia-telangiectasia mutated
(
ATM
) gene. Two of the mutations activated cryptic 5′ or 3′ splice sites within exonic regions; the third mutation activated a downstream 5′ splice site leading to pseudoexon inclusion of a portion of intron 28. AMOs were targeted to aberrant splice sites created by the mutations; this effectively restored normal ATM splicing at the mRNA level and led to the translation of full-length, functional ATM protein for at least 84 h in the three cell lines examined, as demonstrated by immunoblotting, ionizing irradiation-induced autophosphorylation of ATM, and transactivation of ATM substrates. Ionizing irradiation-induced cytotoxicity was markedly abrogated after AMO exposure. The
ex vivo
data strongly suggest that the disease-causing molecular pathogenesis of such prototypic mutations is not the amino acid change of the protein but the mutated DNA code itself, which alters splicing. Such prototypic splicing mutations may be correctable
in vivo
by systemic administration of AMOs and may provide an approach to customized, mutation-based treatment for ataxia-telangiectasia and other genetic disorders.
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
Authors: Wolf-Yadlin Alejandro , Hautaniemi Sampsa , Lauffenburger Douglas A. , White Forest M.
Published: March 2007

Although recent developments in MS have enabled the identification and quantification of hundreds of phosphorylation sites from a given biological sample, phosphoproteome analysis by MS has been plagued by inconsistent reproducibility arising from automated selection of precursor ions for fragmentation, identification, and quantification. To address this challenge, we have developed a new MS-based strategy, based on multiple reaction monitoring of stable isotope-labeled peptides, that enables highly reproducible quantification of hundreds of nodes (phosphorylation sites) within a signaling network and across multiple conditions simultaneously. We have applied this strategy to quantify temporal phosphorylation profiles of 222 tyrosine phosphorylated peptides across seven time points following EGF treatment, including 31 tyrosine phosphorylation sites not previously known to be regulated by EGF stimulation. With this approach, 88% of the signaling nodes were reproducibly quantified in four analyses, as compared with only 34% by typical information-dependent analysis. As a result of the improved reproducibility, full temporal phosphorylation profiles were generated for an additional 104 signaling nodes with the multiple reaction monitoring strategy, an 88% increase in our coverage of the signaling network. This method is broadly applicable to multiple signaling networks and to a variety of samples, including quantitative analysis of signaling networks in clinical samples. Using this approach, it should now be possible to routinely monitor the phosphorylation status of hundreds of nodes across multiple biological conditions.
Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting
Authors: Hansen Thomas M. , Reihani S. Nader S. , Oddershede Lene B. , Sørensen Michael A.
Published: March 2007

Programmed ribosomal frameshifting is often used by viral pathogens including HIV. Slippery sequences present in some mRNAs cause the ribosome to shift reading frame. The resulting protein is thus encoded by one reading frame upstream from the slippery sequence and by another reading frame downstream from the slippery sequence. Although the mechanism is not well understood, frameshifting is known to be stimulated by an mRNA structure such as a pseudoknot. Here, we show that the efficiency of frameshifting relates to the mechanical strength of the pseudoknot. Two pseudoknots derived from the Infectious Bronchitis Virus were used, differing by one base pair in the first stem. In
Escherichia coli
, these two pseudoknots caused frameshifting frequencies that differed by a factor of two. We used optical tweezers to unfold the pseudoknots. The pseudoknot giving rise to the highest degree of frameshifting required a nearly 2-fold larger unfolding force than the other. The observed energy difference cannot be accounted for by any existing model. We propose that the degree of ribosomal frameshifting is related to the mechanical strength of RNA pseudoknots. Our observations support the “9 Å model” that predicts some physical barrier is needed to force the ribosome into the −1 frame. Also, our findings support the recent observation made by cryoelectron microscopy that mechanical interaction between a ribosome and a pseudoknot causes a deformation of the A-site tRNA. The result has implications for the understanding of genetic regulation, reading frame maintenance, tRNA movement, and unwinding of mRNA secondary structures by ribosomes.
Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme
Authors: Smith M. Duane , Collins Richard A.
Published: March 2007

A fast-cleaving version of the Varkud satellite ribozyme, called RG, shows an apparent
cis
-cleavage rate constant of 5 sec
−1
, similar to the rates of protein enzymes that catalyze similar reactions. Here, we describe mutational, pH-rate, and kinetic solvent isotope experiments that investigate the identity and rate constant of the rate-limiting step in this reaction. Self-cleavage of RG exhibits a bell-shaped rate vs. pH profile with apparent pK
a
s of 5.8 and 8.3, consistent with the protonation state of two nucleotides being important for the rate of cleavage. Cleavage experiments in heavy water (D
2
O) revealed a kinetic solvent isotope effect consistent with proton transfer in the rate-limiting step. A mutant RNA that disrupts a peripheral loop–loop interaction involved in RNA folding exhibits pH- and D
2
O-independent cleavage ≈10
3
-fold slower than wild type, suggesting that this mutant is limited by a different step than wild type. Substitution of adenosine 756 in the putative active-site loop with cytosine also decreases the cleavage rate ≈10
3
-fold, but the A756C mutant retains pH- and D
2
O-sensitivity similar to wild type, consistent with this mutant and wild type being limited by the chemical step of the reaction. These results suggest that the RG ribozyme provides a good experimental system to investigate the nature of fast, rate-limiting steps in a ribozyme cleavage reaction.
Homer 1a uncouples metabotropic glutamate receptor 5 from postsynaptic effectors
Authors: Kammermeier Paul J. , Worley Paul F.
Published: March 2007

Metabotropic glutamate receptors (mGluRs) and Homer proteins play critical roles in neuronal functions including plasticity, nociception, epilepsy, and drug addiction. Furthermore, Homer proteins regulate mGluR1/5 function by acting as adapters and facilitating coupling to effectors such as the inositol triphosphate receptor. However, although Homer proteins and their interaction with mGluRs have been the subject of intense study, direct measurements of Homer-induced changes in postsynaptic mGluR–effector coupling have not been reported. This question was addressed here by examining glutamatergic excitatory postsynaptic currents (EPSCs) in rat autaptic hippocampal cultures. In most neurons, the group I mGluR agonist (S)-3,5-dihydroxyphenylglycine strongly inhibited the EPSC acutely. This modulation occurred postsynaptically, was mediated primarily by mGluR5, and was inositol triphosphate receptor-dependent. Expression of the dominant negative, immediate early form of Homer, Homer 1a, strongly reduced EPSC modulation, but the W24A mutant of Homer 1a, which cannot bind mGluRs, had no effect. (S)-3,5-dihydroxyphenylglycine-mediated intracellular calcium responses in the processes of Homer 1a-expressing neurons were reduced compared with those in Homer 1a W24A-expressing cells. However, neither the distribution of mGluR5 nor the modulation of somatic calcium channels was altered by Homer 1a expression. These data demonstrate that Homer 1a can reduce mGluR5 coupling to postsynaptic effectors without relying on large changes in the subcellular distribution of the receptor. Thus, alteration of mGluR signaling by changes in Homer protein expression may represent a viable mechanism for fine-tuning synaptic strength in neurons.
Ethnobotanical knowledge is associated with indices of child health in the Bolivian Amazon
Authors: McDade T. W. , Reyes-García V. , Blackinton P. , Tanner S. , Huanca T. , Leonard W. R.
Published: March 2007

Culture is a critical determinant of human behavior and health, and the intergenerational transmission of knowledge regarding the use of available plant resources has historically been an essential function of culture. Local ethnobotanical knowledge is important for health and nutrition, particularly in rural low-resource settings, but cultural and economic transitions associated with globalization threaten such knowledge. This prospective study investigates the association between parental ethnobotanical knowledge and child health among the Tsimane', a horticulturalist and foraging society in Amazonian Bolivia. Anthropometric data and capillary blood samples were collected from 330 Tsimane' 2- to 10-year-olds, and mothers and fathers were interviewed to assess ethnobotanical knowledge and skills. Comprehensive measures of parental schooling, acculturation, and economic activities were also collected. Dependent variables included three measures of child health: (i) C-reactive protein, assayed in whole-blood spots as an indicator of immunostimulation; (ii) skinfold thickness, to estimate subcutaneous fat stores necessary to fuel growth and immune function; and (iii) height-for-age, to assess growth stunting. Each child health measure was associated with maternal ethnobotanical knowledge, independent of a wide range of potentially confounding variables. Each standard deviation of maternal ethnobotanical knowledge increased the likelihood of good child health by a factor of >1.5. Like many populations around the world, the Tsimane' are increasingly facing the challenges and opportunities of globalization. These results underscore the importance of local cultural factors to child health and document a potential cost if ethnobotanical knowledge is lost.
A look inside of diamond-forming media in deep subduction zones
Authors: Dobrzhinetskaya Larissa F. , Wirth Richard , Green Harry W.
Published: March 2007

Geologists have “known” for many years that continental crust is buoyant and cannot be subducted very deep. Microdiamonds 10–80 μm in size discovered in the 1980s within metamorphic rocks related to continental collisions clearly refute this statement, suggesting that material of continental crust has been subducted to a minimum depth of >150 km and incorporated into mountain chains during tectonic exhumation. Over the past decade, the rapidly moving technological advancement has made it possible to examine these diamonds in detail, and to learn that they contain nanometric multiphase inclusions of crystalline and fluid phases and are characterized by a “crustal” signature of carbon stable isotopes. Scanning and transmission electron microscopy, focused ion beam techniques, synchrotron infrared spectroscopy, and nano-secondary ion mass spectrometry studies of these diamonds provide evidence that they were crystallized from a supercritical carbon-oxygen-hydrogen fluid. These microdiamonds preserve evidence of the pathway by which carbon and water can be subducted to mantle depths and returned back to the earth's surface.
Exercise reverses preamyloid oligomer and prolongs survival in αB-crystallin-based desmin-related cardiomyopathy
Authors: Maloyan Alina , Gulick James , Glabe Charles G. , Kayed Rakez , Robbins Jeffrey
Published: March 2007

The R120G mutation in the small heat shock-like protein αB-crystallin (CryAB
R120G
) causes desmin-related myopathy (DRM), which is characterized by the formation of desmin- and CryAB-containing aggregates within muscle fibers. Mice with cardiac-specific overexpression of CryAB
R120G
develop cardiomyopathy at 3 months and die at 6–7 months from heart failure (HF). Previous studies showed that overexpression of CryAB
R120G
results in accumulation of preamyloid oligomer (PAO). PAO is considered to be the cytotoxic entity in many of the protein misfolding-based neurodegenerative diseases. On the basis of data from mouse models of neurodegenerative diseases showing that exercise or environmental enrichment reduces the amyloid oligomer level and improves cognitive ability, we hypothesized that CryAB
R120G
-induced DRM would also respond favorably to prolonged voluntary exercise, reducing HF symptoms and rescuing the mice from premature death. Six months of voluntary exercise in CryAB
R120G
animals resulted in 100% survival at a time when all unexercised mice had died. After 22 weeks of exercise, PAO levels were decreased by 47% compared with the unexercised CryAB
R120G
control mice (
P
= 0.00001). Although CryAB
R120G
expression led to decreased levels of the metallomembrane endopeptidase neprilysin, normal levels were maintained in the exercised CryAB
R120G
mice, and
in vitro
loss-of-function and gain-of-function experiments using adenovirus-infected cardiomyocytes confirmed the importance of neprilysin in ameliorating PAO accumulation. The data demonstrate that voluntary exercise slows the progression to HF in the CryAB
R120G
DRM model and that PAO accumulation is mediated, at least in part, by decreased neprilysin activity.
An NMR study oftransligand influence in rhodium η2triphenyltin hydride complexes
Authors: Carlton Laurence , Fernandes Manuel A. , Sitabule Enos
Published: March 2007

The complex [Rh(O2Cisoq)(H)(SnPh3)(PPh3)2] (O2Cisoq = isoquinoline-1-carboxylate), characterized by x-ray crystallography, was used as a precursor to three-center bonded complexes [Rh(O2Cisoq)(η2-HSnPh3)(PPh3)(4-Rpy)] (R = carbomethoxy, acyl, bromo, aldehyde, hydrogen, methoxy, dimethylamino), which were preparedin situfrom the bis(phosphine) complex in dichloromethane by addition of the pyridine. Of two isomeric forms of [Rh(O2Cisoq)(η2-HSnPh3)(PPh3)(4-Rpy)], one, with 4-Rpy positionedtransto tin, is formed at 0°C; the other, with isoquinoline positionedtransto tin, is formed by partial (25–50%) conversion of the first isomer (in solution) upon warming to 30–35°C for a few minutes. The relative coordination geometries of the two isomers were established by using a15N-enriched pyridine. NMR parameters (1H,31P,103Rh, and119Sn) for the pyridine-containing complexes show trends consistent with a significantly greater SnH interaction in complexes having isoquinoline lyingtransto tin and a threshold of σ donor strength for the pyridine below which the influence on Rh(SnH) bonding is minimal and above which the influence is to enhance the SnH interaction. Possible reasons for these effects are discussed.
Molecular and electrophysiological characterization of a mechanosensitive channel expressed in the chloroplasts of
Chlamydomonas
Authors: Nakayama Yoshitaka , Fujiu Kenta , Sokabe Masahiro , Yoshimura Kenjiro
Published: March 2007

MscS is a mechanosensitive channel that is ubiquitous among bacteria. Recent progress in the genome projects has revealed that homologs of MscS are also present in eukaryotes, but whether they operate as ion channels is unknown. In this study we cloned
MSC1
, a homolog of MscS in
Chlamydomonas
, and examined its function when expressed in
Escherichia coli
. Full-length MSC1 was not functional when expressed in
E. coli
cells. However, removal of the N-terminal signal sequence (ΔN-MSC1) reversed this effect. ΔN-MSC1 was found to open in response to membrane stretch and displayed a preference for anions over cations as permeable ions. ΔN-MSC1 exhibited marked hysteretic behavior in response to ascending and descending stimuli. That is, channel gating occurred in response to significant stimuli but remained open until the stimulus was almost completely removed. Indirect immunofluorescence revealed that MSC1 is present as punctate spots in the cytoplasm and chloroplasts. Moreover, knockdown of
MSC1
expression resulted in the abnormal localization of chlorophyll. These findings show that MSC1 is an intracellular mechanosensitive channel and is responsible for the organization of chloroplast in
Chlamydomonas
.
Structural basis for the selection of glycosylated substrates by SCF
Fbs1
ubiquitin ligase
Authors: Mizushima Tsunehiro , Yoshida Yukiko , Kumanomidou Taichi , Hasegawa Yuko , Suzuki Atsuo , Yamane Takashi , Tanaka Keiji
Published: March 2007

The ubiquitin ligase complex SCF
Fbs1
, which contributes to the ubiquitination of glycoproteins, is involved in the endoplasmic reticulum-associated degradation pathway. In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate specificity. Fbs1/Fbx2, a member of the F-box protein family, recognizes high-mannose oligosaccharides. To elucidate the structural basis of SCF
Fbs1
function, we determined the crystal structures of the Skp1–Fbs1 complex and the sugar-binding domain (SBD) of the Fbs1–glycoprotein complex. The mechanistic model indicated by the structures appears to be well conserved among the SCF ubiquitin ligases. The structure of the SBD–glycoprotein complex indicates that the SBD primarily recognizes Man
3
GlcNAc
2
, thereby explaining the broad activity of the enzyme against various glycoproteins. Comparison of two crystal structures of the Skp1–Fbs1 complex revealed the relative motion of a linker segment between the F-box and the SBD domains, which might underlie the ability of the complex to recognize different acceptor lysine residues for ubiquitination.
High-pressure/low-temperature neutron scattering of gas inclusion compounds: Progress and prospects
Authors: Zhao Yusheng , Xu Hongwu , Daemen Luke L. , Lokshin Konstantin , Tait Kimberly T. , Mao Wendy L. , Luo Junhua , Currier Robert P. , Hickmott Donald D.
Published: March 2007

Alternative energy resources such as hydrogen and methane gases are becoming increasingly important for the future economy. A major challenge for using hydrogen is to develop suitable materials to store it under a variety of conditions, which requires systematic studies of the structures, stability, and kinetics of various hydrogen-storing compounds. Neutron scattering is particularly useful for these studies. We have developed high-pressure/low-temperature gas/fluid cells in conjunction with neutron diffraction and inelastic neutron scattering instruments allowing
in situ
and real-time examination of gas uptake/release processes. We studied the formation of methane and hydrogen clathrates, a group of inclusion compounds consisting of frameworks of hydrogen-bonded H
2
O molecules with gas molecules trapped inside the cages. Our results reveal that clathrate can store up to four hydrogen molecules in each of its large cages with an intermolecular H
2
–H
2
distance of only 2.93 Å. This distance is much shorter than that in the solid/metallic hydrogen (3.78 Å), suggesting a strong densification effect of the clathrate framework on the enclosed hydrogen molecules. The framework-pressurizing effect is striking and may exist in other inclusion compounds such as metal-organic frameworks (MOFs). Owing to the enormous variety and flexibility of their frameworks, inclusion compounds may offer superior properties for storage of hydrogen and/or hydrogen-rich molecules, relative to other types of compounds. We have investigated the hydrogen storage properties of two MOFs, Cu
3
[Co(CN)
6
]
2
and Cu
3
(BTC)
2
(BTC = benzenetricarboxylate), and our preliminary results demonstrate that the developed neutron-scattering techniques are equally well suited for studying MOFs and other inclusion compounds.
Timing of estrogen therapy after ovariectomy dictates the efficacy of its neuroprotective and antiinflammatory actions
Authors: Suzuki Shotaro , Brown Candice M. , Dela Cruz Christopher D. , Yang Enhua , Bridwell David A. , Wise Phyllis M.
Published: March 2007

Recent studies describing the seemingly contradictory actions of estrogens in ischemic stroke injury have led us to reevaluate the circumstances under which estrogen therapy (ET) provides benefits against cerebral stroke and decipher its mechanisms of action. One prominent feature that follows stroke injury is massive central and peripheral inflammatory responses. Evidence now suggests that postischemic inflammatory responses strongly contribute to the extent of brain injury, and 17β-estradiol (E
2
) may protect the ischemic brain by exerting antiinflammatory actions. In an attempt to explain recently reported dichotomous effects of E
2
in stroke injury, we tested the hypothesis that an extended period of hypoestrogenicity both prevents E
2
from protecting the brain against ischemia and simultaneously suppresses its antiinflammatory actions. We report that E
2
exerts profound neuroprotective action when administered immediately upon ovariectomy, but not when administered after 10 weeks of hypoestrogenicity. Consistently, E
2
treatment given immediately at the time of ovariectomy attenuated central and peripheral production of proinflammatory cytokines after ischemic stroke. In contrast, E
2
did not suppress production of proinflammatory molecules when it was administered after 10 weeks postovariectomy. These results demonstrate that a prolonged period of hypoestrogenicity disrupts both neuroprotective and antiinflammatory actions of E
2
. Our findings may help to explain the results of the Women's Health initiative that reported no beneficial effect of ET against stroke because the majority of the subjects initiated ET after an extended period of hypoestrogenicity.
Transgenerational epigenetic imprints on mate preference
Authors: Crews David , Gore Andrea C. , Hsu Timothy S. , Dangleben Nygerma L. , Spinetta Michael , Schallert Timothy , Anway Matthew D. , Skinner Michael K.
Published: March 2007

Environmental contamination by endocrine-disrupting chemicals (EDC) can have epigenetic effects (by DNA methylation) on the germ line and promote disease across subsequent generations. In natural populations, both sexes may encounter affected as well as unaffected individuals during the breeding season, and any diminution in attractiveness could compromise reproductive success. Here we examine mate preference in male and female rats whose progenitors had been treated with the antiandrogenic fungicide vinclozolin. This effect is sex-specific, and we demonstrate that females three generations removed from the exposure discriminate and prefer males who do not have a history of exposure, whereas similarly epigenetically imprinted males do not exhibit such a preference. The observations suggest that the consequences of EDCs are not just transgenerational but can be “transpopulational”, because in many mammalian species, males are the dispersing sex. This result indicates that epigenetic transgenerational inheritance of EDC action represents an unappreciated force in sexual selection. Our observations provide direct experimental evidence for a role of epigenetics as a determinant factor in evolution.
The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes
Authors: Achard Patrick , Baghour Mourad , Chapple Andrew , Hedden Peter , Van Der Straeten Dominique , Genschik Pascal , Moritz Thomas , Harberd Nicholas P.
Published: March 2007

The length of the
Arabidopsis thaliana
life cycle depends on the timing of the floral transition. Here, we define the relationship between the plant stress hormone ethylene and the timing of floral initiation. Ethylene signaling is activated by diverse environmental stresses, but it was not previously clear how ethylene regulates flowering. First, we show that ethylene delays flowering in
Arabidopsis
, and that this delay is partly rescued by loss-of-function mutations in genes encoding the DELLAs, a family of nuclear gibberellin (GA)-regulated growth-repressing proteins. This finding suggests that ethylene may act in part by modulating DELLA activity. We also show that activated ethylene signaling reduces bioactive GA levels, thus enhancing the accumulation of DELLAs. Next, we show that ethylene acts on DELLAs via the CTR1-dependent ethylene response pathway, most likely downstream of the transcriptional regulator EIN3. Ethylene-enhanced DELLA accumulation in turn delays flowering via repression of the floral meristem-identity genes
LEAFY
(
LFY
) and
SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1
(
SOC1
). Our findings establish a link between the CTR1/EIN3-dependent ethylene and GA–DELLA signaling pathways that enables adaptively significant regulation of plant life cycle progression in response to environmental adversity.
Overexpression of CCS in G93A-SOD1 mice leads to accelerated neurological deficits with severe mitochondrial pathology
Authors: Son Marjatta , Puttaparthi Krishna , Kawamata Hibiki , Rajendran Bhagya , Boyer Philip J. , Manfredi Giovanni , Elliott Jeffrey L.
Published: March 2007

Cu, Zn superoxide dismutase (SOD1) has been detected within spinal cord mitochondria of mutant SOD1 transgenic mice, a model of familial ALS. The copper chaperone for SOD1 (CCS) provides SOD1 with copper, facilitates the conversion of immature apo-SOD1 to a mature holoform, and influences in yeast the cytosolic/mitochondrial partitioning of SOD1. To determine how CCS affects G93A-SOD1-induced disease, we generated transgenic mice overexpressing CCS and crossed them to G93A-SOD1 or wild-type SOD1 transgenic mice. Both CCS transgenic mice and CCS/wild-type-SOD1 dual transgenic mice are neurologically normal. In contrast, CCS/G93A-SOD1 dual transgenic mice develop accelerated neurological deficits, with a mean survival of 36 days, compared with 242 days for G93A-SOD1 mice. Immuno-EM and subcellular fractionation studies on the spinal cord show that G93A-SOD1 is enriched within mitochondria in the presence of CCS overexpression. Our results indicate that CCS overexpression in G93A-SOD1 mice produces severe mitochondrial pathology and accelerates disease course.
Lysosomal killing ofMycobacteriummediated by ubiquitin-derived peptides is enhanced by autophagy
Authors: Alonso Sylvie , Pethe Kevin , Russell David G. , Purdy Georgiana E.
Published: March 2007

Mycobacterium tuberculosisparasitizes resting macrophages yet is killed by activated macrophages through both oxidative and nonoxidative mechanisms. Nonoxidative mechanisms are linked to the maturation of the bacteria-containing phagosome into an acidified, hydrolytically active compartment. We describe here a mechanism for killingMycobacteriain the lysosomal compartment through the activity of peptides generated by the hydrolysis of ubiquitin. The induction of autophagy in infected macrophages enhanced the delivery of ubiquitin conjugates to the lysosome and increased the bactericidal capacity of the lysosomal soluble fraction. The accumulation of ubiquitinated proteins in the autophagolysosome provides one possible mechanism behind the antimicrobial activities observed for a range of pathogens in autophagous host cells.
Estimation of critical exponents from cluster coefficients and the application of this estimation to hard spheres
Authors: Eisenberg E. , Baram A.
Published: March 2007

For a large class of repulsive interaction models, the Mayer cluster integrals can be transformed into a tridiagonal real symmetric matrix
R

mn

, whose elements converge to two constants with 1/
n
2
correction. We find exact expressions in terms of these correction terms for the two critical exponents describing the density near the two singular termination points of the fluid phase. We apply the method to the hard-spheres model and find that the metastable fluid phase terminates at ρ
t
= 0.751[5]. The density near the transition is given by ρ
t
-ρ ∼ (
z
t
−
z
)
σ′
, where the critical exponent is predicted to be σ′ = 0.0877[25]. Interestingly, the termination density is close to the observed glass transition; thus, the above critical behavior is expected to be associated with the onset of glassy behavior in hard spheres.
Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays
Authors: Pourmand Nader , Caramuta Stefano , Villablanca Andrea , Mori Silvia , Karhanek Miloslav , Wang Shan X. , Davis Ronald W.
Published: March 2007

The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or column-based approaches to analyze DNA repeats. Individual STR alleles are separated and distinguished according to fragment length; thus the assay is generally hampered by its low multiplex capacity. However, use of DNA microarray would employ a simple hybridization and detection for field forensics and biology. Here we demonstrate a rapid, highly sensitive method for STR analysis that utilizes DNA microarray technology. We describe two adaptations to accomplish this: the use of competitive hybridization to remove unpaired ssDNA from an array and the use of neural network classification to automate the analysis. The competitive displacement technique mimics the branch migration process that occurs during DNA recombination. Our technique will facilitate the rapid deduction of identity, length, and number of repeats for the multiple STRs in an unknown DNA sample.
Signaling-dependent and coordinated regulation of transcription, splicing, and translation resides in a single coregulator, PCBP1
Authors: Meng Qingchang , Rayala Suresh K. , Gururaj Anupama E. , Talukder Amjad H. , O'Malley Bert W. , Kumar Rakesh
Published: March 2007

Transcription, splicing, and translation are potentially coordinately regulatable in a temporospatial-dependent manner, although supporting experimental evidence for this notion is scarce. Yeast two-hybrid screening of a mammary gland cDNA library with human p21-activated kinase 1 (Pak1) as bait identified polyC-RNA-binding protein 1 (PCBP1), which controls translation from mRNAs containing the DICE (differentiation control element). Mitogenic stimulation of human cells phosphorylated PCBP1 on threonines 60 and 127 in a Pak1-sensitive manner. Pak1-dependent phosphorylation of PCBP1 released its binding and translational inhibition from a DICE-minigene. Overexpression of PCBP1 also inhibited the translation of the endogenous L1 cell adhesion molecule mRNA, which contains two DICE motifs in the 3′ untranslated region. We also found that Pak1 activation led to an increased nuclear retention of PCBP1, recruitment to the eukaryotic translation initiation factor 4E (eIF4E) promoter, and stimulation of eIF4E expression in a Pak1-sensitive manner. Moreover, mitogenic stimulation promoted Pak1- and PCBP1-dependent alternative splicing and exon inclusion from a CD44 minigene. The alternative splicing functions of PCBP1 were in turn mediated by its intrinsic interaction with Caper α, a U2 snRNP auxiliary factor-related protein previously implicated in RNA splicing. These findings establish the principle that a single coregulator can function as a signal-dependent and coordinated regulator of transcription, splicing, and translation.
Adaptive TGF-β-dependent regulatory T cells control autoimmune diabetes and are a privileged target of anti-CD3 antibody treatment
Authors: You Sylvaine , Leforban Bertrand , Garcia Corinne , Bach Jean-François , Bluestone Jeffrey A. , Chatenoud Lucienne
Published: March 2007

Previous results have shown that CD4+CD25+regulatory T cells (Tregs) control autoimmunity in a spontaneous model of type 1 diabetes, the nonobese diabetic (NOD) mouse. Moreover, anti-CD3 reverses diabetes in this setting by promoting Tregs that function in a TGF-β-dependent manner. This finding contrasts with a large body of work suggesting that CD4+CD25highTregs act in a cytokine-independent manner, thus suggesting that another type of Treg is operational in this setting. We sought to determine the basis of suppression both in untreated NOD mice and in those treated with anti-CD3. Our present results show that a subset of foxP3+cells present within a CD4+CD25lowlymphocyte subset suppresses T cell immunity in spontaneously diabetic NOD mice in a TGF-β-dependent manner, a functional property typical of “adaptive” regulatory T cells. This distinct Treg subset is evident in NOD, but not normal, mice, suggesting that the NOD mice may generate these adaptive Tregs in an attempt to regulate ongoing autoimmunity. Importantly, in two distinctin vivomodels, these TGF-β-dependent adaptive CD4+CD25lowT cells can be induced from peripheral CD4+CD25−T lymphocytes by anti-CD3 immunotherapy which correlates with the restoration of self-tolerance.
Toll-like receptor-MyD88 and Fc receptor pathways of mast cells mediate the thyroid dysfunctions observed during nonthyroidal illness
Authors: Rocchi Roberto , Kimura Hiroaki , Tzou Shey-Cherng , Suzuki Koichi , Rose Noel R. , Pinchera Aldo , Ladenson Paul W. , Caturegli Patrizio
Published: March 2007

Bacterial infections and other pathologic conditions induce complex dysfunctions of the hypothalamic–pituitary–thyroid axis, collectively known as nonthyroidal illness (NTI). To explore the pathogenesis of bacterial NTI, we injected
Mycobacterium tuberculosis
extracts or
Escherichia coli
LPS in mice lacking key components of the Toll-like receptor or crystallizable fragment (Fc) receptor pathways. In wild-type mice, the bacterial components induced a hypothyroidism characterized by elements of both hypothalamic and thyroidal dysfunction. This NTI hypothyroidism did not develop in mice lacking the MyD88 adaptor or in those with a reduced number of mast cells. The hypothyroid responsiveness to LPS, however, was restored upon reconstitution with mast cells derived from the bone marrow of wild-type donors. In addition to bacterial components, whole immunoglobulins induced NTI hypothyroidism in wild-type mice, but not in those lacking activating Fc receptors or mast cells. The study demonstrates a link between Toll-like and Fc receptor signaling and thyroid gland function, uncovering a role of mast cells in murine NTI.
Unc-51-like kinase 1/2-mediated endocytic processes regulate filopodia extension and branching of sensory axons
Authors: Zhou Xiang , Babu J. Ramesh , da Silva Susana , Shu Qing , Graef Isabella A. , Oliver Tim , Tomoda Toshifumi , Tani Tomomi , Wooten Marie W. , Wang Fan
Published: March 2007

The molecular mechanism and significance of endocytic processes involved in directional axon elongation are not well understood. The Unc-51 family of serine/threonine kinases was shown to be important for axon growth and was also linked to endocytosis, providing an entry point to study this problem. We found that mouse Unc-51-like kinase 1/2 (Ulk1/2) proteins are localized to vesicular structures in growth cones of mouse spinal sensory neurons. RNAi-mediated knockdown of Ulk1 and/or Ulk2 resulted in impaired endocytosis of nerve growth factor (NGF), excessive axon arborization, and severely stunted axon elongation. The evidence also indicates that Ulk1/2 mediates a non-clathrin-coated endocytosis in sensory growth cones. Interestingly, NGF can induce the interaction of Ulk1 with TrkA receptor complexes through promoting K63-polyubiquitination of Ulk1 and binding of Ulk1 to the scaffolding protein p62. These results and additional studies suggest that Ulk1/2 proteins regulate filopodia extension and neurite branching during sensory axon outgrowth, probably through regulating TrkA receptor trafficking and signaling.
Splenic accumulation of IL-10 mRNA in T cells distinct from CD4+CD25+ (Foxp3) regulatory T cells in human visceral leishmaniasis
Authors: Nylén Susanne , Maurya Radheshyam , Eidsmo Liv , Manandhar Krishna Das , Sundar Shyam , Sacks David
Published: March 2007

Visceral leishmaniasis (VL) is a life-threatening disease characterized by uncontrolled parasitization of the spleen, liver, and bone marrow. Interleukin (IL)-10 has been implicated in the suppression of host immunity in human VL based on the elevated levels of IL-10 observed in plasma and lesional tissue, and its role in preventing clearance of Leishmania donovani in murine models of VL. The aim of this study was to identify the cellular source of IL-10 in human VL and determine if CD4+CD25+ (Foxp3high) regulatory T (T reg) cells are associated with active disease. We analyzed surface marker and gene expression in peripheral blood mononuclear cells and splenic aspirates from Indian VL patients before and 3–4 wk after treatment with Amphotericin B. The results did not point to an important role for natural CD4+CD25+ (Foxp3high) T reg cells in human VL. They did not accumulate in and were not a major source of IL-10 in the spleen, and their removal did not rescue antigen-specific interferon γ responses. In contrast, splenic T cells depleted of CD25+ cells expressed the highest levels of IL-10 mRNA and were the predominant lymphocyte population in the VL spleen. The elevated levels of IL-10 in VL plasma significantly enhanced the growth of L. donovani amastigotes in human macrophages. The data implicate IL-10–producing CD25−Foxp3− T cells in the pathogenesis of human VL.
Lymph node topology dictates T cell migration behavior
Authors: Beltman Joost B. , Marée Athanasius F.M. , Lynch Jennifer N. , Miller Mark J. , de Boer Rob J.
Published: March 2007

Adaptive immunity is initiated by T cell recognition of foreign peptides presented on dendritic cells (DCs) by major histocompatibility molecules. These interactions take place in secondary lymphoid tissues, such as lymph nodes (LNs) and spleen, and hence the anatomical structure of these tissues plays a crucial role in the development of immune responses. Two-photon microscopy (2PM) imaging in LNs suggests that T cells walk in a consistent direction for several minutes, pause briefly with a regular period, and then take off in a new, random direction. Here, we construct a spatially explicit model of T cell and DC migration in LNs and show that all dynamical properties of T cells could be a consequence of the densely packed LN environment. By means of 2PM experiments, we confirm that the large velocity fluctuations of T cells are indeed environmentally determined rather than resulting from an intrinsic motility program. Our simulations further predict that T cells self-organize into microscopically small, highly dynamic streams. We present experimental evidence for the presence of such turbulent streams in LNs. Finally, the model allows us to estimate the scanning rates of DCs (2,000 different T cells per hour) and T cells (100 different DCs per hour).