bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in water flows and water productivity upon vegetation regeneration on degraded hillslopes in northern Ethiopia: a water balance modelling exercise
Authors: Descheemaeker Katrien , Raes Dirk , Nyssen Jan , Poesen Jean , Haile Mitiku , Deckers Jozef
Published: June 2009

The establishment of exclosures (i.e. areas closed for grazing and agriculture) is a common practice to reverse land degradation through vegetation regeneration in the semiarid highland areas of northern Ethiopia. In order to assess the effect of exclosures on water flows, the water balance components for different vegetation regeneration stages were assessed through field measurements and modelling. Successful model calibration and validation was done based on soil water content measurements conducted during 2 years in 22 experimental plots. In the protected areas, vegetation regeneration leads to an increase in infiltration and transpiration and a more productive use of water for biomass production. In areas where additional lateral water (runon) infiltrates, source–sink systems are created. Here, up to 30% of the annual rainfall percolates through the root-zone towards the groundwater table. Increased biomass production in exclosures leads to possibilities for wood harvesting and cut and carry of grasses for livestock feeding. Together with water conservation and more productive use of water, the latter contributes to increased livestock water productivity. At the landscape scale, the creation of vegetation filters, capturing resources like water and nutrients, reinforces the rehabilitation process and healthy landscape functioning.
Factors affecting livestock water productivity: animal scale analysis using previous cattle feeding trials in Ethiopia
Authors: Gebreselassie S. , Peden D. , Haileslassie A. , Mpairwe D.
Published: June 2009

Availability and access to fresh water will likely constrain future food production in many countries. Thus, it is frequently suggested that the limited amount of water should be used more productively. In this study we report the results of our investigation on effects of feed, age and weight on livestock water productivity (LWP). The main objective is to identify technologies that will help enhance LWP. We combined empirical knowledge and literature values to estimate the amount of water depleted to produce beef, milk, traction power and manure. We estimated the LWP as the ratio of livestock products and services to the depleted water. In the feeding trials, various combinations of maize and oat stover, vetch, lablab and wheat bran were combined in different proportions to make 16 unique rations that were fed to the experimental animals of different age and weight groups. We observed differences of LWP across feed type, age and weight of dairy cows. The value of LWP tended to increase with increasing age and weight: the lowest LWP (0.34 US$/m3) for cows less than five years whereas the highest LWP value was 0.41 US$/m3 for those cows in the age category of 8 years and above. Similarly, there was an increase in LWP as weight of the animal increased, i.e. LWP was lowest (0.32 US$/m3) for lower weight groups (300–350 kg) and increased for larger animals.
There were apparent impacts of feed composition on LWP values. For example, the highest LWP value was observed for oat, vetch and wheat bran mixes. Taking livestock services and products into account, the overall livestock water productivity ranged from 0.25 to 0.39 US$/m3 and the value obtained from a cow appeared to be higher than for an ox. In conclusion, some strategies and technological options such as improved feeds, better herd management, appropriate heard structure can be adapted to enhance LWP.
Influence of the coupling of interdomain and overall motions on NMR relaxation
Authors: Wong Vance , Case David A. , Szabo Attila
Published: June 2009

Most theoretical models for NMR relaxation in liquids assume that overall rotational motion can be described as rotational diffusion with a single diffusion tensor. Such models cannot handle motions (such as between “closed” and “open” states of an enzyme, or between conformers of a partially disordered system) where the shape of the molecule (and hence its rotational diffusion behavior) fluctuates. We provide here a formalism for dealing with such problems. The model involves jumps between discrete conformers with different overall diffusion tensors, and a master (rate) equation to describe the transitions between these conformers. Numerical examples are given for a two-site jump model where global and local motions are concerted, showing how the rate of conformational transitions (relative to the rate of rotational diffusion) affects the observed relaxation parameters.
The endocannabinoid system and pivotal role of the CB
2
receptor in mouse spermatogenesis
Authors: Grimaldi Paola , Orlando Pierangelo , Di Siena Sara , Lolicato Francesca , Petrosino Stefania , Bisogno Tiziana , Geremia Raffaele , De Petrocellis Luciano , Di Marzo Vincenzo
Published: June 2009

The exact role of the endocannabinoid system (ECS) during spermatogenesis has not been clarified. We used purified germ cell fractions representative of all phases of spermatogenesis and primary cultures of spermatogonia. This approach allowed the precise quantification of the cannabinoid receptor ligands, anandamide and 2-arachidonoylglycerol, and of the expression at transcriptional and transductional levels of their metabolic enzymes and receptors. Our data indicate that male mouse germ cells possess an active and complete ECS, which is modulated during meiosis, and suggest the presence of an autocrine endocannabinoid signal during spermatogenesis. Mitotic cells possess higher levels of 2-arachidonoylglycerol, which decrease in spermatocytes and spermatids. Accordingly, spermatogonia express higher and lower levels of 2-arachidonoylglycerol biosynthetic and degrading enzymes, respectively, as compared to meiotic and postmeiotic cells. This endocannabinoid likely plays a pivotal role in promoting the meiotic progression of germ cells by activating CB
2
receptors. In fact, we found that the selective CB
2
receptor agonist, JWH133, induced the Erk 1/2 MAPK phosphorylation cascade in spermatogonia and their progression toward meiosis, because it increased the number of cells positive for SCP3, a marker of meiotic prophase, and the expression of early meiotic prophase genes.
Discrete molecular states in the brain accompany changing responses to a vocal signal
Authors: Dong Shu , Replogle Kirstin L. , Hasadsri Linda , Imai Brian S. , Yau Peter M. , Rodriguez-Zas Sandra , Southey Bruce R. , Sweedler Jonathan V. , Clayton David F.
Published: June 2009

New experiences can trigger changes in gene expression in the brain. To understand this phenomenon better, we studied zebra finches hearing playbacks of birdsong. Earlier research had shown that initial playbacks of a novel song transiently increase the ZENK (ZIF-268,EGR1,NGFIA,KROX-24) mRNA in the auditory forebrain, but the response selectively habituates after repetition of the stimulus. Here, using DNA microarray analysis, we show that novel song exposure induces rapid changes in thousands of RNAs, with even more RNAs decreasing than increasing. Habituation training leads to the emergence of a different gene expression profile a day later, accompanied by loss of essentially all of the rapid “novel” molecular responses. The novel molecular profile is characterized by increases in genes involved in transcription and RNA processing and decreases in ion channels and putative noncoding RNAs. The “habituated” profile is dominated by changes in genes for mitochondrial proteins. A parallel proteomic analysis [2-dimensional difference gel electrophoresis (2D-DIGE) and sequencing by mass spectrometry] also detected changes in mitochondrial proteins, and direct enzyme assay demonstrated changes in both complexes I and IV in the habituated state. Thus a natural experience, in this case hearing the sound of birdsong, can lead to major shifts in energetics and macromolecular metabolism in higher centers in the brain.
Evaluating β-turn mimics as β-sheet folding nucleators
Authors: Fuller Amelia A. , Du Deguo , Liu Feng , Davoren Jennifer E. , Bhabha Gira , Kroon Gerard , Case David A. , Dyson H. Jane , Powers Evan T. , Wipf Peter , Gruebele Martin , Kelly Jeffery W.
Published: June 2009

β-Turns are common conformations that enable proteins to adopt globular structures, and their formation is often rate limiting for folding. β-Turn mimics, molecules that replace the
i
+ 1 and
i
+ 2 amino acid residues of a β-turn, are envisioned to act as folding nucleators by preorganizing the pendant polypeptide chains, thereby lowering the activation barrier for β-sheet formation. However, the crucial kinetic experiments to demonstrate that β-turn mimics can act as strong nucleators in the context of a cooperatively folding protein have not been reported. We have incorporated 6 β-turn mimics simulating varied β-turn types in place of 2 residues in an engineered β-turn 1 or β-bulge turn 1 of the Pin 1 WW domain, a three-stranded β-sheet protein. We present 2 lines of kinetic evidence that the inclusion of β-turn mimics alters β-sheet folding rates, enabling us to classify β-turn mimics into 3 categories: those that are weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong nucleators accelerate folding relative to WW domains incorporating all α-amino acid sequences. A solution NMR structure reveals that the native Pin WW β-sheet structure is retained upon incorporating a strong
E
-olefin nucleator. These β-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other β-turn mimics.
mTOR and HIF-1α-mediated tumor metabolism in an LKB1 mouse model of Peutz-Jeghers syndrome
Authors: Shackelford David B. , Vasquez Debbie S. , Corbeil Jacqueline , Wu Shulin , Leblanc Mathias , Wu Chin-Lee , Vera David R. , Shaw Reuben J.
Published: June 2009

Peutz-Jeghers syndrome (PJS) is a familial cancer disorder due to inherited loss of function mutations in the LKB1/ STK11 serine/threonine kinase. PJS patients develop gastrointestinal hamartomas with 100% penetrance often in the second decade of life, and demonstrate an increased predisposition toward the development of a number of additional malignancies. Among mitogenic signaling pathways, the mammalian-target of rapamycin complex 1 (mTORC1) pathway is hyperactivated in tissues and tumors derived from LKB1-deficient mice. Consistent with a central role for mTORC1 in these tumors, rapamycin as a single agent results in a dramatic suppression of preexisting GI polyps in LKB1+/− mice. However, the key targets of mTORC1 in LKB1-deficient tumors remain unknown. We demonstrate here that these polyps, and LKB1- and AMPK-deficient mouse embryonic fibroblasts, show dramatic up-regulation of the HIF-1α transcription factor and its downstream transcriptional targets in an rapamycin-suppressible manner. The HIF-1α targets hexokinase II and Glut1 are up-regulated in these polyps, and using FDG-PET, we demonstrate that LKB1+/− mice show increased glucose utilization in focal regions of their GI tract corresponding to these gastrointestinal hamartomas. Importantly, we demonstrate that polyps from human Peutz-Jeghers patients similarly exhibit up-regulated mTORC1 signaling, HIF-1α, and GLUT1 levels. Furthermore, like HIF-1α and its target genes, the FDG-PET signal in the GI tract of these mice is abolished by rapamycin treatment. These findings suggest a number of therapeutic modalities for the treatment and detection of hamartomas in PJS patients, and potential for the screening and treatment of the 30% of sporadic human lung cancers bearing LKB1 mutations.
Zinc is an essential trace element for spermatogenesis
Authors: Yamaguchi Sonoko , Miura Chiemi , Kikuchi Kazuya , Celino Fritzie T. , Agusa Tetsuro , Tanabe Shinsuke , Miura Takeshi
Published: June 2009

Zinc (Zn) plays important roles in various biological activities but there is little available information regarding its functions in spermatogenesis. In our current study, we further examined the role of Zn during spermatogenesis in the Japanese eel (
Anguilla japonica
). Human CG (hCG) was injected into the animals to induce spermatogenesis, after which the concentration of Zn in the testis increased in tandem with the progression of spermatogenesis. Staining of testicular cells with a Zn-specific fluorescent probe revealed that Zn accumulates in germ cells, particularly in the mitochondria of spermatogonia and spermatozoa. Using an in vitro testicular organ culture system for the Japanese eel, production of a Zn deficiency by chelation with
N
,
N
,
N
′,
N
′-tetrakis (2-pyridylemethyl)ethylenediamine (TPEN) caused apoptosis of the germ cells. However, this cell death was rescued by the addition of Zn to the cultures. Furthermore, an induced deficiency of Zn by TPEN chelation was found to inhibit the germ cell proliferation induced by 11-ketotestosterone (KT), a fish specific androgen, 17α,20β-dihydroxy-4-pregnen-3-one (DHP), the initiator of meiosis in fish, and estradiol-17β (E2), an inducer of spermatogonial stem-cell renewal. We also investigated the effects of Zn deficiency on sperm motility and observed that TPEN treatment of eel sperm suppressed the rate and duration of their motility but that co-treatment with Zn blocked the effects of TPEN. Our present results thus suggest that Zn is an essential trace element for the maintenance of germ cells, the progression spermatogenesis, and the regulation of sperm motility.
Stress increases putative gonadotropin inhibitory hormone and decreases luteinizing hormone in male rats
Authors: Kirby Elizabeth D. , Geraghty Anna C. , Ubuka Takayoshi , Bentley George E. , Kaufer Daniela
Published: June 2009

The subjective experience of stress leads to reproductive dysfunction in many species, including rodents and humans. Stress effects on reproduction result from multilevel interactions between the hormonal stress response system, i.e., the hypothalamic–pituitary–adrenal (HPA) axis, and the hormonal reproductive system, i.e., the hypothalamic–pituitary–gonadal (HPG) axis. A novel negative regulator of the HPG axis known as gonadotropin-inhibitory hormone (GnIH) was recently discovered in quail, and orthologous neuropeptides known as RFamide-related peptides (RFRPs) have also been identified in rodents and primates. It is currently unknown, however, whether GnIH/RFRPs influence HPG axis activity in response to stress. We show here that both acute and chronic immobilization stress lead to an up-regulation of RFRP expression in the dorsomedial hypothalamus (DMH) of adult male rats and that this increase in RFRP is associated with inhibition of downstream HPG activity. We also show that adrenalectomy blocks the stress-induced increase in RFRP expression. Immunohistochemistry revealed that 53% of RFRP cells express receptors for glucocorticoids (GCs), indicating that adrenal GCs can mediate the stress effect through direct action on RFRP cells. It is thought that stress effects on central control of reproduction are largely mediated by direct or indirect effects on GnRH-secreting neurons. Our data show that stress-induced increases in adrenal GCs cause an increase in RFRP that contributes to hypothalamic suppression of reproductive function. This novel insight into HPA-HPG interaction provides a paradigm shift for work on stress-related reproductive dysfunction and infertility, and indicates that future work on stress and reproductive system interactions must include investigation of the role of GnIH/RFRP.
Oviposition preference for and positional avoidance of acetic acid provide a model for competing behavioral drives in
Drosophila
Authors: Joseph Ryan M. , Devineni Anita V. , King Ian F. G. , Heberlein Ulrike
Published: June 2009

Selection of appropriate oviposition sites is essential for progeny survival and fitness in generalist insect species, such as
Drosphila melanogaster
, yet little is known about the mechanisms regulating how environmental conditions and innate adult preferences are evaluated and balanced to yield the final substrate choice for egg-deposition. Female
D. melanogaster
are attracted to food containing acetic acid (AA) as an oviposition substrate. However, our observations reveal that this egg-laying preference is a complex process, as it directly opposes an otherwise strong, default behavior of positional avoidance for the same food. We show that 2 distinct sensory modalities detect AA. Attraction to AA-containing food for the purpose of egg-laying relies on the gustatory system, while positional repulsion depends primarily on the olfactory system. Similarly, distinct central brain regions are involved in AA attraction and repulsion. Given this unique situation, in which a single environmental stimulus yields 2 opposing behavioral outputs, we propose that the interaction of egg-laying attraction and positional aversion for AA provides a powerful model for studying how organisms balance competing behavioral drives and integrate signals involved in choice-like processes.
Signaling dynamics of the KSR1 scaffold complex
Authors: McKay Melissa M. , Ritt Daniel A. , Morrison Deborah K.
Published: June 2009

Scaffold proteins contribute to the spatiotemporal control of MAPK signaling and KSR1 is an ERK cascade scaffold that localizes to the plasma membrane in response to growth factor treatment. To better understand the molecular mechanisms of KSR1 function, we examined the interaction of KSR1 with each of the ERK cascade components, Raf, MEK, and ERK. Here, we identify a hydrophobic motif within the proline-rich sequence (PRS) of MEK1 and MEK2 that is required for constitutive binding to KSR1 and find that MEK binding and residues in the KSR1 CA1 region enable KSR1 to form a ternary complex with B-Raf and MEK following growth factor treatment that enhances MEK activation. We also find that docking of active ERK to the KSR1 scaffold allows ERK to phosphorylate KSR1 and B-Raf on feedback S/TP sites. Strikingly, feedback phosphorylation of KSR1 and B-Raf promote their dissociation and result in the release of KSR1 from the plasma membrane. Together, these findings provide unique insight into the signaling dynamics of the KSR1 scaffold and reveal that through regulated interactions with Raf and ERK, KSR1 acts to both potentiate and attenuate ERK cascade activation, thus regulating the intensity and duration of ERK cascade signaling emanating from the plasma membrane during growth factor signaling.
A metastable
DWARF1
epigenetic mutant affecting plant stature in rice
Authors: Miura Kotaro , Agetsuma Masakazu , Kitano Hidemi , Yoshimura Atsushi , Matsuoka Makoto , Jacobsen Steven E. , Ashikari Motoyuki
Published: June 2009

Epigenetic mutations confer heritable changes in gene expression that are not due to changes in the underlying sequence of the DNA. We identified a spontaneous rice mutant,
Epi-d1
, that shows a metastable dwarf phenotype. The phenotype is mitotically and meiotically inheritable and corresponds to the metastable epigenetic silencing of the
DWARF1
(
D1
) gene. The silenced state is correlated with repressive histone and DNA methylation marks in the
D1
promoter region but is not associated with DNA sequence alterations. Compared with other known epigenetic silenced loci in plants such as paramutable maize alleles and silent
Arabidopsis
genes, the
Epi-d1
silencing phenomenon shows a high level of bidirectional metastable mutability. Epigenetic alleles such as
Epi-d1
could thus provide for rapid adaptation under selective conditions.
Protein tyrosine phosphatase activity in the neural crest is essential for normal heart and skull development
Authors: Nakamura Tomoki , Gulick James , Colbert Melissa C. , Robbins Jeffrey
Published: June 2009

Mutations within the protein tyrosine phosphatase, SHP2, which is encoded by
PTPN11
, cause a significant proportion of Noonan syndrome (NS) cases, typically presenting with both cardiac disease and craniofacial abnormalities. Neural crest cells (NCCs) participate in both heart and skull formation, but the role of SHP2 signaling in NCC has not yet been determined. To gain insight into the role of SHP2 in NCC function, we ablated
PTPN11
specifically in premigratory NCCs. SHP2-deficient NCCs initially exhibited normal migratory and proliferative patterns, but in the developing heart failed to migrate into the developing outflow tract. The embryos displayed persistent truncus arteriosus and abnormalities of the great vessels. The craniofacial deficits were even more pronounced, with large portions of the face and cranium affected, including the mandible and frontal and nasal bones. The data show that SHP2 activity in the NCC is essential for normal migration and differentiation into the diverse lineages found in the heart and skull and demonstrate the importance of NCC-based normal SHP2 activity in both heart and skull development, providing insight into the syndromic presentation characteristic of NS.
SPLUNC1 regulates airway surface liquid volume by protecting ENaC from proteolytic cleavage
Authors: Garcia-Caballero Agustin , Rasmussen Julia E. , Gaillard Erol , Watson Michael J. , Olsen John C. , Donaldson Scott H. , Stutts M. Jackson , Tarran Robert
Published: June 2009

Many epithelia, including the superficial epithelia of the airways, are thought to secrete “volume sensors,” which regulate the volume of the mucosal lining fluid. The epithelial Na
+
channel (ENaC) is often the rate limiting factor in fluid absorption, and must be cleaved by extracellular and/or intracellular proteases before it can conduct Na
+
and absorb excess mucosal liquid, a process that can be blocked by proteases inhibitors. In the airways, airway surface liquid dilution or removal activates ENaC. Therefore, we hypothesized that endogenous proteases are membrane-anchored, whereas endogenous proteolysis inhibitors are soluble and can function as airway surface liquid volume sensors to inhibit ENaC activity. Using a proteomic approach, we identified short palate, lung, and nasal epithelial clone (SPLUNC)1 as a candidate volume sensor. Recombinant SPLUNC1 inhibited ENaC activity in both human bronchial epithelial cultures and
Xenopus
oocytes. Knockdown of SPLUNC1 by shRNA resulted in a failure of bronchial epithelial cultures to regulate ENaC activity and airway surface liquid volume, which was restored by adding recombinant SPLUNC1 to the airway surface liquid. Despite being able to inhibit ENaC, recombinant SPLUNC1 had little effect on extracellular serine protease activity. However, SPLUNC1 specifically bound to ENaC, preventing its cleavage and activation by serine proteases. SPLUNC1 is highly expressed in the airways, as well as in colon and kidney. Thus, we propose that SPLUNC1 is secreted onto mucosal surfaces as a soluble volume sensor whose concentration and dilution can regulate ENaC activity and mucosal volumes, including that of airway surface liquid.
An icosahedral algal virus has a complex unique vertex decorated by a spike
Authors: Cherrier Mickaël V. , Kostyuchenko Victor A. , Xiao Chuan , Bowman Valorie D. , Battisti Anthony J. , Yan Xiaodong , Chipman Paul R. , Baker Timothy S. , Van Etten James L. , Rossmann Michael G.
Published: June 2009

Paramecium bursaria Chlorella
virus-1 is an icosahedrally shaped, 1,900-Å-diameter virus that infects unicellular eukaryotic green algae. A 5-fold symmetric, 3D reconstruction using cryoelectron microscopy images has now shown that the quasiicosahedral virus has a unique vertex, with a pocket on the inside and a spike structure on the outside of the capsid. The pocket might contain enzymes for use in the initial stages of infection. The unique vertex consists of virally coded proteins, some of which have been identified. Comparison of shape, size, and location of the spike with similar features in bacteriophages T4 and P22 suggests that the spike might be a cell-puncturing device. Similar asymmetric features may have been missed in previous analyses of many other viruses that had been assumed to be perfectly icosahedral.
Non-blinking and photostable upconverted luminescence from single lanthanide-doped nanocrystals
Authors: Wu Shiwei , Han Gang , Milliron Delia J. , Aloni Shaul , Altoe Virginia , Talapin Dmitri V. , Cohen Bruce E. , Schuck P. James
Published: June 2009

The development of probes for single-molecule imaging has dramatically facilitated the study of individual molecules in cells and other complex environments. Single-molecule probes ideally exhibit good brightness, uninterrupted emission, resistance to photobleaching, and minimal spectral overlap with cellular autofluorescence. However, most single-molecule probes are imperfect in several of these aspects, and none have been shown to possess all of these characteristics. Here we show that individual lanthanide-doped upconverting nanoparticles (UCNPs)—specifically, hexagonal phase NaYF
4
(β-NaYF
4
) nanocrystals with multiple Yb
3+
and Er
3+
dopants—emit bright anti-Stokes visible upconverted luminescence with exceptional photostability when excited by a 980-nm continuous wave laser. Individual UCNPs exhibit no on/off emission behavior, or “blinking,” down to the millisecond timescale, and no loss of intensity following an hour of continuous excitation. Amphiphilic polymer coatings permit the transfer of hydrophobic UCNPs into water, resulting in individual water-soluble nanoparticles with undiminished photophysical characteristics. These UCNPs are endocytosed by cells and show strong upconverted luminescence, with no measurable anti-Stokes background autofluorescence, suggesting that UCNPs are ideally suited for single-molecule imaging experiments.
Nature of the protein universe
Authors: Levitt Michael
Published: June 2009

The protein universe is the set of all proteins of all organisms. Here, all currently known sequences are analyzed in terms of families that have single-domain or multidomain architectures and whether they have a known three-dimensional structure. Growth of new single-domain families is very slow: Almost all growth comes from new multidomain architectures that are combinations of domains characterized by ≈15,000 sequence profiles. Single-domain families are mostly shared by the major groups of organisms, whereas multidomain architectures are specific and account for species diversity. There are known structures for a quarter of the single-domain families, and >70% of all sequences can be partially modeled thanks to their membership in these families.
Crystal structure of type I ryanodine receptor amino-terminal β-trefoil domain reveals a disease-associated mutation “hot spot” loop
Authors: Amador Fernando J. , Liu Shuang , Ishiyama Noboru , Plevin Michael J. , Wilson Aaron , MacLennan David H. , Ikura Mitsuhiko
Published: June 2009

Muscle contraction and relaxation is regulated by transient elevations of myoplasmic Ca
2+
. Ca
2+
is released from stores in the lumen of the sarco(endo)plasmic reticulum (SER) to initiate formation of the Ca
2+
transient by activation of a class of Ca
2+
release channels referred to as ryanodine receptors (RyRs) and is pumped back into the SER lumen by Ca
2+
-ATPases (SERCAs) to terminate the Ca
2+
transient. Mutations in the type 1 ryanodine receptor gene,
RYR1
, are associated with 2 skeletal muscle disorders, malignant hyperthermia (MH), and central core disease (CCD). The evaluation of proposed mechanisms by which RyR1 mutations cause MH and CCD is hindered by the lack of high-resolution structural information. Here, we report the crystal structure of the N-terminal 210 residues of RyR1 (RyR
NTD
) at 2.5 Å. The RyR
NTD
structure is similar to that of the suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor (IP
3
Rsup), but lacks most of the long helix-turn-helix segment of the “arm” domain in IP
3
Rsup. The N-terminal β-trefoil fold, found in both RyR and IP
3
R, is likely to play a critical role in regulatory mechanisms in this channel family. A disease-associated mutation “hot spot” loop was identified between strands 8 and 9 in a highly basic region of RyR1. Biophysical studies showed that 3 MH-associated mutations (C36R, R164C, and R178C) do not adversely affect the global stability or fold of RyR
NTD
, supporting previously described mechanisms whereby mutations perturb protein–protein interactions.
Cost-Effectiveness Analysis of a Silver-Coated Endotracheal Tube to Reduce the Incidence of Ventilator-Associated Pneumonia
Authors: Shorr Andrew F. , Zilberberg Marya D. , Kollef Marin
Published: June 2009

Objective.

To conduct a cost-effectiveness analysis of the economic outcomes of ventilator-associated pneumonia (VAP) prevention associated with silver-coated endotracheal tubes versus uncoated endotracheal tubes.

Design.

We used a simple decision model based on a hypothetical 1,000-patient cohort intubated with silver-coated or uncoated endotracheal tubes. The primary end point was marginal hospital savings per case of VAP prevented (savings from using silver-coated endotracheal tubes minus acquisition cost divided by number of VAP cases prevented).

Methods.

We followed each branch of the decision model to VAP or no VAP and conducted Monte Carlo simulations and sensitivity analyses. Inputs for VAP incidence, relative risk reduction, and hospital costs were derived from publicly available sources. Relative risk reduction was derived from the pivotal study of the silver-coated endotracheal tube.

Results.

In the base-case analysis, we reduced the pivotal study relative risk in incidence of microbiologically confirmed VAP in patients intubated ≥24 hours from 35.9% to 24%. Thus, 23 of 97 expected cases of VAP could be prevented with silver-coated endotracheal tubes. The savings per case of VAP prevented was $12,840 in the base case, with assumed marginal VAP cost of $16,620 and costs of $90.00 for coated and $2.00 for uncoated endotracheal tubes. Estimates were most sensitive to assumptions regarding VAP cost and relative risk reduction with silver-coated endotracheal tubes. Nonetheless, in multivariate sensitivity analyses, the silver-coated endotracheal tubes yielded persistent savings (95% confidence interval, $9,630-$16,356) per case of VAP prevented. With other base-case inputs held constant, breakeven cost for silver-coated endotracheal tubes was $388.

Conclusions.

The silver-coated endotracheal tube represents a strategy for preventing VAP that may yield hospital savings.
Cytotoxic Activities of Physalis minima L. Chloroform Extract on Human Lung Adenocarcinoma NCI‐H23 Cell Lines by Induction of Apoptosis
Authors: Leong Ooi Kheng , Muhammad Tengku Sifzizul Tengku , Sulaiman Shaida Fariza
Published: June 2009

Physalis minima L. is reputed for having anticancer property. In this study, the chloroform extract of this plant exhibited remarkable cytotoxic activities on NCI‐H23 (human lung adenocarcinoma) cell line at dose‐ and time‐dependent manners (after 24, 48 and 72 h of incubation). Analysis of cell‐death mechanism demonstrated that the extract exerted apoptotic programed cell death in NCI‐H23 cells with typical DNA fragmentation, which is a biochemical hallmark of apoptosis. Morphological observation using transmission electron microscope (TEM) also displayed apoptotic characteristics in the treated cells, including clumping and margination of chromatins, followed by convolution of the nuclear and budding of the cells to produce membrane‐bound apoptotic bodies. Different stages of apoptotic programed cell death as well as phosphatidylserine externalization were confirmed using annexin V and propidium iodide staining. Furthermore, acute exposure to the extract produced a significant regulation of c‐myc, caspase‐3 and p53 mRNA expression in this cell line. Due to its apoptotic effect on NCI‐H23 cells, it is strongly suggested that the extract could be further developed as an anticancer drug.
Thermal Decomposition of Corn Starch with Different Amylose/Amylopectin Ratios in Open and Sealed Systems
Authors: Liu Xingxun , Yu Long , Liu Hongsheng , Chen Ling , Li Lin
Published: June 2009

Thermal decomposition of corn starches with different amylose to amylopectin ratios (0:100 waxy, 23:77 maize, 50:50 Gelose 50, 80:20 Gelose 80) were studied by thermogravimetric analysis (TGA) in an open system and differential scanning calorimetry (DSC) in a sealed system using stainless steel high‐pressure pans with varying water content (9–75%). The initial water content did not affect the decomposition temperature in the open system because all water evaporated from samples before reaching the decomposition temperature. The sequence of decomposition temperature of different starches is waxy > maize > G50 > G80 in an open system. The moisture content in starch remains constant during the degradation process in a sealed system. Two decomposition temperatures were observed in the sealed system: the first at lower temperature represents long chain scission and the second at higher temperature involves decomposition of the glucose ring. The sequence of the first degradation is waxy > maize > G50 > G80. There is no observable difference of the second degradation for the samples containing different amylose to amylopectin ratios. The higher the moisture content, the lower the second decomposition temperature. Decomposition of glucose was used to confirm the mechanisms proposed for the starch degradation.
Evidence-based gene predictions in plant genomes
Authors: Liang Chengzhi , Mao Long , Ware Doreen , Stein Lincoln
Published: June 2009

Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidence—known proteins, full-length cDNAs, or expressed sequence tags (ESTs)—in the species of interest. This limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of EST- and cDNA-sequencing projects. To overcome this limitation, we have developed an evidence-based gene build system (the Gramene pipeline) that can use transcriptional evidence across related species. The Gramene pipeline uses the Ensembl computing infrastructure with a novel data processing scheme. Using the previously annotated plant genomes, the dicotArabidopsis thalianaand the monocotOryza sativa, we show that the cross-species ESTs from within monocot or dicot class are a valuable source of evidence for gene predictions. We also find that, using only EST and cross-species evidence, the Gramene pipeline can generate a plant gene set that is comparable in quality to the human genes based on known proteins and full-length cDNAs. We compare the Gramene pipeline to several widely used ab initio gene prediction programs in rice; this comparison shows the pipeline performs favorably at both the gene and exon levels with cross-species gene products only. We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and discuss potential application of the pipeline to other genomes.
Genome-wide comparisons of variation in linkage disequilibrium
Authors: Teo Yik Y. , Fry Andrew E. , Bhattacharya Kanishka , Small Kerrin S. , Kwiatkowski Dominic P. , Clark Taane G.
Published: June 2009

Current genome-wide surveys of common diseases and complex traits fundamentally aim to detect indirect associations where the single nucleotide polymorphisms (SNPs) carrying the association signals are not biologically active but are in linkage disequilibrium (LD) with some unknown functional polymorphisms. Reproducing any novel discoveries from these genome-wide scans in independent studies is now a prerequisite for the putative findings to be accepted. Significant differences in patterns of LD between populations can affect the portability of phenotypic associations when the replication effort or meta-analyses are attempted in populations that are distinct from the original population in which the genome-wide study is performed. Here, we introduce a novel method for genome-wide analyses of LD variations between populations that allow the identification of candidate regions with different patterns of LD. The evidence of LD variation provided by the introduced method correlated with the degree of differences in the frequencies of the most common haplotype across the populations. Identified regions also resulted in greater variation in the success of replication attempts compared with random regions in the genome. A separate permutation strategy introduced for assessing LD variation in the absence of genome-wide data also correctly identified the expected variation in LD patterns in two well-established regions undergoing strong population-specific evolutionary pressure. Importantly, this method addresses whether a failure to reproduce a disease association in a disparate population is due to underlying differences in LD structure with an unknown functional polymorphism, which is vital in the current climate of replicating and fine-mapping established findings from genome-wide association studies.
Circos: An information aesthetic for comparative genomics
Authors: Krzywinski Martin , Schein Jacqueline , Birol İnanç , Connors Joseph , Gascoyne Randy , Horsman Doug , Jones Steven J. , Marra Marco A.
Published: June 2009

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
Authors: Freeman J. Douglas , Warren René L. , Webb John R. , Nelson Brad H. , Holt Robert A.
Published: June 2009

T-cell receptor (TCR) genomic loci undergo somatic V(D)J recombination, plus the addition/subtraction of nontemplated bases at recombination junctions, in order to generate the repertoire of structurally diverse T cells necessary for antigen recognition. TCR beta subunits can be unambiguously identified by their hypervariable CDR3 (Complement Determining Region 3) sequence. This is the site of V(D)J recombination encoding the principal site of antigen contact. The complexity and dynamics of the T-cell repertoire remain unknown because the potential repertoire size has made conventional sequence analysis intractable. Here, we use 5′-RACE, Illumina sequencing, and a novel short read assembly strategy to sample CDR3βdiversity in human T lymphocytes from peripheral blood. Assembly of 40.5 million short reads identified 33,664 distinct TCRβclonotypes and provides precise measurements of CDR3βlength diversity, usage of nontemplated bases, sequence convergence, and preferences forTRBV(T-cell receptor beta variable gene) andTRBJ(T-cell receptor beta joining gene) gene usage and pairing. CDR3 length between conserved residues ofTRBVandTRBJranged from 21 to 81 nucleotides (nt).TRBVgene usage ranged from 0.01% forTRBV17to 24.6% forTRBV20-1.TRBJgene usage ranged from 1.6% forTRBJ2-6to 17.2% forTRBJ2-1. We identified 1573 examples of convergence where the same amino acid translation was specified by distinct CDR3βnucleotide sequences. Direct sequence-based immunoprofiling will likely prove to be a useful tool for understanding repertoire dynamics in response to immune challenge, without a priori knowledge of antigen.
Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
Authors: Lau Nelson C. , Robine Nicolas , Martin Raquel , Chung Wei-Jen , Niki Yuzo , Berezikov Eugene , Lai Eric C.
Published: June 2009

Piwi proteins, a subclass of Argonaute-family proteins, carry ∼24–30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piRNAs in abundance. In contrast to intact gonads, which contain mixtures of germline and somatic cell types that express different Piwi-class proteins, OSS cells are a homogenous somatic cell population that expresses only PIWI and primary piRNAs. Detailed examination of its TE-derived piRNAs and endo-siRNAs revealed aspects of TE defense that do not rely upon ping-pong amplification. In particular, we provide evidence that a subset of piRNA master clusters, including flamenco, are specifically expressed in OSS and ovarian follicle cells. These data indicate that the restriction of certain TEs in somatic gonadal cells is largely mediated by a primary piRNA pathway.
Phase transformation in nanocrystalline Sm2Co17permanent magnet material
Authors: Song Xiaoyan , Lu Nianduan , Xu Wenwu , Zhang Zhexu , Zhang Jiuxing
Published: June 2009

Single-phase ultrafine nanocrystalline Sm2Co17, a candidate material for permanent magnets, was prepared by a novel simple route based on a home-built `oxygen-free'in situfabrication system. The as-prepared nanocrystalline Sm2Co17has the stable hexagonal Th2Ni17-type (2:17 H) crystal structure at room temperature, which is distinctly different from the conventional polycrystalline Sm2Co17having the rhombohedral Th2Zn17-type (2:17 R) crystal structure at room temperature. Phase transformations in the nanocrystalline Sm2Co17alloy were investigated systematically by a series of annealing experiments. It was found that, along with the nanograin growth in the heat-treatment process, the crystal structure of the room-temperature phase transforms from 2:17 H to 2:17 R. The magnetization behavior of Sm2Co17alloys in different structural states was characterized. The relationship between the magnetic performance and the structure characteristics was analyzed. Understanding the phase transformation of Sm2Co17nanocrystals facilitates the development of nanocrystalline Sm2Co17-type magnets for high-temperature applications.
Rigorous filtration for protein crystallization
Authors: Chayen Naomi E.
Published: June 2009

Centrifugation or filtration of protein samples through 0.22 µm mesh size filters is standard procedure before setting up trials for crystallization. This note concerns other, mostly unused filters, namely 0.1 µm and 100 000–300 000 molecular weight cut-off filters, which have proved to aid in obtaining single high-quality crystals. It serves to pool together information concerning filtration which has been scattered, and somewhat concealed, in various publications over the years and to add information that has not yet been published. Filtration is relevant to all methods of crystallization for both screening and optimization.
Parabolic category O, perverse sheaves on Grassmannians, Springer fibres and Khovanov homology
Authors: Stroppel Catharina
Published: June 2009

For a fixed parabolic subalgebra 𝔭 of $\mathfrak {gl}(n,\mathbb {C})$ we prove that the centre of the principal block 𝒪0𝔭 of the parabolic category 𝒪 is naturally isomorphic to the cohomology ring H*(ℬ𝔭) of the corresponding Springer fibre. We give a diagrammatic description of 𝒪0𝔭 for maximal parabolic 𝔭 and give an explicit isomorphism to Braden’s description of the category PervB(G(k,n)) of Schubert-constructible perverse sheaves on Grassmannians. As a consequence Khovanov’s algebra ℋn is realised as the endomorphism ring of some object from PervB(G(n,n)) which corresponds under localisation and the Riemann–Hilbert correspondence to a full projective–injective module in the corresponding category 𝒪0𝔭. From there one can deduce that Khovanov’s tangle invariants are obtained from the more general functorial invariants in [C. Stroppel, Categorification of the Temperley Lieb category, tangles, and cobordisms via projective functors, Duke Math. J. 126(3) (2005), 547–596] by restriction.
Penumbral Structure and Outflows in Simulated Sunspots
Authors: Rempel M. , Schüssler M. , Cameron R. H. , Knölker M.
Published: June 2009

Sunspots Before Your Eyes

Sunspots have a dark central region, the umbra, surrounded by a region of lighter radial filaments, the penumbra, along which there are outward horizontal mass flows that are still not fully understood despite their discovery 100 years ago. Now

Rempel
et al.

(p.
171
, published online 18 June; see the Perspective by

Scharmer

) present comprehensive numerical simulations of a pair of sunspots that show the development of an outer penumbra with systematic radial outflows along channels of nearly horizontal magnetic field in regions where the average field inclination is greater than 45 degrees. The outflows result from rising hot plasma that turns over and is guided outward by the strong and inclined magnetic field. The simulations reproduce observed properties throughout the entire penumbra and show that the penumbral structure and outflows in sunspots can be understood in terms of convective flow in a magnetic field with varying inclination.
Consistency Between Satellite-Derived and Modeled Estimates of the Direct Aerosol Effect
Authors: Myhre Gunnar
Published: June 2009

Cooling Down

Some aerosols, such as sulfates, reflect solar radiation and have a cooling effect on climate, while others, such as black carbon, have a warming effect because they absorb solar radiation. The preponderance of reflective aerosols causes the net effect to be one of cooling, but the amount of cooling is uncertain, owing to a large difference in estimates of the effect of aerosols in global aerosol models compared with estimates based on observations.
Myhre
(p.
187
, published online 18 June; see the Perspective by

Quaas

) uses a combination of observational data and modeling to reconcile the two approaches, drawing particular attention to relative increases in the aerosol fraction of black carbon. Taken together, the results suggest a best estimate of the cooling effect of aerosols that is 60% of previous reports.
Successful Conservation of a Threatened
Maculinea
Butterfly
Authors: Thomas J. A. , Simcox D. J. , Clarke R. T.
Published: June 2009

Bringing Back the Large Blue

Flagship endangered species, such as the Large Blue butterfly have driven conservation programs worldwide. However, the Large Blue butterfly (
Maculinea arion
) became extinct in the United Kingdom. The apparent driver of this extinction was a complex set of events documented by Thomas
et al.
(p.
80
, published online 18 June; see the Perspective by
Settele and Kühn
). Life-tables and modeling demonstrate how ecological changes, affecting multiple species, cascaded to negatively impact Large Blue populations. When the changes that cause these extinctions were addressed, reintroduction efforts proved successful. Other insects have experienced similar declines and, hopefully, on sites where their known resources remain abundant, a similar approach may be applied.