bluuebunny/crossref_metadata_2025 huggingface dataset:
Trading-off fish biodiversity, food security, and hydropower in the Mekong River Basin
Authors: Ziv Guy , Baran Eric , Nam So , Rodríguez-Iturbe Ignacio , Levin Simon A.
Published: March 2012

The Mekong River Basin, site of the biggest inland fishery in the world, is undergoing massive hydropower development. Planned dams will block critical fish migration routes between the river's downstream floodplains and upstream tributaries. Here we estimate fish biomass and biodiversity losses in numerous damming scenarios using a simple ecological model of fish migration. Our framework allows detailing trade-offs between dam locations, power production, and impacts on fish resources. We find that the completion of 78 dams on tributaries, which have not previously been subject to strategic analysis, would have catastrophic impacts on fish productivity and biodiversity. Our results argue for reassessment of several dams planned, and call for a new regional agreement on tributary development of the Mekong River Basin.
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism
Authors: Band Leah R. , Wells Darren M. , Larrieu Antoine , Sun Jianyong , Middleton Alistair M. , French Andrew P. , Brunoud Géraldine , Sato Ethel Mendocilla , Wilson Michael H. , Péret Benjamin , Oliva Marina , Swarup Ranjan , Sairanen Ilkka , Parry Geraint , Ljung Karin , Beeckman Tom , Garibaldi Jonathan M. , Estelle Mark , Owen Markus R. , Vissenberg Kris , Hodgman T. Charlie , Pridmore Tony P. , King John R. , Vernoux Teva , Bennett Malcolm J.
Published: March 2012

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
Improvement of islet function in a bioartificial pancreas by enhanced oxygen supply and growth hormone releasing hormone agonist
Authors: Ludwig Barbara , Rotem Avi , Schmid Janine , Weir Gordon C. , Colton Clark K. , Brendel Mathias D. , Neufeld Tova , Block Norman L. , Yavriyants Karina , Steffen Anja , Ludwig Stefan , Chavakis Triantafyllos , Reichel Andreas , Azarov Dimitri , Zimermann Baruch , Maimon Shiri , Balyura Mariya , Rozenshtein Tania , Shabtay Noa , Vardi Pnina , Bloch Konstantin , de Vos Paul , Schally Andrew V. , Bornstein Stefan R. , Barkai Uriel
Published: March 2012

Islet transplantation is a feasible therapeutic alternative for metabolically labile patients with type 1 diabetes. The primary therapeutic target is stable glycemic control and prevention of complications associated with diabetes by reconstitution of endogenous insulin secretion. However, critical shortage of donor organs, gradual loss in graft function over time, and chronic need for immunosuppression limit the indication for islet transplantation to a small group of patients. Here we present a promising approach to address these limitations by utilization of a macrochamber specially engineered for islet transplantation. The s.c. implantable device allows for controlled and adequate oxygen supply and provides immunological protection of donor islets against the host immune system. The minimally invasive implantable chamber normalized blood glucose in streptozotocin-induced diabetic rodents for up to 3 mo. Sufficient graft function depended on oxygen supply. Pretreatment with the growth hormone-releasing hormone (GHRH) agonist, JI-36, significantly enhanced graft function by improving glucose tolerance and increasing β-cell insulin reserve in rats thereby allowing for a reduction of the islet mass required for metabolic control. As a result of hypervascularization of the tissue surrounding the device, no relevant delay in insulin response to glucose changes has been observed. Consequently, this system opens up a fundamental strategy for therapy of diabetes and may provide a promising avenue for future approaches to xenotransplantation.
Molecular basis for complement recognition by integrin αXβ2
Authors: Chen Xing , Yu Yamei , Mi Li-Zhi , Walz Thomas , Springer Timothy A.
Published: March 2012

Integrin αXβ2functions as complement receptor for iC3b and mediates recognition and phagocytosis of pathogens. We used negative-stain EM to examine the αXβ2interaction with iC3b. EM class averages of αXβ2in complex with iC3b define the binding sites on both the integrin and iC3b. iC3b contains C3c and thioester domain moieties linked by a long flexible linker. The binding site is on the key ring of the C3c moiety, at the interface between the MG3 and MG4 domains. Similar complexes are seen between αXβ2and the C3c fragment. αXβ2binds through the αXαI domain, on the face known to bear the metal ion-dependent adhesion site, at the opposite end of the αI domain from its site of insertion in the β-propeller domain.
Dysmyelination not demyelination causes neurological symptoms in preweaned mice in a murine model of Cockayne syndrome
Authors: Revet Ingrid , Feeney Luzviminda , Tang Amy A. , Huang Eric J. , Cleaver James E.
Published: March 2012

Cockayne syndrome (CS) is a rare autosomal recessive neurodegenerative disease that is associated with mutations in either of two transcription-coupled DNA repair genes,
CSA
or
CSB
. Mice with a targeted mutation in the
Csb
gene (Cs-b
m/m
) exhibit a milder phenotype compared with human patients with mutations in the orthologous
CSB
gene. Mice mutated in
Csb
were crossed with mice lacking
Xpc
(Xp-c
−/−
), the global genome repair gene, to enhance the pathological symptoms. These Cs-b
m/m
.Xp-c
−/−
mice were normal at birth but exhibited progressive failure to thrive, whole-body wasting, and ataxia and died at approximately postnatal day 21. Characterization of Cs-b
m/m
.Xp-c
−/−
brains at postnatal stages demonstrated widespread reduction of myelin basic protein (MBP) and myelin in the sensorimotor cortex, the stratum radiatum, the corpus callosum, and the anterior commissure. Quantification of individual axons by electron microscopy showed a reduction in both the number of myelinated axons and the average diameter of myelin surrounding the axons. There were no significant differences in proliferation or oligodendrocyte differentiation between Cs-b
m/m
.Xp-c
−/−
and Cs-b
m/+
.Xp-c
−/−
mice. Rather, Cs-b
m/m
.Xp-c
−/−
oligodendrocytes were unable to generate sufficient MBP or to maintain the proper myelination during early development. Csb is a multifunctional protein regulating both repair and the transcriptional response to reactive oxygen through its interaction with histone acetylase p300 and the hypoxia-inducible factor (HIF)1 pathway. On the basis of our results, combined with that of others, we suggest that in Csb the transcriptional response predominates during early development, whereas a neurodegenerative response associated with repair deficits predominates in later life.
Tagging Models for Estimating Survival Rates When Tag Visibility Changes over Time: Partial-Year Tabulation of Recaptures
Authors: Waterhouse Lynn , Hoenig John M.
Published: March 2012

Brownie tagging models are commonly used for estimating survival rates from multiyear tagging studies. The basic model, model 1, assumes that all tags have the same recovery rate. An alternative, model 0, allows newly tagged animals to have a different tag recovery rate than previously tagged animals. This feature might be necessary because new tags are less fouled and more visible than previously applied tags and thus have a higher reporting rate. Model 0 accommodates the different recovery rates through the use of additional parameters, which leads to larger standard errors than in model 1. Model 0′, a new model, also allows newly tagged animals to have a different tag recovery rate than previously tagged ones. It makes use of a known fouling time (the time it takes for tags on newly tagged animals to have the same visibility as tags on previously tagged animals) to divide the year into two parts. During the first part of the year the tags on newly tagged animals are more visible than those on previously tagged ones, while in the second part all tags have the same visibility. Dividing the year into parts and recording the recaptures in each part avoids the failure of the assumption that the reporting rate is constant for all tagged animals, achieves greater precision, and provides estimates of the survival rate at the end of the second year instead of at the end of the third year (as in model 0). The superiority of model 0′ over models 0 and 1 is demonstrated for several cases using Monte Carlo simulation. Simulations were based on the queen conch Strombus gigas fishery of the Turks and Caicos Islands, British West Indies. For that fishery, if the tag reporting rate is altered by 25% or more by fouling, it is beneficial to use model 0′ instead of model 1.

Received January 6, 2011; accepted October 6, 2011
Population Size of Hatchery-Reared and Wild Pallid Sturgeon in the Lower Missouri River
Authors: Steffensen Kirk D. , Powell Larkin A. , Pegg Mark A.
Published: March 2012

The population size of pallid sturgeon Scaphirhynchus albus is currently unknown throughout much of the Missouri River. Listed as federally endangered in 1990, the pallid sturgeon remains one of the rarest fishes in the Missouri and Mississippi River basins, and little to no natural recruitment occurs. Artificial population supplementation via a hatchery propagation program was initiated, necessitating the collection of sexually mature pallid sturgeon. Therefore, the Nebraska Game and Parks Commission maintained an intensive broodstock collection and mark–recapture effort from 2008 to 2010 to capture reproductively ready adults for the propagation program. Coordinated crews fished baited trotlines from the confluence of the Platte and Missouri rivers at river kilometer (rkm) 957.6 to a point about 80.5 rkm downstream. A total of 438 pallid sturgeon were captured, which amounts to a 7.8% recapture rate. The objectives of the study were to (1) use these data to estimate the annual population sizes of wild-origin and hatchery-reared pallid sturgeon within the above-mentioned 80.5-rkm reach of the lower Missouri River and (2) compare current population levels with the Pallid Sturgeon Recovery Team's population objective. We used the mark–recapture data in a robust-design analysis to derive population estimates and annual survival, capture, and temporary emigration rates. The annual population estimate for wild pallid sturgeon varied from 5.4 to 8.9 fish/rkm, whereas the estimate for known hatchery-reared fish varied from 28.6 to 32.3 fish/rkm. The robust-design approach to our analysis resulted in useful estimates of population size and other variables important to quantifying species recovery and management targets; the approach may be suitable for other fisheries management data sets.

Received February 24, 2011; accepted October 13, 2011
Teaching (about) Britishness? An investigation into trainee teachers' understanding of Britishness in relation to citizenship and the discourse of civic nationalism
Authors: Jerome Lee , Clemitshaw Gary
Published: March 2012

This research was prompted by the developing political discourse proposing the teaching of Britishness and British values in the context of the United Kingdom. This discourse will be reviewed in the first part of the article, in the context of previous work which has sought to assess how Britishness and related concepts might be promoted through education. The second part will be based on questionnaire responses from a sample of students following post‐graduate initial teacher training programmes in a number of higher education partnerships. It indicates that, while political discourse and educational policy have sensitised trainee teachers to the agenda, there remains a deep uncertainty and misgiving about this as an educational objective.
The ebb and flow of curriculum construction in physical education: a Scottish narrative
Authors: Gray Shirley , Mulholland Rosemary , MacLean Justine
Published: March 2012

Within Scotland's new curriculum, a Curriculum for Excellence, physical education (PE) has been relocated from ‘Expressive Arts' to ‘Health and Wellbeing'. The repositioning of PE could result in a shift in the way PE is conceptualised. In order to understand this shift, we conducted in‐depth, one‐to‐one interviews with 10 participants who contributed to the development of the new policy text for PE. The results from this study provide a narrative that describes the process of developing policy text for PE. Additionally, the participants described a process of consultation and debate, and referred to decision‐making based on national initiatives linked to improving children%s health. However, there was also evidence to suggest that the government controlled the process and that this control limited the extent to which the participants could make a genuine contribution to shaping the vision for PE. In making the process of developing curriculum text for PE more explicit, it is hoped that this study will encourage teachers and other key stakeholders to read the documentation that was produced in a critical way and have a greater understanding of the policy development process.
Fly wing cells choose sides
Authors: Leslie Mitch
Published: March 2012

Kinase guides membrane trafficking to specify where wing hairs emerge.
Orna Cohen-Fix: Playing with nuclear morphology
Authors: Sedwick Caitlin
Published: March 2012

Cohen-Fix studies how cells determine and maintain their nuclear morphology.
Vinculin associates with endothelial VE-cadherin junctions to control force-dependent remodeling
Authors: Huveneers Stephan , Oldenburg Joppe , Spanjaard Emma , van der Krogt Gerard , Grigoriev Ilya , Akhmanova Anna , Rehmann Holger , de Rooij Johan
Published: March 2012

To remodel endothelial cell–cell adhesion, inflammatory cytokine- and angiogenic growth factor–induced signals impinge on the vascular endothelial cadherin (VE-cadherin) complex, the central component of endothelial adherens junctions. This study demonstrates that junction remodeling takes place at a molecularly and phenotypically distinct subset of VE-cadherin adhesions, defined here as focal adherens junctions (FAJs). FAJs are attached to radial F-actin bundles and marked by the mechanosensory protein Vinculin. We show that endothelial hormones vascular endothelial growth factor, tumor necrosis factor α, and most prominently thrombin induced the transformation of stable junctions into FAJs. The actin cytoskeleton generated pulling forces specifically on FAJs, and inhibition of Rho-Rock-actomyosin contractility prevented the formation of FAJs and junction remodeling. FAJs formed normally in cells expressing a Vinculin binding-deficient mutant of α-catenin, showing that Vinculin recruitment is not required for adherens junction formation. Comparing Vinculin-devoid FAJs to wild-type FAJs revealed that Vinculin protects VE-cadherin junctions from opening during their force-dependent remodeling. These findings implicate Vinculin-dependent cadherin mechanosensing in endothelial processes such as leukocyte extravasation and angiogenesis.
Neutrophil depletion impairs natural killer cell maturation, function, and homeostasis
Authors: Jaeger Baptiste N. , Donadieu Jean , Cognet Céline , Bernat Claire , Ordoñez-Rueda Diana , Barlogis Vincent , Mahlaoui Nizar , Fenis Aurore , Narni-Mancinelli Emilie , Beaupain Blandine , Bellanné-Chantelot Christine , Bajénoff Marc , Malissen Bernard , Malissen Marie , Vivier Eric , Ugolini Sophie
Published: March 2012

Natural killer (NK) cells are bone marrow (BM)–derived granular lymphocytes involved in immune defense against microbial infections and tumors. In an N-ethyl N-nitrosourea (ENU) mutagenesis strategy, we identified a mouse mutant with impaired NK cell reactivity both in vitro and in vivo. Dissection of this phenotype showed that mature neutrophils were required both in the BM and in the periphery for proper NK cell development. In mice lacking neutrophils, NK cells displayed hyperproliferation and poor survival and were blocked at an immature stage associated with hyporesponsiveness. The role of neutrophils as key regulators of NK cell functions was confirmed in patients with severe congenital neutropenia and autoimmune neutropenia. In addition to their direct antimicrobial activity, mature neutrophils are thus endowed with immunoregulatory functions that are conserved across species. These findings reveal novel types of cooperation between cells of the innate immune system and prompt examination of NK cell functional deficiency in patients suffering from neutropenia-associated diseases.
Primary Epstein-Barr virus infection does not erode preexisting CD8+ T cell memory in humans
Authors: Odumade Oludare A. , Knight Jennifer A. , Schmeling David O. , Masopust David , Balfour Henry H. , Hogquist Kristin A.
Published: March 2012

Acute Epstein-Barr virus (EBV) infection results in an unusually robust CD8+ T cell response in young adults. Based on mouse studies, such a response would be predicted to result in attrition of preexisting memory to heterologous infections like influenza A (Flu) and cytomegalovirus (CMV). Furthermore, many studies have attempted to define the lymphocytosis that occurs during acute EBV infection in humans, but it is unclear whether bystander T cells contribute to it. To address these issues, we performed a longitudinal prospective study of primary EBV infection in humans. During acute EBV infection, both preexisting CMV- and Flu-specific memory CD8+ T cells showed signs of bystander activation, including up-regulation of granzyme B. However, they generally did not expand, suggesting that the profound CD8+ lymphocytosis associated with acute EBV infection is composed largely of EBV-specific T cells. Importantly, the numbers of CMV- and Flu-specific T cells were comparable before and after acute EBV infection. The data support the concept that, in humans, a robust CD8+ T cell response creates a new memory CD8+ T cell niche without substantially depleting preexisting memory for heterologous infections.
Temperature-dependent demagnetization behaviour in perpendicular exchange-coupled SmCo5/FeCo multilayers
Authors: Belemuk A M , Chui S T
Published: March 2012

We study with finite temperature Monte Carlo simulation the temperature-dependent demagnetization behaviour of exchange-coupled multilayers of hard (SmCo5) and soft (FeCo) magnetic materials. The easy axis of the hard phase is perpendicular to the layers, as is motivated by recent experimental results. We perform simulations with and without the dipolar interaction and study the effect of finite temperature on the coercivity, the remanence and the energy density of the composites. We investigate these properties as functions of the soft layer thickness. We find that as the temperature is increased, the increase in the energy product with the addition of soft material becomes progressively smaller than expected because the increase in the remanent magnetization is less than anticipated for two reasons. Because of the different magnetization densities between the hard and the soft phases, magnetic charges are created at the hard–soft boundaries. To reduce the corresponding dipolar energy, at moderate temperatures the magnetization of the soft phase becomes tilted with respect to that of the hard phase; at relatively high temperatures vortex-like structures are created in the soft phase. Furthermore, the addition of soft material reduces the spin wave stiffness and increases the amount of thermal fluctuation. These two effects reduce the rate of increase of the magnetic moment and hence the maximum energy product. At low temperatures, the hysteresis curve shows a two-stage magnetization reversal process. Simulation results for the first instability field H
c1 are in reasonable agreement with theoretical nucleation field H
n estimates for a moderate amount of soft materials. The difference between H
c1 and H
n when the amount of soft material is small is explained. As the temperature is increased, the two-stage process disappears, most likely due to the formation of vortex-like structures in the soft phase.
Development of polymer MEMS process technology as an approach to a sustainable production system
Authors: Sugiyama Susumu , Amaya Satoshi , Viet Dao Dzung
Published: March 2012

Polymethyl methacrylate (PMMA) has been proposed as a material for micro-electromechanical systems (MEMS) to initiate the research on environmentally friendly micro-nano machining technology using polymer materials. A polymer MEMS process has been developed using hot embossing and precision machining. MEMS structures less than 2 μm were successfully embossed. The PMMA layer that remained after hot embossing was removed by a polishing process to release the movable parts. A PMMA electrostatic comb-drive microactuator was fabricated. Both finger width and gap between fingers were 5 μm, and thickness was larger than 70 μm. An operated displacement of 11 μm at a drive voltage of 100 V was obtained. It was 20 times larger than that of an identical silicon device. A torsional micro mirror device driving with vertical comb actuator was fabricated. The size of the mirror was 1×1 mm
2. The maximum tilt angle of 5.6 was obtained with driving voltage of 100 V and frequency up to 100 Hz. A chevron-shaped PMMA thermal actuator with a thickness of about 50 μm has been fabricated and tested successfully. The displacement was about 5 times larger than that of a Si counterpart at the same power consumption.
Fabrication and properties of terbium phosphate nanorods
Authors: Tran Thu Huong , Tran Kim Anh , Hoang Thi Khuyen , Pham Thu Hien , Le Quoc Minh
Published: March 2012

Recently, luminescent nanomaterials with one-dimensional (1D) structured form have been extensively investigated as fluorescent label agents in biology. Among them, 1D nanostructured terbium compounds (for example terbium phosphate) have attracted great attention due to their high-emission efficiency in water. In this report, terbium phosphate nanorods were successfully prepared by hydrothermal method in autoclave for the first time. This method is a simple one, which permits obtaining large-scale, uniform and pure product. The size of the rods can be controlled precisely. The nanorods have diameters from 15 to 50 nm, and lengths from 300 to 500 nm. Based on the effects of change of pH values to the size, crystalline structure and morphology of terbium phosphate nanorods, field emission scanning electron microscopy (FE-SEM) and x-ray diffraction (XRD) data of the as-synthesized samples have been elucidated. The photoluminescent (PL) spectra of TbPO
4 nanorods have been measured at room temperature under ultraviolet excitation and show four high luminescence main peaks at 490, 545, 585 and 620 nm.
The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression
Authors: Sadasivam Subhashini , Duan Shenghua , DeCaprio James A.
Published: March 2012

Cell cycle progression is dependent on two major waves of gene expression. Early cell cycle gene expression occurs during G1/S to generate factors required for DNA replication, while late cell cycle gene expression begins during G2 to prepare for mitosis. Here we demonstrate that the MuvB complex—comprised of LIN9, LIN37, LIN52, LIN54, and RBBP4—serves an essential role in three distinct transcription complexes to regulate cell cycle gene expression. The MuvB complex, together with the Rb-like protein p130, E2F4, and DP1, forms the DREAM complex during quiescence and represses expression of both early and late genes. Upon cell cycle entry, the MuvB complex dissociates from p130/DREAM, binds to B-Myb, and reassociates with the promoters of late genes during S phase. MuvB and B-Myb are required for the subsequent recruitment of FoxM1 to late gene promoters during G2. The MuvB complex remains bound to FoxM1 during peak late cell cycle gene expression, while B-Myb binding is lost when it undergoes phosphorylation-dependent, proteasome-mediated degradation during late S phase. Our results reveal a novel role for the MuvB complex in recruiting B-Myb and FoxM1 to promote late cell cycle gene expression and in regulating cell cycle gene expression from quiescence through mitosis.
AMD1 is essential for ESC self-renewal and is translationally down-regulated on differentiation to neural precursor cells
Authors: Zhang Dawei , Zhao Tianyun , Ang Haw Siang , Chong Peini , Saiki Ryotaro , Igarashi Kazuei , Yang Henry , Vardy Leah A.
Published: March 2012

The gene expression networks governing embryonic stem cell (ESC) pluripotency are complex and finely regulated during differentiation toward specific lineages. We describe a new role for Amd1 (adenosyl methionine decarboxylase), a key enzyme in the polyamine synthesis pathway, in regulating both ESC self-renewal and differentiation to the neural lineage. Amd1 is highly expressed in ESCs and is translationally down-regulated by the neural precursor cell (NPC)-enriched microRNA miR-762 during NPC differentiation. Overexpression of Amd1 or addition of the polyamine spermine blocks ESC-to-NPC conversion, suggesting Amd1 must be down-regulated to decrease the levels of inhibitory spermine during differentiation. In addition, we demonstrate that high levels of Amd1 are required for maintenance of the ESC state. We show that forced overexpression of Amd1 in ESCs results in maintenance of high Myc levels and a delay in differentiation on removal of LIF. We propose that Amd1 is a major regulator of ESC self-renewal and that its essential role lies in its regulation of Myc levels within the cell.
On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1
Authors: Luo Xin , Kraus W. Lee
Published: March 2012

Cellular stress responses are mediated through a series of regulatory processes that occur at the genomic, transcriptional, post-transcriptional, translational, and post-translational levels. These responses require a complex network of sensors and effectors from multiple signaling pathways, including the abundant and ubiquitous nuclear enzyme poly(ADP-ribose) (PAR) polymerase-1 (PARP-1). PARP-1 functions at the center of cellular stress responses, where it processes diverse signals and, in response, directs cells to specific fates (e.g., DNA repair vs. cell death) based on the type and strength of the stress stimulus. Many of PARP-1's functions in stress response pathways are mediated by its regulated synthesis of PAR, a negatively charged polymer, using NAD+ as a donor of ADP-ribose units. Thus, PARP-1's functions are intimately tied to nuclear NAD+ metabolism and the broader metabolic profile of the cell. Recent studies in cell and animal models have highlighted the roles of PARP-1 and PAR in the response to a wide variety of extrinsic and intrinsic stress signals, including those initiated by oxidative, nitrosative, genotoxic, oncogenic, thermal, inflammatory, and metabolic stresses. These responses underlie pathological conditions, including cancer, inflammation-related diseases, and metabolic dysregulation. The development of PARP inhibitors is being pursued as a therapeutic approach to these conditions. In this review, we highlight the newest findings about PARP-1's role in stress responses in the context of the historical data.
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
Authors: Marquez Yamile , Brown John W.S. , Simpson Craig , Barta Andrea , Kalyna Maria
Published: March 2012

Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis. We detect ∼150,000 splice junctions derived mostly from typical plant introns, including an eightfold increase in the number of U12 introns (2069). Around 61% of multiexonic genes are alternatively spliced under normal growth conditions. Moreover, we provide experimental validation of 540 AS transcripts (from 256 genes coding for important regulatory factors) using high-resolution RT-PCR and Sanger sequencing. Intron retention (IR) is the most frequent AS event (∼40%), but many IRs have relatively low read coverage and are less well-represented in assembled transcripts. Additionally, ∼51% of Arabidopsis genes produce AS transcripts which do not involve IR. Therefore, the significance of IR in generating transcript diversity was generally overestimated in previous assessments. IR analysis allowed the identification of a large set of cryptic introns inside annotated coding exons. Importantly, a significant fraction of these cryptic introns are spliced out in frame, indicating a role in protein diversity. Furthermore, we show extensive AS coupled to nonsense-mediated decay in AFC2, encoding a highly conserved LAMMER kinase which phosphorylates splicing factors, thus establishing a complex loop in AS regulation. We provide the most comprehensive analysis of AS to date which will serve as a valuable resource for the plant community to study transcriptome complexity and gene regulation.
Sodium (1R)-D-glucit-1-ylsulfonate monohydrate
Authors: Haines Alan H. , Hughes David L.
Published: March 2012

The title salt, Na+·C6H13O9S−·H2O, crystallizes with three independent cations, molecular anions and solvent water molecules in the asymmetric unit. This crystalline monohydrate addition product, formed by reaction of D-glucose and sodium hydrogen sulfite in water, forms a three-dimensional network through complex cation coordination and extensive intermolecular hydrogen bonding. Each of the independent molecules has an open-chain structure with the carbon chains adopting a sickle-like conformation, similar to that found in the potassium salt [Coleet al.(2001).Carbohydr. Res.335, 1–10], but there are significant differences in the patterns of complexation.
(Z)-2-(5-Chloro-2-oxoindolin-3-ylidene)-N-methylhydrazinecarbothioamide
Authors: Qasem Ali Amna , Eltayeb Naser Eltaher , Teoh Siang Guan , Salhin Abdussalam , Fun Hoong-Kun
Published: March 2012

In the title compound, C10H9ClN4OS, an intramolecular N—H...O hydrogen-bonding interaction and an N—H...N interaction generate ring motifs [graph setsS(6) andS(5), respectively]. In the crystal, molecules form a chain through N—H...O hydrogen bonds, and these are extended by N—H...S hydrogen-bonding interactions into an infinite three-dimensional network. The crystal structure also exhibits weak C—H...π interactions.
1,2-Bis(4-methylbenzyl)diselane
Authors: Zhou Mei-Yun , Li Yi-Qun , Zheng Wen-Jie
Published: March 2012

The title molecule, C16H18Se2, features a diselenide bridge between two 4-methylbenzyl units, in which the central C—Se—Se—C torsion angle is 88.1 (3)°, while the two Se—Se—C—C fragments assumegaucheconformations, with torsion angles of −51.8 (5) and 59.1 (4)°. The dihedral angle between the benzene rings is 78.9 (2)°.
Poly[(μ2-2-aminopyrimidine-κ2N1:N3)di-μ2-chlorido-mercury(II)]
Authors: Eshtiagh-Hosseini Hossein , Yousefi Zakieh , Janiak Agnieszka
Published: March 2012

The title compound, [HgCl2(C4H5N3)]n, features a two-dimensional network parallel to (001) that is based on an HgIIatom octahedrally coordinated by four μ2-Cl atoms and two μ2-2-aminopyrimidine (apym) ligands intranspositions, yielding a distorted HgCl4N2octahedron. The coordination network can be described as an uninodal 4-connected net with the sql topology. The HgIIion lies on a site of -1 symmetry and the apym ligand lies on sites ofmsymmetry with the mirror plane perpendicular to the pyrimidine plane and passing through the NH2group N atom. This polymeric structure is stabilized by N—H...Cl hydrogen bonds and columnar π–π stacking of pyrimidine rings, with a centroid–centroid distance of 3.832 (2) Å.
2-(2,5-Dimethoxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]acetamide
Authors: Choi Hyeong , Shim Yong Suk , Han Byung Hee , Kang Sung Kwon , Sung Chang Keun
Published: March 2012

In the title compound, C18H21NO4, the dihedral angles between the acetamide group and the methoxy- and hydroxy-substitured benzene rings are 80.81 (5) and 8.19 (12)°, respectively. The benzene rings are twisted with respect to each other, making a dihedral angle of 72.89 (5)°. In the crystal, N—H...O and O—H...O hydrogen bonds link the molecules into a three-dimensional network.
1-[3-(4-Chlorophenyl)-5-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl]butan-1-one
Authors: Fun Hoong-Kun , Quah Ching Kheng , Samshuddin S. , Narayana B. , Sarojini B. K.
Published: March 2012

In the title compound, C20H21ClN2O2, the benzene rings form dihedral angles of 6.35 (5) and 81.82 (5)° with the mean plane of the 4,5-dihydro-1H-pyrazole ring (r.m.s. deviation = 0.145 Å). This latter ring adopts an envelope conformation with the CH grouping as the flap. The dihedral angle between the benzene rings is 75.63 (4)°. In the crystal, molecules are linked by C—H...Cl and C—H...O hydrogen bonds into chains along [-201]. The crystal structure also features C—H...π interactions.
Bis(guanidinium) naphthalene-1,5-disulfonate–18-crown-6 (1/1)
Authors: Wei Bin
Published: March 2012

In the crystal of the title compound, 2CH6N3+·C10H6O6S22−·C12H24O6, the 1,5-naphthnalenedisulfonate anion and the 18-crown-6 molecule lie across inversion centers. The guanidinium cation links with the 1,5-naphthnalenedisulfonate anion and 18-crown-6 moleculeviaN—H...O hydrogen bonds.
4-[(Z)-(n-Butylamino)(phenyl)methylidene]-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one
Authors: Wang Hai-Wen
Published: March 2012

The title compound, C21H23N3O, exists in an enamine–keto form with the amino group involved in an intramolecular N—H...O hydrogen bond. The dihedral angle between the phenyl rings is 73.59 (6)°. The five-membered ring is nearly planar, the largest deviation being 0.0004 (7) Å, and makes dihedral angles of 4.81 (6) and 69.81 (5)° wth the phenyl rings. In the crystal, pairs of weak C—H...O interactions link the molecules into centrosymmetric dimers.
Aquachlorido(3,5-dinitro-2-oxidobenzoato-κ2O1,O2)(1,10-phenanthroline-κ2N,N′)chromium(III)
Authors: Meng Zhao-Hui , Lian Hui , Zhang Shu-Shen , Feng Yu-Quan
Published: March 2012

In the title compound, [Cr(C7H2N2O7)Cl(C12H8N2)(H2O)], the CrIIIatom displays a distorted octahedral coordination geometry, with the chelating phenantroline and 3,5-dinitrosalicylate ligands intranspositions. In the crystal, molecules are connectedviaO—H...O hydrogen bonds into a two-dimensional framework parallel to (100). In addition, there are π–π stacking interactions between phenanthroline ligands along thecaxis, with a mean interplanar distance of 3.456 (4) Å.
Characterization of yellow grouper Epinephelus awoara (Serranidae) karyotype by chromosome bandings and fluorescence in situ hybridization
Authors: Wang S. F. , Cai Y. , Qin Y. X. , Zhou Y. C. , Su Y. Q. , Wang J.
Published: March 2012

The cytogenetics of yellow grouper Epinephelus awoara was studied using multiple cytogenetic markers [Giemsa staining, C‐banding, Ag‐NORs and fluorescence in situ hybridization (FISH)]. Giemsa staining results showed that the karyotypic formula of E. awoara was 2n = 48a, FN (fundamental number) = 48. Faint C‐bandings were only detected at the centromeric regions of chromosome pair number 24, being almost indiscernible on the other chromosome pairs. After Ag‐NOR staining, one pair of nucleolar organizer regions (NOR) was observed in the subcentromeric region of pair number 24. FISH results showed that 5S rDNA was located at a pair of medium‐sized chromosomes, while 18S rDNA appeared at the same location in the subcentromeric region of pair number 24 where Ag‐NORs were detected. The telomeric sequence (TTAGGG)n detected by FISH was located at both ends of each chromosome. The results suggested that E. awoara has retained general karyotypic structure stability during the evolutionary diversification process.
Promising option in the prevention of idiopathic anaphylaxis: Omalizumab
Authors: DEMIRTÜRK Mustafa , GELINCIK Asli , ÇOLAKOĞLU Bahattin , DAL Murat , BÜYÜKÖZTÜRK Suna
Published: March 2012

Anaphylaxis is a serious and probably lethal systemic reaction which occurs instantaneously after exposure to an allergen. It can occur after exposure to various triggers including allergic and non‐allergic factors. When a trigger cannot be determined, idiopathic anaphylaxis is considered. In idiopathic anaphylaxis presenting with frequent attacks, long‐term prophylaxis with H1 antihistamine and steroid treatment are recommended. Omalizumab, a humanized monoclonal antibody drug which decreases free immunoglobulin E molecules in the circulation, is approved for the treatment of chronic severe persistent allergic asthma. We report a 46‐year‐old female patient with severe uncontrolled allergic asthma and idiopathic anaphylaxis presenting with attacks of abdominal pain, generalized urticaria, feeling of strangulation in her throat and unconsciousness. Omalizumab at a dose of 375 mg once every 2 weeks was administrated and at the end of 3 months anaphylactic attacks had ceased. At the end of the sixth month of omalizumab therapy, her injection intervals were extended to 4 weeks. After she began experiencing moderate attacks of urticaria and hoarsening, however, initial treatment plan was reestablished. Currently, she has completed her first year of treatment without further attacks.
Analysis of chimeric ribosomal stalk complexes from eukaryotic and bacterial sources: structural features responsible for specificity of translation factors
Authors: Mochizuki Masahiro , Kitamyo Masumi , Miyoshi Tomohiro , Ito Kosuke , Uchiumi Toshio
Published: March 2012

Ribosomal protein P0 forms a pentameric complex with two heterodimers of the flexible stalk proteins P1•P2 and plays a role in the functional interaction of eukaryotic ribosomes with translational factors. To investigate the functionality of domains of P0 characteristic to eukaryotes, we constructed various chimeras between silkworm P0 and Escherichia coli counterpart L10. Replacement of the C‐terminal region of L10 with that of P0 allowed the binding of two P1•P2 heterodimers, which supported ribosomal activity dependent on eukaryotic elongation factors eEF‐2/eEF‐1α, but not activity dependent on bacterial factors EF‐G/EF‐Tu. Conversely, replacement of the C‐terminal region of P0 with that of L10 allowed binding of two bacterial L12 homodimers, which resulted in a low level of activity dependent on bacterial factors. Insertion of the extended region of P0 that is absent in the bacterial counterpart into L10 did not affect L12 binding or bacterial factor‐dependent activity, but deletion of this region from P0 resulted in a 40% reduction in eukaryotic factor‐dependent activity. The results indicate that the C‐terminal regions of P0 and L10 are responsible for binding of the cognate stalk dimers and ribosomal specificity for translation factors and suggest that the extended region participates in accessibility only for eukaryotic factors.
The effect of experimental warming and precipitation change on proteolytic enzyme activity: positive feedbacks to nitrogen availability are not universal
Authors: Brzostek Edward R. , Blair John M. , Dukes Jeffrey S. , Frey Serita D. , Hobbie Sarah E. , Melillo Jerry M. , Mitchell Robert J. , Pendall Elise , Reich Peter B. , Shaver Gaius R. , Stefanski Artur , Tjoelker Mark G. , Finzi Adrien C.
Published: March 2012

Nitrogen regulates the Earth's climate system by constraining the terrestrial sink for atmospheric CO2. Proteolytic enzymes are a principal driver of the within‐system cycle of soil nitrogen, yet there is little to no understanding of their response to climate change. Here, we use a single methodology to investigate potential proteolytic enzyme activity in soils from 16 global change experiments. We show that regardless of geographical location or experimental manipulation (i.e., temperature, precipitation, or both), all sites plotted along a single line relating the response ratio of potential proteolytic activity to soil moisture deficit, the difference between precipitation and evapotranspiration. In particular, warming and reductions in precipitation stimulated potential proteolytic activity in mesic sites – temperate and boreal forests, arctic tundra – whereas these manipulations suppressed potential activity in dry grasslands. This study provides a foundation for a simple representation of the impacts of climate change on a central component of the nitrogen cycle.
DNA methyltransferase 3B expression is associated with poor outcome of stage I testicular seminoma
Authors: Arai Eri , Nakagawa Tohru , Wakai‐Ushijima Saori , Fujimoto Hiroyuki , Kanai Yae
Published: March 2012

Arai E, Nakagawa T, Wakai‐Ushijima S, Fujimoto H & Kanai Y

(2012) Histopathology 60, E12–E18

DNA methyltransferase 3B expression is associated with poor outcome of stage I testicular seminoma

Aims:  To examine in testicular seminomas the expression of DNA methyltransferase 3B (DNMT3B), which is known to be associated with early embryonic development and carcinogenesis, and to obtain a predictive marker for relapse of stage I seminomas.

Methods and results:  Immunohistochemical examination of DNMT3B was performed in 88 cases of seminoma, 35 (39.8%) of which showed widely scattered nuclear immunoreactivity for DNMT3B, and 53 (60.2%) of which were completely negative. The incidence of focal DNMT3B expression was higher in stage III seminomas (5/5, 100%) than in stage I (25/70, 35.7%) or stage II (5/13, 38.5%) seminomas (P = 0.011). In stage I seminomas there were no significant correlations between DNMT3B expression and tumour size, invasion of the rete testis, or lymphatic or vascular involvement. Six of 25 cases (24%) showing DNMT3B expression relapsed, whereas only 3/45 cases (6.7%) lacking such expression did so (P = 0.037). Patients with seminomas showing DNMT3B expression had a significantly lower relapse‐free survival rate than patients whose tumours lacked this feature (P = 0.0464).

Conclusions:  Patients with seminomas showing focal DNMT3B expression are at increased risk of relapse, and should be followed up carefully.
Fallopian tube metastases of non‐gynaecological origin: a series of 20 cases emphasizing patterns of involvement including intra‐epithelial spread
Authors: Stewart Colin J R , Leung Yee C , Whitehouse Ann
Published: March 2012

Stewart C J R, Leung Y C & Whitehouse A

(2012) Histopathology 60, E106–E114

Fallopian tube metastases of non‐gynaecological origin: a series of 20 cases emphasizing patterns of involvement including intra‐epithelial spread

Aims:  To determine the frequency and distribution of Fallopian tube involvement in patients with ovarian metastases of non‐gynaecological origin.

Methods and results:  All Fallopian tube tissue was processed for histological examination in a consecutive series of 31 patients with ovarian metastases of non‐gynaecological origin. The most common primary sites were appendix (n = 10) colon (n = 7), stomach (n = 6) and breast (n = 4). Twenty cases (65%) showed at least one type of tubal spread. Mural involvement was most common (14 cases) but serosal, intra‐vascular, intra‐epithelial and intra‐lumenal spread were also identified in 12, 9, 8 and 11 cases respectively. Intra‐epithelial involvement was restricted to the fimbrial epithelium and mimicked tubal carcinoma in situ (CIS) architecturally. Pagetoid invasion was noted in two of the cases.

Conclusions:  The Fallopian tubes are commonly involved in patients who have neoplasms metastatic to the ovaries. Metastases may show a CIS‐like pattern of intra‐epithelial spread and therefore small serous CIS‐type lesions may not represent proof of tubal tumour origin in patients who have high‐stage pelvic serous carcinomas. The frequency of intra‐lumenal tumour cells supports transtubal spread as a likely mechanism for mucosal involvement by metastatic tumours involving the lower genital tract.
The diagnostic value of immunohistochemically detected methylthioadenosine phosphorylase deficiency in malignant pleural mesotheliomas
Authors: Zimling Zarah Glad , Jørgensen Anne , Santoni‐Rugiu Eric
Published: March 2012

Zimling Z G, Jørgensen A & Santoni‐Rugiu E

(2012) Histopathology 60, E96–E105

The diagnostic value of immunohistochemically detected methylthioadenosine phosphorylase deficiency in malignant pleural mesotheliomas

Aims:  Malignant pleural mesothelioma (MPM) often causes diagnostic difficulties for pathologists. We assessed whether loss of methylthioadenosine phosphorylase (MTAP), a key enzyme in the intracellular recycling of adenosine triphosphate (ATP) often deleted in MPM, could be detected with immunohistochemistry (IHC) and used as a diagnostic marker for MPM.

Methods and results:  We used IHC to detect MTAP in a cohort of 99 MPMs and 39 reactive mesothelial proliferations (RP) (reactive mesothelial hyperplasia n = 33, reactive pleural fibrosis n = 6). MTAP staining was assessed by an H score. The median H score of the RP cohort was set as a reference point. Cases with H scores below this reference point were considered to have decreased MTAP expression. We found that 64 of 99 (65%) of the investigated MPMs had decreased MTAP expression, while this was only true for nine of 39 (23%) of the RPs (P = 0.001). We further evaluated MTAP expression in a cohort of coagulated pleural effusions from 14 patients with MPM and 20 patients with RP by using a double‐staining technique with Wilms tumour 1 (WT1) as a mesothelial marker. In these samples, decreased MTAP expression diagnosed MPM with a sensitivity of 71% and a specificity of 90%.

Conclusions:  Decreased MTAP expression could potentially be useful in combination with other markers in the diagnosis of MPM.