bluuebunny/crossref_metadata_2025 huggingface dataset:
Truncated β-amyloid peptide channels provide an alternative mechanism for Alzheimer’s Disease and Down syndrome
Authors: Jang Hyunbum , Arce Fernando Teran , Ramachandran Srinivasan , Capone Ricardo , Azimova Rushana , Kagan Bruce L. , Nussinov Ruth , Lal Ratnesh
Published: March 2010

Full-length amyloid beta peptides (Aβ
1–40/42
) form neuritic amyloid plaques in Alzheimer’s disease (AD) patients and are implicated in AD pathology. However, recent transgenic animal models cast doubt on their direct role in AD pathology. Nonamyloidogenic truncated amyloid-beta fragments (Aβ
11–42
and Aβ
17–42
) are also found in amyloid plaques of AD and in the preamyloid lesions of Down syndrome, a model system for early-onset AD study. Very little is known about the structure and activity of these smaller peptides, although they could be the primary AD and Down syndrome pathological agents. Using complementary techniques of molecular dynamics simulations, atomic force microscopy, channel conductance measurements, calcium imaging, neuritic degeneration, and cell death assays, we show that nonamyloidogenic Aβ
9–42
and Aβ
17–42
peptides form ion channels with loosely attached subunits and elicit single-channel conductances. The subunits appear mobile, suggesting insertion of small oligomers, followed by dynamic channel assembly and dissociation. These channels allow calcium uptake in amyloid precursor protein-deficient cells. The channel mediated calcium uptake induces neurite degeneration in human cortical neurons. Channel conductance, calcium uptake, and neurite degeneration are selectively inhibited by zinc, a blocker of amyloid ion channel activity. Thus, truncated Aβ fragments could account for undefined roles played by full length Aβs and provide a unique mechanism of AD and Down syndrome pathologies. The toxicity of nonamyloidogenic peptides via an ion channel mechanism necessitates a reevaluation of the current therapeutic approaches targeting the nonamyloidogenic pathway as avenue for AD treatment.
Neurons sense nanoscale roughness with nanometer sensitivity
Authors: Brunetti V. , Maiorano G. , Rizzello L. , Sorce B. , Sabella S. , Cingolani R. , Pompa P. P.
Published: March 2010

The interaction between cells and nanostructured materials is attracting increasing interest, because of the possibility to open up novel concepts for the design of smart nanobiomaterials with active biological functionalities. In this frame we investigated the response of human neuroblastoma cell line (SH-SY5Y) to gold surfaces with different levels of nanoroughness. To achieve a precise control of the nanoroughness with nanometer resolution, we exploited a wet chemistry approach based on spontaneous galvanic displacement reaction. We demonstrated that neurons sense and actively respond to the surface nanotopography, with a surprising sensitivity to variations of few nanometers. We showed that focal adhesion complexes, which allow cellular sensing, are strongly affected by nanostructured surfaces, leading to a marked decrease in cell adhesion. Moreover, cells adherent on nanorough surfaces exhibit loss of neuron polarity, Golgi apparatus fragmentation, nuclear condensation, and actin cytoskeleton that is not functionally organized. Apoptosis/necrosis assays established that nanoscale features induce cell death by necrosis, with a trend directly related to roughness values. Finally, by seeding SH-SY5Y cells onto micropatterned flat and nanorough gold surfaces, we demonstrated the possibility to realize substrates with cytophilic or cytophobic behavior, simply by fine-tuning their surface topography at nanometer scale. Specific and functional adhesion of cells occurred only onto flat gold stripes, with a clear self-alignment of neurons, delivering a simple and elegant approach for the design and development of biomaterials with precise nanostructure-triggered biological responses.
HLA-A alleles and infectious mononucleosis suggest a critical role for cytotoxic T-cell response in EBV-related Hodgkin lymphoma
Authors: Hjalgrim Henrik , Rostgaard Klaus , Johnson Paul C. D. , Lake Annette , Shield Lesley , Little Ann-Margaret , Ekstrom-Smedby Karin , Adami Hans-Olov , Glimelius Bengt , Hamilton-Dutoit Stephen , Kane Eleanor , Taylor G. Malcolm , McConnachie Alex , Ryder Lars P. , Sundstrom Christer , Andersen Paal Skytt , Chang Ellen T. , Alexander Freda E. , Melbye Mads , Jarrett Ruth F.
Published: March 2010

A proportion of classical Hodgkin lymphoma (HL) is believed to be causally related to infection with the ubiquitous lymphotropic EBV. The determining factors for development of EBV-related HL remain poorly understood, but likely involve immunological control of the viral infection. Accordingly, markers of the HLA class I region have been associated with risk of EBV-related HL. To study the host genetic component of EBV-related HL further, we investigated the lymphoma's association with HLA-A*01 and HLA-A*02 simultaneously in the setting of infectious mononucleosis (IM), a risk factor for EBV-related HL, in a case-series analysis including 278 EBV-related and 656 EBV-unrelated cases of HL. By logistic regression, HLA-A*01 alleles [odds ratio (OR) per allele, 2.15; 95% CI, 1.60–2.88] were associated with increased and HLA-A*02 alleles (OR per allele, 0.70; 95% CI, 0.51–0.97) with decreased risk of EBV-related HL. These allele-specific associations corresponded to nearly 10-fold variation in risk of EBV-related HL between HLA-A*01 and HLA-A*02 homozygotes. History of IM was also associated with risk of EBV-related HL (OR, 3.40; 95% CI, 1.74–6.66). The association between history of IM and EBV-related HL was not seen in the presence of HLA-A*02 because this allele appeared to neutralize the effect of IM on EBV-related HL risk. Our findings suggest that HLA class I-restricted EBV-specific cytotoxic T-cell responses and events in the early immune response to EBV infection in IM play critical roles in the pathogenesis of EBV-related HL.
Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo
Authors: Morris Samantha A. , Teo Roy T. Y. , Li Huiliang , Robson Paul , Glover David M. , Zernicka-Goetz Magdalena
Published: March 2010

A crucial question in mammalian development is how cells of the early embryo differentiate into distinct cell types. The first decision is taken when cells undertake waves of asymmetric division that generate one daughter on the inside and one on the outside of the embryo. After this division, some cells on the inside remain pluripotent and give rise to the epiblast, and hence the future body, whereas others develop into the primitive endoderm, an extraembryonic tissue. How the fate of these inside cells is decided is unknown: Is the process random, or is it related to their developmental origins? To address this question, we traced all cells by live-cell imaging in intact, unmanipulated embryos until the epiblast and primitive endoderm became distinct. This analysis revealed that inner cell mass (ICM) cells have unrestricted developmental potential. However, cells internalized by the first wave of asymmetric divisions are biased toward forming pluripotent epiblast, whereas cells internalized in the next two waves of divisions are strongly biased toward forming primitive endoderm. Moreover, we show that cells internalized by the second wave up-regulate expression of Gata6 and Sox17, and changing the expression of these genes determines whether the cells become primitive endoderm. Finally, with our ability to determine the origin of cells, we find that inside cells that are mispositioned when they are born can sort into the correct layer. In conclusion, we propose a model in which the timing of cell internalization, cell position, and cell sorting combine to determine distinct lineages of the preimplantation mouse embryo.
Ribosome-associated peroxiredoxins suppress oxidative stress–induced de novo formation of the [

PSI
+

] prion in yeast
Authors: Sideri Theodora C. , Stojanovski Klement , Tuite Mick F. , Grant Chris M.
Published: March 2010

Peroxiredoxins (Prxs) are ubiquitous antioxidants that protect cells against oxidative stress. We show that the yeast Tsa1/Tsa2 Prxs colocalize to ribosomes and function to protect the Sup35 translation termination factor against oxidative stress–induced formation of its heritable [

PSI
+

] prion conformation. In a
tsa1 tsa2
[

psi
-

] [

PIN
+

] strain, the frequency of [

PSI
+

] de novo formation is significantly elevated. The Tsa1/Tsa2 Prxs, like other 2-Cys Prxs, have dual activities as peroxidases and chaperones, and we show that the peroxidase activity is required to suppress spontaneous de novo [

PSI
+

] prion formation. Molecular oxygen is required for [

PSI
+

] prion formation as growth under anaerobic conditions prevents prion formation in the
tsa1 tsa2
mutant. Conversely, oxidative stress conditions induced by exposure to hydrogen peroxide elevates the rate of de novo [

PSI
+

] prion formation leading to increased suppression of all three termination codons in the
tsa1 tsa2
mutant. Altered translational fidelity in [

PSI
+

] strains may provide a mechanism that promotes genetic variation and phenotypic diversity (True HL, Lindquist SL (2000)
Nature
407:477–483). In agreement, we find that prion formation provides yeast cells with an adaptive advantage under oxidative stress conditions, as elimination of the [
PSI
+
] prion from
tsa1 tsa2
mutants renders the resulting [
psi
-
] [

pin
-

] cells hypersensitive to hydrogen peroxide. These data support a model in which Prxs function to protect the ribosomal machinery against oxidative damage, but when these systems become overwhelmed, [

PSI
+

] prion formation provides a mechanism for uncovering genetic traits that aid survival during oxidative stress conditions.
Xenopus Bsxlinks daily cell cycle rhythms and pineal photoreceptor fate
Authors: D'Autilia Silvia , Broccoli Vania , Barsacchi Giuseppina , Andreazzoli Massimiliano
Published: March 2010

In the developing central nervous system, the cell cycle clock plays a crucial role in determining cell fate specification. A second clock, the circadian oscillator, generates daily rhythms of cell cycle progression. Although these two clocks interact, the mechanisms linking circadian cell cycle progression and cell fate determination are still poorly understood. A convenient system to address this issue is the pineal organ of lower vertebrates, which contains only two neuronal types, photoreceptors and projection neurons. In particular, photoreceptors constitute the core of the pineal circadian system, being able to transduce daily light inputs into the rhythmical production of melatonin. However, the genetic program leading to photoreceptor fate largely remains to be deciphered. Here, we report a previously undescribed function for the homeobox geneBsxin controlling pineal proliferation and photoreceptor fate inXenopus. We show thatXenopus Bsx(Xbsx) is expressed rhythmically in postmitotic photoreceptor precursors, reaching a peak during the night, with a cycle that is complementary to the daily rhythms of S-phase entry displayed by pineal cells.Xbsxknockdown results in increased night levels of pineal proliferation, whereas activation of a GR-Xbsx protein flattens the daily rhythms of S-phase entry to the lowest level. Furthermore, evidence is presented thatXbsxis necessary and sufficient to promote a photoreceptor fate. Altogether, these data indicate thatXbsxplays a dual role in contributing to shape the profile of the circadian cell cycle progression and in the specification of pineal photoreceptors, thus acting as a unique link between these two events.
Aberrant temporal and spatial brain activity during rest in patients with chronic pain
Authors: Malinen Sanna , Vartiainen Nuutti , Hlushchuk Yevhen , Koskinen Miika , Ramkumar Pavan , Forss Nina , Kalso Eija , Hari Riitta
Published: March 2010

In the absence of external stimuli, human hemodynamic brain activity displays slow intrinsic variations. To find out whether such fluctuations would be altered by persistent pain, we asked 10 patients with unrelenting chronic pain of different etiologies and 10 sex- and age-matched control subjects to rest with eyes open during 3-T functional MRI. Independent component analysis was used to identify functionally coupled brain networks. Time courses of an independent component comprising the insular cortices of both hemispheres showed stronger spectral power at 0.12 to 0.25 Hz in patients than in control subjects, with the largest difference at 0.16 Hz. A similar but weaker effect was seen in the anterior cingulate cortex, whereas activity of the precuneus and early visual cortex, used as a control site, did not differ between the groups. In the patient group, seed point-based correlation analysis revealed altered spatial connectivity between insulae and anterior cingulate cortex. The results imply both temporally and spatially aberrant activity of the affective pain-processing areas in patients suffering from chronic pain. The accentuated 0.12- to 0.25-Hz fluctuations in the patient group might be related to altered activity of the autonomic nervous system.
Compound-specific carbon isotopes from Earth’s largest flood basalt eruptions directly linked to the end-Triassic mass extinction
Authors: Whiteside Jessica H. , Olsen Paul E. , Eglinton Timothy , Brookfield Michael E. , Sambrotto Raymond N.
Published: March 2010

A leading hypothesis explaining Phanerozoic mass extinctions and associated carbon isotopic anomalies is the emission of greenhouse, other gases, and aerosols caused by eruptions of continental flood basalt provinces. However, the necessary serial relationship between these eruptions, isotopic excursions, and extinctions has never been tested in geological sections preserving all three records. The end-Triassic extinction (ETE) at 201.4 Ma is among the largest of these extinctions and is tied to a large negative carbon isotope excursion, reflecting perturbations of the carbon cycle including a transient increase in CO
2
. The cause of the ETE has been inferred to be the eruption of the giant Central Atlantic magmatic province (CAMP). Here, we show that carbon isotopes of leaf wax derived lipids (
n
-alkanes), wood, and total organic carbon from two orbitally paced lacustrine sections interbedded with the CAMP in eastern North America show similar excursions to those seen in the mostly marine St. Audrie’s Bay section in England. Based on these results, the ETE began synchronously in marine and terrestrial environments slightly before the oldest basalts in eastern North America but simultaneous with the eruption of the oldest flows in Morocco, a CO
2
super greenhouse, and marine biocalcification crisis. Because the temporal relationship between CAMP eruptions, mass extinction, and the carbon isotopic excursions are shown in the same place, this is the strongest case for a volcanic cause of a mass extinction to date.
Drosophila
topo IIIα is required for the maintenance of mitochondrial genome and male germ-line stem cells
Authors: Wu Jianhong , Feng Liping , Hsieh Tao-shih
Published: March 2010

Topoisomerase IIIα (topo IIIα), a member of the conserved Type IA subfamily of topoisomerases, is required for the cell proliferation in mitotic tissues, but has a lesser effect on DNA endoreplication. The
top3α
gene encodes two forms of protein by utilizing alternative translation initiation sites: one (short form) with the nuclear localization signal only, exclusively localized in the nuclei, and the other (long form), retaining a mitochondrial import sequence at the N-terminus and the nuclear localization sequence at the C-terminus, localized primarily in the mitochondria, though with a small portion in the nuclei. Both forms of topo IIIα can rescue the viability of null mutants of
top3α
. No apparent defect is associated with the flies rescued by the long form; short-form-rescued flies (referred to as
M1L
), however, exhibit defects in fertilities.
M1L
females are sterile. They can lay eggs but with mitochondrial DNA (mtDNA) copy number and ATP content decreased by 20- and 2- to 3-fold, respectively, and they fail to hatch. Of the newly eclosed
M1L
males, 33% are completely sterile, whereas the rest have residual fertilities that are quickly lost in 6 days. The fertility loss of
M1L
males is caused by the disruption of the individualization complex and a progressive loss of germ-line stem cells. This study implicates topo IIIα in the maintenance of mtDNA and male germ-line stem cells, and thus is a causative candidate for genetic disorders associated with mtDNA depletion.
Gonadotropin-positive pituitary tumors accompanied by ovarian tumors in aging female ERβ
−/−
mice
Authors: Fan Xiaotang , Gabbi Chiara , Kim Hyun-Jin , Cheng Guojun , Andersson Leif C. , Warner Margaret , Gustafsson Jan-Åke
Published: March 2010

At 2 years of age, 100% (23/23) of ERβ
−/−
female mice have developed large pituitary and ovarian tumors. The pituitary tumors are gonadotropin-positive and the ovarian tumors are sex cord (less differentiated) and granulosa cell tumors (differentiated and estrogen secreting). No male mice had pituitary tumors and no pituitary or ovarian tumors developed in ERα
−/−
mice or in ERαβ
−/−
double knockout mice. The tumors have high proliferation indices, are ERα-positive, ERβ-negative, and express high levels of nuclear phospho-SMAD3. Mice with granulosa cell tumors also had hyperproliferative endometria. The cause of the pituitary tumors appeared to be excessive secretion of gonadotropin releasing hormone (GnRH) from the hypothalamus resulting from high expression of NPY. The ovarian phenotype is similar to that seen in mice where inhibin is ablated. The data indicate that ERβ plays an important role in regulating GnRH secretion. We suggest that in the absence of ERβ, the proliferative action of FSH/SMAD3 is unopposed and the high proliferation leads to the development of ovarian tumors. The absence of tumors in the ERαβ
−/−
mice suggests that tumor development requires the presence of ERα.
Dynamic evolution of translation initiation mechanisms in prokaryotes
Authors: Nakagawa So , Niimura Yoshihito , Miura Kin-ichiro , Gojobori Takashi
Published: March 2010

It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5′ UTR of an mRNA and the anti-SD sequence in the 3′ end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5′ UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.
Tin-containing zeolites are highly active catalysts for the isomerization of glucose in water
Authors: Moliner Manuel , Román-Leshkov Yuriy , Davis Mark E.
Published: March 2010

The isomerization of glucose into fructose is a large-scale reaction for the production of high-fructose corn syrup (HFCS; reaction performed by enzyme catalysts) and recently is being considered as an intermediate step in the possible route of biomass to fuels and chemicals. Here, it is shown that a large-pore zeolite that contains tin (Sn-Beta) is able to isomerize glucose to fructose in aqueous media with high activity and selectivity. Specifically, a 10% (wt/wt) glucose solution containing a catalytic amount of Sn-Beta (1∶50 Sn:glucose molar ratio) gives product yields of approximately 46% (wt/wt) glucose, 31% (wt/wt) fructose, and 9% (wt/wt) mannose after 30  min and 12 min of reaction at 383 K and 413 K, respectively. This reactivity is achieved also when a 45 wt% glucose solution is used. The properties of the large-pore zeolite greatly influence the reaction behavior because the reaction does not proceed with a medium-pore zeolite, and the isomerization activity is considerably lower when the metal centers are incorporated in ordered mesoporous silica (MCM-41). The Sn-Beta catalyst can be used for multiple cycles, and the reaction stops when the solid is removed, clearly indicating that the catalysis is occurring heterogeneously. Most importantly, the Sn-Beta catalyst is able to perform the isomerization reaction in highly acidic, aqueous environments with equivalent activity and product distribution as in media without added acid. This enables Sn-Beta to couple isomerizations with other acid-catalyzed reactions, including hydrolysis/isomerization or isomerization/dehydration reaction sequences [starch to fructose and glucose to 5-hydroxymethylfurfural (HMF) demonstrated here].
A genome-scale protein interaction profile of
Drosophila
p53 uncovers additional nodes of the human p53 network
Authors: Lunardi Andrea , Di Minin Giulio , Provero Paolo , Dal Ferro Marco , Carotti Marcello , Del Sal Giannino , Collavin Licio
Published: March 2010

The genome of the fruitfly
Drosophila melanogaster
contains a single p53-like protein, phylogenetically related to the ancestor of the mammalian p53 family of tumor suppressors. We reasoned that a comprehensive map of the protein interaction profile of
Drosophila
p53 (Dmp53) might help identify conserved interactions of the entire p53 family in man. Using a genome-scale in vitro expression cloning approach, we identified 91 previously unreported Dmp53 interactors, considerably expanding the current
Drosophila
p53 interactome. Looking for evolutionary conservation of these interactions, we tested 41 mammalian orthologs and found that 37 bound to one or more p53-family members when overexpressed in human cells. An RNAi-based functional assay for modulation of the p53 pathway returned five positive hits, validating the biological relevance of these interactions. One p53 interactor is GTPBP4, a nucleolar protein involved in 60S ribosome biogenesis. We demonstrate that GTPBP4 knockdown induces p53 accumulation and activation in the absence of nucleolar disruption. In breast tumors with wild-type p53, increased expression of GTPBP4 correlates with reduced patient survival, emphasizing a potential relevance of this regulatory axis in cancer.
Do the Poor Pay More for Food? Evidence from the United Kingdom
Authors: Beatty Timothy K.M.
Published: March 2010

Does food cost more for low‐income households? This paper compares two well‐known approaches to answering this question. I find that quantity discounts for a broad range of foods are statistically significant and economically important. However quantity discounting does not lead to the poor paying more for food. I find that the poor pay less than average for the food they purchase. This is explained by the poor spending a greater share of their income on foods where quantity discounting occurs.
varLD: a program for quantifying variation in linkage disequilibrium patterns between populations
Authors: Ong Rick Twee-Hee , Teo Yik-Ying
Published: March 2010

Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studies (GWAS). However, such inter-population LD differences can be leveraged to narrow the search for common causal variants responsible for the association signals observed. The ability to assess and quantify LD variations among populations is thus expected to contribute to both replication and fine-mapping stages of GWAS.

Availability: The program varLD is available for download from http://www.nus-cme.org.sg/software/varld.html

Contact:  statyy@nus.edu.sg
A comparison of bathymetry mapped with the Simrad ME70 multibeam echosounder operated in bathymetric and fisheries modes
Authors: Cutter George R. , Berger Laurent , Demer David A.
Published: March 2010

Cutter, G. R. Jr, Berger, L., and Demer, D. A. 2010. A comparison of bathymetry mapped with the Simrad ME70 multibeam echosounder operated in bathymetric and fisheries modes. – ICES Journal of Marine Science, 67: 1301–1309. The Simrad ME70 multibeam echosounder was designed for quantitative fisheries research and is currently installed on Ifremer's fishery survey vessel (FSV) “Thalassa” and each of the new, quiet, NOAA FSVs. The ME70 has configurable beams and transmits in the range 70–120 kHz to provide calibrated, acoustic-backscattering data throughout the detection range (fisheries mode, FM). With optional hardware and software, the ME70 can also collect soundings that potentially meet International Hydrographic Organization's S–44 Order 1 standards (bathymetric mode, BM). Furthermore, with custom algorithms and software, bathymetric data can be obtained from the ME70 operating in FM, and volume backscatter can be sampled from the ME70 operating in BM. This flexibility allows data to be concurrently collected on fish and their seabed habitat. A method is described for processing the echo amplitude and phase data from multiple split-beams formed in FM to estimate seabed range, slope, and roughness. The resulting bathymetry is compared with that collected with the ME70 operating in BM in the same area of the Bay of Biscay. A proposal is made for software development to facilitate dual-use data processing.
Age, growth, and mortality of Loligo vulgaris wild paralarvae: implications for understanding of the life cycle and longevity
Authors: González Ángel F. , Otero Jaime , Pierce Graham J. , Guerra Ángel
Published: March 2010

González, Á. F., Otero, J., Pierce, G. J., and Guerra, Á. 2010. Age, growth, and mortality of Loligo vulgaris wild paralarvae: implications for understanding of the life cycle and longevity. – ICES Journal of Marine Science, 67: 1119–1127. Age, growth, and mortality were estimated for the first time in wild paralarvae of the common squid, Loligo vulgaris, by examining growth increments in the statoliths of 273 animals collected off the Ría de Vigo (NW Spain, NE Atlantic). Hatching was all year round for the period 2003–2005, with a peak during late spring and a secondary peak during early autumn. Paralarvae varied from 1260 to 7580 µm, and their abundance decreased abruptly as they grew. Statolith increments were clearly visible without grinding in almost all material, allowing reliable estimation of age. Paralarvae are planktonic for at least 3 months. Growth in dorsal mantle length (DML) during that period fitted an exponential equation. The instantaneous relative growth rates were 2.11, 2.15, and 1.82% DML d−1 for 2003, 2004, and 2005, respectively, and there were no significant differences in size-at-age between the 3 years. Taking into account the growth rates estimated for the whole cycle of L. vulgaris, we suggest that the lifespan may previously have been underestimated by 3 months, because the proximity of the rings deposited during paralarval and early juvenile stages would prevent accuracy in enumerating the number of growth increments in later stages. The estimated instantaneous rate of total mortality during the first 90 d of a paralarva life was 9.6, 5.3, and 4.8% d−1 for 2003, 2004, and 2005, respectively. Eye diameter was a reliable and rapid way of estimating DML and age.
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
Authors: Sheldrick George M.
Published: March 2010

The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXE by the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue α-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap.
With phases: how two wrongs can sometimes make a right
Authors: Roversi Pietro , Johnson Steven , Lea Susan M.
Published: March 2010

In isolation, both weak isomorphous/anomalous difference signals from heavy-atom derivatization and phases from partial molecular-replacement solutions for a subset of the asymmetric unit often fall short of producing interpretable electron-density maps. Phases generated from very partial molecular-replacement models (if generated carefully) can be used to reliably locate heavy-atom sites, even if the signal is not sufficiently strong to allow robust finding of the sites using Patterson interpretation or direct methods. Additional advantages are that using molecular-replacement phases to define the heavy-atom substructure avoids the need for subsequent hand determination and/or origin-choice reconciliation and that the partial model can be used to aid the mask determination during solvent flattening. Two case studies are presented in which it was only by combining experimental and molecular-replacement phasing approaches that the crystal structures could be determined.
`Broken symmetries' in macromolecular crystallography: phasing from unmerged data
Authors: Schiltz Marc , Bricogne Gérard
Published: March 2010

The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the symmetry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information.
Temperature-dependent macromolecular X-ray crystallography
Authors: Weik Martin , Colletier Jacques-Philippe
Published: March 2010

X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.
Experimental phasing: best practice and pitfalls
Authors: McCoy Airlie J. , Read Randy J.
Published: March 2010

Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real–imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.
The minimum crystal size needed for a complete diffraction data set
Authors: Holton James M. , Frankel Kenneth A.
Published: March 2010

In this work, classic intensity formulae were united with an empirical spot-fading model in order to calculate the diameter of a spherical crystal that will scatter the required number of photons per spot at a desired resolution over the radiation-damage-limited lifetime. The influences of molecular weight, solvent content, WilsonBfactor, X-ray wavelength and attenuation on scattering power and dose were all included. Taking the net photon count in a spot as the only source of noise, a complete data set with a signal-to-noise ratio of 2 at 2 Å resolution was predicted to be attainable from a perfect lysozyme crystal sphere 1.2 µm in diameter and two different models of photoelectron escape reduced this to 0.5 or 0.34 µm. These represent 15-fold to 700-fold less scattering power than the smallest experimentally determined crystal size to date, but the gap was shown to be consistent with the background scattering level of the relevant experiment. These results suggest that reduction of background photons and diffraction spot size on the detector are the principal paths to improving crystallographic data quality beyond current limits.
Features and development of Coot
Authors: Emsley P. , Lohkamp B. , Scott W. G. , Cowtan K.
Published: March 2010

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
Phymatotrichum (cotton) root rot caused by Phymatotrichopsis omnivora: retrospects and prospects
Authors: UPPALAPATI SRINIVASA RAO , YOUNG CAROLYN A. , MAREK STEPHEN M. , MYSORE KIRANKUMAR S.
Published: March 2010

Phymatotrichum (cotton or Texas) root rot is caused by the soil‐borne fungus Phymatotrichopsis omnivora (Duggar) Hennebert. The broad host range of the fungus includes numerous crop plants, such as alfalfa and cotton. Together with an overview of existing knowledge, this review is aimed at discussing the recent molecular and genomic approaches that have been undertaken to better understand the disease development at the molecular level with the ultimate goal of developing resistant germplasm.

Taxonomy: Phymatotrichopsis omnivora (Duggar) Hennebert [synonym Phymatotrichum omnivorum (Shear) Duggar] is an asexual fungus with no known sexual stage. Mitosporic botryoblastospores occasionally form on epigeous spore mats in nature, but perform no known function and do not contribute to the disease cycle. The fungus has been affiliated erroneously with the polypore basidiomycete Sistotrema brinkmannii (Bres.) J. Erikss. Recent phylogenetic studies have placed this fungus in the ascomycete order Pezizales.

Host range and disease symptoms: The fungus infects most dicotyledonous field crops, causing significant losses to cotton, alfalfa, grape, fruit and nut trees and ornamental shrubs in the south‐western USA, northern Mexico and possibly parts of central Asia. However, this fungus does not cause disease in monocotyledonous plants. Symptoms include an expanding tissue collapse (rot) of infected taproots. In above‐ground tissues, the root rot results in vascular discoloration of the stem and rapid wilting of the leaves without abscission, and eventually the death of the plant. Characteristic mycelial strands of the pathogen are typically present on the root's surface, aiding diagnosis.

Pathogenicity: Confocal imaging of P. omnivora interactions with Medicago truncatula roots revealed that infecting hyphae do not form any specialized structures for penetration and mainly colonize cortical cells and eventually form a mycelial mantle covering the root's surfaces. Cell wall‐degrading enzymes have been implicated in penetration and symptom development. Global gene expression profiling of infected M. truncatula revealed roles for jasmonic acid, ethylene and the flavonoid pathway during disease development. Phymatotrichopsis omnivora apparently evades induced host defences and may suppress the host's phytochemical defences at later stages of infection to favour pathogenesis.

Disease control: No consistently effective control measures are known. The long‐lived sclerotia and facultative saprotrophism of P. omnivora make crop rotation ineffective. Chemical fumigation methods are not cost‐effective for most crops. Interestingly, no genetic resistance has been reported in any of the susceptible crop species.
Expression patterns and association analysis of the porcine DHX58 gene
Authors: Li X. Y. , Han C. M. , Wang Y. , Liu H. Z. , Wu Z. F. , Gao Q. H. , Zhao S. H.
Published: March 2010

RIG‐1 signalling is responsible for the detection of cytoplasmic viral RNA molecules. DEXH (Asp‐Glu‐X‐His) box polypeptide 58 (encoded by DHX58) is a negative regulator of the RIG‐1 signalling pathway. In human, the DHX58 gene can be upregulated and can inhibit the RIG‐1 signalling pathway during viral infection. In this study, porcine DHX58 gene expression patterns were studied. According to our results, the porcine DHX58 gene was upregulated not only by the stimulation of Poly I:C but also by the stimulation of 1ipopolysaccharides (LPS). One polymorphism (g.4919G>C), detected in the ninth intron, was significantly associated with some blood parameters including the red cell distribution width of 1‐day‐old pigs and white blood cell counts, lymphocyte absolute counts, and platelet distribution width of 17‐day‐old pigs (P < 0.05). Moreover, the individuals with the genotype GG have a significantly higher mean white blood cell count than individuals with genotype CC or GC (P < 0.05). Our study indicates that DHX58 is an important gene that is associated with the immune response in swine.
Dietary habits and health status of African‐Caribbean adults
Authors: Earland J. , Campbell J. , Srivastava A.
Published: March 2010

Background:  Although African‐Caribbeans in the UK are more likely to suffer from a number of diet‐related health conditions, including obesity, hypertension and type II diabetes, there have been few dietary studies on this group. The present study is based on a small survey of food and nutrient intakes and traditional dietary habits of African‐Caribbean adults living in Staffordshire.

Methods:  A questionnaire, designed to collect demographic data and information on medical status, physical activities, dietary, cooking and food shopping habits was administered to a convenience sample of 39 adults. Detailed information on food intakes was gathered using a modified existing Food Frequency Questionnaire with 169 items. Height and weight were measured for the calculation of body mass index.

Results:  The average age of the subjects was 47 years (range 19–65 years). The prevalence of obesity was 39% and one‐third of subjects reported having at least one health condition. Physical activities, outside of work, were undertaken by 95% of the sample. Traditional foods were used by 92% of respondents, including fruit and vegetables purchased at markets outside of their local area. A wide variety of foods were consumed and the percentages of energy provided by fats and carbohydrates (30% and 53%, respectively) appeared to be meeting government recommendations. However, absolute energy intakes were high and salt consumption, often in the form of commercial seasonings, exceeded government recommendations.

Conclusions:  The positive aspects of the diets of this population need to be encouraged. Interventions need to focus on ways of reducing total energy intakes, as well as levels of salt consumption.
Attitudes to breastfeeding among adolescents
Authors: Giles M. , Connor S. , McClenahan C. , Mallet J.
Published: March 2010

Background:  Breastfeeding is a major public health concern and a decision to breastfeed has important health benefits for both the infant and mother. Breastfeeding rates are low in many Western countries, and evidence is accumulating to suggest that breastfeeding should be promoted in schools. The present study aimed to employ the theory of planned behaviour (TPB) to predict and explain young people’s motivations to breastfeed with a view to designing an intervention to positively promote breastfeeding among adolescents.

Methods:  Senior schools in Northern Ireland were sorted by a number of key stratification variables, and then randomly sampled. In anticipation of a nonresponse, a first and second reserve list was drawn using matched replacements. Selected schools were contacted by letter, followed by a telephone call. Thirty‐six schools agreed to take part in the research, and a cross‐sectional survey was conducted with 2021 Year 10 pupils.

Results:  Having been breastfed as a child and having seen a mother breastfeeding significantly correlated with intention among both females and males. In descending order of importance, the TPB direct constructs were all significantly correlated with intention among males and females. A hierarchical multiple regression was performed with the intention to breastfeed/encourage partner to breastfeed as the dependent variable, and the TPB successfully predicted intention among males and females.

Conclusions:  The findings obtained in the present study suggest that the TPB is a useful framework on which to base the design of an intervention to promote attitude change, and highlight the importance of key theoretical constructs in predicting intentions to breastfeed.
Nutritional status, nutrition practices and post‐operative complications in patients with gastrointestinal cancer
Authors: Garth A. K. , Newsome C. M. , Simmance N. , Crowe T. C.
Published: March 2010

Background:  Malnutrition and its associated complications are a considerable issue for surgical patients with upper gastrointestinal and colorectal cancer. The present study aimed to determine whether specific perioperative nutritional practices and protocols are associated with improved patient outcomes in this group.

Methods:  Patients admitted for elective upper gastrointestinal or colorectal cancer surgery (n = 95) over a 19‐month period underwent a medical history audit assessing weight changes, nutritional intake, biochemistry, post‐operative complications and length of stay. A subset of patients (n = 25) underwent nutritional assessment by subjective global assessment prior to surgery in addition to assessment of post‐operative medical outcomes, nutritional intake and timing of dietetic intervention.

Results:  Mean (SD) length of stay for patients was 14.0 (12.2) days, with complication rates at 35%. Length of stay was significantly longer in patients who experienced significant preoperative weight loss compared to those who did not [17.0 (15.8) days versus 10.0 (6.8) days, respectively; P < 0.05]. Low albumin and post‐operative weight loss were also predictive of increased length of stay. Of patients who underwent nutritional assessment, 32% were classified as mild–moderately malnourished and 16% severely malnourished. Malnourished patients were hospitalised twice as long as well‐nourished patients [15.8 (12.8) days versus 7.6 (3.5) days; P < 0.05]. Time taken [6.9 (3.6) days] to achieve adequate nutrition post surgery was a factor in post‐operative outcomes, with a positive correlation with length of stay (r = 0.493; P < 0.01), a negative correlation with post‐operative weight change (r = −0.417; P < 0.05) and a greater risk of complications (52% versus 13%; P < 0.01).

Conclusions:  Malnutrition is prevalent among surgical patients with gastrointestinal cancer. Poor nutritional status coupled with delayed and inadequate post‐operative nutrition practices are associated with worse clinical outcomes.
Diet and exercise in the prevention of diabetes
Authors: Walker K. Z. , O’Dea K. , Gomez M. , Girgis S. , Colagiuri R.
Published: March 2010

Background:  Individuals with impaired fasting glucose or impaired glucose tolerance are at high risk of progression to type 2 diabetes. Lifestyle modification through change to diet and exercise habit has considerable potential to prevent or delay the onset of this disease.

Methods:  A systematic literature search was undertaken of Medline, EMBASE, the Cochrane library and the Cumulative Index to Nursing and Allied Health Literature for journal articles relevant to the question of whether type 2 diabetes can be prevented by lifestyle change.

Results:  Four cohort studies in a total of 4864 high risk individuals followed for a period of 2.5–6 years were identified. These showed that lifestyle change may reduce the incidence of type 2 diabetes by 28–59%. Moreover, follow‐up studies also indicate that diabetes incidence rates continue to be depressed many years after the discontinuation of a lifestyle intervention. Evidence from a meta‐analysis confirms this evidence and suggests that it would be necessary to treat 6.4 (95% confidence interval 5.0–8.4) individuals to prevent or delay one case of diabetes through lifestyle intervention. An examination of weight loss diets (low fat, high protein or Mediterranean) suggests each may be effective but each has limitations requiring care in food selection. Evidence also suggests that the maintenance of weight loss also requires regular exercise with an additional expenditure of approximately 8.4 MJ week−1 (2000 kcal week−1).

Conclusions:  Diabetes can be prevented by lifestyle change. The challenge is to develop public health approaches to support individuals with respect to incorporating the lifestyle changes needed to reduce the risk of diabetes into their everyday life.