bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering a protein–protein interface using a computationally designed library
Authors: Guntas Gurkan , Purbeck Carrie , Kuhlman Brian 
Published: October 2010

Computational algorithms for protein design can sample large regions of sequence space, but suffer from undersampling of conformational space and energy function inaccuracies. Experimental screening of combinatorial protein libraries avoids the need for accurate energy functions, but has limited access to vast amounts of sequence space. Here, we test if these two traditionally alternative, but potentially complementary approaches can be combined to design a variant of the ubiquitin-ligase E6AP that will bind to a nonnatural partner, the NEDD8-conjugating enzyme Ubc12. Three E6AP libraries were constructed: (
i
) a naive library in which all 20 amino acids were allowed at every position on the target-binding surface of E6AP (13 positions), (
ii
) a semidirected library that varied the same residue positions as in the naive library but disallowed mutations computationally predicted to destabilize E6AP, and (
iii
) a directed library that used docking and sequence optimization simulations to identify mutations predicted to be favorable for binding Ubc12. Both of the directed libraries showed > 30-fold enrichment over the naive library after the first round of screening with a split-dihydrofolate reductase complementation assay and produced multiple tight binders (
K

d

< 100 nM) after four rounds of selection. Four rounds of selection with the naive library failed to produce any binders with
K

d

’s lower than 50 μM. These results indicate that protein design simulations can be used to create directed libraries that are enriched in tight binders and that in some cases it is sufficient to computationally screen for well-folded sequences without explicit binding calculations.
Elementary steps at the surface of ice crystals visualized by advanced optical microscopy
Authors: Sazaki Gen , Zepeda Salvador , Nakatsubo Shunichi , Yokoyama Etsuro , Furukawa Yoshinori 
Published: October 2010

Due to the abundance of ice on earth, the phase transition of ice plays crucially important roles in various phenomena in nature. Hence, the molecular-level understanding of ice crystal surfaces holds the key to unlocking the secrets of a number of fields. In this study we demonstrate, by laser confocal microscopy combined with differential interference contrast microscopy, that elementary steps (the growing ends of ubiquitous molecular layers with the minimum height) of ice crystals and their dynamic behavior can be visualized directly at air-ice interfaces. We observed the appearance and lateral growth of two-dimensional islands on ice crystal surfaces. When the steps of neighboring two-dimensional islands coalesced, the contrast of the steps always disappeared completely. We were able to discount the occurrence of steps too small to detect directly because we never observed the associated phenomena that would indicate their presence. In addition, classical two-dimensional nucleation theory does not support the appearance of multilayered two-dimensional islands. Hence, we concluded that two-dimensional islands with elementary height (0.37 and 0.39 nm on basal and prism faces, respectively) were visualized by our optical microscopy. On basal and prism faces, we also observed the spiral growth steps generated by screw dislocations. The distance between adjacent spiral steps on a prism face was about 1/20 of that on a basal face. Hence, the step ledge energy of a prism face was 1/20 of that on a basal face, in accord with the known lower-temperature roughening transition of the prism face.
RETRACTED: Phospholipid bilayers are viscoelastic
Authors: Harland Christopher W. , Bradley Miranda J. , Parthasarathy Raghuveer 
Published: October 2010

Lipid bilayers provide the structural framework for cellular membranes, and their character as two-dimensional fluids enables the mobility of membrane macromolecules. Though the existence of membrane fluidity is well established, the nature of this fluidity remains poorly characterized. Three-dimensional fluids as diverse as chocolates and cytoskeletal networks show a rich variety of Newtonian and non-Newtonian dynamics that have been illuminated by contemporary rheological techniques. Applying particle-tracking microrheology to freestanding phospholipid bilayers, we find that the membranes are not simply viscous but rather exhibit viscoelasticity, with an elastic modulus that dominates the response above a characteristic frequency that diverges at the fluid–gel (
L

α

-
L

β

) phase-transition temperature. These findings fundamentally alter our picture of the nature of lipid bilayers and the mechanics of membrane environments.
Uterine epithelial estrogen receptor α is dispensable for proliferation but essential for complete biological and biochemical responses
Authors: Winuthayanon Wipawee , Hewitt Sylvia C. , Orvis Grant D. , Behringer Richard R. , Korach Kenneth S. 
Published: October 2010

Female fertility requires estrogen to specifically stimulate estrogen receptor α (ERα)-dependent growth of the uterine epithelium in adult mice, while immature females show proliferation in both stroma and epithelium. To address the relative roles of ERα in mediating estrogen action in uterine epithelium versus stroma, a uterine epithelial-specific ERα knockout (UtEpiαERKO) mouse line was generated by crossing
Esr
mice with
Wnt7a
-Cre mice. Expression of
Wnt7a
directed Cre activity generated selective deletion of ERα in uterine epithelium, and female UtEpiαERKO are infertile. Herein, we demonstrate that 17β-estradiol (
E
2
)-induced uterine epithelial proliferation was independent of uterine epithelial ERα because DNA synthesis and up-regulation of mitogenic mediators were sustained in UtEpiαERKO uteri after
E
2
treatment. IGF-1 treatment resulted in ligand-independent ER activation in both wild-type (WT) and UtEpiαERKO and mimicked the
E
2
stimulatory effect on DNA synthesis in uterine epithelium. Uterine epithelial ERα was necessary to induce lactoferrin, an
E
2
-regulated secretory protein selectively synthesized in the uterine epithelium. However, loss of uterine epithelial ERα did not alter the
E
2
-dependent progesterone receptor (PR) down-regulation in epithelium. Strikingly, the uterine epithelium of UtEpiαERKO had robust evidence of apoptosis after 3 d of
E
2
treatment. Therefore, we surmise that estrogen induced uterine hyperplasia involves a dispensable role for uterine epithelial ERα in the proliferative response, but ERα is required subsequent to proliferation to prevent uterine epithelial apoptosis assuring the full uterine epithelial response, illustrating the differential cellular roles for ERα in uterine tissue and its contribution during pregnancy.
Determining Weight and Moisture Properties of Sound and Fusarium‐Damaged Single Wheat Kernels by Near‐Infrared Spectroscopy
Authors: Peiris K. H. S. , Dowell F. E. 
Published: October 2010

ABSTRACTSingle kernel moisture content (MC) is important in the measurement of other quality traits in single kernels because many traits are expressed on a dry weight basis. MC also affects viability, storage quality, and price. Also, if near‐infrared (NIR) spectroscopy is used to measure grain traits, the influence of water must be accounted for because water is a strong absorber throughout the NIR region. The feasibility of measurement of MC, fresh weight, dry weight, and water mass of single wheat kernels with or without Fusarium damage was investigated using two wheat cultivars with three visually selected classes of kernels with Fusarium damage and a range of MC. Calibration models were developed either from all kernel classes or from only undamaged kernels of one cultivar that were then validated using all spectra of the other cultivar. A calibration model developed for MC when using all kernels from the wheat cultivar Jagalene had a coefficient of determination (R2) of 0.77 and standard error of cross validation (SECV) of 1.03%. This model predicted the MC of the wheat cultivar 2137 with R2 of 0.81 and a standard error of prediction (SEP) of 1.02% and RPD of 2.2. Calibration models developed using all kernels from both cultivars predicted MC, fresh weight, dry weight, or water mass in kernels better than models that used only undamaged kernels from both cultivars. Single kernel water mass was more accurately estimated using the actual fresh weight of kernels and MC predicted by calibrations that used all kernels or undamaged kernels. The necessity for evaluating and expressing constituent levels in single kernels on a mass/kernel basis rather than a percentage basis was elaborated. The need to overcome the effects of kernel size and water mass on single kernel spectra before using in calibration model development was also highlighted.
pex5Mutants That Differentially Disrupt PTS1 and PTS2 Peroxisomal Matrix Protein Import in Arabidopsis
Authors: Khan Bibi Rafeiza , Zolman Bethany K. 
Published: October 2010

AbstractPEX5 and PEX7 are receptors required for the import of peroxisome-bound proteins containing one of two peroxisomal targeting signals (PTS1 or PTS2). To better understand the role of PEX5 in plant peroxisomal import, we characterized the Arabidopsis (Arabidopsis thaliana) pex5-10 mutant, which has a T-DNA insertion in exon 5 of the PEX5 gene. Sequencing results revealed that exon 5, along with the T-DNA, is removed in this mutant, resulting in a truncated pex5 protein. The pex5-10 mutant has germination defects and is completely dependent on exogenous Suc for early seedling establishment, based on poor utilization of seed-storage fatty acids. This mutant also has delayed development and reduced fertility, although adult pex5-10 plants appear normal. Peroxisomal metabolism of indole-3-butyric acid, propionate, and isobutyrate also is disrupted. The pex5-10 mutant has reduced import of both PTS1 and PTS2 proteins, and enzymatic processes that occur in peroxisomes are disrupted. To specifically study the import and importance of PTS1 proteins, we made a truncated PEX5 construct lacking the PTS1-binding region (PEX5454). Transformation of this construct into pex5-10 resulted in the rescue of PTS2 import, thereby creating a line with PTS1-specific import defects. The pex5-10 (PEX5454) plants still had developmental defects, although restoring PTS2 import resulted in a less severe mutant phenotype. Comparison of pex5-10 and pex5-10 (PEX5454) phenotypes can separate the import mechanisms for enzymes acting in different peroxisomal processes, including indole-3-butyric acid/2,4-dichlorophenoxybutyric acid oxidation, isobutyrate and propionate metabolism, and photorespiration.
Osmoregulation in Lilium Pollen Grains Occurs via Modulation of the Plasma Membrane H+ ATPase Activity by 14-3-3 Proteins
Authors: Pertl Heidi , Pöckl Magdalena , Blaschke Christian , Obermeyer Gerhard 
Published: October 2010

Abstract
To allow successful germination and growth of a pollen tube, mature and dehydrated pollen grains (PGs) take up water and have to adjust their turgor pressure according to the water potential of the surrounding stigma surface. The turgor pressure of PGs of lily (Lilium longiflorum) was measured with a modified pressure probe for simultaneous recordings of turgor pressure and membrane potential to investigate the relation between water and electrogenic ion transport in osmoregulation. Upon hyperosmolar shock, the turgor pressure decreased, and the plasma membrane (PM) hyperpolarizes in parallel, whereas depolarization of the PM was observed with hypoosmolar treatment. An acidification and alkalinization of the external medium was monitored after hyper- and hypoosmotic treatments, respectively, and pH changes were blocked by vanadate, indicating a putative role of the PM H+ ATPase. Indeed, an increase in PM-associated 14-3-3 proteins and an increase in PM H+ ATPase activity were detected in PGs challenged by hyperosmolar medium. We therefore suggest that in PGs the PM H+ ATPase via modulation of its activity by 14-3-3 proteins is involved in the regulation of turgor pressure.
Natural Variation in Arabidopsis Leads to the Identification of REME1, a Pentatricopeptide Repeat-DYW Protein Controlling the Editing of Mitochondrial Transcripts
Authors: Bentolila Stéphane , Knight Walter , Hanson Maureen 
Published: October 2010

Abstract
In vascular plants, organelle RNAs are edited by C-to-U base modification. Hundreds of mitochondrial C residues are targeted for editing in flowering plants. In this study, we exploited naturally occurring variation in editing extent to identify Required for Efficiency of Mitochondrial Editing1 (REME1), an Arabidopsis (Arabidopsis thaliana) pentatricopeptide repeat protein-encoding gene belonging to the DYW subclass that promotes editing of at least two C residues on different mitochondrial transcripts. Positional cloning identified REME1 unambiguously as the gene controlling editing of nad2-558. Virus-induced gene silencing of REME1 confirmed its role in editing of nad2-558 and allowed us to identify orfX-552 as a second C whose editing is positively controlled by REME1. An unexpected outcome of REME1 silencing was the finding of a number of mitochondrial C targets whose editing extent exhibits a significant and reproducible increase in silenced tissues. That increase was shown to be partly due to the virus inoculation and partly to REME1-specific silencing. Analysis of an insertional T-DNA mutant within the REME1 coding sequence confirmed the findings of the virus-induced gene silencing experiments: decrease in editing extent of nad2-558 and orfX-552 and increase in editing extent of two sites, matR-1771 and rpl5-92. Transgenic complementation of the low-edited accession (Landsberg erecta) restored the editing of nad2-558 and orfX-552 to high-edited accession (Columbia)-type levels or to even higher levels than Columbia. There was no effect of the transgene on editing extent of matR-1771 and rpl5-92. The strategy and tools used in this report can be applied to identify additional genes that affect editing extent in plant mitochondria.
Phylogenetic analysis of the latitude‐niche breadth hypothesis in the butterfly subfamily Nymphalinae
Authors: SLOVE JESSICA , JANZ NIKLAS 
Published: October 2010

1. One possible explanation for the latitudinal gradient in species richness often demonstrated is a related gradient in niche breadth, which may allow for denser species packing in the more stable environments at low latitudes.2. The evidence for such a gradient is, however, ambiguous, and the results have varied as much as the methods. Several studies have considered the non‐independence of species, but few have performed explicit phylogenetic analyses.3. In the present study, we tested for a correlation between diet breadth and latitude of distribution in Nymphalinae butterflies using generalised estimating equations (GEE) and accounting for phylogenetic independence.4. Using a simple model with only latitude of distribution as a predictor variable revealed a significant positive relationship with diet breadth. Previous studies, however, have shown that diet breadth is also correlated with butterfly range size, and in turn, that range size may be correlated with latitude of distribution. Including geographical range size in the model also turned out to have a profound effect on the results – to the extent that the relationship between latitude of distribution and diet breadth was effectively reversed.5. We conclude that, at least for this group of butterflies, there is no evidence for a positive correlation between latitude of species distribution and diet breadth when controlling for range size, and that the effect may actually even be reversed.
Fidelity to clinical guidelines using a care pathway in the treatment of first episode psychosis
Authors: Petrakis Melissa , Hamilton Bridget , Penno Steve , Selvendra Ajit , Laxton Simon , Doidge Graeme , Svenson Megan , Castle David 
Published: October 2010

AbstractObjective  To evaluate the implementation of clinical practice guidelines in the initial stages of treatment of first episode psychosis, through use of a care pathway within one area mental health service.Methods  A fidelity audit was undertaken using data from local Early Psychosis Care Pathway documents, completed for the cohort of clients with early psychosis seen in the first 2 years of an integrated early psychosis programme model, at St Vincent's Mental Health Service, Melbourne, Australia.Results  The utilisation of a care pathway greatly supported both the documentation of clinical process and fidelity to clinical guidelines in early psychosis treatment. Excellent adherence (over 80%) was achieved for therapeutic alliance with the client, conducting a comprehensive bio‐psychosocial assessment, medical investigations, reduction of client trauma and increased orientation to the service and the mental health systems of care, and for contact with family. Good adherence (over 70%) was achieved for client re‐integration to the community and promotion of carer well‐being; the service plans to focus on these areas in future service improvement initiatives, along with a focus on physical health assessment and enhancing primary care liaison.Conclusions  The process of formally operationalizing and implementing clinical guidelines utilizing a care pathway within an area mental health service has proved to be an effective way to ensure fidelity with standard agency practices and protocols. The integrated approach, supported by quality assurance initiatives, provides an excellent goodness‐of‐fit within an established area mental health service.
Taking the PACIC back to basics: the structure of the Patient Assessment of Chronic Illness Care
Authors: Spicer John , Budge Claire , Carryer Jenny 
Published: October 2010

AbstractRationale, aims and objectives  The Patient Assessment of Chronic Illness Care (PACIC) is a widely used 20‐item measure consisting of five subscales. Published factor analyses of PACIC scores have produced conflicting results on the measure's factorial validity, and therefore some confusion as to the utility of its subscales. We aim to reduce this confusion by reviewing the evidence on the PACIC's factorial validity, exploring the statistical issues it raises, and considering more broadly what such analyses can reveal about the validity of the PACIC.Methods  To achieve these aims we review six published studies on the PACIC's factorial validity, present confirmatory factor analyses of our own PACIC data from 251 chronic care patients, and assess the PACIC with respect to its status as a reflective or a formative measure.Results  Our statistical analyses support the view that a 5‐factor model does not fit the structure of the PACIC, and highlight a variety of technical issues that confront researchers who wish to factor analyse the measure. However, we argue that, as the PACIC is more accurately seen as a formative measure, such analyses do not provide information that should be used to assess the PACIC's validity.Conclusions  We conclude that, while it is important to continue examining the reliability and validity of the PACIC in a variety of ways, traditional analyses of its factorial validity (and internal consistency) are inappropriate. Meanwhile, use of the subscales is defensible as long as they continue to meet other types of reliability and validity requirements.
Psychometric properties of a scale to measure investment in the sick role: the Illness Cognitions Scale
Authors: Berk Michael , Berk Lesley , Dodd Seetal , Jacka Felice N. , Fitzgerald Paul B. , de Castella Anthony R. , Filia Sacha , Filia Kate , Kulkarni Jayashri , Jackson Henry J. , Stafford Lesley 
Published: October 2010

AbstractRationale, aims and objectives A person's beliefs about their illness may contribute to recovery and prognosis. Some degree of acceptance of illness and its impact is necessary to integrate the presence of a chronic disorder into one's lifestyle and adhere to necessary components of illness management; however, some individuals can become ‘stuck’ and have difficulty adjusting out of the sick role. Inventories exist to measure illness cognitions, attitudes and behaviours as they relate to hypochondria and psychosomatic illness, but there is no extant measure of sick role inertia. We describe the psychometric properties of a new scale, the Illness Cognitions Scale (ICS), a metric of investment in the sick role.Methods The ICS was administered to 97 individuals with bipolar or schizoaffective disorder, and the psychometric properties of the scale measured. Dimensionality was assessed using Principal Components Analysis with Oblimin rotation.Results The scale has a strong internal consistency, with a Cronbach's alpha of 0.858. Results of a factor analysis suggested the presence of one main factor, with three other smaller, related sub‐factors, capturing aspects of maladaptive illness beliefs.Conclusion The ICS is a 17‐item, internally validated scale measuring difficulty adjusting out of the sick role. The scale predominantly measures a single construct. Further research on external validity of the ICS is required as well as determination of the clinical significance and patient acceptability of the scale.
Genetic evidence for male‐biased dispersal in the Siberian jay (Perisoreus infaustus) based on autosomal and Z‐chromosomal markers
Authors: LI M.‐H. , MERILÄ J. 
Published: October 2010

AbstractSex‐bias in natal dispersal patterns can have important genetic and evolutionary consequences; however, reliable information about sex‐biased dispersal can be difficult to obtain with observational methods. We analysed the sex‐specific patterns of genetic differentiation among three Siberian jay (Perisoreus infaustus) populations, using 11 autosomal and six Z‐chromosomal microsatellite markers. Irrespective of marker‐type and indices used (viz. FST, average pairwise relatedness and effective number of immigrants), all analyses provided strong evidence for male‐biased dispersal. Population structuring at autosomal loci (FST = 0.046, P < 0.05) exceeded that at Z‐chromosomal loci (FST = 0.033, P < 0.05), and levels of introgression were inferred to be significantly higher for Z‐chromosomal when compared to autosomal loci. Of the three populations studied, levels of genetic variability were the lowest in the southernmost fringe population, despite the fact that it harboured a group of divergent Z‐chromosomal haplotypes that were not found in the other two populations. In general, the results provide strong genetic evidence for male‐biased dispersal in Siberian jays, where observational data have previously suggested male philopatry. The results also highlight the utility of Z‐chromosomal markers for gaining insights into the genetic diversity and structuring of populations.
Intestinal immune response of Silurus glanis and Barbus barbus naturally infected with Pomphorhynchus laevis (Acanthocephala)
Authors: DEZFULI B. S. , CASTALDELLI G. , BO T. , LORENZONI M. , GIARI L. 
Published: October 2010

SummaryImmunopathological and ultrastructural studies were conducted on the intestine of barbel Barbus barbus and sheatfish Silurus glanis that were naturally infected with the acanthocephalan Pomphorhynchus laevis. Enteric helminths often cause inflammation of the digestive tract, inducing the recruitment of different types of immune cells at the site of infection. The results of our study clearly demonstrated that mast cells (MC) were the dominant immune cells which occur at the site of inflammation in both hosts. MC were associated with fibroblasts and were found in close proximity to, and inside, the capillaries of the intestine, thus, migration of mast cells via the bloodstream was suggested. Significant degranulation of MC was present. Immunohistochemical staining revealed met‐enkephalin and serotonin (5‐HT) in intestinal MC of both uninfected and infected barbel and the absence of the antimicrobial peptides piscidin 3 and piscidin 4 in both species. Data are discussed with respect to host immune response to an intestinal helminth and compared with other host‐parasite systems.