bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of cerebral white matter changes on cardiovascular responses to cognitive and physical activity in a stroke population
Authors: Williamson J. B. , Lewis G. F. , Nyenhuis D. L. , Stebbins G. T. , Murphy C. , Handelman M. , Harden E. , Heilman K. M. , Gorelick P. B. , Porges S. W.
Published: October 2012

Autonomic nervous system (ANS) control may be disrupted by cerebrovascular disease. We investigated the relationship between alterations in white matter integrity and regulation of the ANS in 23 participants who sustained a stroke within 5 years. These participants underwent diffusion tensor imaging, and fractional anisotropy values were calculated (DTI‐FA) for each hemisphere and lobe. Cognitive and physical exertion tasks were performed while recording an electrocardiogram. Respiratory sinus arrhythmia (RSA) decreased more during a verbal fluency task with lower left hemisphere DTI‐FA. Further, the physical stressor yielded decreases in RSA with lower frontal DTI‐FA and higher temporal lobe DTI‐FA, p < .05 (perhaps a release effect on the central autonomic network). Decrements in ANS regulation may have functional consequences that alter behavior, as well as potentially increasing the risk for further vascular disease.
The Backroom Effect in Retail Operations
Authors: Eroglu Cuneyt , Williams Brent D. , Waller Matthew A.
Published: October 2012

Traditional inventory models fail to take into account the dynamics between the retail sales floor and the backroom, commonly used by retailers for extra storage. When a replenishment order for a given item arrives at a retail store, it may not fit on the allocated shelf space, making backroom storage necessary. In this article, we introduce the backroom effect (BRE) as a consequence of misalignment of case pack size, shelf space, and reorder point. This misalignment results from the fragmented nature of inventory policy decision making in the retail industry and affects basic trade‐offs in inventory models. We specify conditions under which the BRE exists, quantify the expected amount of backroom inventory, derive an optimal short‐term inventory policy, and assess the impact of the BRE on the optimal inventory policy and total costs. Our results indicate that ignoring the BRE leads to artificially high reorder points and higher total costs. The paper concludes with a discussion of theoretical and managerial implications.
Effects of Meloxicam and Phenylbutazone on Equine Gastric Mucosal Permeability
Authors: D'Arcy‐Moskwa E. , Noble G.K. , Weston L.A. , Boston R. , Raidal S.L.
Published: October 2012

Background

NewerNSAIDs that more selectively target the induced isoform of the cyclooxygenase enzyme (COX2) activity might reduce adverse effects while preserving therapeutic benefits of these drugs.

Objectives

To compare the effect of oral administration of multiple dose rates of meloxicam and phenylbutazone (PBZ) on gastric mucosal integrity in horses.

Animals

Twenty‐five light breed horses.

Methods

In vivo toxicity study. Horses were randomly assigned to 5 treatment groups, receiving placebo,PBZ(4.4 mg/kgPOq12h day 1, 2.2 mg/kgPOq12h for 4 days, 2.2 mg/kgPOq24h for 9 days), or 3 dose rates of meloxicam (0.6 mg/kg q24h, 1.8 mg/kg q24h, 3.0 mg/kg q24h) for 14 days. Sucrose permeability testing was performed on Day 0 (before treatment) and on Day 13. All personnel involved with data collection or analysis were blinded to treatment.

Results

Administration ofPBZat the above dose rate significantly increased gastric permeability to sucrose, evidenced by increased peak serum sucrose concentrations (280–1,580 pg/μL,P = .001) after treatment. Similar changes were not evident after administration of meloxicam at any dose rate tested, or in control horses (P > .05). Treatment was not associated with significant differences in ulceration of the squamous or glandular mucosa. Peak sucrose concentrations were not correlated with serum total protein or albumin concentrations (R2 = −0.07,P = .61, R2 = −0.08,P = .58, respectively).

Conclusion and Clinical Importance

These results suggest thatPBZwas associated with greater compromise to gastric mucosal integrity than meloxicam.
Suicide Attempts and Suicide among Marines: A Decade of Follow‐up
Authors: Gradus Jaimie L. , Shipherd Jillian C. , Suvak Michael K. , Giasson Hannah L. , Miller Matthew
Published: October 2012

Suicidal behavior among military personnel is of paramount public health importance because of the increased risk of death from suicide in this population. Pre‐ and post‐Marine recruit training risk factors for suicide attempts among current and former Marines were examined in 10 years following recruit training. The characteristics of the subsample of current and former Marines who died by suicide during this time are also described. Stressful and traumatic life events (e.g., childhood physical, sexual, and emotional abuse, sexual harassment during recruit training) and pre‐recruit training suicide attempts emerged as having strong associations with post‐recruit training attempts. Half of those who died by suicide in the 10 years following recruit training endorsed at least one significant life stressor prior to joining the Marines. This study highlights the importance of screening for stressful and potentially traumatic experiences occurring both before and during military service as part of a comprehensive suicide risk assessment in military samples.
Predictors of Suicidal Ideation in Late Childhood and Adolescence: A 5‐Year Follow‐Up of Two Nationally Representative Cohorts in the Republic of Korea
Authors: Park Sunhee
Published: October 2012

This study explores the trajectory of suicidal ideation in childhood and adolescence and identifies its strong predictors. Secondary data obtained from two nationally representative cohorts of South Korean youth were longitudinally analyzed using frequencies, percentages, and discrete time survival analysis. This study revealed an increase in the occurrence of suicidal ideation in adolescence, a higher prevalence of suicidal ideation among females than among males, and differences in predictors of suicide ideation by developmental stages and gender. The results suggest that multifaceted factors specific to developmental stages and gender should be simultaneously considered to diminish the occurrences of suicidal ideation.
Emotional and behavioural outcomes later in childhood and adolescence for children with specific language impairments: meta‐analyses of controlled prospective studies
Authors: Yew Shaun Goh Kok , O’Kearney Richard
Published: October 2012

Background:  Prospective evidence on psychological outcomes for children with specific language impairments (SLI) is accumulating. To date, there has been no attempt to summarise what this evidence says about the strength of link between SLI and later child and adolescent emotional and behavioural (EB) outcomes.

Methods:  We undertook a systematic review and meta‐analysis (following PRISMA guidelines and involving a literature search to June 2012 of seven databases, including MEDLINE and PsychAPA) of prospective, cohort studies of children with SLI and typical language development (TLD) reporting on the incidence and severity of EB problems later in childhood or adolescence.

Results:  Nineteen follow‐up reports of eight cohorts with 553 SLI children and 1533 TLD controls were identified. Initial assessment was at 3–8.8 years of age and follow‐up duration from 2 to 12 years. Pooled across comparable studies, SLI children were about two times more likely to show disorder levels of overall internalising problems, overall externalising and ADHD problems than TLD children. Compared with the average TLD child (50 percentile), at follow‐up, the symptom severity of the average SLI child was at the 72 percentile (95% CI 65–79 percentile) on internalising symptoms, the 69 percentile (95% CI 63–74 percentile) on externalising symptoms and the 60 percentile (95% CI 52–68 percentile) on AHDH severity. The findings about risk to specific mental disorders and the severity of specific problems were inconclusive.

Conclusions:  Relative to typical children, SLI children experience clinically important increases in the severity of diverse emotional, behavioural and ADHD symptoms and more frequently show a clinical level of these problems. The small number of studies included in pooled analysis and methodological heterogeneity reduce the precision and generalisability of the findings. Most studies do not account for initial levels of EB problems.
Element mobility during continental collision: insights from polymineralic metamorphic vein within UHP eclogite in the Dabie orogen
Authors: SHENG Y.‐M. , ZHENG Y‐F. , LI S‐N. , HU Z.
Published: October 2012

Metamorphic dehydration and partial melting are two important processes during continental collision. They have significant bearing on element transport at the slab interface under subduction‐zone P–T conditions. Petrological and geochemical insights into the two processes are provided by a comprehensive study of leucocratic veins in ultrahigh‐pressure (UHP) metamorphic rocks. This is exemplified by this study of a polymineralic vein within phengite‐bearing UHP eclogite in the Dabie orogen. The vein is primarily composed of quartz, kyanite, epidote and phengite, with minor accessory minerals such as garnet, rutile and zircon. Primary multiphase solid inclusions occur in garnet and epidote from the both vein and host eclogite. They are composed of quartz ± K‐feldspar ± plagioclase ± K‐bearing glass and exhibit irregular to negative crystal shapes that are surrounded by weak radial cracks. This suggests their precipitation from solute‐rich metamorphic fluid/melt that involved the reaction of phengite breakdown. Zircon U–Pb dating for the vein gave two groups of concordant ages at 217 ± 2 and 210 ± 2 Ma, indicating two episodes of zircon growth in the Late Triassic. The same minerals from the two rocks give consistent δ18O and δD values, suggesting that the vein‐forming fluid was directly derived from the host UHP eclogite. The vein is much richer in phengite and epidote than the host eclogite, suggesting that the fluid is associated with remarkable concentration of such water‐soluble elements as LILE and LREE migration. Garnet and rutile in the vein exhibit much higher contents of HREE (2.2–5.7 times) and Nb–Ta (1.8–2.0 times) than those in the eclogite, indicating that these normally water‐insoluble elements became mobile and then were sunken in the vein minerals. Thus, the vein‐forming agent would be primarily composed of the UHP aqueous fluid with minor amounts of the hydrous melt, which may even become a supercritical fluid to have a capacity to transport not only LILE and LREE but also HREE and HFSE at subduction‐zone metamorphic conditions. Taken together, significant amounts of trace elements were transported by the vein‐forming fluid due to the phengite breakdown inside the UHP eclogite during exhumation of the deeply subducted continental crust.
Synaptosomes secrete and uptake functionally active microRNAs via exocytosis and endocytosis pathways
Authors: Xu Jie , Chen Qun , Zen Ke , Zhang Chenyu , Zhang Qipeng
Published: October 2012

In this study, we first characterized synaptosome microRNA (miRNA) profiles using microarray and qRT‐PCR. MicroRNAs were detected in isolated synaptic vesicles, and Ago2 immunoprecipitation studies revealed an association between miRNAs and Ago2. Second, we found that miR‐29a, miR‐99a, and miR‐125a were significantly elevated in synaptosome supernatants after depolarization. MiRNA secretion by the synaptosome was Ca2+‐dependent and was inhibited by the exocytosis inhibitor, okadaic acid. Furthermore, application of nerve growth factor increased miRNA secretion without altering the spontaneous release of miRNAs. Conversely, kainic acid decreased miRNA secretion and enhanced the spontaneous release of miRNAs. These results indicate that synaptosomes could secrete miRNAs. Finally, synthesized miRNAs were taken up by synaptosomes, and the endocytosis inhibitor Dynasore blocked this process. After incubation with miR‐125a, additional miR‐125a was bound to Ago2 in the synaptosome, and expression of the miR‐125a target gene (PSD95 mRNA) was decreased; these findings suggest that the ingested miRNAs were assembled in the RNA‐induced silencing complex, resulting in the degradation of target mRNAs. To our knowledge, this is the first study that demonstrates the secretion of miRNAs by synaptosomes under physiological stimulation and demonstrates that secreted miRNAs might be functionally active after being taken up by the synaptic fraction via the endocytic pathway.
SMRT‐mediated co‐shuttling enables export of class IIa HDACs independent of their CaM kinase phosphorylation sites
Authors: Soriano Francesc X. , Chawla Sangeeta , Skehel Paul , Hardingham Giles E.
Published: October 2012

The Class IIa histone deacetylases (HDAC)4 and HDAC5 play a role in neuronal survival and behavioral adaptation in the CNS. Phosphorylation at 2/3 N‐terminal sites promote their nuclear export. We investigated whether non‐canonical signaling routes to Class IIa HDAC export exist because of their association with the co‐repressor Silencing Mediator Of Retinoic And Thyroid Hormone Receptors (SMRT). We found that, while HDAC5 and HDAC4 mutants lacking their N‐terminal phosphorylation sites (HDAC4MUT, HDAC5MUT) are constitutively nuclear, co‐expression with SMRT renders them exportable by signals that trigger SMRT export, such as synaptic activity, HDAC inhibition, and Brain Derived Neurotrophic Factor (BDNF) signaling. We found that SMRT's repression domain 3 (RD3) is critical for co‐shuttling of HDAC5MUT, consistent with the role for this domain in Class IIa HDAC association. In the context of BDNF signaling, we found that HDAC5WT, which was more cytoplasmic than HDAC5MUT, accumulated in the nucleus after BDNF treatment. However, co‐expression of SMRT blocked BDNF‐induced HDAC5WT import in a RD3‐dependent manner. In effect, SMRT‐mediated HDAC5WT export was opposing the BDNF‐induced HDAC5 nuclear accumulation observed in SMRT's absence. Thus, SMRT's presence may render Class IIa HDACs exportable by a wider range of signals than those which simply promote direct phosphorylation.
Cyclooxygenase‐1 inhibition reduces amyloid pathology and improves memory deficits in a mouse model of Alzheimer's disease
Authors: Choi Sang‐Ho , Aid Saba , Caracciolo Luca , Sakura Minami S. , Niikura Takako , Matsuoka Yasuji , Turner R. Scott , Mattson Mark P. , Bosetti Francesca
Published: October 2012

Several epidemiological and preclinical studies suggest that non‐steroidal anti‐inflammatory drugs (NSAIDs), which inhibit cyclooxygenase (COX), reduce the risk of Alzheimer's disease (AD) and can lower β‐amyloid (Aβ) production and inhibit neuroinflammation. However, follow‐up clinical trials, mostly using selective cyclooxygenase (COX)‐2 inhibitors, failed to show any beneficial effect in AD patients with mild to severe cognitive deficits. Recent data indicated that COX‐1, classically viewed as the homeostatic isoform, is localized in microglia and is actively involved in brain injury induced by pro‐inflammatory stimuli including Aβ, lipopolysaccharide, and interleukins. We hypothesized that neuroinflammation is critical for disease progression and selective COX‐1 inhibition, rather than COX‐2 inhibition, can reduce neuroinflammation and AD pathology. Here, we show that treatment of 20‐month‐old triple transgenic AD (3 × Tg‐AD) mice with the COX‐1 selective inhibitor SC‐560 improved spatial learning and memory, and reduced amyloid deposits and tau hyperphosphorylation. SC‐560 also reduced glial activation and brain expression of inflammatory markers in 3 × Tg‐AD mice, and switched the activated microglia phenotype promoting their phagocytic ability. The present findings are the first to demonstrate that selective COX‐1 inhibition reduces neuroinflammation, neuropathology, and improves cognitive function in 3 × Tg‐AD mice. Thus, selective COX‐1 inhibition should be further investigated as a potential therapeutic approach for AD.
Differential expression of parvalbumin in neonatal phencyclidine‐treated rats and socially isolated rats
Authors: Kaalund Sanne S. , Riise Jesper , Broberg Brian V. , Fabricius Katrine , Karlsen Anna S. , Secher Thomas , Plath Niels , Pakkenberg Bente
Published: October 2012

Decreased parvalbumin expression is a hallmark of the pathophysiology of schizophrenia and has been associated with abnormal cognitive processing and decreased network specificity. It is not known whether this decrease is due to reduced expression of the parvalbumin protein or degeneration of parvalbumin‐positive interneurons (PV+ interneurons). In this study, we examined PV+ expression in two rat models of cognitive dysfunction in schizophrenia: the environmental social isolation (SI) and pharmacological neonatal phencyclidine (neoPCP) models. Using a stereological method, the optical fractionator, we counted neurons, PV+ interneurons, and glial cells in the medial prefrontal cortex (mPFC) and hippocampus (HPC). In addition, we quantified the mRNA level of parvalbumin in the mPFC. There was a statistically significant reduction in the number of PV+ interneurons (p = 0.021) and glial cells (p = 0.024) in the mPFC of neonatal phencyclidine rats, but not in SI rats. We observed no alterations in the total number of neurons, hippocampal PV+ interneurons, parvalbumin mRNA expression or volume of the mPFC or HPC in the two models. Thus, as the total number of neurons remains unchanged following phencyclidine (PCP) treatment, we suggest that the decreased number of counted PV+ interneurons represents a reduced parvalbumin protein expression below immunohistochemical detection limit rather than a true cell loss. Furthermore, these results indicate that the effect of neonatal PCP treatment is not limited to neuronal populations.
A Molecular Survey of Ulva (Chlorophyta) in Temperate Australia Reveals Enhanced Levels of Cosmopolitanism
Authors: Kirkendale Lisa , Saunders Gary W. , Winberg Pia
Published: October 2012

The green algal genus Ulva includes a speciose group of marine macroalgae inhabiting shallow seas worldwide. Although algal blooms in Asia highlight the opportunistic nature of several “nuisance” species, recent research clearly reveals important positive benefits of Ulva. Applied research requires accurate, reliable, and rapid identification, however, identification of Ulva spp. has met with con‐siderable difficulty. Consequently, many have turned to molecular markers to aid in taxonomy. Previous studies of plants and algae have relied heavily on ITS and rbcL. Recently, tufA has been presented as a suitable barcoding gene to facilitate species‐level identification of green macroalgae and it is used here to explore the diversity of Ulva spp. in temperate Australia. Ninety Ulva specimens collected from 38 sites across five states were sequenced for this gene region with exemplars from each genetic group also sequenced for rbcL to test for congruence. Collections of Australian Ulva spp. were compared to samples from Asia and North America and exhibited trends consistent with recent studies in terms of species relationships. Results support an overwhelmingly cosmopolitan flora in temperate Australia that contrasts with other Australasian surveys of Ulva that report a greater number of endemics and new species. Four new records, as well as numerous range extensions for taxa already known from the country, are documented. Evidence for three nonindigenous Ulva species in temperate Australia is discussed.
Algal Parasite Herpodiscus durvillaeae (Phaeophyceae: Sphacelariales) Inferred to have Traversed the Pacific Ocean with its Buoyant Host
Authors: Fraser Ceridwen I. , Waters Jonathan M.
Published: October 2012

The parasitic phaeophycean endophyte Herpodiscus durvillaeae (Lindauer) G. R. South has previously only been recorded from New Zealand, in association with a single host species, Durvillaea antarctica (Chamisso) Hariot (southern bull‐kelp). Here we use DNA sequence data from plastid and nuclear markers (chloroplast rbcL, ribosomal LSU, and a nuclear pseudogene copy of COI) to test for the presence of H. durvillaeae beyond the New Zealand region, and on host species other than D. antarctica. Analyses of samples from the Falkland Islands confirm the first record of H. durvillaeae from the Atlantic Ocean. We report that Falkland Islands H. durvillaeae are genetically indistinguishable from samples of this species from New Zealand's sub‐Antarctic Campbell Island, suggesting recent dispersal of the parasite across the Pacific Ocean, presumably by rafting with its buoyant macroalgal host. We also here record H. durvillaeae from New Zealand endemics Durvillaea poha Fraser et al. and D. willana Lindauer.
Phylogenetic Reappraisal of the Genus Monomorphina (Euglenophyceae) Based on Molecular and Morphological Data
Authors: Kim Jong Im , Shin Woongghi , Triemer Richard E.
Published: October 2012

A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakryś, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.
Fully Unconscious and Prone to Habit: The Characteristics of Agency in the Structure and Agency Dialectic
Authors: Akram Sadiya
Published: October 2012

While the human agent must have the capacity for reflexivity, intentionality and consciousness, the same agent must also be affected by the social world in which she lives: herein lies the essence of the structure and agency dialectic. This paper argues that while some realists are in principle committed to a dialectical relationship between structure and agency, there is some dissonance between this commitment and the concepts of agency that they develop. I highlight the exclusion of the unconscious and habit from realist notions of agency and argue that this oversight serves to unbalance the dialectic between structure and agency thereby leading to the over‐empowerment of agency. The concepts of agency developed by Margaret Archer, Anthony Giddens and Pierre Bourdieu are discussed in this paper. Archer's concept of agency is argued to focus exclusively on reflexivity whilst neglecting to include the unconscious and habit. Giddens is shown to develop a much improved concept of agency, which includes the unconscious, however, his rejection of the independent causal powers of structure and agency problematises his commitment to the dialectic. A much improved approach to theorising agency, developed within a critical realist framework, is offered drawing on Bourdieu's concept of habitus. The paper concludes with a discussion of gender, and considers how the unconscious and habit can help to better understand the myriad ways in which gender functions in society.
Relationship between the microsatellite D2S388‐5 and D2S2232 polymorphisms and chronic obstructive pulmonary disease in the Chinese Kazakh population
Authors: GUAN JIAN , LIU XIAN‐SHENG , XU YONG‐JIAN , XU XI‐LIN , YANG YONG‐SHENG , WANG RAN
Published: October 2012

Background and objective:  Chronic obstructive pulmonary disease (COPD) is influenced by multiple genetic and environmental factors. The role of genetic susceptibility in the pathogenesis of COPD has recently gained more attention. The surface lung surfactant protein B plays an important role in COPD pathogenesis. Microsatellite DNA has been characterized in the surfactant protein B alleles D2S388‐5 and D2S2232. The aim of this research was to investigate the distribution of the D2S388‐5 and D2S2232 microsatellite polymorphisms in smokers of the Kazakh ethnic group in Xinjiang, China, with and without COPD to assess whether such polymorphisms are associated with COPD susceptibility.

Methods:  DNA was extracted from the blood of 197 smokers with COPD and 236 control smokers of Kazakh ethnicity. The smokers diagnosed with COPD were registered at the Department of Respiratory Medicine from four different hospitals. The control group was recruited at the medical examination centre from the same area. The polymorphisms of the D2S388‐5 and D2S2232 microsatellite loci were measured by multiple short tandem repeat amplification using fluorescence‐labelled polymerase chain reaction and capillary electrophoresis.

Results:  Nine alleles and 32 genotypes were identified in D2S388‐5, while 9 alleles and 31 genotypes were identified in D2S2232. Both genotype distributions in control smokers were in accordance with Hardy–Weinberg equilibrium. The frequency of the 254 bp allele from the D2S388‐5 locus was significantly higher in the COPD group versus the control (P < 0.001, odds ratio = 5.942).

Conclusions:  D2S388‐5 microsatellite polymorphism may be associated with susceptibility to COPD in Xinjiang Kazakhs.
Phytosulfokine control of growth occurs in the epidermis, is likely to be non‐cell autonomous and is dependent on brassinosteroids
Authors: Hartmann Jens , Stührwohldt Nils , Dahlke Renate I. , Sauter Margret
Published: October 2012

Phytosulfokine (PSK) is a secreted disulfated pentapeptide that controls root and shoot growth. The ubiquitous expression of PSK precursor and of the LRR receptor kinase genes in Arabidopsis raised the question of whether PSK acts as an autocrine growth factor in planta. Expression of PSKR1 under the control of tissue‐ and cell type‐specific promoters in a receptor null background strongly suggests that PSK is a non‐cell autonomous signal that controls growth through localized activity in the epidermis. pskr1–3 pskr2–1 seedlings had shorter roots and hypocotyls than the wild type, whereas 35S: PSKR1 or 35S: PSKR2 seedlings were larger, indicating that receptor abundance limits growth in planta. The preferential expression of PSKR1 in the epidermis of CER6: PSKR1 pskr1–3 pskr2–1 seedlings was sufficient to promote wild‐type growth. Moreover, in GL2:PSKR1 pskr1–3 pskr2–1 seedlings that express PSKR1 in atrichoblasts of the root epidermis, root growth was restored to wild‐type levels. In pskr1–3 pskr2–1 seedlings, trichoblasts and atrichoblasts were shorter than in the wild type. Trichoblasts of GL2:PSKR1 pskr1–3 pskr2–1 seedlings, which are unable to sense PSK, nonetheless had acquired wild‐type length, suggesting that PSK acts as a non‐cell autonomous signal. Inhibition of brassinosteroid (BR) biosynthesis with brassinazole (BZ) caused a loss of responsiveness to PSK in wild‐type, tpst–1 (tyrosylprotein sulfotransferase–1), PSKR1ox12 and CER6:PSKR1–3–1 seedlings, as did the genetic knock‐out of BR synthesis in det2–1 and of BR perception in bri1–9, suggesting that BR mediates PSK‐dependent growth. Quantitative PCR analysis of BR‐related genes in wild‐type, pskr1–3 pskr2–1, PSKR1ox and tpst–1 seedlings showed largely unchanged transcript levels of BR biosynthesis genes.
Validation of deformable registration in head and neck cancer using analysis of variance
Authors: Mencarelli A. , van Beek S. , van Kranen S. , Rasch C. , van Herk M. , Sonke J.‐J.
Published: October 2012

Purpose:

Deformable image registration (DIR) is often validated based on a distance‐to‐agreement (DTA) criterion of automatically propagated anatomical landmarks that were manually identified. Due to human observer variability, however, the performance of the registration method is diluted. The purpose of this study was to evaluate an analysis of variance (ANOVA) based validation to account for such observer variation.

Methods:

Weekly cone beam CTs (CBCTs) of ten head and neck cancer patients undergoing five weeks of radiotherapy were used. An expert identified 23 anatomical features (landmarks) on the planning CT. The landmarks were automatically propagated to the CBCT using multiregion‐of‐interest (mROI) registration. Additionally, two human observers independently localized these landmarks on the CBCTs. Subsequently, ANOVA was used to compute the variance of each observer on the pairwise distance (PWD).

Results:

ANOVA based analysis demonstrated that a classical DTA approach underestimated the precision for the mROI due to human observer variation by about 25%. The systematic error (accuracy) of mROI ranged from 0.13 to 0.17 mm; the variability (1 SD) (precision) ranged from 1.3 to 1.5 mm demonstrating that its performance is dominated by the precision.

Conclusions:

The PWD‐ANOVA method accounts for human observer variation allowing a better estimation of the of DIR errors.
Tricking the Guard: Exploiting Plant Defense for Disease Susceptibility
Authors: Lorang J. , Kidarsa T. , Bradford C. S. , Gilbert B. , Curtis M. , Tzeng S.-C. , Maier C. S. , Wolpert T. J.
Published: October 2012

Necrophilic Bandit Fungi

The immune systems that plants use to defend against pathogens normally deflect attack. However,

Lorang
et al.

(p.
659
, published online 18 October) have identified a rearguard susceptibility that a necrotrophic fungus exploits. The fungal toxin victorin interacts with the defense protein LOV1 in
Arabidopsis
and activates it, but the result, counterintuitively, is that the plant succumbs to the disease rather than fighting it off. What seems to be happening is that victorin targets a thioredoxin that regulates the systemic acquired resistance pathway. That interaction triggers activity of LOV1, which in turn incites cell death. The invading fungus then benefits from the ready access to dead cells.
Dedifferentiation of Neurons and Astrocytes by Oncogenes Can Induce Gliomas in Mice
Authors: Friedmann-Morvinski Dinorah , Bushong Eric A. , Ke Eugene , Soda Yasushi , Marumoto Tomotoshi , Singer Oded , Ellisman Mark H. , Verma Inder M.
Published: October 2012

Cancer Stem Cells: A Moving Target?

Glioblastoma multiforme (GBM) is a highly aggressive human brain tumor. The prevailing “cancer stem cell hypothesis” posits that GBMs arise primarily from neuronal stem cells. Now,

Friedmann-Morvinski
et al.

(p.
1080
, published online 18 October; see the Perspective by
Krivtsov and Armstrong
) suggest that this hypothesis may be too restrictive. In mouse models, brain tumors resembling human GBMs could form from fully differentiated cells such as astrocytes and neurons. Upon acquiring certain genetic alterations, mature brain cells may thus be capable of dedifferentiating into a progenitor-like cell, which could then initiate and maintain tumor growth.
Structural Basis of Transcription Initiation
Authors: Zhang Yu , Feng Yu , Chatterjee Sujoy , Tuske Steve , Ho Mary X. , Arnold Eddy , Ebright Richard H.
Published: October 2012

The bacterial transcription initiation complex preorganizes promoter DNA for nucleotide binding and RNA synthesis.
Structure and Ecological Roles of a Novel Exopolysaccharide from the Arctic Sea Ice Bacterium Pseudoalteromonas sp. Strain SM20310
Authors: Liu Sheng-Bo , Chen Xiu-Lan , He Hai-Lun , Zhang Xi-Ying , Xie Bin-Bin , Yu Yong , Chen Bo , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: October 2012

The structure and ecological roles of the exopolysaccharides (EPSs) from sea ice microorganisms are poorly studied. Here we show that strain SM20310, with an EPS production of 567 mg liter
−1
, was screened from 110 Arctic sea ice isolates and identified as a
Pseudoalteromonas
strain. The EPS secreted by SM20310 was purified, and its structural characteristics were studied. The predominant repeating unit of this EPS is a highly complicated α-mannan with a molecular mass greater than 2 × 10
6
Da. The backbone of the EPS consists of 2-α-, 6-α-mannosyl residues, in which a considerable part of the 6-α-mannosyl residues are branched at the 2 position with either single
t
-mannosyl residues or two mannosyl residues. The structure of the described EPS is different from the structures of EPSs secreted by other marine bacteria. Analysis of the ecological roles of the identified EPS showed that the EPS could significantly enhance the high-salinity tolerance of SM20310 and improve the survival of SM20310 after freeze-thaw cycles. These results suggest that the EPS secreted by strain SM20310 enables the strain to adapt to the sea ice environment, which is characterized by low temperature, high salinity, and repeated freeze-thaw cycles. In addition to its functions in strain SM20310, this EPS also significantly improved the tolerance of
Escherichia coli
to freeze-thaw cycles, suggesting that it may have a universal impact on microorganism cryoprotection.
Depth-Related Differences in Organic Substrate Utilization by Major Microbial Groups in Intertidal Marine Sediment
Authors: Miyatake Tetsuro , MacGregor Barbara J. , Boschker Henricus T. S.
Published: October 2012

Stable isotope probing of magnetic-bead-captured rRNA (Mag-SIP) indicated clear differences in
in situ
organic substrate utilization by major microbial groups between the more oxidized (0 to 2 cm) and sulfate-reducing (2 to 5 cm) horizons of marine intertidal sediment. We also showed that cyanobacteria and diatoms may survive by glucose utilization under dark anoxic conditions.
Behavior of Different Shiga Toxin-Producing Escherichia coli Serotypes in Various Experimentally Contaminated Raw-Milk Cheeses
Authors: Miszczycha Stéphane D. , Perrin Frédérique , Ganet Sarah , Jamet Emmanuel , Tenenhaus-Aziza Fanny , Montel Marie-Christine , Thevenot-Sergentet Delphine
Published: October 2012

Shiga toxin-producing
Escherichia coli
(STEC) is an important cause of food-borne illness. The public health implication of the presence of STEC in dairy products remains unclear. Knowledge of STEC behavior in cheeses would help to evaluate the human health risk. The aim of our study was to observe the growth and survival of experimentally inoculated STEC strains in raw-milk cheeses manufactured and ripened according to five technological schemes: blue-type cheese, uncooked pressed cheese with long ripening and with short ripening steps, cooked cheese, and lactic cheese. Cheeses were contaminated with different STEC serotypes (O157:H7, O26:H11, O103:H2, and O145:H28) at the milk preparation stage. STEC growth and survival were monitored on selective media during the entire manufacturing process. STEC grew (2 to 3 log
10
CFU · g
−1
) in blue-type cheese and the two uncooked pressed cheeses during the first 24 h of cheese making. Then, STEC levels progressively decreased in cheeses that were ripened for more than 6 months. In cooked cheese and in lactic cheese with a long acidic coagulation step (pH < 4.5), STEC did not grow. Their levels decreased after the cooking step in the cooked cheese and after the coagulation step in the lactic cheese, but STEC was still detectable at the end of ripening and storage. A serotype effect was found: in all cheeses studied, serotype O157:H7 grew less strongly and was less persistent than the others serotypes. This study improves knowledge of the behavior of different STEC serotypes in various raw-milk cheeses.
Co-Occurring Anammox, Denitrification, and Codenitrification in Agricultural Soils
Authors: Long Andrew , Heitman Joshua , Tobias Craig , Philips Rebecca , Song Bongkeun
Published: October 2012

Anammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N
2
gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N
2
in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N
2
production, molecular and
15
N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (
nosZ
) and hydrazine oxidase (
hzo
) genes, respectively, while the internal transcribed spacer (ITS) of
Fusarium oxysporum
was quantified to estimate the abundance of codenitrifying and denitrifying fungi.
15
N tracer incubation experiments with
15
NO
3
−
or
15
NH
4
+
addition were conducted to measure the N
2
production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N
2
production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed by
F. oxysporum
based on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N
2
-N g
−1
day
−1
, while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N
2
-N g
−1
day
−1
. Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N
2
production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle.
Identification of a Residue Affecting Fatty Alcohol Selectivity in Wax Ester Synthase
Authors: Barney Brett M. , Mann Rachel L. , Ohlert Janet M.
Published: October 2012

The terminal enzyme in the bacterial wax ester biosynthetic pathway is the bifunctional wax ester synthase/acyl-coenzyme A:diacylglycerol acyltransferase (WS/DGAT), which utilizes a fatty alcohol and a fatty acyl-coenzyme A (CoA) to synthesize the corresponding wax ester. In this report, we identify a specific residue in WS/DGAT enzymes obtained from
Marinobacter aquaeolei
VT8 and
Acinetobacter baylyi
that alters fatty alcohol selectivity and kinetic parameters when modified to alternative residues.
Biochemical Properties and Crystal Structure of a β-Phenylalanine Aminotransferase from Variovorax paradoxus
Authors: Crismaru Ciprian G. , Wybenga Gjalt G. , Szymanski Wiktor , Wijma Hein J. , Wu Bian , Bartsch Sebastian , de Wildeman Stefaan , Poelarends Gerrit J. , Feringa Ben L. , Dijkstra Bauke W. , Janssen Dick B.
Published: October 2012

By selective enrichment, we isolated a bacterium that can use β-phenylalanine as a sole nitrogen source. It was identified by 16S rRNA gene sequencing as a strain ofVariovorax paradoxus. Enzyme assays revealed an aminotransferase activity. Partial genome sequencing and screening of a cosmid DNA library resulted in the identification of a 1,302-bp aminotransferase gene, which encodes a 46,416-Da protein. The gene was cloned and overexpressed inEscherichia coli. The recombinant enzyme was purified and showed a specific activity of 17.5 U mg−1for (S)-β-phenylalanine at 30°C and 33 U mg−1at the optimum temperature of 55°C. The β-specific aminotransferase exhibits a broad substrate range, acceptingortho-,meta-, andpara-substituted β-phenylalanine derivatives as amino donors and 2-oxoglutarate and pyruvate as amino acceptors. The enzyme is highly enantioselective toward (S)-β-phenylalanine (enantioselectivity [E], >100) and derivatives thereof with different substituents on the phenyl ring, allowing the kinetic resolution of various racemic β-amino acids to yield (R)-β-amino acids with >95% enantiomeric excess (ee). The crystal structures of the holoenzyme and of the enzyme in complex with the inhibitor 2-aminooxyacetate revealed structural similarity to the β-phenylalanine aminotransferase fromMesorhizobiumsp. strain LUK. The crystal structure was used to rationalize the stereo- and regioselectivity ofV. paradoxusaminotransferase and to define a sequence motif with which new aromatic β-amino acid-converting aminotransferases may be identified.
Form and Function of Clostridium thermocellum Biofilms
Authors: Dumitrache Alexandru , Wolfaardt Gideon , Allen Grant , Liss Steven N. , Lynd Lee R.
Published: October 2012

The importance of bacterial adherence has been acknowledged in microbial lignocellulose conversion studies; however, few reports have described the function and structure of biofilms supported by cellulosic substrates. We investigated the organization, dynamic formation, and carbon flow associated with biofilms of the obligately anaerobic cellulolytic bacterium
Clostridium thermocellum
27405. Using noninvasive,
in situ
fluorescence imaging, we showed biofilms capable of near complete substrate conversion with a characteristic monolayered cell structure without an extracellular polymeric matrix typically seen in biofilms. Cell division at the interface and terminal endospores appeared throughout all stages of biofilm growth. Using continuous-flow reactors with a rate of dilution (2 h
−1
) 12-fold higher than the bacterium's maximum growth rate, we compared biofilm activity under low (44 g/liter) and high (202 g/liter) initial cellulose loading. The average hydrolysis rate was over 3-fold higher in the latter case, while the proportions of oligomeric cellulose hydrolysis products lost from the biofilm were 13.7% and 29.1% of the total substrate carbon hydrolyzed, respectively. Fermentative catabolism was comparable between the two cellulose loadings, with ca. 4% of metabolized sugar carbon being utilized for cell production, while 75.4% and 66.7% of the two cellulose loadings, respectively, were converted to primary carbon metabolites (ethanol, acetic acid, lactic acid, carbon dioxide). However, there was a notable difference in the ethanol-to-acetic acid ratio (g/g), measured to be 0.91 for the low cellulose loading and 0.41 for the high cellulose loading. The results suggest that substrate availability for cell attachment rather than biofilm colonization rates govern the efficiency of cellulose conversion.
Development of Quantitative PCR Assays Targeting the 16S rRNA Genes of Enterococcus spp. and Their Application to the Identification of Enterococcus Species in Environmental Samples
Authors: Ryu Hodon , Henson Michael , Elk Michael , Toledo-Hernandez Carlos , Griffith John , Blackwood Denene , Noble Rachel , Gourmelon Michèle , Glassmeyer Susan , Santo Domingo Jorge W.
Published: October 2012

The detection of environmental enterococci has been determined primarily by using culture-based techniques that might exclude some enterococcal species as well as those that are nonculturable. To address this, the relative abundances of enterococci were examined by challenging fecal and water samples against a currently available genus-specific assay (Entero1). To determine the diversity of enterococcal species, 16S rRNA gene-based group-specific quantitative PCR (qPCR) assays were developed and evaluated against eight of the most common environmental enterococcal species. Partial 16S rRNA gene sequences of 439 presumptive environmental enterococcal strains were analyzed to study further the diversity of enterococci and to confirm the specificities of group-specific assays. The group-specific qPCR assays showed relatively high amplification rates with targeted species (>98%), although some assays cross-amplified with nontargeted species (1.3 to 6.5%). The results with the group-specific assays also showed that different enterococcal species co-occurred in most fecal samples. The most abundant enterococci in water and fecal samples were
Enterococcus faecalis
and
Enterococcus faecium
, although we identified more water isolates as
Enterococcus casseliflavus
than as any of the other species. The prevalence of the Entero1 marker was in agreement with the combined number of positive signals determined by the group-specific assays in most fecal samples, except in gull feces. On the other hand, the number of group-specific assay signals was lower in all water samples tested, suggesting that other enterococcal species are present in these samples. While the results highlight the value of genus- and group-specific assays for detecting the major enterococcal groups in environmental water samples, additional studies are needed to determine further the diversity, distributions, and relative abundances of all enterococcal species found in water.
A Pericentrin-Related Protein Homolog in Aspergillus nidulans Plays Important Roles in Nucleus Positioning and Cell Polarity by Affecting Microtubule Organization
Authors: Chen Peiying , Gao Rongsui , Chen Shaochun , Pu Li , Li Pin , Huang Ying , Lu Ling
Published: October 2012

Pericentrin is a large coiled-coil protein in mammalian centrosomes that serves as a multifunctional scaffold for anchoring numerous proteins. Recent studies have linked numerous human disorders with mutated or elevated levels of pericentrin, suggesting unrecognized contributions of pericentrin-related proteins to the development of these disorders. In this study, we characterized AnPcpA, a putative homolog of pericentrin-related protein in the model filamentous fungus
Aspergillus nidulans
, and found that it is essential for conidial germination and hyphal development. Compared to the hyphal apex localization pattern of calmodulin (CaM), which has been identified as an interactive partner of the pericentrin homolog, GFP-AnPcpA fluorescence dots are associated mainly with nuclei, while the accumulation of CaM at the hyphal apex depends on the function of AnPcpA. In addition, the depletion of AnPcpA by an inducible
alcA
promoter repression results in severe growth defects and abnormal nuclear segregation. Most interestingly, in mature hyphal cells, knockdown of pericentrin was able to significantly induce changes in cell shape and cytoskeletal remodeling; it resulted in some enlarged compartments with condensed nuclei and anucleate small compartments as well. Moreover, defects in AnPcpA significantly disrupted the microtubule organization and nucleation, suggesting that AnPcpA may affect nucleus positioning by influencing microtubule organization.
Microsporidian Infection in a Free-Living Marine Nematode
Authors: Ardila-Garcia A. M. , Fast N. M.
Published: October 2012

Microsporidia are unicellular fungi that are obligate endoparasites. Although nematodes are one of the most abundant and diverse animal groups, the only confirmed report of microsporidian infection was that of the “nematode killer” (Nematocida parisii).N. parisiiwas isolated from a wildCaenorhabditissp. and causes an acute and lethal intestinal infection in a lab strain ofCaenorhabditis elegans. We set out to characterize a microsporidian infection in a wild nematode to determine whether the infection pattern ofN. parisiiin the lab is typical of microsporidian infections in nematodes. We describe a novel microsporidian species namedSporanauta perivermis(marine spore of roundworms) and characterize its infection in its natural host, the free-living marine nematodeOdontophora rectangula. S. perivermisis not closely related toN. parisiiand differs strikingly in all aspects of infection. Examination by transmission electron microscopy (TEM) revealed that the infection was localized in the hypodermal and muscle tissues only and did not involve the intestines. Fluorescentin situhybridization (FISH) confirmed infection in the muscle and hypodermis, and surprisingly, it also revealed that the parasite infectsO. rectangulaeggs, suggesting a vertical mode of transmission. Our observations highlight the importance of studying parasites in their natural hosts and indicate that not all nematode-infecting microsporidia are “nematode killers”; instead, microsporidiosis can be more versatile and chronic in the wild.