bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth
Authors: Hotto Amber M , Huston Zoe E , Stern David B
Published: September 2010

Background

The roles of non-coding RNAs in regulating gene expression have been extensively studied in both prokaryotes and eukaryotes, however few reports exist as to their roles in organellar gene regulation. Evidence for accumulation of natural antisense RNAs (asRNAs) in chloroplasts comes from the expressed sequence tag database and cDNA libraries, while functional data have been largely obtained from artificial asRNAs. In this study, we used Nicotiana tabacum to investigate the effect on sense strand transcripts of overexpressing a natural chloroplast asRNA, AS5, which is complementary to the region which encodes the 5S rRNA and tRNAArg.

Results

AS5-overexpressing (AS5ox) plants obtained by chloroplast transformation exhibited slower growth and slightly pale green leaves. Analysis of AS5 transcripts revealed four distinct species in wild-type (WT) and AS5ox plants, and additional AS5ox-specific products. Of the corresponding sense strand transcripts, tRNAArg overaccumulated several-fold in transgenic plants whereas 5S rRNA was unaffected. However, run-on transcription showed that the 5S-trnR region was transcribed four-fold more in the AS5ox plants compared to WT, indicating that overexpression of AS5 was associated with decreased stability of 5S rRNA. In addition, polysome analysis of the transformants showed less 5S rRNA and rbcL mRNA associated with ribosomes.

Conclusions

Our results suggest that AS5 can modulate 5S rRNA levels, giving it the potential to affect Chloroplast translation and plant growth. More globally, overexpression of asRNAs via chloroplast transformation may be a useful strategy for defining their functions.
Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women
Authors: El Aila Nabil A , Tency Inge , Claeys Geert , Saerens Bart , Cools Piet , Verstraelen Hans , Temmerman Marleen , Verhelst Rita , Vaneechoutte Mario
Published: September 2010

Background

Streptococcus agalactiae (group B streptococcus; GBS) is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics), followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS.

Methods

A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA), group B streptococcus differential agar (GBSDA) (Granada Medium) and chromID Strepto B agar (CA), with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination.

Results

The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100%) was significantly higher than detection on the basis of vaginal sampling (50%), but not significantly higher than for rectal sampling (82%). Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95%) detected more carriers than Lim broth enrichment and subculture onto CNA (77%). One false negative isolate was observed on GBSDA, and three false positives on CA.

Conclusions

In conclusion, rectovaginal sampling increased the number GBS positive women detected, compared to vaginal and/or rectal sampling. Direct plating on CA and/or GBSDA provided rapid detection of GBS that was at least as sensitive and specific as the CDC recommended method of Lim broth subcultured onto non chromogenic agar.
Population uptake of antiretroviral treatment through primary care in rural South Africa
Authors: Cooke Graham S , Tanser Frank C , Bärnighausen Till W , Newell Marie-Louise
Published: September 2010

Background

KwaZulu-Natal is the South African province worst affected by HIV and the focus of early modeling studies investigating strategies of antiretroviral treatment (ART) delivery. The reality of antiretroviral roll-out through primary care has differed from that anticipated and real world data are needed to inform the planning of further scaling up of services. We investigated the factors associated with uptake of antiretroviral treatment through a primary healthcare system in rural South Africa.

Methods

Detailed demographic, HIV surveillance and geographic information system (GIS) data were used to estimate the proportion of HIV positive adults accessing antiretroviral treatment within northern KwaZulu-Natal, South Africa in the period from initiation of antiretroviral roll-out until the end of 2008. Demographic, spatial and socioeconomic factors influencing the likelihood of individuals accessing antiretroviral treatment were explored using multivariable analysis.

Results

Mean uptake of ART among HIV positive resident adults was 21.0% (95%CI 20.1-21.9). Uptake among HIV positive men (19.2%) was slightly lower than women (21.8%, P = 0.011). An individual's likelihood of accessing ART was not associated with level of education, household assets or urban/rural locale. ART uptake was strongly negatively associated with distance from the nearest primary healthcare facility (aOR = 0.728 per square-root transformed km, 95%CI 0.658-0.963, P = 0.002).

Conclusions

Despite concerns about the equitable nature of antiretroviral treatment rollout, we find very few differences in ART uptake across a range of socio-demographic variables in a rural South African population. However, even when socio-demographic factors were taken into account, individuals living further away from primary healthcare clinics were still significantly less likely to be accessing ART
Efficacy and safety of combined prolonged-release oxycodone and naloxone in the management of moderate/severe chronic non-malignant pain: results of a prospectively designed pooled analysis of two randomised, double-blind clinical trials
Authors: Löwenstein Oliver , Leyendecker Petra , Lux Eberhard A , Blagden Mark , Simpson Karen H , Hopp Michael , Bosse Björn , Reimer Karen
Published: September 2010

Background

Two randomised 12-week, double-blind, parallel-group, multicenter studies comparing oxycodone PR/naloxone PR and oxycodone PR alone on symptoms of opioid-induced bowel dysfunction in patients with moderate/severe non-malignant pain have been conducted.

Methods

These studies were prospectively designed to be pooled and the primary outcome measure of the pooled data analysis was to demonstrate non-inferiority in 12-week analgesic efficacy of oxycodone PR/naloxone PR versus oxycodone PR alone. Patients with opioid-induced constipation were switched to oxycodone PR and then randomised to fixed doses of oxycodone PR/naloxone PR (n = 292) or oxycodone PR (n = 295) for 12 weeks (20-80 mg/day).

Results

No statistically significant differences in analgesic efficacy were observed for the two treatments (p = 0.3197; non-inferiority p < 0.0001; 95% CI -0.07, 0.23) and there was no statistically significant difference in frequency of analgesic rescue medication use. Improvements in Bowel Function Index score were observed for oxycodone PR/naloxone PR by Week 1 and at every subsequent time point (-15.1; p < 0.0001; 95% CI -17.3, -13.0). AE incidence was similar for both groups (61.0% and 57.3% of patients with oxycodone PR/naloxone PR and oxycodone PR alone, respectively).

Conclusions

Results of this pooled analysis confirm that oxycodone PR/naloxone PR provides effective analgesia and suggest that oxycodone PR/naloxone PR improves bowel function without compromising analgesic efficacy.

Trial registration numbers

ClinicalTrials.gov identifier: NCT00412100 and NCT00412152
Therapeutic versus neuroinflammatory effects of passive immunization is dependent on Aβ/amyloid burden in a transgenic mouse model of Alzheimer's disease
Authors: Minami S Sakura , Sidahmed Elkhansa , Aid Saba , Shimoji Mika , Niikura Takako , Mocchetti Italo , Rebeck G William , Prendergast Jay S , Dealwis Chris , Wetzel Ronald , Bosetti Francesca , Matsuoka Yasuji , Hoe Hyang-Sook , Turner R Scott
Published: September 2010

Background

Passive immunization with antibodies directed to Aβ decreases brain Aβ/amyloid burden and preserves memory in transgenic mouse models of Alzheimer's disease (AD). This therapeutic strategy is under intense scrutiny in clinical studies, but its application is limited by neuroinflammatory side effects (autoimmune encephalitis and vasogenic edema).

Methods

We intravenously administered the monoclonal Aβ protofibril antibody PFA1 to aged (22 month) male and female 3 × tg AD mice with intermediate or advanced AD-like neuropathologies, respectively, and measured brain and serum Aβ and CNS cytokine levels. We also examined 17 month old 3 × tg AD female mice with intermediate pathology to determine the effect of amyloid burden on responses to passive immunization.

Results

The 22 month old male mice immunized with PFA1 had decreased brain Aβ, increased serum Aβ, and no change in CNS cytokine levels. In contrast, 22 month old immunized female mice revealed no change in brain Aβ, decreased serum Aβ, and increased CNS cytokine levels. Identical experiments in younger (17 month old) female 3 × tg AD mice with intermediate AD-like neuropathologies revealed a trend towards decreased brain Aβ and increased serum Aβ accompanied by a decrease in CNS MCP-1.

Conclusions

These data suggest that passive immunization with PFA1 in 3 × tg AD mice with intermediate disease burden, regardless of sex, is effective in mediating potentially therapeutic effects such as lowering brain Aβ. In contrast, passive immunization of mice with a more advanced amyloid burden may result in potentially adverse effects (encephalitis and vasogenic edema) mediated by certain proinflammatory cytokines.
Guidelines for the diagnosis and management of chylomicron retention disease based on a review of the literature and the experience of two centers
Authors: Peretti Noel , Sassolas Agnès , Roy Claude C , Deslandres Colette , Charcosset Mathilde , Castagnetti Justine , Pugnet-Chardon Laurence , Moulin Philippe , Labarge Sylvie , Bouthillier Lise , Lachaux Alain , Levy Emile
Published: September 2010

Familial hypocholesterolemia, namely abetalipoproteinemia, hypobetalipoproteinemia and chylomicron retention disease (CRD), are rare genetic diseases that cause malnutrition, failure to thrive, growth failure and vitamin E deficiency, as well as other complications. Recently, the gene implicated in CRD was identified. The diagnosis is often delayed because symptoms are nonspecific. Treatment and follow-up remain poorly defined.

The aim of this paper is to provide guidelines for the diagnosis, treatment and follow-up of children with CRD based on a literature overview and two pediatric centers 'experience.

The diagnosis is based on a history of chronic diarrhea with fat malabsorption and abnormal lipid profile. Upper endoscopy and histology reveal fat-laden enterocytes whereas vitamin E deficiency is invariably present. Creatine kinase (CK) is usually elevated and hepatic steatosis is common. Genotyping identifies theSar1bgene mutation.

Treatment should be aimed at preventing potential complications. Vomiting, diarrhea and abdominal distension improve on a low-long chain fat diet. Failure to thrive is one of the most common initial clinical findings. Neurological and ophthalmologic complications in CRD are less severe than in other types of familial hypocholesterolemia. However, the vitamin E deficiency status plays a pivotal role in preventing neurological complications. Essential fatty acid (EFA) deficiency is especially severe early in life. Recently, increased CK levels and cardiomyopathy have been described in addition to muscular manifestations. Poor mineralization and delayed bone maturation do occur. A moderate degree of macrovesicular steatosis is common, but no cases of steatohepatitis cirrhosis.

Besides a low-long chain fat diet made up uniquely of polyunsaturated fatty acids, treatment includes fat-soluble vitamin supplements and large amounts of vitamin E. Despite fat malabsorption and the absence of postprandial chylomicrons, the oral route can prevent neurological complications even though serum levels of vitamin E remain chronically low. Dietary counseling is needed not only to monitor fat intake and improve symptoms, but also to maintain sufficient caloric and EFA intake.

Despite a better understanding of the pathogenesis of CRD, the diagnosis and management of the disease remain a challenge for clinicians. The clinical guidelines proposed will helpfully lead to an earlier diagnosis and the prevention of complications.
Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
Authors: Ptitsyn Andrey , Schlater Amber , Kanatous Shane
Published: September 2010

Background

The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.

Results

Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation.

Conclusion

In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.
Mothers' knowledge and utilization of prevention of mother to child transmission services in northern Tanzania
Authors: Falnes Eli Fjeld , Tylleskär Thorkild , de Paoli Marina Manuela , Manongi Rachel , Engebretsen Ingunn MS
Published: September 2010

Background

More than 90% of children living with HIV have been infected through mother to child transmission. The aims of our present study were to: (1) assess the utilization of the prevention of mother to child transmission (PMTCT) services in five reproductive and child health clinics in Moshi, northern Tanzania, after the implementation of routine counselling and testing; (2) explore the level of knowledge the postnatal mothers had about PMTCT; and (3) assess the quality of the counselling given.

Methods

This study was conducted in 2007 and 2008 in rural and urban areas of Moshi in the Kilimanjaro region of Tanzania. Mixed methods were used. We interviewed 446 mothers when they brought their four‐week‐old infants to five reproductive and child health clinics for immunization. On average, the urban clinics included in the study had implemented the programme two years earlier than the rural clinics. We also conducted 13 in‐depth interviews with mothers and nurses, four focus group discussions with mothers, and four observations of mothers receiving counselling.

Results

Nearly all mothers (98%) were offered HIV testing, and all who were offered accepted. However, the counselling was hasty with little time for clarifications. Mothers attending urban antenatal clinics tended to be more knowledgeable about PMTCT than the rural attendees. Compared with previous studies in the area, our study found that PMTCT knowledge had increased and the counsellors had greater confidence in their counselling.

Conclusions

Routine counselling and testing for HIV at the antenatal clinics was greatly accepted and included practically every mother in this time period. However, the counselling was suboptimal due to time and resource constraints. We interpret the higher level of PMTCT knowledge among the urban as opposed to the rural attendees as a result of differences in the start up of the PMTCT programme and, thus, programme maturation. After comparison with earlier studies conducted in this setting, we conclude that when the programme has had time to get established, both its acceptance and the understanding of the topics dealt with during the counselling increases.
The rate of the molecular clock and the cost of gratuitous protein synthesis
Authors: Plata Germán , Gottesman Max E , Vitkup Dennis
Published: September 2010

Background

The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve slowly in all species mainly to maintain robustness to translation errors that generate toxic misfolded proteins. Here we investigate this hypothesis experimentally by comparing the growth rate of Escherichia coli expressing wild type and misfolding-prone variants of the LacZ protein.

Results

We show that the cost of toxic protein misfolding is small compared to other costs associated with protein synthesis. Complementary computational analyses demonstrate that there is also a relatively weaker, but statistically significant, selection for increasing solubility and polarity in highly expressed E. coli proteins.

Conclusions

Although we cannot rule out the possibility that selection against misfolding toxicity significantly affects the protein clock in species other than E. coli, our results suggest that it is unlikely to be the dominant and universal factor determining the clock rate in all organisms. We find that in this bacterium other costs associated with protein synthesis are likely to play an important role. Interestingly, our experiments also suggest significant costs associated with volume effects, such as jamming of the cellular environment with unnecessary proteins.
The Wheatstone Concertina and Symmetrical Arrangements of Tonal Space
Authors: Gawboy Anna
Published: September 2010

The English concertina, invented by the physicist Charles Wheatstone, enjoyed a modest popularity as a parlor and concert instrument in Victorian Britain. Wheatstone designed several button layouts for the concertina consisting of pitch lattices of interlaced fifths and thirds, which he described in patents of 1829 and 1844. Like the later tonal spaces of the German dualist theorists, the concertina's button layouts were inspired by the work of eighteenth-century mathematician Leonhard Euler, who used a lattice to show relationships among pitches in just intonation. Wheatstone originally tuned the concertina according to Euler's diatonic-chromatic genus before switching to meantone and ultimately equal temperament for his commercial instruments. Among members of the Royal Society, the concertina became an instrument for research on acoustics and temperament. Alexander Ellis, translator of Hermann von Helmholtz's On the Sensations of Tone, used the concertina as a demonstration tool in public lectures intended to popularize Helmholtz's acoustic theories. The English concertina's history reveals the peculiar fissures and overlaps between scientific and popular cultures, speculative harmonics and empirical acoustics, and music theory and musical practice in the mid-nineteenth century.
On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development
Authors: Wollmann Heike , Mica Erica , Todesco Marco , Long Jeff A. , Weigel Detlef
Published: September 2010

The ABC model of flower development explains how three classes of homeotic genes confer identity to the four types of floral organs. In Arabidopsis thaliana, APETALA2 (AP2) and AGAMOUS (AG) represent A- and C-class genes that act in an antagonistic fashion to specify perianth and reproductive organs, respectively. An apparent paradox was the finding that AP2 mRNA is supposedly uniformly distributed throughout young floral primordia. Although miR172 has a role in preventing AP2 protein accumulation, miR172 was reported to disappear from the periphery only several days after AG activation in the center of the flower. Here, we resolve the enigmatic behavior of AP2 and its negative regulator miR172 through careful expression analyses. We find that AP2 mRNA accumulates predominantly in the outer floral whorls, as expected for an A-class homeotic gene. Its pattern overlaps only transiently with that of miR172, which we find to be restricted to the center of young floral primordia from early stages on. MiR172 also accumulates in the shoot meristem upon floral induction, compatible with its known role in regulating AP2-related genes with a role in flowering. Furthermore, we show that AP2 can cause striking organ proliferation defects that are not limited to the center of the floral meristem, where its antagonist AG is required for terminating stem cell proliferation. Moreover, AP2 never expands uniformly into the center of ag mutant flowers, while miR172 is largely unaffected by loss of AG activity. We present a model in which the decision whether stamens or petals develop is based on the balance between AP2 and AG activities, rather than the two being mutually exclusive.
Oct1 regulates trophoblast development during early mouse embryogenesis
Authors: Sebastiano Vittorio , Dalvai Mathieu , Gentile Luca , Schubart Karin , Sutter Julien , Wu Guang-Ming , Tapia Natalia , Esch Daniel , Ju Jin-Young , Hübner Karin , Bravo Marcos Jesus Arauzo , Schöler Hans Robert , Cavaleri Fatima , Matthias Patrick
Published: September 2010

Oct1 (Pou2f1) is a transcription factor of the POU-homeodomain family that is unique in being ubiquitously expressed in both embryonic and adult mouse tissues. Although its expression profile suggests a crucial role in multiple regions of the developing organism, the only essential function demonstrated so far has been the regulation of cellular response to oxidative and metabolic stress. Here, we describe a loss-of-function mouse model for Oct1 that causes early embryonic lethality, with Oct1-null embryos failing to develop beyond the early streak stage. Molecular and morphological analyses of Oct1 mutant embryos revealed a failure in the establishment of a normal maternal-embryonic interface due to reduced extra-embryonic ectoderm formation and lack of the ectoplacental cone. Oct1–/– blastocysts display proper segregation of trophectoderm and inner cell mass lineages. However, Oct1 loss is not compatible with trophoblast stem cell derivation. Importantly, the early gastrulation defect caused by Oct1 disruption can be rescued in a tetraploid complementation assay. Oct1 is therefore primarily required for the maintenance and differentiation of the trophoblast stem cell compartment during early post-implantation development. We present evidence that Cdx2, which is expressed at high levels in trophoblast stem cells, is a direct transcriptional target of Oct1. Our data also suggest that Oct1 is required in the embryo proper from late gastrulation stages onwards.
The rotation of cellulose synthase trajectories is microtubule dependent and influences the texture of epidermal cell walls inArabidopsis hypocotyls
Authors: Chan Jordi , Crowell Elizabeth , Eder Magdalena , Calder Grant , Bunnewell Susan , Findlay Kim , Vernhettes Samantha , Höfte Herman , Lloyd Clive
Published: September 2010

Plant shoots have thick, polylamellate outer epidermal walls based on crossed layers of cellulose microfibrils, but the involvement of microtubules in such wall lamellation is unclear. Recently, using a long-term movie system in which Arabidopsis seedlings were grown in a biochamber, the tracks along which cortical microtubules move were shown to undergo slow rotary movements over the outer surface of hypocotyl epidermal cells. Because microtubules are known to guide cellulose synthases over the short term, we hypothesised that this previously unsuspected microtubule rotation could, over the longer term, help explain the cross-ply structure of the outer epidermal wall. Here, we test that hypothesis using Arabidopsis plants expressing the cellulose synthase GFP-CESA3 and show that cellulose synthase trajectories do rotate over several hours. Neither microtubule-stabilising taxol nor microtubule-depolymerising oryzalin affected the linear rate of GFP-CESA3 movement, but both stopped the rotation of cellulose synthase tracks. Transmission electron microscopy revealed that drug-induced suppression of rotation alters the lamellation pattern, resulting in a thick monotonous wall layer. We conclude that microtubule rotation, rather than any hypothetical mechanism for wall self-assembly, has an essential role in developing cross-ply wall texture.
The microtubule plus-end localization ofAspergillusdynein is important for dynein–early-endosome interaction but not for dynein ATPase activation
Authors: Zhang Jun , Zhuang Lei , Lee Young , Abenza Juan F. , Peñalva Miguel A. , Xiang Xin
Published: September 2010

Cytoplasmic dynein in filamentous fungi accumulates at microtubule plus-ends near the hyphal tip, which is important for minus-end-directed transport of early endosomes. It was hypothesized that dynein is switched on at the plus-end by cargo association. Here, we show in Aspergillus nidulans that kinesin-1-dependent plus-end localization is not a prerequisite for dynein ATPase activation. First, the Walker A and Walker B mutations in the dynein heavy chain AAA1 domain implicated in blocking different steps of the ATPase cycle cause different effects on dynein localization to microtubules, arguing against the suggestion that ATPase is inactive before arriving at the plus-end. Second, dynein from ΔkinA (kinesin 1) mutant cells has normal ATPase activity despite the absence of dynein plus-end accumulation. In ΔkinA hyphae, dynein localizes along microtubules and does not colocalize with abnormally accumulated early endosomes at the hyphal tip. This is in contrast to the colocalization of dynein and early endosomes in the absence of NUDF/LIS1. However, the Walker B mutation allows dynein to colocalize with the hyphal-tip-accumulated early endosomes in the ΔkinA background. We suggest that the normal ability of dyenin to interact with microtubules as an active minus-end-directed motor demands kinesin-1-mediated plus-end accumulation for effective interactions with early endosomes.
Complexity of the microRNA repertoire revealed by next-generation sequencing
Authors: Lee Lik Wee , Zhang Shile , Etheridge Alton , Ma Li , Martin Dan , Galas David , Wang Kai
Published: September 2010

MicroRNAs (miRNAs) have been implicated to play key roles in normal physiological functions, and altered expression of specific miRNAs has been associated with a number of diseases. It is of great interest to understand their roles and a prerequisite for such study is the ability to comprehensively and accurately assess the levels of the entire repertoire of miRNAs in a given sample. It has been shown that some miRNAs frequently have sequence variations termed isomirs. To better understand the extent of miRNA sequence heterogeneity and its potential implications for miRNA function and measurement, we conducted a comprehensive survey of miRNA sequence variations from human and mouse samples using next generation sequencing platforms. Our results suggest that the process of generating this isomir spectrum might not be random and that heterogeneity at the ends of miRNA affects the consistency and accuracy of miRNA level measurement. In addition, we have constructed a database from our sequencing data that catalogs the entire repertoire of miRNA sequences (http://galas.systemsbiology.net/cgi-bin/isomir/find.pl). This enables users to determine the most abundant sequence and the degree of heterogeneity for each individual miRNA species. This information will be useful both to better understand the functions of isomirs and to improve probe or primer design for miRNA detection and measurement.
Selectivity and Tolerance (“Invariance”) Both Increase as Visual Information Propagates from Cortical Area V4 to IT
Authors: Rust Nicole C. , DiCarlo James J.
Published: September 2010

Our ability to recognize objects despite large changes in position, size, and context is achieved through computations that are thought to increase both the shape selectivity and the tolerance (“invariance”) of the visual representation at successive stages of the ventral pathway [visual cortical areas V1, V2, and V4 and inferior temporal cortex (IT)]. However, these ideas have proven difficult to test. Here, we consider how well population activity patterns at two stages of the ventral stream (V4 and IT) discriminate between, and generalize across, different images. We found that both V4 and IT encode natural images with similar fidelity, whereas the IT population is much more sensitive to controlled, statistical scrambling of those images. Scrambling sensitivity was proportional to receptive field (RF) size in both V4 and IT, suggesting that, on average, the number of visual feature conjunctions implemented by a V4 or IT neuron is directly related to its RF size. We also found that the IT population could better discriminate between objects across changes in position, scale, and context, thus directly demonstrating a V4-to-IT gain in tolerance. This tolerance gain could be accounted for by both a decrease in single-unit sensitivity to identity-preserving transformations (e.g., an increase in RF size) and an increase in the maintenance of rank-order object selectivity within the RF. These results demonstrate that, as visual information travels from V4 to IT, the population representation is reformatted to become more selective for feature conjunctions and more tolerant to identity preserving transformations, and they reveal the single-unit response properties that underlie that reformatting.
Transient Receptor Potential Canonical 3 (TRPC3) Mediates Thrombin-Induced Astrocyte Activation and Upregulates Its Own Expression in Cortical Astrocytes
Authors: Shirakawa Hisashi , Sakimoto Shinya , Nakao Kenji , Sugishita Aiko , Konno Masakazu , Iida Shota , Kusano Ayaka , Hashimoto Emina , Nakagawa Takayuki , Kaneko Shuji
Published: September 2010

Reactive astrogliosis, defined by abnormal morphology and excessive cell proliferation, is a characteristic response of astrocytes to CNS injuries, including intracerebral hemorrhage. Thrombin, a major blood-derived serine protease, leaks into the brain parenchyma upon blood–brain barrier disruption and can induce brain injury and astrogliosis. Transient receptor potential canonical (TRPC) channels, Ca2+-permeable, nonselective cation channels, are expressed in astrocytes and involved in Ca2+influx after receptor stimulation; however, their pathophysiological functions in reactive astrocytes remain unknown. We investigated the pathophysiological roles of TRPC in thrombin-activated cortical astrocytes. Application of thrombin (1 U/ml, 20 h) upregulated TRPC3 protein, which was associated with increased Ca2+influx after thapsigargin treatment. Pharmacological manipulations revealed that the TRPC3 upregulation was mediated by protease-activated receptor 1 (PAR-1), extracellular signal-regulated protein kinase, c-Jun NH2-terminal kinase, and nuclear factor-κB signaling and requiredde novoprotein synthesis. The Ca2+signaling blockers BAPTA-AM, cyclopiazonic acid, and 2-aminoethoxydiphenyl borate and a selective TRPC3 inhibitor, pyrazole-3, attenuated TRPC3 upregulation, suggesting that Ca2+signaling through TRPC3 contributes to its increased expression. Thrombin-induced morphological changes at 3 h upregulated S100B, a marker of reactive astrocytes, at 20 h and increased astrocytic proliferation by 72 h, all of which were inhibited by Ca2+-signaling blockers and specific knockdown of TRPC3 using small interfering RNA. Intracortical injection of SFLLR-NH2, a PAR-1 agonist peptide, induced proliferation of astrocytes, most of which were TRPC3 immunopositive. These results suggest that thrombin dynamically upregulates TRPC3 and that TRPC3 contributes to the pathological activation of astrocytes in part through a feedforward upregulation of its own expression.
Hierarchical Auditory Processing Directed Rostrally along the Monkey's Supratemporal Plane
Authors: Kikuchi Yukiko , Horwitz Barry , Mishkin Mortimer
Published: September 2010

Connectional anatomical evidence suggests that the auditory core, containing the tonotopic areas A1, R, and RT, constitutes the first stage of auditory cortical processing, with feedforward projections from core outward, first to the surrounding auditory belt and then to the parabelt. Connectional evidence also raises the possibility that the core itself is serially organized, with feedforward projections from A1 to R and with additional projections, although of unknown feed direction, from R to RT. We hypothesized that area RT together with more rostral parts of the supratemporal plane (rSTP) form the anterior extension of a rostrally directed stimulus quality processing stream originating in the auditory core area A1. Here, we analyzed auditory responses of single neurons in three different sectors distributed caudorostrally along the supratemporal plane (STP): sector I, mainly area A1; sector II, mainly area RT; and sector III, principally RTp (the rostrotemporal polar area), including cortex located 3 mm from the temporal tip. Mean onset latency of excitation responses and stimulus selectivity to monkey calls and other sounds, both simple and complex, increased progressively from sector I to III. Also, whereas cells in sector I responded with significantly higher firing rates to the “other” sounds than to monkey calls, those in sectors II and III responded at the same rate to both stimulus types. The pattern of results supports the proposal that the STP contains a rostrally directed, hierarchically organized auditory processing stream, with gradually increasing stimulus selectivity, and that this stream extends from the primary auditory area to the temporal pole.
TRPA1 Is a Component of the Nociceptive Response to CO2
Authors: Wang Yuanyuan Y. , Chang Rui B. , Liman Emily R.
Published: September 2010

In humans, high concentrations of CO2, as found in carbonated beverages, evoke a mixture of sensations that include a stinging or pungent quality. The stinging sensation is thought to originate with the activation of nociceptors, which innervate the respiratory, nasal, and oral epithelia. The molecular basis for this sensation is unknown. Here we show that CO2specifically activates a subpopulation of trigeminal neurons that express TRPA1, a mustard oil- and cinnamaldehyde-sensitive channel, and that these responses are dependent on a functional TRPA1 gene. TRPA1 is sufficient to mediate responses to CO2as TRPA1 channels expressed in HEK-293 cells, but not TRPV1 channels, were activated by bath-applied CO2. CO2can diffuse into cells and produce intracellular acidification, which could gate TRPA1 channels. Consistent with this mechanism, TRPA1 channels in excised patches were activated in a dose-dependent manner by intracellular protons. We conclude that TRPA1, by sensing intracellular acidification, constitutes an important component of the nociceptive response to CO2.
The Synaptic Organization of the Claustral Projection to the Cat's Visual Cortex
Authors: da Costa Nuno Maçarico , Fürsinger David , Martin Kevan A. C.
Published: September 2010

The claustrum is a subcortical structure reciprocally connected with most areas of neocortex. This strategic location suggests an integrative role of the claustrum across different sensory modalities. However, our knowledge of the synaptic relationship between the neocortex and the claustrum is basic. In this study, we address this question through a structural investigation of the claustral projection to the ipsilateral primary visual cortex of the cat. Light microscopic reconstructions of axons from the entire thickness of cortex showed a very sparse innervation of the entire cortical depth, with most synaptic boutons in layers 2/3 and 6. Axons bearing numerous boutonsterminauxand boutonsen passantbranched in these laminae. The sparse innervation did not seem to be compensated by particularly large synapses, given that the postsynaptic densities in the superficial layers are of comparable sizes (0.1 μm2) to other cortical synapses. All claustral synapses were asymmetric and in most cases targeted spines (87% in layer 4, 94% in layers 2/3 and 97% in layer 6). The pattern of innervation together with the known physiology of this projection suggests that the claustrum has a modulatory effect on visual cortex.
Induction of Vertebrate Regeneration by a Transient Sodium Current
Authors: Tseng Ai-Sun , Beane Wendy S. , Lemire Joan M. , Masi Alessio , Levin Michael
Published: September 2010

Amphibians such as frogs can restore lost organs during development, including the lens and tail. To design biomedical therapies for organ repair, it is necessary to develop a detailed understanding of natural regeneration. Recently, ion transport has been implicated as a functional regulator of regeneration. Whereas voltage-gated sodium channels play a well known and important role in propagating action potentials in excitable cells, we have identified a novel role in regeneration for the ion transport function mediated by the voltage-gated sodium channel, NaV1.2. A local, early increase in intracellular sodium is required for initiating regeneration followingXenopus laevistail amputation, and molecular and pharmacological inhibition of sodium transport causes regenerative failure. NaV1.2 is absent under nonregenerative conditions, but misexpression of human NaV1.5 can rescue regeneration during these states. Remarkably, pharmacological induction of a transient sodium current is capable of restoring regeneration even after the formation of a nonregenerative wound epithelium, confirming that it is the regulation of sodium transport that is critical for regeneration. Our studies reveal a previously undetected competency window in which cells retain their intrinsic regenerative program, identify a novel endogenous role for NaVin regeneration, and show that modulation of sodium transport represents an exciting new approach to organ repair.
The Architecture of Reward Value Coding in the Human Orbitofrontal Cortex
Authors: Sescousse Guillaume , Redouté Jérôme , Dreher Jean-Claude
Published: September 2010

To ensure their survival, animals exhibit a number of reward-directed behaviors, such as foraging for food or searching for mates. This suggests that a core set of brain regions may be shared by many species to process different types of rewards. Conversely, many new brain areas have emerged over the course of evolution, suggesting potential specialization of specific brain regions in the processing of more recent rewards such as money. Here, using functional magnetic resonance imaging in humans, we identified the common and distinct brain systems processing the value of erotic stimuli and monetary gains. First, we provide evidence that a set of neural structures, including the ventral striatum, anterior insula, anterior cingulate cortex, and midbrain, encodes the subjective value of rewards regardless of their type, consistent with a general hedonic representation. More importantly, our results reveal reward-specific representations in the orbitofrontal cortex (OFC): whereas the anterior lateral OFC, a phylogenetically recent structure, processes monetary gains, the posterior lateral OFC, phylogenetically and ontogenetically older, processes more basic erotic stimuli. This dissociation between OFC representations of primary and secondary rewards parallels current views on lateral prefrontal cortex organization in cognitive control, suggesting an increasing trend in complexity along a postero-anterior axis according to more abstract representations. Together, our results support a modular view of reward value coding in the brain and propose that a unifying principle of postero-anterior organization can be applied to the OFC.
Regulatory mechanism underlying cyclic changes in mouse uterine bicarbonate secretion: role of estrogen
Authors: He Qiong , Chen Hui , Wong Connie Hau Yan , Tsang Lai Ling , Chan Hsiao Chang
Published: September 2010

Our previous study has demonstrated that bicarbonate in the uterine fluid plays an indispensable role in sperm capacitation. However, the cellular mechanisms underlying the formation of bicarbonate-rich uterine fluid and the regulatory mechanism remained largely unknown. In this study, the expression profiles of bicarbonate transport/production proteins, the cystic fibrosis transmembrane conductance regulator (CFTR), SLC26A6, carbonic anhydrase 2 (CAR2, CA2) and CAR12 (CA12), throughout the estrous cycle, were examined in the mouse uterus by western blot. The results showed that the maximum expression levels of the proteins examined were observed at estrus. Luminal surface pH measurements showed that the resting uterine surface pH at estrus was significantly higher than that at diestrus, which could be reduced significantly by CFTR blocker, diphenylamine-2,2′-dicarboxylic acid, SLC26A6 inhibitor, 4′,4′-diisothiocyanostilbene-2′,2′-disulfonic acid, and CA inhibitor, acetazolamide. In ovariectomized mice and primary culture of endometrial epithelial cells, estrogen could upregulate CFTR, SLC26A6, CAR2, and CAR12 expression with a corresponding increase in the bicarbonate-dependent short-circuit current (Isc) and endometrial surface pH. The present results have demonstrated dynamic changes in uterine bicarbonate secretion and expression of the proteins involved in bicarbonate secretion during the estrous cycle and suggested a novel role of estrogen in regulating uterine bicarbonate transport, which may be important for successful reproduction.
Demonstration of 3C-SiC MEMS Structures on Polysilicon-on-oxide Substrates
Authors: Locke Christopher , Frewin Christopher , Abbati Luca , Saddow Stephen E.
Published: September 2010

Silicon carbide has robust mechanical, electrical, and chemical properties which make it an attractive material candidate for micro- and nano-electromechanical systems (MEMS and NEMS). 3C-SiC films grown via a polysilicon seed-layer CVD-deposited on an oxide coated (111) Si substrate offers an innovative method to overcome the residual film stress issues associated with 3C-SiC heteroepitaxy and the difficulties of fabricating structures from 3C-SiC films. The oxide plays a dual role by permitting film relaxation with respect to the supporting substrate and functioning as a MEMS release layer, allowing MEMS structures such as cantilevers and diaphragms, to be easily fabricated from the 3C-SiC film. The impact of the oxide layer on the relaxation of the film stress was investigated by comparing direction-sensitive MEMS stress sensors fabricated from 3C-SiC films grown via a polysilicon-on-oxide-coated-substrate and a polysilicon-on-crystalline Si substrate. Scanning Electron Microscopy (SEM) analysis of bridge structures fabricated on the polysilicon-on-oxide substrate revealed evidence of film strain relaxation when compared to bridge structures fabricated on the polysilicon-on-crystalline Si substrate. However, the upward-curled cantilever and comb structures fabricated on both substrates indicate the presence of a strain gradient in the 3C-SiC film grown on both substrates.
When Organometallic Chemistry and Metal Oxide Nanoparticles Meet Optimized Silicon-based Gas Sensor
Authors: Yoboue Pamela , Menini Philippe , Maisonnat Andre , Kahn Myrtil , Fajerwerg Katia , Chaudret Bruno , Fau Pierre
Published: September 2010

A robust silicon gas sensor chip (platinum heater, low deformation membrane) has been designed and successfully operated with various metal oxide nanoparticles synthesized by an organometallic route (SnO2, ZnO) and deposited by a generic ink-jet method. High quality and micron thick layers are obtained and the CO gas sensitivity is presented.
Synthesis of Size and Shape Controlled Silver Nanoparticles Coated by a Thin Layer of Gold and Their Use as Ultrasensitive Biomolecular Probes
Authors: Mott Derrick , Thuy Nguyen Thi Bich , Aoki Yoshiya , Maenosono Shinya
Published: September 2010

Silver nanoparticles coated by a layer of gold (Ag@Au) have received much attention because of their potential application as ultra sensitive probes for the detection of biologically important molecules such as DNA, proteins, amino acids and many others. However, the ability to control the size, shape, and monodispersity of the Ag@Au structure has met with limited success. In our own research we have addressed this challenge by creating an aqueous wet chemical synthesis technique towards size and shape controllable Ag@Au nanoparticles. These materials are highly interesting because of the tunable silver core size, and the tunable gold shell thickness, opening many avenues to the modification of the particle properties in terms of bio-molecular sensing. The resulting nanoparticle probes were functionalized with two complementary stranded DNA oligonucleotides. When combined, the complementary strands hybridized, causing the Ag@Au nanoparticles to assemble into large nano-structures. The presence of the oligonucleotide was confirmed through a series of techniques including UV-Vis and RAMAN spectroscopy, as well as HR-TEM, XPS, DLS, and many others. The results reflect the role that the nanoparticle physical properties play in the detection of the bio-molecules, as well as elucidate the characteristics of the bio-molecule/nanoparticle interaction.
Resistance Sensor Based on Thermophoresis for Soot in Diesel Exhaust
Authors: Bjorklund Robert , Johansson Mats L. , Grant Ann , Jozsa Peter , Fägerman Per-Erik , Paaso Jaska , Larsson Andreas , Lutic Doina , Lloyd Spetz Anita
Published: September 2010

A resistance sensor for use in diesel exhaust is reported. Several soot deposition mechanisms contribute to collection on the sensing electrodes. The sensor is designed to enhance the temperature difference between the electrode surface and the ambient. The resulting thermophoretic force on nanoparticles enhances soot deposition. Exhaust soot concentrations were shown to correlate with resistance decreases and the effect of thermophoresis was studied.
Preparation and Characterization of Periodically Poled Ferroelectric Lithium Niobate (LiNbO3)
Authors: Zhang Zhengzheng , Borca Camelia N , Wu D , Gruverman Alexei , Kizikaya Orhan , Xiao Jie , Dowben Peter A
Published: September 2010

No compositional variations of periodically poled lithium niobate (PPLN) (period of ~28 μm) are found using spatially resolved near edge X-ray adsorption fine structure (XANES) spectra taken at the Nb K-edge. The periodicity the ferroelectric domain patterns can be imaged using piezoresponse force microscopy (PFM) and atomic force microscopy (AFM) and the periodic variations in the optical properties of PPLN result in a nonlinear optical response in the IR region at a fixed scattering angle.