bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of published single nucleotide polymorphisms associated with acute GVHD
Authors: Chien Jason W. , Zhang Xinyi Cindy , Fan Wenhong , Wang Hongwei , Zhao Lue Ping , Martin Paul J. , Storer Barry E. , Boeckh Michael , Warren Edus H. , Hansen John A.
Published: January 2012

Candidate genetic associations with acute GVHD (aGVHD) were evaluated with the use of genotyped and imputed single-nucleotide polymorphism data from genome-wide scans of 1298 allogeneic hematopoietic cell transplantation (HCT) donors and recipients. Of 40 previously reported candidate SNPs, 6 were successfully genotyped, and 10 were imputed and passed criteria for analysis. Patient and donor genotypes were assessed for association with grades IIb-IV and III-IV aGVHD, stratified by donor type, in univariate and multivariate allelic, recessive and dominant models. Use of imputed genotypes to replicate previous IL10 associations was validated. Similar to previous publications, the IL6 donor genotype for rs1800795 was associated with a 20%-50% increased risk for grade IIb-IV aGVHD after unrelated HCT in the allelic (adjusted P = .011) and recessive (adjusted P = .0013) models. The donor genotype was associated with a 60% increase in risk for grade III-IV aGVHD after related HCT (adjusted P = .028). Other associations were found for IL2, CTLA4, HPSE, and MTHFR but were inconsistent with original publications. These results illustrate the advantages of using imputed single-nucleotide polymorphism data in genetic analyses and demonstrate the importance of validation in genetic association studies.
TNF-α promoter polymorphism: a factor contributing to the different immunological and clinical phenotypes in Japanese encephalitis
Authors: Pujhari Sujit Kumar , Ratho Radha Kanta , Prabhakar Sudesh , Mishra Baijayantimala , Modi Manish
Published: January 2012

Background

More than three billion populations are living under the threat of Japanese encephalitis in South East Asian (SEA) countries including India. The pathogenesis of this disease is not clearly understood and is probably attributed to genomic variations in viral strains as well as the host genetic makeup. The present study is to determine the role of polymorphism of TNF-alpha promoter regions at positions -238G/A, -308G/A, -857C/T and -863C/A in the severity of Japanese encephalitis patients.

Methods

Total of 142 patients including 66 encephalitis case (IgM/RT-PCR positive), 16 fever cases (IgM positive) without encephalitis and 60 apparently healthy individuals (IgG positive) were included in the study. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) using site specific restriction enzymes were implemented for polymorphism study of TNF alpha promoter.

Results

Following the analysis of the digestion patterns of four polymorphic sites of the TNF- alpha promoter region, a significant association was observed between the allele -308A and -863C with the patients of Japanese encephalitis.

Conclusions

TNF- alpha 308 G/A has been shown to be associated with elevated TNF- alpha transcriptional activity. On the other hand, polymorphism at position -863C/A in the promoter region has been reported to be associated with reduced TNF- alpha promoter activity and lower plasma TNF levels. As per the literature search, this is the first study to identify the role of TNF- alpha promoter in JE infection. Our results show that subjects with - 308A and -863C alleles are more vulnerable to the severe form of JE infection.
A local outbreak of dengue caused by an imported case in Dongguan China
Authors: Peng Hong-Juan , Lai Hui-Bing , Zhang Qiao-Li , Xu Ba-Yi , Zhang Hao , Liu Wen-Hua , Zhao Wei , Zhou Yuan-Ping , Zhong Xin-Guang , Jiang Shu , Duan Jin-Hua , Yan Gui-Yun , He Jian-Feng , Chen Xiao-Guang
Published: January 2012

Background

Dengue, a mosquito-borne febrile viral disease, is found in tropical and sub-tropical regions around the world. Since the first occurrence of dengue was confirmed in Guangdong, China in 1978, dengue outbreaks have been reported sequentially in different provinces in South China transmitted by.peridomestic Ae. albopictus mosquitoes, diplaying Ae. aegypti, a fully domestic vector that transmits dengue worldwide. Rapid and uncontrolled urbanization is a characteristic change in developing countries, which impacts greatly on vector habitat, human lifestyle and transmission dynamics on dengue epidemics. In September 2010, an outbreak of dengue was detected in Dongguan, a city in Guangdong province characterized by its fast urbanization. An investigation was initiated to identify the cause, to describe the epidemical characteristics of the outbreak, and to implement control measures to stop the outbreak. This is the first report of dengue outbreak in Dongguan, even though dengue cases were documented before in this city.

Methods

Epidemiological data were obtained from local Center of Disease Control and prevention (CDC). Laboratory tests such as real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR), the virus cDNA sequencing, and Enzyme-Linked immunosorbent assay (ELISA) were employed to identify the virus infection and molecular phylogenetic analysis was performed with MEGA5. The febrile cases were reported every day by the fever surveillance system. Vector control measures including insecticidal fogging and elimination of habitats of Ae. albopictus were used to control the dengue outbreak.

Results

The epidemiological studies results showed that this dengue outbreak was initiated by an imported case from Southeast Asia. The outbreak was characterized by 31 cases reported with an attack rate of 50.63 out of a population of 100,000. Ae. albopictus was the only vector species responsible for the outbreak. The virus cDNA sequencing analysis showed that the virus responsible for the outbreak was Dengue Virus serotype-1 (DENV-1).

Conclusions

Several characterized points of urbanization contributed to this outbreak of dengue in Dongguan: the residents are highly concentrated; the residents' life habits helped to form the habitats of Ae. albopictus and contributed to the high Breteau Index; the self-constructed houses lacks of mosquito prevention facilities. This report has reaffirmed the importance of a surveillance system for infectious diseases control and aroused the awareness of an imported case causing the epidemic of an infectious disease in urbanized region.
TNF-α protein synthesis inhibitor restores neuronal function and reverses cognitive deficits induced by chronic neuroinflammation
Authors: Belarbi Karim , Jopson Timothy , Tweedie David , Arellano Carla , Luo Weiming , Greig Nigel H , Rosi Susanna
Published: January 2012

Background

Chronic neuroinflammation is a hallmark of several neurological disorders associated with cognitive loss. Activated microglia and secreted factors such as tumor necrosis factor (TNF)-α are key mediators of neuroinflammation and may contribute to neuronal dysfunction. Our study was aimed to evaluate the therapeutic potential of a novel analog of thalidomide, 3,6'-dithiothalidomide (DT), an agent with anti-TNF-α activity, in a model of chronic neuroinflammation.

Methods

Lipopolysaccharide or artificial cerebrospinal fluid was infused into the fourth ventricle of three-month-old rats for 28 days. Starting on day 29, animals received daily intraperitoneal injections of DT (56 mg/kg/day) or vehicle for 14 days. Thereafter, cognitive function was assessed by novel object recognition, novel place recognition and Morris water maze, and animals were euthanized 25 min following water maze probe test evaluation.

Results

Chronic LPS-infusion was characterized by increased gene expression of the proinflammatory cytokines TNF-α and IL-1β in the hippocampus. Treatment with DT normalized TNF-α levels back to control levels but not IL-1β. Treatment with DT attenuated the expression of TLR2, TLR4, IRAK1 and Hmgb1, all genes involved in the TLR-mediated signaling pathway associated with classical microglia activation. However DT did not impact the numbers of MHC Class II immunoreactive cells. Chronic neuroinflammation impaired novel place recognition, spatial learning and memory function; but it did not impact novel object recognition. Importantly, treatment with DT restored cognitive function in LPS-infused animals and normalized the fraction of hippocampal neurons expressing the plasticity-related immediate-early gene Arc.

Conclusion

Our data demonstrate that the TNF-α synthesis inhibitor DT can significantly reverse hippocampus-dependent cognitive deficits induced by chronic neuroinflammation. These results suggest that TNF-α is a critical mediator of chronic neuroinflammation-induced neuronal dysfunction and cognitive impairment and targeting its synthesis could provide an effective therapeutic approach to several human neurodegenerative diseases.
High prevalence of gastroesophageal reflux symptoms in type 2 diabetics with hypoadiponectinemia and metabolic syndrome
Authors: Hirata Ayumu , Kishida Ken , Nakatsuji Hideaki , Inoue Kana , Hiuge-Shimizu Aki , Funahashi Tohru , Shimomura Iichiro
Published: January 2012

Background

The prevalence of gastroesophageal reflux disease (GERD) has been increasing worldwide. Abdominal obesity or visceral fat accumulation rather than simple obesity is associated with GERD. Previous reports demonstrated the association between GERD and type 2 diabetes mellitus (T2DM). Signification of visceral fat accumulation and adiponectin in T2DM patients with GERD remains unclear. The present study investigated the relationships between GERD symptoms, visceral fat accumulation and adiponectin in subjects with T2DM.

Findings

The study (ADMIT study) subjects were 66 Japanese T2DM outpatients, who answered the questionnaire regarding GERD symptoms in Frequency Scale for the Symptoms of GERD (FSSG), and were measured visceral fat area by bioelectrical impedance analysis. Patients with FSSG scores of more than 8 were considered as positive. The prevalence of FSSG score ≥ 8 and average FSSG score in T2DM subjects with the metabolic syndrome (Mets) were significantly higher compared to those without Mets. The prevalence of FSSG score ≥ 8 and average FSSG score in T2DM subjects with low levels of serum adiponectin were significantly higher compared to those with high levels of serum adiponectin. Moreover, the combination of Mets and hypoadiponectinemia had a multiplicative effect on GERD symptom score (p = 0.047).

Conclusions

Our study showed that the coexistence of MetS and low levels of serum adiponectin was associated with the higher prevalence of FSSG score ≥ 8 and the higher scores of GERD symptom in subjects with T2DM.

Trial Registration

UMIN 000002271.
Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments
Authors: Helal Manal , Kong Fanrong , Chen Sharon CA , Zhou Fei , Dwyer Dominic E , Potter John , Sintchenko Vitali
Published: January 2012

Background

Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets.

Results

A novel method that combines the linear mapping hash function and multiple sequence alignment (MSA) was developed. This method takes advantage of the already sorted by similarity sequences from the MSA output, and identifies the optimal number of clusters, clusters cut-offs, and clusters centroids that can represent reference gene vouchers for the different species. The linear mapping hash function can map an already ordered by similarity distance matrix to indices to reveal gaps in the values around which the optimal cut-offs of the different clusters can be identified. The method was evaluated using sets of closely related (16S rRNA gene sequences of Nocardia species) and highly variable (VP1 genomic region of Enterovirus 71) sequences and outperformed existing unsupervised machine learning clustering methods and dimensionality reduction methods. This method does not require prior knowledge of the number of clusters or the distance between clusters, handles clusters of different sizes and shapes, and scales linearly with the dataset.

Conclusions

The combination of MSA with the linear mapping hash function is a computationally efficient way of gene sequence clustering and can be a valuable tool for the assessment of similarity, clustering of different microbial genomes, identifying reference sequences, and for the study of evolution of bacteria and viruses.
Reprogramming of TAM toward proimmunogenic type through regulation of MAP kinases using a redox-active copper chelate
Authors: Chakraborty Paramita , Chatterjee Shilpak , Ganguly Avishek , Saha Piu , Adhikary Arghya , Das Tanya , Chatterjee Mitali , Choudhuri Soumitra Kumar
Published: January 2012

TAMs, present in the tumor microenvironment, play an immunosuppressive role, leading to tumor progression and metastasis. Recently, numerous attempts have been made to switch immunosuppressive TAMs into an immunostimulatory type. Previously, we showed that a copper chelate, viz., copper N-(2-hydroxy acetophenone) glycinate [CuNG], can reprogram TAMs toward the proimmunogenic type to mount an antitumor immune response, but the underlying molecular mechanisms of skewing TAMs toward the proimmunogenic type remain elusive. Herein, we tried to explore the signaling mechanisms responsible for the reprogramming of TAMs. We observed that CuNG-induced ROS generation triggers activation of two MAPKs, i.e., p38MAPK and ERK1/2, and also causes up-regulation of intracellular glutathione. Furthermore, activation of p38 MAPK up-regulated the initial IL-12 production and the activation of ERK1/2 in tandem with GSH, found responsible for IFN-γ production by TAMs. This IFN-γ, in turn, prolonged IL-12 production and down-regulated TGF-β production and thus, plays the decisive role in CuNG-mediated reprogramming of regulatory cytokine production by TAMs. Our work highlights that ROS-mediated activation of MAPKs can convert suppressive macrophages toward the proimmunogenic type. Thus, the present study opens the possibility of targeting TAMs by the use of redox-active compounds for designing a novel, therapeutic strategy against cancer.
CLM94, a Novel Cyclic Amide with Anti-VEGFR-2 and Antiangiogenic Properties, Is Active against Primary Anaplastic Thyroid Cancer in Vitro and in Vivo
Authors: Antonelli Alessandro , Bocci Guido , La Motta Concettina , Ferrari Silvia Martina , Fallahi Poupak , Ruffilli Ilaria , Di Domenicantonio Andrea , Fioravanti Anna , Sartini Stefania , Minuto Michele , Piaggi Simona , Corti Alessandro , Alì Greta , Di Desidero Teresa , Berti Piero , Fontanini Gabriella , Danesi Romano , Da Settimo Federico , Miccoli Paolo
Published: January 2012

Context and Objective:

We have studied the antitumor activity of a novel cyclic amide, CLM94, with anti-vascular endothelial growth factor (VEGF) receptor-2 and antiangiogenic activity in primary anaplastic thyroid cancer (ATC) cells in vitro and in vivo.

Design and Main Outcome Measures:

CLM94 was tested: 1) in two human cell lines (HMVEC-d, dermal microvascular endothelial cells; and 8305C, undifferentiated thyroid cancer) at 0.001–100 μm; 2) in ATC cells at the concentrations of 10, 30, and 50 μm; and 3) in an ATC cell line (AF) in CD nu/nu mice.

Results:

CLM94 significantly inhibited VEGF receptor-2 and epidermal growth factor receptor phosphorylation in HMVEC-d and proliferation in HMVEC-d and 8305C cells. A significant reduction of proliferation with CLM94 in ATC cells (P < 0.01, ANOVA) and a slight but significant reduction of proliferation with CLM94 30 and 50 μm in normal thyroid follicular cells (P < 0.01, ANOVA) were shown. CLM94 increased the percentage of apoptotic ATC cells dose-dependently (P < 0.001, ANOVA) and inhibited migration (P < 0.01) and invasion (P < 0.001). AF cell line was injected sc in CD nu/nu mice, and tumor masses became detectable 25 d afterward. CLM94 (40 mg/kg · d) significantly inhibited tumor growth (starting 10 d after the beginning of treatment). CLM94 significantly decreased the VEGF-A gene expression in the AF cell line and the VEGF-A protein and microvessel density in AF tumor tissues.

Conclusions:

The antitumor and antiangiogenic activity of a new “cyclic amide” compound, CLM94, is very promising in ATC, opening the way to a future clinical evaluation.
Langland on the Church and the End of the Cardinal Virtues
Authors: Aers David
Published: January 2012

This essay argues that William Langland’s great poem Piers Plowman poses serious questions both to the tradition of the virtues that Langland inherited and to the possibility of their authentic embodiment in the contemporary Church Langland knew. Moving from Thomas Aquinas to Thomas Hobbes and back again to Langland, the essay finds Langland imagining a troubling history in which the meaning of moral concepts is transformed and the powers of moral discernment baffled. Langland’s pictures of response to this scenario are enigmatic and elusive but potentially figure forth a revolutionary transformation of a Church embroiled in Constantinian forms of Christianity. The essay therefore posits a Langlandian vision contrary to some recent trends in the historiography of the late medieval Church and some recent accounts of Piers Plowman itself. Crucial to Langland’s concerns is the question of what sort of agents revolution might require, as well as what sort of eschatology might sustain them and what sort of community they might inhabit. In its search for answers Langland’s poem discredits ideologies of magisterial reformation. Langland offers instead significant gestures toward alternative forms of Christian community and authority, while likewise refusing to relinquish his abiding commitment to the Christian Church as a visible, historical polity.
Virtues in Elizabethan and Early Stuart Grammar Schools
Authors: Peltonen Markku
Published: January 2012

This article examines the role and place of virtues in early modern English grammar schools (ca. 1558 – 1640). It argues that schoolboys were exposed to the questions of moral philosophy and virtues throughout their time in the grammar school. From their elementary classes in Latin grammar to moral philosophy and rhetoric classes in the uppermost forms, students received training in the four cardinal virtues. The training took place, however, in an overwhelmingly linguistic and rhetorical context. It follows that early modern schoolboys learned that virtues were not so much intrinsic values of morality as much as instrumental values of rhetoric. This has important consequences for our understanding of early modern educational and intellectual culture.
Milton and Literary Virtue
Authors: Fallon Stephen M.
Published: January 2012

In a famous passage, the Son of God in Paradise Regained dismisses classical philosophers for their ignorance of “how man fell” and for their confidence in human sufficiency to attain virtue. “In themselves,” the Son says dismissively, they “seek virtue.” By putting this argument in the mouth of a spokesperson whose authority could hardly be surpassed, Milton aligns himself firmly with Augustine and other Christian theologians who questioned classical magnanimity and emphasized humility. But at other places in both his poetry and prose, Milton comes close to suggesting human ethical sufficiency and to echoing Aristotle on magnanimity. Milton’s thinking on the virtues and their acquisition is eclectic. This essay traces the effect on Milton’s thinking of the gravitational pull of the literary in two senses: Milton’s conception of himself as inspired author and his attraction to an understanding of virtue that can be captured in narrative form.
Relational Virtue: Anne Bradstreet, Edward Taylor, and Puritan Marriage
Authors: Furey Constance
Published: January 2012

This essay seeks to understand the assumptions about marriage bequeathed to us by early modern Protestants by exploring the Puritan interest in mandated affection. For Puritans, obligatory love was the foundation for the covenant between believers and God and the reason why the covenant was itself understood as a marriage. Focusing especially on poems by two canonical Puritan poets, Anne Bradstreet and Edward Taylor, this essay argues that this fascination with the interplay between freedom and restraint — manifest in the form as well as the content of their poetry — produced a distinctive form of relational virtue. The soteriological uncertainty that motivated the Puritans’ restless economic activity (as Weber so influentially discerned) and relentless introspection (evident in works like John Bunyan’s Grace Abounding to the Chief of Sinners) thus also inspired a richly relational alternative still valuable for anyone interested in rooting ethics in the rich loam of relational dynamics.
SHP-2 acts via ROCK to regulate the cardiac actin cytoskeleton
Authors: Langdon Yvette , Tandon Panna , Paden Erika , Duddy Jennifer , Taylor Joan M. , Conlon Frank L.
Published: January 2012

Noonan syndrome is one of the most common causes of human congenital heart disease and is frequently associated with missense mutations in the protein phosphatase SHP-2. Interestingly, patients with acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), juvenile myelomonocytic leukemia (JMML) and LEOPARD syndrome frequently carry a second, somatically introduced subset of missense mutations in SHP-2. To determine the cellular and molecular mechanisms by which SHP-2 regulates heart development and, thus, understand how Noonan-associated mutations affect cardiogenesis, we introduced SHP-2 encoding the most prevalent Noonan syndrome and JMML mutations into Xenopus embryos. Resulting embryos show a direct relationship between a Noonan SHP-2 mutation and its ability to cause cardiac defects in Xenopus; embryos expressing Noonan SHP-2 mutations exhibit morphologically abnormal hearts, whereas those expressing an SHP-2 JMML-associated mutation do not. Our studies indicate that the cardiac defects associated with the introduction of the Noonan-associated SHP-2 mutations are coupled with a delay or arrest of the cardiac cell cycle in M-phase and a failure of cardiomyocyte progenitors to incorporate into the developing heart. We show that these defects are a result of an underlying malformation in the formation and polarity of cardiac actin fibers and F-actin deposition. We show that these defects can be rescued in culture and in embryos through the inhibition of the Rho-associated, coiled-coil-containing protein kinase 1 (ROCK), thus demonstrating a direct relationship between SHP-2N308D and ROCK activation in the developing heart.
The establishment of asymmetry in Arabidopsis lateral root founder cells is regulated by LBD16/ASL18 and related LBD/ASL proteins
Authors: Goh Tatsuaki , Joi Shunpei , Mimura Tetsuro , Fukaki Hidehiro
Published: January 2012

In most dicot plants, lateral root (LR) formation, which is important for the construction of the plant root system, is initiated from coordinated asymmetric cell divisions (ACD) of the primed LR founder cells in the xylem pole pericycle (XPP) of the existing roots. In Arabidopsis thaliana, two AUXIN RESPONSE FACTORs (ARFs), ARF7 and ARF19, positively regulate LR formation through activation of the plant-specific transcriptional regulators LATERAL ORGAN BOUNDARIES-DOMAIN 16/ASYMMETRIC LEAVES2-LIKE 18 (LBD16/ASL18) and the other related LBD/ASL genes. The exact biological role of these LBD/ASLs in LR formation is still unknown. Here, we demonstrate that LBD16/ASL18 is specifically expressed in the LR founder cells adjacent to the XPP before the first ACD and that it functions redundantly with the other auxin-inducible LBD/ASLs in LR initiation. The spatiotemporal expression of LBD16/ASL18 during LR initiation is dependent on the SOLITARY-ROOT (SLR)/IAA14-ARF7-ARF19 auxin signaling module. In addition, XPP-specific expression of LBD16/ASL18 in arf7 arf19 induced cell divisions at XPP, thereby restoring the LR phenotype. We also demonstrate that expression of LBD16-SRDX, a dominant repressor of LBD16/ASL18 and its related LBD/ASLs, does not interfere in the specification of LR founder cells with local activation of the auxin response, but it blocks the polar nuclear migration in LR founder cells before ACD, thereby blocking the subsequent LR initiation. Taken together, these results indicate that the localized activity of LBD16/ASL18 and its related LBD/ASLs is involved in the symmetry breaking of LR founder cells for LR initiation, a key step for constructing the plant root system.
Cell-autonomous FGF signaling regulates anteroposterior patterning and neuronal differentiation in the mesodiencephalic dopaminergic progenitor domain
Authors: Lahti Laura , Peltopuro Paula , Piepponen T. Petteri , Partanen Juha
Published: January 2012

The structure and projection patterns of adult mesodiencephalic dopaminergic (DA) neurons are one of the best characterized systems in the vertebrate brain. However, the early organization and development of these nuclei remain poorly understood. The induction of midbrain DA neurons requires sonic hedgehog (Shh) from the floor plate and fibroblast growth factor 8 (FGF8) from the isthmic organizer, but the way in which FGF8 regulates DA neuron development is unclear. We show that, during early embryogenesis, mesodiencephalic neurons consist of two distinct populations: a diencephalic domain, which is probably independent of isthmic FGFs; and a midbrain domain, which is dependent on FGFs. Within these domains, DA progenitors and precursors use partly different genetic programs. Furthermore, the diencephalic DA domain forms a distinct cell population, which also contains non-DA Pou4f1+ cells. FGF signaling operates in proliferative midbrain DA progenitors, but is absent in postmitotic DA precursors. The loss of FGFR1/2-mediated signaling results in a maturation failure of the midbrain DA neurons and altered patterning of the midbrain floor. In FGFR mutants, the DA domain adopts characteristics that are typical for embryonic diencephalon, including the presence of Pou4f1+ cells among TH+ cells, and downregulation of genes typical of midbrain DA precursors. Finally, analyses of chimeric embryos indicate that FGF signaling regulates the development of the ventral midbrain cell autonomously.
The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub
Authors: Trofka Anna , Schwendinger-Schreck Jamie , Brend Tim , Pontius William , Emonet Thierry , Holley Scott A.
Published: January 2012

Using in vitro and in vivo assays, we define a network of Her/Hes dimers underlying transcriptional negative feedback within the zebrafish segmentation clock. Some of the dimers do not appear to be DNA-binding, whereas those dimers that do interact with DNA have distinct preferences for cis regulatory sequences. Dimerization is specific, with Hes6 serving as the hub of the network. Her1 binds DNA only as a homodimer but will also dimerize with Hes6. Her12 and Her15 bind DNA both as homodimers and as heterodimers with Hes6. Her7 dimerizes strongly with Hes6 and weakly with Her15. This network structure engenders specific network dynamics and imparts greater influence to the Her7 node. Computational analysis supports the hypothesis that Her7 disproportionately influences the availability of Hes6 to heterodimerize with other Her proteins. Genetic experiments suggest that this regulation is important for operation of the network. Her7 therefore has two functions within the zebrafish segmentation clock. Her7 acts directly within the delayed negative feedback as a DNA-binding heterodimer with Hes6. Her7 also has an emergent function, independent of DNA binding, in which it modulates network topology via sequestration of the network hub.
S6K links cell fate, cell cycle and nutrient response inC. elegansgermline stem/progenitor cells
Authors: Korta Dorota Z. , Tuck Simon , Hubbard E. Jane Albert
Published: January 2012

Coupling of stem/progenitor cell proliferation and differentiation to organismal physiological demands ensures the proper growth and homeostasis of tissues. However, in vivo mechanisms underlying this control are poorly characterized. We investigated the role of ribosomal protein S6 kinase (S6K) at the intersection of nutrition and the establishment of a stem/progenitor cell population using the C. elegans germ line as a model. We find that rsks-1 (which encodes the worm homolog of mammalian p70S6K) is required germline-autonomously for proper establishment of the germline progenitor pool. In the germ line, rsks-1 promotes cell cycle progression and inhibits larval progenitor differentiation, promotes growth of adult tumors and requires a conserved TOR phosphorylation site. Loss of rsks-1 and ife-1 (eIF4E) together reduces the germline progenitor pool more severely than either single mutant and similarly to reducing the activity of let-363 (TOR) or daf-15 (RAPTOR). Moreover, rsks-1 acts in parallel with the glp-1 (Notch) and daf-2 (insulin-IGF receptor) pathways, and does not share the same genetic dependencies with its role in lifespan control. We show that overall dietary restriction and amino acid deprivation cause germline defects similar to a subset of rsks-1 mutant phenotypes. Consistent with a link between diet and germline proliferation via rsks-1, loss of rsks-1 renders the germ line largely insensitive to the effects of dietary restriction. Our studies establish the C. elegans germ line as an in vivo model to understand TOR-S6K signaling in proliferation and differentiation and suggest that this pathway is a key nutrient-responsive regulator of germline progenitors.
Dusky-like functions as a Rab11 effector for the deposition of cuticle duringDrosophilabristle development
Authors: Nagaraj Ranganayaki , Adler Paul N.
Published: January 2012

The morphogenesis of Drosophila sensory bristles is dependent on the function of their actin and microtubule cytoskeleton. Actin filaments are important for bristle shape and elongation, while microtubules are thought to mediate protein and membrane trafficking to promote growth. We have identified an essential role for the bristle cuticle in the maintenance of bristle structure and shape at late stages of bristle development. We show that the small GTPase Rab11 mediates the organized deposition of chitin, a major cuticle component in bristles, and disrupting Rab11 function leads to phenotypes that result from bristle collapse rather than a failure to elongate. We further establish that Rab11 is required for the plasma membrane localization of the ZP domain-containing Dusky-like (Dyl) protein and that Dyl is also required for cuticle formation in bristles. Our data argue that Dyl functions as a Rab11 effector for mediating the attachment of the bristle cell membrane to chitin to establish a stable cuticle. Our studies also implicate the exocyst as a Rab11 effector in this process and that Rab11 trafficking along the bristle shaft is mediated by microtubules.
Extracellular leucine-rich repeat proteins are required to organize the apical extracellular matrix and maintain epithelial junction integrity inC. elegans
Authors: Mancuso Vincent P. , Parry Jean M. , Storer Luke , Poggioli Corey , Nguyen Ken C. Q. , Hall David H. , Sundaram Meera V.
Published: January 2012

Epithelial cells are linked by apicolateral junctions that are essential for tissue integrity. Epithelial cells also secrete a specialized apical extracellular matrix (ECM) that serves as a protective barrier. Some components of the apical ECM, such as mucins, can influence epithelial junction remodeling and disassembly during epithelial-to-mesenchymal transition (EMT). However, the molecular composition and biological roles of the apical ECM are not well understood. We identified a set of extracellular leucine-rich repeat only (eLRRon) proteins in C. elegans (LET-4 and EGG-6) that are expressed on the apical surfaces of epidermal cells and some tubular epithelia, including the excretory duct and pore. A previously characterized paralog, SYM-1, is also expressed in epidermal cells and secreted into the apical ECM. Related mammalian eLRRon proteins, such as decorin or LRRTM1-3, influence stromal ECM or synaptic junction organization, respectively. Mutants lacking one or more of the C. elegans epithelial eLRRon proteins show multiple defects in apical ECM organization, consistent with these proteins contributing to the embryonic sheath and cuticular ECM. Furthermore, epithelial junctions initially form in the correct locations, but then rupture at the time of cuticle secretion and remodeling of cell-matrix interactions. This work identifies epithelial eLRRon proteins as important components and organizers of the pre-cuticular and cuticular apical ECM, and adds to the small but growing body of evidence linking the apical ECM to epithelial junction stability. We propose that eLRRon-dependent apical ECM organization contributes to cell-cell adhesion and may modulate epithelial junction dynamics in both normal and disease situations.
Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters
Authors: Tschopp Patrick , Christen Alix J. , Duboule Denis
Published: January 2012

The importance of Hox genes in the specification of neuronal fates in the spinal cord has long been recognized. However, the transcriptional controls underlying their collinear expression domains remain largely unknown. Here we show in mice that the correspondence between the physical order of Hoxd genes and their rostral expression boundaries, although respecting spatial collinearity, does not display a fully progressive distribution. Instead, two major anteroposterior boundaries are detected, coinciding with the functional subdivision of the spinal cord. Tiling array analyses reveal two distinct blocks of transcription, regulated independently from one another, that define the observed expression boundaries. Targeted deletions in vivo that remove the genomic fragments separating the two blocks induce ectopic expression of posterior genes. We further evaluate the independent regulatory potential and transcription profile of each gene locus by a tiling array approach using a contiguous series of transgenes combined with locus-specific deletions. Our work uncovers a bimodal type of HoxD spatial collinearity in the developing spinal cord that relies on two separate ‘enhancer mini-hubs’ to ensure correct Hoxd gene expression levels while maintaining their appropriate anteroposterior boundaries.
An enhancer from the 8q24 prostate cancer risk region is sufficient to direct reporter gene expression to a subset of prostate stem-like epithelial cells in transgenic mice
Authors: Ting Man-Chun , Liao Chun-Peng , Yan Chunli , Jia Li , Groshen Susan , Frankel Baruch , Roy-Burman Pradip , Coetzee Gerhard A. , Maxson Robert
Published: January 2012

Regions in the 8q24 gene desert contribute significantly to the risk of prostate cancer and other adult cancers. This region contains several DNA regions with enhancer activity in cultured cells. One such segment, histone acetylation peak 10 (AcP10), contains a risk single nucleotide polymorphism (SNP) that is significantly associated with the pathogenesis of colorectal, prostate and other cancers. The mechanism by which AcP10 influences cancer risk remains unknown. Here we show that AcP10 contains a sequence that is highly conserved across terrestrial vertebrates and is capable in transgenic mice of directing reporter gene expression to a subset of prostate lumenal epithelial cells. These cells include a small population of Nkx3.1-positive cells that persist even after androgen ablation. Castration-resistant Nkx3.1-positive (CARN) cells were shown by others to function both as stem cells and cells of origin of prostate cancer. Our results thus provide a mechanism by which AcP10 could influence prostate cancer risk.
Interspecies pair housing of macaques in a research facility
Authors: DiVincenti L , Rehrig A , Wyatt J
Published: January 2012

The eighth edition of The Guide for the Care and Use of Laboratory Animals establishes social housing as the ‘default’ for social species including non-human primates. The advantages of social housing for primates have been well established, but small research facilities housing few primates in indoor cages have struggled with social housing as a result of limitations on appropriate housing and availability of compatible monkeys. Here, we report a novel approach to pair housing macaques – crossing species. We have successfully pair housed an intact male rhesus macaque with an intact male cynomolgus macaque, and an adult female rhesus macaque with numerous subadult female cynomolgus macaques. Monkeys in these pairs established dominant–subordinate relationships similar to same-species pairs. Rhesus and cynomolgus macaques can be successfully paired for the purpose of social housing in facilities with limited numbers of monkeys.
Role of helix 44 of 16S rRNA in the fidelity of translation initiation
Authors: Qin Daoming , Liu Qi , Devaraj Aishwarya , Fredrick Kurt
Published: January 2012

The molecular mechanisms that govern translation initiation to ensure accuracy remain unclear. Here, we provide evidence that the subunit-joining step of initiation is controlled in part by a conformational change in the 1408 region of helix h44. First, chemical probing of 30S initiation complexes formed with either a cognate (AUG) or near-cognate (AUC) start codon shows that an IF1-dependent enhancement at A1408 is reduced in the presence of AUG. This change in reactivity is due to a conformational change rather than loss of IF1, because other portions of the IF1 footprint are unchanged and high concentrations of IF1 fail to diminish the reactivity difference seen at A1408. Second, mutations in h44 such as A1413C stimulate 50S docking and cause reduced reactivity at A1408. Third, streptomycin, which has been shown by Rodnina and coworkers to stimulate 50S docking by reversing the inhibitory effects of IF1, also causes reduced reactivity at A1408. Collectively, these data support a model in which IF1 alters the A1408 region of h44 in a way that makes 50S docking unfavorable, and canonical codon–anticodon pairing in the P site restores h44 to a docking-favorable conformation. We also find that, in the absence of factors, the cognate 30S•AUG•fMet-tRNA ternary complex is >1000-fold more stable than the near-cognate 30S•AUC•fMet-tRNA complex. Hence, the selectivity of ternary complex formation is inherently high, exceeding that of initiation in vivo by more than 10-fold.
Single Molecule Sequencing of Free DNA from Maternal Plasma for Noninvasive Trisomy 21 Detection
Authors: van den Oever Jessica M E , Balkassmi Sahila , Verweij E Joanne , van Iterson Maarten , van Scheltema Phebe N Adama , Oepkes Dick , van Lith Jan M M , Hoffer Mariëtte J V , den Dunnen Johan T , Bakker Egbert , Boon Elles M J
Published: January 2012

BACKGROUND

Noninvasive fetal aneuploidy detection by use of free DNA from maternal plasma has recently been shown to be achievable by whole genome shotgun sequencing. The high-throughput next-generation sequencing platforms previously tested use a PCR step during sample preparation, which results in amplification bias in GC-rich areas of the human genome. To eliminate this bias, and thereby experimental noise, we have used single molecule sequencing as an alternative method.

METHODS

For noninvasive trisomy 21 detection, we performed single molecule sequencing on the Helicos platform using free DNA isolated from maternal plasma from 9 weeks of gestation onwards. Relative sequence tag density ratios were calculated and results were directly compared to the previously described Illumina GAII platform.

RESULTS

Sequence data generated without an amplification step show no GC bias. Therefore, with the use of single molecule sequencing all trisomy 21 fetuses could be distinguished more clearly from euploid fetuses.

CONCLUSIONS

This study shows for the first time that single molecule sequencing is an attractive and easy to use alternative for reliable noninvasive fetal aneuploidy detection in diagnostics. With this approach, previously described experimental noise associated with PCR amplification, such as GC bias, can be overcome.
Hope, Meaning and Responsibility across Stages of Recovery for Individuals Living With an Enduring Mental Illness
Authors: Copic Vedrana , Deane Frank P. , Crowe Trevor P. , Oades Lindsay G.
Published: January 2012

This study reports on the relationship between stage of recovery and hope, meaning and responsibility for individuals diagnosed with severe mental illness.Methods:Seventy-seven people with a diagnosis of a psychotic disorder of at least 6 months' duration participated in the study. Participants completed the Self-Identified Stage of Recovery (SISR) scale, measures of component processes of recovery (Hope Scale; Positive Interpretation of Disease, SpREUK; Active Involvement, Personal Health Management Questionnaire (PHMQ) and the Recovery Assessment Scale-short (RAS).Results:Hope, meaning,Personal Confidence and HopeandNot Being Dominated by Symptomsvaried significantly across stages of recovery; however, neither in a parallel nor linear fashion. Hopefulness and sense of meaning in relation to the experience of mental illness increase before personal confidence and resilience in the face of setbacks.Conclusions and implications:Symptoms appear to take less prominence in individuals' lives in later stages of recovery. Greater insight into the relationship between stage of recovery and component processes may allow for more targeted recovery-oriented support for individuals at different stages of recovery.
Encoding of Coordinated Reach and Grasp Trajectories in Primary Motor Cortex
Authors: Saleh Maryam , Takahashi Kazutaka , Hatsopoulos Nicholas G.
Published: January 2012

Though the joints of the arm and hand together comprise 27 degrees of freedom, an ethological movement like reaching and grasping coordinates many of these joints so as to operate in a reduced dimensional space. We used a generalized linear model to predict single neuron responses in primary motor cortex (MI) during a reach-to-grasp task based on 40 features that represent positions and velocities of the arm and hand in joint angle and Cartesian coordinates as well as the neurons' own spiking history. Two rhesus monkeys were trained to reach and grasp one of five objects, located at one of seven locations while we used an infrared camera motion-tracking system to track markers placed on their upper limb and recorded single-unit activity from a microelectrode array implanted in MI. The kinematic trajectories that described hand shaping and transport to the object depended on both the type of object and its location. Modeling the kinematics as temporally extensive trajectories consistently yielded significantly higher predictive power in most neurons. Furthermore, a model that included all feature trajectories yielded more predictive power than one that included any single feature trajectory in isolation, and neurons tended to encode feature velocities over positions. The predictive power of a majority of neurons reached a plateau for a model that included only the first five principal components of all the features' trajectories, suggesting that MI has evolved or adapted to encode the natural kinematic covariations associated with prehension described by a limited set of kinematic synergies.
Novelty Detection in the Human Auditory Brainstem
Authors: Slabu Lavinia , Grimm Sabine , Escera Carles
Published: January 2012

Auditory deviance detection has been associated with a human auditory-evoked potential (AEP), the mismatch negativity, generated in the auditory cortex 100–200 ms from sound change onset. Yet, single-unit recordings in animals suggest much earlier (∼20–40 ms), and anatomically lower (i.e., thalamus and midbrain) deviance detection. In humans, recordings of the scalp middle-latency AEPs have confirmed early (∼30–40 ms) deviance detection. However, involvement of the human auditory brainstem in deviance detection has not yet been demonstrated. Here we recorded the auditory brainstem frequency-following response (FFR) to consonant-vowel stimuli (/ba/, /wa/) in young adults, with stimuli arranged in oddball and reversed oddball blocks (deviant probability,p= 0.2), allowing for the comparison of FFRs to the same physical stimuli presented in different contextual roles. Whereas no effect was observed for the /wa/ syllable, we found for the /ba/ syllable a reduction in the brainstem FFR to deviant stimuli compared with standard ones and to similar stimuli arranged in a control block, with five equiprobable, rarely occurring sounds. These findings demonstrate that the human auditory brainstem is able to encode regularities in the recent auditory past to detect novel events, and confirm the multiple anatomical and temporal scales of human deviance detection.
Cav2.1 in Cerebellar Purkinje Cells Regulates Competitive Excitatory Synaptic Wiring, Cell Survival, and Cerebellar Biochemical Compartmentalization
Authors: Miyazaki Taisuke , Yamasaki Miwako , Hashimoto Kouichi , Yamazaki Maya , Abe Manabu , Usui Hiroshi , Kano Masanobu , Sakimura Kenji , Watanabe Masahiko
Published: January 2012

In the adult cerebellum, each Purkinje cell (PC) is innervated by a single climbing fiber (CF) in proximal dendrites and 105-106parallel fibers (PFs) in distal dendrites. This organized wiring is established postnatally through heterosynaptic competition between PFs and CFs and homosynaptic competition among multiple CFs. Using PC-specific Cav2.1 knock-out mice (PC-Cav2.1 KO mice), we have demonstrated recently that postsynaptic Cav2.1 plays a key role in the homosynaptic competition by promoting functional strengthening and dendritic translocation of single “winner” CFs. Here, we report that Cav2.1 in PCs, but not in granule cells, is also essential for the heterosynaptic competition. In PC-Cav2.1 KO mice, the extent of CF territory was limited to the soma and basal dendrites, whereas PF territory was expanded reciprocally. Consequently, the proximal somatodendritic domain of PCs displayed hyperspiny transformation and fell into chaotic innervation by multiple CFs and numerous PFs. PC-Cav2.1 KO mice also displayed patterned degeneration of PCs, which occurred preferentially in aldolase C/zebrin II-negative cerebellar compartments. Furthermore, the mutually complementary expression of phospholipase Cβ3 (PLCβ3) and PLCβ4 was altered such that their normally sharp boundary was blurred in the PCs of PC-Cav2.1 KO mice. This blurring was caused by an impaired posttranscriptional downregulation of PLCβ3 in PLCβ4-dominant PCs during the early postnatal period. A similar alteration was noted in the banded expression of the glutamate transporter EAAT4 in PC-Cav2.1 KO mice. Therefore, Cav2.1 in PCs is essential for competitive synaptic wiring, cell survival, and the establishment of precise boundaries and reciprocity of biochemical compartments in PCs.