bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetochore–microtubule attachment throughout mitosis potentiated by the elongated stalk of the kinetochore kinesin CENP-E
Authors: Vitre Benjamin , Gudimchuk Nikita , Borda Ranier , Kim Yumi , Heuser John E. , Cleveland Don W. , Grishchuk Ekaterina L.
Published: June 2014

Centromere protein E (CENP-E) is a highly elongated kinesin that transports pole-proximal chromosomes during congression in prometaphase. During metaphase, it facilitates kinetochore–microtubule end-on attachment required to achieve and maintain chromosome alignment. In vitro CENP-E can walk processively along microtubule tracks and follow both growing and shrinking microtubule plus ends. Neither the CENP-E–dependent transport along microtubules nor its tip-tracking activity requires the unusually long coiled-coil stalk of CENP-E. The biological role for the CENP-E stalk has now been identified through creation of “Bonsai” CENP-E with significantly shortened stalk but wild-type motor and tail domains. We demonstrate that Bonsai CENP-E fails to bind microtubules in vitro unless a cargo is contemporaneously bound via its C-terminal tail. In contrast, both full-length and truncated CENP-E that has no stalk and tail exhibit robust motility with and without cargo binding, highlighting the importance of CENP-E stalk for its activity. Correspondingly, kinetochore attachment to microtubule ends is shown to be disrupted in cells whose CENP-E has a shortened stalk, thereby producing chromosome misalignment in metaphase and lagging chromosomes during anaphase. Together these findings establish an unexpected role of CENP-E elongated stalk in ensuring stability of kinetochore–microtubule attachments during chromosome congression and segregation.
Subcellular optogenetic inhibition of G proteins generates signaling gradients and cell migration
Authors: O'Neill Patrick R. , Gautam N.
Published: June 2014

Cells sense gradients of extracellular cues and generate polarized responses such as cell migration and neurite initiation. There is static information on the intracellular signaling molecules involved in these responses, but how they dynamically orchestrate polarized cell behaviors is not well understood. A limitation has been the lack of methods to exert spatial and temporal control over specific signaling molecules inside a living cell. Here we introduce optogenetic tools that act downstream of native G protein–coupled receptor (GPCRs) and provide direct control over the activity of endogenous heterotrimeric G protein subunits. Light-triggered recruitment of a truncated regulator of G protein signaling (RGS) protein or a Gβγ-sequestering domain to a selected region on the plasma membrane results in localized inhibition of G protein signaling. In immune cells exposed to spatially uniform chemoattractants, these optogenetic tools allow us to create reversible gradients of signaling activity. Migratory responses generated by this approach show that a gradient of active G protein αi and βγ subunits is sufficient to generate directed cell migration. They also provide the most direct evidence so for a global inhibition pathway triggered by Gi signaling in directional sensing and adaptation. These optogenetic tools can be applied to interrogate the mechanistic basis of other GPCR-modulated cellular functions.
Common regulatory control of CTP synthase enzyme activity and filament formation
Authors: Noree Chalongrat , Monfort Elena , Shiau Andrew K. , Wilhelm James E.
Published: June 2014

The ability of enzymes to assemble into visible supramolecular complexes is a widespread phenomenon. Such complexes have been hypothesized to play a number of roles; however, little is known about how the regulation of enzyme activity is coupled to the assembly/disassembly of these cellular structures. CTP synthase is an ideal model system for addressing this question because its activity is regulated via multiple mechanisms and its filament-forming ability is evolutionarily conserved. Our structure–function studies of CTP synthase in Saccharomyces cerevisiae reveal that destabilization of the active tetrameric form of the enzyme increases filament formation, suggesting that the filaments comprise inactive CTP synthase dimers. Furthermore, the sites responsible for feedback inhibition and allosteric activation control filament length, implying that multiple regions of the enzyme can influence filament structure. In contrast, blocking catalysis without disrupting the regulatory sites of the enzyme does not affect filament formation or length. Together our results argue that the regulatory sites that control CTP synthase function, but not enzymatic activity per se, are critical for controlling filament assembly. We predict that the ability of enzymes to form supramolecular structures in general is closely coupled to the mechanisms that regulate their activity.
Women, Race, and the Law in Early America
Authors: Snyder Terri L.
Published: June 2014

Everywhere across European and Indigenous settlements in 17th- and 18th-century North America and the Caribbean, the law or legal practices shaped women’s status and conditioned their dependency, regardless of race, age, marital status, or place of birth. Historians have focused much of their attention on the legal status, powers, and experiences of women of European origin across the colonies and given great consideration to the law of domestic relations, the legal disabilities of coverture, and women’s experiences as plaintiffs and defendants, both civil and criminal, in colonial courts. Early American legalities, however, differed markedly for women of color—whether free, indentured, or enslaved, and whether Native or African in origin or descent—whose relationships to the legal regimes of early America were manifold and complex. In their status under the law, experiences at the bar, and, as a result, positions in household polities, women of color reckoned with a set of legalities that differed from those of their European counterparts. The diversity of women’s experiences of the law was shaped not only by race but also by region: Indigenous people had what one historian has labeled jurispractices, while Europeans brought and created a jurisprudence of race and status that shaped treatments of women of color across imperial spaces. A widely comparative analysis of women and the law reflects ways in which race shaped women’s status under and experiences of the law as well as the legalities of their marriages in pre-Revolutionary America.
Muslim-Jewish Relations
Authors: Firestone Reuven
Published: June 2014

Muslim-Jewish relations began with the emergence of Islam in 7th-century Arabia, but contacts between pre-Jewish Israelites and pre-Muslim Arabs had been common for nearly two millennia previously. These interactions inform the earliest relations between Muslims and Jews and serve as precursors to the social, cultural, religious, political, and institutional relations between Muslims and Jews from the 7th century to the present. Areas and periods of particular importance are 7th-century Arabia with first contacts between Jews and the earliest Muslims, 8th–9th-century Middle East with the establishment of legal and social status of Jews in Islam, the 9th to 14th centuries in many parts of the Muslim world with the development of great Jewish intellectual advances under Islamic influence, the subsequent decline of the Muslim world and its negative impact on Jews and other minorities, the period under colonial powers with the rise of national movements and the subsequent transition to independent nation-states that includes the rise of both Jewish and Palestinian nationalisms, and the current status of Muslim-Jewish relations today. Common issues include language production; cultural production including literature, hermeneutics, and systematic thinking; legal developments, political relations, religious commonalities and differences, and economic relations and partnerships.
The History of the Modern Liturgical Movement
Authors: Pecklers Keith F.
Published: June 2014

The 20th-century liturgical movement grew in tandem with the biblical, ecumenical, ecclesiological, and patristic movements, all part of a wider movement of resourcement—a return to biblical and patristic sources. Indeed, the success of the liturgical movement in the 20th century, ultimately ratified in the liturgical reforms of the Second Vatican Council (1962–1965), can be seen precisely in its collaboration with those other ecclesial movements for church reform. Especially important was the ecumenical liturgical cooperation that grew across denominational lines as the movement took shape in different churches.

Belgian Benedictine Lambert Beauduin (d. 1960) of Mont César is considered the founder of the Roman Catholic liturgical movement; during a national Catholic labor conference, held in Malines in September 1909, he delivered a conference on the liturgy as the “true prayer of the Church.” Taking his cue from Pope Pius X’s 1903 motu proprio “Tra le sollecitudini,” in which he spoke of the liturgy as “the true and indispensible source” for the Christian life, Beauduin argued that liturgy was foundational for Christian mission and social outreach. This message was consistent with the parish communion movement within the Church of England at the dawn of the 20th century and, indeed, in what the founder of the liturgical movement within the Church of England, A. Gabriel Hebert, S. S. M., wrote in his classic 1935 text Liturgy and Society.

In Germany, the movement centered on the Benedictine monastery of Maria Laach and was more scientific in scope. Soon the movement took hold in Austria, France, and the rest of Europe, as well as in the Americas, in Anglican, Lutheran, and Roman Catholic churches in particular. It is precisely because of this common return to the sources that the 20th-century liturgical movement can only be understood in its wider ecumenical context.
Ritual Studies
Authors: Post Paul
Published: June 2014

Ritual studies is not a school, nor is it a theory or a method; it is a multi- or interdisciplinary platform for the academic, critical, and systematic study of ritual, or in the words of the founding father of ritual studies, Ronald Grimes: it is a field. The platform of ritual studies, which emerged in the mid-1970s, initially combined the fields of religious studies, anthropology, liturgical studies, and theater studies.

The emergence of ritual studies as a field of research of its own fits seamlessly into a broader development in academia that took place in three phases. The first phase took place during the second half of the 19th and the first half of the 20th centuries, when academic disciplines came into being and formed distinct profiles. The study of ritual plays a prominent role in (comparative) religious studies (Eliade, Otto, Van der Leeuw), in philosophy (ritual and symbol, Ricoeur), in anthropology and sociology (Durkheim, Turner), in psychology (Jung), and in cultural history (Huizinga). There was at this time remarkably little interest in ritual among theologians. It was not until the influence of the Liturgical Movement that a change occurred. The second phase took place during the long decade of the 1960s, which saw the start of a fruitful interdisciplinary phase. Rituals were thought to offer an effective entrance into a culture, allowing one to penetrate it deeply. The liturgical renewal project also took place after Vaticanum II, and it was in this setting that the term “ritual studies” was first used by the American Academy of Religion in 1977. The beginning of the 21st century saw the start of a new phase, during which different disciplines have been connected and integrated into large, multidisciplinary thematic clusters. In this context, the field of ritual studies features in a broad range of studies, including cultural memory studies, media and communication studies, death studies, leisure studies, material religion studies, migration studies, and many others.
Christian Worship and Gender Practices
Authors: Berger Teresa
Published: June 2014

The foundational materiality in Christian worship is the bodily presence of worshippers. Gender differences—and the manifold ways in which they are embodied and performed in different cultural contexts—are therefore inscribed into the very fabric of liturgical practices, past and present. In Christian worship today, the workings of gender are evident across a broad spectrum of ecclesial traditions. Some churches have authorized rituals for the blessing of same-sex unions; some are ordaining openly transgender priests. Other churches continue to struggle with the ordination of women, while a few aim for explicitly “masculine” worship experiences. Feminist concerns over liturgical language mark some communities, while churches rooted in more traditional contexts maintain seating arrangements that separate women and men. Clearly, the workings of gender in Christian worship today span a broad spectrum of quite dissimilar concerns. At the root of all these concerns, however, lies the same vital reality, namely that worship is an embodied practice and therefore never gender-free.

What often goes unnoticed in contemporary discussions is the fact that gender differences have marked liturgical practices in Christian communities since earliest times. The workings of gender, in other words, have a genealogy in Christian worship. Scholars have only recently begun to map this terrain, by bringing the interpretive tools of gender theory to bear on liturgical historiography. Paramount among these interpretive tools is an understanding of gender as attending to all gendered particularities and sexualities (e.g., eunuchs in Byzantium, ascetic virgins in Merovingian Gaul, transgender people in contemporary North America, etc.). Gender, in other words, is understood to encompass much more than the traditional binary of “women” and “men.”

The emerging gender-attentive insights into liturgical history have been intriguing and at times quite surprising. These insights span the whole of liturgy’s past, from ways in which gender shaped early baptismal practices (e.g., in the choreography of the rite, in questions surrounding the minister of baptism, in the bodily proprieties considered appropriate at the font) to the workings of gender in the 20th-century Liturgical Movement (e.g., its first important text, Tra le Sollecitudine (1903)—usually hailed for its evocation of an “active participation” of the faithful in worship—also sought to discontinue the presence of castrati singers in the Sistine Chapel choir while ensuring that women would not take their place).

In between earliest glimpses of the workings of gender in Christian worship and our own times lie approximately a thousand years of a complex history. Tracing this history of the interplay between gender differences and Christian worship not only constitutes an important task for historians of liturgy, but also provides rich resources for addressing contemporary issues.
Early Modern Afro-Caribbean Healers
Authors: Gómez Pablo F.
Published: June 2014

In the early modern Spanish Caribbean, ritual practitioners of African descent were essential providers of health care for Caribbean people of all origins. Arriving from West and West Central Africa, Europe, and other Caribbean and New World locales, black healers were some of the most important shapers of practices related to the human body in the region. They openly performed bodily rituals of African, European, and Native American inspiration. Theirs is not a history uniquely defined by resistance or attempts at cultural survival, but rather by the creation of political and social capital through healing practices. Such a project was only possible through their exploration of and engagement with early modern Caribbean human and natural landscapes.
Predicting dynamic signaling network response under unseen perturbations
Authors: Zhu Fan , Guan Yuanfang
Published: June 2014

Motivation: Predicting trajectories of signaling networks under complex perturbations is one of the most valuable, but challenging, tasks in systems biology. Signaling networks are involved in most of the biological pathways, and modeling their dynamics has wide applications including drug design and treatment outcome prediction.

Results: In this paper, we report a novel model for predicting the cell type-specific time course response of signaling proteins under unseen perturbations. This algorithm achieved the top performance in the 2013 8th Dialogue for Reverse Engineering Assessments and Methods (DREAM 8) subchallenge: time course prediction in breast cancer cell lines. We formulate the trajectory prediction problem into a standard regularization problem; the solution becomes solving this discrete ill-posed problem. This algorithm includes three steps: denoising, estimating regression coefficients and modeling trajectories under unseen perturbations. We further validated the accuracy of this method against simulation and experimental data. Furthermore, this method reduces computational time by magnitudes compared to state-of-the-art methods, allowing genome-wide modeling of signaling pathways and time course trajectories to be carried out in a practical time.

Availability and implementation: Source code is available at http://guanlab.ccmb.med.umich.edu/DREAM/code.html and as supplementary file online.

Contact:  gyuanfan@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Johan Hjort: The Canadian Fisheries Expedition, International Scientific Networks, and the challenge of modernization
Authors: Hubbard Jennifer
Published: June 2014

By leading the Canadian Fisheries Expedition of 1914–1915 Johan Hjort took the opportunity to do far more than just survey herring, other fish stocks, and the hydrography of Canadian Atlantic waters. He also attempted to improve the backward fish-processing technologies used in the local fisheries, an agenda blocked by the Canadian government. Hjort did succeed markedly, however, in introducing Canadian scientists to the International Council for the Exploration of the Sea's new scientific methods for fisheries research. He and his colleagues offered training in the new dynamic oceanography as well as population demographic studies and biometrics for studying fish populations, races, and other units. His extroverted leadership-initiated lasting linkages between Canadian and Scandinavian scientists, and created an international network of fisheries biologists.
Ground-truthing the ground-truth: reply to Garibaldi et al.'s comment on “Managing fisheries from space: Google Earth improves estimates of distant fish catches”
Authors: Al-Abdulrazzak Dalal , Pauly Daniel
Published: June 2014

There has been a growing interest in the potential of Google Earth for scientific inquiries, and our previous paper (Al-Abdulrazzak and Pauly, 2014. Managing fisheries from space: Google Earth improves estimates of distant fish catches. ICES Journal of Marine Science, 71: 450–454) on weirs and their catch in the Persian Gulf is a case in point. Garibaldi et al. (2014. Comment on: “Managing fisheries from space: Google Earth improves estimates of distant fish catchs” by Al-Abdulrazzak and Pauly. ICES Journal of Marine Science), while agreeing in principle with using Google Earth for fisheries-related purposes, criticized the assumptions, data, methodology, and results of this paper. Here, we refute their criticisms, notably by showing that the “derelict weirs” that they thought they had “ground-truthed” are not weirs at all, but another type of fishing gear in one case, and debris from a boat anchoring system in the other. We develop the theme that ground-truthing requires local knowledge, and provide recommendations for using Google Earth images in fisheries management.
Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil
Authors: Kim Soo-Jin , Park Joo-Hyeon , Lim Jun-Muk , Ahn Jae-Hyung , Anandham Rangasamy , Weon Hang-Yeon , Kwon Soon-Wo
Published: June 2014

A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family

Chitinophagaceae

, and exhibited the highest sequence similarities with members of the genera

Terrimonas

(89.2–92.6 %),

Sediminibacterium

(90.8–91.4 %) and

Chitinophaga

(89.2–91.7 %),

Filimonas lacunae

YT21T (91.7 %), members of the genus

Segetibacter

(90.2–91.6 %),

Parasegetibacter luojiensis

RHYL-37T (90.9 %) and

Flavihumibacter petaseus

T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family

Chitinophagaceae

, for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).
Barnettozyma siamensis f.a., sp. nov., a lipid-accumulating ascomycete yeast species
Authors: Polburee Pirapan , Yongmanitchai Wichien , Ohashi Takao , Fujiyama Kazuhito , Limtong Savitree
Published: June 2014

Two strains, DMKU-UbN24(1)T and DMKU-CPN24(1), of a novel yeast species were obtained from soil and palm oil fruit, respectively, collected in Thailand by an enrichment isolation technique using a nitrogen-limited medium containing glycerol as the sole source of carbon. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were found to represent a novel species of the genus Barnettozyma although the formation of ascospores was not observed. The novel species was related most closely to the type strain of Candida montana but differed by 5.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and by 10.3–10.5 % nucleotide substitutions in the ITS region. The name Barnettozyma siamensis f.a., sp. nov. is proposed. The type strain is DMKU-UbN24(1)T ( = BCC 61189T = NBRC 109701T = CBS 13392T).
Structural proteins of West Nile virus are a major determinant of infectious particle production and fitness in astrocytes
Authors: Hussmann Katherine L. , Vandergaast Rianna , Zheng Kang , Hoover Lisa I. , Fredericksen Brenda L.
Published: June 2014

The molecular basis for the increased resistance of astrocytes to a non-neuropathogenic strain of West Nile virus (WNV), WNV-MAD78, compared with the neuropathogenic strain WNV-NY remains unclear. Here, we demonstrated that the reduced susceptibility of astrocytes to WNV-MAD78 is due to a combination of both cellular activities as well as viral determinants. Analyses of the viral particle indicated that astrocyte-derived WNV-MAD78 particles were less infectious than those of WNV-NY. Additionally, inhibition of cellular furin-like proteases increased WNV-MAD78 infectious particle production in astrocytes, suggesting that high levels of furin-like protease activity within these cells acted in a cell- and strain-specific manner to inhibit WNV-MAD78 replication. Moreover, analysis of recombinant viruses indicated that the structural proteins of WNV-MAD78 were responsible for decreased particle infectivity and the corresponding reduction in infectious particle production compared with WNV-NY. Thus, the composition of the WNV virion was also a major determinant for viral fitness within astrocytes and may contribute to WNV propagation within the central nervous system. Whether the WNV-MAD78 structural genes reduce virus replication and particle infectivity through the same mechanism as the cellular furin-like protease activity or whether these two determinants function through distinct pathways remains to be determined.
Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses
Authors: Schwessinger Benjamin , Bahar Ofir , Nicolas Thomas , Holton Nicolas , Nekrasov Vladimir , Ruan Randy , Canlas Patrick , Daudi Arsalan , Petzold Christopher , Singan Vasanth , Kuo Rita , Chovatia Mansi , Daum Chris , Heazlewood Joshua , Zipfel Cyril , Ronald Pamela
Published: June 2014

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
Authors: Banovich Nicholas E. , Lan Xun , McVicker Graham , van de Geijn Bryce , Degner Jacob F. , Blischak John D. , Roux Julien , Pritchard Jonathan K. , Gilad Yoav
Published: June 2014

DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ∼300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915cismethylation QTLs (meQTLs)—i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.

Author Summary

DNA methylation is an important epigenetic mark that contributes to many biological processes including the regulation of gene expression. Genetic variation has been associated with quantitative changes in DNA methylation (meQTLs). We identified thousands of meQTLs using an assay that allowed us to measure methylation levels at around 300 thousand cytosines. We found that meQTLs are enriched with loci that is also associated with quantitative changes in gene expression, DNase I hypersensitivity, PolII occupancy, and a number of histone marks. This suggests that many molecular events are likely regulated in concert. Finally, we found that changes in transcription factor binding as well as transcription factor abundance are associated with changes in DNA methylation near transcription factor binding sites. This work contributes to our understanding of the regulation of DNA methylation in the larger context of gene regulatory landscape.
Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state
Authors: Katz Yarden , Li Feifei , Lambert Nicole , Sokol Ethan , Tam Wai-Leong , Cheng Albert W. , Airoldi Edoardo M. , Lengner Christopher J. , Gupta Piyush B. , Yu Zhengquan , Jaenisch Rudolf , Burge Christopher B.
Published: June 2014

The conserved Musashi (Msi) family of RNA binding proteins are expressed in stem/progenitor and cancer cells, but mostly absent from differentiated cells, consistent with a role in cell state regulation. We found that Msi genes are rarely mutated but frequently overexpressed in human cancers, and associated with an epithelial-luminal cell state. Using ribosome footprint profiling and RNA-seq analysis of genetic mouse models in neuronal and mammary cell types, we found that Msis regulate translation of genes implicated in epithelial cell biology and epithelial-to-mesenchymal transition (EMT) and promote an epithelial splicing pattern. Overexpression of Msi proteins inhibited translation of genes required for EMT, including Jagged1, and repressed EMT in cell culture and in mammary glandin vivo, while knockdown in epithelial cancer cells led to loss of epithelial identity. Our results show that mammalian Msi proteins contribute to an epithelial gene expression program and promote an epithelial-luminal state in both neural and breast cell types.

Highlights

Msi proteins bind UAG motifs in vitro and in 3’ UTRs of mRNAs

Msi proteins are markers of epithelial state in brain and breast tumors, and cell lines

The Notch regulatorJag1mRNA is bound and translationally repressed by Msi

Msi overexpression represses EMT in the mammary glandin vivo
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family
Authors: Roppolo Daniele , Boeckmann Brigitte , Pfister Alexandre , Boutet Emmanuel , Rubio Maria C. , Dénervaud-Tendon Valérie , Vermeer Joop E.M. , Gheyselinck Jacqueline , Xenarios Ioannis , Geldner Niko
Published: June 2014

CASPARIAN STRIP MEMBRANE DOMAIN PROTEINS (CASPs) are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. CASPs show high stability in their membrane domain, which presents all the hallmarks of a membrane scaffold. Here, we characterized the large family of CASP-like (CASPL) proteins. CASPLs were found in all major divisions of land plants as well as in green algae; homologs outside of the plant kingdom were identified as members of the MARVEL protein family. When ectopically expressed in the endodermis, most CASPLs were able to integrate the CASP membrane domain, which suggests that CASPLs share with CASPs the propensity to form transmembrane scaffolds. Extracellular loops are not necessary for generating the scaffold, since CASP1 was still able to localize correctly when either one of the extracellular loops was deleted. The CASP first extracellular loop was found conserved in euphyllophytes but absent in plants lacking Casparian strips, an observation that may contribute to the study of Casparian strip and root evolution. In Arabidopsis (Arabidopsis thaliana), CASPL showed specific expression in a variety of cell types, such as trichomes, abscission zone cells, peripheral root cap cells, and xylem pole pericycle cells.
REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis
Authors: Zhao Yusheng , Xie Shaojun , Li Xiaojie , Wang Chunlei , Chen Zhongzhou , Lai Jinsheng , Gong Zhizhong
Published: June 2014

In Arabidopsis thaliana, active DNA demethylation is initiated by the DNA glycosylase REPRESSOR OF SILENCING1 (ROS1) and its paralogs DEMETER, DEMETER-LIKE2 (DML2), and DML3. How these demethylation enzymes are regulated, however, is poorly understood. Here, using a transgenic Arabidopsis line harboring the stress-inducible RESPONSIVE TO DEHYDRATION29A (RD29A) promoter–LUCIFERASE (LUC) reporter gene and the cauliflower mosaic virus 35S promoter (35S)–NEOMYCIN PHOSPHOTRANSFERASE II (NPTII) antibiotic resistance marker gene, we characterize a ROS locus, ROS5, that encodes a protein in the small heat shock protein family. ROS5 mutations lead to the silencing of the 35S-NPTII transgene due to DNA hypermethylation but do not affect the expression of the RD29A-LUC transgene. ROS5 physically interacts with the histone acetyltransferase ROS4/INCREASED DNA METHYLATION1 (IDM1) and is required to prevent the DNA hypermethylation of some genes that are also regulated by ROS1 and IDM1. We propose that ROS5 regulates DNA demethylation by interacting with IDM1, thereby creating a chromatin environment that facilitates the binding of ROS1 to erase DNA methylation.
4-[(4-Bromophenyl)amino]-2-methylidene-4-oxobutanoic acid
Authors: Narayana B. , Nayak Prakash S. , Sarojini Balladka K. , Jasinski Jerry P.
Published: June 2014

In the title compound, C11H10BrNO3, two independent molecules (AandB) crystallize in the asymmetric unit. The dihedral angles between the mean planes of the 4-bromophenyl ring and amide group are 24.8 (7) in moleculeAand 77.1 (6)° in moleculeB. The mean plane of the methylidene group is further inclined by 75.6 (4) in moleculeAand 72.5 (6)° in moleculeBfrom that of the amide group. In the crystal, N—H...O hydrogen bonds formed by amide groups and O—H...O hydrogen bonds formed by carboxylic acid groups are observed and supported additionally by weak C—H...O interactions between the methylidene and amide groups. Together, these link the molecules into chains of dimers along [110] and formR22(8) graph-set motifs.
(18-Crown-6)potassium(I) diphenylstibate(−1)
Authors: Kaas Marina , Friedrich Ute , Korber Nikolaus
Published: June 2014

Red crystals of the title salt, [K(C12H24O6)][Sb(C6H5)2], were obtained by the reaction of SbPh3, KSnBi and 18-crown-6 in liquid ammonia. The asymmetric unit contains one half of a [K(18-crown-6)]+cation and one half of an SbPh2−anion, with the central element lying on a twofold axis and a centre of inversion, respectively. In the crystal structure, the sequestered potassium cations show weak interactions with the π-electrons of the phenyl groups of the SbPh2−anion [shortest K...C distances = 3.190 (2) and 3.441 (2) Å], leading to one-dimensional strands along the crystallographiccaxis. These strands are aligned in a pseudo-hexagonal packing perpendicular to theabplane.
Redetermination of diaquatris(4-oxopent-2-en-2-olato-κ2O,O′)lanthanum(III)
Authors: Okawara Toru , Ishihama Kohei , Takehara Kenji
Published: June 2014

The structure of the title compound, [La(C5H7O2)3(H2O)2], has been redetermined to modern standards with anisotropic displacement parameters for all non-H atoms and the hydrogen-bonding pattern unambiguously established [for the previous study, see Phillipset al.(1968).Inorg. Chem.7, 2295–2299]. The La3+ion is coordinated by threeO,O′-bidentate acetylacetate (acac−) ligands and two water molecules, resulting in a fairly regular square-antiprismatic LaO8coordination geometry, with both aqua ligands part of the same square face. In the crystal, the neutral complex molecules are linked into [110] chains by O—H...O hydrogen bonds.
N-Methyl-N-nitroso-p-toluenesulfonamide
Authors: Rai Kartik , Wu Vincent , Gupta Priya , Laviska David A. , Chan Benny C.
Published: June 2014

The crystal structure of the title compound, C8H10N2O3S, displays predominant C—H...O hydrogen-bonding and π–π stacking interactions. The hydrogen bonds are between the O atoms of the sulfonyl group and H atoms on methyl groups. The π–π stacking interactions occur between adjacent aromatic rings, with a centroid–centroid distance of 3.868 (11) Å. These interactions lead to the formation of chains parallel to (101).
2-[(3S,3aS,5R,8S,8aS)-3,8-Dimethylhexahydro-1H,4H-3a,8a-epoxyazulen-5-yl]propan-2-ol
Authors: Burrett Stacey , Taylor Dennis K. , Tiekink Edward R. T.
Published: June 2014

Four independent molecules (A–D) comprise the asymmetric unit of the title compound, C15H26O2, which differ only in the relative orientations of the terminal –C(Me)2OH groups [e.g.the range of Cmethylene—Cmethine—Cquaternary—Ohydroxytorsion angles is 52.7 (7)–57.1 (6)°, where the Cmethyleneatom is bound to an epoxide C atom]. The five-membered rings adopt envelope conformations, with the methylene C atom adjacent to the methine C atom being the flap atom in each case. In each molecule, the conformation of the seven-membered ring is a half-chair, with the Cmethylene—Cmethinebond, flanked by methylene C atoms, being the back of the chair. Supramolecular helical chains along thebaxis are found in the crystal packing, sustained by hydroxy–epoxide O—H...O hydrogen bonding. Molecules ofAself-associate into a chain as do those ofD. A third independent chain comprisingBandCmolecules is also formed. The studied crystal is a pseudo-merohedral twin (minor componentca21%).
Hydrogen bonding in 4-nitrobenzene-1,2-diamine and two hydrohalide salts
Authors: Geiger David K. , Parsons Dylan E.
Published: June 2014

The structures of 4-nitrobenzene-1,2-diamine [C6H7N3O2, (I)], 2-amino-5-nitroanilinium chloride [C6H8N3O2+·Cl−, (II)] and 2-amino-5-nitroanilinium bromide monohydrate [C6H8N3O2+·Br−·H2O, (III)] are reported and their hydrogen-bonded structures described. The amine groupparato the nitro group in (I) adopts an approximately planar geometry, whereas themetaamine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine groupmetato the nitro group is protonated. Compound (I) displays a pleated-sheet hydrogen-bonded two-dimensional structure withR22(14) andR44(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three-dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo-inversion center. The dominant hydrogen-bonding interactions involve the chloride ion and result inR42(8) rings linked to form a ladder-chain structure. The chains are joined by N—H...Cl and N—H...O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to formR42(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternatingR55(15) andR64(24) rings. Ammonium N—H...Br interactions join the sheets to form a three-dimensional extended structure. Energy-minimized structures obtained using DFT and MP2 calculations are consistent with the solid-state structures. Consistent with (II) and (III), calculations show that protonation of the amine groupmetato the nitro group results in a structure that is about 1.5 kJ mol−1more stable than that obtained by protonation of thepara-amine group. DFT calculations on single molecules and hydrogen-bonded pairs of molecules based on structural results obtained for (I) and for 3-nitrobenzene-1,2-diamine, (IV) [Betz & Gerber (2011).Acta Cryst.E67, o1359] were used to estimate the strength of the N—H...O(nitro) interactions for three observed motifs. The hydrogen-bonding interaction between the pairs of molecules examined was found to correspond to 20–30 kJ mol−1.
(E)-3-{4-[(7-Chloroquinolin-4-yl)oxy]-3-methoxyphenyl}-1-(4-methylphenyl)prop-2-en-1-one: a ladder-like structure resulting solely from π–π stacking interactions
Authors: Montoya Alba , Insuasty Braulio , Cobo Justo , Glidewell Christopher
Published: June 2014

In the title compound, C26H20ClNO3, the quinoline fragment is nearly orthogonal to the adjacent aryl ring, while the rest of the molecular skeleton is close to being planar. The crystal structure contains no hydrogen bonds of any sort, but there are two π–π stacking interactions present. One, involving the quinoline ring, links molecules related by inversion, while the other, involving the two nonfused aryl rings, links molecules related by translation, so together forming a ladder-type arrangement
Natural enemy ecology: comparing the effects of predation risk, infection risk and disease on host behaviour
Authors: Preston Daniel L. , Boland Clara E. , Hoverman Jason T. , Johnson Pieter T. J.
Published: June 2014

Growing interest in unifying the field of natural enemy ecology has revealed similarities between predation and parasitism. In parallel with predation, parasite infection – and even the threat of infection – can alter host traits and indirectly affect community interactions. Nonetheless, few studies have considered multiple mechanisms of natural enemy‐induced behavioural alteration in parallel (e.g. effects before and after enemy contact) or the factors that drive variation in behavioural responses.

We first evaluated how the threat of infection by a virulent trematode (Ribeiroia ondatrae) compared to the well studied risk of predation in triggering inducible defences in amphibian hosts, prior to direct contact with either enemy. We then evaluated five separate factors that influenced the magnitude of parasite‐induced behavioural changes after successful transmission.

In both the laboratory and an outdoor mesocosm experiment, we found no evidence that tadpoles of two species (Pseudacris regillaandAnaxyrus boreas) altered their activity levels in response to chemical cues from uninfected host snails, trematode‐infected snails, or from conspecifics actively becoming infected. In contrast, tadpoles sharply reduced their activity in response to lethal predation risks posed by caged dragonfly larvae.

After infection, however,Ribeiroiacaused strong decreases in host activity and escape distance that correlated positively with infection intensity and negatively with host size and developmental stage. Five days after infection with a one‐time pulse exposure, hosts recovered to near‐normal activity levels. Hosts exposed to a chronic daily exposure of equal intensity, however, continued to decrease activity. UnlikeRibeiroia, two less virulent trematodes had no detectable effects on host behaviour.

Our results highlight key distinctions between predation and parasitism. The contrasting effects prior to enemy contact may stem from the fact that unlike predation, the consequences of macroparasite infection are intensity‐dependent and unpredictable. In contrast, the strong changes in host behaviour after infection are more similar to non‐consumptive predator effects in terms of their potential influences on host fitness and community interactions.
The influence of fracturing process on microseismic propagation
Authors: Zhang Xiaolin , Zhang Feng , Li Xiang‐Yang
Published: June 2014

In the hydraulic fracturing process, the velocity model for microseismic location is usually constructed by well logs, seismic data or calibration shots which ignore the influence of the fracturing process. In this work, we examine its influence by simulating microseismic events and pore pressure variation in the fracturing process. Besides the microseismicity produced by hydraulic fracture extension, we also simulate the microseismicity caused by fluid leakage by means of the critical pore pressure criterion. The Coates‐Schoenberg method and fracture compliances are then applied to calculate the real‐time velocity in the fracturing process, and 3D ray tracing method is applied to compare the microseismic propagation variation in the different stages of the fracturing process. The results of the simulation show that the deviation caused by the fracturing process varies considerably between different receiver locations, and the overall deviation increases with the fracturing process. Finally, a new method is constructed to evaluate the travel time deviation in real data.
Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics
Authors: Moitinho‐Silva Lucas , Seridi Loqmane , Ryu Taewoo , Voolstra Christian R. , Ravasi Timothy , Hentschel Ute
Published: June 2014

Sponges are important components of marine benthic environments and are associated with microbial symbionts that carry out ecologically relevant functions. Stylissa carteri is an abundant, low‐microbial abundance species in the Red Sea. We aimed to achieve the functional and taxonomic characterization of the most actively expressed prokaryotic genes in S. carteri. Prokaryotic mRNA was enriched from sponge total RNA, sequenced using Illumina HiSeq technology and annotated using the metagenomics Rapid Annotation using Subsystem Technology (MG‐RAST) pipeline. We detected high expression of archaeal ammonia oxidation and photosynthetic carbon fixation by members of the genus Synechococcus. Functions related to stress response and membrane transporters were among the most highly expressed by S. carteri symbionts. Unexpectedly, gene functions related to methylotrophy were highly expressed by gammaproteobacterial symbionts. The presence of seawater‐derived microbes is indicated by the phylogenetic proximity of organic carbon transporters to orthologues of members from the SAR11 clade. In summary, we revealed the most expressed functions of the S. carteri‐associated microbial community and linked them to the dominant taxonomic members of the microbiome. This work demonstrates the applicability of metatranscriptomics to explore poorly characterized symbiotic consortia and expands our knowledge of the ecologically relevant functions carried out by coral reef sponge symbionts.
The impact of dynamic assessment: an exploration of the views of children, parents and teachers
Authors: Lawrence Nicola , Cahill Sharon
Published: June 2014

A qualitative research project was carried out to explore the views of children with special educational needs, their parents and teachers about one aspect of educational psychology practice: the dynamic assessment of cognitive skills. The research was carried out in a highly diverse and inclusive borough in East London, by Nicola Lawrence from Hounslow Educational Psychology Service, and Sharon Cahill from the University of East London. The views of nine children were sought through semi‐structured interviews regarding the process of dynamic assessment, supported with tools and techniques to facilitate discussion. The views of eight parents and seven teachers were also sought, through semi‐structured interviews and focus groups, regarding the psychological reports produced from dynamic assessment. Of the original findings acquired through thematic analysis of the data, those pertaining to the perceived impact of dynamic assessment of cognitive skills are reported. Dynamic assessment was reported to impact positively upon the child's emotional well‐being, self‐perceptions, approach to learning and social relationships, both directly, and through the subsequent intervention of parents and educators. Dynamic assessment, as well as providing instructionally useful information for parents and teachers, encouraged them to move beyond locating the problem within the child, to reconceptualising their special educational needs in context. As a result, parents and teachers became more positive and optimistic about the child, the current situation and the child's future. Dynamic assessment impacted upon the child's holistic needs, parenting and the development of inclusive practice in the classroom. It is concluded that from the perspective of service users, dynamic assessment forms a worthwhile and valuable part of educational psychology practice.