bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative analysis of genomic element interactions by molecular colony technique
Authors: Gavrilov Alexey A. , Chetverina Helena V. , Chermnykh Elina S. , Razin Sergey V. , Chetverin Alexander B.
Published: December 2013

Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde–cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA–protein complex cannot be stabilized by formaldehyde cross-linking.
The contribution of pseudouridine to stabilities and structure of RNAs
Authors: Kierzek Elzbieta , Malgowska Magdalena , Lisowiec Jolanta , Turner Douglas H. , Gdaniec Zofia , Kierzek Ryszard
Published: December 2013

Thermodynamic data are reported revealing that pseudouridine (Ψ) can stabilize RNA duplexes when replacing U and forming Ψ-A, Ψ-G, Ψ-U and Ψ-C pairs. Stabilization is dependent on type of base pair, position of Ψ within the RNA duplex, and type and orientation of adjacent Watson–Crick pairs. NMR spectra demonstrate that for internal Ψ-A, Ψ-G and Ψ-U pairs, the N3 imino proton is hydrogen bonded to the opposite strand nucleotide and the N1 imino proton may also be hydrogen bonded. CD spectra show that general A-helix structure is preserved, but there is some shifting of peaks and changing of intensities. Ψ has two hydrogen donors (N1 and N3 imino protons) and two hydrogen bond acceptors because the glycosidic bond is C-C rather than C-N as in uridine. This greater structural potential may allow Ψ to behave as a kind of structurally driven universal base because it can enhance stability relative to U when paired with A, G, U or C inside a double helix. These structural and thermodynamic properties may contribute to the biological functions of Ψ.
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors
Authors: Ye Zhenqing , Chen Zhong , Lan Xun , Hara Stephen , Sunkel Benjamin , Huang Tim H.-M. , Elnitski Laura , Wang Qianben , Jin Victor X.
Published: December 2013

Alternative splicing (AS), in higher eukaryotes, is one of the mechanisms of post-transcriptional regulation that generate multiple transcripts from the same gene. One particular mode of AS is the skipping event where an exon may be alternatively excluded or constitutively included in the resulting mature mRNA. Both transcript isoforms from this skipping event site, i.e. in which the exon is either included (inclusion isoform) or excluded (skipping isoform), are typically present in one cell, and maintain a subtle balance that is vital to cellular function and dynamics. However, how the prevailing conditions dictate which isoform is expressed and what biological factors might influence the regulation of this process remain areas requiring further exploration. In this study, we have developed a novel computational method, graph-based exon-skipping scanner (GESS), for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites. We have applied our method to publicly available RNA-seq data in GM12878 and K562 cells from the ENCODE consortium and experimentally validated several skipping site predictions by RT-PCR. Furthermore, we integrated other sequencing-based genomic data to investigate the impact of splicing activities, transcription factors (TFs) and epigenetic histone modifications on splicing outcomes. Our computational analysis found that splice sites within the skipping-isoform-dominated group (SIDG) tended to exhibit weaker MaxEntScan-calculated splice site strength around middle, ‘skipping’, exons compared to those in the inclusion-isoform-dominated group (IIDG). We further showed the positional preference pattern of splicing factors, characterized by enrichment in the intronic splice sites immediately bordering middle exons. Finally, our analysis suggested that different epigenetic factors may introduce a variable obstacle in the process of exon–intron boundary establishment leading to skipping events.
A new epoch of quantum manipulation
Authors: Han Yongjian , Wang Zhen , Guo Guang-Can
Published: December 2013

The behavior of individual microscopic particles, such as an atom (or a photon), predicted using quantum mechanics, is dramatically different from the behavior of classical particles, such as a planet, determined using classical mechanics. How can the counter-intuitive behavior of the microscopic particle be verified and manipulated experimentally? David Wineland and Serge Haroche, who were awarded the Nobel Prize in physics in 2012, developed a set of methods to isolate the ions and photons from their environment to create a genuine quantum system. Furthermore, they also developed methods to measure and manipulate these quantum systems, which open a path not only to explore the fundamental principles of quantum mechanics, but also to develop a much faster computer: a quantum computer.
Streptomyces zhaozhouensis sp. nov., an actinomycete isolated from candelabra aloe (Aloe arborescens Mill)
Authors: He Hairong , Liu Chongxi , Zhao Junwei , Li Wenjun , Pan Tong , Yang Lingyu , Wang Xiangjing , Xiang Wensheng
Published: December 2013

A novel endophytic actinomycete, designated strain NEAU-LZS-5T, was isolated from the leaf of candelabra aloe (Aloe arborescens Mill) and characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that strain NEAU-LZS-5T belongs to the genus

Streptomyces

and exhibited 99.51 and 97.37 % similarity to

Streptomyces sedi

YIM 65188T and

Streptomyces specialis

GW41-1564T, respectively, whereas low similarity values (<97 %) distinguished strain NEAU-LZS-5T from all other species of the genus

Streptomyces

with validly published names. Two tree-making algorithms also supported the position that strain NEAU-LZS-5T formed a distinct clade with

Streptomyces sedi

YIM 65188T and

Streptomyces specialis

GW41-1564T. However, levels of DNA–DNA relatedness between strain NEAU-LZS-5T and

Streptomyces sedi

YIM 65188T and

Streptomyces specialis

GW41-1564T were 45.59 and 31.90 %, respectively. A comparative study between strain NEAU-LZS-5T and the type strains of closest related species of the genus

Streptomyces

revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, strain NEAU-LZS-5T represents a novel species of the genus

Streptomyces

, for which the name Streptomyces zhaozhouensis sp. nov. is proposed. The type strain is NEAU-LZS-5T ( = CGMCC 4.7095T = DSM 42101T).
Nonomuraea fuscirosea sp. nov., an actinomycete isolated from the rhizosphere soil of rehmannia (Rehmannia glutinosa Libosch)
Authors: Zhang Xinhui , Zhang Yuejing , Zhao Junwei , Liu Chongxi , Wang Shurui , Yang Lingyu , He Hairong , Xiang Wensheng , Wang Xiangjing
Published: December 2013

A novel actinomycete, designated strain NEAU-dht8T, was isolated from the rhizosphere soil of rehmannia (Rehmannia glutinosa Libosch) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus

Nonomuraea

. The G+C content of the DNA was 68.47 mol%. On the basis of 16S rRNA gene sequence similarity studies, strain NEAU-dht8T was most closely related to

Nonomuraea maheshkhaliensis

16-5-14T (99.31 %),

Nonomuraea kuesteri

GW 14-1925T (98.77 %),

Nonomuraea coxensis

JCM 13931T (98.71 %),

Nonomuraea wenchangensis

210417T (98.44 %),

Nonomuraea bangladeshensis

5-10-10T (98.36 %) and

Nonomuraea salmonea

DSM 43678T (98.0 %); similarities to other species of the genus

Nonomuraea

were lower than 98 %. Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with its closest neighbour

N. maheshkhaliensis

16-5-14T. However, the low level of DNA–DNA relatedness allowed the novel isolate to be differentiated from

N. maheshkhaliensis

16-5-14T. Strain NEAU-dht8T could also be differentiated from other species of the genus

Nonomuraea

showing high 16S rRNA gene sequence similarity (98–98.77 %) by morphological and physiological characteristics. Thus, strain NEAU-dht8T is considered to represent a novel species of the genus

Nonomuraea

, for which the name Nonomuraea fuscirosea sp. nov. is proposed. The type strain is NEAU-dht8T ( = CGMCC 4.7104T = DSM 45880T).
Gluconobacter cerevisiae sp. nov., isolated from the brewery environment
Authors: Spitaels Freek , Wieme Anneleen , Balzarini Tom , Cleenwerck Ilse , Van Landschoot Anita , De Vuyst Luc , Vandamme Peter
Published: December 2013

Three strains, LMG 27748T, LMG 27749 and LMG 27882 with identical MALDI-TOF mass spectra were isolated from samples taken from the brewery environment. Analysis of the 16S rRNA gene sequence of strain LMG 27748Trevealed that the taxon it represents was closely related to type strains of the speciesGluconobacter albidus(100 % sequence similarity),Gluconobacter kondonii(99.9 %),Gluconobacter sphaericus(99.9 %) andGluconobacter kanchanaburiensis(99.5 %). DNA–DNA hybridization experiments on the type strains of these species revealed moderate DNA relatedness values (39–65 %). The three strains usedd-fructose,d-sorbitol,meso-erythritol, glycerol,l-sorbose, ethanol (weakly), sucrose and raffinose as a sole carbon source for growth (weak growth on the latter two carbon sources was obtained for strains LMG 27748Tand LMG 27882). The strains were unable to grow on glucose-yeast extract medium at 37 °C. They produced acid frommeso-erythritol and sucrose, but not from raffinose.d-Gluconic acid, 2-keto-d-gluconic acid and 5-keto-d-gluconic acid were produced fromd-glucose, but not 2,5-diketo-d-gluconic acid. These genotypic and phenotypic characteristics distinguish strains LMG 27748T, LMG 27749 and LMG 27882 from species of the genusGluconobacterwith validly published names and, therefore, we propose classifying them formally as representatives of a novel species,Gluconobacter cerevisiaesp. nov., with LMG 27748T( = DSM 27644T) as the type strain.
Morphometrics of a wild Asian elephant exhibiting disproportionate dwarfism
Authors: de Silva Shermin , Weerathunga U. S. , Kumara T. V.
Published: December 2013

Dwarfism is a condition characterized by shorter stature, at times accompanied by differential skeletal growth pro-portions relative to the species-typical physical conformation. Causes vary and well-documented in humans as well as certain mammalian species in captive or laboratory conditions, but rarely observed in the wild. Here we report on a single case of apparent dwarfism in a free-ranging adult male Asian elephant (Elephas maximus) in Sri Lanka, comparing physical dimensions to those of other males in the same population, males in other populations, and records in previous literature. The subject was found to have a shoulder height of approximately 195cm, is shorter than the average height of typical mature males, with a body length of 218cm. This ratio of body length to height deviates from what is typically observed, which is approximately 1:1. In absolute height the subject was similar to the attributes of a captive elephant documented in 1955 in Sri Lanka, also said to be a dwarf, however the two specimens differed in the relative proportions of height vs. body length. The subject also exhibits a slight elongation of the skull. We discuss how this phenotype compares to cases of dwarfism in other non-human animals.
Using Targeted Variants of Aequorin to Measure Ca2+ Levels in Intracellular Organelles
Authors: Granatiero Veronica , Patron Maria , Tosatto Anna , Merli Giulia , Rizzuto Rosario
Published: December 2013

Aequorin is a Ca2+-sensitive photoprotein isolated from the jellyfish Aequorea victoria. It is an ideal probe for measuring Ca2+ concentration ([Ca2+]) in intracellular organelles because it can be modified to include specific targeting sequences. On the binding of Ca2+ to three high-affinity sites in aequorin, an irreversible reaction occurs in which the prosthetic group coelenterazine is released and a photon is emitted. This protocol presents procedures for expressing, targeting, and reconstituting aequorin in intact and permeabilized mammalian cells and describes how to use this photoprotein to measure intracellular [Ca2+] in various subcellular compartments.
Purification of VDAC1 from Rat Liver Mitochondria
Authors: Ben-Hail Danya , Shoshan-Barmatz Varda
Published: December 2013

To make biophysical measurements of functions such as the pore-forming activity of mitochondrial voltage-dependent anion-selective channel protein 1 (VDAC1), it is first necessary to obtain a source of purified VDAC protein. In this protocol, we present a method for obtaining rat liver mitochondria as a source of VDAC1 and then describe two methods, one using a nonionic detergent and the other an ionic detergent, for purifying VDAC1 from the isolated mitochondria. This produces a source of VDAC1 proteins that are suitable for subsequent incorporation into artificially prepared phospholipid bilayers. Furthermore, the isolated mitochondria can be used for assaying the mitochondrial permeability transition pore (MPTP).
Of Model Pets and Cancer Models: An Introduction to Mouse Models of Cancer
Authors: Lunardi Andrea , Nardella Caterina , Clohessy John G. , Pandolfi Pier Paolo
Published: December 2013

The extraordinary endeavor to faithfully model human disorders in mice began in the early 1900s, and in the century since has delivered fundamental advances in our understanding and treatment of human disease. Although it could not be appreciated at the time, 99% of mouse protein-coding genes have an equivalent homolog in the human genome, despite the striking differences in appearance between mouse and man. This remarkable genetic similarity, together with our ability to finely engineer the murine genome, has made the mouse the ideal animal in which to model and analyze human biology and disease. Here we describe this remarkable shared journey between human and mouse, and envisage the next generation of mouse models, which will no doubt prove increasingly sophisticated and even more faithful to human disease. We also address the strategic use of mice in the fight against cancer, and the role they will play in the development of therapies to eradicate this disease.
Purification and Culture of Central Nervous System Endothelial Cells
Authors: Zhou Lu , Sohet Fabien , Daneman Richard
Published: December 2013

Blood vessels are critical for delivering oxygen and nutrients to all tissues in the body. This is especially important in the central nervous system, which is extremely sensitive to hypoxia and ischemia. Blood vessels are made of two main cell types: endothelial cells and mural cells. Endothelial cells form the walls of the blood vessels that generate a lumen through which blood flows. Mural cells are support cells thought to be involved in vessel contractility, vascular remodeling, and regulation of endothelial permeability. On large vessels, including arteries and veins, mural cells are termed vascular smooth muscle cells. On the small vessels of the capillary bed, they are called pericytes. Here, we provide a brief introduction to the methods for purification of endothelial cells, including an immunopanning method that we developed for isolating these cells from the rodent brain and optic nerve.
CELLULOSE SYNTHASE INTERACTIVE3 Regulates Cellulose Biosynthesis in Both a Microtubule-Dependent and Microtubule-Independent Manner inArabidopsi s
Authors: Lei Lei , Li Shundai , Du Juan , Bashline Logan , Gu Ying
Published: December 2013

Anisotropic plant cell growth depends on the coordination between the orientation of cortical microtubules and the orientation of nascent cellulose microfibrils. CELLULOSE SYNTHASE INTERACTIVE1 (CSI1) is a key scaffold protein that guides primary cellulose synthase complexes (CSCs) along cortical microtubules during cellulose biosynthesis. Here, we investigated the function of the CSI1-like protein, CSI3, in Arabidopsis thaliana. Similar to CSI1, CSI3 associates with primary CSCs in vitro, colocalizes with CSCs in vivo, and exhibits the same plasma membrane localization and bidirectional motility as CSI1. However, ProCSI1:GFP-CSI3 cannot complement the anisotropic cell growth defect in csi1 mutants, suggesting that CSI3 is not functionally equivalent to CSI1. Also, the colocalization ratio between CSI1 and CSI3 is low, which may suggest heterogeneity within the CSC population. csi1 csi3 double mutants showed an enhanced cell expansion defect as well as an additive reduction of CSC velocities, and CSI3 dynamics are dependent on CSI1 function. We propose that CSI3 is an important regulator of plant cellulose biosynthesis and plant anisotropic cell growth that modulates the velocity of CSCs in both a microtubule-dependent and microtubule-independent manner.
Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling
Authors: Miller J. Benjamin , Pratap Amitesh , Miyahara Akira , Zhou Liang , Bornemann Stephen , Morris Richard J. , Oldroyd Giles E.D.
Published: December 2013

The establishment of symbiotic associations in plants requires calcium oscillations that must be decoded to invoke downstream developmental programs. In animal systems, comparable calcium oscillations are decoded by calmodulin (CaM)–dependent protein kinases, but symbiotic signaling involves a calcium/CaM–dependent protein kinase (CCaMK) that is unique to plants. CCaMK differs from the animal CaM kinases by its dual ability to bind free calcium, via calcium binding EF-hand domains on the protein, or to bind calcium complexed with CaM, via a CaM binding domain. In this study, we dissect this dual regulation of CCaMK by calcium. We find that calcium binding to the EF-hand domains promotes autophosphorylation, which negatively regulates CCaMK by stabilizing the inactive state of the protein. By contrast, calcium-dependent CaM binding overrides the effects of autophosphorylation and activates the protein. The differential calcium binding affinities of the EF-hand domains compared with those of CaM suggest that CCaMK is maintained in the inactive state at basal calcium concentrations and is activated via CaM binding during calcium oscillations. This work provides a model for decoding calcium oscillations that uses differential calcium binding affinities to create a robust molecular switch that is responsive to calcium concentrations associated with both the basal state and with oscillations.
TheTrans-Acting Short Interfering RNA3 Pathway and NO APICAL MERISTEM Antagonistically Regulate Leaf Margin Development and Lateral Organ Separation, as Revealed by Analysis of anargonaute7/lobed leaflet1Mutant inMedicago truncatula
Authors: Zhou Chuanen , Han Lu , Fu Chunxiang , Wen Jiangqi , Cheng Xiaofei , Nakashima Jin , Ma Junying , Tang Yuhong , Tan Yang , Tadege Million , Mysore Kirankumar S. , Xia Guangmin , Wang Zeng-Yu
Published: December 2013

Leaf shape elaboration and organ separation are critical for plant morphogenesis. We characterized the developmental roles of LOBED LEAFLET1 by analyzing a recessive mutant in the model legume Medicago truncatula. An ortholog of Arabidopsis thaliana ARGONAUTE7 (AGO7), Mt-AGO7/LOBED LEAFLET1, is required for the biogenesis of a trans-acting short interfering RNA (ta-siRNA) to negatively regulate the expression of AUXIN RESPONSE FACTORs in M. truncatula. Loss of function in AGO7 results in pleiotropic phenotypes in different organs. The prominent phenotype of the ago7 mutant is lobed leaf margins and more widely spaced lateral organs, suggesting that the trans-acting siRNA3 (TAS3) pathway negatively regulates the formation of boundaries and the separation of lateral organs in M. truncatula. Genetic interaction analysis with the smooth leaf margin1 (slm1) mutant revealed that leaf margin formation is cooperatively regulated by the auxin/SLM1 (ortholog of Arabidopsis PIN-FORMED1) module, which influences the initiation of leaf margin teeth, and the TAS3 ta-siRNA pathway, which determines the degree of margin indentation. Further investigations showed that the TAS3 ta-siRNA pathway and NO APICAL MERISTEM (ortholog of Arabidopsis CUP-SHAPED COTYLEDON) antagonistically regulate both leaf margin development and lateral organ separation, and the regulation is partially dependent on the auxin/SLM1 module.
ArabidopsisPhosphoglycerate Dehydrogenase1 of the Phosphoserine Pathway Is Essential for Development and Required for Ammonium Assimilation and Tryptophan Biosynthesis
Authors: Benstein Ruben Maximilian , Ludewig Katja , Wulfert Sabine , Wittek Sebastian , Gigolashvili Tamara , Frerigmann Henning , Gierth Markus , Flügge Ulf-Ingo , Krueger Stephan
Published: December 2013

In plants, two independent serine biosynthetic pathways, the photorespiratory and glycolytic phosphoserine (PS) pathways, have been postulated. Although the photorespiratory pathway is well characterized, little information is available on the function of the PS pathway in plants. Here, we present a detailed characterization of phosphoglycerate dehydrogenases (PGDHs) as components of the PS pathway in Arabidopsis thaliana. All PGDHs localize to plastids and possess similar kinetic properties, but they differ with respect to their sensitivity to serine feedback inhibition. Furthermore, analysis of pgdh1 and phosphoserine phosphatase mutants revealed an embryo-lethal phenotype and PGDH1-silenced lines were inhibited in growth. Metabolic analyses of PGDH1-silenced lines grown under ambient and high CO2 conditions indicate a direct link between PS biosynthesis and ammonium assimilation. In addition, we obtained several lines of evidence for an interconnection between PS and tryptophan biosynthesis, because the expression of PGDH1 and PHOSPHOSERINE AMINOTRANSFERASE1 is regulated by MYB51 and MYB34, two activators of tryptophan biosynthesis. Moreover, the concentration of tryptophan-derived glucosinolates and auxin were reduced in PGDH1-silenced plants. In essence, our results provide evidence for a vital function of PS biosynthesis for plant development and metabolism.
Genome-Wide Analysis of Branched-Chain Amino Acid Levels inArabidopsisSeeds
Authors: Angelovici Ruthie , Lipka Alexander E. , Deason Nicholas , Gonzalez-Jorge Sabrina , Lin Haining , Cepela Jason , Buell Robin , Gore Michael A. , DellaPenna Dean
Published: December 2013

Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two BRANCHED-CHAIN AMINO ACID TRANSFERASES, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds.
CAROTENOID CLEAVAGE DIOXYGENASE4Is a Negative Regulator of β-Carotene Content inArabidopsisSeeds
Authors: Gonzalez-Jorge Sabrina , Ha Sun-Hwa , Magallanes-Lundback Maria , Gilliland Laura Ullrich , Zhou Ailing , Lipka Alexander E. , Nguyen Yen-Nhu , Angelovici Ruthie , Lin Haining , Cepela Jason , Little Holly , Buell C. Robin , Gore Michael A. , DellaPenna Dean
Published: December 2013

Experimental approaches targeting carotenoid biosynthetic enzymes have successfully increased the seed β-carotene content of crops. However, linkage analysis of seed carotenoids in Arabidopsis thaliana recombinant inbred populations showed that only 21% of quantitative trait loci, including those for β-carotene, encode carotenoid biosynthetic enzymes in their intervals. Thus, numerous loci remain uncharacterized and underutilized in biofortification approaches. Linkage mapping and genome-wide association studies of Arabidopsis seed carotenoids identified CAROTENOID CLEAVAGE DIOXYGENASE4 (CCD4) as a major negative regulator of seed carotenoid content, especially β-carotene. Loss of CCD4 function did not affect carotenoid homeostasis during seed development but greatly reduced carotenoid degradation during seed desiccation, increasing β-carotene content 8.4-fold relative to the wild type. Allelic complementation of a ccd4 null mutant demonstrated that single-nucleotide polymorphisms and insertions and deletions at the locus affect dry seed carotenoid content, due at least partly to differences in CCD4 expression. CCD4 also plays a major role in carotenoid turnover during dark-induced leaf senescence, with β-carotene accumulation again most strongly affected in the ccd4 mutant. These results demonstrate that CCD4 plays a major role in β-carotene degradation in drying seeds and senescing leaves and suggest that CCD4 orthologs would be promising targets for stabilizing and increasing the level of provitamin A carotenoids in seeds of major food crops.
Abscisic Acid–Responsive Guard Cell Metabolomes of Arabidopsis Wild-Type and gpa1 G-Protein Mutants
Authors: Jin Xiaofen , Wang Rui-Sheng , Zhu Mengmeng , Jeon Byeong Wook , Albert Reka , Chen Sixue , Assmann Sarah M.
Published: December 2013

Individual metabolites have been implicated in abscisic acid (ABA) signaling in guard cells, but a metabolite profile of this specialized cell type is lacking. We used liquid chromatography–multiple reaction monitoring mass spectrometry for targeted analysis of 85 signaling-related metabolites in Arabidopsis thaliana guard cell protoplasts over a time course of ABA treatment. The analysis utilized ∼350 million guard cell protoplasts from ∼30,000 plants of the Arabidopsis Columbia accession (Col) wild type and the heterotrimeric G-protein α subunit mutant, gpa1, which has ABA-hyposensitive stomata. These metabolomes revealed coordinated regulation of signaling metabolites in unrelated biochemical pathways. Metabolites clustered into different temporal modules in Col versus gpa1, with fewer metabolites showing ABA-altered profiles in gpa1. Ca2+-mobilizing agents sphingosine-1-phosphate and cyclic adenosine diphosphate ribose exhibited weaker ABA-stimulated increases in gpa1. Hormone metabolites were responsive to ABA, with generally greater responsiveness in Col than in gpa1. Most hormones also showed different ABA responses in guard cell versus mesophyll cell metabolomes. These findings suggest that ABA functions upstream to regulate other hormones, and are also consistent with G proteins modulating multiple hormonal signaling pathways. In particular, indole-3-acetic acid levels declined after ABA treatment in Col but not gpa1 guard cells. Consistent with this observation, the auxin antagonist α-(phenyl ethyl-2-one)-indole-3-acetic acid enhanced ABA-regulated stomatal movement and restored partial ABA sensitivity to gpa1.
Structural basis for adaptation of lactobacilli to gastrointestinal mucus
Authors: Etzold Sabrina , Kober Olivia I. , MacKenzie Donald A. , Tailford Louise E. , Gunning A. Patrick , Walshaw John , Hemmings Andrew M. , Juge Nathalie
Published: December 2013

The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the underpinning mechanisms of these interactions are not understood. Here, we provide structural and functional insights into the canonical mucus‐binding protein (MUB), a multi‐repeat cell‐surface adhesin found in Lactobacillus inhabitants of the GI tract. X‐ray crystallography together with small‐angle X‐ray scattering demonstrated a ‘beads on a string’ arrangement of repeats, generating 174 nm long protein fibrils, as shown by atomic force microscopy. Each repeat consists of tandemly arranged Ig‐ and mucin‐binding protein (MucBP) modules. The binding of full‐length MUB was confined to mucus via multiple interactions involving terminal sialylated mucin glycans. While individual MUB domains showed structural similarity to fimbrial proteins from Gram‐positive pathogens, the particular organization of MUB provides a structural explanation for the mechanisms in which lactobacilli have adapted to their host niche by maximizing interactions with the mucus receptors, potentiating the retention of bacteria within the mucus layer. Together, this study reveals functional and structural features which may affect tropism of microbes across mucus and along the GI tract, providing unique insights into the mechanisms adopted by commensals and probiotics to adapt to the mucosal environment.
Estate management and institutional constraints in pre‐industrialEngland: the ecclesiastical estates ofDurham, c. 1400–1640
Authors: BROWN A. T.
Published: December 2013

This article explores how far estate management and institutional constraints help to explain the transformations of rural society inEngland from the fourteenth to the seventeenth centuries. The monks ofDurhamCathedralPriory and the bishops ofDurham faced many of the same exogenous pressures in the fourteenth and fifteenth centuries but they responded differently to these challenges. By the seventeenth century all of the dean and chapter's lands were consolidated holdings on 21‐year leases, whereas a confused mixture of copyhold and leasehold land had developed on the bishops' estate. This had a significant impact upon the challenges and opportunities facing their tenants. Institutional constraints were often crucial factors in the transformation of the English countryside: these two neighbouring ecclesiastical estates faced broadly the same problems and yet the composition of their estates diverged significantly across this period, having a profound effect not only on levels of rent, but also on the tenure of holdings and ultimately their relative size; three of the most important factors in the formation of agrarian capitalism. This article also argues that how rural society adapted to the fifteenth‐century recession greatly affected the ability of their sixteenth‐century counterparts to respond to inflation.
Risk of maternal and neonatal complications in subsequent pregnancy after planned caesarean section in a first birth, compared with emergency caesarean section: a nationwide comparative cohort study
Authors: Kok N , Ruiter L , Hof M , Ravelli A , Mol BW , Pajkrt E , Kazemier B
Published: December 2013

Objective

To compare the difference in risks of neonatal and maternal complications, including uterine rupture, in a second birth following a planned caesarean section versus emergency caesarean section in the first birth.

Design

Prospective cohort study.

Setting

Population‐based cohort in the Netherlands.

Population

Linked data set of outcomes for term caesarean section in a first birth followed by a consecutive delivery.

Methods

We conducted a prospective cohort analysis using data from the Dutch Perinatal Registry. We included primiparous women who gave birth to term singleton infants through planned or emergency caesarean from January 2000 through December 2007, and who had a second singleton delivery during the same period (n = 41 109). Odds ratios and adjusted odds ratios were calculated.

Main outcome measures

Maternal and neonatal complications, specifically uterine rupture, in second births associated with planned and emergency caesareans in the first birth.

Results

Women with a history of a planned caesarean section in the first birth (n = 11 445) had a 0.24% risk for uterine rupture, compared with a 0.16% risk for women with a history of emergency caesarean section (n = 29 664; aOR 1.4, 95% CI 0.8–2.4). In multivariate logistic regression, women with planned caesareans in a first birth had a significantly increased risk of stillbirth (aOR 1.5, 95% CI 1.0–2.2) and postpartum haemorrhage (aOR 1.1, 95% CI 1.0–1.2) in second births, compared with women with emergency caesareans in the first birth.

Conclusions

We found a moderately increased risk of postpartum haemorrhage and a small to moderately increased risk of uterine rupture and stillbirth as a long‐term effect of prior planned caesarean delivery on second births.
Gross Lease Premiums
Authors: Wiley Jonathan A.
Published: December 2013

The premium for the gross lease relative to the net lease is estimated using a large sample of leasing data for office properties in seven U.S. markets during 2011. After matching gross leases with net leases on propensity scores, analysis for the matched sample of 9,860 lease observations reports the gross lease premium estimated at 12.9%. The relative premium of a gross lease responds to property‐specific characteristics, including tenant size, property size and property class, and is increasing with operating expense expectations. Gross lease premiums are increased in low‐vacancy markets. The findings support theoretical predictions from the existing literature.
Sustained improvement in health‐related quality of life measures in patients with inflammatory bowel disease receiving prolonged anti‐tumor necrosis factor therapy
Authors: Sherman Michael , Tsynman Donald N , Kim Albert , Arora Jyoti , Pietras Timothy , Messing Susan , St Hilaire Lydia , Yoon Sonia , Decross Arthur , Shah Ashok , Saubermann Lawrence
Published: December 2013

Objective

The aim of this study was to determine whether the effects of prolonged therapy (≥1 year) with anti‐tumor necrosis factor (TNF) agents were sustained on the health‐related quality of life (HRQoL) in patients with inflammatory bowel disease (IBD).

Methods

A cross‐sectional survey of patients with IBD who were treated with anti‐TNF agents was performed. Results of the validated HRQoL measures (inflammatory bowel disease questionnaire [IBDQ], EuroQoL‐5 dimensions [EQ‐5D], health status visual analogue scale [VAS] and the Zung self‐rating depression scale) were recorded and compared between patients treated with anti‐TNF agents for <1 year and ≥1 year.

Results

A total of 41 patients were finally enrolled in the study. Among them, 11 (26.8%) had received anti‐TNF therapy for less than one year with a median duration of 7 months (range 3–11 months), while the other 30 (73.2%) had been treated for ≥1 year with a median duration of 42 months (range 12–104 months). Crohn's disease was the most common type in both groups. None of the mean IBDQ, EQ‐5D and EQ‐5D plus VAS, or Zung self‐rating depression scale scores differed significantly between the two groups of patients.

Conclusions

Improvements in HRQoL for IBD patients on anti‐TNF therapy were sustained for longer than one year. HRQoL measures for IBD patients treated with anti‐TNF therapy for <1 year do not differ significantly from those treated for ≥1 year, but a trend towards improved HRQoL measures with prolonged therapy can be obtained.
Mutation discovery forMendelian traits in non‐laboratory animals: a review of achievements up to 2012
Authors: Nicholas Frank W. , Hobbs Matthew
Published: December 2013

Within two years of the re‐discovery ofMendelism,Bateson andSaunders had described six traits in non‐laboratory animals (five in chickens and one in cattle) that show single‐locus (Mendelian) inheritance. In the ensuing decades, much progress was made in documenting an ever‐increasing number of such traits. In 1987 came the first discovery of a causal mutation for aMendelian trait in non‐laboratory animals: a non‐sense mutation in thethyroglobulingene (TG), causing familial goitre in cattle. In the years that followed, the rate of discovery of causal mutations increased, aided mightily by the creation of genome‐wide microsatellite maps in the 1990s and even more mightily by genome assemblies and single‐nucleotide polymorphism (SNP) chips in the 2000s. With sequencing costs decreasing rapidly, by 2012 causal mutations were being discovered in non‐laboratory animals at a rate of more than one per week. By the end of 2012, the total number of Mendelian traits in non‐laboratory animals with known causal mutations had reached 499, which was half the number of published single‐locus (Mendelian) traits in those species. The distribution of types of mutations documented in non‐laboratory animals is fairly similar to that in humans, with almost half being missense or non‐sense mutations. The ratio of missense to non‐sense mutations in non‐laboratory animals to the end of 2012 was 193:78. The fraction of non‐sense mutations (78/271 = 0.29) was not very different from the fraction of non‐stop codons that are just one base substitution away from a stop codon (21/61 = 0.34).
Evaluation of driving confidence in post‐stroke older drivers in South Australia
Authors: McNamara Annabel , Ratcliffe Julie , George Stacey
Published: December 2013

Aim

To determine whether self‐perceived driving confidence levels are lower in the post‐stroke driving population than their aged‐matched non‐stroke driving peers. A lack of driving confidence has been linked to self‐limiting driving behaviours.

Method

Adelaide Driving Self‐Efficacy Scale (ADSES) scores were collected for a stroke population who returned to driving (N = 40, 25 men) with a mean age of 65 (SD = 12.17) years and an older non‐stroke driver population (N = 114, 56 men) with a mean age of 72 (SD = 5.2) years.

Results

The non‐stroke and stroke groups showed no significant differences in ADSES scores (t(153) = 0.32, P = 0.58).

Conclusion

Stroke survivors who return to driving have no differences in their driving confidence to their aged‐matched non‐stroke driving peers. Timely recognition of lack of driving confidence might allow for appropriately targeted intervention strategies and prevent premature driving cessation.
Percutaneous Penetration ‐ Methodological Considerations
Authors: Holmgaard Rikke , Benfeldt Eva , Nielsen Jesper B.
Published: December 2013

Studies on percutaneous penetration are needed to assess the hazards after unintended occupational skin exposures to industrial products as well as the efficacy after intended consumer exposure to topically applied medicinal or cosmetic products. During recent decades, a number of methods have been developed to replace methods involving experimental animals. The results obtained from these methods are decided not only by the chemical or product tested, but to a significant degree also by the experimental set‐up and decisions made by the investigator during the planning phase. The present MiniReview discusses some of the existing and well‐known experimental in vitro and in vivo methods for studies of percutaneous penetration together with some more recent and promising methods. After this, some considerations and recommendations about advantages and limitations of the different methods and their relevance for the prediction of percutaneous penetration are given. Which method to prefer will depend on the product to be tested and the question asked. Regulatory guidelines exist for studies on percutaneous penetration, but researchers as well as regulatory bodies need to pay specific attention to the vehicles and solvents used in donor and sampling fluids so that it reflects in‐use conditions as closely as possible. Based on available experimental data, mathematical models have been developed to aid predictions of skin penetration. The authors question the general use of the present mathematical models in hazard assessment, as they seem to ignore outliers among chemicals as well as the heterogeneity of skin barrier properties and skin conditions within the exposed populations.
Implicit Decals: Interactive Editing of Repetitive Patterns on Surfaces
Authors: de Groot Erwin , Wyvill Brian , Barthe Loïc , Nasri Ahmad , Lalonde Paul
Published: December 2013

Texture mapping is an essential component for creating 3D models and is widely used in both the game and the movie industries. Creating texture maps has always been a complex task and existing methods carefully balance flexibility with ease of use. One difficulty in using texturing is the repeated placement of individual textures over larger areas. In this paper, we propose a method which uses decals to place images onto a model. Our method allows the decals to compete for space and to deform as they are being pushed by other decals. A spherical field function is used to determine the position and the size of each decal and the deformation applied to fit the decals. The decals may span multiple objects with heterogeneous representations. Our method does not require an explicit parametrization of the model. As such, varieties of patterns, including repeated patterns like rocks, tiles and scales can be mapped. We have implemented the method using the GPU where placement, size and orientation of thousands of decals are manipulated in real time.
Projection Mapping on Arbitrary Cubic Cell Complexes
Authors: Apaza‐Agüero K. , Silva L. , Bellon O. R. P. 
Published: December 2013

This work presents a new representation used as a rendering primitive of surfaces. Our representation is defined by an arbitrary cubic cell complex: a projection‐based parameterization domain for surfaces where geometry and appearance information are stored as tile textures. This representation is used by our ray casting rendering algorithm called projection mapping, which can be used for rendering geometry and appearance details of surfaces from arbitrary viewpoints. The projection mapping algorithm uses a fragment shader based on linear and binary searches of the relief mapping algorithm. Instead of traditionally rendering the surface, only front faces of our rendering primitive (our arbitrary cubic cell complex) are drawn, and geometry and appearance details of the surface are rendered back by using projection mapping. Alternatively, another method is proposed for mapping appearance information on complex surfaces using our arbitrary cubic cell complexes. In this case, instead of reconstructing the geometry as in projection mapping, the original mesh of a surface is directly passed to the rendering algorithm. This algorithm is applied in the texture mapping of cultural heritage sculptures.
Implications of Macroalgal Isolation by Distance for Networks of Marine Protected Areas
Authors: DURRANT HALLEY M. S. , BURRIDGE CHRISTOPHER P. , KELAHER BRENDAN P. , BARRETT NEVILLE S. , EDGAR GRAHAM J. , COLEMAN MELINDA A.
Published: December 2013

The global extent of macroalgal forests is declining, greatly affecting marine biodiversity at broad scales through the effects macroalgae have on ecosystem processes, habitat provision, and food web support. Networks of marine protected areas comprise one potential tool that may safeguard gene flow among macroalgal populations in the face of increasing population fragmentation caused by pollution, habitat modification, climate change, algal harvesting, trophic cascades, and other anthropogenic stressors. Optimal design of protected area networks requires knowledge of effective dispersal distances for a range of macroalgae. We conducted a global meta‐analysis based on data in the published literature to determine the generality of relation between genetic differentiation and geographic distance among macroalgal populations. We also examined whether spatial genetic variation differed significantly with respect to higher taxon, life history, and habitat characteristics. We found clear evidence of population isolation by distance across a multitude of macroalgal species. Genetic and geographic distance were positively correlated across 49 studies; a modal distance of 50–100 km maintained FST < 0.2. This relation was consistent for all algal divisions, life cycles, habitats, and molecular marker classes investigated. Incorporating knowledge of the spatial scales of gene flow into the design of marine protected area networks will help moderate anthropogenic increases in population isolation and inbreeding and contribute to the resilience of macroalgal forests.

Implicaciones del Aislamiento por Distancia de Macroalgas para Redes de Áreas Marinas Protegidas
Selection of Multiple Umbrella Species for Functional and Taxonomic Diversity to Represent Urban Biodiversity
Authors: SATTLER T. , PEZZATTI G. B. , NOBIS M. P. , OBRIST M. K. , ROTH T. , MORETTI M.
Published: December 2013

Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty‐one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within‐ and across‐taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity.

Selección de Múltiples Especies Paraguas para la Diversidad Funcional y Taxonómica para Representar la Biodiversidad Urbana