bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Authors: King David C. , Taylor James , Zhang Ying , Cheng Yong , Lawson Heather A. , Martin Joel ,   ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis, Chiaromonte Francesca , Miller Webb , Hardison Ross C.
Published: June 2007

Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity of evolutionary histories can be captured, at least in part, by the suite of available comparative genomics tools, especially after correction for regional differences in the neutral substitution rate. Putative transcriptional regulatory regions show alignability in different clades, and the genes associated with them are enriched for distinct functions. Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation.
Transcription factor binding and modified histones in human bidirectional promoters
Authors: Lin Jane M. , Collins Patrick J. , Trinklein Nathan D. , Fu Yutao , Xi Hualin , Myers Richard M. , Weng Zhiping
Published: June 2007

Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of ∼11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcription factors, and modified histones as overrepresented, shared, or underrepresented in bidirectional promoters with respect to unidirectional promoters. We found that a small set of motifs, including GABPA, MYC, E2F1, E2F4, NRF-1, CCAAT, YY1, and ACTACAnnTCC are overrepresented in bidirectional promoters, while the majority (73%) of known vertebrate motifs are underrepresented. We performed chromatin-immunoprecipitation (ChIP), followed by quantitative PCR for GABPA, on 118 regions in the human genome and showed that it binds to bidirectional promoters more frequently than unidirectional promoters, and its position-specific scoring matrix is highly predictive of binding. Signatures of active transcription, such as occupancy of RNA polymerase II and the modified histones H3K4me2, H3K4me3, and H3ac, are overrepresented in regions around bidirectional promoters, suggesting that a higher fraction of divergent genes are transcribed in a given cell than the fraction of other genes. Accordingly, analysis of whole-genome microarray data indicates that 68% of divergent genes are transcribed compared with 44% of all human genes. By combining the analysis of publicly available ENCODE data and a detailed study of GABPA, we survey bidirectional promoters with breadth and depth, leading to biological insights concerning their motif composition and bidirectional regulatory mode.
Structured RNAs in the ENCODE selected regions of the human genome
Authors: Washietl Stefan , Pedersen Jakob S. , Korbel Jan O. , Stocsits Claudia , Gruber Andreas R. , Hackermüller Jörg , Hertel Jana , Lindemeyer Manja , Reiche Kristin , Tanzer Andrea , Ucla Catherine , Wyss Carine , Antonarakis Stylianos E. , Denoeud France , Lagarde Julien , Drenkow Jorg , Kapranov Philipp , Gingeras Thomas R. , Guigó Roderic , Snyder Michael , Gerstein Mark B. , Reymond Alexandre , Hofacker Ivo L. , Stadler Peter F.
Published: June 2007

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic–stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to ∼2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3′-UTRs. While we estimate a significant false discovery rate of ∼50%–70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
Authors: Denoeud France , Kapranov Philipp , Ucla Catherine , Frankish Adam , Castelo Robert , Drenkow Jorg , Lagarde Julien , Alioto Tyler , Manzano Caroline , Chrast Jacqueline , Dike Sujit , Wyss Carine , Henrichsen Charlotte N. , Holroyd Nancy , Dickson Mark C. , Taylor Ruth , Hance Zahra , Foissac Sylvain , Myers Richard M. , Rogers Jane , Hubbard Tim , Harrow Jennifer , Guigó Roderic , Gingeras Thomas R. , Antonarakis Stylianos E. , Reymond Alexandre
Published: June 2007

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5′ rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5′ distal to the annotated 5′ terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be “noncoding,” ultimately relating to the identification of disease-related sequence alterations.
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Authors: Rozowsky Joel S. , Newburger Daniel , Sayward Fred , Wu Jiaqian , Jordan Greg , Korbel Jan O. , Nagalakshmi Ugrappa , Yang Jin , Zheng Deyou , Guigó Roderic , Gingeras Thomas R. , Weissman Sherman , Miller Perry , Snyder Michael , Gerstein Mark B.
Published: June 2007

For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount of “unannotated transcription.” We use a number of disparate features to classify the 6988 novel TARs—array expression profiles across cell lines and conditions, sequence composition, phylogenetic profiles (presence/absence of syntenic conservation across 17 species), and locations relative to genes. In the classification, we first filter out TARs with unusual sequence composition and those likely resulting from cross-hybridization. We then associate some of those remaining with proximal exons having correlated expression profiles. Finally, we cluster unclassified TARs into putative novel loci, based on similar expression and phylogenetic profiles. To encapsulate our classification, we construct a Database of Active Regions and Tools (DART.gersteinlab.org). DART has special facilities for rapidly handling and comparing many sets of TARs and their heterogeneous features, synchronizing across builds, and interfacing with other resources. Overall, we find that ∼14% of the novel TARs can be associated with known genes, while ∼21% can be clustered into ∼200 novel loci. We observe that TARs associated with genes are enriched in the potential to form structural RNAs and many novel TAR clusters are associated with nearby promoters. To benchmark our classification, we design a set of experiments for testing the connectivity of novel TARs. Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously.
The landscape of histone modifications across 1% of the human genome in five human cell lines
Authors: Koch Christoph M. , Andrews Robert M. , Flicek Paul , Dillon Shane C. , Karaöz Ulaş , Clelland Gayle K. , Wilcox Sarah , Beare David M. , Fowler Joanna C. , Couttet Phillippe , James Keith D. , Lefebvre Gregory C. , Bruce Alexander W. , Dovey Oliver M. , Ellis Peter D. , Dhami Pawandeep , Langford Cordelia F. , Weng Zhiping , Birney Ewan , Carter Nigel P. , Vetrie David , Dunham Ian
Published: June 2007

We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including the ENCODE Consortium common cell lines GM06990 (lymphoblastoid) and HeLa-S3, as well as K562, HFL-1, and MOLT4, we identified clear patterns of histone modification profiles with respect to genomic features. H3K4me3, H3K4me2, and H3ac modifications are tightly associated with the transcriptional start sites (TSSs) of genes, while H3K4me1 and H4ac have more widespread distributions. TSSs reveal characteristic patterns of both types of modification present and the position relative to TSSs. These patterns differ between active and inactive genes and in particular the state of H3K4me3 and H3ac modifications is highly predictive of gene activity. Away from TSSs, modification sites are enriched in H3K4me1 and relatively depleted in H3K4me3 and H3ac. Comparison between cell lines identified differences in the histone modification profiles associated with transcriptional differences between the cell lines. These results provide an overview of the functional relationship among histone modifications and gene expression in human cells.
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
Authors: Kim Jong Hyun , Waterman Michael S. , Li Lei M.
Published: June 2007

One of the main goals in genome sequencing projects is to determine a haploid consensus sequence even when clone libraries are constructed from homologous chromosomes. However, it has been noticed that haplotypes can be inferred from genome assemblies by investigating phase conservation in sequenced reads. In this study, we seek to infer haplotypes, a diploid consensus sequence, from the genome assembly of an organism, Ciona intestinalis. The Ciona intestinalis genome is an ideal resource from which haplotypes can be inferred because of the high polymorphism rate (1.2%). The haplotype estimation scheme consists of polymorphism detection and phase estimation. The core step of our method is a Gibbs sampling procedure. The mate-pair information from two-end sequenced clone inserts is exploited to provide long-range continuity. We estimate the polymorphism rate of Ciona intestinalis to be 1.2% and 1.5%, according to two different polymorphism counting schemes. The distribution of heterozygosity number is well fit by a compound Poisson distribution. The N50 length of haplotype segments is 37.9 kb in our assembly, while the N50 scaffold length of the Ciona intestinalis assembly is 190 kb. We also infer diploid gene sequences from haplotype segments. According to our reconstruction, 85.4% of predicted gene sequences are continuously covered by single haplotype segments. Our results indicate 97% accuracy in haplotype estimation, based on a simulated data set. We conduct a comparative analysis with Ciona savignyi, and discover interesting patterns of conserved DNA elements in chordates.
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
Authors: Ruan Yijun , Ooi Hong Sain , Choo Siew Woh , Chiu Kuo Ping , Zhao Xiao Dong , Srinivasan K.G. , Yao Fei , Choo Chiou Yu , Liu Jun , Ariyaratne Pramila , Bin Wilson G.W. , Kuznetsov Vladimir A. , Shahab Atif , Sung Wing-Kin , Bourque Guillaume , Palanisamy Nallasivam , Wei Chia-Lin
Published: June 2007

Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5′ and 3′ transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.
Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes
Authors: Tsuritani Katsuki , Irie Takuma , Yamashita Riu , Sakakibara Yuta , Wakaguri Hiroyuki , Kanai Akinori , Mizushima-Sugano Junko , Sugano Sumio , Nakai Kenta , Suzuki Yutaka
Published: June 2007

Although recent studies have revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also demonstrated that roughly half of the human RefSeq genes examined contain putative alternative promoters (PAPs). Here we report large-scale comparative studies of PAPs between human and mouse counterpart genes. Detailed sequence comparison of the 17,245 putative promoter regions (PPRs) in 5463 PAP-containing human genes revealed that PPRs in only a minor fraction of genes (807 genes) showed clear evolutionary conservation as one or more pairs. Also, we found that there were substantial qualitative differences between conserved and non-conserved PPRs, with the latter class being AT-rich PPRs of relative minor usage, enriched in repetitive elements and sometimes producing transcripts that encode small or no proteins. Systematic luciferase assays of these PPRs revealed that both classes of PPRs did have promoter activity, but that their strength ranges were significantly different. Furthermore, we demonstrate that these characteristic features of the non-conserved PPRs are shared with the PPRs of previously discovered putative non-protein coding transcripts. Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution.
Identification of higher-order functional domains in the human ENCODE regions
Authors: Thurman Robert E. , Day Nathan , Noble William S. , Stamatoyannopoulos John A.
Published: June 2007

It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. We hypothesized that diverse experimental data types generated by The ENCODE Project Consortium could be combined to delineate active and quiescent or repressed functional domains and thereby illuminate the higher-order functional architecture of the genome. To address this, we coupled wavelet analysis with hidden Markov models for unbiased discovery of “domain-level” behavior in high-resolution functional genomic data, including activating and repressive histone modifications, RNA output, and DNA replication timing. We find that higher-order patterns in these data types are largely concordant and may be analyzed collectively in the context of HeLa cells to delineate 53 active and 62 repressed functional domains within the ENCODE regions. Active domains comprise ∼44% of the ENCODE regions but contain ∼75%–80% of annotated genes, transcripts, and CpG islands. Repressed domains are enriched in certain classes of repetitive elements and, surprisingly, in evolutionarily conserved nonexonic sequences. The functional domain structure of the ENCODE regions appears to be largely stable across different cell types. Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture.
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
Authors: Faux Noel G. , Huttley Gavin A. , Mahmood Khalid , Webb Geoffrey I. , Garcia de la Banda Maria , Whisstock James C.
Published: June 2007

Over 3% of human proteins contain single amino acid repeats (repeat-containing proteins, RCPs). Many repeats (homopeptides) localize to important proteins involved in transcription, and the expansion of certain repeats, in particular poly-Q and poly-A tracts, can also lead to the development of neurological diseases. Previous studies have suggested that the homopeptide makeup is a result of the presence of G+C-rich tracts in the encoding genes and that expansion occurs via replication slippage. Here, we have performed a large-scale genomic analysis of the variation of the genes encoding RCPs in 13 species and present these data in an online database (http://repeats.med.monash.edu.au/genetic_analysis/). This resource allows rapid comparison and analysis of RCPs, homopeptides, and their underlying genetic tracts across the eukaryotic species considered. We report three major findings. First, there is a bias for a small subset of codons being reiterated within homopeptides, and there is no G+C or A+T bias relative to the organism’s transcriptome. Second, single base pair transversions from the homocodon are unusually common and may represent a mechanism of reducing the rate of homopeptide mutations. Third, homopeptides that are conserved across different species lie within regions that are under stronger purifying selection in contrast to nonconserved homopeptides.
What is a gene, post-ENCODE? History and updated definition
Authors: Gerstein Mark B. , Bruce Can , Rozowsky Joel S. , Zheng Deyou , Du Jiang , Korbel Jan O. , Emanuelsson Olof , Zhang Zhengdong D. , Weissman Sherman , Snyder Michael
Published: June 2007

While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.
IRECS: A new algorithm for the selection of most probable ensembles of side‐chain conformations in protein models
Authors: Hartmann Christoph , Antes Iris , Lengauer Thomas
Published: June 2007

We introduce a new algorithm, IRECS (Iterative REduction of Conformational Space), for identifying ensembles of most probable side‐chain conformations for homology modeling. On the basis of a given rotamer library, IRECS ranks all side‐chain rotamers of a protein according to the probability with which each side chain adopts the respective rotamer conformation. This ranking enables the user to select small rotamer sets that are most likely to contain a near‐native rotamer for each side chain. IRECS can therefore act as a fast heuristic alternative to the Dead‐End‐Elimination algorithm (DEE). In contrast to DEE, IRECS allows for the selection of rotamer subsets of arbitrary size, thus being able to define structure ensembles for a protein. We show that the selection of more than one rotamer per side chain is generally meaningful, since the selected rotamers represent the conformational space of flexible side chains. A knowledge‐based statistical potential ROTA was constructed for the IRECS algorithm. The potential was optimized to discriminate between side‐chain conformations of native and rotameric decoys of protein structures. By restricting the number of rotamers per side chain to one, IRECS can optimize side chains for a single conformation model. The average accuracy of IRECS for the χ1 and χ1 + 2 dihedral angles amounts to 84.7% and 71.6%, respectively, using a 40° cutoff. When we compared IRECS with SCWRL and SCAP, the performance of IRECS was comparable to that of both methods. IRECS and the ROTA potential are available for download from the URL http://irecs.bioinf.mpi‐inf.mpg.de.
Solvent‐induced differentiation of protein backbone hydrogen bonds in calmodulin
Authors: Juranić Nenad , Atanasova Elena , Streiff John H. , Macura Slobodan , Prendergast Franklyn G.
Published: June 2007

In apo and holoCaM, almost half of the hydrogen bonds (H‐bonds) at the protein backbone expected from the corresponding NMR or X‐ray structures were not detected by h3 JNC′ couplings. The paucity of the h3 JNC′ couplings was considered in terms of dynamic features of these structures. We examined a set of seven proteins and found that protein‐backbone H‐bonds form two groups according to the h3 JNC′ couplings measured in solution. H‐bonds that have h3 JNC′ couplings above the threshold of 0.2 Hz show distance/angle correlation among the H‐bond geometrical parameters, and appear to be supported by the backbone dynamics in solution. The other H‐bonds have no such correlation; they populate the water‐exposed and flexible regions of proteins, including many of the CaM helices. The observed differentiation in a dynamical behavior of backbone H‐bonds in apo and holoCaM appears to be related to protein functions.
o‐Nitrotyrosine andp‐iodophenylalanine as spectroscopic probes for structural characterization of SH3 complexes
Authors: De Filippis Vincenzo , Draghi Annamaria , Frasson Roberta , Grandi Claudio , Musi Valeria , Fontana Angelo , Pastore Annalisa
Published: June 2007

High‐throughput screening of protein–protein and protein–peptide interactions is of high interest both for biotechnological and pharmacological applications. Here, we propose the use of the noncoded amino acidso‐nitrotyrosine andp‐iodophenylalanine as spectroscopic probes in combination with circular dichroism and fluorescence quenching techniques (i.e., collisional quenching and resonance energy transfer) as a means to determine the peptide orientation in complexes with SH3 domains. Proline‐rich peptides bind SH3 modules in two alternative orientations, according to their sequence motifs, classified as class I and class II. The method was tested on an SH3 domain from a yeast myosin that is known to recognize specifically class I peptides. We exploited the fluorescence quenching effects induced byo‐nitrotyrosine andp‐iodophenylalanine on the fluorescence signal of a highly conserved Trp residue, which is the signature of SH3 domains and sits directly in the binding pocket. In particular, we studied how the introduction of the two probes at different positions of the peptide sequence (i.e., N‐terminally or C‐terminally) influences the spectroscopic properties of the complex. This approach provides clear‐cut evidence of the orientation of the binding peptide in the SH3 pocket. The chemical strategy outlined here can be easily extended to other protein modules, known to bind linear sequence motifs in a highly directional manner.
The three‐dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans‐aconitate: Insights into its biological function
Authors: Garvey Graeme S. , Rocco Christopher J. , Escalante‐Semerena Jorge C. , Rayment Ivan
Published: June 2007

In bacteria, the dehydration of 2‐methylcitrate to yield 2‐methylaconitate in the 2‐methylcitric acid cycle is catalyzed by a cofactor‐less (PrpD) enzyme or by an aconitase‐like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three‐dimensional crystal structure of the PrpF protein from the bacterium Shewanella oneidensis was solved at 2.0 Å resolution. The protein fold of PrpF is strikingly similar to those of the non‐PLP‐dependent diaminopimelate epimerase from Haemophilus influenzae, a putative proline racemase from Brucella melitensis, and to a recently deposited structure of a hypothetical protein from Pseudomonas aeruginosa. Results from in vitro studies show that PrpF isomerizes trans‐aconitate to cis‐aconitate. It is proposed that PrpF catalysis of the cis–trans isomerization proceeds through a base‐catalyzed proton abstraction coupled with a rotation about C2–C3 bond of 2‐methylaconitate, and that residue Lys73 is critical for PrpF function. The newly identified function of PrpF as a non‐PLP‐dependent isomerase, together with the fact that PrpD‐containing bacteria do not require PrpF, suggest that the isomer of 2‐methylaconitate that serves as a substrate of aconitase must have the same stereochemistry as that synthesized by PrpD. From this, it follows that the 2‐methylaconitate isomer generated by AcnD is not a substrate of aconitase, and that PrpF is required to generate the correct isomer. As a consequence, the isomerase activity of PrpF may now be viewed as an integral part of the 2‐methylcitric acid cycle.
The crystal structure of the tumor suppressor protein pp32 (Anp32a): Structural insights into Anp32 family of proteins
Authors: Huyton Trevor , Wolberger Cynthia
Published: June 2007

The tumor suppressor protein pp32 is highly overexpressed in many cancers of the breast and prostate, and has also been implicated in the neurodegenerative disease spinocerebellar ataxias type 1 (SCA1). Pp32 is a multifunctional protein that is involved in the regulation of transcription, apoptosis, phosphorylation, and cell cycle progression, the latter through its association with the hyperphosphorylated form of the retinoblastoma tumor suppressor. We have determined the structure of an N‐terminal pp32 fragment comprising a capped leucine‐rich repeat (LRR) domain, which provides insight into the structural and biochemical properties of the pp32 (Anp32) family of proteins.
Resolution analysis of geophysical images: Comparison between point spread function and region of data influence measures
Authors: Miller Carlyle R. , Routh Partha S.
Published: June 2007

Practical decisions are often made based on the subsurface images obtained by inverting geophysical data. Therefore it is important to understand the resolution of the image, which is a function of several factors, including the underlying geophysical experiment, noise in the data, prior information and the ability to model the physics appropriately. An important step towards interpreting the image is to quantify how much of the solution is required to satisfy the data observations and how much exists solely due to the prior information used to stabilize the solution. A procedure to identify the regions that are not constrained by the data would help when interpreting the image. For linear inverse problems this procedure is well established, but for non‐linear problems the procedure is more complicated. In this paper we compare two different approaches to resolution analysis of geophysical images: the region of data influence index and a resolution spread computed using point spread functions. The region of data influence method is a fully non‐linear approach, while the point spread function analysis is a linearized approach. An approximate relationship between the region of data influence and the resolution matrix is derived, which suggests that the region of data influence is connected with the rows of the resolution matrix. The point‐spread‐function spread measure is connected with the columns of the resolution matrix, and therefore the point‐spread‐function spread and the region of data influence are fundamentally different resolution measures. From a practical point of view, if two different approaches indicate similar interpretations on post‐inversion images, the confidence in the interpretation is enhanced. We demonstrate the use of the two approaches on a linear synthetic example and a non‐linear synthetic example, and apply them to a non‐linear electromagnetic field data example.
Liveweight gains of lambs from Caucasian clover/ryegrass and white clover/ryegrass swards on soils of high and low fertility
Authors: Black A. D. , Lucas R. J. , Moot D. J. , Sedcole J. R.
Published: June 2007

The high nutritive value and persistence under a wide range of climatic and soil fertility conditions make Caucasian clover a potentially useful forage legume but there is little information about the performance of livestock grazing Caucasian clover/grass swards. This study compared liveweight gains of lambs grazing Caucasian clover/perennial ryegrass and white clover/perennial ryegrass swards on high fertility (Olsen P 20 mg L−1, SO4‐S 12 mg kg−1) and low fertility (Olsen P 11 mg L−1, SO4‐S 7 mg kg−1) soils from 1998 to 2001 in the South Island of New Zealand. Mean annual liveweight gains were 1178 kg ha−1 for Caucasian clover/perennial ryegrass and 1069 kg ha−1 for white clover/perennial ryegrass swards at high fertility compared with 1094 kg ha−1 and 1015 kg ha−1, respectively, at low fertility. There was a higher mean proportion of clover in Caucasian clover/perennial ryegrass (0·19) than white clover/perennial ryegrass (0·11) swards, but there were no differences in total herbage production between the two clover/perennial ryegrass swards. The mean concentration of crude protein in the herbage of Caucasian clover (302 g kg DM−1) was higher than that in white clover (287 g kg DM−1) and grass herbage (227 g kg DM−1). Estimated mean metabolizable energy concentrations in the herbage were 12·5 MJ kg DM−1 for the two clovers and 11·6 MJ kg DM−1 for grass herbage. The difference in liveweight gain between swards on soils of high and low fertility was associated with an increase in total herbage production of similar composition and nutritive value, giving a greater number of grazing days for the swards on soils of high than low fertility.
Mineral concentrations in herbage and soil in a Pinus radiata silvopastoral system in north‐west Spain after sewage sludge and lime application
Authors: Rigueiro‐Rodríguez A. , Mosquera‐Losada M. R. , López‐Díaz M. L.
Published: June 2007

Silvopastoral systems in north‐west Spain can reduce the risk of fires and promote multi‐purpose forest land use. Fertilizer application is important for optimal pasture and tree production. The application rate of sewage sludge as a fertilizer is regulated and is based on its nutrient concentration, especially nitrogen. The aim of this study was to assess the effect of three consecutive years of application of different application rates of sewage sludge and inorganic fertilizer, with or without lime (2·5 t CaCO3 ha−1) on the ammonium, nitrate and exchangeable K, Ca and Mg contents in soil, and on the crude protein (CP), K, Ca and Mg concentrations in herbage in a silvopastoral system established under a 5‐year‐old Pinus radiata D. Don plantation with a density of 1667 trees ha−1. The experiment was started in autumn 1997, when a pasture mixture was sown (25 kg ha−1Lolium perenne, 10 kg ha−1Dactylis glomerata and 4 kg ha−1Trifolium repens). Changes in ammonium and nitrate content in the soil in response to liming and sewage sludge application reflected the initial pH of the soil. In general, liming increased the available Ca and Mg content in soil, and CP and Ca concentrations in herbage, but reduced exchangeable K content in the soil in the first year. Application of sewage sludge increased all of the measured nutrients in both soil and herbage.
Effects of livestock breed and grazing intensity on biodiversity and production in grazing systems. 2. Diet selection
Authors: Dumont B. , Rook A. J. , Coran Ch. , Röver K.‐U.
Published: June 2007

Reduction in grazing intensity and the use of traditional instead of commercial breeds have frequently been recommended to meet biodiversity and production goals in sustainable grazing systems. The impact of such practices within a range of contrasting grassland vegetation types was studied. This paper describes the effects on foraging behaviour in a study conducted over three years on mesotrophic or semi‐natural grasslands in UK (steers), Germany (steers), France (heifers) and Italy (sheep). Three treatments were performed: (i) a moderate grazing intensity using a commercial breed, (ii) a more lenient grazing intensity with a commercial breed and (iii) a more lenient intensity with a traditional breed. Livestock at all sites preferentially selected bites containing legumes and forbs, and also short rather than tall vegetative patches. Grazing intensity affected not only diet consumed, largely reflecting the different availabilities of dietary components, but also some differences in diet selection. Livestock grazing the more productive mesotrophic grasslands more frequently exploited short patches of higher nutritive value, which is expected to reinforce the spatial heterogeneity of the pastures. Studies in the UK and Germany also revealed that steers showed a more pronounced selection for short patches at the lenient grazing intensity. More homogeneous grazing by livestock on the semi‐natural grasslands with fine‐scale heterogeneity is likely to decrease their spatial heterogeneity. There were few differences in the choices made by commercial and traditional breed livestock. North Devon steers in the UK expressed a greater selection for tall grass‐forb bites than Charolais × Holstein crossbreds, whereas traditional breeds appeared slightly less selective than commercial breeds at the other three sites.
Seasonal patterns of diet composition, herbage intake and digestibility limit the performance of cattle grazing native pasture in the Falkland Islands
Authors: Miller S. M. , Thompson R. P.
Published: June 2007

The botanical composition, intake and digestibility of the diet consumed by mature lactating and non‐lactating cows grazing a native white grass (Cortaderia pilosa) plant community in the Falkland Islands was measured in four periods between September 1998 and June 1999. Five lactating and five non‐lactating cows were used in the summer, autumn and winter; five non‐lactating cows were used in the spring. Different cows were used in each period. Plant cuticle patterns in the faeces of cattle were used, in conjunction with the patterns of concentrations of n‐alkanes in the faeces, to estimate the botanical composition of the diet and predicted concentrations of C32‐ and C33‐alkanes in the herbage allowed herbage intake and digestibility to be estimated using the n‐alkane technique. White grass, sedges and rushes comprised 0·78, 0·64 and 0·63 of the diet in autumn, winter and spring respectively. Fine grasses, smooth‐stalked meadow grass (Poa pratensis L.), annual meadow grass (Poa annua L.), bent grass (Agrostis capillaris L.), native fescue (Festuca magellanica Lam.), Yorkshire fog (Holcus lanatus L.), wavy hair grass [Deschampsia flexuosa (L) Trin.] and early hair grass (Aira praecox L.), were consumed at the expense of sedges and rushes in summer and this coincided with the period of greatest estimated metabolizable energy and crude protein intakes by cows. Lactating cows suffered substantial liveweight loss during autumn and winter and this reflected the low quality of the diet consumed. Phosphorus intakes were insufficient and there was an estimated deficiency of vitamin D in the winter and early spring in cattle that were grazed with the experimental cows. The nutrient restrictions imposed on cattle by the low quality of native pasture during autumn and winter are likely to impair the reproductive potential of breeding females and methods should be investigated to improve the diet consumed by cows during these critical periods if cattle systems are to become sustainable in the Falkland Islands.
Implications of climate change for grassland in Europe: impacts, adaptations and mitigation options: a review
Authors: Hopkins A. , Del Prado A.
Published: June 2007

Climate change associated with greenhouse gas (GHG) emissions may have important implications for Europe's grasslands. Projected scenarios indicate that increased temperatures and CO2 concentrations have the potential to increase herbage growth and to favour legumes more than grasses, but changes in seasonal precipitation would reduce these benefits particularly in areas with low summer rainfall. Further implications for grasslands may arise from increased frequency of droughts, storms and other extreme events. Potential farm‐scale adaptive responses to climate change are identified. Grassland agriculture also contributes to GHG emissions, particularly methane and nitrous oxide, and management of grassland affects net carbon balances and carbon sequestration. Management options are identified for mitigating grassland's contribution to GHG emissions which need to be developed in a holistic way that also considers other pressures.
The choice of a fitting model for in sacco degradation curves of some temperate and tropical grasses
Authors: Nivyobizi A. , Deswysen A. G. , Moreau B. , Dehareng D. , Larondelle Y. , Peeters A.
Published: June 2007

The objective was to compare alternative models for fitting to data on degradation of dry matter (DM), organic matter (OM) and crude protein (CP) in the rumen of two harvests of four temperate grasses, made into hay in Belgium, and one harvest of three tropical grasses commonly used in Burundi. Fifteen non‐linear models were used and these included generalized Mitscherlich, simple Mitscherlich (or exponential), generalized Michaelis–Menten, Gompertz, logistic, simple Michaelis–Menten, segmented Van Milgen and von Bertalanffy models. Degradation profiles of DM, OM and CP obtained in sacco from the rumen of three mature sheep were fitted to all the models. The convergence success rate along with acceptable parameters was used as a first tool to eliminate models. Comparisons between the remaining twelve models were then made using the run test of sign, the root mean square prediction error, the root mean square error, the lack of fit test and the variance ratio test criteria. On the basis of an overall assessment using these tests, the Gompertz lagged model was the best suited to fit the degradation data of both temperate and tropical grasses. This study confirmed the superiority of sigmoid type functions over diminishing return‐type models.
Financial Compensation for Victims of Catastrophes: A Law and Economics Perspective
Authors: FAURE MICHAEL G.
Published: June 2007

This article examines the various approaches legislators may use to compensate victims of catastrophes. Traditional law and economics of insurance literature, with respect to government relief and insurance solutions towards financial compensation, is used to analyze (highly diverging) approaches in Europe and the United States. First, the importance of liability (insurance) is discussed in cases where a liable injurer can be identified; second, the possibilities of first‐party insurance are examined, whereby various regulatory solutions (particularly the French model of providing mandatory coverage for catastrophes) is critically discussed. The (first‐party) insurance solution is compared with public intervention, and a distinction is made between ad hoc government relief on an ex‐post basis and structural compensation funds. The solutions applied and discussed in many countries are critically analyzed for their ability to provide adequate compensation at low costs and their effects on incentives for prevention and for developing private (insurance) solutions.
Where Have All of the Pro‐Choice Lawyers Gone? An Analysis of Post‐Roe Reproductive Rights Lawyering
Authors: O’CONNOR KAREN , YANUS ALIXANDRA B.
Published: June 2007

A body of scholarship attests to the importance of experienced litigators before the U.S. Supreme Court. In this article, we specifically consider the role of experienced litigators in the thirty years of reproductive rights litigation that followed Roe v Wade. To that end, we divide the lawyers by their pro‐choice or pro‐life affiliations and ask (1) how often individual lawyers appear before the Court in reproductive rights cases, (2) who the lawyers arguing these case before the Supreme Court are, and (3) how their participation has changed over time. We find changes in the pro‐choice and pro‐life bars that mirror the reproductive rights movement at large. Pro‐choice groups, which once employed a stable of elite lawyers with significant expertise, have been decimated by the retirements of pro‐choice counsel with no lawyers emerging to replace them. At the same time, the pro‐life bar and pro‐life groups appear to be developing a strong litigation campaign complete with experienced litigators.
Computer Aided Design in Industrial Design Education
Authors: CHAPMAN GILL
Published: June 2007

In general, Industrial Design BA courses have been slow to formulate a coherent strategy for the inclusion, implementation and integration of computers into their teaching. CAD hardware and software has appeared in many institutions as a result of the enthusiasm of one or two individuals who have used a particular CAD system themselves or been bowled over by an impressive demonstration. The possession of the equipment then to a large extent determines what kind of use can be made of it, and this is also subject to the vagaries of staff time and expertise, both of which are often in short supply.

Basic questions, such as ‘What is the purpose of CAD education in this course?’ or ‘What kind of computing do the students really need?’ are often by‐passed until it is too late. Over the last three years at Sheffield Hallam University a conscious attempt has been made to evolve an approach which begins with questions such as these and results in a coherent teaching and learning strategy for our students.
Controlling the Masses: the Reinvention of a ‘National’ Curriculum
Authors: SWIFT JOHN
Published: June 2007

Educational policies and their curricula are inevitably political in their intent and design. The reintroduction of a supposed ‘national’ curriculum for British education reveals a strange notion of nationhood which retains privilege, and indeed accelerates it through the lure of (mainly) spurious competition to meet predetermined and externally defined standards. Art education does not escape this: it reflects the larger picture. Through comparing the educational policies and practices of Victorian education and art education with our own, this paper hopes to reveal commonalities and differences, and what these disclose about current values concerning the individual and the ‘nation’.
Beyond Local Cultures: Towards a Cosmopolitan Art Education
Authors: BURTONWOOD NEIL
Published: June 2007

What kind of art education best takes up the educational opportunity of cultural diversity? This article draws on Merton's distinction between local and cosmopolitan perspectives on culture to contrast different models of art education in a multicultural society. An example is given to illustrate a local perspective on education which seeks to affirm pupils in their own culture. This model is underpinned by a particular view of culture, pluralism, art and education. Alternative views on each of these constituent elements are explored in order to make a case for an alternative model of art education ‐ one which goes beyond culture and which can more properly be described as cosmopolitan.
Primary Children's Understanding of Early Modern Artists' Concepts
Authors: GILBERT JEAN
Published: June 2007

This paper reports on the first three weeks of a piece of classroom action research that took place over a period of eight weeks. It involved three primary classes: 5 year olds, 7/8 year olds and 11 year olds. The research was carried out in two contrasting settings: inner city Toxteth, Liverpool, with two classes of 5 and 11 year olds, and a leafy suburban setting in Cheshire, with one class of 7/8 year olds. The research sought answers to the following questions: Can young children understand some aspects of the concepts that inform modern art? Could that understanding be used to bring about cognitive development in their artwork? How are the developmental differences between 5, 7/8, and 11 year olds demonstrated? Do inner‐city children perform less well than suburban children in art? Could each child's learning be assessed in art? For reasons of brevity this paper gives evidence of the 5 and 11 year old children's work and reports on the 7/8 year olds response in the conclusion.