bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution
Authors: Emrich Scott J , Li Li , Wen Tsui-Jung , Yandeau-Nelson Marna D , Fu Yan , Guo Ling , Chou Hui-Hsien , Aluru Srinivas , Ashlock Daniel A , Schnable Patrick S 
Published: November 2006

Abstract
As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum of 10% over time. Nearly identical paralogs (NIPs) are defined as paralogous genes that exhibit ≥98% identity. Sequence analyses of the “gene space” of the maize inbred line B73 genome, coupled with wet lab validation, have revealed that, conservatively, at least ∼1% of maize genes have a NIP, a rate substantially higher than that in Arabidopsis. In most instances, both members of maize NIP pairs are expressed and are therefore at least potentially functional. Of evolutionary significance, members of many NIP families also exhibit differential expression. The finding that some families of maize NIPs are closely linked genetically while others are genetically unlinked is consistent with multiple modes of origin. NIPs provide a mechanism for the maize genome to circumvent the inherent limitation that diploid genomes can carry at most two “alleles” per “locus.” As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species.
Mutations Leading to Loss of Sporulation Ability in Bacillus subtilis Are Sufficiently Frequent to Favor Genetic Canalization
Authors: Masel Joanna , Maughan Heather 
Published: November 2006

Abstract
We measured the rate of mutations impairing sporulation ability in Bacillus subtilis as 0.003 in a mutator population, following 6000 generations of strong selection for sporulation that have previously been described. This means that the product of the population size and the functional mutation rate is ∼105, well within the parameter range for which genetic canalization of sporulation ability is expected.
Temporal Estimates of Effective Population Size in Species With Overlapping Generations
Authors: Waples Robin S , Yokota Masashi 
Published: November 2006

AbstractThe standard temporal method for estimating effective population size (Ne) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\hat{N}}_{\mathrm{e}}\) \end{document}$ caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age-structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\hat{N}}_{\mathrm{e}}\) \end{document}$. The direction and magnitude of the bias are shown to depend on the sampling method and the species' life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde–Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.
An Ectopic Expression Screen Reveals the Protective and Toxic Effects of Drosophila Seminal Fluid Proteins
Authors: Mueller Jacob L , Page Jennifer L , Wolfner Mariana F 
Published: November 2006

AbstractIn Drosophila melanogaster, seminal fluid regulates the reproductive and immune responses of mated females. Some seminal fluid proteins may provide protective functions to mated females, such as antimicrobial activity and/or stimulation of antimicrobial gene expression levels, while others appear to have negative effects, contributing to a “cost of mating.” To identify seminal proteins that could participate in these phenomena, we used a systemic ectopic expression screen to test the effects on unmated females of proteins normally produced by the male accessory gland (Acps). Of the 21 ectopically expressed Acps that we tested for ability to assist in the clearance of a bacterial infection with Serratia marcescens, 3 Acps significantly reduced the bacterial counts of infected females, suggesting a protective role. Of the 23 Acps that we tested for toxicity, 3 were toxic, including one that has been implicated in the cost of mating in another study. We also tested ectopic expression females for other Acp-induced effects, but found no additional Acps that affected egg laying or receptivity upon ectopic expression.
Cytogenetic and Molecular Characterization of Heterochromatin Gene Models in Drosophila melanogaster
Authors: Rossi Fabrizio , Moschetti Roberta , Caizzi Ruggiero , Corradini Nicoletta , Dimitri Patrizio 
Published: November 2006

Abstract
In the past decade, genome-sequencing projects have yielded a great amount of information on DNA sequences in several organisms. The release of the Drosophila melanogaster heterochromatin sequence by the Drosophila Heterochromatin Genome Project (DHGP) has greatly facilitated studies of mapping, molecular organization, and function of genes located in pericentromeric heterochromatin. Surprisingly, genome annotation has predicted at least 450 heterochromatic gene models, a figure 10-fold above that defined by genetic analysis. To gain further insight into the locations and functions of D. melanogaster heterochromatic genes and genome organization, we have FISH mapped 41 gene models relative to the stained bands of mitotic chromosomes and the proximal divisions of polytene chromosomes. These genes are contained in eight large scaffolds, which together account for ∼1.4 Mb of heterochromatic DNA sequence. Moreover, developmental Northern analysis showed that the expression of 15 heterochromatic gene models tested is similar to that of the vital heterochromatic gene Nipped-A, in that it is not limited to specific stages, but is present throughout all development, despite its location in a supposedly “silent” region of the genome. This result is consistent with the idea that genes resident in heterochromatin can encode essential functions.
Chi Hotspot Activity in Escherichia coli Without RecBCD Exonuclease Activity: Implications for the Mechanism of Recombination
Authors: Amundsen Susan K , Smith Gerald R 
Published: November 2006

Abstract
The major pathway of genetic recombination and DNA break repair in Escherichia coli requires RecBCD enzyme, a complex nuclease and DNA helicase regulated by Chi sites (5′-GCTGGTGG-3′). During its unwinding of DNA containing Chi, purified RecBCD enzyme has two alternative nucleolytic reactions, depending on the reaction conditions: simple nicking of the Chi-containing strand at Chi or switching of nucleolytic degradation from the Chi-containing strand to its complement at Chi. We describe a set of recC mutants with a novel intracellular phenotype: retention of Chi hotspot activity in genetic crosses but loss of detectable nucleolytic degradation as judged by the growth of mutant T4 and λ phages and by assay of cell-free extracts. We conclude that RecBCD enzyme's nucleolytic degradation of DNA is not necessary for intracellular Chi hotspot activity and that nicking of DNA by RecBCD enzyme at Chi is sufficient. We discuss the bearing of these results on current models of RecBCD pathway recombination.
The Saccharomyces cerevisiae ATP22 Gene Codes for the Mitochondrial ATPase Subunit 6-Specific Translation Factor
Authors: Zeng Xiaomei , Hourset Audrey , Tzagoloff Alexander 
Published: November 2006

Abstract
Mutations in the Saccharomyces cerevisiae ATP22 gene were previously shown to block assembly of the F0 component of the mitochondrial proton-translocating ATPase. Further inquiries into the function of Atp22p have revealed that it is essential for translation of subunit 6 of the mitochondrial ATPase. The mutant phenotype can be partially rescued by the presence in the same cell of wild-type mitochondrial DNA and a ρ− deletion genome in which the 5′-UTR, first exon, and first intron of COX1 are fused to the fourth codon of ATP6. The COX1/ATP6 gene is transcribed and processed to the mature mRNA by splicing of the COX1 intron from the precursor. The hybrid protein translated from the novel mRNA is proteolytically cleaved at the normal site between residues 10 and 11 of the subunit 6 precursor, causing the release of the polypeptide encoded by the COX1 exon. The ability of the ρ− suppressor genome to express subunit 6 in an atp22 null mutant constitutes strong evidence that translation of subunit 6 depends on the interaction of Atp22p with the 5′-UTR of the ATP6 mRNA.
Accumulation of Deleterious Mutations in Small Abiotic Populations of RNA
Authors: Soll Steven J , Arenas Carolina Díaz , Lehman Niles 
Published: November 2006

Abstract
The accumulation of slightly deleterious mutations in populations leads to the buildup of a genetic load and can cause the extinction of populations of small size. Mutation-accumulation experiments have been used to study this process in a wide variety of organisms, yet the exact mutational underpinnings of genetic loads and their fitness consequences remain poorly characterized. Here, we use an abiotic system of RNA populations evolving continuously in vitro to examine the molecular events that can instigate a genetic load. By tracking the fitness decline of ligase ribozyme populations with bottleneck sizes between 100 and 3000 molecules, we detected the appearance and subsequent fixation of both slightly deleterious mutations and advantageous mutations. Smaller populations went extinct in significantly fewer generations than did larger ones, supporting the notion of a mutational meltdown. These data suggest that mutation accumulation was an important evolutionary force in the prebiotic RNA world and that mechanisms such as recombination to ameliorate genetic loads may have been in place early in the history of life.
Teaching How to Prepare a Manuscript by Means of Rewriting Published Scientific Papers
Authors: Tomaska Lubomir 
Published: November 2006

Abstract
The objective of the course described here is to train undergraduate students to write a scientific manuscript. The students participate in selection of a current topic in contemporary genetics or molecular biology by choosing the most interesting paper of a given year. After the teacher provides all essential background about the selected subject, he or she selects a recent article from the corresponding field and presents the students with all the necessary information contained in the paper without revealing its title and author. The data presented in the paper are reviewed by the class so that each student understands every experiment and the main points of the work. Simultaneously, the students are informed about the basic rules of writing the individual sections of a scientific paper. They are then asked to write and formally submit a manuscript summarizing the data. Finally, the students act as reviewers of their colleagues' manuscripts and compare their papers with the original published articles. This enables them to identify both the strengths and the weaknesses of their manuscripts and to gain confidence in the writing skills that will be so critical for their future scientific activities.
A Modified Algorithm for the Improvement of Composite Interval Mapping
Authors: Li Huihui , Ye Guoyou , Wang Jiankang 
Published: November 2006

AbstractComposite interval mapping (CIM) is the most commonly used method for mapping quantitative trait loci (QTL) with populations derived from biparental crosses. However, the algorithm implemented in the popular QTL Cartographer software may not completely ensure all its advantageous properties. In addition, different background marker selection methods may give very different mapping results, and the nature of the preferred method is not clear. A modified algorithm called inclusive composite interval mapping (ICIM) is proposed in this article. In ICIM, marker selection is conducted only once through stepwise regression by considering all marker information simultaneously, and the phenotypic values are then adjusted by all markers retained in the regression equation except the two markers flanking the current mapping interval. The adjusted phenotypic values are finally used in interval mapping (IM). The modified algorithm has a simpler form than that used in CIM, but a faster convergence speed. ICIM retains all advantages of CIM over IM and avoids the possible increase of sampling variance and the complicated background marker selection process in CIM. Extensive simulations using two genomes and various genetic models indicated that ICIM has increased detection power, a reduced false detection rate, and less biased estimates of QTL effects.
The Membrane‐Bound Lon Protease from Thermoplasma Displays Unfolding Activity
Authors: Besche Henrike , Navon Amiel , Zwickl Peter 
Published: November 2006

AbstractThe membrane‐bound Lon protease from Thermoplasma acidophilum (Ta Lon) was shown to unfold and degrade a fusion of the green fluorescent protein with calmodulin (GFP—CaM). Unfolding and degradation were ATP‐dependent reactions and could be inhibited by calcium ions, which are known to stabilize calmodulin. Notably, an inverse fusion of the same proteins, i.e., CaM—GFP, as well as GFP or GFP‐SsrA, was neither unfolded nor degraded. Thus, Ta Lon seems to unfold and degrade preferentially protein substrates with an extended unstructured C‐terminus. A set of Ta Lon variants mutated in critical residues of the AAA+ domain, were tested for their respective ATPase and GFP—CaM unfolding activity. This analysis revealed that the rate of ATP hydrolysis correlated with the efficiency of the GFP—CaM unfolding activity. In summary, we show here that the membrane‐bound Ta Lon protease displays an unfolding activity, which is correlated with the rate of ATP hydrolysis.
The E3 Ubiquitin Ligases HRD1 and SCFFbs2 Recognize the Protein Moiety and Sugar Chains, Respectively, of an ER‐Associated Degradation Substrate
Authors: Groisman Bella , Avezov Edward , Lederkremer Gerardo Z. 
Published: November 2006

AbstractSeveral E3 ubiquitin ligases have been identified that participate in endoplasmic reticulum‐associated degradation (ERAD) of misfolded membrane and secretory proteins. Sometimes two ligases were shown to share the same substrate. However, it is not known whether they recognize the same structural determinants and constitute alternative pathways for ubiquitination or if they can act sequentially on different determinants on the substrate. Here we have analyzed in cells in vivo interactions of the recently identified mammalian HRD1 and SCFFbs2 with a model ERAD substrate, uncleaved precursor of asialoglycoprotein receptor H2a, and their involvement in its degradation. As Fbs2 had been shown to bind sugar chains, we studied the influence of glycosylation of the substrate by analyzing the effect of dominant negative mutants of HRD1 and Fbs2 on ERAD of H2a and of a mutant lacking all three of its glycosylation sites. Both HRD1 and Fbs2 were found to associate with H2a, and their mutants inhibited its degradation, but only dominant negative HRD1 blocked the degradation of the unglycosylated version of H2a.This suggests a cooperative action of the two ligases that target the glycans (Fbs2) and a protein motif (HRD1). In addition, our results suggest the need for retrotranslocation of the luminal glycosylated domain of the substrate prior to interaction with cytosolic Fbs2.
The Origins of the Ubiquitin Field
Authors: Varshavsky Alexander 
Published: November 2006

AbstractThis is a personal account of the early history of ubiquitin research by one of its protagonists. The field of ubiquitin and regulated protein degradation was created in the 1980s, largely through the complementary discoveries by the laboratory of A. Hershko (Technion, Haifa, Israel) and by my laboratory, then at MIT (Cambridge, MA, USA). I describe the elegant insights by Hershko and his colleagues that yielded the initial understanding of the chemistry of ubiquitin conjugation and ubiquitin‐mediated proteolysis in cell extracts, including the identifcation of E1, E2, and E3 enzymes. These advances were followed by a set of interconnected discoveries in my laboratory that revealed the biology of the ubiquitin system, i.e., its necessity for protein degradation in vivo, its specific physiological functions (in the cell cycle, DNA repair, protein synthesis, transcriptional regulation, and stress responses), the source of its selectivity (specific degradation signals in short‐lived proteins), and its key mechanistic attributes, such as the polyubiquitin chain and the subunit selectivity of protein degradation. The above biological (function‐based) insights produced the main discovery of the physiological regulation by intracellular protein degradation. These advances caused the enormous expansion of the ubiquitin field in the 1990s. Together with the initial discovery of ubiquitin‐mediated proteolysis by Hershko and coworkers, our biological discoveries in the 1980s led to a radically changed understanding of the logic of intracellular circuits, as it became clear that the control through regulated protein degradation rivals, and often surpasses in significance, the classical regulation through transcription and translation.
Multiple Forms of the 26S Proteasome‐Associated Protein Ecm29 in the Mouse Brain
Authors: Gorbea Carlos , Kaufmann Anthony G. , Pratt Gregory , Rechsteiner Martin , Rogers Scott W. 
Published: November 2006

AbstractEcm29 is an ˜200‐K HEAT‐repeat protein that associates with the 26S proteasome in yeast and HeLa cells. Whereas in most mouse organs Ecm29 is present as a single 200‐K protein, in the brain there are eleven species, ranging from 55 K to greater than 250 K, that react with anti‐Ecm29 antibodies. Since the largest brain‐specific Ecm29 variant reacts with antibodies to sequences within the N‐terminal and C‐terminal regions of the protein, but not to the antibody directed to its central region, this putative isoform likely arises by alternative splicing. Some of the smaller Ecm29‐positive forms appear to arise by proteolytic processing, but extraction of minced brain fragments in boiling SDS‐PAGE sample buffer reveals that all forms are present prior to homogenization. Only the 220‐K Ecm29 species is clearly associated with the 26S proteasome; with one exception, the other variants sediment slower than 20S. Direct dissection and immunohistochemistry reveal that these putative Ecm29 isoforms are present throughout the central nervous system. However, anti‐Ecm29 immunoreactivity is differentially distributed within subregions of the mouse brain and among cell types, suggesting that Ecm29 isoform distribution contributes to the complexity and regional specificity of brain function.
Characterization and Purification of Kinase Activities against Arabidopsis COP9 Signalosome Subunit 7
Authors: Malec Przemyslaw , Chamovitz Daniel A. 
Published: November 2006

AbstractThe COP9 signalosome (CSN) is a multisubunit protein complex that intersects the ubiquitin (Ub)–proteasome pathway at several junctions. The CSN associates with several protein kinases that target key regulatory proteins that themselves are targets for Ub‐dependent degradation, and several subunits themselves are phosphoproteins. We previously reported that Arabidopsis CSN7 is a phosphoprotein. To identify the kinases responsible for CSN7 phosphorylation, we biochemically purified CSN7‐kinsae activities from cauliflower through a four‐step purification procedure that resulted in a ca. 300‐fold enrichment. One of these activities is Ca2+ dependent, while the second is not. Peptide fingerprint analysis of the purified proteins identified three putative CSN7 kinases.
Lost Watersheds: Barriers, Aquatic Habitat Connectivity, and Salmon Persistence in the Willamette and Lower Columbia River Basins
Authors: Sheer M. B. , Steel E. A. 
Published: November 2006

AbstractLarge portions of watersheds and streams are lost to anadromous fishes because of anthropogenic barriers to migration. The loss of these streams and rivers has shifted the distribution of accessible habitat, often reducing the diversity of accessible habitat and the quantity of high‐quality habitat. We combined existing inventories of barriers to adult fish passage in the Willamette and Lower Columbia River basins and identified 1,491 anthropogenic barriers to fish passage blocking 14,931 km of streams. We quantified and compared the stream quality, land cover, and physical characteristics of lost versus currently accessible habitat by watershed, assessed the effect of barriers on the variability of accessible habitats, and investigated potential impacts of habitat reduction on endangered or threatened salmonid populations. The majority of the study watersheds have lost more than 40% of total fish stream habitat. Overall, 40% of the streams with spawning gradients suitable for steelhead (anadromous rainbow trout Oncorhynchus mykiss), 60% of streams with riparian habitat in good condition, and 30% of streams draining watersheds with all coniferous land cover are no longer accessible to anadromous fish. Across watersheds, hydrologic and topographic watershed characteristics were correlated with barrier location, barrier density, and the impacts of barriers on habitat. Population‐based abundance scores for spring Chinook salmon O. tshawytscha were strongly correlated with the magnitude of habitat lost and the number of lowland fish passage barriers. The characteristics of barrier and habitat distribution presented in this paper indicate that barrier removal projects and mitigation for instream barriers should consider both the magnitude and quality of the lost habitat.