bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato
Authors: Iovene Marina , Wielgus Susan M , Simon Philipp W , Buell C Robin , Jiang Jiming 
Published: September 2008

Abstract
Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for ∼28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.
Role of Recombination in the Long-Term Retention of Transposable Elements in rRNA Gene Loci
Authors: Zhang Xian , Eickbush Michael T , Eickbush Thomas H 
Published: September 2008

AbstractMultiple theoretical studies have focused on the concerted evolution of the tandemly repeated rRNA genes of eukaryotes; however, these studies did not consider the transposable elements that interrupt the rRNA genes in many organisms. For example, in insects, R1 and R2 have been stable components of the rDNA locus for hundreds of millions of years, suggesting either that they have minimal effects on fitness or that they are unable to be eliminated. We constructed a simulation model of recombination and retrotransposition within the rDNA locus that addresses the population dynamics and fitness consequences associated with R1 and R2 insertions. The simulations suggest that even without R1 and R2 retrotransposition the frequent sister chromatid exchanges postulated from various empirical studies will, in combination with selection, generate rDNA loci that are much larger than those needed for transcription. These large loci enable the host to tolerate high levels of R1 and R2 insertions with little fitness consequences. Changes in retrotransposition rates are likely to be accommodated by adjustments in sister chromatid exchange (SCE) rate, rather than by direct selection on the number of uninserted rDNA units. These simulations suggest that the rDNA locus serves as an ideal niche for the long-term survival of transposable elements.
Transcriptional Control and Protein Specialization Have Roles in the Functional Diversification of Two Dicer-Like Proteins in Magnaporthe oryzae
Authors: Kadotani Naoki , Murata Toshiki , Quoc Nguyen Bao , Adachi Yusuke , Nakayashiki Hitoshi 
Published: September 2008

Abstract
Quantitative RT–PCR and overexpression studies of two Dicer-like proteins, MoDcl1 and MoDcl2, in Magnaporthe oryzae indicated that the functional diversification of the MoDcl1 and MoDcl2 proteins in RNA-mediated gene silencing pathways was likely to have arisen from both transcriptional control and protein specialization.
Insulator and Ovo Proteins Determine the Frequency and Specificity of Insertion of the gypsy Retrotransposon in Drosophila melanogaster
Authors: Labrador Mariano , Sha Ky , Li Alice , Corces Victor G 
Published: September 2008

Abstract
The gypsy retrovirus of Drosophila is quite unique among retroviruses in that it shows a strong preference for integration into specific sites in the genome. In particular, gypsy integrates with a frequency of &gt;10% into the regulatory region of the ovo gene. We have used in vivo transgenic assays to dissect the role of Ovo proteins and the gypsy insulator during the process of gypsy site-specific integration. Here we show that DNA containing binding sites for the Ovo protein is required to promote site-specific gypsy integration into the regulatory region of the ovo gene. Using a synthetic sequence, we find that Ovo binding sites alone are also sufficient to promote gypsy site-specific integration into transgenes. These results indicate that Ovo proteins can determine the specificity of gypsy insertion. In addition, we find that interactions between a gypsy provirus and the gypsy preintegration complex may also participate in the process leading to the selection of gypsy integration sites. Finally, the results suggest that the relative orientation of two integrated gypsy sequences has an important role in the enhancer-blocking activity of the gypsy insulator.
The DNA End-Binding Protein Ku Regulates Silencing at the InternalHMLandHMRLoci inSaccharomyces cerevisiae
Authors: Vandre Catherine L , Kamakaka Rohinton T , Rivier David H 
Published: September 2008

AbstractHeterochromatin resides near yeast telomeres and at the cryptic mating-type loci, HML and HMR, where it silences transcription of the α- and a-mating-type genes, respectively. Ku is a conserved DNA end-binding protein that binds telomeres and regulates silencing in yeast. The role of Ku in silencing is thought to be limited to telomeric silencing. Here, we tested whether Ku contributes to silencing at HML or HMR. Mutant analysis revealed that yKu70 and Sir1 act collectively to silence the mating-type genes at HML and HMR. In addition, loss of yKu70 function leads to expression of different reporter genes inserted at HMR. Quantitative chromatin-immunoprecipitation experiments revealed that yKu70 binds to HML and HMR and that binding of Ku to these internal loci is dependent on Sir4. The interaction between yKu70 and Sir4 was characterized further and found to be dependent on Sir2 but not on Sir1, Sir3, or yKu80. These observations reveal that, in addition to its ability to bind telomeric DNA ends and aid in the silencing of genes at telomeres, Ku binds to internal silent loci via protein–protein interactions and contributes to the efficient silencing of these loci.
Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes
Authors: Ueki Noriko , Nishii Ichiro 
Published: September 2008

Abstract
A cold-inducible transposon called Jordan has previously been used to tag and recover genes controlling key aspects of Volvox development, including the process called inversion. In a search for additional genes, we isolated 17 new inversionless mutants from cultures grown at 24° (the temperature that activates Jordan transposition). These mutants were stable at 32°, but generated revertants at 24°. DNA blots revealed that one mutant had a transposon unrelated to Jordan inserted in invA (“inversionless A”). This new transposon, which we named Idaten, has terminal inverted repeats (TIRs) beginning with CCCTA, and upon insertion it creates a 3-bp target-site duplication. It appears to belong to the CACTA superfamily of class II DNA transposons, which includes En/Spm. No significant open reading frames were in the Idaten sequence, but we retrieved another element with Idaten-type TIRs encoding a protein similar to the En/Spm transposase as a candidate for an Idaten-specific transposase. We found that in five of the new inversionless strains we could not find any Jordan insertions causing the phenotype to possess insertions of an Idaten family member in a single locus (invC). This clearly indicates that Idaten is a potentially powerful alternative to Jordan for tagging developmentally important genes in Volvox.
A Genomewide Survey Argues That Every Zygotic Gene Product Is Dispensable for the Initiation of Somatic Homolog Pairing in Drosophila
Authors: Bateman Jack R , Wu C-ting 
Published: September 2008

AbstractStudies from diverse organisms show that distinct interchromosomal interactions are associated with many developmental events. Despite recent advances in uncovering such phenomena, our understanding of how interchromosomal interactions are initiated and regulated is incomplete. During the maternal-to-zygotic transition (MZT) of Drosophila embryogenesis, stable interchromosomal contacts form between maternal and paternal homologous chromosomes, a phenomenon known as somatic homolog pairing. To better understand the events that initiate pairing, we performed a genomewide assessment of the zygotic contribution to this process. Specifically, we took advantage of the segregational properties of compound chromosomes to generate embryos lacking entire chromosome arms and, thus, all zygotic gene products derived from those arms. Using DNA fluorescence in situ hybridization (FISH) to assess the initiation of pairing at five separate loci, this approach allowed us to survey the entire zygotic genome using just a handful of crosses. Remarkably, we found no defect in pairing in embryos lacking any chromosome arm, indicating that no zygotic gene product is essential for pairing to initiate. From these data, we conclude that the initiation of pairing can occur independently of zygotic control and may therefore be part of the developmental program encoded by the maternal genome.
EXPORTIN1 Genes Are Essential for Development and Function of the Gametophytes in Arabidopsis thaliana
Authors: Blanvillain Robert , Boavida Leonor C , McCormick Sheila , Ow David W 
Published: September 2008

Abstract
Gametes are produced in plants through mitotic divisions in the haploid gametophytes. We investigated the role of EXPORTIN1 (XPO1) genes during the development of both female and male gametophytes of Arabidopsis. Exportins exclude target proteins from the nucleus and are also part of a complex recruited at the kinetochores during mitosis. Here we show that double mutants in Arabidopsis XPO1A and XPO1B are gametophytic defective. In homozygous–heterozygous plants, 50% of the ovules were arrested at different stages according to the parental genotype. Double-mutant female gametophytes of xpo1a-3/+; xpo1b-1/xpo1b-1 plants failed to undergo all the mitotic divisions or failed to complete embryo sac maturation. Double-mutant female gametophytes of xpo1a-3/xpo1a-3; xpo1b-1/+ plants had normal mitotic divisions and fertilization occurred; in most of these embryo sacs the endosperm started to divide but an embryo failed to develop. Distortions in male transmission correlated with the occurrence of smaller pollen grains, poor pollen germination, and shorter pollen tubes. Our results show that mitotic divisions are possible without XPO1 during the haploid phase, but that XPO1 is crucial for the maternal-to-embryonic transition.
An Age‐Dependent Tag Return Model for Estimating Mortality and Selectivity of an Estuarine‐Dependent Fish with High Rates of Catch and Release
Authors: Bacheler Nathan M. , Hightower Joseph E. , Paramore Lee M. , Buckel Jeffrey A. , Pollock Kenneth H. 
Published: September 2008

AbstractRed drum Sciaenops ocellatus support commercial and recreational fisheries in North Carolina, but the stock was overfished in the 1980s because fishing was unregulated. Subsequent fishery regulations increased subadult survival into adult age‐classes, but overall stock status is difficult to assess because of migration to ocean waters, prohibited harvest of older fish, and relative importance of catch and release. We analyzed 24 years of tagging data from the North Carolina Division of Marine Fisheries to assess the effects of two regulation changes (effected in 1991 and 1998) on fishing mortality rate (F) and selectivity (SEL) patterns of red drum. We used an age‐dependent tag return model that accounted for both harvest and catch‐and‐release fishing. Using external estimates of natural mortality (M) and annual tag retention rate, we obtained precise estimates of annual F; an overall tag reporting rate (λ); and fate‐specific, age‐specific, and regulation‐period‐specific SEL. Estimated F of fully selected red drum was high and variable before 1991 (mean F = 2.38) but decreased in magnitude and variability after 1991. A dome‐shaped pattern of SEL was observed for harvested fish in all regulation periods; maximum SEL occurred at age 2, when red drum were of harvestable size and found in more‐accessible estuarine waters. Selectivity for caught‐and‐released red drum generally decreased for younger ages and increased for older ages in later regulation periods. The λ was estimated at 18% and was generally insensitive to changes in the inputs of M or tag retention rate. As catch‐and‐release fishing increases, tag return models may be important tools for studying fish populations, as long as practical issues, such as λ, tag loss, timing of tagging, and hooking and tagging mortality, are addressed.
Separation and determination of inorganic cations in beverages by capillary electrophoresis with indirect UV detection
Authors: Gao Jinzhang , Fan Haifeng , Yang Wu , Sun Xiangli , Li Chongyang , Mao Xuefeng , Wang Jie , Wang Rong , Jia Zhengping 
Published: September 2008

Abstract
A rapid, simple and reliable capillary electrophoresis method for the separation and quantitation of inorganic cations with indirect UV detection at 214 nm was developed. The electrolyte was: 12 mM imidazole as background absorbance provider; 5 mM malic acid and 1.0 mM 18-crown-6 ether as complexing agents; and 20% D2O (v/v) to improve ion mobility. The pH was 4.25. The applied voltage was 22 kV at 22°C. Nine ions were completely separated and determined with correlation coefficients of 0.9979-0.9992. The relative standard deviations (RSD) were less than 0.5% for migration time and less than 5.2% for peak area (n=8). The detection limits (S/N=3) were from 0.08 mg L−1 (for Na+) to 0.51 mg L−1 (for Cu2+). To assess the reliability atomic absorption (AA) was also used to determine the same samples. Satisfactory results were obtained for real samples of jasmine tea drink and coconut milk.
Morphometric and molecular characterization of Parapharyngodon echinatus (Nematoda, Pharyngodonidae) from the Senegal gecko (Tarentola parvicarinata)
Authors: Mašová Šárka , Baruš Vlastimil , Hodová Iveta , Matějusová Iveta , Koubek Petr , Koubková Božena 
Published: September 2008

AbstractA West African species of gecko, Tarentola parvicarinata Joger (Gekkonidae), collected in the Niokolo Koba National Park in East Senegal is a new host species for the nematode Parapharyngodon echinatus (Rudolphi, 1819). Fifty one specimens of P. echinatus were studied under a light microscope and thirteen specimens were studied for the first time by a scanning electron microscope. The main differences between P. echinatus and other African species, especially Parapharyngodon micipsae (Seurat, 1917), were in the shape of annules on body cuticle, broad lateral alae and their terminations, the shape of the distal extremity of the spicule and number of outgrowths at the anterior cloacal lip. For the purposes of DNA characterization, partial sequence of the small subunit ribosomal RNA gene (SSU rRNA) was obtained from two specimens of P. echinatus. This is the first published sequence of a species from the family Pharyngodonidae.
Gyrodactylus species (Monogenea) infecting alpine bullhead (Cottus poecilopus Heckel, 1837) in Norway and Slovakia, including the description of Gyrodactylus mariannae sp. nov.
Authors: Winger Anja , Hansen Haakon , Bachmann Lutz , Bakke Tor 
Published: September 2008

AbstractGyrodactylus specimens infecting the skin and fins of two alpine bullhead (Cottus poecilopus) populations from the rivers Signaldalselva (North Norway) and Rena (South-East Norway) were characterized by both morphological and molecular means. Morphometrical differences were minor and the nucleotide sequences of the internal transcribed spacers (ITS) of the nuclear rDNA cluster were identical for parasites from both localities. Based on earlier descriptions, the relatively closest species are Gyrodactylus hrabei Ergens, 1957, described from common bullhead (Cottus gobio) in Slovakia and G. sp. Malmberg, 1973, from alpine bullhead in Sweden. The Norwegian Gyrodactylus specimens from the two alpine bullhead populations were morphometrically different from both the type material of G. hrabei from Slovakia and newly collected Gyrodactylus specimens from alpine bullhead in two Slovakian localities. The Slovakian Gyrodactylus specimens were found to be identical with type material of G. hrabei. The nucleotide sequences of the ITS of the Norwegian Gyrodactylus species were different from the Slovakian material. Hence, the Norwegian Gyrodactylus specimens from the alpine bullhead represent a new species, G. mariannae sp. nov.
κB‐Ras proteins are fast‐exchanging GTPases and function via nucleotide‐independent binding of Ral GTPase‐activating protein complexes
Authors: Rasche René , Apken Lisa Helene , Michalke Esther , Kümmel Daniel , Oeckinghaus Andrea 
Published: April 2024

κB‐Ras (NF‐κB inhibitor‐interacting Ras‐like protein) GTPases are small Ras‐like GTPases but harbor interesting differences in important sequence motifs. They act in a tumor‐suppressive manner as negative regulators of Ral (Ras‐like) GTPase and NF‐κB signaling, but little is known about their mode of function. Here, we demonstrate that, in contrast to predictions based on primary structure, κB‐Ras GTPases possess hydrolytic activity. Combined with low nucleotide affinity, this renders them fast‐cycling GTPases that are predominantly GTP‐bound in cells. We characterize the impact of κB‐Ras mutations occurring in tumors and demonstrate that nucleotide binding affects κB‐Ras stability but is not strictly required for RalGAP (Ral GTPase‐activating protein) binding. This demonstrates that κB‐Ras control of RalGAP/Ral signaling occurs in a nucleotide‐binding‐ and switch‐independent fashion.
Constructing Nerve Guidance Conduit using dECM‐Doped Conductive Hydrogel to Promote Peripheral Nerve Regeneration
Authors: Yan Lizhao , Liu Shuang , Wang Jianwen , Ding Xiaoyue , Zhao Yingsong , Gao Nan , Xia Zishen , Li Ming , Wei Qianqian , Okoro Oseweuba Valentine , Sun Yanfang , Nie Lei , Shavandi Amin , Jiang Guohua , Chen Jianghai , Fan Lihong , Weng Yuxiong 
Published: April 2024

AbstractPeripheral nerve injury often leads to the loss of neurological functions due to the slow regeneration rate and inefficient functional reconstruction. Current clinical treatments using nerve guidance conduits (NGCs) still face challenges in providing a biomimetic microenvironment to promote nerve repair. Herein, decellularized extracellular matrix (dECM) is obtained from porcine Achilles tendon and crosslinked with 3‐amino‐4‐methoxybenzoic acid grafted gelatin (PAMB‐G) to obtain conductive hydrogels. Then, a novel nerve guidance conduit is developed by assembling poly(vinyl alcohol) (PVA) conduit and conductive ECM@PAMB‐G hydrogel. This bioengineered ECM@PAMB‐G/PVA conduit demonstrated excellent cytocompatibility, electrical conductivity, mechanical properties, and biodegradability. In vitro experiments confirmed that the ECM@PAMB‐G hydrogel significantly promotes the proliferation and migration of PC12 cells and primary Schwann cells, as well as the growth of dorsal root ganglion (DRG) axons. Furthermore, in vivo studies in a rat sciatic nerve model exhibited improvements in axonal regeneration, Schwann cell migration, myelin sheath formation, and functional recovery mediated by the ECM@PAMB‐G/PVA conduit. This work demonstrates the synergistic effects of extracellular matrix and electrical cues in enhancing peripheral nerve regeneration. The ECM@PAMB‐G/PVA nerve guidance conduit shows potential as an alternative to autografts for supporting peripheral nerve reconstruction.
Simultaneous Enhancement of Electrical Conductivity and Porosity of a Metal–Organic Framework Toward Thermoelectric Applications
Authors: Olorunyomi Joseph F. , Dyett Brendan P. , Murdoch Billy J. , Ahmed Al Jumlat , Rosengarten Gary , Caruso Rachel A. , Doherty Cara M. , Mulet Xavier 
Published: April 2024

AbstractMetal–organic frameworks (MOFs) exhibit large surface areas and low thermal conductivity, making them promising for thermoelectric generation. However, their limited electrical conductivity poses a significant hurdle to be practically useful. Traditionally, enhancing the electrical conductivity of MOFs typically comes at the cost of reducing surface area, thereby increasing thermal conductivity. This study introduces an approach to simultaneously boost the electrical conductivity and porosity of a MOF‐based material while maintaining remarkably low thermal conductivity. The electrically conductive poly(3,4‐ethylenedioxythiophene)‐poly(styrenesulfonate) (PEDOT:PSS) is deployed to nucleate the growth of Cu3(BTC)2 (or simply CuBTC, where BTC = benzene‐1,3,5‐tricarboxylic acid), resulting in the synthesis of composites labeled CPP‐y (where y denotes wt% PEDOT:PSS). Predictably, the CPP‐y composites are more electrically conductive than pure CuBTC, achieving an electrical conductivity exceeding 1.40 S cm−1 at room temperature. Furthermore, the CPP‐y composites exhibit consistently high Brunauer–Emmett–Teller (BET) surface areas of ≈1600 m2 g−1, comparable to pristine CuBTC, while maintaining thermal conductivities below 0.04 W m−1 K−1 at room temperature. With a high Seebeck coefficient in the range 180–373 µV K−1, CPP‐15 and CPP‐23 demonstrate a figure‐of‐merit (zT) of 0.25 and 0.11, respectively, at 285 K, marking a substantial achievement for MOF‐based materials.
Forty years of struggle in North Carolina: Workplace segregation and fatal occupational injury rates
Authors: McClure Elizabeth S. , Martin Amelia T. , Ranapurwala Shabbar I. , Nocera Maryalice , Cantrell John , Marshall Stephen , Richardson David B. 
Published: April 2024

AbstractObjectiveTo assess workplace segregation in fatal occupational injury from 1992 to 2017 in North Carolina.MethodsWe calculated occupational fatal injury rates within categories of occupation, industry, race, age, and sex; and estimated expected numbers of fatalities among Black and Hispanic male workers had they experienced the rates of White male workers. We also estimated the contribution of workforce segregation to disparities by estimating the expected number of fatalities among Black and Hispanic male workers had they experienced the industry and occupation patterns of White male workers. We assessed person‐years of life‐lost, using North Carolina life expectancy estimates.ResultsHispanic workers contributed 32% of their worker‐years and experienced 58% of their fatalities in construction. Black workers were most overrepresented in the food manufacturing industry. Hispanic males experienced 2.11 (95% CI: 1.86–2.40) times the mortality rate of White males. The Black‐White and Hispanic‐White disparities were widest among workers aged 45 and older, and segregation into more dangerous industries and occupations played a substantial role in driving disparities. Hispanic workers who suffered occupational fatalities lost a median 47 life‐years, compared to 37 among Black workers and 36 among White workers.ConclusionsIf Hispanic and Black workers experienced the workplace safety of their White counterparts, fatal injury rates would be substantially reduced. Workforce segregation reflects structural racism, which also contributes to mortality disparities. Root causes must be addressed to eliminate disparities.