bluuebunny/crossref_metadata_2025 huggingface dataset:
Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution
Authors: Durrett Rick , Schmidt Deena
Published: September 2008

Results of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced two prespecified mutations and the time until this mutant phenotype becomes fixed in the population. In this article we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans. In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take >100 million years. In addition, we use these results to expose flaws in some of Michael Behe's arguments concerning mathematical limits to Darwinian evolution.
Distributions of Hardy–Weinberg Equilibrium Test Statistics
Authors: Rohlfs R V , Weir B S
Published: September 2008

It is well established that test statistics and P-values derived from discrete data, such as genetic markers, are also discrete. In most genetic applications, the null distribution for a discrete test statistic is approximated with a continuous distribution, but this approximation may not be reasonable. In some cases using the continuous approximation for the expected null distribution may cause truly null test statistics to appear nonnull. We explore the implications of using continuous distributions to approximate the discrete distributions of Hardy–Weinberg equilibrium test statistics and P-values. We derive exact P-value distributions under the null and alternative hypotheses, enabling a more accurate analysis than is possible with continuous approximations. We apply these methods to biological data and find that using continuous distribution theory with exact tests may underestimate the extent of Hardy–Weinberg disequilibrium in a sample. The implications may be most important for the widespread use of whole-genome case–control association studies and Hardy–Weinberg equilibrium (HWE) testing for data quality control.
The Genetic Architecture of Complex Traits in Teosinte (Zea maysssp.parviglumis): New Evidence From Association Mapping
Authors: Weber Allison L , Briggs William H , Rucker Jesse , Baltazar Baltazar M , de Jesús Sánchez-Gonzalez José , Feng Ping , Buckler Edward S , Doebley John
Published: September 2008

Previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (<10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte.
Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses
Authors: Lam Alex C , Fu Jingyuan , Jansen Ritsert C , Haley Chris S , de Koning Dirk-Jan
Published: September 2008

Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type of study is high. For those organisms where recombinant inbred lines are available for mapping, the “distant pair design” maximizes the number of informative contrasts over all marker loci. Here, we describe an extension of this design, named the “optimal pair design,” for use with F2 crosses between outbred lines. The performance of this design is investigated by simulation and compared to several other two-color microarray designs. We show that, for a given number of microarrays, the optimal pair design outperforms all other designs considered for detection of expression quantitative trait loci (eQTL) with additive effects by linkage analysis. We also discuss the suitability of this design for outbred crosses in organisms with large genomes and for detection of dominance.
Identification of Single-Nucleotide Polymorphism in the Progesterone Receptor Gene and Its Association With Reproductive Traits in Rabbits
Authors: Peiró R , Merchán M , Santacreu M A , Argente M J , García M L , Folch J M , Blasco A
Published: September 2008

A total of 598 F2 does from a cross between the high and low lines selected divergently for uterine capacity during 10 generations were used in a candidate gene analysis. The presence of major genes affecting the number of implanted embryos and uterine capacity has been suggested in lines divergently selected for uterine capacity. Uterine capacity is a main component of litter size. The progesterone receptor gene was tested as a candidate gene to determine whether polymorphisms explain differences in litter size and its components. Fragments of the promoter region and exons 1–8 were amplified and sequenced. One SNP was found in the promoter region, 2464G>A, three SNPs in the 5′-UTR exon 1, and a silence SNP in exon 7. The first four SNPs were segregated in two haplotypes. The allele G found in the promoter region was found in 75% of the high-line parental animals and in 29% of the low-line parental animals. The GG genotype had 0.5 kits and 0.5 implanted embryos more than the AA genotype. At 48 hr of gestation, the difference in early embryo survival and embryonic stage of development was small. However, at 72 hr of gestation, the GG genotype had 0.36 embryos more than the AA genotype and also had a more advanced embryonic stage of development, showing a lower percentage of compacted morulae and a higher percentage of blastocysts. The difference in litter size between the GG and GA genotypes was similar to the difference found between homozygote genotypes; however, differences in implanted embryos, early embryo survival, and embryo development were not detected between the GG and GA genotypes.
Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans
Authors: Teschke Meike , Mukabayire Odette , Wiehe Thomas , Tautz Diethard
Published: September 2008

Genome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation rates should remove signatures of older events. We assess this concept here in a large-scale study. We have analyzed two population pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M. m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of neutral expectation. For eight loci from each population pair we have determined the size of the potential sweep window and applied a second statistical procedure (linked locus statistics). For the two population pairs, we find five and four significant sweep loci, respectively, with an average estimated window size of 120 kb. On the basis of the analysis of individual allele frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of 400–600 years ago. Given the known population history for the French–German population pair, we infer that the average frequency of selective sweeps in these populations is higher than 1 in 100 generations across the whole genome. We discuss the implications for adaptation processes in natural populations.
unc-44 Ankyrin and stn-2 γ-Syntrophin Regulate sax-7 L1CAM Function in Maintaining Neuronal Positioning in Caenorhabditis elegans
Authors: Zhou Shan , Opperman Karla , Wang Xuelin , Chen Lihsia
Published: September 2008

The L1 family of single-pass transmembrane cell adhesion molecules (L1CAMs) is conserved from Caenorhabditis elegans and Drosophila to vertebrates and is required for axon guidance, neurite outgrowth, and maintenance of neuronal positions. The extracellular region of L1CAMs mediates cell adhesion via interactions with diverse cell-surface and extracellular matrix proteins. In contrast, less is known regarding the function of the intracellular domains in the L1CAM cytoplasmic tail. Previously, we identified a role of the C. elegans L1CAM homolog, SAX-7, in maintaining neuronal and axonal positioning. Here, we demonstrate that this function is dependent on three conserved motifs that reside in the SAX-7 cytoplasmic tail: (1) the FERM-binding motif, (2) the ankyrin-binding domain, and (3) the PDZ-binding motif. Furthermore, we provide molecular and genetic evidence that UNC-44 ankyrin and STN-2 γ-syntrophin bind SAX-7 via the respective ankyrin-binding and PDZ-binding motifs to regulate SAX-7 function in maintaining neuronal positioning.
Proteasomal Regulation of the Proliferation vs. Meiotic Entry Decision in the Caenorhabditis elegans Germ Line
Authors: MacDonald Lindsay D , Knox Aaron , Hansen Dave
Published: September 2008

Reproductive fitness in many animals relies upon a tight balance between the number of cells that proliferate in the germ line and the number of cells that enter meiosis and differentiate as gametes. In the Caenorhabditis elegans germ line, the GLP-1/Notch signaling pathway controls this balance between proliferation and meiotic entry. Here we describe the identification of the proteasome as an additional regulator of this balance. We show that a decrease in proteasome activity, through either genetic mutation or RNAi to core components of the proteasome, shifts this balance toward excess germ-line proliferation. We further demonstrate that there are likely two or more proteasome targets that contribute to excess germ-line proliferation when proteasome activity is reduced. One of these targets is likely a component or regulator of the Notch-signaling pathway, while the other functions on one of the two major redundant genetic pathways downstream of GLP-1/Notch signaling. We propose a model in which the proteasome degrades proteins that are necessary for proliferation as cells switch from proliferation to meiotic entry.
Controlling Type-I Error of the McDonald–Kreitman Test in Genomewide Scans for Selection on Noncoding DNA
Authors: Andolfatto Peter
Published: September 2008

Departures from the assumption of homogenously interdigitated neutral and putatively selected sites in the McDonald–Kreitman test can lead to false rejections of the neutral model in the presence of intermediate levels of recombination. This problem is exacerbated by small sample sizes, nonequilibrium demography, recombination rate variation, and in comparisons involving more recently diverged species. I propose that establishing significance levels by coalescent simulation with recombination can improve the fidelity of the test in genomewide scans for selection on noncoding DNA.
Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids
Authors: Li Lanzhi , Lu Kaiyang , Chen Zhaoming , Mu Tongmin , Hu Zhongli , Li Xinqi
Published: September 2008

Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter- (IJ) and intrasubspecific (II) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation (L1 + L2) and by subtraction (L1 − L2) of two backcross populations (L1 and L2). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-to-complete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis.
The Different Sources of Variation in Inbreeding Depression, Heterosis and Outbreeding Depression in a Metapopulation ofPhysa acuta
Authors: Escobar Juan Sebastián , Nicot Antoine , David Patrice
Published: September 2008

Understanding how parental distance affects offspring fitness, i.e., the effects of inbreeding and outbreeding in natural populations, is a major goal in evolutionary biology. While inbreeding is often associated with fitness reduction (inbreeding depression), interpopulation outcrossing may have either positive (heterosis) or negative (outbreeding depression) effects. Within a metapopulation, all phenomena may occur with various intensities depending on the focal population (especially its effective size) and the trait studied. However, little is known about interpopulation variation at this scale. We here examine variation in inbreeding depression, heterosis, and outbreeding depression on life-history traits across a full-life cycle, within a metapopulation of the hermaphroditic snail Physa acuta. We show that all three phenomena can co-occur at this scale, although they are not always expressed on the same traits. A large variation in inbreeding depression, heterosis, and outbreeding depression is observed among local populations. We provide evidence that, as expected from theory, small and isolated populations enjoy higher heterosis upon outcrossing than do large, open populations. These results emphasize the need for an integrated theory accounting for the effects of both deleterious mutations and genetic incompatibilities within metapopulations and to take into account the variability of the focal population to understand the genetic consequences of inbreeding and outbreeding at this scale.
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

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

Multiple 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

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

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 >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

Heterochromatin 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

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

Studies 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

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

Red 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

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

A 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

Gyrodactylus 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.
Serum lactate dehydrogenase level in childhood acute lymphoblastic leukemia
Authors: Hafiz Md Golam , Mannan MA
Published: September 2008

Serum lactate dehydrogenase (LDH) level was estimated in 44 childhood (age range 1-15 years) acute lymphoblastic leukemia (ALL) on admission, day 14 and day 29 of induction. Another 25 children without ALL were included as control. On admission, the level of serum LDH was significantly high in ALL cases than control (p<0.001). Total WBC count was significantly decreased along with serum LDH level at day 14 and day 29 of induction (p<0.001). A significant rise of platelet count was observed at day 29 of induction in relation to significant decrease of serum LDH level (p<0.001). A significant decrease of peripheral and bone marrow blast cell percentages were also observed at day 29 of induction along with significant decrease level of serum LDH (p<0.001). So, the measurement of serum LDH level can be accepted as an enzymatic tool for presumption of childhood ALL and the response to chemotherapy during induction of remission.DOI = 10.3329/bmrcb.v33i3.1139Bangladesh Med Res Counc Bull 2007; 33: 88-91
A modified formula for defining tissue phantom ratio of photon beams
Authors: Alam M Jahangir , Rabbani KS , Zakaria GA , Hussain SM Akram , Kiber Adnan , Baig Tanvir
Published: September 2008

Tissue phantom ratio (TPR), for square fields of various dimensions has been determined at varying depths in water. The dose in water has been measured at a fixed source-to-surface distance (SSD) of 100 cm and reference depth of 5 cm for 6 MV photon beam of Siemens Linear Accelerator Primus II in German Cancer Research Center (DKFZ), Heidelberg, Germany. A modified formula has been developed to calculate the TPR value for isocentric treatment. The present article describes the conversion of the measured data values into a comprehensive and consistent data set by the modified formula, that gives the TPR from Percentage Depth Dose (PDD) with depth as a function of field sizes from 10 mm x 10 mm up to 300 mm x 300 mm) and depth (from 0 mm to 300 mm).DOI = 10.3329/bmrcb.v33i3.1140Bangladesh Med Res Counc Bull 2007; 33: 92-97
Serum complement (C3, C4) levels in patients with acute myocardial infarction and angina pectoris
Authors: Giasuddin ASM , ElMahdawi Jamila M , ElHassadi Fakhri M
Published: September 2008

Serum complement (C3, C4) levels in Libyan patients with acute myocardial infarction (AMI; 31 patients) and angina pectoris (AP; 11 patients) at the 1st day and 7th day of attack were estimated. A group of 26 healthy Libyans were taken as control subjects (CS). Serum C3 and C4 levels (mean Â± SD, mg/dl) were elevated at the 1st day in AMI as well as AP patients (C3 â AMI1: 154.0 Â± 28.5, AP1: 152.0 Â± 45.0, CS: 132.0 Â± 8.0, ANOVA: p=0.0072; C4â AMI1: 38 Â± 13, AP1: 37 Â± 17, CS: 29 Â± 6, ANOVA: p=0.0160). No significant differences for the elevated C3 and C4 levels at the 1st day were observed between the two diseases groups (AMI1 vs AP1 â C3: p=0.879, C4: p=0.818). At the 7th day, C3 and C4 levels were further elevated in AMI, while they remained at the similar elevated levels in AP (C3 â AMI 7: 173.1 Â± 28.0, AP 7: 149.0 Â± 41.0, CS: 132.0 Â± 8.0, ANOVA: p=0.0000; C4 â AMI 7: 46.0 Â± 7.0, AP 7: 36.0 Â± 15.0, CS: 29.0 Â± 6.0, ANOVA: p=0.0000). Again, no significance differences for the raised C3 and C4 levels at the 7th day was observed between AMI and AP patients (AMI 7 vs AP 7 â C3: P=0.059, C4: p=0.06). The C3 elevation showed significant positive correlation in AMI group (r=0.522, p=0.003) while it was insignificant in AP patients (r=0.037, p=0.915). Regarding C4 levels, it was significantly correlated in AMI (r=0.483, p=0.006), and in AP, although it was positively correlated (r=0.656, P=0.028) the observed difference was not significant (t=0.29, p=0.778). In conclusion, serum C3 and C4 levels were more profoundly elevated in AMI compared to AP patients suggestive of an acute phase and inflammatory response.DOI = 10.3329/bmrcb.v33i3.1141Bangladesh Med Res Counc Bull 2007; 33: 98-102
Seropositivity and pattern of viral hepatitis in clinically suspected cases of hepatitis in Dhaka city
Authors: Rahman Md. Tahminur , Sultana Rosy , Chowdhury Sohel Reza
Published: September 2008

An attempt was made to see the seropositivity and pattern of four common hepatotrophic viruses (HBV, HCV, HEV, HAV) in patients suspected to have been suffering from viral hepatitis. Blood samples from 2,995 cases of suspected HBV infection, 331 from HCV, 155 from HEV and 24 from HAV were tested for these viral markers. Of these a total of 245 (8.1%) were positive for HBsAg, 18 (5.4%) for HCV, 87 (56.1%) for HEV and 8 (33.3%) were positive for HAV infection. The predominant age group affected in HBV is 25-40 years, for HCV >61 years, HEV 26-50 years and HAV under 11 years. Seropositivity for HBsAg was statistically higher (near double) in males than females (p<0.05). HCV showed more seropositivity in males than females. HEV showed slight male preponderance and for HAV the female showed preponderance. The seropositivity rate was higher in Bangladesh in comparison to other developed and developing countries.DOI = 10.3329/bmrcb.v33i3.1142Bangladesh Med Res Counc Bull 2007; 33: 103-106
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.
The “Third Body” Approach to Joining of Metals by Simple Shear under Pressure
Authors: Beygelzimer Yan , Grötzinger Karl C. , Liewald Mathias , Estrin Yuri , Kulagin Roman
Published: April 2024

A continuum mechanics approach to cold welding (CW) of metals under shear is considered. The main idea is to treat a weld joint as an extra material—a “third body” in its own right. Its properties stem from plastic co‐deformation of the two contacting alloys. The mechanical characteristics of the weld joint, i.e., its strength and plasticity in the complex stress state, are determined by the deformation history of the “third body.” The proposed approach enables a unified description of the CW process itself, as well as the subsequent variation of shape of the composite material with the weld joint.
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

Peripheral 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

Metal–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

Objective

To assess workplace segregation in fatal occupational injury from 1992 to 2017 in North Carolina.

Methods

We 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.

Results

Hispanic 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.

Conclusions

If 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.
Working and impacting local communities as establishing the start of a conservation initiative: American Society of Primatology conservation committee webinar
Authors: Dobson Kaelyn , Gerstner Katie , Oktaviani Rahayu , Shaffer Christopher , Pruetz Jill
Published: April 2024

Nonhuman primate species currently face human‐induced pressures and will continue to face them in the modern landscape. These pressures require conservation projects in primate habitat countries to aid in protection, preservation, and conservation. Though there are several examples of primate conservation projects, starting up an initiative can be a daunting task. The American Society of Primatology (ASP) Conservation Committee hosted a video webinar presenting on the first steps of developing, running and continuing a primate conservation program. Dr. Christopher Shaffer, Rahayu Oktaviani, and Dr. Jill Pruetz presented their early program experiences establishing wild primate conservation projects to educate primatologists around the world. The running themes of the presentations included establishing community, working locally, impacting locally and preparing for the future.
Current State of Evidence for Neuroimaging Paradigms in Management of Acute Ischemic Stroke
Authors: Sarraj Amrou , Pujara Deep K , Campbell Bruce CV
Published: April 2024

Stroke is the chief differential diagnosis in patient presenting to the emergency room with abrupt onset focal neurological deficits. Neuroimaging, including non‐contrast computed tomography (CT), magnetic resonance imaging (MRI), vascular and perfusion imaging, is a cornerstone in the diagnosis and treatment decision‐making. This review examines the current state of evidence behind the different imaging paradigms for acute ischemic stroke diagnosis and treatment, including current recommendations from the guidelines. Non‐contrast CT brain, or in some centers MRI, can help differentiate ischemic stroke and intracerebral hemorrhage (ICH), a pivotal juncture in stroke diagnosis and treatment algorithm, especially for early window thrombolytics. Advanced imaging such as MRI or perfusion imaging can also assist making a diagnosis of ischemic stroke versus mimics such as migraine, Todd's paresis, or functional disorders. Identification of medium‐large vessel occlusions with CT or MR angiography triggers consideration of endovascular thrombectomy (EVT), with additional perfusion imaging help identify salvageable brain tissue in patients who are likely to benefit from reperfusion therapies, particularly in the ≥6 h window. We also review recent advances in neuroimaging and ongoing trials in key therapeutic areas and their imaging selection criteria to inform the readers on potential future transitions into use of neuroimaging for stroke diagnosis and treatment decision making. ANN NEUROL 2024;95:1017–1034