bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactive gene networks with KNIT
Authors: Magruder D S , Liebhoff A M , Bethune J , Bonn S 
Published: January 2021

Abstract

Summary
KNIT is a web application that provides a hierarchical, directed graph on how a set of genes is connected to a particular gene of interest. Its primary aim is to aid researchers in discerning direct from indirect effects that a gene might have on the expression of other genes and molecular pathways, a very common problem in omics analysis. As such, KNIT provides deep contextual information for experiments where gene or protein expression might be changed, such as gene knock-out and overexpression experiments.

Availability and implementation
KNIT is publicly available at http://knit.ims.bio. It is implemented with Django and Nuxtjs, with all major browsers supported.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sleep apnoea has a dose-dependent effect on atrial remodelling in paroxysmal but not persistent atrial fibrillation: a high-density mapping study
Authors: Nalliah Chrishan Joseph , Wong Geoffrey R , Lee Geoffrey , Voskoboinik Aleksandr , Kee Kirk , Goldin Jeremy , Watts Troy , Linz Dominik , Wirth Daniel , Parameswaran Ramanathan , Sugumar Hariharan , Prabhu Sandeep , McLellan Alex , Ling Han , Joseph Stephen , Morton Joseph B , Kistler Peter , Sanders Prashanthan , Kalman Jonathan M 
Published: January 2021

Abstract

Aims
Obstructive sleep apnoea (OSA) associates with atrial fibrillation (AF), but the relationship of OSA severity and AF phenotype with the atrial substrate remains poorly defined. We sought to define the atrial substrate across the spectrum of OSA severity utilizing high-density mapping.

Methods and results
Sixty-six consecutive patients (male 71%, age 61 ± 9) having AF ablation (paroxysmal AF 36, persistent AF 30) were recruited. All patents underwent formal overnight polysomnography and high-density left atrial (LA) mapping (mean 2351 ± 1244 points) in paced rhythm. Apnoea–hypopnoea index (AHI) (mean 21 ± 18) associated with lower voltage (−0.34, P = 0.005), increased complex points (r = 0.43, P &lt; 0.001), more low-voltage areas (r = 0.42, P &lt; 0.001), and greater voltage heterogeneity (r = 0.39, P = 0.001), and persisted after multivariable adjustment. Atrial conduction heterogeneity (r = 0.24, P = 0.025) but not conduction velocity (r = −0.09, P = 0.50) associated with AHI. Patchy regions of low voltage that co-localized with slowed conduction defined the atrial substrate in paroxysmal AF, while a diffuse atrial substrate predominated in persistent AF. The association of AHI with remodelling was most apparent among paroxysmal AF [LA voltage: paroxysmal AF −0.015 (−0.025, −0.005), P = 0.004 vs. persistent AF −0.006 (−0.017, 0.005), P = 0.30]. Furthermore, in paroxysmal AF an AHI ≥ 30 defined a threshold at which atrial remodelling became most evident (nil–mild vs. moderate vs. severe: 1.92 ± 0.42 mV vs. 1.84 ± 0.28 mV vs. 1.34 ± 0.41 mV, P = 0.006). In contrast, significant remodelling was observed across all OSA categories in persistent AF (1.67 ± 0.55 mV vs. 1.50 ± 0.66 mV vs. 1.55 ± 0.67 mV, P = 0.82).

Conclusion
High-density mapping observed that OSA associates with marked atrial remodelling, predominantly among paroxysmal AF cohorts with severe OSA. This may facilitate the identification of AF patients that stand to derive the greatest benefit from OSA management.
REGULATION OF A BACTERIOPHAGE T4 LATE GENE, soc, WHICH MAPS IN AN EARLY REGION
Authors: Macdonald Paul M , Kutter Elizabeth , Mosig Gisela 
Published: January 2021

ABSTRACT
We have sequenced and analyzed the expression of an early region of the bacteriophage T4 genome that surprisingly contains a late gene, soc. soc is oriented in the same direction as early genes, like the T4 lysozyme gene. Northern hybridization of early and late T4 RNA, using cloned T4 restriction fragments as probes, identified two long early transcripts and a short late transcript, all containing the soc-coding sequence. Thus, soc is transcribed both early and late. It is, however, translated only late. The inhibition of soc translation from the long early transcripts can be explained by formation of a hairpin in the RNA that sequesters the soc ribosome-binding site. The transcript initiated at the late promoter cannot form this hairpin and is, therefore, translated.
MUTAGENIC SPECIFICITY OF A NOVEL T4 DNA POLYMERASE MUTANT
Authors: Reha-Krantz Linda J , Liesner Evelyn M 
Published: January 2021

ABSTRACT
The in vivo mutational specificity of a novel T4 DNA polymerase mutator mutant, tsM19, was determined. Two genetic tester systems were used to characterize the mutant. Results of our studies indicate that tsM19 promotes transition and transversion mutagenesis and, possibly, frameshift mutagenesis. Central G:C base pairs in runs of three or more consecutive G:C base pairs may be target sites for tsM19-induced transitions.
A GENETIC ANALYSIS OF TARGETED GROWTH IN MICE
Authors: Riska Bruce , Atchley William R , Rutledge J J 
Published: January 2021

ABSTRACT
Effects of normal growth regulation on components of phenotypic variance and covariance of body weight were examined in a cross-fostering study of growth between 2 and 10 wk of age in ICR randombred mice. Different early growth rates caused genetic, postnatal maternal and residual environmental variances to increase, but these variances were subsequently reduced by negative autocorrelation between early and later growth. Postnatal maternal variance continued to increase for about 1 wk after weaning but then decreased substantially. Genetic variance caused by preweaning growth followed a pattern of increase and decrease very similar to that of postnatal maternal variance, but this pattern was masked by new genetic variance. Normal growth regulation affects the magnitudes of genetic variances and serial autocorrelations. The timing of these changes suggests that regulation of cell numbers reduces variance near the end of exponential growth, but this may be obscured by subsequent increase in cell size. In contrast with earlier studies, we find that targeted growth reduces both genetically and environmentally determined differences among early growth trajectories. Final size may be determined by an antagonistic balance between early growth rate and age at initiation of puberty.
MODIFICATIONS OF MEAN OVARIOLE NUMBER, FRESH WEIGHT OF ADULT FEMALES AND DEVELOPMENTAL TIME IN DROSOPHILA MELANOGASTER INDUCED BY DROSOPHILA C VIRUS
Authors: Thomas-Orillard Michele 
Published: January 2021

ABSTRACT
Drosophila C virus, a picornavirus that has some influence on ovarian morphogenesis, was discovered in a French strain of Drosophila melanogaster. When the strain was infected by Drosophila C virus (DCV), the mean number of ovarian tubes and weights of the adult females increased, but the developmental time from egg to imago decreased. The maternal effects observed when DCV was present disappeared when the strain was DCV free but were restored by experimental contamination.
SHORTVEIN, A NEW COMPONENT OF THE DECAPENTAPLEGIC GENE COMPLEX IN DROSOPHILA MELANOGASTER
Authors: Segal Daniel , Gelbart William M 
Published: January 2021

ABSTRACT
Our laboratory has been concerned with the structure and function of the decapentaplegic gene complex (DPP-C) in Drosophila melanogaster . To define the boundaries of the complex, we have studied the genetics of mutations allelic to a previously discovered mutation shortvein (shv), known to reside near decapentaplegic. We found that shortvein resides distal to Hin-d and dpp within the same polytene chromosome doublet, 22F1-2. Lesions in shv can affect not only the formation of the wing veins but also can interfere with normal development of parts of the adult and/or be lethal. Like those of dpp mutants, the shv-associated adult abnormalities affect distal epidermal structures. Some shv lesions cause a larval lethal syndrome which is associated with an unusually long larval stage (ca. five to six times its normal duration). Lesions in shv exhibit an involved pattern of complementation with dpp mutations, indicating that both shv and dpp are parts of a single gene complex. A subset of the array of mutant phenotypes displayed by shv/dpp trans-heterozygotes appear to be dpp-specific phenotypes; we interpret these as reflecting an inactivation effect of certain shv alleles on dpp functions. The other abnormalities displayed by these trans-heterozygotes appear to be shv-specific defects; we view these as indicating an inactivation effect of certain dpp mutations on shv functions. Furthermore, embryonic lethal (EL) mutations within the DPP-C exhibit allelic interactions with all shv mutations. We conclude that the shortvein region represents a newly identified integrated portion of the DPP-C.
GENETIC ANALYSIS OF MUTANTS OF SACCHAROMYCES CEREVISIAE RESISTANT TO THE HERBICIDE SULFOMETURON METHYL
Authors: Falco S C , Dumas K S 
Published: January 2021

ABSTRACT
Sulfometuron methyl (SM), a potent new sulfonylurea herbicide, inhibits growth of the yeast Saccharomyces cerevisiae on minimal media. Sixty-six spontaneous mutants resistant to SM were isolated. All of the resistance mutations segregate 2:2 in tetrads; 51 of the mutations are dominant, five are semidominant and ten are recessive. The mutations occur in three linkage groups, designated SMR1, smr2 and smr3. Several lines of evidence demonstrate that the SMR1 mutations (47 dominant and four semidominant) are alleles of ILV2 which encodes acetolactate synthase (ALS), the target of SM. First, SMR1 mutations result in the production of ALS enzyme activity with increased resistance to SM. Second, molecular cloning of the ILV2 gene permitted the isolation of mutations in the cloned gene which result in the production of SM-resistant ALS. Finally, SMR1 mutations map at the ILV2 locus. The smr2 mutations (four recessive, two dominant and one semidominant) map at the pdr1 (pleiotropic drug resistance) locus and show cross-resistance to other inhibitors, typical of mutations at this locus. The smr3 mutations (six recessive and two dominant) define a new gene which maps approximately midway between ADE2 and HIS3 on the right arm of chromosome XV.
THE GENE STRUCTURES OF SPONTANEOUS MUTATIONS AFFECTING A CAENORHABDITIS ELEGANS MYOSIN HEAVY CHAIN GENE
Authors: Eide David , Anderson Philip 
Published: January 2021

ABSTRACT
We have isolated spontaneous mutations affecting the unc-54 major myosin heavy chain gene of Caenorhabditis elegans (variety Bristol). Spontaneous unc-54 mutants occur in C. elegans populations at a frequency of approximately 3 × 10-7. We have studied the gene structure of 65 independent unc-54 mutations using filter-transfer hybridization techniques. Most unc-54 mutations (50 of 65) exhibit no abnormalities detected with these techniques; these mutations are small lesions affecting less than 100 base pairs. Approximately 17% of the mutations (11 of 65) are simple deletions, ranging in size from less than 100 base pairs to greater than 17 kilobases. One isolate contains two separate deletions, each of which affects unc-54. Two mutants contain tandem genetic duplications that include a portion of unc-54 and extend 8-10 kilobases beyond the 5' terminus of the mRNA. Conspicuously absent from our collection of spontaneous unc-54 mutations are any resulting from insertion of transposable genetic elements. Such mutants, if they occur, must arise at a frequency of less than 5 × 10-9
GENE CONVERSION AT THE GRAY LOCUS OF SORDARIA FIMICOLA: FIT OF THE EXPERIMENTAL DATA TO A HYBRID DNA MODEL OF RECOMBINATION
Authors: Kalogeropoulos Angelos , Thuriaux Pierre 
Published: January 2021

ABSTRACT
A hybrid DNA (hDNA) model of recombination has been algebraically formulated, which allows the prediction of frequencies of postmeiotic segregation and conversion of a given allele and their probability of being associated with a crossing over. The model considered is essentially the "Aviemore model." In contrast to some other interpretations of recombination, it states that gene conversion can only result from the repair of heteroduplex hDNA, with postmeiotic segregation resulting from unrepaired heteroduplexes. The model also postulates that crossing over always occurs distally to the initiation site of the hDNA. Eleven types of conversion and postmeiotic segregation with or without associated crossover were considered. Their theoretical frequencies are given by 11 linear equations with ten variables, four describing heteroduplex repair, four giving the probability of hDNA formation and its topological properties and two giving the probability that crossing over occurs at the left or right of the converting allele.—Using the experimental data of Kitani and coworkers on conversion at the six best studied gray alleles of Sordaria fimicola, we found that the model considered fit the data at a P level above or very close (allele h4) to the 5% level of sampling error provided that the hDNA is partly asymmetric. The best fitting solutions are such that the hDNA has an equal probability of being formed on either chromatid or, alternatively, that both DNA strands have the same probability of acting as the invading strand during hDNA formation. The two mismatches corresponding to a given allele are repaired with different efficiencies. Optimal solutions are found if one allows for repair to be more efficient on the asymmetric hDNA than on the symmetric one. In the case of allele g1, our data imply that the direction of repair is nonrandom with respect to the strand on which it occurs.
SPONTANEOUS IR DUPLICATIONS GENERATED AT MITOSIS IN ASPERGILLUS NIDULANS: FURTHER EVIDENCE OF A PREFERENTIAL SITE OF TRANSPOSED ATTACHMENT
Authors: Daud F , Ortori G S , Roper J A 
Published: January 2021

ABSTRACT
A radiation-induced translocation, T(IIR → IIIL), has been shown to be nonreciprocal and to have most of IIR, including its terminus, attached uninverted to the terminus of IIIL.—Progeny with the IIR segment in duplicate, obtained from crosses of T(IIR → IIIL) to strains with a standard genome, were unstable at mitosis; like earlier duplication strains, they suffered deletions from either duplicate segment. Frequent mitotic crossing over occurred between the duplicate IIR segments so that, following deletions, more than two classes of stable, balanced products arose from each heterozygous duplication strain.— Spontaneous, mitotically arising duplications of the IR segment, bearing the rate-limiting adE20 allele, can be selected on adenine-free medium on which they emerge as vigorous sectors from the stunted adE20 colony. It was shown previously that most such duplications, when selected from a strain with standard genome, had the terminal IR segment attached to the end of IIR. Selection has now been made from an adE20 strain carrying T(IIR → IIIL), and seven of the 13 independent IR duplications were linked to the III-IIR translocation complex. In three strains analyzed further, the duplicate IR segments, which included the IR terminus, were attached uninverted to the terminus of IIR; the segments of IR were of approximately equal genetic length.—This supports earlier suggestions that there is a preferential site for the initiation of IR duplications and a preferential site, the IIR terminus, for their attachment.
POPULATION BOTTLENECKS AND NONEQUILIBRIUM MODELS IN POPULATION GENETICS. II. NUMBER OF ALLELES IN A SMALL POPULATION THAT WAS FORMED BY A RECENT BOTTLENECK
Authors: Maruyama Takeo , Fuerst Paul A 
Published: January 2021

ABSTRACT
A model is presented in which a large population in mutation/drift equilibrium undergoes a severe restriction in size and subsequently remains at the small size. The rate of loss of genetic variability has been studied. Allelic loss occurs more rapidly than loss of genic heterozygosity. Rare alleles are lost especially rapidly. The result is a transient deficiency in the total number of alleles observed in samples taken from the reduced population when compared with the number expected in a sample from a steady-state population having the same observed heterozygosity. Alternatively, the population can be considered to posses excess gene diversity if the number of alleles is used as the statistical estimator of mutation rate. The deficit in allele number arises principally from a lack of those alleles that are expected to appear only once or twice in the sample. The magnitude of the allelic deficiency is less, however, than the excess that an earlier study predicted to follow a rapid population expansion. This suggests that populations that have undergone a single bottleneck event, followed by rapid population growth, should have an apparent excess number of alleles, given the observed level of genic heterozygosity and provided that the bottleneck has not occurred very recently. Conversely, such populations will be deficient for observed heterozygosity if allele number is used as the sufficient statistic for the estimation of 4Nev. Populations that have undergone very recent restrictions in size should show the opposite tendencies.
LETHAL MUTATIONS FLANKING THE 68C GLUE GENE CLUSTER ON CHROMOSOME 3 OF DROSOPHILA MELANOGASTER
Authors: Crosby Madeline A , Meyerowitz Elliot M 
Published: January 2021

ABSTRACT
We have conducted a genetic analysis of the region flanking the 68C glue gene cluster in Drosophila melanogaster by isolating lethal and semilethal mutations uncovered by deficiencies which span this region. Three different mutagens were used: ethyl methanesulfonate (EMS), ethyl nitrosourea (ENU) and diepoxybutane (DEB). In the region from 68A3 to 68C11, 64 lethal, semilethal, and visible mutations were recovered. These include alleles of 13 new lethal complementation groups, as well as new alleles of rotated, low xanthine dehydrogenase, lethal(3)517 and lethal(3)B76. Six new visible mutations from within this region were recovered on the basis of their reduced viability; all proved to be semiviable alleles of lethal complementation groups. No significant differences were observed in the distributions of lethals recovered using the three different mutagens. Each lethal was mapped on the basis of complementation with overlapping deficiencies; mutations that mapped within the same interval were tested for complementation, and the relative order of the lethal groups within each interval was determined by recombination. The cytological distribution of genes within the 68A3-68C11 region is not uniform: the region from 68A2,3 to 68B1,3 (seven to ten polytene chromosome bands) contains at least 13 lethal complementation groups and the mutation low xanthine dehydrogenase; the adjoining region from 68B1,3 to 68C5,6 (six to nine bands) includes the 68C glue gene cluster, but no known lethal or visible complementation groups; and the interval from 68C5,6 to 68C10,11 (three to five bands) contains at least three lethal complementation groups and the visible mutation rotated. The developmental stage at which lethality is observed was determined for a representative allele from each lethal complementation group.
LIMITS TO THE RELATIONSHIP AMONG RECOMBINATION, DISEQUILIBRIUM AND EPISTASIS IN TWO-LOCUS MODELS
Authors: Hastings Alan 
Published: January 2021

ABSTRACT
I determine limits to the equilibrium relationship among epistasis, recombination and disequilibrium in two-locus, two-allele models using linear programming techniques. I show that when allele frequencies are one-half at each locus, the symmetric model is the fitness pattern that generates the most disequilibrium for the smallest level of epistasis. When allele frequencies deviate from one-half, much larger levels of epistasis are required to generate similar levels of disequilibrium. I determine the level of epistasis required to generate observed significant levels of disequilibrium in natural populations. The overall implication is that disequilibrium will be large at equilibrium only between strongly interacting, closely linked loci.
ESTERASE GENES IN PARALLEL COMPOSITE CROSS BARLEY POPULATIONS
Authors: Luckett D J , Edwards K J R 
Published: January 2021

ABSTRACT
The California population of Composite Cross V of barley was used as the source of three subpopulations that were started from generations 10, 20 and 30, respectively, and were grown in parallel environmental conditions in Cambridge for eight generations. Outcrossing rates (0.2%) were even lower than in the California material, and heterozygotes were correspondingly rare, so that the populations were essentially mixtures of homozygous lines. Four esterase loci that were polymorphic in the base Composite Cross V remained so in all the derived populations, but showed considerable changes in allelic frequency over time, particularly at two of the genes. Multilocus analysis showed that strong directional changes occurred in all three populations, but they were not consistent. One particular genotype became predominant in the population derived from generation 10, whereas in the other two populations it was a genotype with different alleles at the Est1 and Est3 loci that rose to frequencies of more than 50%. Strong directional selection undoubtedly occurred in these populations, but did not cause parallel changes in esterase gene frequencies. These data do not facilitate a discrimination between the alternative explanations of hitchhiking or multilocus selection at these loci.
FRAMESHIFT SUPPRESSION BY thyA MUTANTS OF ESCHERICHIA COLI K-12
Authors: Herrington Muriel B , Kohli Anjali , Faraci Maria 
Published: January 2021

ABSTRACT
We have extended our previous study on the suppression of frameshift mutants by Escherichia coli thyA mutants by assaying suppression of 15 rIIB frameshift mutants of bacteriophage T4 on one of our suppressing thyA mutant strains. The majority of insertion mutants were suppressible, whereas none of the deletion mutants tested was suppressible. Frameshift suppression could be inhibited by adding thymidine to the assay medium, but was not affected by the presence of a restrictive rpsL mutation in the host strain. We suggest that the frameshift suppression event occurs at a nonsense codon generated by the frameshift mutation.
WHAT CAN BE LEARNT ABOUT SELECTION FROM GENE FREQUENCY DISTRIBUTION?
Authors: Mani G S , Cook L M , Marvdashti R 
Published: January 2021

ABSTRACT
Polymorphism has been studied at the Esterase 6 locus in the Yellow Fever mosquito Aedes aegypti (L.) in laboratory stocks. At least 12 alleles are present, with up to four coexisting in a stock. The allele frequency distribution is quite sharply peaked at a mode of about 0.25. The experimental data are compared with the results of simulation based on two models, one in which the initial global distribution is taken to be the stationary distribution obtained from the neutral model assuming M = 4μ Ne = 1 and the other in which the initial global distribution is generated from the experimental populations studied. The results suggest that the patterns observed are not likely to arise through random fluctuation of frequencies in neutral alleles, but that some kind of selection maintains polymorphism, either in the wild or in the laboratory, or both.