bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of REO1, a gene involved in negative regulation of COX5b and ANB1 in aerobically grown Saccharomyces cerevisiae.
Authors: Trueblood C E , Poyton R O 
Published: January 2021

Abstract
In Saccharomyces cerevisiae, the COX5a and COX5b genes constitute a small gene family that encodes two forms of cytochrome c oxidase subunit V, Va and Vb, either of which can provide a function essential for cytochrome c oxidase activity and respiration. In aerobically grown wild-type yeast cells, Va is the predominant form of subunit V. The COX5b gene alone does not produce enough Vb to support a respiration rate sufficient to allow growth on nonfermentable carbon sources. By selecting for mutations that increase the respiratory capacity of a strain deleted for COX5a, we have identified a gene that is involved in negative regulation of COX5b expression under aerobic growth conditions. Each of four independently isolated reo1 mutations are shown to be recessive, unlinked to COX5b, but dependent on COX5b for phenotypic expression. The mutations define a single complementation and linkage group: designated as REO1 for regulator of expression of oxidase. reo1 mutations increase expression of COX5b in aerobically grown cells, but not in anaerobically grown cells, where expression is already elevated. These mutations have no effect on COX5a, the other member of this small gene family which is positively regulated by heme and oxygen. The REO1 gene does play a role in repression of ANB1, a gene that is normally repressed under aerobic but not anaerobic conditions. Neither rox1 or rox3 mutations, which have previously been shown to increase ANB1 expression, are in the same complementation group as reo1 mutations.
Sequence amplification and gene rearrangement in parasitic nematode mitochondrial DNA.
Authors: Hyman B C , Beck J L , Weiss K C 
Published: January 2021

Abstract
The nematode Romanomermis culicivorax, an obligate mosquito parasite, possesses a 26 kilobase (kb) mitochondrial genome. The unusually large size is due to transcriptionally active DNA sequences present as 3.0 kb direct tandem repeats and as inverted portions of the repeating unit located elsewhere in the mitochondrial DNA (mtDNA). The genome rearrangements involved in establishing this unusual sequence organization may have dramatically altered conventional mitochondrial gene order. Genes for subunits of the cytochrome c oxidase complex (COI and COII) are normally closely linked in animal mtDNAs, but are separated by approximately 8 kb in this mitochondrial genome.
Design and analysis of experiments on random drift and inbreeding depression.
Authors: Lynch M 
Published: January 2021

Abstract
While the genetic consequences of inbreeding and small population size are of fundamental importance in many areas of biology, empirical research on these phenomena has proceeded in the absence of a well-developed statistical methodology. The usual approach is to compare observed means and variances with the expectations of Wright's neutral, additive genetic model for quantitative characters. If the observations deviate from the expectations more than can be accounted for by sampling variance of the parameter estimates, the null hypothesis is routinely rejected in favor of alternatives invoking evolutionary forces such as selection or nonadditive gene action. This is a biased procedure because it treats sequential samples from the same populations as independent, and because it ignores the fact that the expectations of the neutral additive genetic model will rarely be realized when only a finite number of lines are studied. Even when genes are perfectly additive and neutral, the variation among the properties of founder populations, the random development of linkage disequilibrium within lines, and the variance in inbreeding between lines reduce the likelihood that Wright's expectations will be realized in any particular set of lines. Under most experimental designs, these sources of variation are much too large to be ignored. Formulas are presented for the variance-covariance structure of the realized within- and between-line variance under the neutral additive genetic model. These results are then used to develop statistical tests for detecting the operation of selection and/or inbreeding depression in small populations. A number of recommendations are made for the optimal design of experiments on drift and inbreeding, and a method is suggested for the correction of data for general environmental effects. In general, it appears that we can best understand the response of populations to inbreeding and finite population size by studying a very large number (&gt;100) of self-fertilizing or full-sib mated lines in parallel with one or more stable control populations.
A genetic analysis of suppressors of the PF10 mutation in Chlamydomonas reinhardtii.
Authors: Dutcher S K , Gibbons W , Inwood W B 
Published: January 2021

Abstract
A mutation at the PF10 locus of the unicellular green alga Chlamydomonas reinhardtii leads to abnormal cell motility. The asymmetric form of the ciliary beat stroke characteristic of wild-type flagella is modified by this mutation to a nearly symmetric beat. We report here that this abnormal motility is a conditional phenotype that depends on light intensity. In the absence of light or under low light intensities, the motility is more severely impaired than at higher light intensities. By UV mutagenesis we obtained 11 intragenic and 70 extragenic strains that show reversion of the pf10 motility phenotype observed in low light. The intragenic events reverted the motility phenotype of the pf10 mutation completely. The extragenic events define at least seven suppressor loci; these map to linkage groups IV, VII, IX, XI, XII and XVII. Suppressor mutations at two of the seven loci (LIS1 and LIS2) require light for their suppressor activity. Forty-eight of the 70 extragenic suppressors were examined in heterozygous diploid cells; 47 of these mutants were recessive to the wild-type allele and one mutant (bop5-1) was dominant to the wild-type allele. Complementation analysis of the 47 recessive mutants showed unusual patterns. Most mutants within a recombinationally defined group failed to complement one another, although there were pairs that showed intra-allelic complementation. Additionally, some of the mutants at each recombinationally defined locus failed to complement mutants at other loci. They define dominant enhancers of one another.
INTRAGENIC DELETIONS AND SALIVARY BAND RELATIONSHIPS IN DROSOPHILA
Authors: Welshons W J , Keppy D O 
Published: January 2021

ABSTRACT
In the absence of assumptions pertaining to the organization and function of chromomeric DNA, the cytogenetic analysis of intragenic deletions that start at Notch and spread to the right or left of the locus suggests that the recombinational gene is bilaterally associated with salivary band 3C7. Either there are two genes resolved as a single cistron, or one must seek an alternative interpretation that allows some modicum of independent in the relationship between gene and band. Although we momentarily lean toward the hypothesis that gene and salivary band are separate entities on a binemic chromosome, alternative views can be devised, and the data must remain open to reinterpretation.—The recessive visible allele faswb behaves as a point mutant at the left end of the map and seems to be a deletion in the interval 3C6 to 7; we suspect some part of the band is missing. We have used the aberration in faswb as a cytological marker, isolated intragenic recombinants, and subjected them to examination. The analysis indicates that the chromosomal interchanges occurred to the right of 3C7.
REQUIREMENT FOR CELL DISPERSION PRIOR TO SELECTION OF INDUCED AZAGUANINE-RESISTANT COLONIES OF CHINESE HAMSTER CELLS
Authors: Myhr B C , DiPaolo J A 
Published: January 2021

ABSTRACT
With V79 Chinese hamster cell cultures treated with a mutagen, the maximum frequency of colonies resistant to 8-azaguanine (AZG) was attained when the cells were dispersed after a suitable expression time before adding the selection medium. V79–4 cells were exposed to 500 µM MMS, 7 µM AFAA, or 10 µM MNNG and allowed to multiply before being reseeded at 4 × 104 cells/60 mm dish and selected with 10 µg/ml AZG. Maximum frequencies of 4 × 10-5, 4 × 10-4, and 2.4 × 10-3 were obtained about 100, 130, and 200 hrs after exposure to MMS, AFAA, and MNNG, respectively. The maximum frequencies following MMS or MNNG treatments were about 10-fold greater than those obtained when induction and selection of AZG-resistant colonies were performed in the same culture dish. The reseeding of treated cells eliminated the possibility of metabolic cooperation within mosaic colonies of wild-type and mutant cells and achieved expression of the induced changes before intercolony crossfeeding reduced the frequency of resistant colonies.—AZG-resistant colonies were selected in medium containing dialyzed fetal bovine serum, and the selection medium was replaced at least twice. Both serum dialysis and selection medium replacement were necessary for consistent achievement of background frequencies of resistant colonies near 10-6. Reconstruction experiments with AZG-resistant V79 lines showed that the efficiency of recovery of resistant cells in the selection medium was constant over a range of 0–20 colonies observed/dish. A mixed population of V79 and AZG-resistant cells was also correctly analyzed by the procedure used in mutagenesis studies.
PRIMARY HOMOTHALLISM—RELATION TO HETEROTHALLISM IN THE REGULATION OF SEXUAL MORPHOGENESIS IN SISTOTREMA
Authors: Ullrich Robert C , Raper John R 
Published: January 2021

ABSTRACT
The wood-rotting basidiomycete, Sistotrema brinkmannii, is an aggregate of biological species possessing several variations—homothallism, bipolar heterothallism and tetrapolar heterothallism—on the genetic regulation of a critical phase of development. Nutritionally forced intra- and interspecific matings provide genetic information about the relatedness of homothallic isolates, the relation of the various species to one another, the genetic basis of homothallism, and its relationship to heterothallism. Most homothallic isolates are interfertile when nutritionally forced. Successful hybridization between species is restricted to particular combinations of homothallic × bipolar isolates. Significant findings of these studies include: (1) documentation of hybridization of biological species in the Homobasidiomycetes, (2) documentation of the relatedness of two naturally occurring, variant systems, homothallism and bipolar heterothallism, that regulate sexual morphogenesis in the higher fungi, (3) evidence for definite, but limited, evolutionary divergence of the polygenic, regulated components of the respective systems, and (4) indication that the genetic basis of homothallism in this system is essentially due to constitutive function and consequently is fundamentally different from presently understood mechanisms in other self-fertile systems.
THE EVOLUTION OF SELECTIVELY SIMILAR ELECTRO-PHORETICALLY DETECTABLE ALLELES IN FINITE NATURAL POPULATIONS
Authors: Wehrhahn C F 
Published: January 2021

Abstract
Most of the models of population genetics are not realistic when applied to data on electrophoretic variants of proteins because the same net charge may result from any of several amino acid combinations. In the absence of realistic models they have, however, been widely used to test competing hypotheses about the origin and maintenance of genetic variation in populations. In this paper I present a general method for determining probability generating functions for electrophoretic state differences. Then I use the method to find allelic state difference distributions for selectively similar electrophoretically detectable alleles in finite natural populations.
Predicted patterns of genetic variation, both within and among species, are in reasonable accord with those found in the Drosophila willistoni group by Ayala et al. (1972) and by Ayala and Tracey (1974).
GENETIC ANALYSIS OF COPPER RESISTANCE IN PARAMECIUM AURELIA SYNGEN 4
Authors: Nyberg Dennis 
Published: January 2021

ABSTRACT
Measurement of the median tolerance limit to cupric ion of 28 wild stocks of Paramecium aurelia syngen 4 revealed a phenotypic polymorphism; two stocks showed a much greater resistance than the others. Genetic analysis showed the resistant phenotype was produced by a recessive allele, cur, identical in both resistant wild stocks. No modification of the phenotypic expression of this allele could be detected after backcrossing into different genetic backgrounds. The results are interpreted to support the importance of mutational adaptation in this inbreeding species. Possible patterns of internal genetic organization of species which rely on mutation for adaptation are discussed.
TEMPERATURE-SENSITIVE MUTANTS OF A CHINESE HAMSTER CELL LINE. I. SELECTION OF CLONES WITH DEFECTIVE MACROMOLECULAR BIOSYNTHESIS
Authors: Roufa Donald J , Reed Susan J 
Published: January 2021

ABSTRACT
Temperature-sensitive clones have been selected from a mutagenized culture of Chinese hamster lung cells by a procedure involving bromodeoxy-uridine (BrdU) incorporation and irradiation with black light. The selection procedure used in these studies was adapted from methods developed by others to yield mutants that cease DNA replication within a short time after they are transferred to nonpermissive temperature. After mutagenesis with ethyl methanosulfonate ten clones survived the selection procedure. Three of the clones (mutants) were temperature-sensitive as measured by growth properties. Two mutants ceased DNA synthesis within six hours of being shifted to 39° and the third mutant continued to synthesize DNA at nonpermissive temperature at a reduced rate for at least 24 hours. Thus, all three mutants survived the selection procedure for understandable reasons, since each was unable to incorporate sufficient BrdU at 39° to lethally protosensitize its DNA during the standard exposure period. The two mutants that cease DNA synthesis at high temperature (clones 115-47 and 115-53) also stop incorporating radioactive amino acids and uridine within six hours at 39°. Their complex phenotype, i.e. defective DNA, RNA and protein biosynthesis, is reversible. When these mutants were returned to 33° after 8 hours at 39°, both resumed DNA synthesis immediately (&lt; 1 hour). Reversal of defective DNA synthesis in both mutants was sensitive to drugs that inhibit protein biosynthesis specifically. Those same drugs, as well as toxic amino acids analogs, also effected a striking mutant phenocopy in wild-type cells. The phenocopy produced by amino acid analogs that are incorporated into mammalian proteins suggested that one or more proteins must be synthesized continuously to support mammalian cells engaged in programmed DNA replication.
LIMITS TO THE ADVANTAGE OF RECOMBINATION IN INCREASING THE RATE OF INCORPORATION OF FAVORABLE MUTANTS
Authors: Nyberg Dennis 
Published: January 2021

ABSTRACT
The advantage of recombination in increasing the rate of incorporation of favorable mutants is shown to disappear for large NU if substitution is occurring at only two loci. Recombination will, on the average, destroy all double favorable individuals in a haploid population until the product of the frequencies of the single favorable mutants exceeds 1/N. As NU increases there is an increasing probability of the occurrence of the double favorable my mutation alone. Recombination provides a significant advantage in the rate of incorporation of favorable mutants only if 2 s/lnN&lt;NU&lt;2c when substitution is occurring at only two loci. If substitution is occurring at more than two loci the recombining population apparently has a substantial advantage for large NU.
Should we be measuring DNA damage in human spermatozoa? New light on an old question
Authors: Aitken R John , Bakos Hassan W 
Published: January 2021

Abstract
Assessments of sperm DNA damage are controversial because of perceived uncertainties over the relationship with pregnancy and the limited range of therapies available should positive results be returned. In this article, we highlight recent data supporting a chain of associations between oxidative stress in the male germ line, DNA damage in spermatozoa, defective DNA repair in the oocyte, the mutational load carried by the resulting embryo and the long-term health trajectory of the offspring. Any condition capable of generating oxidative damage in spermatozoa (age, obesity, smoking, prolonged abstinence, varicocele, chemical exposures, radiation etc.) is capable of influencing offspring health in this manner, creating a range of pathologies in the progeny including neuropsychiatric disorders and cancer. If sperm DNA damage is detected, there are several therapeutic interventions that can be introduced to improve DNA quality prior to the use of these cells in ART. We therefore argue that infertility specialists should be engaged in the diagnosis and remediation of sperm DNA damage as a matter of best practice, in order to minimize the risk of adverse health outcomes in children conceived using ART.
Rivers of gas – I. Unveiling the properties of high redshift filaments
Authors: Ramsøy Marius , Slyz Adrianne , Devriendt Julien , Laigle Clotilde , Dubois Yohan 
Published: January 2021

ABSTRACT
At high redshift, the cosmic web is widely expected to have a significant impact on the morphologies, dynamics, and star formation rates of the galaxies embedded within it, underscoring the need for a comprehensive study of the properties of such a filamentary network. With this goal in mind, we perform an analysis of high-z gas and dark matter (DM) filaments around a Milky Way-like progenitor simulated with the ramses adaptive mesh refinement (AMR) code from cosmic scales (∼1 Mpc) down to the virial radius of its DM halo host (∼20 kpc at z = 4). Radial density profiles of both gas and DM filaments are found to have the same functional form, namely a plummer-like profile modified to take into account the wall within which these filaments are embedded. Measurements of the typical filament core radius r0 from the simulation are consistent with that of isothermal cylinders in hydrostatic equilibrium. Such an analytic model also predicts a redshift evolution for the core radius of filaments in fair agreement with the measured value for DM [r0∝ (1 + z)−3.18 ± 0.28]. Gas filament cores grow as [r0∝ (1 + z)−2.72 ± 0.26]. In both gas and DM, temperature and vorticity sharply drop at the edge of filaments, providing an excellent way to constrain the outer filament radius. When feedback is included, the gas temperature and vorticity fields are strongly perturbed, hindering such a measurement in the vicinity of the galaxy. However, the core radius of the filaments as measured from the gas density field is largely unaffected by feedback; and the median central density is only reduced by about 20 per cent.
Bank Concentration and Product Market Competition
Authors: Saidi Farzad , Streitz Daniel 
Published: January 2021

Abstract
This paper documents a link between bank concentration and markups in nonfinancial sectors. We exploit concentration-increasing bank mergers and variation in banks’ market shares across industries and show that higher credit concentration is associated with higher markups and that high-market-share lenders charge lower loan rates. We argue that this is due to the greater incidence of competing firms sharing common lenders that induce less aggressive product market behavior among their borrowers, thereby internalizing potential adverse effects of higher rates. Consistent with our conjecture, the effect is stronger in industries with competition in strategic substitutes where negative product market externalities are greatest.
Voluntary wheel running improves outcomes in an early life stress–induced model of urologic chronic pelvic pain syndrome in male mice
Authors: Fuentes Isabella M. , Jones Brittni M. , Brake Aaron D. , Pierce Angela N. , Eller Olivia C. , Supple Rachel M. , Wright Douglas E. , Christianson Julie A. 
Published: January 2021

Abstract
Patients with a history of early life stress (ELS) exposure have an increased risk of developing chronic pain and mood disorders later in life. The severity of ELS in patients with urologic chronic pelvic pain syndrome (UCPPS) is directly correlated with symptom severity and increased comorbidity, and is inversely related to likelihood of improvement. Voluntary exercise improves chronic pain symptoms, and our group and others have shown that voluntary wheel running can improve outcomes in stress-induced UCPPS models, suggesting that exercise may negate some of the outcomes associated with ELS. Here, we provide further evidence that voluntary wheel running can attenuate increased perigenital mechanical sensitivity, bladder output, and mast cell degranulation in the bladder and prostate in male mice that underwent neonatal maternal separation (NMS). Sedentary male NMS mice had reduced serum corticosterone, which was not impacted by voluntary wheel running, although stress-related regulatory gene expression in the hypothalamus and hippocampus was significantly increased after exercise. Neurogenesis in the dentate gyrus of the hippocampus was diminished in sedentary NMS mice and significantly increased in both exercised naïve and NMS mice. Sucrose consumption increased in exercised naïve but not NMS mice, and anxiety behaviors measured on an elevated plus maze were increased after exercise. Together these data suggest that voluntary wheel running is sufficient to normalize many of the UCPPS-related outcomes resulting from NMS. Exercise also increased hippocampal neurogenesis and stress-related gene expression within the hypothalamic–pituitary–adrenal axis, further supporting exercise as a nonpharmacological intervention for attenuating outcomes related to ELS exposure.
Relationship Between Retinal Layer Thickness and Disability Worsening in Relapsing-Remitting and Progressive Multiple Sclerosis
Authors: Cellerino Maria , Priano Luca , Bruschi Nicolò , Boffa Giacomo , Petracca Maria , Novi Giovanni , Lapucci Caterina , Sbragia Elvira , Uccelli Antonio , Inglese Matilde 
Published: January 2021

Background:
Data regarding the predictive value of optical coherence tomography (OCT)-derived measures are lacking, especially in progressive multiple sclerosis (PMS). Accordingly, we aimed at investigating whether a single OCT assessment can predict a disability risk in both relapsing-remitting MS (RRMS) and PMS.

Methods:
One hundred one patients with RRMS and 79 patients with PMS underwent Spectral-Domain OCT, including intraretinal layer segmentation. All patients had at least 1 Expanded Disability Status Scale (EDSS) measurement during the subsequent follow-up (FU). Differences in terms of OCT metrics and their association with FU disability were assessed by analysis of covariance and linear regression models, respectively.

Results:
The median FU was 2 years (range 1–5.5 years). The baseline peripapillary retinal nerve fiber layer (pRNFL) and ganglion cell + inner plexiform layer (GCIPL) were thinner in PMS compared with RRMS (P = 0.02 and P = 0.003, respectively). In the RRMS population, multivariable models showed that the GCIPL significantly correlated with FU disability (0.04 increase in the EDSS for each 1-μm decrease in the baseline GCIPL, 95% confidence interval: 0.006–0.08; P = 0.02). The baseline GCIPL was thinner in patients with RRMS with FU-EDSS >4 compared with those with FU-EDSS ≤4, and individuals in the highest baseline GCIPL tertile had a significantly lower FU-EDSS score than those in the middle and lowest tertile (P = 0.01 and P = 0.001, respectively). These findings were not confirmed in analyses restricted to patients with PMS.

Conclusions:
Among OCT-derived metrics, GCIPL thickness had the strongest association with short-medium term disability in patients with RRMS. The predictive value of OCT metrics in the longer term will have to be further investigated, especially in PMS.