bluuebunny/crossref_metadata_2025 huggingface dataset:
Bipartite structure of the 5S ribosomal gene family in a Drosophila melanogaster strain, and its evolutionary implications.
Authors: Samson M L , Wegnez M
Published: January 2021

Knowledge of multigenic family organization should provide insight into their mode of evolution. Accordingly, we characterized the 5S ribosomal gene family in the Drosophila melanogaster strain ry506. The 5S genes in this strain display a striking HindIII restriction difference compared to the "standard" D. melanogaster 5S genes. The sequence of three ry506 5S genes was determined. We show that the HindIII restriction site heterogeneity within the ry506 5S family most probably results from the same point mutation, suggesting that a single 5S variant was propagated into the 5S cluster of this strain. Furthermore, we demonstrate that the structural organization of the 5S genes in ry506 is a bipartite structure, i.e., that about 40% of the 5S genes constitute a HindIII+/HindIII- mixed cluster, while those remaining constitute an homogeneous HindIII- cluster. The events which might lead to such an heterogeneous pattern are discussed from an evolutionary point of view.
Conditions under Which the Mean Fertility Is Maximized When a Population Is at a Stable Equilibrium.
Authors: Scott M E , Scott D M , Pollak E
Published: January 2021

It is assumed that there is a population with two alleles at one locus, random mating of adults and selection only involving differential fertilities. By making use of the Kuhn-Tucker theory of optimization under constraints, conditions are derived under which stable equilibrium frequencies x, y and z of the three genotypes are the same as those that maximize the mean fertility of the population. We derive all sets of frequencies of this type for the Hadeler-Liberman symmetric fertility model and all such sets for which at least one genotype is missing for the general model. If the population has frequencies that are initially near those at which there is both a stable equilibrium and maximization of the mean fertility, then the mean fertility phi(t) at time t is nondecreasing with t as t -> &. It is found that it is possible for the stable equilibrium maximum points (x, y, z) to be one or two points on a ridge on which the mean fertility phi is maximized or the entire set of points on the ridge. Furthermore, phi may be smaller on this ridge than at another stable equilibrium point at which phi is not even locally maximized.
P element insertions and rearrangements at the singed locus of Drosophila melanogaster.
Authors: Roiha H , Rubin G M , O'Hare K
Published: January 2021

DNA from the singed gene of Drosophila melanogaster was isolated using an inversion between a previously cloned P element at cytological location 17C and the hypermutable allele singed-weak. Five out of nine singed mutants examined have alterations in their DNA maps in this region. The singed locus is a hotspot for mutation during P-M hybrid dysgenesis, and we have analyzed 22 mutations induced by P-M hybrid dysgenesis. All 22 have a P element inserted within a 700-bp region. The precise positions of 10 P element insertions were determined and they define 4 sites within a 100-bp interval. During P-M hybrid dysgenesis, the singed-weak allele is destabilized, producing two classes of phenotypically altered derivatives at high frequency. In singed-weak, two defective P elements are present in a "head-to-head" or inverse tandem arrangement. Excision of one element results in a more extreme singed bristle phenotype while excision of the other leads to a wild-type bristle phenotype.
Unlinked noncomplementation: isolation of new conditional-lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae.
Authors: Stearns T , Botstein D
Published: January 2021

Mutations in genes of Saccharomyces cerevisiae that code for proteins that interact with beta-tubulin were sought by screening for unlinked mutations that fail to complement mutations in the single beta-tubulin-encoding gene (TUB2). Among the first three noncomplementing mutations examined, two are linked to TUB2 while one is unlinked. The unlinked mutation was shown to be a conditional-lethal allele of the major alpha-tubulin-encoding gene (TUB1) and represents the first such mutation in that gene. The tub1-1 mutation itself causes a cold-sensitive cell-cycle arrest, and confers supersensitivity to the antimicrotubule drug benomyl. These phenotypes occur in the presence of a wild-type copy of the minor alpha-tubulin-encoding gene, TUB3; the combination of tub1-1 and a tub3 null mutation is inviable in haploids. Through further application of this method, new mutations in TUB2 and TUB3 were isolated as unlinked noncomplementers of tub1-1. The noncomplementation between tub1 and tub2 mutations is gene specific and allele specific, suggesting that the phenotype is due to an interaction at the protein level. We conclude that isolation of unlinked noncomplementing mutations is likely to be a generally useful method for isolating mutations in interacting gene products.
Spontaneous mitotic recombination in yeast: the hyper-recombinational rem1 mutations are alleles of the RAD3 gene.
Authors: Montelone B A , Hoekstra M F , Malone R E
Published: January 2021

The RAD3 gene of Saccharomyces cerevisiae is required for UV excision-repair and is essential for cell viability. We have identified the rem1 mutations (enhanced spontaneous mitotic recombination and mutation) of Saccharomyces cerevisiae as alleles of RAD3 by genetic mapping, complementation with the cloned wild-type gene, and DNA hybridization. The high levels of spontaneous mitotic gene conversion, crossing over, and mutation conferred upon cells by the rem1 mutations are distinct from the effects of all other alleles of RAD3. We present preliminary data on the localization of the rem1 mutations within the RAD3 gene. The interaction of the rem1 mutant alleles with a number of radiation-sensitive mutations is also different than the interactions reported for previously described (UV-sensitive) alleles of RAD3. Double mutants of rem1 and a defect in the recombination-repair pathway are inviable, while double mutants containing UV-sensitive alleles of RAD3 are viable. The data presented here demonstrate that: (1) rem1 strains containing additional mutations in other excision-repair genes do not exhibit elevated gene conversion; (2) triple mutants containing rem1 and mutations in both excision-repair and recombination-repair are viable; (3) such triple mutants containing rad52 have reduced levels of gene conversion but wild-type frequencies of crossing over. We have interpreted these observations in a model to explain the effects of rem1. Consistent with the predictions of the model, we find that the size of DNA from rem1 strains, as measured by neutral sucrose gradients, is smaller than wild type.
Quantitative Genetics of Drosophila Melanogaster. II. Heritabilities and Genetic Correlations between Sexes for Head and Thorax Traits.
Authors: Cowley D E , Atchley W R
Published: January 2021

A quantitative genetic analysis is reported for traits on the head and thorax of adult fruit flies, Drosophila melanogaster. Females are larger than males, and the magnitude of sexual dimorphism is similar for traits derived from the same imaginal disc, but the level of sexual dimorphism varies widely across discs. The greatest difference between males and females occurs for the dimensions of the sclerotized mouthparts of the proboscis. Most of the traits studied are highly heritable with heritabilities ranging from 0.26 to 0.84 for males and 0.27 to 0.81 for females. In general, heritabilities are slightly higher for males, possibly reflecting the effect of dosage compensation on X-linked variance. The X chromosome contributes substantially to variance for many of these traits, and including results reported elsewhere, the variance for over two-thirds of the traits studied includes X-linked variance. The genetic correlations between sexes for the same trait are generally high and close to unity. Coupled with the small differences in the traits between sexes for heritabilities and phenotypic variances, these results suggest that selection would be very slow to change the level of sexual dimorphism in size of various body parts.
Unidirectional incompatibility in Drosophila simulans: inheritance, geographic variation and fitness effects.
Authors: Hoffmann A A , Turelli M
Published: January 2021

In California, Drosophila simulans females from some populations (type W) produce relatively few adult progeny when crossed to males from some other populations (type R), but the productivity of the reciprocal cross is comparable to within-population controls. These two incompatibility types are widespread in North America and are also present elsewhere. Both types sometimes occur in the same population. Type R females always produce type R progeny irrespective of the father's type. However, matings between R males and females from stocks classified as type W produce type R progeny at low frequency. This suggests rare paternal transmission of the R incompatibility type, as we have found no evidence for segregation of incompatibility types in the W stocks. There is quantitative variation among type R lines for compatibility with W females, but not vice versa. Population cage studies and productivity tests suggest that deleterious side effects are associated with the type R cytoplasm.
Microgeographic genetic variation in the apple maggot rhagoletis pomonella.
Authors: McPheron B A , Smith D C , Berlocher S H
Published: January 2021

We examined electrophoretic variability at five enzyme loci in the apple maggot fly, Rhagoletis pomonella, on a microgeographic scale. Treating flies from individual hawthorn trees as separate populations, we estimated F(ST) values from allele frequencies. The results indicate that there is significant allele frequency heterogeneity among fly populations over a small spatial scale at some loci but not at others. This variation among loci in degree of differentiation is itself statistically significant, casting doubt on the role of genetic drift in maintaining the heterogeneity. There is also heterogeneity between years in flies from a given tree. These data provide a baseline with which future work on genetic differentiation among apple maggot populations associated with different species of host plants may be compared.
Effects of an intercultivaral chromosome substitution on winterhardiness and vernalization in wheat.
Authors: Zemetra R S , Morris R
Published: January 2021

During a study on the genetic control of winterhardiness in winter wheat (Triticum aestivum L. group aestivum), a gene that affected vernalization was found on chromosome 3B in the winter wheat cultivar ;Wichita.' When chromosome 3B from Wichita was substituted into the winter wheat cultivar ;Cheyenne,' the resultant substitution line exhibited a spring growth habit. This is unusual since a cross between the cultivars Wichita and Cheyenne results in progeny that exhibit the winter growth habit. The F(2) plants from a cross of the 3B substitution line to Cheyenne, the recipient parent, segregated 3:1 for heading/no heading response in the absence of vernalization (chi(2) = 2.44). Earliness of heading appeared to be due to an additive effect of the 3B gene as shown by the segregation ratio 1:2:1 (early heading-later heading-no heading) (chi(2) = 2.74). This vernalization gene differs from previously described vernalization genes because, while dominant in a Cheyenne background, its expression is suppressed in Wichita. The gene may have an effect on winter hardiness in Wichita. In a field test for winter survival the 3B substitution line had only 5% survival, while Wichita and Cheyenne had 50 and 80% survival, respectively. No other substitution line significantly reduced winter survival. The difference between Wichita and Cheyenne in winterhardiness may be due to the vernalization gene carried on the 3B chromosome.
Isolation and characterization of mutants which show an oversecretion phenotype in Saccharomyces cerevisiae.
Authors: Sakai A , Shimizu Y , Hishinuma F
Published: January 2021

We have isolated mutants responsible for an oversecretion phenotype in Saccharomyces cerevisiae, using a promoter of SUC2 and the gene coding for alpha-amylase from mouse as a marker of secretion. These mutations defined two complementation groups, designated as ose1 (over secretion) and rgr1 (resistant to glucose repression). The ose1 mutant produced an oversecretion of amylase by 12- to 15-fold under derepressing conditions; however, the amylase mRNA was present at nearly the same amount as it was in the parent cells. No expression of the amylase gene was detected under repressing conditions. The rgr1 mutant oversecreted amylase by 11- to 13-fold under repressing conditions by 15- to 18-fold under derepressing conditions. The rgr1 mutant showed pleiotropic effects on the following cellular functions: (1) resistance to glucose repression, (2) temperature-sensitive lethality, (3) sporulation deficieny in homozygous diploid cells, and (4) abnormal cell morphology. The rgr1 mutation was not allelic with ssn6 and cyc9, and failed to suppress snf1.
Genetic analysis of chromosomal region 67A-D of Drosophila melanogaster.
Authors: Leicht B G , Bonner J J
Published: January 2021

In an effort to (1) characterize the 67 interval of chromosome 3 of Drosophila melanogaster genetically and (2) isolate mutations of the 67B1 small heat shock protein (hsp) gene cluster specifically, we undertook a mutational analysis of the 67A-D subinterval. Using a deficiency of the 67A2 to 67D11-13 region, Df(3L)AC1, we screened 8700 diepoxybutane-treated chromosomes and 7800 ethyl methanesulfonate-treated chromosomes for visible and lethal mutations throughout this interval and recovered 74 independent recessive lethal mutations, but no visible mutations. One of the lethal mutations, d29A6, was identified as an overlapping deficiency extending from 66F3 to 67B1. An additional 6000 diepoxybutane-treated chromosomes were screened for lethality over d29A6, yielding another four lethal mutations within the 67A2-B1 subinterval. These 78 lethal mutations, along with two others isolated in other laboratories, define 23 essential loci--6 within the 67A2-B1 subinterval and 17 within the 67A2 to D11-13 subinterval. Many of these loci appear to be required for imaginal development only, exhibiting late larval to pharate adult lethal phases. Examination of the 67A2-B1 lethal complementation groups for (1) earlier onset of lethality following a heat shock, (2) missing or altered small hsps on two-dimensional protein gels, and (3) restoration of viability by transformed wild-type copies of the small hsp genes indicates that none of these mutations affect the small hsps. On the basis of this analysis and the known homology of the genes, we conclude that the small hsps are functionally equivalent.
A genetic analysis of male-predominant pheromones in Drosophila melanogaster.
Authors: Scott D , Richmond R C
Published: January 2021

Chemical signals from males play an important role in stimulating Drosophila melanogaster females to mate, and male-predominant pheromones may influence a female's choice of mates. Male-predominant pheromones also inhibit courtship, thereby functioning as antiaphrodisiacs. Interstrain variation in the ratio of two male-predominant pheromones (7-tricosene and 7-pentacosene) has been reported, but the genetic basis for this potentially important variation has not been examined. In a series of crosses between strains that differ radically in the amounts of 7-tricosene and 7-pentacosene, we have identified both X-linked and autosomal contributions to interstrain variation in the amounts of these compounds. The X-linked loci act as enhancers for production of the compound predominant in the strain from which the X chromosome originated. Autosomal factors for each of the two compounds appear to segregate as high vs. low, with incomplete dominance of high 7-tricosene over low, and low 7-pentacosene over high. A significant negative correlation between the quantities of 7-pentacosene and 7-tricosene in the F2 and backcross progeny, but not in the F1s or parentals, indicates linkage between autosomal loci regulating the expression of each compound. However, the phenotypic distributions of the backcross progeny indicate that additional unlinked loci are also directly involved in the production of these two hydrocarbons.
Estimation of mutation rates based on the analysis of polypeptide constituents of cultured human lymphoblastoid cells.
Authors: Chu E H , Boehnke M , Hanash S M , Kuick R D , Lamb B J , Neel J V , Niezgoda W , Pivirotto S , Sundling G
Published: January 2021

A subclone of a human diploid lymphoblastoid cell line, TK-6, with consistently high cloning efficiency has been used to estimate the rates of somatic mutations on the basis of protein variation detected by two-dimensional polyacrylamide gel electrophoresis. A panel of 267 polypeptide spots per gel was screened, representing the products of approximately 263 unselected loci. The rate of human somatic mutation in vitro was estimated by measuring the proportion of protein variants among cell clones isolated at various times during continuous exponential growth of a TK-6 cell population. Three mutants of spontaneous origin were observed, giving an estimated spontaneous rate of 6 x 10(-8) electrophoretic mutations per allele per cell generation (i.e., 1.2 x 10(-7) per locus per cell generation). Following treatment of cells with N-ethyl-N-nitrosourea, a total of 74 confirmed variants at 54 loci were identified among 1143 clones analyzed (approximately 601,000 allele tests). The induced variants include 65 electromorphs which exhibit altered isoelectric charge and/or apparent molecular weight and nine nullimorphs for each of which a gene product was not detected at its usual location on the gel. The induced frequency for these 65 structural gene mutants is 1.1 x 10(-4) per allele. An excess of structural gene mutations at ten known polymorphic loci and repeat mutations at these and other loci suggest nonrandomness of mutation in human somatic cells. Nullimorphs occurring at three heterozygous loci in TK-6 cells may be caused by genetic processes other than structural gene mutation.
Genetic control of intrachromosomal recombination in Saccharomyces cerevisiae. I. Isolation and genetic characterization of hyper-recombination mutations.
Authors: Aguilera A , Klein H L
Published: January 2021

Eight complementation groups have been defined for recessive mutations conferring an increased mitotic intrachromosomal recombination phenotype (hpr genes) in Saccharomyces cerevisiae. Some of the mutations preferentially increase intrachromosomal gene conversion (hpr4, hpr5 and hpr8) between repeated sequences, some increase loss of a marker between duplicated genes (hpr1 and hpr6), and some increase both types of events (hpr2, hpr3 and hpr7). New alleles of the CDC2 and CDC17 genes were recovered among these mutants. The mutants were also characterized for sensitivity to DNA damaging agents and for mutator activity. Among the more interesting mutants are hpr5, which shows a biased gene conversion in a leu2-112::URA3::leu2-k duplication; and hpr1, which has a much weaker effect on interchromosomal mitotic recombination than on intrachromosomal mitotic recombination. These analyses suggest that gene conversion and reciprocal exchange can be separated mutationally. Further studies are required to show whether different recombination pathways or different outcomes of the same recombination pathway are controlled by the genes identified in this study.
An efficient selection producing structural gene mutants of yeast alcohol dehydrogenase resistant to pyrazole.
Authors: Wills C , Hom D
Published: January 2021

Selection for resistance to allyl alcohol in respiration-incompetent Saccharomyces cerevisiae produces a high proportion of mutants that can be localized within the ADH2 structural gene and that still, because of the type of selection employed, retain enzyme activity. We show here that a similar type of selection produces a similarly high proportion of mutants resistant to the competitive inhibitor pyrazole. The first four mutants examined, picked at random from a collection of spontaneous pyrazole-resistant mutants, show altered--usually increased--KM values for ethanol and NAD+, and markedly increased K1 values for pyrazole, compared with the wild type. When these kinetic measures and their electrophoretic mobilities were compared, all the mutants could be clearly distinguished from each other as well as from wild type. Genetic analysis shows these mutants to be close to and probably resident in the structural gene. For a variety of reasons, these mutants are even more favorable subjects for population genetic analysis and the dissection of molecular microevolution than are allyl alcohol-resistant mutants.
Adaptation at specific loci. V. Metabolically adjacent enzyme loci may have very distinct experiences of selective pressures.
Authors: Carter P A , Watt W B
Published: January 2021

The polymorphic phosphoglucomutase (PGM) and glucose-6-phosphate dehydrogenase (G6PD) loci have been studied in parallel to experimental work on the phosphoglucose isomerase (PGI) polymorphism in Colias butterflies. PGI, PGM and G6PD are also autosomal in Colias. PGM and G6PD are loosely linked (and represent the first identified autosomal linkage group in Colias); they assort independently from PGI. Recombination occurs in both sexes. Neither PGM nor G6PD shows large, consistent differences in flight capacity through the day among its genotypes, as PGI does. PGM shows some change of allele frequencies, and match to Hardy-Weinberg expectation, with air temperature in middle and latter parts of the season, but not early in the season. G6PD may show some heterozygote excess over Hardy-Weinberg expectation early in the day, but more testing is needed. No evidence for differential survivorship was seen at PGM or G6PD, in contrast to PGI. At the PGM and G6PD loci, male heterozygotes are advantaged in mating with females, but without the evidence of female choice which occurs for PGI. These effects are not correlated among the three loci. There is no assortative mating at G6PD (nor at PGI). There is minor positive assortative mating of PGM heterozygotes, but it is too weak to account for the PGM-genotype-specific male mating advantage. No trends of multilocus genotype frequencies involving PGI are seen. Certain PGM-G6PD two-locus genotypes are over-represented, and others under-represented, in wild adult samples, particularly among males and uniformly among successfully mating males. Our results emphasize that enzyme loci sharing a substrate need not have common experience of the existence or strength of natural selection, and suggest initial food-resource processing and allocation as a possible context for fitness-related effects of the PGM and G6PD polymorphisms.
Heterochronic mutations affecting shoot development in maize.
Authors: Poethig R S
Published: January 2021

Three semidominant, nonallelic mutations of maize, Teopod 1 (Tp1), Teopod 2 (Tp2) and Teopod 3 (Tp3), have a profound effect on both vegetative and reproductive development. Although each mutation is phenotypically distinct, they all (1) increase the number of vegetative phytomers; (2) increase the number of phytomers producing ears, tillers and prop roots; (3) increase the number of leaves bearing epidermal wax; (4) decrease the size of leaves and internodes; (5) decrease the size of both the ear and tassel; and (6) transform reproductive structures into vegetative ones. The analysis presented here suggests that this phenotype reflects the prolonged expression of a juvenile, vegetative developmental program which overlaps with the reproductive developmental program. The expression of these mutations is different in each of the four inbred backgrounds used in this study. Tp1 and Tp2 have similar phenotypes and are more highly expressed in the A632 and Oh51a inbred backgrounds than in W23 and Mo17. Tp3 has less extreme effects than either of these mutations and has the opposite modification pattern; i.e., it is more highly expressed in W23 and Mo17 than in A632 and Oh51a. The expression of Tp1 and Tp2 in the presence of varying doses of their wild-type alleles indicate that both are gain-of-function mutations. The phenotypes of Tp1 and Tp2 and the nature of their response to variation in gene dose suggest that they control related, but nonidentical functions. The developmental and evolutionary implications of the heterochronic phenotype of these mutations is discussed.
Developmental genetics of chromosome I spermatogenesis-defective mutants in the nematode Caenorhabditis elegans.
Authors: L'Hernault S W , Shakes D C , Ward S
Published: January 2021

Mutations affecting Caenorhabditis elegans spermatogenesis can be used to dissect the processes of meiosis and spermatozoan morphological maturation. We have obtained 23 new chromosome I mutations that affect spermatogenesis (spe mutations). These mutations, together with six previously described mutations, identify 11 complementation groups, of which six are defined by multiple alleles. These spe mutations are all recessive and cause normally self-fertile hermaphrodites to produce unfertilized oocytes that can be fertilized by wild-type male sperm. Five chromosome I mutation/deficiency heterozygotes have similar phenotypes to the homozygote showing that the probable null phenotype of these genes is defective sperm. Spermatogenesis is disrupted at different steps by mutations in these genes. The maturation of 1 degree spermatocytes is disrupted by mutations in spe-4 and spe-5. Spermatids from spe-8 and spe-12 mutants develop into normal spermatozoa in males, but not in hermaphrodites. fer-6 spermatids are abnormal, and fer-1 spermatids look normal but subsequently become abnormal spermatozoa. Mutations in five genes (fer-7, spe-9, spe-11, spe-13 and spe-15) allow formation of normal looking motile spermatozoa that appear to be defective in either sperm-spermathecal or sperm-oocyte interactions.
Organization of the Tgm family of transposable elements in soybean.
Authors: Rhodes P R , Vodkin L O
Published: January 2021

We have compared the organization of six Tgm elements that were selected from a genomic library of soybean DNA on the basis of hybridization with subcloned regions of Tgm 1 (transposon, Glycine max) from the seed lectin gene. These elements ranged in size from 1.6 kbp to greater than 12 kbp. Tgm2, Tgm3, Tgm4 and Tgm5 represent partial isolates in which the genomic clone contained a 3' but not a 5' terminus of the element; while Tgm6 and Tgm7, like Tgm1, were small isolates flanked by both 5' and 3' nonelement sequences. Cross-hybridization studies between subcloned portions of these seven elements identified regions of homology which suggest that the Tgm transposable elements of soybean form a family of deletion derivatives. In addition to internal deletion events, numerous deletions and base substitutions are also present within the borders of these elements which are comprised of the same tandemly repeated sequence. The 39% amino acid homology between a 1 kb portion of an open reading frame in Tgm4 and Tgm5 and ORF1, an open frame from the first intron of the maize Enhancer (Suppressor-mutator) transposable element, suggests that both elements encode a common function that requires a high degree of protein conservation.
Chronic Exposure to Cadmium Induces Differential Methylation in Mice Spermatozoa
Authors: Saintilnord Wesley N , Tenlep Sara Y N , Preston Joshua D , Duregon Eleonora , DeRouchey Jason E , Unrine Jason M , de Cabo Rafael , Pearson Kevin J , Fondufe-Mittendorf Yvonne N
Published: January 2021

Cadmium exposure is ubiquitous and has been linked to diseases including cancers and reproductive defects. Since cadmium is nonmutagenic, it is thought to exert its gene dysregulatory effects through epigenetic reprogramming. Several studies have implicated germline exposure to cadmium in developmental reprogramming. However, most of these studies have focused on maternal exposure, while the impact on sperm fertility and disease susceptibility has received less attention. In this study, we used reduced representation bisulfite sequencing to comprehensively investigate the impact of chronic cadmium exposure on mouse spermatozoa DNA methylation. Adult male C57BL/J6 mice were provided water with or without cadmium chloride for 9 weeks. Sperm, testes, liver, and kidney tissues were collected at the end of the treatment period. Cadmium exposure was confirmed through gene expression analysis of metallothionein-1 and 2, 2 well-known cadmium-induced genes. Analysis of sperm DNA methylation changes revealed 1788 differentially methylated sites present at regulatory regions in sperm of mice exposed to cadmium compared with vehicle (control) mice. Furthermore, most of these differential methylation changes positively correlated with changes in gene expression at both the transcription initiation stage as well as the splicing levels. Interestingly, the genes targeted by cadmium exposure are involved in several critical developmental processes. Our results present a comprehensive analysis of the sperm methylome in response to chronic cadmium exposure. These data, therefore, highlight a foundational framework to study gene expression patterns that may affect fertility in the exposed individual as well as their offspring, through paternal inheritance.
Identification of Pectobacterium versatile Causing Blackleg of Potato in New York State
Authors: Ma Xing , Stodghill Paul , Gao Miao , Perry Keith L. , Swingle Bryan
Published: January 2021

Soft rot bacteria classified in the Pectobacteriaceae (SRP), including Pectobacterium and Dickeya spp., are responsible for soft rot and blackleg diseases of potato. Since 2014, blackleg outbreaks caused by D. dianthicola have increased in the United States and Canada. Our previous study found that the most abundant causal organisms of blackleg disease in New York State were P. parmentieri and D. dianthicola, with the latter being the only Dickeya species reported. In the present study, we identified and characterized pathogenic SRP bacteria from 19 potato samples collected in New York State during the 2017 growing season. We used genome sequence comparison to determine the pathogens’ species. We found eight P. versatile, one P. atrosepticum, two P. carotovorum, two P. parmentieri, and six D. dianthicola isolates in our 2017 SRP collection. This is the first time that P. versatile has been reported to cause potato blackleg disease in New York State. We determined the phylogenetic relationships between the SRP strains by using 151 single-copy orthologous gene sequences shared among the set of bacteria in our analysis, which provided better resolution than phylogenies constructed with the dnaX gene.
Patterns of Approach to Activity in 851 Patients With Severe Chronic Pain
Authors: Titze Christina , Hasenbring Monika I. , Kristensen Lotte , Bendix Laila , Vaegter Henrik B.
Published: January 2021

Objectives:

The Avoidance-Endurance Fast-Screen (AEFS) is a 9-item self-report questionnaire that classifies patients with back pain into 4 activity-related subgroups, based on the Avoidance-Endurance Model of pain. The objective of this study was to translate the AEFS into Danish and investigate its discriminative abilities in a large, diverse patient sample.

Materials and Methods:

A total of 851 specialist care-seeking patients with severe chronic pain conditions participated in this cross-sectional study. Participants were categorized as showing a “distress-endurance” (DER), “eustress-endurance” (EER), “fear-avoidance” (FAR), or “adaptive” (AR) pattern. Principal component analysis reduced a large number of psychological variables beforehand. Construct and outcome-based validity were explored using multivariate analysis of variance.

Results:

Of the participants, 33.6% were categorized as DER, 29.4% as EER, 22% as FAR, and 15% as adaptive. Principal component analysis showed the factors activity-related pain behavior, affective distress, and dysfunctional pain thoughts. The AEFS-DK discriminated all 4 subgroups in terms or their pain behavior with EER>DER>AR>FAR. FAR showed less moderate/vigorous activity than DER and EER and more sedentary time than EER. DER and FAR showed higher affective distress, dysfunctional pain thoughts, and poorer outcomes than AR and EER.

Conclusion:

The results indicate good construct validity of the AEFS-DK discriminating the 4 avoidance-endurance model-related subgroups with respect to approach to activity behavior, psychological variables, and reported physical activity. Concerning outcome-based validity, 2 subgroups DER/FAR and AR/EER could be distinguished with inconclusive results for the eustress-endurance subgroup. Future studies are warranted using longitudinal research designs investigating whether AEFS subgroups differ in terms of treatment effects and long-term prognosis.
Evaluating Social Media Use Among Active American Members of the Cervical Spine Research Society
Authors: Bernstein David N. , Melone Giresse , Jubril Ayodeji , Zhang Jun , Mesfin Addisu
Published: January 2021

Study Design:

Observational study.

Objectives:

The objectives of this study are (1) to quantify social media use among active American Cervical Spine Research Society (CSRS) members; (2) to determine if there is an association between practice setting, region, or years of active membership and social media use.

Summary of Background Data:

Many patients now seek health and physician information online, including on social media. Indeed, social media use by orthopedic surgeons has been shown to be associated with more and improved ratings on physician review websites. Further, social media can provide a means for improved doctor-patient relationships, educational endeavors, and professional networking. However, there is a paucity of literature examining social media use among spine surgeons.

Materials and Methods:

In January 2019, the CSRS membership directory was used to identify all active American spine surgeon members. Through a Google search, social media use of each spine surgeon on the following platforms was identified: provider page/official website; Facebook; Twitter; Instagram; LinkedIn; and YouTube. In addition, surgeon characteristics were recorded. The percentage of spine surgeons using each social media platform was reported. Bivariate analysis was used to compare social media use by practice setting, region, and years of active CSRS membership.

Results:

Nearly all spine surgeons have a provider page/official website (98%) and over half (56%) have a LinkedIn presence. Less than one third of spine surgeons are on any of the remaining social media platforms analyzed. The least frequently used social media platform was Instagram (3.2%). There was no difference in any social media platform use by practice setting, region, and years of active CSRS membership.

Conclusions:

As social media becomes even more common place and the role of it in medical care continues to be better defined, there is notable room for increased social media use among active American members of the CSRS.

Level of Evidence:

Level IV—observational study.
Non‐invasive Predictors of Esophageal Varices With a High Risk of Bleeding in Pediatric Cirrhotic Patients
Authors: Lopes José Ricardo Borém , Ferreira Alexandre Rodrigues , Liu Priscila Menezes Ferri , Queiroz Thaís Costa Nascentes , Fagundes Eleonora Druve Tavares , Pimenta Júlio Rocha , Neto José Andrade Franco , Carvalho Simone Diniz , Borges Maria Eduarda Marques , Colin Lucas Garcia de Figueiredo
Published: January 2021

Objectives:

To evaluate non‐invasive predictive factors of varices with a high risk of bleeding in pediatric cirrhotic patients.

Methods:

This retrospective, cross‐sectional study included data from 158 children with cirrhosis, median age of 5.38 years (interquartile [IQ] 2.08−11.52 years), and no history of upper gastrointestinal bleeding. Patients underwent an endoscopy to screen for esophageal varices. Varices with a high risk of bleeding were defined as those with a medium to large caliber, presence of red spots, or the presence of gastric varices and identified as high‐risk varices (HRV). Laboratory and clinical factors were evaluated as possible predictors of HRV.

Results:

HRV were detected in 30 children (19%) after the first endoscopy. In the multivariate analysis, only the risk score (RS), as described by Park et al, and the aspartate aminotransferase‐to‐platelet ratio index (APRi) were predictive of HRV. The best non‐invasive predictor of HRV was the RS with an area under the receiver operating characteristic curve of 0.764. When used a cut‐off point of −1.2, the sensitivity of the RS was 90% and specificity was 53%. The use of RS or APRi correctly identified 96% of children with HRV.

Conclusions:

The described predictors allow the correct identification of patients with HRV. The association of RS >−1.2 or APRi >1.4 has a good sensitivity to identify HRV and to prevent unnecessary endoscopy in about one‐third of children with no HRV.
Performance of a True Point-of-Care Assay for HIV-1/2 Viral Load Measurement at Antenatal and Postpartum Services
Authors: Meggi Bindiya , Bollinger Timothy , Zitha Alcina , Mudenyanga Chishamiso , Vubil Adolfo , Mutsaka Dadirayi , Nhachigule Carina , Mabunda Nedio , Loquiha Osvaldo , Kroidl Arne , Jani Ilesh V.
Published: January 2021

Background:

Timely viral load (VL) results during pregnancy and the postpartum period are crucial for HIV disease management and for preventing mother-to-child transmission. Point-of-care (POC) VL testing could reduce turnaround times and streamline patient management. We evaluated the diagnostic performance of the novel m-PIMA HIV-1/2 VL assay (Abbott, Chicago, IL) in Mozambique.

Setting:

The study was conducted in prenatal and postpartum consultation rooms in 2 primary health care clinics. Sample collection and testing on m-PIMA were performed by trained nurses.

Methods:

HIV-infected pregnant and postpartum women on antiretroviral treatment (ART) or ART naive were tested using both on-site m-PIMA POC and referral laboratory-based real-time VL assays. Linear regression analysis and Bland–Altman plots were used to calculate the agreement between both.

Findings:

Correlation between venous blood plasma POC and plasma laboratory-based VL was strong (r2 = 0.850, P < 0.01), with good agreement between the methods [overall bias 0.202 log copies/mL (95% CI: 0.366 to 0.772 log copies/mL)]. Using the threshold of 1000 copies/mL, which is used to determine ART failure, the sensitivity and specificity of the POC VL assay were 95.0% (95% CI: 91.6% to 97.3%) and 96.5% (95% CI: 94.2% to 98.0%), respectively. The correlation coefficient between the venous and capillary sample types was 0.983 (r2 = 0.966).

Conclusions:

On-site, nurse-performed POC VL testing is feasible and accurate in resource-limited primary health care settings. The operational challenge of plasma separation within clinics for POC testing was successfully overcome using minicentrifuges. The use of capillary blood could simplify the execution of the assay in a clinical environment.
2020: the year of living cautiously
Authors: Inglis Timothy J. J.
Published: January 2021

2020 was the year when microbiology burst onto the world stage, not just as the science of small living things, but as the prism through which we understood global events. Clinical logic suffered under pressure arising from an urgent need to confirm or exclude severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This is a generation’s Hobbesian moment in which the public concern for safety and security from infection outweighs the pursuit of personal freedom. The strangeness of a world in which a minute particle wields superhuman power has generated its list of unlikely heroes and mendacious villains. As the year comes to an end, there are glimmers of light amid the gloom: the prospect of an effective vaccine, and life after the pandemic.
Alzheimer’s genetic risk effects on cerebral blood flow are spatially consistent and proximal to gene expression across the lifespan
Authors: Chandler H.L , Wise R.G , Linden D.E , Williams J , Murphy K , Lancaster T.M ,   Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: January 2021

Cerebrovascular dysregulation is a hallmark feature of Alzheimer’s disease (AD), where alterations in cerebral blood flow (CBF) are observed decades prior to symptom onset. Genome-wide association studies (GWAS) show that AD has a polygenic aetiology, providing a tool for studying AD susceptibility across the lifespan. Here, we ascertain whether AD genetic risk effects on CBF previously observed (Chandler et al., 2019) remain consistent across the lifespan. We further provide a causal mechanism to AD genetic risk scores (AD-GRS) effects by establishing spatial convergence between AD-GRS associated regional reductions in CBF and mRNA expression of the proximal AD transcripts using independent data from the Allen Brain Atlas. We analysed grey matter (GM) CBF in a young cohort (N=75; aged 18-35) and an older cohort (N=90; aged 55-85). Critically, we observed that AD-GRS was negatively associated with whole brain GM CBF in the older cohort (standardised β −0.38 [−0.68 – −0.09], P = 0.012), consistent with our prior observation in younger healthy adults (Chandler et al., 2019). We then demonstrate that the regional impact of AD-GRS on GM CBF was spatially consistent across the younger and older samples (r = 0.233, P = 0.035). Finally, we show that CBF across the cortex was related to the regional expression of the genes proximal to SNP’s used to estimate AD-GRS in both younger and older cohorts (ZTWO-TAILED= −1.99, P= 0.047; ZTWO-TAILED= −2.153 P = 0.032, respectively). These observations collectively demonstrate that AD risk alleles have a negative influence on brain vascular function and likely contribute to cerebrovascular changes preceding the onset of clinical symptoms, potentially driven by regional expression of proximal AD risk genes across the brain. Our observations suggest that reduced CBF is an early antecedent of AD and a key modifiable target for therapeutic intervention in individuals with a higher cumulative genetic risk for AD. This study will further enable identification of key molecular processes that underpin AD genetic risk related reductions in CBF that could be targeted decades prior to the onset of neurodegeneration.
Predicting Stroke and Mortality in Mitral Regurgitation: A Gradient Boosting Approach
Authors: Zhou Jiandong , Lee Sharen , Liu Yingzhi , Liu Tong , Tse Gary , Zhang Qingpeng
Published: January 2021

Introduction

We hypothesized that an interpretable gradient boosting machine (GBM) model considering comorbidities, P-wave and echocardiographic measurements, can better predict mortality and cerebrovascular events in mitral regurgitation (MR).

Methods

Patients from a tertiary center were analyzed. The GBM model was used as an interpretable statistical approach to identify the leading indicators of high-risk patients with either outcome of CVAs and all-cause mortality.

Results

A total of 706 patients were included. GBM analysis showed that age, systolic blood pressure, diastolic blood pressure, plasma albumin levels, mean P-wave duration (PWD), MR regurgitant volume, left ventricular ejection fraction (LVEF), left atrial dimension at end-systole (LADs), velocity-time integral (VTI) and effective regurgitant orifice were significant predictors of TIA/stroke. Age, sodium, urea and albumin levels, platelet count, mean PWD, LVEF, LADs, left ventricular dimension at end systole (LVDs) and VTI were significant predictors of all-cause mortality. The GBM demonstrates the best predictive performance in terms of precision, sensitivity c-statistic and F1-score compared to logistic regression, decision tree, random forest, support vector machine, and artificial neural networks.

Conclusion

Gradient boosting model incorporating clinical data from different investigative modalities significantly improves risk prediction performance and identify key indicators for outcome prediction in MR.
Hydroxyzine inhibits SARS-CoV-2 Spike protein binding to ACE2 in a qualitativein vitroassay
Authors: Rivas Maria Dolores , Saponi-Cortes Jose Maria Rafael , Zamorano Jose
Published: January 2021

COVID-19 currently represents a major public health problem. Multiple efforts are being performed to control this disease. Vaccinations are already in progress. However, no effective treatments have been found so far. The disease is caused by the SARS-CoV-2 coronavirus that through the Spike protein interacts with its cell surface receptor ACE2 to enter into the host cells. Therefore, compounds able to block this interaction may help to stop disease progression. In this study, we have analyzed the effect of compounds reported to interact and modify the activity of ACE2 on the binding of the Spike protein. Among the compounds tested, we found that hydroxyzine could inhibit the binding of the receptor-binding domain of Spike protein to ACE2 in a qualitativein vitroassay. This finding supports the reported clinical data showing the benefits of hydroxyzine on COVID-19 patients, raising the need for further investigation into its effectiveness in the treatment of COVID-19 given its well-characterized medical properties and affordable cost.
Reciprocal Priming between Receptor Tyrosine Kinases at Recycling Endosomes Orchestrates Cellular Signalling Outputs
Authors: Smith Michael P. , Ferguson Harriet R. , Ferguson Jennifer , Zindy Egor , Kowalczyk Katarzyna M. , Kedward Thomas , Bates Christian , Parsons Joseph , Watson Joanne , Chandler Sarah , Fullwood Paul , Warwood Stacey , Knight David , Clarke Robert B. , Francavilla Chiara
Published: January 2021

Integration of signalling downstream of individual receptor tyrosine kinases (RTKs) is crucial to fine tune cellular homeostasis during development and in pathological conditions, including breast cancer. However, how signalling integration is regulated and whether the endocytic fate of single receptors controls such signalling integration remains poorly elucidated. Combining quantitative phosphoproteomics and targeted assays, we generated a detailed picture of recycling-dependent fibroblast growth factor (FGF) signalling in breast cancer cells, with a focus on distinct FGF receptors (FGFRs). We discovered reciprocal priming between FGFRs and epidermal growth factor (EGF) receptor (EGFR) that is coordinated at recycling endosomes. FGFR recycling ligands induce EGFR phosphorylation on threonine 693. This phosphorylation event alters both FGFR and EGFR trafficking and primes FGFR-mediated proliferation but not cell invasion. In turn, FGFR signalling primes EGF-mediated outputs via EGFR threonine 693 phosphorylation. This reciprocal priming between distinct families of RTKs from recycling endosomes exemplifies a novel signalling integration hub where recycling endosomes orchestrate cellular behaviour. Therefore, targeting reciprocal priming over individual receptors may improve personalized therapies in breast and other cancers.