bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethanol production process driving changes on industrial strains
Authors: Nagamatsu Sheila Tiemi , Coutouné Natalia , José Juliana , Fiamenghi Mateus Bernabe , Pereira Gonçalo Amarante Guimarães , Oliveira Juliana Velasco de Castro , Carazzolle Marcelo Falsarella 
Published: January 2021

ABSTRACT
Ethanol production has key differences between the two largest producing countries of this biofuel, Brazil and the USA, such as feedstock source, sugar concentration and ethanol titers in industrial fermentation. Therefore, it is highly probable that these specificities have led to genome adaptation of the Saccharomyces cerevisiae strains employed in each process to tolerate different environments. In order to identify particular adaptations, in this work, we have compared the genomes of industrial yeast strains widely used to produce ethanol from sugarcane, corn and sweet sorghum, and also two laboratory strains as reference. The genes were predicted and then 4524 single-copy orthologous were selected to build the phylogenetic tree. We found that the geographic location and industrial process were shown as the main evolutionary drivers: for sugarcane fermentation, positive selection was identified for metal homeostasis and stress response genes, whereas genes involved in membrane modeling have been connected with corn fermentation. In addition, the corn specialized strain Ethanol Red showed an increased number of copies of MAL31, a gene encoding a maltose transporter. In summary, our work can help to guide new strain chassis selection for engineering strategies, to produce more robust strains for biofuel production and other industrial applications.
The crest phenotype in domestic chicken is caused by a 195 bp duplication in the intron of HOXC10
Authors: Li Jingyi , Lee Mi-Ok , Davis Brian W , Wu Ping , Hsieh Li Shu-Man , Chuong Cheng-Ming , Andersson Leif 
Published: January 2021

Abstract
The Crest mutation in chicken shows incomplete dominance and causes a spectacular phenotype in which the small feathers normally present on the head are replaced by much larger feathers normally present only in dorsal skin. Using whole-genome sequencing, we show that the crest phenotype is caused by a 195 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33. A diagnostic test showed that the duplication was present in all 54 crested chickens representing eight breeds and absent from all 433 non-crested chickens representing 214 populations. The mutation causes ectopic expression of at least five closely linked HOXC genes, including HOXC10, in cranial skin of crested chickens. The result is consistent with the interpretation that the crest feathers are caused by an altered body region identity. The upregulated HOXC gene expression is expanded to skull tissue of Polish chickens showing a large crest often associated with cerebral hernia, but not in Silkie chickens characterized by a small crest, both homozygous for the duplication. Thus, the 195 bp duplication is required for the development of a large crest and susceptibility to cerebral hernia because only crested chicken show this malformation. However, this mutation is not sufficient to cause herniation because this malformation is not present in breeds with a small crest, like Silkie chickens.
The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment
Authors: Rogers Anna R , Dunne Jeffrey C , Romay Cinta , Bohn Martin , Buckler Edward S , Ciampitti Ignacio A , Edwards Jode , Ertl David , Flint-Garcia Sherry , Gore Michael A , Graham Christopher , Hirsch Candice N , Hood Elizabeth , Hooker David C , Knoll Joseph , Lee Elizabeth C , Lorenz Aaron , Lynch Jonathan P , McKay John , Moose Stephen P , Murray Seth C , Nelson Rebecca , Rocheford Torbert , Schnable James C , Schnable Patrick S , Sekhon Rajandeep , Singh Maninder , Smith Margaret , Springer Nathan , Thelen Kurt , Thomison Peter , Thompson Addie , Tuinstra Mitch , Wallace Jason , Wisser Randall J , Xu Wenwei , Gilmour A R , Kaeppler Shawn M , De Leon Natalia , Holland James B 
Published: January 2021

AbstractHigh-dimensional and high-throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments. For grain yield, dominance variance was similar in magnitude to additive variance, and genetic-by-environment variances were more important than genetic main effect variances. Models involving both additive and dominance relationships best fit the data and modeling unique genetic covariances among all environments provided the best characterization of the genotype-by-environment interaction patterns. Similarity of relative hybrid performance among environments was modeled as a function of underlying weather variables, permitting identification of weather covariates driving correlations of genetic effects across environments. The resulting models can be used for genomic prediction of mean hybrid performance across populations of environments tested or for environment-specific predictions. These results can also guide efforts to incorporate high-throughput environmental data into genomic prediction models and predict values in new environments characterized with the same environmental characteristics.
RECESSIVE UAA SUPPRESSORS OF THE YEAST SACCHAROMYCES CEREVISIAE
Authors: Ono Bun-Ichiro , Tanaka Mitsuaki , Kominami Masayo , Ishino Yumiko , Shinoda Sumio 
Published: January 2021

ABSTRACT
Recessive lysine-independent revertants were isolated from a ψ+ haploid strain of the yeast Saccharomyces cerevisiae containing one of the leucine-inserting UAA suppressors, SUP29, and various UAA mutations including lys1-1. The majority of the revertants were found to have recessive suppressors in addition to the pre-existing SUP29 mutation. The recessive suppressors were able to suppress only a very limited number of UAA mutations, and none of the UAG mutations thus far examined. The recessive inefficient UAA suppressors were assigned to three complementation groups, sup111, sup112, and sup113. A high incidence of gene conversion was observed for an allele of sup111. An antisuppressor acting on sup111, but not detectably on SUP29, was inadvertently obtained during the course of the study. Interactions between SUP29, sup111 and the antisuppressor asu12 were studied.
MEIOSIS IN DROSOPHILA MELANOGASTER. III. THE EFFECT OF ORIENTATION DISRUPTOR (ord) ON GONIAL MITOTIC AND THE MEIOTIC DIVISIONS IN MALES
Authors: Lin Hsiu-Ping P , Church Kathleen 
Published: January 2021

ABSTRACT
Orientation disruptor (ord), a meiotic mutant that is recombination defective in females and disjunction defective in males and females, has been analyzed using serial section electron and light microscopy. From analysis of primary spermatocytes we have confirmed that ord males are defective in some aspect of the mechanism(s) that holds sister chromatids together during meiosis. In addition, we have determined that ord causes high frequencies of nondisjunction during spermatogonial mitotic divisions, as well as during the meiotic divisions. Mitotic nondisjunction involves the large autosomes more frequently than the sex chromosomes or chromosome 4 and results in high frequencies of primary spermatocytes that are either monosomic or trisomic for chromosome 2 or 3. Abnormalities in spermatocyte cyst formation are also observed in males homozygous for ord. These abnormalities include loss of regulation of meiotic synchrony and the number of gonial cell divisions.
FRAMESHIFT SUPPRESSION IN SACCHAROMYCES CEREVISIAE VI. COMPLETE GENETIC MAP OF TWENTY-FIVE SUPPRESSOR GENES
Authors: Gaber Richard F , Mathison Lorilee , Edelman Irv , Culbertson Michael R 
Published: January 2021

ABSTRACT
Five previously unmapped frameshift suppressor genes have been located on the yeast genetic map. In addition, we have further characterized the map positions of two suppressors whose approximate locations were determined in an earlier study. These results represent the completion of genetic mapping studies on all 25 of the known frameshift suppressor genes in yeast.—The approximate location of each suppressor gene was initially determined through the use of a set of mapping strains containing 61 signal markers distributed throughout the yeast genome. Standard meiotic linkage was assayed in crosses between strains carrying the suppressors and the mapping strains. Subsequent to these approximate linkage determinations, each suppressor gene was more precisely located in multi-point crosses. The implications of these mapping results for the genomic distribution of frameshift suppressor genes, which include both glycine and proline tRNA genes, are discussed.
ADAPTATION AT SPECIFIC LOCI. III. FIELD BEHAVIOR AND SURVIVORSHIP DIFFERENCES AMONG COLIAS PGI GENOTYPES ARE PREDICTABLE FROM IN VITRO BIOCHEMISTRY
Authors: Watt Ward B , Cassin Richard C , Swan Mary S 
Published: January 2021

ABSTRACT
Previous work on the phosphoglucose isomerase (PGI) polymorphism of Colias butterflies led to predictions concerning aspects of differential survivorship and fecundity among the polymorphic genotypes in the wild. Explicit assumptions underlying these predictions were that functional differences among genotypes at the in vitro biochemical level reflected roughly corresponding differences in vivo, and that the interaction of such differences with the thermal dependence of flight capacity was correctly understood. All those predictions tested were confirmed. We now report experimental designs for testing three more of these predictions. They concern both differential survivorship and the flight activity component of differential fecundity. We find, as predicted: (1) certain heterozygotes, kinetically most effective at low temperature, begin flight earlier in the day than do other genotypes (six replicates); (2) among the three most common genotypes, the order of kinetic effectiveness, i.e., 3/4 &gt; 3/3 &gt;&gt; 4/4, is reflected in asymmetric order of heterotic advantage, 3/4&gt; 3/3 &gt;&gt; 4/4, in time of flight initiation, breadth of flight time and/or overall flight density through the day (six replicates); (3) under high temperature stress, the usual survivorship advantage of kinetically favored genotypes is reversed, and the three most thermally stable genotypes show better survivorship.——These results strengthen further the case for direct natural selection on this locus. Implications for population sampling practices, for studies of the adaptive organization of metabolism, and for studies of the interaction of genetic variation with patterns of environmental variability are discussed.
INVOLVEMENT OF GENE 49 IN RECOMBINATION OF BACTERIOPHAGE T4
Authors: Miyazaki Junichi , Ryo Yeikou , Minagawa Teiichi 
Published: January 2021

ABSTRACT
The role of T4 gene 49 in recombination was investigated using its conditional-lethal amber (am) and temperature-sensitive (ts) mutants. When measured in genetic tests, defects in gene 49 produced a recombination-deficient phenotype. However, DNA synthesized in cells infected with a ts mutant (tsC9) at a nonpermissive temperature appeared to be in a recombinogenic state: after restitution of gene function by shifting to a permissive temperature, the recombinant frequency among progeny increased rapidly even when DNA replication was blocked by an inhibitor. Growth of a gene 49-defective mutant was suppressed by an additional mutation in gene uvs X, but recombination between rII markers was not.
A MUTATION ALLOWING EXPRESSION OF NORMALLY SILENT a MATING-TYPE INFORMATION IN SACCHAROMYCES CEREVISIAE
Authors: Gruenspan Harry , Eaton Norman R 
Published: January 2021

ABSTRACT
Mating type in haploid cells of the yeast Saccharomyces cerevisiae is determined by a pair of alleles MAT a and MATα. Under various conditions haploid mating types can be interconverted. It has been proposed that transpositions of silent cassettes of mating-type information from HML or HMR to MAT are the source of mating type conversions. A mutation described in this work, designated AON1, has the following properties. (1) MATα cells carring AON1 are defective in mating. (2) AON1 allows MATα/MATα but not MAT a/MAT a diploids to sporulate; thus, AON1 mimics the MAT a requirement for sporulation. (3) mat a-1 cells that carry AON1 are MAT a phenocopies, i.e., MATα/mat a-1 AON1 diploids behave as standard MATα/MAT a cells; therefore, AON1 suppresses the defect of mat a-1. (4) AON1 maps at or near HMR a. (5) Same-site revertants from AON1 lose the ability to convert mating type to MAT a, indicating that reversion is associated with the loss of a functional HMR a locus. In addition, AON1 is a dominant mutation. We conclude that AON1 is a regulatory mutation, probably cis-acting, that leads to the constitutive expression of silent a mating-type information located at HMR a.
EVOLUTIONARY RELATIONSHIPS OF FOUR SPECIES OF HAWAIIAN DROSOPHILA AS MEASURED BY DNA REASSOCIATION
Authors: Hunt John A , Carson Hampton L 
Published: January 2021

ABSTRACT
Four species of the Hawaiian Drosophila planitibia subgroup which are homosequential in their polytene chromosomes are resident on the islands of Molokai, Maui and Hawaii. Comparisons of DNA sequence divergence in these four have been made by hybridization of total single-copy radiolabeled tracer DNA from each of the species with excess nonlabeled DNA from each of the species, and measurement of the reduction of average melting temperature (ΔTma) was made in 2.4 m tetraethyl ammonium chloride. The mean ΔTma between either D. heteroneura or D. silvestris and either D. planitibia or D. differens was found to be 1.06°, whereas the difference between D. planitibia and D. differens in 0.65° and between D. heteroneura and D. silvestris is 0.75°. These measurements taken together with the distances calculated from isozyme studies, chromosomal relationships, as well as the island locations indicate that the ancestor of these species diverged from other planitibia subgroup flies on Molokai [age 1.8 million years before present, (My BP)]. We hypothesize that one line became the present-day D. differens and diverged probably at the time of formation of East Maui (0.8-1 My BP) to form the species D. planitibia. Flies from the other line migrated to Hawaii soon after its formation (0.7 My BP) to form the two species D. heteroneura and D. silvestris.
PATTERNS OF MITOCHONDRIAL DNA VARIATION IN INDIGENOUS MAIZE RACES OF LATIN AMERICA
Authors: Weissinger A K , Timothy D H , Levings C S , Goodman M M 
Published: January 2021

ABSTRACT
Mitochondrial DNAs (mtDNAs) were isolated from 93 diverse races of maize from Latin America. DNAs were examined by agarose gel electrophoresis of undigested DNA and by BamHI and EcoRI cleavage fragment analysis. Eighteen races contained plasmid-like mtDNAs. One race contained the S-1 and S-2 molecules associated with the S cytoplasmic male-sterile, and 17 were found to have the R-1 and R-2 plasmid-like DNAs. BamHI digestion of mtDNAs generated ten distinct electrophoretograms, and EcoRI digestion produced eight different fragment patterns. Races were assigned to one of 18 groups according to EcoRI and BamHI fragment patterns and whether or not they contained plasmid-like DNAs. Eight races produced restriction patterns similar to one of the characterized cytoplasmic male-steriles C, T, or S. Races from Meso-America and some from South America with Meso-American affinities were separated from other South American races. South American races were placed in three general classes of related groups. There was considerable agreement among the groupings here and those based on morphological and cytological affinities.
NATURAL SELECTION AND DENSITY-DEPENDENT POPULATION GROWTH
Authors: Desharnais R A , Costantino R F 
Published: January 2021

ABSTRACT
Natural selection was studied in the context of density-dependent population growth using a single locus, continuous time model for the rates of change of population size and allele frequency. The maximization principle of density-dependent selection was applied to a class of fitness expressions with explicit recruitment and mortality terms. Three general results were obtained: First, at low population densities, the genetic basis of selection is the difference between the mean recruitment rate and the mean mortality rate. Second, at densities much higher than the equilibrium population size, selection is expected to act to minimize the mean mortality rate. Third, as the population approaches its equilibrium density, selection is predicted to maximize the ratio of the mean recruitment rate to the mean mortality rate.
GENETIC CONTROL OF Adh EXPRESSION IN DROSOPHILA MELANOGASTER
Authors: Maroni G , Laurie-Ahlberg C C 
Published: January 2021

ABSTRACT
Natural variants displaying different levels of expression of the gene for alcohol dehydrogenase (Adh) were subjected to genetic mapping experiments. The strains studied carry one of the two common electrophoretic forms of the enzyme. The difference among Adh - fast strains appears to be due to multiple loci with trans-acting effects. Differences among Adh - slow strains are due to modifiers or quantitative sites located very close to the structural gene (less than 0.05 map unit) or part of it. The modifiers detected in the Adhs strains seem to operate only on the structural allele in the cis-position.—A modifier that affects the ratio of ADH levels in larvae and adults was also detected in the Adhs strains. This modifier is also closely linked to Adh and is cis-acting.
Incomes and Child Health in Sub-Saharan Africa, 1990–2018
Authors: Grogan Louise , Moers Luc 
Published: January 2021

Abstract
This paper investigates the relationship between real incomes in Sub-Saharan African countries during 1990–2018 and child wellbeing. A new UNICEF-WHO-World Bank database of child growth and malnutrition and annual measures of child mortality from the World Development Indicators are employed. Changes in real incomes are related to changes in these measures. Real incomes are found to be strongly negatively conditionally associated with stunting, underweight and child mortality. The fraction of each country’s export revenue derived from major non-agricultural export commodities in 1990 is then used to construct a counterfactual value of export revenues. This measure is used to predict real incomes in a country in a year. The impact of incomes on child mortality outcomes is then assessed. Instrumental variables results suggest that improved incomes may have causally reduced neonatal and under-five mortality.
Do Age and Sex Influence Anorectal Manometry Parameters?
Authors: Jutras Gabrielle , Wahba George , Ayuso Eloise , Neshkova Elissaveta , Bouin Mickael 
Published: January 2021

Abstract

Background
High-resolution anorectal manometry (HRM) is widely used in the evaluation of anal incontinence and constipation, which become increasingly prevalent with age. However, the impact of age and comorbidities on physiological digestive parameters remains poorly understood. In this study, we aimed to evaluate the effect of age on anorectal function.

Methods
We conducted a retrospective study on patients at our digestive motility clinic between January 2016 and May 2019. All patients with a normal HRM were included. Clinical data and HRM parameters were collected in a database. Multivariate regression analyses were performed to evaluate the effects of age, sex, medical comorbidities and obstetric history on anorectal HRM parameters.

Key Results
One hundred and forty-four patients were included (mean age: 53 ± 16 years, 72% females). The main indications for anorectal HRM were incontinence (44%), constipation (37%) and anorectal pain (9%). Age was significantly associated with higher maximum tolerable volume (β = +0.48 mL year-1, P = 0.04) and higher rectal compliance (β = +0.04 mL year-1, P = 0.01). Independently from age and medical comorbidities, female demonstrated significantly lower mean endurance squeeze pressure (β = −44.4 mmHg, P &lt; 0.001), maximal squeeze pressure (β = −62.3 mmHg; P &lt; 0.001), volume at first urge (β = −16.7 mL, P = 0.02) and maximum tolerable volume (β = −16.1 mL, P = 0.046). Vaginal birth was associated with lower tolerable maximum pressure (β = −39.4 mmHg, P = 0.046).

Conclusion
Age and sex are independent factors which influence anorectal HRM parameters. These findings should be taken into consideration when interpreting anorectal HRM.
The Role of Law in Enforcing Peace Agreements: Lessons Learned from Colombia
Authors: Müller C Sophia 
Published: January 2021

Abstract
Peace agreements are frequently violated. These violations can result in the resumption of armed conflict. Yet, while there is an entire body of political science literature on the factors that influence the success or failure of peace agreements, there are only few legal scholars who deal with the implementation and enforcement of peace agreements. Law has the potential to play a critical role in peace agreement enforcement. At present, however, it is prevented from fulfilling this potential due to controversies on the legal nature of peace agreements, and the limited number of available legal enforcement mechanisms. This article will address some of these controversies on the basis of a Colombian case study. Compared to other contemporary peace agreements, the Colombian peace agreement of 24 November 2016 with the FARC is detailed and comprehensive. It created a range of monitoring mechanisms, such as two UN political missions, a comprehensive follow-up commission (CSIVI), and an international observation mechanism. Despite the abundance of these monitoring mechanisms, gaps in protection remain. An analysis of the mechanisms shows that some peace agreement violations could not be adequately addressed by any of the available mechanisms—be it due to their political nature, or due to their limited mandates. Bearing in mind the relative sophistication of the Colombian peace agreement, this is reason for concern. The article aims to demonstrate the role that law could play in enforcing peace agreements, while also discussing persisting systemic shortcomings in the applicable legal framework.
Reasoning about strategic voting in modal logic quickly becomes undecidable
Authors: Parmann Erik , Ågotnes Thomas 
Published: January 2021

AbstractIn this paper, we show that modal logics for reasoning about social choice quickly become undecidable. In particular, we study modal logics that can be used to reason about situations involving both actual and claimed preferences in the context of a social choice function and argue that reasoning on this level often occurs in social choice. We formally define a particular logic, interpreted in such situations, that can express the properties involved in the Gibbard–Satterthwaite theorem. We then, however, demonstrate that any modal logic interpreted in such situations having a certain natural expressive power, in particular a modality quantifying over all possible claimed preferences, becomes undecidable when there are enough agents in the system. We also discuss a decidable special case and provide a complete axiomatization of fragment of the language.