bluuebunny/crossref_metadata_2025 huggingface dataset:
A multi-modal data harmonisation approach for discovery of COVID-19 drug targets
Authors: Chen Tyrone , Philip Melcy , Lê Cao Kim-Anh , Tyagi Sonika
Published: April 2021

Despite the volume of experiments performed and data available, the complex biology of coronavirus SARS-COV-2 is not yet fully understood. Existing molecular profiling studies have focused on analysing functional omics data of a single type, which captures changes in a small subset of the molecular perturbations caused by the virus. As the logical next step, results from multiple such omics analysis may be aggregated to comprehensively interpret the molecular mechanisms of SARS-CoV-2. An alternative approach is to integrate data simultaneously in a parallel fashion to highlight the inter-relationships of disease-driving biomolecules, in contrast to comparing processed information from each omics level separately. We demonstrate that valuable information may be masked by using the former fragmented views in analysis, and biomarkers resulting from such an approach cannot provide a systematic understanding of the disease aetiology. Hence, we present a generic, reproducible and flexible open-access data harmonisation framework that can be scaled out to future multi-omics analysis to study a phenotype in a holistic manner. The pipeline source code, detailed documentation and automated version as a R package are accessible. To demonstrate the effectiveness of our pipeline, we applied it to a drug screening task. We integrated multi-omics data to find the lowest level of statistical associations between data features in two case studies. Strongly correlated features within each of these two datasets were used for drug–target analysis, resulting in a list of 84 drug–target candidates. Further computational docking and toxicity analyses revealed seven high-confidence targets, amsacrine, bosutinib, ceritinib, crizotinib, nintedanib and sunitinib as potential starting points for drug therapy and development.
doubletD: detecting doublets in single-cell DNA sequencing data
Authors: Weber Leah L , Sashittal Palash , El-Kebir Mohammed
Published: April 2021

Motivation

While single-cell DNA sequencing (scDNA-seq) has enabled the study of intratumor heterogeneity at an unprecedented resolution, current technologies are error-prone and often result in doublets where two or more cells are mistaken for a single cell. Not only do doublets confound downstream analyses, but the increase in doublet rate is also a major bottleneck preventing higher throughput with current single-cell technologies. Although doublet detection and removal are standard practice in scRNA-seq data analysis, options for scDNA-seq data are limited. Current methods attempt to detect doublets while also performing complex downstream analyses tasks, leading to decreased efficiency and/or performance.

Results

We present doubletD, the first standalone method for detecting doublets in scDNA-seq data. Underlying our method is a simple maximum likelihood approach with a closed-form solution. We demonstrate the performance of doubletD on simulated data as well as real datasets, outperforming current methods for downstream analysis of scDNA-seq data that jointly infer doublets as well as standalone approaches for doublet detection in scRNA-seq data. Incorporating doubletD in scDNA-seq analysis pipelines will reduce complexity and lead to more accurate results.

Availability and implementation

https://github.com/elkebir-group/doubletD.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effects of rapid and slow maxillary expansion on root resorption: a micro-computed tomography study
Authors: Colak Canan , Aras Banu , Cheng Lam L , Elekdag-Turk Selma , Turk Tamer , Darendeliler M Ali
Published: April 2021

Aim

To compare root resorption (RR) after rapid maxillary expansion (RME) and slow maxillary expansion (SME) through micro-computed tomography (micro-CT).

Subjects and methods

Twenty-six subjects who required maxillary expansion and bilateral upper first premolar extraction were randomly assigned to RME (n = 13, mean age: 13.25 ± 0.88 years) or SME (n = 13, mean age: 13.53±1.28 years) group. A hyrax-type acrylic bonded expansion appliance was used. The Hyrax screw was activated ¼ turn twice a day for 20 days in the RME group and ¼ turn every second day for 80 days in the SME group. One randomly selected upper first premolar was extracted in each patient after active expansion. The appliance was left in situ for a 24-week retention period then the contralateral upper first premolar was extracted. Extracted teeth were scanned with micro-CT and the volume of the resorption craters was analysed with a specialized software. Transversal skeletal and dental widths were measured on posteroanterior radiographs taken before and after expansion and retention periods.

Results

The resorption craters were concentrated mostly on the buccal surface and middle level in all samples. The total RR in the RME group was less post-expansion (P ≤ 0.05) and more post-retention (P > 0.05) than the SME group. During retention, there was a significant decrease in the total RR in the SME group (P > 0.05) and an increase in the RME group. Both RME and SME groups displayed a similar increase in skeletal transverse dimensions, but inter-molar width increased significantly more in the SME group during the whole experimental period.

Conclusion

RME does not have an advantage over SME in terms of skeletal expansion and the amount of RR when a retention period of six months is followed.
Cartelization and firm performance in Upper Silesia 1880–1913
Authors: Beyer Christian
Published: April 2021

In this article the effects of cartelization on firms’ efficiency are investigated using the example of an early twentieth century coal-mining cartel in Upper Silesia: the Upper Silesian Coal Convention. Established in 1898, the cartel comprised various types of private, as well as state-owned, mining enterprises. Using a microeconomic dataset based on firm-level data of the Upper Silesian mines, I focus on the cartel’s effect on efficiency. The cartel did not significantly reduce technical efficiency among mines. This finding confirms previous research on cartels’ effects on efficiency.
Transcriptomic response ofCryptococcus neoformansto ecologically relevant nitrogen concentrations
Authors: Bosch Caylin , Bhana Zoë , Toplis Barbra , Volschenk Heinrich , Botha Alfred
Published: April 2021

Nitrogen availability is vital for the growth and survival of Cryptococcus neoformans in the natural environment. Two major ecological reservoirs were previously described for C. neoformans, namely, pigeon guano and the woody debris of various tree species. In contrast to the abundance of available nitrogen in guano, C. neoformans must adapt to severely limited nitrogen conditions within arboreal ecological niches. Previously, we demonstrated the role of nitrogen limitation in the production of cryptococcal virulence factors and drug tolerance. The genetic response underlying this adaptation to nitrogen deficiency, however, remains to be determined. Therefore, in the present study we investigated the transcriptomic response of C. neoformans to ecologically relevant nitrogen concentrations using RNA-sequencing. Our data revealed that low nitrogen conditions modulate the expression of numerous virulence genes in C. neoformans. Among these were, CTR4 and CGP1, which showed highly significant modulation under low nitrogen conditions. Furthermore, data analysis revealed the upregulation of antifungal tolerance-related genes in low nitrogen conditions, including genes involved in ergosterol biosynthetic processes and cell wall integrity. Overall, our findings provide insight into the survival of C. neoformans in nitrogen-poor ecological niches and suggest that pre-adaptation to these conditions may influence the pathobiology of this yeast.
Is the transperineal ultrasonography approach effective for the diagnosis of rectocele?
Authors: Yao Yi-Bo , Yin Hao-Qiang , Wang Hai-Jun , Liang Hong-Tao , Wang Bo , Wang Chen
Published: April 2021

Background

Transperineal ultrasonography has been used as a diagnostic imaging modality for rectocele for many years. However, the consistency of ultrasonography and defecography in evaluating the severity of rectocele was not satisfactory. This study aimed to evaluate the agreement in the measurement of rectocele parameters between the two methods in different positions and provide clinical implications for the diagnosis of rectocele.

Methods

In this pilot study, participants were recruited in an outpatient clinic of a tertiary hospital between December 2017 and December 2019. All participants separately underwent defecation proctography at sitting and squatting positions, and undertook transperineal ultrasonography at left lateral, sitting, and squatting positions. The consistency of ultrasonography and defecography was evaluated.

Results

Thirty female volunteers with rectocele were included in this study. The degree of anorectal angle was significantly larger at rest and during contraction, maximal Valsalva, and evacuation; the depth of the rectocele was significantly deeper during maximal Valsalva and evacuation; and the length of the perineum descending was significantly longer during contraction and maximal Valsalva in using squatting position compared to the sitting position when performing the defecation proctography. The degree of anorectal angle, the depth of rectocele, the area of levator hiatus, and the volume of the rectocele were significantly different in using squatting, sitting, and left lateral positions when performing the transperineal ultrasonography. Bland-Altman semi-quantitative plots showed good consistency in the measurement of the anorectal angle and the depth of the rectocele between proctography and ultrasonography in both sitting and squatting positions.

Conclusions

The findings of our study may be considered as the preliminary evidence to support the use of transperineal ultrasonography with sitting and squatting positions as the imaging test of choice for evaluating patients with rectocele.
A multicenter study assessing the prevalence of germline genetic alterations in Chinese gastric-cancer patients
Authors: Zhang Yin-Jie , Yang Yang , Wei Qing , Xu Ting , Zhang Xiao-Tian , Gao Jing , Tan Si-Yi , Liu Bao-Rui , Zhang Jing-Dong , Chen Xiao-Bing , Wang Zhao-Jie , Qiu Meng , Wang Xin , Shen Lin , Wang Xi-Cheng
Published: April 2021

Background

Approximately 10% of patients with gastric cancer (GC) have a genetic predisposition toward the disease. However, there is scant knowledge regarding germline mutations in predisposing genes in the Chinese GC population. This study aimed to determine the spectrum and distribution of predisposing gene mutations among Chinese GC patients known to have hereditary high-risk factors for cancer.

Methods

A total of 40 GC patients from 40 families were recruited from seven medical institutions in China. Next-generation sequencing was performed on 171 genes associated with cancer predisposition. For probands carrying pathogenic/likely pathogenic germline variants, Sanger sequencing was applied to validate the variants in the probands as well as their relatives.

Results

According to sequencing results, 25.0% (10/40) of the patients carried a combined total of 10 pathogenic or likely pathogenic germline variants involving nine different genes: CDH1 (n = 1), MLH1 (n = 1), MSH2 (n = 1), CHEK2 (n = 1), BLM (n = 1), EXT2 (n = 1), PALB2 (n = 1), ERCC2 (n = 1), and SPINK1 (n = 2). In addition, 129 variants of uncertain significance were identified in 27 patients.

Conclusions

This study indicates that approximately one in every four Chinese GC patients with hereditary high risk factors may harbor pathogenic/likely pathogenic germline alterations in cancer-susceptibility genes. The results further indicate a unique genetic background for GC among Chinese patients.
Distinguishing Between Selection and Population Expansion in an Experimental Lineage of Bacteriophage T7
Authors: Hahn Matthew W , Rausher Mark D , Cunningham Clifford W
Published: April 2021

Experimental evolution of short-lived organisms offers the opportunity to study the dynamics of polymorphism over time in a controlled environment. Here, we characterize DNA polymorphism data over time for four genes in bacteriophage T7. Our experiment ran for 2500 generations and populations were sampled after 500, 2000, and 2500 generations. We detect positive selection, purifying (“negative”) selection, and population expansion in our experiment. We also present a statistical test that is able to distinguish demographic from selective events, processes that are hard to identify individually because both often produce an excess of rare mutations. Our “heterogeneity test” modifies common statistics measuring the frequency spectrum of polymorphism (e.g., Fu and Li’s D) by looking for processes producing different patterns on nonsynonymous and synonymous mutations. Test results agree with the known conditions of the experiment, and we are therefore confident that this test offers a tool to evaluate natural populations. Our results suggest that instances of segregating deleterious mutations may be common, but as yet undetected, in nature.
Increased or Decreased Levels ofCaenorhabditis elegans lon-3, a Gene Encoding a Collagen, Cause Reciprocal Changes in Body Length
Authors: Nyström Josefin , Shen Zai-Zhong , Aili Margareta , Flemming Anthony J , Leroi Armand , Tuck Simon
Published: April 2021

Body length in C. elegans is regulated by a member of the TGFβ family, DBL-1. Loss-of-function mutations in dbl-1, or in genes encoding components of the signaling pathway it activates, cause worms to be shorter than wild type and slightly thinner (Sma). Overexpression of dbl-1 confers the Lon phenotype characterized by an increase in body length. We show here that loss-of-function mutations in dbl-1 and lon-1, respectively, cause a decrease or increase in the ploidy of nuclei in the hypodermal syncytial cell, hyp7. To learn more about the regulation of body length in C. elegans we carried out a genetic screen for new mutations causing a Lon phenotype. We report here the cloning and characterization of lon-3. lon-3 is shown to encode a putative cuticle collagen that is expressed in hypodermal cells. We show that, whereas putative null mutations in lon-3 (or reduction of lon-3 activity by RNAi) causes a Lon phenotype, increasing lon-3 gene copy number causes a marked reduction in body length. Morphometric analyses indicate that the lon-3 loss-of-function phenotype resembles that caused by overexpression of dbl-1. Furthermore, phenotypes caused by defects in dbl-1 or lon-3 expression are in both cases suppressed by a null mutation in sqt-1, a second cuticle collagen gene. However, whereas loss of dbl-1 activity causes a reduction in hypodermal endoreduplication, the reduction in body length associated with overexpression of lon-3 occurs in the absence of defects in hypodermal ploidy.
Mutational Bisection of the Mitochondrial DNA Stability and Amino Acid Biosynthetic Functions of Ilv5p of Budding Yeast
Authors: Bateman Joseph M , Perlman Philip S , Butow Ronald A
Published: April 2021

Ilv5p is a bifunctional yeast mitochondrial enzyme required for branched chain amino acid biosynthesis and for the stability of mitochondrial DNA (mtDNA) and its parsing into nucleoids. The latter occurs when the general amino acid control (GAC) pathway is activated. We have isolated ilv5 mutants that lack either the enzymatic (a−D+) or the mtDNA stability function (a+D−) of the protein. The affected residues in these two mutant classes cluster differently when mapped to the 3-D structure of the spinach ortholog of Ilv5p. a−D+ mutations map to conserved internal domains known to be important for substrate and cofactor binding, whereas the a+D− mutations map to a C-terminal region on the surface of the protein. The a+D− mutants also have a temperature-sensitive phenotype when grown on a glycerol medium, which correlates with their degree of mtDNA instability. Analysis of an a+D− mutant with a strong mtDNA instability phenotype shows that it is also unable to parse mtDNA into nucleoids when activated by the GAC pathway. Finally, the wild-type Escherichia coli ortholog of Ilv5p behaves like a+D− mutants when expressed and targeted to mitochondria in ilv5Δ yeast cells, suggesting that yeast Ilv5p acquired its mtDNA function after the endosymbiotic event.
Role of the Tsc1-Tsc2 Complex in Signaling and Transport Across the Cell Membrane in the Fission YeastSchizosaccharomyces pombe
Authors: Matsumoto Sanae , Bandyopadhyay Amitabha , Kwiatkowski David J , Maitra Umadas , Matsumoto Tomohiro
Published: April 2021

Heterozygous inactivation of either human TSC1 or TSC2 causes tuberous sclerosis (TSC), in which development of benign tumors, hamartomas, occurs via a two-hit mechanism. In this study, fission yeast genes homologous to TSC1 and TSC2 were identified, and their protein products were shown to physically interact like the human gene products. Strains lacking tsc1+ or tsc2+ were defective in uptake of nutrients from the environment. An amino acid permease, which is normally positioned on the plasma membrane, aggregated in the cytoplasm or was confined in vacuole-like structures in Δtsc1 and Δtsc2 strains. Deletion of tsc1+ or tsc2+ also caused a defect in conjugation. When a limited number of the cells were mixed, they conjugated poorly. The conjugation efficiency was improved by increased cell density. Δtsc1 cells were not responsive to a mating pheromone, P-factor, suggesting that Tsc1 has an important role in the signal cascade for conjugation. These results indicate that the fission yeast Tsc1-Tsc2 complex plays a role in the regulation of protein trafficking and suggest a similar function for the human proteins. We also show that fission yeast Int6 is involved in a similar process, but functions in an independent genetic pathway.
Chromosomal Elements Evolve at Different Rates in the Drosophila Genome
Authors: González Josefa , Ranz José María , Ruiz Alfredo
Published: April 2021

Recent results indicate that the rate of chromosomal rearrangement in the genus Drosophila is the highest found so far in any eukaryote. This conclusion is based chiefly on the comparative mapping analysis of a single chromosomal element (Muller's element E) in two species, D. melanogaster and D. repleta, representing the two farthest lineages within the genus (the Sophophora and Drosophila subgenera, respectively). We have extended the analysis to two other chromosomal elements (Muller's elements A and D) and tested for differences in rate of evolution among chromosomes. With this purpose, detailed physical maps of chromosomes X and 4 of D. repleta were constructed by in situ hybridization of 145 DNA probes (gene clones, cosmids, and P1 phages) and their gene arrangements compared with those of the homologous chromosomes X and 3L of D. melanogaster. Both chromosomal elements have been extensively reshuffled over their entire length. The number of paracentric inversions fixed has been estimated as 118 ± 17 for element A and 56 ± 8 for element D. Comparison with previous data for elements E and B shows that there are fourfold differences in evolution rate among chromosomal elements, with chromosome X exhibiting the highest rate of rearrangement. Combining all results, we estimated that 393 paracentric inversions have been fixed in the whole genome since the divergence between D. repleta and D. melanogaster. This amounts to an average rate of 0.053 disruptions/Mb/myr, corroborating the high rate of rearrangement in the genus Drosophila.
Deriving Evolutionary Relationships Among Populations Using Microsatellites and (δμ)2: All Loci Are Equal, but Some Are More Equal Than Others …
Authors: Landry Pierre-Alexandre , Koskinen Mikko T , Primmer Craig R
Published: April 2021

Numerous studies have relied on microsatellite DNA data to assess the relationships among populations in a phylogenetic framework, converting microsatellite allelic composition of populations into evolutionary distances. Among other coefficients, (δμ)2 and Rst are often employed because they make use of the differences in allele sizes on the basis of the stepwise mutation model. While it has been recognized that some microsatellites can yield disproportionate interpopulation distance estimates, no formal investigation has been conducted to evaluate to what extent such loci could affect the topology of the corresponding dendrograms. Here we show that single loci, displaying extremely large among-population variance, can greatly bias the topology of the phylogenetic tree, using data from European grayling (Thymallus thymallus, Salmonidae) populations. Importantly, we also demonstrate that the inclusion of a single disproportionate locus will lead to an overestimation of the stability of trees assessed using bootstrapping. To avoid this bias, we introduce a simple statistical test for detecting loci with significantly disproportionate variance prior to phylogenetic analyses and further show that exclusion of offending loci eliminates the false increase in phylogram stability.
Evidence That Selected Amplification of a Bacterial lac Frameshift Allele Stimulates Lac+ Reversion (Adaptive Mutation) With or Without General Hypermutability
Authors: Slechta E Susan , Liu Jing , Andersson Dan I , Roth John R
Published: April 2021

In the genetic system of Cairns and Foster, a nongrowing population of an E. coli lac frameshift mutant appears to specifically accumulate Lac+ revertants when starved on medium including lactose (adaptive mutation). This behavior has been attributed to stress-induced general mutagenesis in a subpopulation of starved cells (the hypermutable state model). We have suggested that, on the contrary, stress has no direct effect on mutability but favors only growth of cells that amplify their leaky mutant lac region (the amplification mutagenesis model). Selection enhances reversion primarily by increasing the mutant lac copy number within each developing clone on the selection plate. The observed general mutagenesis is attributed to a side effect of growth with an amplification—induction of SOS by DNA fragments released from a tandem array of lac copies. Here we show that the S. enterica version of the Cairns system shows SOS-dependent general mutagenesis and behaves in every way like the original E. coli system. In both systems, lac revertants are mutagenized during selection. Eliminating the 35-fold increase in mutation rate reduces revertant number only 2- to 4-fold. This discrepancy is due to continued growth of amplification cells until some clones manage to revert without mutagenesis solely by increasing their lac copy number. Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process). These observations support the amplification mutagenesis model.
Hybrid Sterility, Haldane's Rule and Speciation in Heliconius cydno and H. melpomene
Authors: Naisbit Russell E , Jiggins Chris D , Linares Mauricio , Salazar Camilo , Mallet James
Published: April 2021

Most genetic studies of Haldane's rule, in which hybrid sterility or inviability affects the heterogametic sex preferentially, have focused on Drosophila. It therefore remains unclear to what extent the conclusions of that work apply more generally, particularly in female-heterogametic taxa such as birds and Lepidoptera. Here we present a genetic analysis of Haldane's rule in Heliconius butterflies. Female F1 hybrids between Heliconius melpomene and H. cydno are completely sterile, while males have normal to mildly reduced fertility. In backcrosses of male F1 hybrids, female offspring range from completely sterile to fully fertile. Linkage analysis using the Z-linked triose-phosphate isomerase locus demonstrates a “large X” (Z) effect on sterility. Expression of female sterility varies among crosses in this and a previous study of Heliconius. Sterility may result from the production of normal but infertile eggs, production of small infertile eggs, or from a complete failure to develop ovarioles, which suggests multiple routes to the evolution of hybrid sterility in these Heliconius species. These results conform to the expectations of the “dominance” rather than “faster male” theories of Haldane's rule and suggest that relatively few loci are responsible. The two species are broadly sympatric and hybridize in the wild, so that female hybrid sterility forms one of several strong but incomplete barriers to gene flow in nature. The effect of female sterility is comparable to that of selection against non-mimetic hybrids, while mate choice forms a much stronger barrier to gene transfer.
Does Stellate Cause Meiotic Drive in Drosophila melanogaster?
Authors: Belloni Massimo , Tritto Patrizia , Bozzetti Maria Pia , Palumbo Gioacchino , Robbins Leonard G
Published: April 2021

Drosophila melanogaster males deficient for the crystal (cry) locus of the Y chromosome that carry between 15 and 60 copies of the X-linked Stellate (Ste) gene are semisterile, have elevated levels of nondisjunction, produce distorted sperm genotype ratios (meiotic drive), and evince hyperactive transcription of Ste in the testes. Ste seems to be the active element in this system, and it has been proposed that the ancestral Ste gene was “selfish” and increased in frequency because it caused meiotic drive. This hypothetical evolutionary history is based on the idea that Ste overexpression, and not the lack of cry, causes the meiotic drive of cry– males. To test whether this is true, we have constructed a Ste-deleted X chromosome and examined the phenotype of Ste–/cry– males. If hyperactivity of Ste were necessary for the transmission defects seen in cry– males, cry– males completely deficient for Ste would be normal. Although it is impossible to construct a completely Ste– genotype, we find that Ste–/cry– males have exactly the same phenotype as Ste+/cry– males. The deletion of all X chromosome Ste copies not only does not eliminate meiotic drive and nondisjunction, but it also does not even reduce them below the levels produced when the X carries 15 copies of Ste.
Mutation Patterns of Mitochondrial H- and L-Strand DNA in Closely Related Cyprinid Fishes
Authors: Bielawski Joseph P , Gold John R
Published: April 2021

Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-strand replication, displacing the parental H-strand as it proceeds along the molecule. The H-strand remains single stranded until light (L)-strand replication is initiated from a second origin of replication. It has been suggested that single-stranded H-strand DNA is more sensitive to mutational damage, giving rise to substitutional rate differences between the two strands and among genes in mammalian mitochondrial DNA. In this study, we analyzed sequences of the cytochrome b, ND4, ND4L, and COI genes of cyprinid fishes to investigate rates and patterns of nucleotide substitution in the mitochondrial genome. To test for strand-asymmetric mutation pressure, a likelihood-ratio test was developed and applied to the cyprinid sequences. Patterns of substitution and levels of strand-asymmetric mutation pressure were largely consistent with a mutation gradient between the H- and L-strand origins of replication. Significant strand bias was observed among rates of transitional substitution. However, biological interpretation of the direction and strength of strand asymmetry for specific classes of substitutions is problematic. The problem occurs because the rate of any single class of substitution inferred from one strand is actually a sum of rates on two strands. The validity of the likelihood-ratio test is not affected by this problem.
Sequence Variation and Haplotype Structure at the Human HFE Locus
Authors: Toomajian Christopher , Kreitman Martin
Published: April 2021

The HFE locus encodes an HLA class-I-type protein important in iron regulation and segregates replacement mutations that give rise to the most common form of genetic hemochromatosis. The high frequency of one disease-associated mutation, C282Y, and the nature of this disease have led some to suggest a selective advantage for this mutation. To investigate the context in which this mutation arose and gain a better understanding of HFE genetic variation, we surveyed nucleotide variability in 11.2 kb encompassing the HFE locus and experimentally determined haplotypes. We fully resequenced 60 chromosomes of African, Asian, or European ancestry as well as one chimpanzee, revealing 41 variable sites and a nucleotide diversity of 0.08%. This indicates that linkage to the HLA region has not substantially increased the level of HFE variation. Although several haplotypes are shared between populations, one haplotype predominates in Asia but is nearly absent elsewhere, causing higher than average genetic differentiation among the three major populations. Our samples show evidence of intragenic recombination, so the scarcity of recombination events within the C282Y allele class is consistent with selection increasing the frequency of a young allele. Otherwise, the pattern of variability in this region does not clearly indicate the action of positive selection at this or linked loci.
General Models of Multilocus Evolution
Authors: Kirkpatrick Mark , Johnson Toby , Barton Nick
Published: April 2021

In 1991, Barton and Turelli developed recursions to describe the evolution of multilocus systems under arbitrary forms of selection. This article generalizes their approach to allow for arbitrary modes of inheritance, including diploidy, polyploidy, sex linkage, cytoplasmic inheritance, and genomic imprinting. The framework is also extended to allow for other deterministic evolutionary forces, including migration and mutation. Exact recursions that fully describe the state of the population are presented; these are implemented in a computer algebra package (available on the Web at http://helios.bto.ed.ac.uk/evolgen). Despite the generality of our framework, it can describe evolutionary dynamics exactly by just two equations. These recursions can be further simplified using a “quasi-linkage equilibrium” (QLE) approximation. We illustrate the methods by finding the effect of natural selection, sexual selection, mutation, and migration on the genetic composition of a population.
Identification of X-Linked Genes Required for Migration and Programmed Cell Death of Drosophila melanogaster Germ Cells
Authors: Coffman Clark R , Strohm Rachel C , Oakley Fredrick D , Yamada Yukiko , Przychodzin Danielle , Boswell Robert E
Published: April 2021

Drosophila germ cells form at the posterior pole of the embryo and migrate to the somatic gonad. Approximately 50% of the germ cells that form reach their target. The errant cells within the embryo undergo developmentally regulated cell death. Prior studies have identified some autosomal genes that regulate germ cell migration, but the genes that control germ cell death are not known. To identify X-linked genes required for germ cell migration and/or death, we performed a screen for mutations that disrupt these processes. Here we report the identification of scattershot and outsiders, two genes that regulate the programmed death of germ cells. The scattershot gene is defined by a mutation that disrupts both germ cell migration and the death of germ cells ectopic to the gonad. Maternal and zygotic expression of scattershot is required, but the migration and cell death functions can be genetically uncoupled. Zygotic expression of wild-type scattershot rescues germ cell pathfinding, but does not restore the programmed death of errant cells. The outsiders gene is required zygotically. In outsiders mutant embryos, the appropriate number of germ cells is incorporated into the gonad, but germ cells ectopic to the gonad persist.
Is a Multivariate Consensus Representation of Genetic Relationships Among Populations Always Meaningful?
Authors: Moazami-Goudarzi K , Laloë D
Published: April 2021

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.
A Mutation in the ATP2 Gene Abrogates the Age Asymmetry Between Mother and Daughter Cells of the Yeast Saccharomyces cerevisiae
Authors: Lai Chi-Yung , Jaruga Ewa , Borghouts Corina , Jazwinski S Michal
Published: April 2021

The yeast Saccharomyces cerevisiae reproduces by asymmetric cell division, or budding. In each cell division, the daughter cell is usually smaller and younger than the mother cell, as defined by the number of divisions it can potentially complete before it dies. Although individual yeast cells have a limited life span, this age asymmetry between mother and daughter ensures that the yeast strain remains immortal. To understand the mechanisms underlying age asymmetry, we have isolated temperature-sensitive mutants that have limited growth capacity. One of these clonal-senescence mutants was in ATP2, the gene encoding the β-subunit of mitochondrial F1, F0-ATPase. A point mutation in this gene caused a valine-to-isoleucine substitution at the ninetieth amino acid of the mature polypeptide. This mutation did not affect the growth rate on a nonfermentable carbon source. Life-span determinations following temperature shift-down showed that the clonal-senescence phenotype results from a loss of age asymmetry at 36°, such that daughters are born old. It was characterized by a loss of mitochondrial membrane potential followed by the lack of proper segregation of active mitochondria to daughter cells. This was associated with a change in mitochondrial morphology and distribution in the mother cell and ultimately resulted in the generation of cells totally lacking mitochondria. The results indicate that segregation of active mitochondria to daughter cells is important for maintenance of age asymmetry and raise the possibility that mitochondrial dysfunction may be a normal cause of aging. The finding that dysfunctional mitochondria accumulated in yeasts as they aged and the propensity for old mother cells to produce daughters depleted of active mitochondria lend support to this notion. We propose, more generally, that age asymmetry depends on partition of active and undamaged cellular components to the progeny and that this “filter” breaks down with age.
Mutations in Homologous Recombination Genes Rescue top3 Slow Growth in Saccharomyces cerevisiae
Authors: Shor Erika , Gangloff Serge , Wagner Marisa , Weinstein Justin , Price Gavrielle , Rothstein Rodney
Published: April 2021

In budding yeast, loss of topoisomerase III, encoded by the TOP3 gene, leads to a genomic instability phenotype that includes slow growth, hyper-sensitivity to genotoxic agents, mitotic hyper-recombination, increased chromosome missegregation, and meiotic failure. Slow growth and other defects of top3 mutants are suppressed by mutation of SGS1, which encodes the only RecQ helicase in S. cerevisiae. sgs1 is epistatic to top3, suggesting that the two proteins act in the same pathway. To identify other factors that function in the Sgs1-Top3 pathway, we undertook a genetic screen for non-sgs1 suppressors of top3 defects. We found that slow growth and DNA damage sensitivity of top3 mutants are suppressed by mutations in RAD51, RAD54, RAD55, and RAD57. In contrast, top3 mutants show extreme synergistic growth defects with mutations in RAD50, MRE11, XRS2, RDH54, and RAD1. We also analyzed recombination at the SUP4-o region, showing that in a rad51, rad54, rad55, or rad57 background top3Δ does not increase recombination to the same degree as in a wild-type strain. These results suggest that the presence of the Rad51 homologous recombination complex in a top3 background facilitates creation of detrimental intermediates by Sgs1. We present a model wherein Rad51 helps recruit Sgs1-Top3 to sites of replicative damage.
Dissection of Upstream Regulatory Components of the Rho1p Effector, 1,3-β-Glucan Synthase, in Saccharomyces cerevisiae
Authors: Sekiya-Kawasaki Mariko , Abe Mitsuhiro , Saka Ayaka , Watanabe Daisuke , Kono Keiko , Minemura-Asakawa Masayo , Ishihara Satoru , Watanabe Takahide , Ohya Yoshikazu
Published: April 2021

In the budding yeast Saccharomyces cerevisiae, one of the main structural components of the cell wall is 1,3-β-glucan produced by 1,3-β-glucan synthase (GS). Yeast GS is composed of a putative catalytic subunit encoded by FKS1 and FKS2 and a regulatory subunit encoded by RHO1. A combination of amino acid alterations in the putative catalytic domain of Fks1p was found to result in a loss of the catalytic activity. To identify upstream regulators of 1,3-β-glucan synthesis, we isolated multicopy suppressors of the GS mutation. We demonstrate that all of the multicopy suppressors obtained (WSC1, WSC3, MTL1, ROM2, LRE1, ZDS1, and MSB1) and the constitutively active RHO1 mutations tested restore 1,3-β-glucan synthesis in the GS mutant. A deletion of either ROM2 or WSC1 leads to a significant defect of 1,3-β-glucan synthesis. Analyses of the degree of Mpk1p phosphorylation revealed that among the multicopy suppressors, WSC1, ROM2, LRE1, MSB1, and MTL1 act positively on the Pkc1p-MAPK pathway, another signaling pathway regulated by Rho1p, while WSC3 and ZDS1 do not. We have also found that MID2 acts positively on Pkc1p without affecting 1,3-β-glucan synthesis. These results suggest that distinct networks regulate the two effector proteins of Rho1p, Fks1p and Pkc1p.
A Unique Class of Conditional sir2 Mutants Displays Distinct Silencing Defects in Saccharomyces cerevisiae
Authors: Garcia Sandra N , Pillus Lorraine
Published: April 2021

Silencing provides a critical means of repressing transcription through the assembly and modification of chromatin proteins. The NAD+-dependent deacetylation of histones by the Sir2p family of proteins lends mechanistic insight into how SIR2 contributes to silencing. Here we describe three locus-specific sir2 mutants that have a spectrum of silencing phenotypes in yeast. These mutants are dependent on SIR1 for silencing function at the HM silent mating-type loci, display distinct phenotypes at the rDNA, and have dominant silencing defects at the telomeres. Telomeric silencing is restored if the mutant proteins are directly tethered to subtelomeric regions, via a Gal4p DNA-binding domain (GBD), or are recruited by tethered GBD-Sir1p. These sir2 mutations are found within conserved residues of the SIR2 family and lead to defects in catalytic activity. Since one of the mutations lies outside the previously defined minimal catalytic core, our results show that additional regions of Sir2p can be important for enzymatic activity and that differences in levels of activity may have distinct effects at the silenced loci.
The Regulatory Regions Required for B′ Paramutation and Expression Are Located Far Upstream of the Maize b1 Transcribed Sequences
Authors: Stam Maike , Belele Christiane , Ramakrishna Wusirika , Dorweiler Jane E , Bennetzen Jeffrey L , Chandler Vicki L
Published: April 2021

Paramutation is an interaction between alleles that leads to a heritable change in the expression of one allele. In B′/B-I plants, B-I (high transcription) always changes to B′ (low transcription). The new B′ allele retains the low expression state in the next generation and paramutates B-I at a frequency of 100%. Comparisons of the structure and expression of B′ with that of a closely related allele that does not participate in paramutation demonstrated that transcription from the same promoter-proximal sequences is not sufficient for paramutation. Fine-structure recombination mapping localized sequences required for B′ expression and paramutation. The entire 110 kb upstream of the B′ transcription start site was cloned and sequenced and the recombination breakpoints were determined for 12 recombinant alleles. Sequences required for expression and paramutation mapped to distinct regions, 8.5-49 kb and 93-106 kb upstream of the B′ transcription start site, respectively. Sequencing and DNA blot analyses indicate that the B′ region required for paramutation is mostly unique or low copy in the maize genome. These results represent the first example of long-distance regulatory elements in plants and demonstrate that paramutation is mediated by long-distance cis and trans interactions.
A Penalized Likelihood Method for Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches
Authors: Boer Martin P , Braak Cajo J F ter , Jansen Ritsert C
Published: April 2021

Epistasis is a common and important phenomenon, as indicated by results from a number of recent experiments. Unfortunately, the discovery of epistatic quantitative trait loci (QTL) is difficult since one must search for multiple QTL simultaneously in two or more dimensions. Such a multidimensional search necessitates many statistical tests, and a high statistical threshold must be adopted to avoid false positives. Furthermore, the large number of (interaction) parameters in comparison with the number of observations results in a serious danger of overfitting and overinterpretation of the data. In this article we present a new statistical framework for mapping epistasis in inbred line crosses. It is based on reducing the high dimensionality of the problem in two ways. First, epistatic QTL are mapped in a one-dimensional genome scan for high interactions between QTL and the genetic background. Second, the dimension of the search is bounded by penalized likelihood methods. We use simulated backcross data to illustrate the new approach.
SIR2-Induced Inviability Is Suppressed by Histone H4 Overexpression
Authors: Matecic Mirela , Stuart Shelagh , Holmes Scott G
Published: April 2021

We have identified histone H4 as a high-expression suppressor of Sir2-induced inviability in yeast cells. Overexpression of histone H3 does not suppress Sir2-induced lethality, nor does overexpression of histone H4 alleles associated with silencing defects. These results suggest a direct and specific interaction between Sir2 and H4 in the silencing mechanism.
Incorporation of Large Heterologies Into Heteroduplex DNA During Double-Strand-Break Repair in Mouse Cells
Authors: Raynard Steven J , Baker Mark D
Published: April 2021

In this study, the formation and repair of large (>1 kb) insertion/deletion (I/D) heterologies during double-strand-break repair (DSBR) was investigated using a gene-targeting assay that permits efficient recovery of sequence insertion events at the haploid chromosomal immunoglobulin (Ig) μ-locus in mouse hybridoma cells. The results revealed that (i) large I/D heterologies were generated on one or both sides of the DSB and, in some cases, formed symmetrically in both homology regions; (ii) large I/D heterologies did not negatively affect the gene targeting frequency; and (iii) prior to DNA replication, the large I/D heterologies were rectified.
Maintenance of Mitochondrial Morphology Is Linked to Maintenance of the Mitochondrial Genome in Saccharomyces cerevisiae
Authors: Hanekamp Theodor , Thorsness Mary K , Rebbapragada Indrani , Fisher Elizabeth M , Seebart Corrine , Darland Monica R , Coxbill Jennifer A , Updike Dustin L , Thorsness Peter E
Published: April 2021

In the yeast Saccharomyces cerevisiae, certain mutant alleles of YME4, YME6, and MDM10 cause an increased rate of mitochondrial DNA migration to the nucleus, carbon-source-dependent alterations in mitochondrial morphology, and increased rates of mitochondrial DNA loss. While single mutants grow on media requiring mitochondrial respiration, any pairwise combination of these mutations causes a respiratory-deficient phenotype. This double-mutant phenotype allowed cloning of YME6, which is identical to MMM1 and encodes an outer mitochondrial membrane protein essential for maintaining normal mitochondrial morphology. Yeast strains bearing null mutations of MMM1 have altered mitochondrial morphology and a slow growth rate on all carbon sources and quantitatively lack mitochondrial DNA. Extragenic suppressors of MMM1 deletion mutants partially restore mitochondrial morphology to the wild-type state and have a corresponding increase in growth rate and mitochondrial DNA stability. A dominant suppressor also suppresses the phenotypes caused by a point mutation in MMM1, as well as by specific mutations in YME4 and MDM10.
Sex-RatioDrive inDrosophila simulans: Variation in Segregation Ratio ofXChromosomes From a Natural Population
Authors: Montchamp-Moreau Catherine , Cazemajor Michel
Published: April 2021

The sex-ratio trait that exists in a dozen Drosophila species is a case of naturally occurring X chromosome drive that causes males to produce female-biased progeny. Autosomal and Y polymorphism for suppressors are known to cause variation in drive expression, but the X chromosome polymorphism has never been thoroughly investigated. We characterized 41 X chromosomes from a natural population of Drosophila simulans that had been transferred to a suppressor-free genetic background. We found two clear-cut groups of chromosomes, sex-ratio and standard. The sex-ratio X chromosomes differed in their segregation ratio (81-96% females in the progeny), the less powerful drivers being less stable in their expression. A sib analysis, using a moderate driver, indicated that within-X variation in drive expression depended on genetic (autosomal) or epigenetic factors and that the age of the males also affected the trait. The other X chromosomes produced equal or roughly equal sex ratios, but again with significant variation. The continuous pattern of variation observed within both groups suggested that, in addition to a major sex-ratio gene, many X-linked loci of small effect modify the segregation ratio of this chromosome and are maintained in a polymorphic state. This was also supported by the frequency distribution of sex ratios produced by recombinant X chromosomes.
Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species
Authors: Sivasundar Arjun , Hey Jody
Published: April 2021

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.