bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest
Authors: Nejidat Ali , Diaz-Reck Damiana , Gelfand Ilya , Zaady Eli 
Published: July 2021

ABSTRACTAt the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1–10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23–26%) than in the other corrals and the control (33–38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1–10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.
Genomic prediction in family bulks using different traits and cross-validations in pine
Authors: Rios Esteban F , Andrade Mario H M L , Resende Marcio F R , Kirst Matias , de Resende Marcos D V , de Almeida Filho Janeo E , Gezan Salvador A , Munoz Patricio 
Published: July 2021

Abstract
Genomic prediction integrates statistical, genomic, and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5–20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values (GEBV) at the individual and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of genomic prediction in these situations.
Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila
Authors: Feuda Roberto , Goulty Matthew , Zadra Nicola , Gasparetti Tiziana , Rosato Ezio , Pisani Davide , Rizzoli Annapaola , Segata Nicola , Ometto Lino , Stabelli Omar Rota 
Published: July 2021

Abstract
Diptera is one of the biggest insect orders and displays a large diversity of visual adaptations. Similarly to other animals, the dipteran visual process is mediated by opsin genes. Although the diversity and function of these genes are well studied in key model species, a comprehensive comparative genomic study across the dipteran phylogeny is missing. Here we mined the genomes of 61 dipteran species, reconstructed the evolutionary affinities of 528 opsin genes, and determined the selective pressure acting in different species. We found that opsins underwent several lineage-specific events, including an independent expansion of Long Wave Sensitive opsins in flies and mosquitoes, and numerous family-specific duplications and losses. Both the Drosophila and the Anopheles complement are derived in comparison with the ancestral dipteran state. Molecular evolutionary studies suggest that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila. Overall, our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations, Anopheles and Drosophila, are characterized by contrasting dynamics in the evolution of this gene family. These results provide a foundation for future studies on the dipteran visual system.
The Transcriptional Regulator Hap1p (Cyp1p) Is Essential for Anaerobic or Heme-Deficient Growth of Saccharomyces cerevisiae: Genetic and Molecular Characterization of an Extragenic Suppressor that Encodes a WD Repeat Protein
Authors: Chantrel Yann , Gaisne Mauricette , Lions Claire , Verdière Jacqueline 
Published: July 2021

Abstract
We report here that Hap1p (originally named Cyp1p) has an essential function in anaerobic or heme-deficient growth. Analysis of intragenic revertants shows that this function depends on the amino acid preceding the first cysteine residue of the DNA-binding domain of Hap1p. Selection of recessive extragenic suppressors of a hap1−hem1− strain allowed the identification, cloning, and molecular analysis of ASC1 (Cyp1 Absence of growth Supressor). The sequence of ASC1 reveals that its ORF is interrupted by an intron that shelters the U24 snoRNA. Deletion of the intron, inactivation of the ORF, and molecular localization of the mutations show unambiguously that it is the protein and not the snoRNA that is involved in the suppressor phenotype. ASC1, which is constitutively transcribed, encodes an abundant, cytoplasmically localized 35-kD protein that belongs to the WD repeat family, which is found in a large variety of eucaryotic organisms. Polysome profile analysis supports the involvement of this protein in translation. We propose that the absence of functional Asc1p allows the growth of hap1−hem1− cells by reducing the efficiency of translation. Based on sequence comparisons, we discuss the possibility that the protein intervenes in a kinase-dependent signal transduction pathway involved in this last function.
Dhh1p, a Putative RNA Helicase, Associates with the General Transcription Factors Pop2p and Ccr4p from Saccharomyces cerevisiae
Authors: Hata Hiroaki , Mitsui Hisayuki , Liu Hong , Bai Yongli , Denis Clyde L , Shimizu Yuki , Sakai Akira 
Published: July 2021

Abstract
The POP2 (Caf1) protein in Saccharomyces cerevisiae affects a variety of transcriptional processes and is a component of the Ccr4p complex. We have isolated five multicopy suppressor genes of a pop2 deletion mutation: CCR4, DHH1 (a putative RNA helicase), PKC1, STM1, and MPT5 (multicopy suppressor of pop two). Overexpression of either the CCR4 or DHH1 genes effectively suppressed phenotypes associated with pop2 mutant cells; overexpression of PKC1, STM1, or MPT5 genes produced only partial suppression. Disruption of the CCR4 or DHH1 genes resulted in phenotypes similar to those observed for pop2 cells. In addition, overexpression of the DHH1 gene also suppressed the ccr4 mutation, suggesting a close relationship between the POP2, CCR4, and DHH1 genes. Two-hybrid analysis and coimmunoprecipitation experiments revealed that Pop2p and Dhh1p interact physically, and these and other data suggest that Dhh1p is also a component of the Ccr4p complex. Finally, we investigated the genetic interaction between factors associated with POP2 and the PKC1 pathway. The temperature-sensitive growth defect of dhh1 or mpt5 cells was suppressed by overexpression of PKC1, and the defect of mpk1 cells was suppressed by overexpression of MPT5. These results and phenotypic analysis of double mutants from the POP2 and PKC1 pathways suggested that the POP2 and the PKC1 pathways are independent but have some overlapping functions.
Yeast Meiotic Mutants Proficient for the Induction of Ectopic Recombination
Authors: Engebrecht JoAnne , Masse Sherie , Davis Luther , Rose Kristine , Kessel Therese 
Published: July 2021

Abstract
A screen was designed to identify Saccharomyces cerevisiae mutants that were defective in meiosis yet proficient for meiotic ectopic recombination in the return-to-growth protocol. Seven mutants alleles were isolated; two are important for chromosome synapsis (RED1, MEK1) and five function independently of recombination (SPO14, GSG1, SPOT8/MUM2, 3, 4). Similar to the spoT8-1 mutant, mum2 deletion strains do not undergo premeiotic DNA synthesis, arrest prior to the first meiotic division and fail to sporulate. Surprisingly, although DNA replication does not occur, mum2 mutants are induced for high levels of ectopic recombination. gsg1 diploids are reduced in their ability to complete premeiotic DNA synthesis and the meiotic divisions, and a small percentage of cells produce spores. mum3 mutants sporulate poorly and the spores produced are inviable. Finally, mum4-1 mutants produce inviable spores. The meiotic/sporulation defects of gsg1, mum2, and mum3 are not relieved by spo11 or spo13 mutations, indicating that the mutant defects are not dependent on the initiation of recombination or completion of both meiotic divisions. In contrast, the spore inviability of the mum4-1 mutant is rescued by the spo13 mutation. The mum4-1 spo13 mutant undergoes a single, predominantly equational division, suggesting that MUM4 functions at or prior to the first meiotic division. Although recombination is variably affected in the gsg1 and mum mutants, we hypothesize that these mutants define genes important for aspects of meiosis not directly related to recombination.
Dominant Alleles of Saccharomyces cerevisiae CDC20 Reveal Its Role in Promoting Anaphase
Authors: Schott Eric J , Hoyt M Andrew 
Published: July 2021

Abstract
We identified an allele of Saccharomyces cerevisiae CDC20 that exhibits a spindle-assembly checkpoint defect. Previous studies indicated that loss of CDC20 function caused cell cycle arrest prior to the onset of anaphase. In contrast, CDC20-50 caused inappropriate cell cycle progression through M phase in the absence of mitotic spindle function. This effect of CDC20-50 was dominant over wild type and was eliminated by a second mutation causing loss of function, suggesting that it encodes an overactive form of Cdc20p. Overexpression of CDC20 was found to cause a similar checkpoint defect, causing bypass of the preanaphase arrest produced by either microtubule-depolymerizing compounds or MPS1 overexpression. CDC20 overexpression was also able to overcome the anaphase delay caused by high levels of the anaphase inhibitor Pds1p, but not a mutant form immune to anaphase-promoting complex- (APC-)mediated proteolysis. CDC20 overexpression was unable to promote anaphase in cells deficient in APC function. These findings suggest that Cdc20p is a limiting factor that promotes anaphase entry by antagonizing Pds1p. Cdc20p may promote the APC-dependent proteolytic degradation of Pds1p and other factors that act to inhibit cell cycle progression through mitosis.
Comparative Analysis of Position–Effect Variegation Mutations in Drosophila melanogaster Delineates the Targets of Modifiers
Authors: Sass Georgette L , Henikoff Steven 
Published: July 2021

AbstractIn Drosophila melanogaster, heterochromatin-induced silencing or position–effect variegation (PEV) of a reporter gene has provided insights into the properties of heterochromatin. Class I modifiers suppress PEV, and class II modifiers enhance PEV when the modifier gene is present in fewer than two doses. We have examined the effects of both class I and class II modifiers on four PEV mutations. These mutations include the inversions In(1)wm4 and In(2R)bwVDe2, which are classical chromosomal rearrangements that typify PEV mutations. The other mutations are a derivative of brownDominant, in which brown+ reporters are inactivated by a large block of heterochromatin, and a P[white+] transposon insertion associated with second chromosome heterochromatin. In general, we find that class I modifiers affect both classical and nonclassical PEV mutations, whereas class II modifiers affect only classical PEV mutations. We suggest that class II modifiers affect chromatin architecture in the vicinity of reporter genes, and only class I modifiers identify proteins that are potentially involved in heterochromatin formation or maintenance. In addition, our observations support a model in which there are different constraints on the process of heterochromatin-induced silencing in classical vs. nonclassical PEV mutations.
Analysis of Temperature-Sensitive Mutants Reveals New Genes Involved in the Courtship Song of Drosophila
Authors: Peixoto Alexandre A , Hall Jeffrey C 
Published: July 2021

Abstract
cacophony (cac), a mutation affecting the courtship song in Drosophila melanogaster, is revealed to cause temperature-sensitive (TS) abnormalities. When exposed to high temperatures (37°), cac flies show frequent convulsions and pronounced locomotor defects. This TS phenotype seems consistent with the idea that cac is a mutation in a calcium-channel gene; it maps to the same X-chromosomal locus that encodes the polypeptide comprising the α-1 subunit of this membrane protein. Analysis of the courtship song of some TS physiological mutants showed that slowpoke mutations, which affect a calcium-activated potassium channel, cause severe song abnormalities. Certain additional TS mutants, in particular parats1 and napts1, exhibit subtler song defects. The results therefore suggest that genes involved in ion-channel function are a potential source of intraspecific genetic variation for song parameters, such as the number of cycles present in “pulses” of tone or the rate at which pulses are produced by the male's courtship wing vibrations. The implications of these findings from the perspective of interspecific lovesong variations in Drosophila are discussed.
A Detailed Linkage Map of Rainbow Trout Produced Using Doubled Haploids
Authors: Young William P , Wheeler Paul A , Coryell Virginia H , Keim Paul , Thorgaard Gary H 
Published: July 2021

Abstract
We report the first detailed genetic linkage map of rainbow trout (Oncorhynchus mykiss). The segregation analysis was performed using 76 doubled haploid rainbow trout produced by androgenesis from a hybrid between the “OSU” and “Arlee” androgenetically derived homozygous lines. Four hundred and seventy-six markers segregated into 31 major linkage groups and 11 small groups (&lt;5 markers/group). The minimum genome size is estimated to be 2627.5 cM in length. The sex-determining locus segregated to a distal position on one of the linkage groups. We analyzed the chromosomal distribution of three classes of markers: (1) amplified fragment length polymorphisms, (2) variable number of tandem repeats, and (3) markers obtained using probes homologous to the 5′ or 3′ end of salmonid-specific small interspersed nuclear elements. Many of the first class of markers were clustered in regions that appear to correspond to centromeres. The second class of markers were more telomeric in distribution, and the third class were intermediate. Tetrasomic inheritance, apparently related to the tetraploid ancestry of salmonid fishes, was detected at one simple sequence repeat locus and suggested by the presence of one extremely large linkage group that appeared to consist of two smaller groups linked at their tips. The double haploid rainbow trout lines and linkage map present a foundation for further genomic studies.
Genetic Interactions Among Late-Flowering Mutants of Arabidopsis
Authors: Koornneef M , Alonso-Blanco C , Vries H Blankestijn-de , Hanhart C J , Peeters A J M 
Published: July 2021

Abstract
Flowering time in Arabidopsis is controlled by a large number of genes, identified by induced mutations. Forty-two double mutants involving 10 of these loci were obtained and analyzed for their flowering behavior under long-day conditions, with and without vernalization, and under short-day conditions. The genetic interactions between the various mutants proved to be complex, although a major epistatic group (called group A) could be identified corresponding to the mutants, which are relatively insensitive to vernalization and daylength. In contrast, the genetic behavior of the mutants much more responsive to these environmental factors (group B) is more complex. The vernalization responsiveness of the group B mutants did not compensate for the lateness of the group A mutants. This indicated that these genes do not control vernalization sensitivity as such, but provide a factor that becomes limiting in short days. The classification of these mutants in different physiological groups is discussed in relation to the detected genetic interactions, and based on these interactions a more detailed model of their role in flowering initiation is proposed.
Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals
Authors: Mughal Mehreen R , DeGiorgio Michael 
Published: July 2021

Abstract
The Patterson F- and D-statistics are commonly used measures for quantifying population relationships and for testing hypotheses about demographic history. These statistics make use of allele frequency information across populations to infer different aspects of population history, such as population structure and introgression events. Inclusion of related or inbred individuals can bias such statistics, which may often lead to the filtering of such individuals. Here, we derive statistical properties of the F- and D-statistics, including their biases due to the inclusion of related or inbred individuals, their variances, and their corresponding mean squared errors. Moreover, for those statistics that are biased, we develop unbiased estimators and evaluate the variances of these new quantities. Comparisons of the new unbiased statistics to the originals demonstrates that our newly derived statistics often have lower error across a wide population parameter space. Furthermore, we apply these unbiased estimators using several global human populations with the inclusion of related individuals to highlight their application on an empirical dataset. Finally, we implement these unbiased estimators in open-source software package funbiased for easy application by the scientific community.
2015–2016 Normative Data for the 3-m Usual Walk, Five Repeated Chair Stands, and Static Balance Components of the SPPB Among U.S. Older Adults Across Two Nationally Representative Data Sets: NSHAP and NHATS
Authors: Huisingh-Scheetz Megan , Buta Brian , Bandeen-Roche Karen , Huang Elbert S , Varadhan Ravi , Walston Jeremy , Wroblewski Kristen , Schumm L Philip , Waite Linda J 
Published: July 2021

Abstract

Objectives
Our primary objective was to examine the distribution of 3-m usual walk, five repeated chair stands, and three static balance stance performances among age and gender subgroups of adults at least 65 years in two national data sets. We secondarily determined whether demographic–function associations varied across data sets, birth cohorts, or models incorporating data from those “unable to do” tasks.

Methods
Two nationally representative data sets were used to generate survey weight-adjusted performance distributions: the 2015–2016 National Social Life Health and Aging Project and the 2016 National Health and Aging Trends Study. We then regressed walk and chair stand performance on age, gender, and race/ethnicity, examining differences across data sets, birth cohorts (1920–1947, 1948–1965), and before/after incorporating the “unable to do” performers.

Results
Findings confirmed the gradual decline in function with age and allowed estimation of “relative” performance within age/gender subgroups. Data set distribution differences were noted, possibly due to recruitment, eligibility, and protocol variations. Demographic associations were similar across data sets but generally weaker among the 1948–1965 cohort and in models including the sizable “unable to do” group.

Discussion
We present the largest, most current Short Physical Performance Battery reference data in U.S. adults aged 65 or older. Findings support standardization of administration protocols in research and clinical care and differentiating absolute from relative performance.
Mining Men: Reflections on Masculinity and Oral History during the Coronavirus Pandemic
Authors: Peirson-Webber Emily 
Published: July 2021

Abstract
The COVID-19 pandemic has disrupted our ability to undertake oral history research as it is traditionally understood, where interviewer and interviewee are in dialogue with each other in a shared physical setting. Reflecting on experiences conducting twenty-seven remote interviews with former British mineworkers, this article explores how meaningful interviews can be produced with certain groups via video conferencing software and over the telephone. While some of the observational benefits of in-person interviewing were lost, there were gains in terms of the comfort of interviewees and interviewer alike. The reciprocity of video conferencing software went some way to disrupt the power dynamics of oral history interviews. Likewise, interviewees seemed more self-reflexive and willing to discuss sensitive topics when talking via online video-conferencing platforms than over the telephone, or inperson. My experience demands that we rethink orthodox methodological advice concerning best practice. The remote oral history interview can allow access to groups who are hard to reach, and offers a means through which vulnerable interviewees can regain some sense of identity and agency in a time of social dislocation.