bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repair of single base-pair transversion mismatches of Escherichia coli in vitro: correction of certain A/G mismatches is independent of dam methylation and host mutHLS gene functions.
Authors: Lu A L , Chang D Y 
Published: January 2021

Abstract
Six different base-pair transversion mismatches are repaired with different efficiencies in an in vitro mismatch repair system. In particular, the T/T and C/C mismatches appear to be less efficiently repaired than the A/A and G/G mismatches. Four A/G and four C/T mismatches at different positions are repaired to different extents. One of the A/G mismatches is repaired equally efficiently when DNA heteroduplexes are fully methylated or hemi-methylated at the d(GATC) sequences. This type of mismatch repair appears to be unidirectional with A to C conversion by acting at A/G mispairs to restore the C/G pairs. This methylation-independent correction is not controlled by the mutH, mutL, mutS, uvrE, uvrB, phr, recA, recF, and recJ gene products. The independence of the transversion mismatch repair of these genes and methylation distinguishes this from the known mismatch repair pathways.
Differential mismatch repair can explain the disproportionalities between physical distances and recombination frequencies of cyc1 mutations in yeast.
Authors: Moore C W , Hampsey D M , Ernst J F , Sherman F 
Published: January 2021

Abstract
Recombination rates have been examined in two-point crosses of various defined cyc1 mutations that cause the loss or nonfunction of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Recombinants arising by three different means were investigated, including X-ray induced mitotic recombination, spontaneous mitotic recombination, and meiotic recombination. Heteroallelic diploid strains were derived by crossing cyc1 mutants containing a series of alterations at or near the same site to cyc1 mutants containing alterations at various distances. Marked disproportionalities between physical distances and recombination frequencies were observed with certain cyc1 mutations, indicating that certain mismatched bases can significantly affect recombination. The marker effects were more pronounced when the two mutational sites of the heteroalleles were within about 20 base pairs, but separated by at least 4 base pairs. Two alleles, cyc1-163 and cyc1-166, which arose by G.C----C.G transversions at nucleotide positions 3 and 194, respectively, gave rise to especially high rates of recombination. Other mutations having different substitutions at the same nucleotide positions were not associated with abnormally high recombination frequencies. We suggest that these marker effects are due to the lack of repair of either G/G or C/C mismatched base pairs, while the other mismatched base pair of the heteroallele undergoes substantial repair. Furthermore, we suggest that diminished recombination frequencies are due to the concomitant repair of both mismatches within the same DNA tract.
fog-2, a germ-line-specific sex determination gene required for hermaphrodite spermatogenesis in Caenorhabditis elegans.
Authors: Schedl T , Kimble J 
Published: January 2021

Abstract
This paper describes the isolation and characterization of 16 mutations in the germ-line sex determination gene fog-2 (fog for feminization of the germ line). In the nematode Caenorhabditis elegans there are normally two sexes, self-fertilizing hermaphrodites (XX) and males (XO). Wild-type XX animals are hermaphrodite in the germ line (spermatogenesis followed by oogenesis), and female in the soma. fog-2 loss-of-function mutations transform XX animals into females while XO animals are unaffected. Thus, wild-type fog-2 is necessary for spermatogenesis in hermaphrodites but not males. The fem genes and fog-1 are each essential for specification of spermatogenesis in both XX and XO animals. fog-2 acts as a positive regulator of the fem genes and fog-1. The tra-2 and tra-3 genes act as negative regulators of the fem genes and fog-1 to allow oogenesis. Two models are discussed for how fog-2 might positively regulate the fem genes and fog-1 to permit spermatogenesis; fog-2 may act as a negative regulator of tra-2 and tra-3, or fog-2 may act positively on the fem genes and fog-1 rendering them insensitive to the negative action of tra-2 and tra-3.
Identification of a putative structural gene for cathepsin D in Caenorhabditis elegans.
Authors: Jacobson L A , Jen-Jacobson L , Hawdon J M , Owens G P , Bolanowski M A , Emmons S W , Shah M V , Pollock R A , Conklin D S 
Published: January 2021

Abstract
Mutants of Caenorhabditis elegans having about 10% of wild-type activity of the aspartyl protease cathepsin D have been isolated by screening. Mutant homozygotes have normal growth rates and no obvious morphological or developmental abnormalities. The mutant gene (cad-1) has been mapped to the right extremity of linkage group II. Heterozygous animals (cad-1/+) show intermediate enzyme levels and animals heterozygous for chromosomal deficiencies of the right extremity of linkage group II have 50% of wild-type activity. Cathepsin D purified from a mutant strain has a lower activity per unit mass of pure enzyme. These data suggest that cad-1 is a structural gene for cathepsin D.
Molecular and genetic characterization of the Drosophila melanogaster 87E actin gene region.
Authors: Manseau L J , Ganetzky B , Craig E A 
Published: January 2021

Abstract
A combined molecular and genetic analysis of the 87E actin gene (Act87E) in Drosophila melanogaster was undertaken. A clone of Act87E was isolated and characterized. The Act87E transcription unit is 1.57 kb and includes a 556-base intervening sequence in the 5' leader of the gene. The protein-coding region is contiguous and encodes a protein that is greater than 93% identical to the other Drosophila actins. By in situ hybridization with a series of deficiencies that break in 87E, Act87E was localized to a region encompassing one to three faint, polytene chromosome bands. The region between the deficiency endpoints that flank the actin gene was isolated and measures approximately 24-30 kb. The closest proximal deficiency endpoint lies 8-10 kb 5' to the actin gene; the closest distal deficiency endpoint lies 16-20 kb 3' to the actin gene. A single, recessive lethal complementation group lies between the deficiency endpoints that flank the actin gene. An EMS mutagenesis screen produced four additional members of this recessive lethal complementation group. Molecular analysis of the members of this complementation group indicated that two of the newly induced mutations have deletions of approximately 1 kb in a transcribed region 4-5 kb 3' (distal) to the actin gene. This result suggests that the recessive lethal complementation group represents a gene separate from and distal to the actin gene. The mutagenesis screen failed to identify additional recessive lethal complementation groups in the actin gene-containing region. The implications of the failure to identify recessive lethal mutations in the actin gene are discussed in reference to studies of other conserved multigene families and other muscle protein mutations.
The estimation of parental genotypes by the analysis of a fixed number of their offspring.
Authors: Barbadilla A , Naveira H 
Published: January 2021

Abstract
When genotypes are cryptic in adult organisms but visible in young life-stages, it is possible to estimate the genotypes in parents after the examination of a fixed number of their offspring. Thus, in Drosophila, males collected in the wild can be crossed to females of a homozygous laboratory stock, and the identification for genotype of seven larvae is largely enough to guarantee a correct diagnosis of the two alleles of the father (P = 0.984). On the other hand, when collected females were inseminated in nature, it should be possible to determine the constitution both the female and her mate, after the analysis of a sufficient number of their offspring. Nevertheless, exact formulas for the probabilities of correct diagnoses of parental genotypes in this case have not yet been published. In this paper we derive such formulas, and illustrate their application. The conclusion we draw from our calculations is that, unless 13 larvae are examined among the offspring, the probability of misdiagnosis is over the 0.05 level. Of course, the errors produced become greater as smaller offspring numbers are analyzed. But in the case of one locus with two alleles, we have derived formulas to correct the observed number of matings and estimate its actual number in the sample, for any offspring sample size. After these corrections, we have been able to calculate estimates of relative mating frequencies in the sampled population, together with their associated errors, which can be subsequently used in studies of adult fitness components, mainly in those dealing with sexual selection.
Homologous recombination involving a large heterology in Escherichia coli.
Authors: Yamamoto K , Takahashi N , Yoshikura H , Kobayashi I 
Published: January 2021

Abstract
Recombination between two different deletion alleles of a gene (neo) for neomycin and kanamycin resistance was studied in an Escherichia coli sbcA- recB-C- strain. The two homologous regions were in an inverted orientation on the same plasmid molecule. Kanamycin-resistant plasmids were selected and analyzed. The rate of recombination to form kanamycin-resistant plasmids was decreased by mutations in the recE, recF and recJ genes, but was not decreased by a mutation in the recA gene. It was found that these plasmids often possessed one wild-type kanamycin-resistant allele (neo+) while the other neo allele was still in its original (deletion) form. Among kanamycin-resistant plasmids with one wild-type and one parental allele it was often found that the region between the inverted repeats had been flipped (turned around) with respect to sites outside the inverted repeats. These results were interpreted as follows. Gene conversion, analogous to gene conversion in eukaryotic meiosis, is responsible for a unidirectional transfer of information from one neo deletion allele to the other. The flipping of the region between the inverted repeats is interpreted as analogous to the crossing over associated with gene conversion in eukaryotic meiosis. In contrast with a rec+ strain, these products cannot be explained by two rounds of reciprocal crossing over involving a dimeric form as an intermediate. In the accompanying paper we present evidence that gene conversion by double-strand gap repair takes place in the same E. coli strain.
Genetics of an unstable white mutant in Drosophila simulans: reversion, suppression and somatic instability.
Authors: Inoue Y H , Taira T , Yamamoto M T 
Published: January 2021

Abstract
A spontaneous white mutation, white-milky (wmky) of Drosophila simulans is moderately unstable and is associated with a 16-kb long DNA insertion into the white gene. wmky, which is an unstable mutation found in D. simulans, has been genetically analyzed. Among nine spontaneous, partial reversions toward wild type, five were white locus mutations. They are phenotypically different from each other and three show eye color sexual dimorphism indicating a failure of the dosage compensation mechanism. Two w locus mutations whose eye color appeared identical between males and females were also isolated. Of the other back-mutants, three were associated with a recessive suppressor of wmky and one was a semidominant suppressor. These suppressor loci are located on the third chromosome at map positions about 90 and 120, respectively. The suppressor mutations demonstrate specific effects on w locus mutations derived from wmky which lack in the gene dosage compensation. Somatic instability was detected at the frequency of 5.6 X 10(-4) in wmky flies heterozygous for the recessive suppressor and the frequency was increased 10-fold when the suppressor mutation was placed in a different genetic background.
Length polymorphisms in human proline-rich protein genes generated by intragenic unequal crossing over.
Authors: Lyons K M , Stein J H , Smithies O 
Published: January 2021

Abstract
Southern blot hybridization analysis of genomic DNAs from 44 unrelated individuals revealed extensive insertion/deletion polymorphisms within the BstNI-type loci (PRB1, PRB2, PRB3 and PRB4) of the human proline-rich protein (PRP) multigene family. Ten length variants were cloned, including alleles at each of the four PRB loci, and in every case the region of length difference was localized to the tandemly repetitious third exon. DNA sequences covering the region of length variation were determined for seven of the alleles. The data indicate (1) that the PRB loci can be divided into two subtypes, PRB1 plus PRB2, and PRB3 plus PRB4, and (2) that the length differences result from different numbers of tandem repeats in the third exons. Variant chromosomes were also identified with different numbers of PRP loci resulting from homologous but unequal exchange between the PRB1 and PRB2 loci. The overall data are compatible with the observed length variants having been generated via homologous but unequal intragenic exchange. The results also indicate that these crossover events are sensitive to the amount of homology shared between the interacting DNA strands. Allelic length variants have arisen independently at least 20 times at the PRB loci, but only one has been detected at a PRH locus. Comparison of the detailed structures of the repetitious regions in PRB and PRH loci shows that the repeats in PRB genes are very similar to each other in sequence and in length. The PRH genes contain fewer repeats, which differ considerably in their individual lengths. These differences suggest that the larger number of length variants in PRB genes is related to their greater ease of homologous but unequal pairing compared to PRH genes.
Mutational analysis of the open reading frames in the transposable element IS1.
Authors: Jakowec M , Prentki P , Chandler M , Galas D J 
Published: January 2021

Abstract
IS1 is one of the smallest transposable elements found in bacteria (768 bp). It contains eight overlapping open-reading-frames (ORFs) greater than 50 codons, designated insA to insG and insB'. To determine which of the ORFs actually code for proteins involved in transposition, we have introduced amber codons into each ORF by site-directed mutagenesis which make neutral changes in the overlapping ORFs. Each mutant IS1 was then tested for its ability to mediate cointegrate formation in Su+ and Su- backgrounds. The mutant elements were also tested for trans-complementation in an IS1-free Salmonella background. Our results show that the products of the insA and insB genes are the only ones essential for cointegrate formation. We suggest that other ORFs may, however, encode accessory proteins.
Alterations in Bile Acid Metabolism Associated With Inflammatory Bowel Disease
Authors: Li Na , Zhan Shukai , Tian Zhenyi , Liu Caiguang , Xie Zonglin , Zhang Shenghong , Chen Minhu , Zeng Zhirong , Zhuang Xiaojun 
Published: January 2021

Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory disorder closely related to gut dysbiosis, which is associated with alterations in an important bacterial metabolite, bile acids (BAs). Although certain findings pertinent to BA changes in IBD vary among studies owing to the differences in sample type, quantitated BA species, study methodology, and patient characteristics, a specific trend concerning variations of BAs in IBD has been identified. In elaborating on this observation, it was noted that primary BAs and conjugated BAs are augmented in fecal samples but there is a reduction in secondary BAs in fecal samples. It is not entirely clear why patients with IBD manifest these changes and what role these changes play in the onset and development of IBD. Previous studies have shown that IBD-associated BA changes may be caused by alterations in BA absorption, synthesis, and bacterial modification. The complex relationship between bacteria and BAs may provide additional and deeper insight into host-gut microbiota interactions in the pathogenesis of IBD. The characteristic BA changes may generate profound effects in patients with IBD by shaping the gut microbiota community, affecting inflammatory processes, causing BA malabsorption associated with diarrhea, and even leading to intestinal dysplasia and cancer. Thus, therapeutic strategies correcting the alterations in the composition of BAs, including the elimination of excess BAs and the supplementation of deficient BAs, may prove promising in IBD.
Ciliate microzooplankton from the Northeastern Gulf of Mexico
Authors: Snyder Richard A , Moss Joseph A , Santoferrara Luciana , Head Marie , Jeffrey Wade H 
Published: January 2021

AbstractMicrozooplankton mediate a critical juncture of autotrophic and heterotrophic microbial production in the water column. Taxonomic and ecological work on this group has been substantial, yet few reports exist for the offshore waters of the Gulf of Mexico (GOM). This report focuses on protists in the phylum Ciliophora collected at stations spanning the continental shelf in the northeastern GOM. We hypothesized that patterns of spatial distribution across the region would be west–east along the coast, rather than north–south coastal to offshore, reflecting major freshwater sources. Samples were obtained by 10 µm plankton net for microscopy and by filtration of seawater for DNA extraction and ciliate-specific clone sequencing. Microscopy and molecular analysis recovered 46 and 156 taxa, respectively. Some visually identified taxa were missing from the sequence analysis and sequences from unknown species dominated molecular results. Differences were apparent with both dominant and rare taxa between February and July sampling and across a trophic gradient from coastal influenced stations to those more representative of the offshore environment. This report provides new data on ciliate microzooplankton richness and distribution in the GOM and adds to our understanding of microzooplankton diversity in the ocean.
Minimally invasive accessory splenectomy for recurrent gastric variceal bleeding due to left-sided portal hypertension: report of the first case
Authors: Schmidt S C , Möller J , Bürgel N , Radke C , Beyer L , Marusch F 
Published: January 2021

Abstract
Upper gastrointestinal bleeding from esophagogastric varices is a common scenario, especially in patients with portal hypertension induced by liver cirrhosis or other diseases with thrombosis of the splenic vein. However, accessory spleen as pathophysiological cause of a regional, left-sided portal hypertension and consecutive development of isolated gastric varices is rare. We report a case of recurrent gastric variceal bleeding resulting from sinistral portal hypertension associated with an accessory spleen in a patient who had traumatic splenectomy many decades before. The accessory spleen is an extremely rare cause for the development of regional, left-sided portal hypertension leading to isolated gastric varices. Minimally invasive splenectomy is a safe and efficient treatment option.
FMR1 expression in human granulosa cells and variable ovarian response: control by epigenetic mechanisms
Authors: Rehnitz Julia , Youness Berthe , Nguyen Xuan Phuoc , Dietrich Jens E , Roesner Sabine , Messmer Birgitta , Strowitzki Thomas , Vogt Peter H 
Published: January 2021

Abstract
In humans, FMR1 (fragile X mental retardation 1) is strongly expressed in granulosa cells (GCs) of the female germline and apparently controls efficiency of folliculogenesis. Major control mechanism(s) of the gene transcription rate seem to be based on the rate of CpG-methylation along the CpG island promoter. Conducting CpG-methylation-specific bisulfite-treated PCR assays and subsequent sequence analyses of both gene alleles, revealed three variably methylated CpG domains (FMR1-VMR (variably methylated region) 1, -2, -3) and one completely unmethylated CpG-region (FMR1-UMR) in this extended FMR1-promoter-region. FMR1-UMR in the core promoter was exclusively present only in female GCs, suggesting expression from both gene alleles, i.e., escaping the female-specific X-inactivation mechanism for the second gene allele. Screening for putative target sites of transcription factors binding with CpG methylation dependence, we identified a target site for the transcriptional activator E2F1 in FMR1-VMR3. Using specific electrophoretic mobility shift assays, we found E2F1 binding efficiency to be dependent on CpG-site methylation in its target sequence. Comparative analysis of these CpGs revealed that CpG 94-methylation in primary GCs of women with normal and reduced efficiency of folliculogenesis statistically significant differences. We therefore conclude that E2F1 binding to FMR1-VMR3 in human GCs is part of an epigenetic mechanism regulating the efficiency of human folliculogenesis. Our data indicate that epigenetic mechanisms may control GC FMR1-expression rates.
Lack of standardization in the use of road counts for surveying raptors
Authors: McClure Christopher J W , Carignan Aaron , Buij Ralph 
Published: January 2021

Abstract
Examination of population trends for raptors is a research priority, especially given recent concern for their conservation status. Road counts—in which raptors are counted from a motorized vehicle moving along the ground—might be an effective method to expand the monitoring of raptor populations and estimation of trends. Here, we review past methods used to perform road counts of raptors and present revised recommendations to aid collaboration, data transfer, and interpretation of results across monitoring programs. We performed a standardized keyword search of online literature databases to obtain 148 past road count studies. The number of studies employing road counts increased per year since the 1970s. Most of these studies occurred in North America. The times of day during which road counts were conducted ranged from sunrise to sunset, and maximum speeds ranged from 10 to 113 km hr–1. The number of observers ranged from 1 (the driver) to 5. Most (93) of the studies used unlimited-width transects and fixed-width transects ranging from 0.02 to 2.50 km wide. Sixteen percent of studies calculated or corrected for the probability of detection. Such broad variation in the methodology used during road counts, coupled with infrequent correction for detection, hampers the interpretation of results across road survey programs. We suggest that road count practitioners should emphasize the collection of data, such as speed, number of observers, and distance to observed raptors, which would allow for the calculation of detection-corrected estimates. Such correction would likely improve trend estimation. Recent technology, including mobile apps, allows researchers to collect such data relatively easily, conducting their own studies while contributing to a broader raptor monitoring initiative. Road counts will likely become more useful as statistical analysis of road count data improves and researchers pool their data in a global effort to monitor raptors.