bluuebunny/crossref_metadata_2025 huggingface dataset:
Mosaic Analysis of Two Genes That Affect Nervous System Structure in Caenorhabditis elegans
Authors: Herman Robert K
Published: January 2021

The mutation mec-4(e1611), identified by M. Chalfie, leads to the degeneration and death of the six neurons, called the microtubule cells, that mediate the response of wild-type animals to light touch. The fates of two of these cells, PLML and PLMR, which are responsible for response to light touch in the tail of the animal, have been monitored in animals mosaic for the mec-4(e1611) mutation. The results are consistent with the view that the mutation behaves cell autonomously in its killing effect; in particular, none of the neurons that make either chemical synapses or gap junctions to PLML or PLMR is responsible for the deaths of PLML or PLMR. The results of gene dosage and dominance tests suggest that the mec-4(+) gene product, which is required for wild-type microtubule cell function, is altered by the e1611 mutation into a novel product that kills the microtubule cells. Mutation in the gene unc-3 leads to the derangement of the processes of the motor neurons of the ventral cord. Mosaic analysis strongly suggests that unc-3(+) expression is required only in the motor neurons themselves for normal neuronal development. In particular, the hypodermis surrounding the ventral cord is not the primary focus of unc-3 action (body muscle was excluded in earlier work). Finally, the mosaic analysis supports an earlier suggestion that a sensory defect caused by a daf-6 mutation is localized to a non-neuronal cell called the sheath cell.
Evolution of Steroid-Inducible RP2 mRNA Expression in the Mouse Kidney
Authors: Tseng-Crank Julie , Berger Franklin G
Published: January 2021

We have examined the structure and expression of mRNAs encoded by the androgen-inducible RP2 gene in the kidneys of nine mouse species within the genus Mus. There is considerable interspecies variation in the lengths of the major RP2 transcripts; some of this variation is due to the presence or absence of a B1 repetitive element in the 3′-untranslated region of the gene. In addition, the extent of RP2 mRNA induction by testosterone differs among the species. Two species show 10-20-fold induction, while others display a reduced response or none at all. Analysis of an interspecific hybrid indicates that the inducibility phenotype is inherited in an additive fashion. A correlation between RP2 inducibility and the time of formation of lineages within the Mus genus suggests that induction evolved in a stepwise fashion, with the acquisition of a modest hormonal response being followed by the appearance of a greater response. The interspecies variations in RP2 mRNA structure and regulation provide a useful model for the identification and study of genetic elements that elicit evolutionary alterations in steroid-modulated gene expression.
Monotonic Change of the Mean Phenotype in Two-Locus Models
Authors: Hastings Alan
Published: January 2021

It is shown that the mean phenotype monotonically approaches the optimum in a class of symmetric, two-locus, two-allele models with stabilizing selection. In this model, mean fitness does not change monotonically. Thus, Fisher's fundamental theorem does not hold, even though another quantity of evolutionary interest, the mean phenotype, can be shown to change monotonically. Using this quantity, it is proven that global stability results for this model.
Polarity effects in the hisG gene of salmonella require a site within the coding sequence.
Authors: Ciampi M S , Roth J R
Published: January 2021

A single site in the middle of the coding sequence of the hisG gene of Salmonella is required for most of the polar effect of mutations in this gene. Nonsense and insertion mutations mapping upstream of this point in the hisG gene all have strong polar effects on expression of downstream genes in the operon; mutations mapping promotor distal to this site have little or no polar effect. Two previously known hisG mutations, mapping in the region of the polarity site, abolish the polarity effect of insertion mutations mapping upstream of this region. New polarity site mutations have been selected which have lost the polar effect of upstream nonsense mutations. All mutations abolishing the function of the site are small deletions; three are identical, 28-bp deletions which have arisen independently. A fourth mutation is a deletion of 16 base pairs internal to the larger deletion. Several point mutations within this 16-bp region have no effect on the function of the polarity site. We believe that a small number of polarity sites of this type are responsible for polarity in all genes. The site in the hisG gene is more easily detected than most because it appears to be the only such site in the hisG gene and because it maps in the center of the coding sequence.
Detection of new MHC mutations in mice by skin grafting, tumor transplantation and monoclonal antibodies: a comparison.
Authors: Egorov I K , Egorov O S
Published: January 2021

Two mechanisms of major histocompatibility complex (MHC) mutations have been described in mice; gene conversion and homologous but unequal recombination. However, our knowledge of mutations in MHC is incomplete because studies have been limited almost exclusively to two haplotypes, H-2b and H-2d, while hundreds of haplotypes exist in nature; it has been biased by the use of only one procedure of screening for mutation, skin grafting. We used three procedures to screen for MHC mutations: (1) conventional techniques of skin grafting, (2) syngeneic tumor transplantation and (3) typing with monoclonal anti-MHC antibodies (mAbs) and complement. The faster technique of tumor transplantation detected mutants similar to those discovered by skin grafting technique. Screening with mAbs allowed us to detect both mutants that are capable of rejecting standard skin grafts and those that are silent in skin grafting tests, and which therefore resulted in a higher apparent mutation frequency. Two mutants of the H-2a haplotype were found that carry concomitant class I and class II antigenic alterations. Both MHC mutants silent in skin grafting tests and mutants carrying concomitant class I and class II alterations have never been studied before and are expected to reveal new mechanisms of generating MHC mutations. 1-Ethyl-1-nitrosourea (ENU) failed to induce de novo MHC mutations in male mice in our skin grafting series.
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

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

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

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

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

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

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

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

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

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

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

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

Microzooplankton 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

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

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

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.
In vivo single-particle tracking of the aquaporin AtPIP2;1 in stomata reveals cell type-specific dynamics
Authors: Cui Yaning , Zhao Yanxia , Lu Yuqing , Su Xiao , Chen Yingying , Shen Yingbai , Lin Jinxing , Li Xiaojuan
Published: January 2021

Aquaporins such as the plasma membrane intrinsic proteins (PIPs) allow water to move through cell membranes and are vital for stomatal movement in plants. Despite their importance, the dynamic changes in aquaporins during water efflux and influx have not been directly observed in real time in vivo. Here, to determine which factors regulate these changes during the bidirectional translocation of water, we examined aquaporin dynamics during the stomatal immune response to the bacterial flagellin-derived peptide flg22. The Arabidopsis (Arabidopsis thaliana) aquaporin mutant pip2;1 showed defects in the flg22-induced stomatal response. Variable-angle total internal reflection fluorescence microscopy revealed that the movement dynamics and dwell times of AQ6]GFP-AtPIP2;1 in guard cells and subsidiary cells exhibited cell type-specific dependencies on flg22. The cytoskeleton, rather than the cell wall, was the major factor regulating AtPIP2;1 dynamics, although both the cytoskeleton and cell wall might form bounded domains that restrict the diffusion of AtPIP2;1 in guard cells and subsidiary cells. Finally, our analysis revealed the different roles of cortical actin and microtubules in regulating AtPIP2;1 dynamics in guard cells, as well as subsidiary cells, under various conditions. Our observations shed light on the heterogeneous mechanisms that regulate membrane protein dynamics in plants in response to pathogens.
Current Management of Cervical Spondylotic Myelopathy
Authors: Donnally Chester J. , Patel Parthik D. , Canseco Jose A. , Vaccaro Alexander R. , Kepler Christopher K.
Published: January 2021

Cervical spondylotic myelopathy (CSM) develops insidiously as degenerative changes of the cervical spine impact the spinal cord. Unfortunately, CSM is a form of spinal cord injury in older patients that often experiences delayed treatment. This summary evaluates the pathophysiology, natural history, diagnosis, and current management of CSM. Frequently, patients do not appreciate or correlate their symptomatology with cervical spine disease, and those with radiographic findings may be clinically asymptomatic. Providers should remember the classic symptoms of CSM—poor hand dexterity, new unsteady gait patterns, new onset and progressive difficulty with motor skills. An magnetic resonance imaging is required in patients with suspected CSM, but computerized tomography myelography is an alternative in patients with implants as contraindications to magnetic resonance imaging. The management of those with CSM has continued to be a controversial topic. In general, patients with incidental findings of cervical cord compression that are asymptomatic can be managed conservatively. Those with daily moderate-severe disease that significantly affects activities of daily living should be treated operatively.
Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease
Authors: Dubanevics Igors , McLeish Tom C. B.
Published: January 2021

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (M
pro
, also known as 3CL
pro
) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an elastic network model (ENM) of the SARS-CoV-2 M
pro
homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.
Polytherapeutic strategies with oncolytic virus–bortezomib and adjuvant NK cells in cancer treatment
Authors: Aspirin Angelica P. , de los Reyes V Aurelio A. , Kim Yangjin
Published: January 2021

Proteasome inhibition and oncolytic virotherapy are two emerging targeted cancer therapies. Bortezomib, a proteasome inhibitor, disrupts the degradation of proteins in the cell leading to accumulation of unfolded proteins inducing apoptosis. On the other hand, oncolytic virotherapy uses genetically modified oncolytic viruses (OV) to infect cancer cells, induce cell lysis, and activate an antitumour response. In this work, optimal control theory is used to minimize the cancer cell population by identifying strategic infusion protocols of bortezomib, OV and natural killer (NK) cells. Three different therapeutic protocols are explored: (i) periodic bortezomib and single administrations of both OV and NK cells therapy; (ii) alternating sequential combination therapy; and (iii) NK cell depletion and infusion therapy. In the first treatment scheme, early OV administration followed by well-timed adjuvant NK cell infusion maximizes antitumour efficacy. The second strategy supports timely OV infusion. The last treatment scheme indicates that transient NK cell depletion followed by appropriate NK cell adjuvant therapy yields the maximal benefits. Relative doses and administrative costs of the three anticancer agents for each approach are qualitatively presented. This study provides potential polytherapeutic strategies in cancer treatment.
Bringing the Ca
2+
sensitivity of myristoylated recoverin into the physiological range
Authors: Marino Valerio , Riva Matteo , Zamboni Davide , Koch Karl-Wilhelm , Dell'Orco Daniele
Published: January 2021

The prototypical Ca
2+
-sensor protein recoverin (Rec) is thought to regulate the activity of rhodopsin kinase (GRK1) in photoreceptors by switching from a relaxed (R) disc membrane-bound conformation in the dark to a more compact, cytosol-diffusing tense (T) conformation upon cell illumination. However, the apparent affinity for Ca
2+
of its physiologically relevant form (myristoylated recoverin) is almost two orders of magnitude too low to support this mechanism
in vivo
. In this work, we compared the individual and synergistic roles of the myristic moiety, the GRK1 target and the disc membrane in modulating the calcium sensitivity of Rec. We show that the sole presence of the target or the disc membrane alone are not sufficient to achieve a physiological response to changes in intracellular [Ca
2+
]. Instead, the simultaneous presence of GRK1 and membrane allows the T to R transition to occur in a physiological range of [Ca
2+
] with high cooperativity via a conformational selection mechanism that drives the structural transitions of Rec in the presence of multiple ligands. Our conclusions may apply to other sensory transduction systems involving protein complexes and biological membranes.
Analytic reproducibility in articles receiving open data badges at the journal
Psychological Science
: an observational study
Authors: Hardwicke Tom E. , Bohn Manuel , MacDonald Kyle , Hembacher Emily , Nuijten Michèle B. , Peloquin Benjamin N. , deMayo Benjamin E. , Long Bria , Yoon Erica J. , Frank Michael C.
Published: January 2021

For any scientific report, repeating the original analyses upon the original data should yield the original outcomes. We evaluated analytic reproducibility in 25
Psychological Science
articles awarded open data badges between 2014 and 2015. Initially, 16 (64%, 95% confidence interval [43,81]) articles contained at least one ‘major numerical discrepancy' (>10% difference) prompting us to request input from original authors. Ultimately, target values were reproducible without author involvement for 9 (36% [20,59]) articles; reproducible with author involvement for 6 (24% [8,47]) articles; not fully reproducible with no substantive author response for 3 (12% [0,35]) articles; and not fully reproducible despite author involvement for 7 (28% [12,51]) articles. Overall, 37 major numerical discrepancies remained out of 789 checked values (5% [3,6]), but original conclusions did not appear affected. Non-reproducibility was primarily caused by unclear reporting of analytic procedures. These results highlight that open data alone is not sufficient to ensure analytic reproducibility.
Dilatancy behaviour and permeability evolution of sandstone subjected to initial confining pressures and unloading rates
Authors: Zhao Honggang , Liu Chao , Huang Gun
Published: January 2021

Mechanical response, deformation behaviour and permeability evolution of surrounding rock under unloading conditions are of significant importance in rock engineering activities. In this research, triaxial experiments of sandstone subjected to different initial confining pressures and unloading rates under fixed axial stress were conducted. The results showed that sandstones experienced shear dilatancy before failure. However, the dilatancy factor did not decrease with increasing confining pressure, i.e. the dilatancy behaviour was not suppressed, which contradicted the phenomenon under increasing axial stress. The crack density also increased with increasing initial confining pressure. Furthermore, the normalized permeability was positively correlated with unloading rates. The sandstone permeability was closely related to the shear dilatancy behaviour. In the accelerated dilatancy stage, the relationship between normalized permeability and volumetric strain was linear at low unloading rates and nonlinear at high unloading rates. The linear/nonlinear relationship between them can directly affect the temporality of respective mutation, so as to guide the prevention of geological disasters at different excavations rates.
Topological charges and conservation laws involving an arbitrary function of time for dynamical PDEs
Authors: Anco Stephen C. , Recio Elena
Published: January 2021

Dynamical PDEs that have a spatial divergence form possess conservation laws that involve an arbitrary function of time. In one spatial dimension, such conservation laws are shown to describe the presence of an
x
-independent source/sink; in two and more spatial dimensions, they are shown to produce a topological charge. Two applications are demonstrated. First, a topological charge gives rise to an associated spatial potential system, allowing non-local conservation laws and symmetries to be found for a given dynamical PDE. This type of potential system has a different form and different gauge freedom compared to potential systems that arise from ordinary conservation laws. Second, when a topological charge arises from a conservation law whose conserved density is non-trivial off of solutions to the dynamical PDE, then this relation yields a constraint on initial/boundary data for which the dynamical PDE will be well posed. Several examples of nonlinear PDEs from applied mathematics and integrable system theory are used to illustrate these results.
Using adjoint-based optimization to enhance ignition in non-premixed jets
Authors: Qadri Ubaid Ali , Magri Luca , Ihme Matthias , Schmid Peter J.
Published: January 2021

Gradient-based optimization is used to reliably and optimally induce ignition in three examples of laminar non-premixed mixture configurations. Using time-integrated heat release as a cost functional, the non-convex optimization problem identified optimal energy source locations that coincide with the stoichiometric local mixture fraction surface for short optimization horizons, while for longer horizons, the hydrodynamics plays an increasingly important role and a balance between flow and chemistry features determines non-trivial optimal ignition locations. Rather than identifying a single optimal ignition location, the results of this study show that there may be several equally good ignition locations in a given flow configuration.
Establishment versus population growth in spatio-temporally varying environments
Authors: Haccou Patsy , Serra Maria Conceição
Published: January 2021

We consider situations where repeated invasion attempts occur from a source population into a receptor population over extended periods of time. The receptor population contains two locations that provide different expected offspring numbers to invaders. There is demographic stochasticity in offspring numbers. In addition, temporal variation causes local invader fitnesses to vary. We show that effects of environmental autocorrelation on establishment success depend on spatial covariance of the receptor subpopulations. In situations with a low spatial covariance this effect is positive, whereas high spatial covariance and/or high migration probabilities between the subpopulations causes the effect to be negative. This result reconciles seemingly contradictory results from the literature concerning effects of temporal variation on population dynamics with demographic stochasticity. We study an example in the context of genetic introgression, where invasions of cultivar plant genes occur through pollen flow from a source population into wild-type receptor populations, but our results have implications in a wider range of contexts, such as the spread of exotic species, metapopulation dynamics and epidemics.
Native biodiversity collapse in the eastern Mediterranean
Authors: Albano Paolo G. , Steger Jan , Bošnjak Marija , Dunne Beata , Guifarro Zara , Turapova Elina , Hua Quan , Kaufman Darrell S. , Rilov Gil , Zuschin Martin
Published: January 2021

Global warming causes the poleward shift of the trailing edges of marine ectotherm species distributions. In the semi-enclosed Mediterranean Sea, continental masses and oceanographic barriers do not allow natural connectivity with thermophilic species pools: as trailing edges retreat, a net diversity loss occurs. We quantify this loss on the Israeli shelf, among the warmest areas in the Mediterranean, by comparing current native molluscan richness with the historical one obtained from surficial death assemblages. We recorded only 12% and 5% of historically present native species on shallow subtidal soft and hard substrates, respectively. This is the largest climate-driven regional-scale diversity loss in the oceans documented to date. By contrast, assemblages in the intertidal, more tolerant to climatic extremes, and in the cooler mesophotic zone show approximately 50% of the historical native richness. Importantly, approximately 60% of the recorded shallow subtidal native species do not reach reproductive size, making the shallow shelf a demographic sink. We predict that, as climate warms, this native biodiversity collapse will intensify and expand geographically, counteracted only by Indo-Pacific species entering from the Suez Canal. These assemblages, shaped by climate warming and biological invasions, give rise to a ‘novel ecosystem’ whose restoration to historical baselines is not achievable.
The most efficient metazoan swimmer creates a ‘virtual wall’ to enhance performance
Authors: Gemmell Brad J. , Du Clos Kevin T. , Colin Sean P. , Sutherland Kelly R. , Costello John H.
Published: January 2021

It has been well documented that animals (and machines) swimming or flying near a solid boundary get a boost in performance. This ground effect is often modelled as an interaction between a mirrored pair of vortices represented by a true vortex and an opposite sign ‘virtual vortex’ on the other side of the wall. However, most animals do not swim near solid surfaces and thus near body vortex–vortex interactions in open-water swimmers have been poorly investigated. In this study, we examine the most energetically efficient metazoan swimmer known to date, the jellyfishAurelia aurita, to elucidate the role that vortex interactions can play in animals that swim away from solid boundaries. We used high-speed video tracking, laser-based digital particle image velocimetry (dPIV) and an algorithm for extracting pressure fields from flow velocity vectors to quantify swimming performance and the effect of near body vortex–vortex interactions. Here, we show that a vortex ring (stopping vortex), created underneath the animal during the previous swim cycle, is critical for increasing propulsive performance. This well-positioned stopping vortex acts in the same way as a virtual vortex during wall-effect performance enhancement, by helping converge fluid at the underside of the propulsive surface and generating significantly higher pressures which result in greater thrust. These findings advocate that jellyfish can generate a wall-effect boost in open water by creating what amounts to a ‘virtual wall’ between two real, opposite sign vortex rings. This explains the significant propulsive advantage jellyfish possess over other metazoans and represents important implications for bio-engineered propulsion systems.