bluuebunny/crossref_metadata_2025 huggingface dataset:
Inseparability of X-Heterochromatic Functions Responsible for X:Y Pairing, Meiotic Drive, and Male Fertility in Drosophila melanogaster
Authors: McKee Bruce , Lindsley Dan L
Published: January 2021

Deficiencies encompassing part or all of the X heterochromatin of Drosophila melanogaster have been linked to three abnormalities in male meiosis and spermatogenesis: X-Y nondisjunction, skewed sperm recovery ratios favoring sperm with reduced chromatin content, and sterility in males carrying either a Y-autosome translocation or mal  +  Y. In this study, 18 X heterochromatic deficiencies of varying sizes were tested in XY males for their spermatogenic phenotypes. All 18 proved to be either mutant for all three phenotypes or wild type for all three. Although variable among mutant deficiencies, expression levels of all three phenotypes were strongly correlated. Deficiencies that cause high levels of nondisjunction also cause severe recovery ratio distortion and are completely sterile in conjunction with mal  +  Y. Low nondisjunction deficiencies cause comparable mild effects for the other phenotypes. The same deficiencies were also tested in males carrying a large heterochromatic free X duplication Dp(1;f)3. For all deficiencies which induce nondisjunction in XY males, the Y and free duplication pair regularly and the X fails to pair in XYDp males. Drive levels are constant across deficiencies in these males. Thus elimination of variability in the pairing phenotype also eliminates variability in sperm recovery ratios.
Characterization of Null Mutants of the RAD55 Gene of Saccharomyces cerevisiae: Effects of Temperature, Osmotic Strength and Mating Type
Authors: Lovett Susan T , Mortimer Robert K
Published: January 2021

RAD55 belongs to a group of genes required for resistance to ionizing radiation, RAD50-RAD57, which are thought to define a pathway of recombinational repair. Since all four alleles of RAD55 are temperature conditional (cold sensitive) for their radiation phenotype, we investigated the phenotype produced by null mutations in the RAD55 gene, constructed in vitro and transplaced to the yeast chromosome. The X-ray sensitivity of these null mutant strains was surprisingly suppressed by increased temperature, osmotic strength of the growth medium and heterozygosity at the mating-type locus. These first two properties, temperature conditionality and osmotic remediability, are commonly associated with missense mutations; these rad55 null mutants are unique in that they exhibit these properties although the mutant gene cannot be expressed. X-ray-induced mitotic recombination was also cold sensitive in rad55 mutant diploids. Although mitotic growth was unaffected in these strains, meiosis was a lethal event at both high and low temperatures. Whereas the phenotype of rad55 null mutants is consistent with a role of RAD55 in recombination and recombinational repair, there is evidence for considerable RAD55-independent recombination, at least in mitotic cells, which is influenced by temperature and MAT. We discuss models for the role of RAD55 in recombination to explain the unusual properties of rad55 mutants.
Polymorphism of Unique Noncoding DNA Sequences in Wild and Laboratory Mice
Authors: Figueroa Felipe , Kasahara Masanori , Tichy Herbert , Neufeld Esther , Ritte Uzi , Klein Jan
Published: January 2021

Two DNA probes, D17Tul and D17Tu2, were isolated from a genomic DNA library containing only two mouse chromosomes, one of which is chromosome 17, carrying the major histocompatibility complex (H-2), as well as the t complex genes. The D17Tul probe was mapped to the centromeric region of chromosome 17 and the D17Tu2 probe to the S region of the H-2 complex. Neither of the two probes appeared to detect any genes, but both contained unique, nonrepetitive sequences. Typing of DNA obtained from a large panel of mice revealed the presence of four D17Tul patterns in inbred mouse strains, one very common, one less common, and two present in one strain each. The two common patterns could not be detected in appreciable frequencies in the European wild mice tested (one of the two patterns was, however, found in Australian wild mice). Conversely, the patterns found frequently in European wild mice are absent in the laboratory mice. We therefore conclude that wild mice from the sampled regions of Europe could not have provided the ancestral stocks from which inbred strains were derived. Only one D17Tul pattern was found in all the populations of Mus musculus tested, while eight patterns were found in Mus domesticus, with virtually all the populations being polymorphic. We suggest that this difference reflects different modes in which the two species colonized Europe. The distribution of the D17Tu2 patterns in inbred strains correlates with the distribution of H-2 haplotypes.
Genetic Organization of the agouti Region of the Mouse
Authors: Siracusa Linda D , Russell Liane B , Eicher Eva M , Corrow Dorcas J , Copeland Neal G , Jenkins Nancy A
Published: January 2021

The agouti locus on mouse chromosome 2 acts via the hair follicle to control the melanic type and distribution of hair pigments. The diverse phenotypes associated with various agouti mutations have led to speculation about the organization of the agouti locus. Earlier studies indicated that two presumed agouti alleles, lethal yellow (Ay) and lethal light-bellied nonagouti(ax), are pseudoallelic. We present genetic data showing probable recombination between Ay and three agouti mutations (at, a, and ax), which suggest that Ay is a pseudoallele of the agouti locus. The close linkage of an endogenous ecotropic murine leukemia provirus, Emv-15, to Ay provides a molecular access to genes at or near the agouti locus. However, previous studies suggested that the Emv-15 locus can recombine with some agouti alleles and therefore we analyzed mice from recombinant inbred strains and backcrosses to measure the genetic distance between various agouti alleles and the Emv-15 locus. Our data indicate that the Emv-15 locus is less than 0.3 cM from the agouti locus. These experiments provide a conceptual framework for initiating chromosome walking experiments designed to retrieve sequences from the agouti locus and give new insight into the genetic organization of the agouti region.
Effects of recA Mutations on Pilus Antigenic Variation and Phase Transitions in Neisseria gonorrhoeae
Authors: Koomey Michael , Gotschlich Emil C , Robbins Ken , Bergström Sven , Swanson John
Published: January 2021

Intragenic recombination between the single complete pilin gene (expression locus) and multiple, distinct, partial pilin gene copies (silent, storage loci) is thought to account for the generation of pilus antigenic diversity and piliation phase (on-off) changes exhibited by Neisseria gonorrhoeae. The mechanisms operating in the genomic rearrangements associated with these forms of pilus variation were investigated through the study of isogenic strains of gonococci bearing either wild-type or altered recA alleles. Examination of the rates of pilus phase variation and the genetic basis for changes in piliation status displayed by these strains show that recA mediated homologous recombination is required for these high frequency events and confirm that the nonpiliated state results from mutations in the expressed pilin gene. In a strain that is deficient in recA mediated homologous recombination, pilus phase variation occurs at a 100-1000-fold reduced rate and results predominantly from one class of spontaneous frameshift mutations within the pilin structural gene.
Genetic organization of the unc-60 region in Caenorhabditis elegans.
Authors: McKim K S , Heschl M F , Rosenbluth R E , Baillie D L
Published: January 2021

We have investigated the chromosomal region around unc-60 V, a gene affecting muscle structure, in the nematode Caenorhabditis elegans. The region studied covers 3 map units and lies at the left end of linkage group (LG) V. Compared to the region around dpy-11 (at the center of LGV), the unc-60 region has relatively few visible genes per map unit. We found the same to be true for essential genes. By screening simultaneously for recessive lethals closely linked to either dpy-11 or unc-60, we recovered ethyl methanesulfonate-induced mutations in 10 essential genes near dpy-11 but in only two genes near unc-60. Four deficiency breakpoints were mapped to the unc-60 region. Using recombination and deficiency mapping we established the following gene order: let-336, unc-34, let-326, unc-60, emb-29, let-426. Regarding unc-60 itself, we compared the effect of ten alleles (including five isolated during this study) on hermaphrodite mobility and fecundity. We used intragenic mapping to position eight of these alleles. The results show that these alleles are not distributed uniformly within the gene, but map to two groups approximately 0.012 map unit apart.
Different reading frames are responsible for IS1-dependent deletions and recombination.
Authors: Braedt G
Published: January 2021

Two classes of plasmids in addition to the parent become apparent when plasmids that contain direct repeats of IS1. One class of plasmids has deleted sequences from the end of IS1 to nonrandom sites within the plasmid. The appearance of these plasmids in the population requires intact insA and insB reading frames, but not insC. The other class of plasmids has undergone an exchange within the direct repeats of IS1 on the plasmid. Their appearance requires InsC but neither InsA nor InsB. The two reactions may represent two distinguishable steps in IS1 transposition. The InsC-catalyzed exchange is independent of RecA and resembles hologous recombination since the frequency of recombinants arising from exchanges in different regions of IS1 appears to be roughly proportional to the size of the region. InsC can also catalyze an exchange between direct repeats of non-IS1 DNA.
Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup.
Authors: Caccone A , Amato G D , Powell J R
Published: January 2021

Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.
Conditional mutants of RPC160, the gene encoding the largest subunit of RNA polymerase C in Saccharomyces cerevisiae.
Authors: Gudenus R , Mariotte S , Moenne A , Ruet A , Memet S , Buhler J M , Sentenac A , Thuriaux P
Published: January 2021

A 18.4-kb fragment of the yeast genome containing the gene of the largest subunit of RNA polymerase C (RPC160) was cloned by hybridization to a previously isolated fragment of that gene. RPC160 maps on chromosome XV, tightly linked but not allelic to the essential gene TSM8740. Temperature sensitive (ts) mutant alleles were constructed by in vitro mutagenesis with NaHSO3 and substituted for the wild-type allele on the chromosome. Four of them were unambiguously identified as rpc160 mutants by failure to complement a fully defective mutation rpc160::URA3. The faithful transcription of a yeast tRNA gene by mutant cell-free extracts is strongly reduced as compared to wild-type. In vivo, the rpc160 mutations specifically affect the synthesis of tRNA in a temperature sensitive way, with comparatively little effect on the synthesis of 5S rRNA and no effect on 5.8S rRNA. An unlinked mutation (pcil-3) suppresses the temperature sensitive phenotype of the rpc160-41 mutation.
A sampling theory of selectively neutral alleles in a subdivided population.
Authors: Tillier E R , Golding G B
Published: January 2021

Ewens' sampling distribution is investigated for a structured population. Samples are assumed to be taken from a single subpopulation that exchanges migrants with other subpopulations. A complete description of the probability distribution for such samples is not a practical possibility but an equilibrium approximation can be found. This approximation extracts the information necessary for constructing a continuous approximation to the complete distribution using known values of the distribution and its derivatives in randomly mating populations. It is shown that this approximation is as complete a description of a single biologically realistic subpopulation as is possible given standard uncertainties about the actual size of the migration rates, relative sizes of each of the subpopulations and other factors that might affect the genetic structure of a subpopulation. Any further information must be gained at the expense of generality. This approximation is used to investigate the effect of population subdivision on Watterson's test of neutrality. It is known that the infinite allele, sample distribution is independent of mutation rate when made conditional on the number of alleles in the sample. It is shown that the conditional, infinite allele, sample distribution from this approximation is also independent of population structure and hence Watterson's test is still approximately valid for subdivided populations.
Autogenous regulation of the regA gene of bacteriophage T4: derepression of translation.
Authors: Liang Y M , Wei R X , Hsu T , Alford C , Dawson M , Karam J
Published: January 2021

The regA gene of phage T4 encodes a translational repressor that inhibits utilization of its own mRNA as well as the translation of a number of other phage-induced mRNAs. In recombinant plasmids, autogenous translational repression limits production of the RegA protein when the cloned structural gene is expressed under control of a strong, plasmid-borne promoter (lambda PL). We have found that a genetic fusion which places the regA ribosome binding domain in proximity to active translation leads to partial derepression of wild-type RegA protein synthesis. The derepression is not due to increased synthesis of regA RNA, suggesting that it occurs at the translational level. Derepressed clones of the wild-type regA gene were used to overproduce and purify the repressor. In an in vitro assay the wild-type target was sensitive and a mutant target was resistant to inhibition by the added protein. The results suggest that the sensitivity of a regA-regulated cistron to translational repression may depend on the competition between ribosomes and RegA protein for overlapping recognition sequences in the translation initiation domain of the mRNA.
Rediscovery of a Mesoamerican greenstone sculpture from the collection of Ulisse Aldrovandi
Authors: Domenici Davide
Published: January 2021

This article presents a pre-Hispanic Mesoamerican greenstone sculpture, formerly held in the collection of Ulisse Aldrovandi (1522–1605) and recently rediscovered by the author in the storerooms of the Museo Civico Medievale in Bologna. After a discussion of Aldrovandi’s general attitude towards natural and cultural specimens from the New World, the article explores the ways in which the Bolognese polymath described and illustrated the sculpture in his Musaeum metallicum (1648), where he named it as ‘Idolum pileatum’. It is argued here that Aldrovandi’s main interest was not so much proto-anthropological as of a taxonomic kind, in line with his interest in material culture as both an antiquary and a natural historian. The last section of the article explores the sculpture’s cultural biography, reconstructing its collection history and also putting forward a hypothesis for the circumstances of its arrival in Bologna.
Association of Daily Alcohol Intake, Volumetric Breast Density, and Breast Cancer Risk
Authors: Rustagi Alison S , Scott Christopher G , Winham Stacey J , Brandt Kathleen R , Norman Aaron D , Jensen Matthew R , Shepherd John A , Hruska Carrie , Heine John J , Pankratz Vernon S , Kerlikowske Karla , Vachon Celine M
Published: January 2021

High alcohol intake and breast density increase breast cancer (BC) risk, but their interrelationship is unknown. We examined whether volumetric density modifies and/or mediates the alcohol-BC association. BC cases (n = 2233) diagnosed from 2006 to 2013 in the San Francisco Bay area had screening mammograms 6 or more months before diagnosis; controls (n = 4562) were matched on age, mammogram date, race or ethnicity, facility, and mammography machine. Logistic regression was used to estimate alcohol-BC associations adjusted for age, body mass index, and menopause; interaction terms assessed modification. Percent mediation was quantified as the ratio of log (odds ratios [ORs]) from models with and without density measures. Alcohol consumption was associated with increased BC risk (2-sided Ptrend = .004), as were volumetric percent density (OR = 1.45 per SD, 95% confidence interval [CI] = 1.36 to 1.56) and dense volume (OR = 1.30, 95% CI = 1.24 to 1.37). Breast density did not modify the alcohol-BC association (2-sided P > .10 for all). Dense volume mediated 25.0% (95% CI = 5.5% to 44.4%) of the alcohol-BC association (2-sided P = .01), suggesting alcohol may partially increase BC risk by increasing fibroglandular tissue.
Global optimization-based reference star differential imaging for high-contrast exoplanet imaging survey
Authors: Ren Deqing , Chen Yili
Published: January 2021

We propose a data reduction approach called global optimization-based reference star differential imaging (G-RDI), which can be used for exoplanet imaging survey, where large numbers of target stars from the same young stellar association are imaged and where no field rotation is needed. One of the unique features of our G-RDI is that we select reference stars from other scientific target stars in the same stellar association to optimize for high-contrast imaging with a target star, which maximizes the observational efficiency and also delivers good performance to remove the speckle noise so that high contrast is achievable even at a small inner working angle (IWA) to the host star of being imaged. We proposed the G-RDI that is optimized for high-contrast exoplanet imaging at a small IWA and to provide a contrast that is significantly better than the current reference star differential imaging (RDI) method. In addition, we also propose the use of multiple reference stars and found that our G-RDI can further deliver better performance in that case. The result was compared with other exoplanet data reduction techniques, including the traditional RDI, and it indicated that our G-RDI with two reference stars can significantly improve the contrast performance at a small IWA with a high observational efficiency – two critical features that current data reduction techniques cannot offer. This approach could be used with both equatorial and alt-azimuth mount telescopes, and provides a new option for future exoplanet imaging surveys with high observational efficiency at a small IWA.
An excess of globular clusters in Ultra-Diffuse Galaxies formed through tidal heating
Authors: Carleton Timothy , Guo Yicheng , Munshi Ferah , Tremmel Michael , Wright Anna
Published: January 2021

To investigate the origin of elevated globular cluster (GC) abundances observed around Ultra-Diffuse Galaxies (UDGs), we simulate GC populations hosted by UDGs formed through tidal heating. Specifically, GC formation is modelled as occurring in regions of dense star formation. Because star formation-rate densities are higher at high redshift, dwarf galaxies in massive galaxy clusters, which formed most of their stars at high redshift, form a large fraction of their stars in GCs. Given that UDGs formed through environmental processes are more likely to be accreted at high redshift, these systems have more GCs than non-UDGs. In particular, our model predicts that massive UDGs have twice the GC mass of non-UDGs of similar stellar mass, in rough agreement with observations. Although this effect is somewhat diminished by GC disruption, we find that the relationship between GC mass fraction and cluster-centric distance, and the relationship between GC mass fraction and galaxy half-light radius are remarkably similar to observations. Among our model objects, both UDGs and non-UDGs present a correlation between halo mass and GC mass, although UDGs have lower dynamical masses at a given GC mass. Furthermore, because of the effectiveness of GC disruption, we predict that GCs around UDGs should have a more top heavy mass function than GCs around non-UDGs. This analysis suggests that dwarfs with older stellar populations, such as UDGs, should have higher GC mass fractions than objects with young stellar populations, such as isolated dwarfs.
A morphological appraisal of the new subfamily Epidesmiinae (Lepidoptera: Geometridae) with an overview of all geometrid subfamilies
Authors: Murillo-Ramos Leidys , Friedrich Egbert , Williams Steve , Wahlberg Niklas , Brehm Gunnar , Sihvonen Pasi
Published: January 2021

Our study revises Epidesmiinae, the first new Geometridae subfamily that has been described in 127 years. We studied the morphological characters of representatives from all genera currently classified into Epidesmiinae, and compared those with all other geometrid subfamilies. Epidesmiinae were found to have an Australasian distribution, with one species occurring in the Indo-Malayan realm. They compose a lineage diagnosable by a combination of the following morphological characters: male antennae unipectinate; labial palps elongated (particularly the second segment), vom Raths’s organ with an elliptical invagination; forewing with two areoles; hindwing with one anal vein; gnathos arms fused, granulate or dentate apically; female genitalia with two signa, one stellate, another an elongated and spinose plate. We also present a summary of diagnostic characters of all geometrid subfamilies, which confirm the lack of single unique morphological characters. The limited information on the biology and ecology of Epidesmiinae species are summarized, indicating that some species fly during the day, most adult records are from the Southern Hemisphere summer months and larvae are found on Myrtaceae. We transfer Arcina Walker, 1863 from Oenochrominae s.l. to Epidesmiinae. Epidesmiinae includes 102 species that are now classified into nine genera: Abraxaphantes, Adeixis, Arcina, Dichromodes, Ecphyas, Epidesmia, Phrataria, Phrixocomes and Systatica.
Parasitic wasps avoid ant-protected hemipteran hosts via the detection of ant cuticular hydrocarbons
Authors: Mouratidis Angelos , Vacas Sandra , Herrero Julieta , Navarro-Llopis Vicente , Dicke Marcel , Tena Alejandro
Published: January 2021

One of the most studied and best-known mutualistic relationships between insects is that between ants and phloem-feeding insects. Ants feed on honeydew excreted by phloem-feeding insects and, in exchange, attack the phloem feeders' natural enemies, including parasitic wasps. However, parasitic wasps are under selection to exploit information on hazards and avoid them. Here, we tested whether parasitic wasps detect the previous presence of ants attending colonies of phloem feeders. Behavioural assays demonstrate that wasps left colonies previously attended by ants more frequently than control colonies. This behaviour has a potential cost for the parasitic wasp as females inserted their ovipositor in fewer hosts per colony. In a further bioassay, wasps spent less time on papers impregnated with extracts of the ant cues than on control papers. Gas chromatography coupled with mass spectrometry analyses demonstrated that ants left a blend of cuticular hydrocarbons when they attended colonies of phloem feeders. These cuticular hydrocarbons are deposited passively when ants search for food. Overall, these results suggest, for the first time, that parasitic wasps of honeydew producers detect the previous presence of mutualistic ants through contact infochemicals. We anticipate such interactions to be widespread and to have implications in numerous ecosystems, as phloem feeders are usually tended by ants.
Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
Authors: Epstein Brendan , Tiffin Peter
Published: January 2021

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.
Deep-diving beaked whales dive together but forage apart
Authors: Alcázar-Treviño Jesús , Johnson Mark , Arranz Patricia , Warren Victoria E. , Pérez-González Carlos J. , Marques Tiago , Madsen Peter T. , Aguilar de Soto Natacha
Published: January 2021

Echolocating animals that forage in social groups can potentially benefit from eavesdropping on other group members, cooperative foraging or social defence, but may also face problems of acoustic interference and intra-group competition for prey. Here, we investigate these potential trade-offs of sociality for extreme deep-diving Blainville′s and Cuvier's beaked whales. These species perform highly synchronous group dives as a presumed predator-avoidance behaviour, but the benefits and costs of this on foraging have not been investigated. We show that group members could hear their companions for a median of at least 91% of the vocal foraging phase of their dives. This enables whales to coordinate their mean travel direction despite differing individual headings as they pursue prey on a minute-by-minute basis. While beaked whales coordinate their echolocation-based foraging periods tightly, individual click and buzz rates are both independent of the number of whales in the group. Thus, their foraging performance is not affected by intra-group competition or interference from group members, and they do not seem to capitalize directly on eavesdropping on the echoes produced by the echolocation clicks of their companions. We conclude that the close diving and vocal synchronization of beaked whale groups that quantitatively reduces predation risk has little impact on foraging performance.
Hearing sensitivity and amplitude coding in bats are differentially shaped by echolocation calls and social calls
Authors: Lattenkamp Ella Z. , Nagy Martina , Drexl Markus , Vernes Sonja C. , Wiegrebe Lutz , Knörnschild Mirjam
Published: January 2021

Differences in auditory perception between species are influenced by phylogenetic origin and the perceptual challenges imposed by the natural environment, such as detecting prey- or predator-generated sounds and communication signals. Bats are well suited for comparative studies on auditory perception since they predominantly rely on echolocation to perceive the world, while their social calls and most environmental sounds have low frequencies. We tested if hearing sensitivity and stimulus level coding in bats differ between high and low-frequency ranges by measuring auditory brainstem responses (ABRs) of 86 bats belonging to 11 species. In most species, auditory sensitivity was equally good at both high- and low-frequency ranges, while amplitude was more finely coded for higher frequency ranges. Additionally, we conducted a phylogenetic comparative analysis by combining our ABR data with published data on 27 species. Species-specific peaks in hearing sensitivity correlated with peak frequencies of echolocation calls and pup isolation calls, suggesting that changes in hearing sensitivity evolved in response to frequency changes of echolocation and social calls. Overall, our study provides the most comprehensive comparative assessment of bat hearing capacities to date and highlights the evolutionary pressures acting on their sensory perception.
Development of a saliva-optimized RT-LAMP assay for SARS-CoV-2
Authors: Yu Albert Dayuan , Galatsis Kristina , Zheng Jian , Le Jasmine Quynh , Ma Dingbang , Perlman Stanley , Rosbash Michael
Published: January 2021

Conventional reverse transcription quantitative polymerase chain reaction (RT-qPCR) technology has struggled to fulfill the unprecedented need for diagnostic testing created by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Complexity and cost hinder access to testing, and long turnaround-time decreases its utility. To ameliorate these issues, we focus on saliva and introduce several advances to colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) technology; RT-LAMP offers a minimal equipment alternative to RT-qPCR. First, we validated the use of the novel dye LAMPShade Violet (LSV), which improves the visual clarity and contrast of the colorimetric readout. Second, we compared different inactivation conditions on infectivity and RNA yield from saliva. Third, we developed a ten-minute RNA purification protocol from saliva. We call this magnetic bead protocol SalivaBeads. Finally, we developed a magnetic stick, StickLAMP, which provides reliable bead-based RNA purification as well as simple and low-cost access to scalable testing from saliva.
The evaluation of a newly developed antigen test (QuickNavi™-COVID19 Ag) for SARS-CoV-2: A prospective observational study in Japan
Authors: Takeuchi Yuto , Akashi Yusaku , Kato Daisuke , Kuwahara Miwa , Muramatsu Shino , Ueda Atsuo , Notake Shigeyuki , Nakamura Koji , Ishikawa Hiroichi , Suzuki Hiromichi
Published: January 2021

Introduction

Several antigen tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed worldwide, but their clinical utility has not been well established. In this study, we evaluated the analytical and clinical performance of QuickNavi™-COVID19 Ag, a newly developed antigen test in Japan.

Methods

This prospective observational study was conducted at a PCR center between October 7 and December 5, 2020. The included patients were referred from a local public health center and 89 primary care facilities. We simultaneously obtained two nasopharyngeal samples with flocked swabs; one was used for the antigen test and the other for real-time reverse transcription PCR (RT-PCR). Using the results of real-time RT-PCR as a reference, the performance of the antigen test was evaluated.

Results

A total of 1186 patients were included in this study, and the real-time RT-PCR detected SARS-CoV-2 in 105 (8.9%). Of these 105 patients, 33 (31.4%) were asymptomatic. The antigen test provided a 98.8% (95% confident interval [CI]: 98.0%-99.4%) concordance rate with real-time RT-PCR, along with a sensitivity of 86.7% (95% CI: 78.6%-92.5%) and a specificity of 100% (95% CI: 99.7%-100%). False-negatives were observed in 14 patients, 8 of whom were asymptomatic and had a low viral load (cycle threshold (Ct) >30). In symptomatic patients, the sensitivity was 91.7% (95% CI: 82.7%-96.9%).

Conclusion

QuickNavi™-COVID19 Ag showed high specificity and sufficient sensitivity for the detection of SARS-CoV-2. This test is a promising potential diagnostic modality especially in symptomatic patients.
Long-term neurological manifestations of COVID-19: prevalence and predictive factors
Authors: Pilotto Andrea , Cristillo Viviana , Piccinelli Stefano Cotti , Zoppi Nicola , Bonzi Giulio , Sattin Davide , Schiavolin Silvia , Raggi Alberto , Canale Antonio , Gipponi Stefano , Libri Ilenia , Frigerio Martina , Bezzi Michela , Leonardi Matilde , Padovani Alessandro
Published: January 2021

Background

Clinical investigations have argued for long-term neurological manifestations in both hospitalized and non-hospitalized COVID-19 patients. It is unclear whether long-term neurological symptoms and features depend on COVID-19 severity.

Methods

from a sample of 208 consecutive non-neurological patients hospitalized for COVID-19 disease, 165 survivors were re-assessed at 6 months according to a structured standardized clinical protocol. Prevalence and predictors of long-term neurological manifestations were evaluated using multivariate logistic regression analyses.

Results

At 6-month follow-up after hospitalisation due to COVID-19 disease, patients displayed a wide array of symptoms; fatigue (34%), memory/attention (31%), and sleep disorders (30%) were the most frequent. At neurological examination, 40% of patients exhibited neurological abnormalities, such as hyposmia (18.0%), cognitive deficits (17.5%), postural tremor (13.8%) and subtle motor/sensory deficits (7.6%). Older age, premorbid comorbidities and severity of COVID-19 were independent predictors of neurological manifestations in logistic regression analyses.

Conclusions

premorbid vulnerability and severity of SARS-CoV-2 infection impact on prevalence and severity of long-term neurological manifestations.
A study of metabolic syndrome in patients of HIV on ART in India
Authors: Sashindran V K , Singh Anchit Raj
Published: January 2021

Metabolic syndrome is a risk factor for cardiovascular disease. With improvement in therapy for HIV, morbidity related to metabolic syndrome becomes a focus of interest. Change in nutritional status and introduction of newer regimens of ART are changing the impact of metabolic syndrome on patients of HIV. Few studies in recent times from developing countries have addressed this question. This is a cross sectional study to study the prevalence of Metabolic Syndrome in patients of HIV on ART from clinics in a tertiary care hospital in India. Data from 1208 patients of HIV on ART was analyzed and metabolic syndrome was seen in 257(21.3%) patients.

The high prevalence of metabolic syndrome in patients of HIV in India found in this study gives an insight on the morbidity of noncommunicable diseases in patients with HIV in India in recent times.
Simulating the Impacts of Interregional Mobility Restriction on the Spatial Spread of COVID-19 in Japan
Authors: Kondo Keisuke
Published: January 2021

This study develops a spatial Susceptible–Exposed–Infectious–Recovered (SEIR) model that analyzes the effect of interregional mobility on the spatial spread of the coronavirus disease 2019 (COVID-19) outbreak in Japan. National and local governments have requested that residents refrain from traveling between 47 prefectures during the state of emergency. However, the extent to which restricting the interregional mobility prevents infection expansion has not been elucidated. Our spatial SEIR model describes the spatial spread pattern of COVID-19 when people commute to a prefecture where they work or study during the daytime and return to their residential prefecture at night. We assume that people are exposed to infection risk during their daytime activities. According to our simulation results, interregional mobility restriction can prevent geographical expansion of the infection. However, in prefectures with many infectious individuals, residents are exposed to higher infection risk when their mobility is restricted. Our simulation results also show that interregional mobility restriction plays a limited role in reducing the national total number of infected individuals.
Animal-to-Animal Variability in Hippocampal Remapping
Authors: Nilchian Parsa , Wilson Matthew A. , Sanders Honi
Published: January 2021

Hippocampal place cells form a map of an animal’s environment. When the animal moves to a new environment, place field locations and firing rates change, a phenomenon known as remapping. Different animals can have different remapping responses to the same environments. This variability across animals in remapping behavior is not well understood. In this work, we analyzed electrophysiological recordings from Alme et al. (2014), in which five male rats were exposed to 11 different environments. To compare the hippocampal maps in two rooms, we computed average rate map correlation coefficients. We discovered that the heterogeneity in animals’ remapping behavior is structured: animals’ remapping behavior is consistent across a range of independent comparisons. Our findings highlight that remapping behavior between repeated environments depends on animal-specific factors.
An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses
Authors: Xie Qingqing , Yu Qi , Jobe Timothy O. , Pham Allis , Ge Chennan , Guo Qianqian , Liu Jianxiu , Liu Honghong , Zhang Huijie , Zhao Yunde , Xue Shaowu , Hauser Felix , Schroeder Julian I.
Published: January 2021

Arsenic stress causes rapid transcriptional responses in plants. However, transcriptional regulators of arsenic-induced gene expression in plants remain less well known. To date, forward genetic screens have proven limited for dissecting arsenic response mechanisms. We hypothesized that this may be due to the extensive genetic redundancy present in plant genomes. To overcome this limitation, we pursued a forward genetics screen for arsenite tolerance using a randomized library of plants expressing >2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants, and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance.
Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer
Authors: Su Xianbin , Zhao Linan , Shi Yi , Zhang Rui , Long Qi , Bai Shihao , Luo Qing , Lin Yingxin , Zou Xin , Ghazanfar Shila , Tao Kun , Yang Guoliang , Wang Lan , He Kun-Yan , Cui Xiaofang , He Jian , Wu Jiao-Xiang , Han Bo , Wang Na , Li Xiaolin , Yang Pengyi , Hou Shangwei , Sun Jielin , Yang Jean Y. H. , Chen Jinhong , Han Ze-Guang
Published: January 2021

Genetic heterogeneity of tumor is closely related to clonal evolution, phenotypic diversity and treatment resistance. Such heterogeneity has been characterized in liver cancer at single-cell sub-chromosomal scale, and a more precise single-variant resolution analysis is lacking. Here we employed a strategy to analyze both the single-cell genomic mutations and transcriptomic changes in 5 patients with liver cancer. Target sequencing was done for a total of 480 single cells in a patient-specific manner. DNA copy number status of point mutations was obtained from single-cell mutational profiling. The clonal structures of liver cancers were then uncovered at single-variant resolution, and mutation combinations in single cells enabled reconstruction of their evolutionary history. A common origin but independent evolutionary fate was revealed for primary liver tumor and intrahepatic metastatic portal vein tumor thrombus. The mutational signature suggested early evolutionary process may be related to specific etiology like aristolochic acids. By parallel single-cell RNA-Seq, the transcriptomic phenotype was found to be related with genetic heterogeneity in liver cancer. We reconstructed the single-cell and single-variant resolution clonal evolutionary history of liver cancer, and dissection of both genetic and phenotypic heterogeneity provides knowledge for mechanistic understanding of liver cancer initiation and progression.
Retroviral Infection of Human Neurospheres and Use of Stem Cell EVs to Repair Cellular Damage
Authors: Branscome Heather , Khatkar Pooja , Sharif Sarah Al , Yin Dezhong , Jacob Sheela , Cowen Maria , Kim Yuriy , Erickson James , Brantner Christine A. , El-Hage Nazira , Liotta Lance A. , Kashanchi Fatah
Published: January 2021

HIV-1 remains an incurable infection that is associated with substantial economic and epidemiologic impacts. HIV-associated neurocognitive disorders (HAND) are commonly linked with HIV-1 infection; despite the development of combination antiretroviral therapy (cART), HAND is still reported to affect at least 50% of HIV-1 infected individuals. It is believed that the over-amplification of inflammatory pathways, along with release of toxic viral proteins from infected cells, are primarily responsible for the neurological damage that is observed in HAND; however, the underlying mechanisms are not well-defined. Therefore, there is an unmet need to develop more physiologically relevant and reliable platforms for studying these pathologies. In recent years, neurospheres derived from induced pluripotent stem cells (iPSCs) have been utilized to model the effects of different neurotropic viruses. Here, we report the generation of neurospheres from iPSC-derived neural progenitor cells (NPCs) and we show that these cultures are permissive to retroviral (e.g. HIV-1, HTLV-1) replication. In addition, we also examine the potential effects of stem cell derived extracellular vesicles (EVs) on HIV-1 damaged cells as there is abundant literature supporting the reparative and regenerative properties of stem cell EVs in the context of various CNS pathologies. Consistent with the literature, our data suggests that stem cell EVs may modulate neuroprotective and anti-inflammatory properties in damaged cells. Collectively, this study demonstrates the feasibility of NPC-derived neurospheres for modeling HIV-1 infection and, subsequently, highlights the potential of stem cell EVs for rescuing cellular damage induced by HIV-1 infection.
Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction
Authors: Subramanian Subu , Gorday Kent , Marcus Kendra , Orellana Matthew R. , Ren Peter , Luo Xiao Ran , O’Donnell Mike , Kuriyan John
Published: January 2021

Clamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Gln 118 forms a hydrogen-bonded junction in a helical unit that we term the central coupler, because it connects the catalytic centers to DNA and the sliding clamp. A suppressor mutation indicates that hydrogen bonding in the junction is important, and molecular dynamics simulations reveal that it maintains rigidity in the central coupler. The glutamine-mediated junction is preserved in diverse AAA+ ATPases, suggesting that a connected network of hydrogen bonds that links ATP molecules is an essential aspect of allosteric communication in these proteins.
Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies
Authors: Dong Hu , Liu Pan , Bai Manyuan , Wang Kang , Feng Rui , Zhu Dandan , Sun Yao , Mu Suyu , Li Haozhou , Harmsen Michiel , Sun Shiqi , Wang Xiangxi , Guo Huichen
Published: January 2021

Outbreaks of Foot-and-mouth disease (FMD) caused by FMD virus result in significant economic losses. Vaccination is helpful, but the benefits are diminished with antigenic diversity within serotypes, instability of the immunogen and inability to confer protection for long durations. Here we have further dissected the mechanisms underpinning the protective efficacy of two previously reported neutralizing antibodies (NAbs), M8 and M170. The atomic details of the epitopes of M8 and M170 unveiled suggest that protection is conferred by disrupting the virus-receptor interactions. Consequently, administration of these NAbs conferred prophylactic and therapeutic benefit in guinea pigs, raising the possibility of administering NAbs before or during vaccination to confer immediate protection; well before the bolstering of the immune response by the vaccine. Differences in the residues and the conformation of elements making up the epitopes explain the differences in specificities of M8 and M170. An ability to bind 146S viral particles specifically, but not 12S degraded components, highlights a likely role for M170 in the quality control of vaccines.
The Crystal Structure of Bromide-BoundGtACR1 Reveals a Pre-Activated State in the Transmembrane Anion Tunnel
Authors: Li Hai , Huang Chia-Ying , Govorunova Elena G. , Sineshchekov Oleg A. , Wang Meitian , Zheng Lei , Spudich John L.
Published: January 2021

The crystal structure of the light-gated anion channelGtACR1 reported in our previous research article (Li et al., 2019) revealed a continuous tunnel traversing the protein from extracellular to intracellular pores. We proposed the tunnel as the conductance channel closed by three constrictions: C1 in the extracellular half, mid-membrane C2 containing the photoactive site, and C3 on the cytoplasmic side. Reported here, the crystal structure of bromide-boundGtACR1 reveals structural changes that relax the C1 and C3 constrictions, including a novel salt-bridge switch mechanism involving C1 and the photoactive site. These findings indicate that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark that facilitates channel opening by reducing free energy in the tunnel constrictions. The results provide direct evidence that the tunnel is the closed form of the channel ofGtACR1 and shed light on the light-gated channel activation mechanism.

Impact Statement

Substrate-induced structural changes inGtACR1 provide new insight into the chemical mechanism of natural light-gated anion conductance, and facilitate its optimization for photoinhibition of neuron firing in optogenetics.