bluuebunny/crossref_metadata_2025 huggingface dataset:
The consequences of differential origin licensing dynamics in distinct chromatin environments
Authors: Mei Liu , Kedziora Katarzyna M. , Song Eun-Ah , Purvis Jeremy E. , Cook Jeanette Gowen
Published: July 2021

MCM complexes are loaded onto chromosomes to license DNA replication origins in G1 phase of the cell cycle, but it is not yet known how mammalian MCM complexes are adequately distributed to both euchromatin and heterochromatin. To address this question, we combined time-lapse live-cell imaging with fixed cell immunofluorescence imaging of single human cells to quantify the relative rates of MCM loading in heterochromatin and euchromatin at different times within G1. We report here that MCM loading in euchromatin is faster than in heterochromatin in very early G1, but surprisingly, heterochromatin loading accelerates relative to euchromatin loading in middle and late G1. These different loading dynamics require ORCA-dependent differences in ORC distribution during G1. A consequence of heterochromatin origin licensing dynamics is that cells experiencing a truncated G1 phase from premature cyclin E expression enter S phase with under-licensed heterochromatin, and DNA damage accumulates preferentially in heterochromatin in the subsequent S/G2 phase. Thus G1 length is critical for sufficient MCM loading, particularly in heterochromatin, to ensure complete genome duplication and to maintain genome stability.
Prediction of antigen-responding VHH antibodies by tracking evolution of antibody along time course of immunization
Authors: Matsuda Tomonari , Akazawa-Ogawa Yoko , Komaba Lilian-Kaede , Kiyose Norihiko , Miyazaki Nobuo , Mizuguchi Yusaku , Fukuta Tetsuo , Ito Yuji , Hagihara Yoshihisa
Published: July 2021

Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that precise observation of this process by high-throughput sequencing along time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additionalin vitroscreening. An alpaca was immunized by IgG fragments using multiple antigen injections and antibody repertoire development was traced via high-throughput sequencing periodically for months. The sequences were processed into clusters and the antibodies in the 16 most abundant clusters were generated to determine whether the clusters included antigen-binding antibodies. The sequences of most antigen-responsive clusters resembled those of germline cells in the early stages. These sequences were observed to accumulate significant mutations and also showed continuous sequence turnover throughout the experimental period. The foregoing characteristics gave us 75% successful prediction of clusters composed of antigen-responding VHHs against IgG fragment. In addition, the prediction method was applied to the data from other alpaca immunized by epidermal growth factor receptor and 77% successful prediction confirmed the generality of the prediction method. Superior to previous studies, we identified the immune responsive but very rare clusters or sequences from the immunized alpaca without any empirical screening data.

Significance Statement

We have developed a method for selecting VHH antibody sequences that react to antigens withoutin vitroscreening by performing a large-scale sequence analysis of VHH along the immunization time course, clustering the sequences, and tracking the evolution of the sequences in the clusters. This method enables the identification of antibodies with low frequencies of occurrence, which has been difficult with existingin silicoantibody identification methods.
Meta-analysis shows both congruence and complementarity of DNA metabarcoding to traditional methods for biological community assessment
Authors: Keck François , Blackman Rosetta C. , Bossart Raphael , Brantschen Jeanine , Couton Marjorie , Hürlemann Samuel , Kirschner Dominik , Locher Nadine , Zhang Heng , Altermatt Florian
Published: July 2021

Assessment of the diversity and composition of biological communities is central to studies in ecology as well as for ecological monitoring. Historically, individual taxonomic groups have been assessed separately, while for an understanding of the state and change of biodiversity under ongoing global change an integrated assessment would be necessary. DNA metabarcoding has been proposed to be a highly promising approach especially for the assessment of aquatic communities, and numerous studies have investigated the consistency of this new technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here we performed the first meta-analysis of all available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including microorganisms, macroinvertebrates, and fish. Across 215 datasets, we found that DNA metabarcoding provides diversity estimates (richness) that are globally consistent to those obtained using traditional methods. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, however, species inventories of microorganisms and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. Our results indicate that DNA metabarcoding is efficient to estimate local and regional richness. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates and microorganisms, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
PhenoExam: an R package and Web application for the examination of phenotypes linked to genes and gene sets
Authors: Cisterna Alejandro , González-Vidal Aurora , Ruiz Daniel , Ortiz Jordi , Gómez-Pascual Alicia , Chen Zhongbo , Nalls Mike , Faghri Faraz , Hardy John , Díez Irene , Maietta Paolo , Álvarez Sara , Ryten Mina , Botía Juan A.
Published: July 2021

Gene set based phenotype enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) can improve the rate of genetic diagnoses amongst other research purposes. To facilitate diverse phenotype analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases. PhenoExam achieves these tasks by integrating databases or resources such as the HPO, MGD, CRISPRbrain, CTD, ClinGen, CGI, OrphaNET, UniProt, PsyGeNET, and Genomics England Panel App. PhenoExam accepts both human and mouse genes as input. We developed PhenoExam to assist a variety of users, including clinicians, computational biologists and geneticists. It can be used to support the validation of new gene-to-disease discoveries, and in the detection of differential phenotypes between two gene sets (a phenotype linked to one of the gene set but no to the other) that are useful for differential diagnosis and to improve genetic panels. We validated PhenoExam performance through simulations and its application to real cases. We demonstrate that PhenoExam is effective in distinguishing gene sets or Mendelian diseases with very similar phenotypes through projecting the disease-causing genes into their annotation-based phenotypic spaces. We also tested the tool with early onset Parkinson’s disease and dystonia genes, to show phenotype-level similarities but also potentially interesting differences. More specifically, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy. Therefore, PhenoExam effectively discovers links between phenotypic terms across annotation databases through effective integration. The R package is available at https://github.com/alexcis95/PhenoExam and the Web tool is accessible at https://snca.atica.um.es/PhenoExamWeb/.
IL-17+ mast cell/T helper cell axis in the early stages of acne
Authors: Eliasse Yoan , Leveque Edouard , Garidou Lucile , Battut Louise , McKenzie Brienne , Nocera Thérèse , Redoules Daniel , Espinosa Eric
Published: July 2021

Acne is a multifactorial disease driven by physiological changes occurring during puberty in the pilosebaceous unit (PSU) that leads to sebum overproduction and a dysbiosis involving notably Cutibacterium acnes. These changes in the PSU microenvironment lead to a shift from a homeostatic to an inflammatory state. Indeed, immunohistochemical analyses have revealed that inflammation and lymphocyte infiltration can be detected even in the infraclinical acneic stages, highlighting the importance of the early stages of the disease. In this study, we utilized a robust multi-pronged approach that included flow cytometry, confocal microscopy, and bioinformatics to comprehensively characterize the evolution of the infiltrating and resident immune cell populations in acneic lesions, beginning in the early stages of their development. Using a discovery cohort of 15 patients, we demonstrated that the composition of immune cell infiltrate is highly dynamic in nature, with the relative abundance of different cell types changing significantly as a function of clinical lesion stage. Within the stages examined, we identified a large population of CD69+ CD4+ T cells, several populations of activated antigen presenting cells, and activated mast cells producing IL-17. IL-17+ mast cells were preferentially located in CD4+ T cell rich areas and we showed that activated CD4+ T cells license mast cells to produce IL-17. Our study reveals that mast cells are the main IL-17 producers in the early stage of acne, underlying the importance of targeting the IL-17+ mast cell/T helper cell axis in therapeutic approaches.
Cherry-picking information: humans actively sample evidence to support prior beliefs
Authors: Kaanders Paula , Sepulveda Pradyumna , Folke Tomas , Ortoleva Pietro , De Martino Benedetto
Published: July 2021

No one likes to be wrong. Previous research has shown that participants may underweight information incompatible with previous choices, a phenomenon called confirmation bias. In this paper we argue that a similar bias exists in the way information is actively sought. We investigate how choice influences information gathering using a perceptual choice task and find that participants sample more information from a previously chosen alternative. Furthermore, the higher the confidence in the initial choice, the more biased information sampling becomes. As a consequence, when faced with the possibility of revising an earlier decision, participants are more likely to stick with their original choice, even when incorrect. Critically, we show that agency controls this phenomenon. The effect disappears in a fixed sampling condition where presentation of evidence is controlled by the experimenter, suggesting that the way in which confirmatory evidence is acquired critically impacts the decision process. These results suggest active information acquisition plays a critical role in the propagation of strongly held beliefs over time.
Stable coexistence in plant-pollinator-herbivore communities requires balanced mutualistic vs antagonistic interactions
Authors: Yacine Youssef , Loeuille Nicolas
Published: July 2021

Ecological communities consist of multiple species interacting in diverse ways. Understanding the mechanisms supporting coexistence requires accounting for such a diversity. Because most works focus either on mutualism or predation, how pollination and herbivory interactively determine the stable coexistence in plant-pollinator-herbivore communities is still poorly understood. Studying the typical three-species module of such communities, we determine the conditions allowing stable coexistence then investigate how its maintenance constrains the relative interaction strengths. Our results show that coexistence is possible if pollination is sufficiently strong relative to herbivory, while its stability is possible if herbivory is sufficiently strong relative to pollination. A balance between pollination and herbivory is therefore required. Interestingly, shared preferences for plant phenotypes, that would favor such balance, have been frequently reported in the empirical literature. The identified ecological trade-off between attracting pollinators and deterring herbivores therefore also appears as an emergent property of stable plant-pollinator-herbivore communities.
Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data
Authors: He Dongze , Zakeri Mohsen , Sarkar Hirak , Soneson Charlotte , Srivastava Avi , Patro Rob
Published: July 2021

The rapid growth of high-throughput single-cell and single-nucleus RNA sequencing technologies has produced a wealth of data over the past few years. The available technologies continue to evolve and experiments continue to increase in both number and scale. The size, volume, and distinctive characteristics of these data necessitate the development of new software and associated computational methods to accurately and efficiently quantify single-cell and single-nucleus RNA-seq data into count matrices that constitute the input to downstream analyses.

We introduce the alevin-fry framework for quantifying single-cell and single-nucleus RNA-seq data. Despite being faster and more memory frugal than other accurate and scalable quantification approaches, alevin-fry does not suffer from the false positive expression or memory scalability issues that are exhibited by other lightweight tools. We demonstrate how alevin-fry can be effectively used to quantify single-cell and single-nucleus RNA-seq data, and also how the spliced and unspliced molecule quantification required as input for RNA velocity analyses can be seamlessly extracted from the same pre-processed data used to generate regular gene expression count matrices.
Fin Shape, Asymmetry, and Evolutionary Ecomorphology in Triggerfishes and Filefishes (Superfamily: Balistoidea)
Authors: George Andrew B. , Westneat Mark W.
Published: July 2021

Triggerfishes and filefishes exhibit a wide range of fin and body morphologies, inhabit many marine habitats, and feed on a variety of benthic and pelagic organisms. Particular morphologies are predicted to provide functional advantages for swimming behaviors that facilitate life in diverse habitats and feeding guilds. Ecomorphological relationships can, in turn, inform evolutionary patterns of morphological convergence. We quantified morphological diversity of 80 balistoid species using geometric morphometrics and assigned each species a primary habitat and feeding mode. Results revealed strong evidence for evolutionary integration among body and fin shapes as well as widespread convergence of both high and low aspect ratio (AR) dorsal and anal fins, the fins that power steady locomotion in these fishes. Dorsal and anal fins were determined to be moderately to highly asymmetrical in most species. Families exhibited considerable overlap in fin and body shapes, but triggerfishes generally exhibited higher AR and more asymmetrical fins than filefishes. Fin asymmetry was not strongly associated with ecology. Planktivorous and offshore-pelagic species exhibited high AR dorsal and anal fins suitable for high endurance swimming performance, while benthic grazing and structured reef species exhibited convergence on low AR median fins more suitable for facilitating maneuverability.
Global distribution and richness of Armillaria and related species inferred from public databases and amplicon sequencing datasets
Authors: Koch Rachel A. , Herr Joshua R.
Published: July 2021

Armillaria is a globally distributed fungal genus most notably recognized as economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.
A simplified method for CRISPR-Cas9 engineering of Bacillus subtilis
Authors: Sachla Ankita J. , Alfonso Alexander J. , Helmann John D.
Published: July 2021

The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system from Streptococcus pyogenes has been widely deployed as a tool for bacterial strain construction. Conventional CRISPR-Cas9 editing strategies require design and molecular cloning of an appropriate guide RNA (gRNA) to target genome cleavage and a repair template for introduction of the desired site-specific genome modification. Here, we present a streamlined method that leverages the existing collection of nearly 4000 Bacillus subtilis strains (the BKE collection) with individual genes replaced by an integrated erythromycin (erm) resistance cassette. A single plasmid (pAJS23) with a gRNA targeted to erm allows cleavage of the genome at any non-essential gene, and at sites nearby to many essential genes. This plasmid can be engineered to include a repair template, or the repair template can be co-transformed with the plasmid as either a PCR product or genomic DNA. We demonstrate the utility of this system for generating gene replacements, site-specific mutations, modification of intergenic regions, and introduction of gene-reporter fusions. In sum, this strategy bypasses the need for gRNA design and allows the facile transfer of mutations and genetic constructions with no requirement for intermediate cloning steps.

Importance

Bacillus subtilis is a well-characterized Gram-positive model organism and a popular platform for biotechnology. Although many different CRISPR-based genome editing strategies have been developed for B. subtilis, they generally involve the design and cloning of a specific gRNA and repair template for each application. By targeting the erm resistance cassette with an anti-erm gRNA, genome-editing can be directed to any of nearly 4000 gene disruptants within the existing BKE collection of strains. Repair templates can be engineered as PCR products, or specific alleles and constructions can be transformed as chromosomal DNA, thereby bypassing the need for plasmid construction. The described method is rapid, free of off-target effects, and facilitates a wide-range of genome manipulations.

“Healing is a matter of time, but it is sometimes also a matter of opportunity.” – Hippocrates
Life history mediates the trade-offs among different components of demographic resilience
Authors: Capdevila Pol , Stott Iain , Cant James , Beger Maria , Rowlands Gwilym , Grace Molly , Salguero-Gómez Roberto
Published: July 2021

Summary paragraph

Accelerating rates of biodiversity loss underscore the need to understand how species achieve resilience –their ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 785 natural populations of animals and plants predict their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance, and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species’ pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, while those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.
Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability
Authors: Gill Peter , Bleka Øyvind , Fonneløp Ane Elida
Published: July 2021

The application of qPCR to estimate the quantity of DNA present is usually based upon a short amplicon (typically c.80bp) and a longer amplicon (typically c.200-300bp) where the latter is used to determine the amount of degradation present in a sample. The data are used to make decisions about a) whether there is sufficient template to amplify? b) how much of the elution volume to forward to PCR? A typical multiplex amplifies template in the region of 100-500bp. Consequently, the results from an 80bp amplicon will tend to overestimate the actual amplifiable quantity that is present in a degraded sample. To compensate, a method is presented that relates the quantity of amplifiable DNA to the average RFU of the amplified fragments. This provides greatly improved accuracy of the estimated quantity of DNA present, which may differ by more than an order of magnitude compared to qPCR. The relative DNA quantities can be apportioned per contributor once mixture proportions are ascertained with probabilistic genotyping software (EuroForMix). The motivation for this work was to provide an improved method to generate data to prepare distributions that are used to inform activity level propositions. However, other applications will benefit, particularly those where extraction and quantification are bypassed: For example direct PCR and Rapid DNA technology. The overall aim of this work was to provide a method of quantification that is standardised and can be used to compare results between different laboratories that use different multiplexes. A software solution “ShinyRFU” is provided to aid calculations.
Deficiency of the ywhaz gene, involved in neurodevelopmental disorders, alters brain activity and behaviour in zebrafish
Authors: Antón-Galindo Ester , Vecchia Elisa Dalla , Orlandi Javier G , Castro Gustavo , Gualda Emilio J , Young Andrew MJ , Aguado Fernando , Loza-Alvarez Pablo , Cormand Bru , Norton William HJ , Fernàndez-Castillo Noèlia
Published: July 2021

Genetic variants in YWHAZ contribute to psychiatric disorders such as autism spectrum disorder and schizophrenia, and have been related to an impaired neurodevelopment in humans and mice. Here, we used zebrafish to further understand the mechanisms by which YWHAZ contributes to neurodevelopmental disorders. We observed that ywhaz expression was panneuronal during developmental stages and restricted to Purkinje cells in the adult cerebellum, cells that are described to be reduced in number in autistic patients. We then performed whole-brain imaging in wild-type and ywhaz CRISPR/Cas9 knockout (KO) larvae and found altered neuronal activity and connectivity in the hindbrain. Adult ywhaz KO fish display decreased levels of monoamines in the hindbrain and freeze when exposed to novel stimuli, a phenotype that can be reversed with drugs that target monoamine neurotransmission. These findings suggest an important role for ywhaz in establishing neuronal connectivity during development and modulating both neurotransmission and behaviour in adults.
Toward an understanding of the chemical ecology of alternative reproductive tactics in the bulb mite (Rhizoglyphus robini)
Authors: Zeeman Adam N. , Smallegange Isabel M. , Steel Emily Burdfield , Groot Astrid T. , Stewart Kathryn A.
Published: July 2021

Background

Under strong sexual selection, certain species evolve distinct intrasexual, alternative reproductive tactics (ARTs). In many cases, ARTs can be viewed as environmentally-cued threshold traits, such that ARTs coexist if their relative fitness alternates over the environmental cue gradient. Surprisingly, the chemical ecology of ARTs has been underexplored in this context. To our knowledge, no prior study has directly quantified pheromone production for ARTs in a male-polymorphic species. Here, we used the bulb mite—in which males are either armed fighters that kill conspecifics, or unarmed scramblers—as a model system to gain insight into the role of pheromones in the evolutionary maintenance of ARTs. Given that scramblers forgo investment into weaponry, we tested whether scramblers produce higher pheromone quantities than fighters, which would improve the fitness of the scrambler phenotype, e.g. through female mimicry to avoid aggression from competitors. To this end, we sampled mites from a rich and a poor nutritional environment and quantified their production of the female sex pheromone α-acaridial through gas chromatography analysis.

Results

We found a positive relationship between pheromone production and body size, but males exhibited a steeper slope in pheromone production with increasing size than females. Females exhibited a higher average pheromone production than males. We found no significant difference in slope of pheromone production over body size between fighters and scramblers. However, scramblers reached larger body sizes and higher pheromone production than fighters, providing some evidence for a potential female mimic strategy adopted by large scramblers. Pheromone production was significantly higher in mites from the rich nutritional environment than the poor environment.

Conclusion

Further elucidation of pheromone functionality in bulb mites, and additional inter-and intrasexual comparisons of pheromone profiles are needed to determine if the observed intersexual and intrasexual differences in pheromone production are adaptive, if they are a by-product of allometric scaling, or diet-mediated pheromone production under weak selection. We argue chemical ecology offers a novel perspective for research on ARTs and other complex life-history traits.
Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2
Authors: Sobitan Adebiyi , Mahase Vidhyanand , Rhoades Raina , Williams Dejaun , Liu Dongxiao , Xie Yixin , Li Lin , Tang Qiyi , Teng Shaolei
Published: July 2021

Severe Acute respiratory syndrome coronavirus (SARS-CoV-1) attaches to the host cell surface to initiate the interaction between the receptor-binding domain (RBD) of its spike glycoprotein (S) and the human Angiotensin-converting enzyme (hACE2) receptor. SARS-CoV-1 mutates frequently because of its RNA genome, which challenges the antiviral development. Here, we performed computational saturation mutagenesis of the S protein of SARS-CoV-1 to identify the residues crucial for its functions. We used the structure-based energy calculations to analyze the effects of the missense mutations on the SARS-CoV-1 S stability and the binding affinity with hACE2. The sequence and structure alignment showed similarities between the S proteins of SARS-CoV-1 and SARS-CoV-2. Interestingly, we found that target mutations of S protein amino acids generate similar effects on their stabilities between SARS-CoV-1 and SARS-CoV-2. For example, G839W of SARS-CoV-1 corresponds to G857W of SARS-CoV-2, which decrease the stability of their S glycoproteins. The viral mutation analysis of the two different SARS-CoV-1 isolates showed that mutations, T487S and L472P, weakened the S-hACE2 binding of the 2003-2004 SARS-CoV-1 isolate. In addition, the mutations of L472P and F360S destabilized the 2003-2004 viral isolate. We further predicted that many mutations on N-linked glycosylation sites would increase the stability of the S glycoprotein. Our results can be of therapeutic importance in the design of antivirals or vaccines against SARS-CoV-1 and SARS-CoV-2.

Author Summary

Severe acute respiratory syndrome coronavirus (SARS-CoV-1) is an RNA virus that undergoes frequent mutations, which may result in more virulent SARS-CoV-1 variants. To prevent another pandemic in the future, scientists must understand the mechanisms of viral mutations and predict if any variants could become a dominant. The infection of SARS-CoV-1 in cells is largely depending on the interactions of the viral Spike (S) and human angiotensin-converting enzyme 2 (hACE2). We applied a computational method to predict S missense mutations that will make SARS-CoV-1 more virulent. We are interested in the variants that can change SARS-CoV-1 spike protein stability and/or change the virus-receptor interactions. We mutated each residue of SARS-CoV-1 spike to all possible amino acids; we calculated the differences between the folding energy and binding energy of each variant and the wildtype and identified the target S mutations with significant effects on protein stability and protein-protein interaction. We found some viral mutations could destabilize S and weaken S-hACE2 binding of SARS-CoV-1 isolate. Our results show that the computational saturation mutagenesis is a reliable approach in the analysis and prediction of missense mutations.
Penetrance estimation ofSORL1loss-of-function variants using a family-based strategy adjusted onAPOEgenotypes suggest a non-monogenic inheritance
Authors: Schramm Catherine , Charbonnier Camille , Zaréa Aline , Lacour Morgane , Wallon David ,   CNRMAJ collaborators, Boland Anne , Deleuze Jean-François , Olaso Robert , Alarcon Flora , Campion Dominique , Nuel Grégory , Nicolas Gaël
Published: July 2021

For complex disorders, estimating the age-related penetrance associated with rare variants of strong effect is essential before a putative use for genetic counseling or disease prevention. However, rarity and co-occurrence with other risk factors make such estimations difficult. In the context of Alzheimer disease, we present a survival model to estimate the penetrance ofSORL1rare (allele frequency< 1%) Loss-of-Function variants (LoF) while accounting forAPOE-ε4, the main risk factor (allele frequency∼ 14% in Caucasians). We developed an efficient strategy to compute penetrance estimates accounting for both common and rare genetic variants based on available penetrance curves associated with common risk factors and using incomplete pedigree data to quantify the additional risk conferred by rare variants. Our model combines: (i) a baseline for non-carriers ofSORL1LoF variants, stratified byAPOEgenotypes derived from the Rotterdam study and (ii) an age-dependent proportional hazard effect forSORL1LoF variants estimated from pedigrees with a proband carrying such a variant. We embed this model into an Expectation-Maximisation algorithm to accommodate for missing genotypes. Confidence intervals were computed by bootstraps. To correct for ascertainment bias, proband phenotypes were omitted. We obtained penetrance curves associated withSORL1LoF variants at the digenic level. By age 70, we estimate a 100% penetrance ofSORL1LoF variants only amongAPOE-ε4ε4 carriers, while penetrance is 56%[40% − 72%] among ε4 heterozygous carriers and 37%[26% − 51%] among ε4 non-carriers. We conclude that rareSORL1LoF variants should not be used for genetic counseling regardless of theAPOEstatus.
Susceptibility to diet induced obesity at thermoneutral conditions is independent of UCP1
Authors: Dieckmann Sebastian , Strohmeyer Akim , Willershäuser Monja , Maurer Stefanie , Wurst Wolfgang , Marschall Susan , de Angelis Martin Hrabe , Kühn Ralf , Worthmann Anna , Fuh Marceline M , Heeren Joerg , Köhler Nikolai , Pauling Josch K. , Klingenspor Martin
Published: July 2021

Objective

Activation of uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) upon cold stimulation leads to substantial increase in energy expenditure to defend body temperature. Increases in energy expenditure after a high caloric food intake, termed diet-induced thermogenesis, are also attributed to BAT. These properties render BAT a potential target to combat diet-induced obesity. However, studies investigating the role of UCP1 to protect against diet-induced obesity are controversial and rely on the phenotyping of a single constitutive UCP1-knockout model.

To address this issue, we generated a novel UCP1-knockout model by Cre-mediated deletion of Exon 2 in the UCP1 gene. We studied the effect of constitutive UCP1 knockout on metabolism and the development of diet-induced obesity.

Methods

UCP1 knockout and wildtype mice were housed at 30°C and fed a control diet for 4-weeks followed by 8-weeks of high-fat diet. Body weight and food intake were monitored continuously over the course of the study and indirect calorimetry was used to determine energy expenditure during both feeding periods.

Results

Based on Western blot analysis, thermal imaging and noradrenaline test, we confirmed the lack of functional UCP1 in knockout mice. However, body weight gain, food intake and energy expenditure were not affected by deletion of UCP1 gene function during both feeding periods.

Conclusion

Conclusively, we show that UCP1 does not protect against diet-induced obesity at thermoneutrality. Further we introduce a novel UCP1-KO mouse enabling the generation of conditional UCP1-knockout mice to scrutinize the contribution of UCP1 to energy metabolism in different cell types or life stages.
Dental caries in wild primates: interproximal cavities on anterior teeth
Authors: Towle Ian , Irish Joel D. , Sabbi Kristin , Loch Carolina
Published: July 2021

Dental caries has been reported in a variety of primates, although is still considered rare in wild populations. In this study, 11 catarrhine primates were studied for the presence of caries. A differential diagnosis of lesions found in interproximal regions of anterior teeth was undertaken, since they had been previously described as both carious and non-carious in origin. Each permanent tooth was examined macroscopically, with severity and position of lesions recorded. Two specimens were micro-CT scanned to assess demineralization. The differential diagnosis confirmed the cariogenic nature of interproximal cavities on anterior teeth (ICAT’s). Overall results show 3.3% of teeth are carious, with prevalence varying among species from 0% to over 7% of teeth affected. ICAT’s occurred in Pan troglodytes (9.8%),Gorilla gorilla gorilla(2.6%),Cercopithecus denti(22.4%),Presbytis femoralis(19.5%) andCercopithecus mitis(18.3%). They make up 87.9% of carious lesions on anterior teeth. These results likely reflect dietary and food processing differences among species, but also between the sexes (e.g., 9.3% of teeth of female chimpanzees were carious vs. 1.8% in males). Processing cariogenic fruits and seeds with the anterior dentition (e.g., wadging) likely contributes to ICAT formation. Further research is needed on living populations to ascertain behavioral/dietary influences on caries occurrence in primates. Given the constancy of ICAT’s in frugivorous primates, their presence in archaeological and paleontological specimens may shed light on diet and food processing behaviors in fossil primates.
Familial Genetic Cancer Risk Assessment with respect to a SilentBRCA2mutation
Authors: Bapat Ashwini , Gahlaut Siddharth , Mishra Rupa , Noor Aijaz Ul , Busheri Laleh , Reddy Ruhi , Shaikh Shahin , Mannan Ashraf , Nare Smeeta , Dixit Santosh , Koppiker Chaitanyanand B.
Published: July 2021

Male Breast Cancer (BC) is relatively rarer, accounting for less than 1% of cancers in men. MBC is hereditary in nature and mainly attributed toBRCA1/2germline mutations. Accordingly, National Comprehensive Cancer Network (NCCN) guidelines advise genetic counselling and testing for all cases of MBCs and their unaffected family members. In this report, we present an uncommon case of male patient primarily diagnosed with pancreatic cancer who later developed asynchronous bilateral hormone positive breast cancer. We describe the genetic screening and clinical management protocol for the proband and family members. Genetic testing with next generation sequencing by uses of a multi-gene germline mutation panel revealed a likely pathogenicBRCA2variant (c.8754G>A, p.E2918E). Subsequently, 34 members of the extended family of the proband were tested for theBRCA2variant by Sanger sequencing. 6 of the family members were identified as carriers of thisBRCA2variant. Of these, three presented with hereditary breast cancer and 3 were unaffected healthy carriers.In silicoanalysis for mechanistic insights in underlying pathogenicity revealed that the silentBRCA2mutation is a spliceogenic variant that is likely to create an aberrant mRNA transcript via alternative splicing ofBRCA2gene. Our study demonstrates the clinical relevance of this silentBRCA2mutation and emphasizes the need for further experimental studies to elucidate its functional role in breast cancer pathology.
Prefrontal stimulation prior to motor sequence learning alters multivoxel patterns in the striatum and the hippocampus
Authors: Gann Mareike A. , King Bradley R. , Dolfen Nina , Veldman Menno P. , Davare Marco , Swinnen Stephan P. , Mantini Dante , Robertson Edwin M. , Albouy Geneviève
Published: July 2021

Motor sequence learning (MSL) is supported by dynamical interactions between hippocampal and striatal networks that are thought to be orchestrated by the prefrontal cortex. In the present study, we tested whether individually-tailored theta-burst stimulation of the dorsolateral prefrontal cortex (DLPFC) prior to MSL, can modulate multivoxel response patterns in the stimulated cortical area, the hippocampus and the striatum. Response patterns were assessed with multivoxel correlation structure analyses of functional magnetic resonance imaging data acquired during task practice and during resting-state scans before and after learning/stimulation. Results revealed that, across stimulation conditions, MSL induced greater modulation of task-related DLPFC multivoxel patterns than random practice. A similar learning-related modulatory effect was observed on sensorimotor putamen patterns under inhibitory stimulation. Furthermore, MSL as well as inhibitory stimulation affected (posterior) hippocampal multivoxel patterns at post-intervention rest. Exploratory analyses showed that MSL-related brain patterns in the posterior hippocampus persisted into post-learning rest preferentially after inhibitory stimulation. These results collectively show that prefrontal stimulation can alter multivoxel brain patterns in deep brain regions that are critical for the MSL process. They also suggest that stimulation influenced early offline consolidation processes as evidenced by a stimulation-induced modulation of the reinstatement of task pattern into post-learning wakeful rest.
Frequent female song in blue tits: behavioural context suggests a role in intrasexual competition
Authors: Sierro Javier , de Kort Selvino R. , Riebel Katharina , Hartley Ian R.
Published: July 2021

The blue tit (Cyanistes caeruleus) is an important avian model in evolutionary ecology (> 20,000 published scientific studies). Song, like in other songbird species, is generally described as a male trait and plays an important role in mate attraction and territory defence. Over the decades, there have been recurring reports of anecdotal female song but these have not led to any quantitative study of female song in blue tits. Our systematic sampling over three years revealed prolific female singing in a northern population of colour ringed blue tits. Daytime singing of females occurred throughout the breeding season during agonistic interactions, solo songs and alarm situations, and these contexts are similar to male song. Notably, female song was absent during the dawn chorus; the period around sunrise when males sing intensively just before mating. Female and male song overlapped substantially in acoustic structure (i.e. same song types, peak frequency or trill rates) but there were also significant differences in that females had smaller repertoires, shorter trills and lower vocal consistency. Differential selections pressures related with contextual (functional) differences in the role of male and female song could explain the observed differences in acoustic structure. The new finding of prolific female singing in such a well-studied species suggests we ought to revise our understanding of male and female vocal communication in this (and probably other) species. Identifying the selection pressures associated to the convergence versus divergence of male and female song may provide important insight in understanding birdsong evolution.

Lay summary

Female song has been anecdotally reported in blue tits but there are no quantitative studies of singing behaviour, song structure or context. Here, we report frequent female singing in blue tits, associated mostly with agonistic interactions and alarm situations. Importantly, female song was not observed during dawn chorus, the period around sunrise when males sing intensively just before mating. Female and male song overlapped substantially in acoustic structure (i.e. same song types) but there were also significant differences (i.e. females sang with lower vocal consistency). We speculate that differences in context (function) of male and female song could explain the observed differences in acoustic structure. The new finding of prolific female singing in such a well-studied species suggests we ought to revise our understanding of male and female vocal communication.
Mitotic chromosome condensation requires phosphorylation of the centromeric protein KNL-2 inC. elegans
Authors: Wenda Joanna M. , Prosée Reinier F. , Gabus Caroline , Steiner Florian A.
Published: July 2021

Centromeres are chromosomal regions that serve as sites for kinetochore formation and microtubule attachment, processes that are essential for chromosome segregation during mitosis. Centromeres are almost universally defined by the histone variant CENP-A. In the holocentric nematodeC. elegans, CENP-A deposition depends on the loading factor KNL-2. Depletion of either CENP-A or KNL-2 results in defects in centromere maintenance, chromosome condensation and kinetochore formation, leading to chromosome segregation failure. Here, we show that KNL-2 is phosphorylated by CDK-1, and that mutation of three C-terminal phosphorylation sites causes chromosome segregation defects and an increase in embryonic lethality. In strains expressing phosphodeficient KNL-2, CENP-A and kinetochore proteins are properly localised, indicating that the role of KNL-2 in centromere maintenance is not affected. Instead, the mutant embryos exhibit reduced mitotic levels of condensin II on chromosomes and significant chromosome condensation impairment. Our findings separate the functions of KNL-2 in CENP-A loading and chromosome condensation and demonstrate that KNL-2 phosphorylation regulates the cooperation between centromeric regions and the condensation machinery inC. elegans.

SUMMARY STATEMENT

Phosphorylation of the essential centromere protein KNL-2 is required for mitotic chromosome condensation, but not for the role of KNL-2 in centromere maintenance and kinetochore formation.
Kinesin-1 captures RNA cargo in its adaptable coils
Authors: Cross Jessica A. , Woolfson Derek. N. , Dodding Mark P.
Published: July 2021

The prototypic and ubiquitous microtubule motor, kinesin-1, uses a variety of adaptor proteins to facilitate the selective transport of diverse cargo within the cell. These cargo adaptors bind to the motor complex through interactions with the kinesin light or heavy chains (KLCs or KHCs). In this issue ofGenes & Development, Dimitrova-Paternoga et al. (pp. 976–991) present the first structural characterization of a KHC–cargo adaptor interface. They describe an antiparallel heterotrimeric coiled-coil complex between the carboxy tail of KHC and Tm1-I/C (aTm1), the atypical tropomyosin that is important foroskarmRNA transport inDrosophilaoocytes. This interaction enhances direct binding between KHC and RNA. Their findings demonstrate the structural plasticity of the KHC tail as a platform for protein–protein interactions and reveal how a cargo adaptor protein can modify a motor–RNA interface to promote transport.
An international study of fast-food dining perceptions: millennial parents, non-millennial parents, and peer judgement during fast-food family dining
Authors: Kellershohn Julie , Walley Keith , Vriesekoop Frank
Published: July 2021

Purpose

This study aims to examine peer perceptions of a parent dining in a fast-food restaurant with their child.

Design/methodology/approach

A vignette approach was used to explore consumer assumptions and normative data using a four-country online survey of parents, with 1,200 respondents (300 from each of Australia, Canada, the UK and the USA). The study included qualitative and quantitative thematic analyses of the responses.

Findings

Family dining in fast-food restaurants was most often associated with an opportunity for family time together (25%), a treat (25%) and an unhealthy food decision (19%). For some, this is a normal meal that should not be judged (11%), for others, this is merely a meal of easy convenience (9%). Fathers, when depicted as the parent in the vignette, were more likely to be praised for spending time with their children, while mothers were more likely to be critiqued for making poor nutritional choices. Respondents from the USA viewed fast-food family dining more favourably than respondents from Australia, Canada or the UK.

Social implications

Despite rising obesity in these four countries, only 19% of respondents focused on the unhealthy element of the food choice, suggesting that perhaps this element is not on the forefront of consumer decision considerations.

Originality/value

This paper confirms parental peer perception differences, based on gender and country, regarding opinions on a child dining with a parent in a fast-food restaurant.