bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

SUMMARYGenetic 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

ABSTRACTBackgroundUnder 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.ResultsWe 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.ConclusionFurther 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

AbstractSevere 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 SummarySevere 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

AbstractFor 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

AbstractObjectiveActivation 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.MethodsUCP1 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.ResultsBased 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.ConclusionConclusively, 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

AbstractDental 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

AbstractMale 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

AbstractMotor 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

ABSTRACTThe 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 summaryFemale 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

ABSTRACTCentromeres 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 STATEMENTPhosphorylation 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.