bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of habitat loss and fragmentation on isolation-by-distance and time
Authors: Sgarlata Gabriele Maria , Maié Tiago , de Zoeten Tiago , Rasteiro Rita , Chikhi Lounès 
Published: October 2022

AbstractThroughout Earth’s natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species and their diversity. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic patterns from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond ‘pattern’ and investigate through simulations some of the ‘processes’ that influence genetic variation in the context of HL&F. Since most species have a geographically restricted dispersal (known as “isolation-by-distance”, IBD), we studied the impact of HL&F on isolation-by-distance. We characterised the behaviour of IBD in the case of i) instantaneous HL&F, ii) gradual (two-steps) HL&F, and iii) instantaneous HL&F following range expansion. In addition, we propose a spatially-explicit theoretical framework by modifying the original theoretical results on isolation-by-distance (Slatkin, 1991; Slatkin, 1993) and apply them to a toroidal stepping-stone model in the context of HL&F. Our results suggest that isolation-by-distance can be maintained for relatively long time after HL&F, thus pointing to the long-term importance of spatial genetic structure in species genetic diversity. In addition, our results may explain why present-day fragmented population still show significant IBD pattern although being disconnected.
Survey of the Phytophthora species diversity revealsP. abietivoraas a potential Phytophthora root rot pathogen in Québec Christmas tree plantations
Authors: Charron Guillaume , Yergeau Julie , Van der Heyden Hervé , Bilodeau Guillaume J. , Beaulieu Carole , Tanguay Philippe 
Published: October 2022

AbstractChristmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those,Phytophthoracauses millions of dollars in damage to plantations annually. In Canada, it is still not known which species are responsible for Phytophthora root rot (PRR) of cultivatedAbiesspecies. Between 2019 and 2021, soil and root samples were collected from 40 Christmas tree plantations in Québec province. We used soil baiting and direct root isolation to assess the diversity of culturablePhytophthoraspp. The obtained isolates were identified with a multi-locus sequencing approach, and we used the sequencing data to place them along thePhytophthoraphylogeny. A total of 44 isolates from six differentPhytophthoraspecies were identified, one fitting the provisional speciesP.sp.□kelmania□. A seventh taxa, represented by a group of 10 isolates, could not be assigned to any knownPhytophthoraspecies. Among the known species,Phytophthora abietivorawas the most prevalent isolated species associated with PRR. Pathogenicity trials confirmed the pathogenicity potential ofP. abietivoraon both Fraser and balsam fir seedlings. Our studies provide a first snapshot of the Phytophthora diversity in Québec’s Christmas tree productions and describe multiple potential first associations betweenPhytophthoraspecies andAbies balsameaandA. fraseri.
Phospholipase C6 Regulates HydroxyprolineO-arabinosyltransferase-mediated Pollen Tube Growth inArabidopsis
Authors: Beuder Steven , Hua Xuesi , Dorchak Alexandria , MacAlister Cora A. 
Published: October 2022

AbstractHydroxyprolineO-arabinosylation is a highly-conserved and plant-specific post-translational modification found on extensins and other structural proteins in the cell wall, and is catalyzed by HydroxyprolineO-arabinosyltransferases (HPATs). InArabidopsis, loss ofHPAT1andHPAT3 (hpat1/3) causes reorganization of components in the pollen tube (PT) cell wall, which compromises cell wall structural integrity and decreases PT growth and fertility. We have previously shown that reduced secretion (caused by loss-of-function mutations in secretory genesEXO70A2, SEC15A, andSEC1A) suppressed cell wall defects and strongly rescued poor growth and fertility inhpat1/3PTs. Here, we show that a missense mutation inPHOSPHOLIPASE C6 (PLC6) also rescueshpat1/3PT growth and fertility. Transgenic insertion mutations that disruptPLC6expression did not improvehpat1/3pollen fertility, and did not affect PT growth or fertility in the wild type background. This data suggests that our missense allele (plc6-4) does not function like a true loss-of-function allele, and that PLC6 is not required for wild type PT growth. However, in the absence ofhpat1/3, plc6-4PTs have defects in transmission and polarized growth, as indicated by meandering growth paths and a resulting crooked appearance.plc6-4PT elongation and straightness are more sensitive to elevated levels of calcium than wild type. This may be due the nature of theplc6-4mutation, which causes an E569K amino acid substitution in the lipid-binding C2 domain. The 569 position is located among conserved residues that bind calcium. The resulting charge inversion caused by the E569K substitution may disrupt PLC6’s lipid binding and phospholipase activities. Here, we show thatPLC6influences polarized PT growth and HPAT-mediated PT growth and fertility, and future studies are necessary to better understand the relationship between calcium andPLC6in PT growth.
Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution inArabidopsis thaliana
Authors: Roberts Miles , Josephs Emily B 
Published: October 2022

AbstractDifferential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data onArabidopsis thalianafrom over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene’s expression and the strength of selection on said gene inA. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.
Persistent lytic bacteriophage infection as a novel strategy for exploitation of nutrient-limited host bacteria
Authors: Dorling Jack , Nhiri Naima , Corral-Lugo Andrés , Jacquet Eric , Tavares Paulo 
Published: October 2022

AbstractWild bacteria, from the open ocean to the gut, experience persistent nutrient limitation. This fundamentally affects bacterial physiology and metabolism and has profound impacts on their infection by bacterial viruses (bacteriophages). For virulent bacteriophages, which cannot enter a lysogenic state, this poses a problem for environmental persistence. Here we demonstrate that virulent bacteriophage SPP1 productively infects nutrient-limited stationary phase cultures of the Gram-positive bacteriumBacillus subtilis. Slow production and release of low numbers of infective viral particles resulted from a prolonged infection of the host population. Extensive culture lysis was greatly delayed, releasing additional viral particles and promoting fresh infections of bacterial survivors. Induced overproduction of cell surface bacteriophage receptor YueB, compensating for its scarcity in stationary phase, expedited infection dynamics under nutrient-limiting conditions, but did not change overall infection productivity. The temporal program of SPP1 gene expression differed from exponential phase, consistent with a prolonged, persistent mode of infection. Reduced expression of genes coding viral structural proteins correlated with the low yield of infectious particles. Importantly, exogenous influx of the carbon source maltose enhanced viral particle production. Our results uncover a novel adaptive strategy of a lytic phage for productive infection of nutrient-limited bacterial populations through persistent, exhaustive infection.
Effects of sensorineural hearing loss on formant-frequency discrimination: Measurements and models
Authors: Carney Laurel H. , Cameron David A. , Kinast Kameron B. , Feld C. Evelyn , Schwarz Douglas M. , Leong U-Cheng , McDonough Joyce M. 
Published: October 2022

ABSTRACTThis study concerns the effect of hearing loss on discrimination of formant frequencies in vowels. In the response of the healthy ear to a harmonic sound, auditory-nerve (AN) rate functions fluctuate at the fundamental frequency, F0. Responses of inner-hair-cells (IHCs) tuned near spectral peaks are captured (or dominated) by a single harmonic, resulting in lower fluctuation depths than responses of IHCs tuned between spectral peaks. Therefore, the depth of neural fluctuations (NFs) varies along the tonotopic axis and encodes spectral peaks, including formant frequencies of vowels. This NF code is robust across a wide range of sound levels and in background noise. The NF profile is converted into a rate-place representation in the auditory midbrain, wherein neurons are sensitive to low-frequency fluctuations. The NF code is vulnerable to sensorineural hearing loss (SNHL) because capture depends upon saturation of IHCs, and thus the interaction of cochlear gain with IHC transduction. In this study, formant-frequency discrimination limens (DLFFs) were estimated for listeners with normal hearing or mild to moderate SNHL. The F0 was fixed at 100 Hz, and formant peaks were either aligned with harmonic frequencies or placed between harmonics. Formant peak frequencies were 600 and 2000 Hz, in the range of first and second formants of several vowels. The difficulty of the task was varied by changing formant bandwidth to modulate the contrast in the NF profile. Results were compared to predictions from model auditory-nerve and inferior colliculus (IC) neurons, with listeners’ audiograms used to individualize the AN model. Correlations between DLFFs, audiometric thresholds near the formant frequencies, age, and scores on the Quick speech-in-noise test are reported. SNHL had a strong effect on DLFFfor the second formant frequency (F2), but relatively small effect on DLFFfor the first formant (F1). The IC model appropriately predicted substantial threshold elevations for changes in F2 as a function of SNHL and little effect of SNHL on thresholds for changes in F1.
Leveraging PDE solver for predicting transient space-use dynamics in ecological and epidemiological systems
Authors: Tao Yun 
Published: October 2022

AbstractModel predictions of animal and human space-use patterns stemming from individual-level movement behaviors have not only contributed significantly to our understanding of population and community dynamics, but they could also inform the development of conservation, natural resource management, and disease control policies. The recent proliferation of high-resolution movement data has ushered in a paradigm shift in how space use is considered: instead of being defined narrowly as the stationary, long-term distribution of individual locations, there is a growing recognition of its transient dynamics, e.g.., how space-use pattern varies before it eventually stabilizes. However, movement models are slow to follow due to longstanding technical challenges in solving transient space-use dynamics. Here, we introduce a numerical framework that enables transient analysis of mechanistic movement models based on partial differential (Fokker-Planck) equations. We demonstrate its potential applications in the context of general research questions in movement ecology using classical and new case studies as illustrations. We demonstrate the framework’s applications and versatility in classical home range models, but also show how it may be extended to address new ecological questions.
Mechanisms of masking by Schroeder-phase harmonic tone complexes in the budgerigar (Melopsittacus undulatus)
Authors: Henry Kenneth S. , Wang Yingxuan , Abrams Kristina S. , Carney Laurel H 
Published: October 2022

AbstractSchroeder-phase harmonic tone complexes can have a flat temporal envelope and either rising or falling instantaneous-frequency sweeps within periods of the fundamental frequency (F0), depending on the phase-scaling parameter C. Human thresholds for tone detection in a concurrent Schroeder masker are 10-15 dB lower for positive C values (rising frequency sweeps) compared to negative (falling sweeps), potentially due to the impulse response of cochlear filtering, though this hypothesis remains controversial. Birds provide an interesting animal model for studies of Schroeder masking because prior reports suggest less behavioral threshold difference between maskers with opposite C values. However, most behavioral studies focused on relatively low masker F0s, and neurophysiological mechanisms in birds have not been explored. We performed behavioral Schroeder-masking experiments in budgerigars (Melopsittacus undulatus) using a wide range of masker F0 and C values. The signal frequency was 2800 Hz. Neural recordings at the midbrain processing level characterized encoding of behavioral stimuli in awake animals. Behavioral thresholds increased with increasing masker F0 and showed minimal difference between opposite C values, consistent with prior studies. Neural recordings showed prominent temporal and rate-based encoding of Schroeder F0, and in many neurons, marked response asymmetry between Schroeder stimuli with opposite C values. Neural thresholds for Schroeder-masked tone detection were (1) in most cases based on a response decrement compared to the masker alone, consistent with prominent modulation tuning in midbrain neurons, and (2) generally similar between opposite masker C values. These results highlight the likely importance of envelope cues in behavioral studies of Schroeder masking.
Spike-phase coupling patterns reveal laminar identity in primate cortex
Authors: Davis Zachary W. , Dotson Nicholas M. , Franken Tom , Muller Lyle , Reynolds John 
Published: October 2022

AbstractThe cortical column is one of the fundamental computational circuits in the brain. In order to understand the role neurons in different layers of this circuit play in cortical function it is necessary to identify the boundaries that separate the laminar compartments. While histological approaches can reveal ground truth they are not a practical means of identifying cortical layersin vivo. The gold standard for identifying laminar compartments in electrophysiological recordings is current-source density (CSD) analysis. However, laminar CSD analysis requires averaging across reliably evoked responses that target the input layer in cortex, which may be difficult to generate in less well studied cortical regions. Further the analysis can be susceptible to noise on individual channels resulting in errors in assigning laminar boundaries. Here, we have analyzed linear array recordings in multiple cortical areas in both the common marmoset and the rhesus macaque. We describe a pattern of laminar spike-field phase relationships that reliably identifies the transition between input and deep layers in cortical recordings from multiple cortical areas in two different non-human primate species. This measure corresponds well to estimates of the location of the input layer using CSDs, but does not require averaging or specific evoked activity. Laminar identity can be estimated rapidly with as little as a minute of ongoing data and is invariant to many experimental parameters. This method may serve to validate CSD measurements that might otherwise be unreliable or to estimate laminar boundaries when other methods are not practical.
Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect barcodes from Colombia
Authors: Baena-Bejarano Nathalie , Reina Catalina , Martínez-Revelo Diego Esteban , Medina Claudia A. , Tovar Eduardo , Uribe-Soto Sandra , Neita-Moreno Jhon Cesar , Gonzalez Mailyn A. 
Published: October 2022

AbstractRecent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems, and GenBank. This was done by comparing the sequence matches between taxonomist identification and the suggested identification from the platforms. We used 1160 sequences in eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus level. The accuracy was higher in BOLD for the orders Coleoptera at family, for Coleoptera and Lepidoptera at genus, and species level. The other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that in this group species were correctly identified when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliable use of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.
Design and characterization of a protein fold switching network
Authors: Ruan Biao , He Yanan , Chen Yingwei , Choi Eun Jung , Chen Yihong , Motabar Dana , Solomon Tsega , Simmerman Richard , Kauffman Thomas , Gallagher D. Travis , Orban John , Bryan Philip N. 
Published: October 2022

AbstractProtein sequences encoding three common small folds (3α, β–grasp, and α/β–plait) were connected in a network with high-identity intersections, termed nodes. The structures of proteins around nodes were determined using NMR spectroscopy and analyzed for stability and binding function. To generate nodes, the amino acid sequence encoding a shorter fold (3a or β–grasp) is embedded in the structure of the~50% longer α/β–plait fold and a new sequence is designed that satisfies two sets of native interactions. This leads to protein pairs with a 3a or β–grasp fold in the shorter form but an α/β–plait fold in the longer form. Further, embedding smaller antagonistic folds in longer folds creates critical states in the longer folds such that single amino acid substitutions can switch both their fold and function. This suggests that abrupt fold switching may be a mechanism of evolving new protein structures and functions.
Modification of Seurat v4 for the development of a phase assignment tool able to distinguish between G2 and Mitotic cells
Authors: Watson Steven , Porter Harry , Sudbery Ian , Thompson Ruth 
Published: October 2022

AbstractSingle cell RNA sequencing (scRNAseq) is a rapidly advancing field which allows for the characterization of the cellular heterogeneity of gene expression profiles within a population. Cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phase to scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as G1, S or G2/M. Discrete cell phase assignment tool are unable to differentiate between G2 and M and continuous phase assignments tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. Bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence activated cell sorting. The gene lists were used to develop a Modified Seurat Mitotic Sort (MoSMiS) methodology which can distinguish G2 and M phase cells in single cell RNA sequencing data. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle identifying a mitotic specific cell population.
At the crossroad of digital and tourism entrepreneurship: mediating effect of digitalization in hospitality industry
Authors: Suder Marcin , Duda Joanna , Kusa Rafał , Mora-Cruz Alexandra 
Published: October 2022

PurposeThis study aims to explore the role of digital technologies in tourism entrepreneurship. In particular, the main objective of this research is to examine the relationships among proactiveness, innovativeness, digitalization, and firm performance and growth in the hotel industry.Design/methodology/approachThe data for this investigation were collected from 110 one- or two-star hotels that were operating in Poland during the time of this research. This study employs PLS-SEM to analyze the relationships among the examined variables.FindingsThe results show that digitalization has a significantly positive impact on a hotel’s performance. Moreover, digitalization mediates the impact of entrepreneurial behaviors on performance. In particular, digitization is a full mediator for the impact of proactiveness on firm growth and innovation on market performance. Additionally, there is a partial complementary mediation effect of digitalization in the case of impact of innovativeness on firm growth; digitization is not a mediator for the impact of proactiveness on firm growth.Originality/valuePrevious studies have not captured the relationships among entrepreneurship, digitalization, and performance; this study helps to fill the gap and examine these associations in the hospitality industry. The outcome of this study provides valuable insights for hoteliers for understanding the role (and importance) of digitalization in the context of proactiveness and innovativeness.