Biology subjects

Becker, D.

Publications and source records attributed to Becker, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Evolutionary paleoecology of European rhinocerotids across the Oligocene-Miocene transition

The Oligocene-Miocene transition witnessed great environmental and faunal changes, but its drivers and consequences on mammals remain poorly understood. Rhinocerotoids are among the most affected taxa, reflected by great taxonomical (extinction of all non-rhinocerotids) and morphological (e.g., more mediportal forms) changes observed during this interval. However, potential associated changes in ecology have not been explored. Here, we investigated the paleoecology of 10 rhinocerotid species coming from 15 localities across Western and Central Europe and ranging from Mammal Paleogene reference level 28 to Mammal Neogene zone 3. We explored evolutionary trends for their diet, physiology, and habitat via dental wear, hypoplasia, body mass estimates, and stable isotopy. Our results (isotopy, dental wear) suggest that all rhinocerotids studied were C3 feeders, whether browsing or mixed-feeding, but niche partitioning was assumed at some localities: distinct dietary preferences and/or habitats were highlighted at Gaimersheim, Ulm-Westtangente, and Rickenbach, whereas a potential competition for the resources or different niche partitioning strategies (body mass, feeding height) are hypothesized at others localities (La Milloque, Thezels, Paulhiac). We reconstructed similar warm conditions at all localities except Gaimersheim, but found greater variations in precipitation. Indeed, a clear shift in {delta}13CCO3, enamel values was noticed at the end of the Oligocene, consistent with climatic changes (Mi-1) and vegetation modifications reported at that time. Despite these great changes, the prevalence of hypoplasia was low (< 10 %) to moderate (< 20 %) except at some localities (Pappenheim, Rickenbach, Engehalde) and for some species (Brachydiceratherium aurelianense and B. lamilloquense). Teleoceratines were particularly affected, suggesting a potential phylogenetic effect. Fourth milk molars and third molars were the most affected loci, indicating stresses around birth and environmental stresses respectively. Body mass co-variated with hypoplasia prevalence, indicating that larger species might be more susceptible to stresses and environmental changes. The tracking of rhinocerotids paleoecological preferences during the Oligocene-Miocene revealed several changes in diet and habitat (temperature, precipitation, vegetation) consistent with global changes during this period.

paleontology↗

bioRxiv2024

A paired analysis of mercury among non-invasive tissues to inform bat conservation monitoring

Contaminant exposure can harm wildlife. However, measuring contaminant exposure in wildlife can be challenging due to accessibility of species and/or sampling tissue matrices needed to answer research questions regarding exposure. For example, in bats and other taxa that roost, it may be best to collect pooled feces from colonies for minimal disturbance to species of conservation concern, but fecal contaminant concentrations do not provide contaminant bioaccumulation estimates. Thus, there is a need for quantifying relationships between sample matrices for measuring contaminant exposure to answer research questions pertaining to wildlife health and addressing conservation needs. Our goal was to determine relationships between fecal and fur total mercury (THg). To do so, we collected paired feces and fur from Mexican free-tailed bats (Tadarida brasiliensis) in summer 2023 in western Oklahoma at a maternity roost with no known Hg point source. We analyzed THg in each sample matrix for each individual (n = 48). We found no relationship between individual fecal and fur THg. However, when averaged, fur THg was 6.11 times greater than fecal THg. This factor can be used as a screening-level risk assessment of under-roost feces, which could then be followed by direct assessments of fur THg concentrations and health impacts. We encourage the use of this conversion factor across other insectivorous bat species and sites for estimating initial risks of contaminant exposure with minimal disturbance to species of conservation concern, when timely research for conservation actions are needed, and when a contaminant point source is not yet known. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/587502v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@4bac41org.highwire.dtl.DTLVardef@1a13deorg.highwire.dtl.DTLVardef@e8e58org.highwire.dtl.DTLVardef@1a33a9d_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract created in BioRender under a free subscription. Cave icon created by artist Freepik at https://www.flaticon.com/free-icons/cave. HighlightsO_LIUnder-roost sampling for contaminant exposure minimizes species disturbance C_LIO_LIContaminant exposure relationships in tissues can aide in measuring wildlife health C_LIO_LIWe sampled Tadarida brasilliensis for paired fecal and fur total Hg (THg) C_LIO_LITHg in fur averaged 6.11 times greater than feces C_LIO_LIThis factor can be used as an initial risk assessment for under-roost fecal sampling C_LIO_LIMore invasive follow-up sampling (bat fur) can be justified following risk assessment C_LI

ecology↗

bioRxiv2024

Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species

Bacterial pathogens remain poorly characterized in bats, especially in North America. We describe novel (and in some cases panmictic) hemoplasmas (10.5% positivity) and bartonellae (25.5% positivity) across three colonies of Mexican free-tailed bats (Tadarida brasiliensis), a partially migratory species that can seasonally travel hundreds of kilometers. Molecular analyses identified three novel Candidatus hemoplasma species most similar to another novel Candidatus species in Neotropical molossid bats. We also detected novel hemoplasmas in sympatric cave myotis (Myotis velifer) and pallid bats (Antrozous pallidus), with sequences in the latter 96.5% related to C. Mycoplasma haemohominis. We identified nine Bartonella genogroups, including those in cave myotis with 96.7% similarity to C. Bartonella mayotimonensis. We also detected Bartonella rochalimae in migratory Mexican free-tailed bats, representing the first report of this human pathogen in the Chiroptera. The seasonality and diversity of these bacteria observed here suggest that additional longitudinal, genomic, and immunological studies in bats are warranted.

ecology↗

bioRxiv2024

Molecular mechanisms underlying single nucleotidepolymorphism-induced reactivity decrease in CYP2D6

Cytochrome P450 2D6 (CYP2D6) is one of the most important enzymes involved in drug metabolism. Genetic polymorphism can influence drug metabolism by CYP2D6 such that a therapy is seriously affected by under- or overdosing of drugs. However, a general explanation at the atomistic level for poor activity is missing so far. Here we show for the 20 most common single nucleotide polymorphisms (SNPs) of CYP2D6 that poor metabolism is driven by four mechanisms. We found in extensive all-atom molecular dynamics simulations that the rigidity of the I-helix (central helix), distance between central phenylalanines (stabilizing bound substrate), availability of basic residues on the surface of CYP2D6 (binding of Cytochrome P450 reductase), and position of arginine 132 (electron transfer to heme) are essential for an extensive function of the enzyme. These results were applied to SNPs with unknown effects and potential SNPs that may lead to poor drug metabolism were identified. The revealed molecular mechanisms might be important for other drug-metabolizing Cytochrome P450 enzymes. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/574226v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@517961org.highwire.dtl.DTLVardef@f7ded3org.highwire.dtl.DTLVardef@1462baaorg.highwire.dtl.DTLVardef@1dcabae_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

The Role of Anthropogenic Roosting Ecology in Shaping Viral Outcomes in Bats

O_LIThe ability of wildlife to live in anthropogenic structures is widely observed across many animal species. As proximity to humans is an important risk factor for pathogen transmission, anthropogenic roosting may have important consequences for predicting the spillover and spillback of viruses. For bats, the influence of roosting in anthropogenic structures on predicting virus hosting ability and diversity is poorly understood. Such information could be useful for optimizing models of virus outcomes to identify species and locations to target for viral discovery at the human-wildlife interface. C_LIO_LIWe integrate novel roosting ecology data into machine learning models to assess the importance of anthropogenic roosting in predicting viral outcomes across bat species. Additionally, we evaluate how this trait affects the prediction of undetected but likely bat host species of viruses. C_LIO_LIThe importance of anthropogenic roosting varies across viral outcomes, being most important for virus hosting ability and less so for zoonotic virus hosting ability, viral family richness, and zoonotic family richness. Across viral outcomes, anthropogenic roosting is less important than human population density but more important than most family, diet, and foraging traits. C_LIO_LIWhile model performance was not affected by inclusion of anthropogenic roosting, models with this novel trait extended the list of undetected host species compared to models excluding this trait. Predicted virus host distributions show distinct spatial patterns between anthropogenic and natural roosting bats, with the greatest proportion of likely novel hosts relative to bat species diversity being anthropogenic roosting bats in Asia. C_LIO_LISynthesis and applications. These findings suggest anthropogenic roosting has a non-trivial role in predicting viral outcomes in bats, specifically for virus hosting ability. Exclusion of this epidemiologically relevant trait could result in underestimation of predicted hosts, particularly in Asia where hotspots of undetected hosts are mostly able to roost in anthropogenic structures. More broadly, these results demonstrate the importance of evaluating the impact of new data on predicting host-pathogen interactions, even for models that already perform well. Such modeling efforts are particularly relevant for assessing spillover or spillback risks at human-wildlife interfaces. C_LI

ecology↗

bioRxiv2023

A general framework for modeling pathogen transmission in co-roosting host communities

Cross-species transmission of pathogens can be facilitated by frequent contact among wildlife. Cross-species transmission is often driven by phylogenetic similarity between host species, but the role this plays when multiple host species co-roost is unknown. We developed a generalizable framework for understanding how cross-species transmission is driven by contact among co-roosting species spanning evolutionary similarities and the net impact on roost-level infection prevalence. We developed ordinary differential equation models describing population and infection dynamics between two and three co-roosting species. We parameterized models using co-roosting Neotropical bat systems, with interspecific transmission exponentially declining with phylogenetic distance. To assess the relative contribution of contact rates and phylogenetic similarity, we co-varied intraspecific transmission rates and phylogenetic distances while considering sensitivity to host and pathogen traits. While our models converged on similar equilibria under high intraspecific transmission or long durations of infection and immunity or latency, simulations with lower intraspecific transmission and shorter such periods revealed roost-level prevalence was greatest when hosts were most closely related. However, we identified regions of parameter space where roost-level prevalence also maximized when hosts were distantly related, driven by species-specific traits. Our generalizable models are adaptable to other co-roosting systems and informs our understanding of pathogen spillover.

ecology↗

bioRxiv2023

Determinants of spring migration departure dates in a New World sparrow: weather variables reign supreme

Numerous factors influence the timing of spring migration in birds, yet the relative importance of intrinsic and extrinsic variables on migration initiation remains unclear. To test for interactions among weather, migration distance, parasitism, and physiology in determining spring departure date, we used Dark-eyed Juncos (Junco hyemalis hyemalis) as a model migratory species known to harbor diverse and common haemosporidian parasites. Prior to spring migration departure from their wintering grounds in Indiana, USA, we quantified the intrinsic variables of fat, body condition (i.e., mass[~]tarsus residuals), physiological stress (i.e., ratio of heterophils to lymphocytes), cellular immunity (i.e., leukocyte composition and total count), migration distance (i.e., distance to the breeding grounds) using stable isotopes of hydrogen from feathers, and haemosporidian parasite intensity. We then attached nanotags to determine the timing of spring migration departure date using the Motus Wildlife Tracking System. We used additive Cox proportional hazard mixed models to test how risk of spring migratory departure was predicted by the combined intrinsic measures, along with meteorological predictors on the evening of departure (i.e., average wind speed and direction, relative humidity, and temperature). Model comparisons found that the best predictor of spring departure date was average nightly wind direction and a principal component combining relative humidity and temperature. Juncos were more likely to depart for spring migration on nights with largely southwestern winds and on warmer and drier evenings (relative to cooler and more humid evenings). Our results indicate that weather conditions at take-off are more critical to departure decisions than the measured physiological and parasitism variables.

ecology↗

bioRxiv2023

Movement-related drivers of exposure to West Nile virus by American robins (Turdus migratorius)

The ecological processes that determine how individual animals become hosts to zoonotic pathogens is a topic of rapidly growing interest. However, how such exposure is mediated by context (e.g., season, location), host behavior (e.g., migration distance) and host demographics is generally poorly understood. We evaluated seasonal exposure to West Nile Virus of American robins sampled in Indiana and compared our results to those of previous studies. Because robins that breed in Indiana are partial migrants (i.e., only a portion of the population migrates), we evaluated their probability of exposure to WNV as a function of whether they migrated or not and of their movement distance. We also tagged a subset of breeding robins with tracking devices to evaluate their potential to disperse the virus between Indiana and other regions of the continent. We found that robins that breed in Indiana are exposed to WNV at a higher rate than that detected in previous studies, but found no correlation between robin exposure and whether a robin migrated or not, nor with migration distance, season, sex, and breeding latitude (for robins overwintering in Indiana). Our tracking data indicate that robins that breed in Indiana migrate several hundred miles to overwinter in the southeastern US. The mean duration of their return to Indiana in spring is 10.3 days, which is less than the maximum infectious period found for robins in previous studies, suggesting that they have the capacity to move WNV long distances in spring. However, we still know little about the physiological capacity of robins to migrate while being infectious, which could inhibit the dispersal of the virus through robin migration. Future research on the physiological, ecological and behavioral factors mediating the exposure of birds to WNV will lend insight into the role that robins and other birds play in the transmission ecology of the virus.

ecology↗

bioRxiv2023

Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico

The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens. O_FIG O_LINKSMALLFIG WIDTH=99 HEIGHT=200 SRC="FIGDIR/small/563347v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@5b100borg.highwire.dtl.DTLVardef@7a59f3org.highwire.dtl.DTLVardef@a78ff3org.highwire.dtl.DTLVardef@dbce25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic abstract:C_FLOATNO Overview of the experimental approach for bird collection and characterization of neotropical ticks microbiome. A) Birds migrating through the Mississippi flyway into the United States were trapped and captured for identification and tick collection and B) immature developmental stages of feeding ticks infesting the birds were carefully removed and stored for morphological and molecular identification of tick species. C) Tick DNA was used for the PCR amplification of arthropods mitochondrial 12S rDNA and amplicons were sequenced and compared to deposited datasets in NCBI database. D) Microbial DNA was isolated using V3-V4 16S primers and unique barcodes attached to amplified 16S sequences prior to Illumina MiSeq sequences. E) Distribution and contribution of birds to tick infestation, and distribution and community profiles of sequenced microbial communities. C_FIG

zoology↗

bioRxiv2023

Disentangling gene expression burden identifies generalizable phenotypes induced by synthetic gene networks

Large-scale genetic circuits are rapidly becoming critical components for the next generation of biotechnologies and living therapeutics. However, the relationship between synthetic and host gene expression is poorly understood. To reveal the impact of genetic circuits on their host, we measure the transcriptional response of wild-type and engineered E. coli MG1655 subject to seven genomically integrated circuits and two plasmid-based circuits across 4 growth time points and 4 circuit input states resulting in 1007 transcriptional profiles. We train a classifier to distinguish profiles from wild-type or engineered strains and use the classifier to identify synthetic construct burdened genes, i.e., genes whose dysregulation is dependent on the presence of a genetic circuit and not what is encoded on the circuit. We develop a deep learning architecture, capable of disentangling influence of combinations of perturbations, to model the impact that synthetic genes have on their host. We use the model to hypothesize a generalizable, synthetic cell state phenotype and validate the phenotype through antibiotic challenge experiments. The synthetic cell state results in increased resistance to {beta}-lactam antibiotics in gram-negative bacteria. This work enhances our understanding of circuit impact by quantifying the disruption of host biological processes and can guide the design of robust genetic circuits with minimal burden or uncover novel biological circuits and phenotypes.

systems biology↗

bioRxiv2023

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype with five complete sets of syntenic chromosomes (2n = 10x = 80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbor three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in trapping pitchers. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes experiencing relaxed purifying selection to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

plant biology↗

bioRxiv2023

Expanded diversity of hemoplasmas in rare and undersampled Neotropical bats

Hemotropic mycoplasmas are emerging as a model system for studying bacterial pathogens in bats, but taxonomic coverage of sampled host species remains biased. We leveraged a long-term field study in Belize to uncover novel hemoplasma diversity in bats by analyzing 80 samples from 19 species, most of which are infrequently encountered. PCR targeting the partial 16S rRNA gene found 41% of bats positive for hemoplasmas. Phylogenetic analyses found two novel host shifts of hemoplasmas, four entirely new hemoplasma genotypes, and the first hemoplasma detections in four bat species. One of these novel hemoplasmas (from Neoeptesicus furinalis) shared 97.6% identity in the partial 16S rRNA gene to a human hemoplasma (Candidatus Mycoplasma haemohominis). Additional analysis of the partial 23S rRNA gene allowed us to also designate two novel hemoplasma species, in Myotis elegans and Phyllostomus discolor, with the proposed names Candidatus Mycoplasma haematomyotis sp. nov. and Candidatus Mycoplasma haematophyllostomi sp. nov., respectively. Our analyses show that additional hemoplasma diversity in bats can be uncovered by targeting rare or undersampled host species.

microbiology↗

bioRxiv2023

S1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs

Plants exhibit an immense plasticity in their architecture. While the impact of hormonal regulation is well-characterised, the importance of sugar-signalling has just recently emerged. Here, we addressed which sugar-signalling components mediate the trade-off between growth of apical versus lateral meristems and how they control organ sink-strength. Thereby, we unravelled a novel developmental function of the sugar-controlled S1 basic-leucine-zipper (S1-bZIP) transcription factors in establishing global source-sink interactions. Applying comprehensive molecular, analytical, and genetic approaches, we demonstrate that S1-bZIPs operate in a redundant manner to control tissue-specific expression of defined SWEET sugar-transporters and the GAT1_2.1 glutaminase. By these means, S1-bZIPs control carbohydrate (C)-channelling from source leaves to apical shoot and root organs and tune systemic organic nitrogen (N)-supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.

plant biology↗

bioRxiv2023

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing

Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programmes. The fine mapping of promoters (transcription start sites [TSS]) and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific phenotypes. To this aim we used Cap Analysis Gene Expression (CAGE) sequencing to define TSS and their co-expressed short-range enhancers (<1kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9) and analysed tissue- and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the three populations (Holstein, Charolais x Holstein and Kinsella beef composite [KC]). In addition, we performed a comparative analysis of our cattle dataset with available data for seven other species to identify TSS and TSS-Enhancers that are specific to cattle. The CAGE dataset will be combined with other transcriptomic information for the same tissues generated in the BovReg project to create a new high-resolution map of transcript diversity across tissues and populations in cattle. Here we provide the CAGE dataset and annotation tracks for TSS and TSS Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programmes.

genomics↗

bioRxiv2023

The impact of patient-specific inlet conditions on oscillatory shear and helicity in haemodynamic simulations of aneurysmal Type-B Aortic Dissection

Type-B Aortic Dissection is a cardiovascular disease in which a tear develops in the intimal layer of the descending aorta, allowing pressurized blood to delaminate the layers of the vessel wall. In medically managed patients, long-term aneurysmal dilatation of the false lumen (FL) is considered virtually inevitable and is associated with poorer disease outcomes. While the pathophysiological mechanisms driving FL dilatation are not yet understood, hemodynamic factors are believed to play a key role. Computational Fluid Dynamics (CFD) and 4D-Flow MRI (4DMR) analyses have revealed correlations between flow helicity, oscillatory wall shear stress, and aneurysmal dilatation of the FL. In this study, we compare CFD simulations using a patient-specific, three-dimensional, three-component inlet velocity profile (3D IVP) extracted from 4DMR data against simulations with flow rate-matched uniform and axial velocity profiles that remain widely used in the absence of 4DMR. We also evaluate the influence of measurement errors in 4DMR data by scaling the 3D IVP to the degree of imaging error detected in prior studies. We observe that oscillatory shear and helicity are highly sensitive to inlet velocity distribution and flow volume throughout the FL and conclude that the choice of IVP may greatly affect the future clinical value of simulations.

bioengineering↗

bioRxiv2023

Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two

BackgroundIn plant genome editing, RNA-guided nucleases such as Cas9 from Streptococcus pyogenes (SpCas9) predominantly induce small insertions or deletions at target sites. This can be used for inactivation of protein-coding genes by frame shift mutations. However, in some cases, it may be advantageous to delete larger chromosomal segments. This is achieved by simultaneously inducing double strand breaks upstream and downstream of the fragment to be deleted. Experimental approaches for deletion induction have not been systematically evaluated. ResultsWe designed three pairs of guide RNAs for deletion of the Arabidopsis WRKY30 locus (~2.2 kb). We tested how the combination of guide RNA pairs and co-expression of the exonuclease TREX2 affect the frequency of wrky30 deletions in editing experiments. Our data demonstrate that compared to one pair of guide RNAs, two pairs increase the frequency of chromosomal deletions. The exonuclease TREX2 enhanced mutation frequency at individual target sites and shifted the mutation profile towards larger deletions. However, TREX2 did not elevate the frequency of chromosomal deletions. ConclusionsMultiplex editing with at least two pairs of guide RNAs (four guide RNAs in total) elevates the frequency of chromosomal deletions, and thus simplifies the selection of corresponding mutants. Co-expression of the TREX2 exonuclease can be used as a general strategy to increase editing efficiency in Arabidopsis without obvious negative effects.

plant biology↗

bioRxiv2022

Ecological drivers of sustained enzootic yellow fever virus transmission in Brazil, 2017-2021

Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV) using qPCR. One sample belonging to a Callithrix, collected in June 2020, was positive for YFV. The viral strain belonged to the same lineage associated with 2017-2018 outbreaks, showing the continued enzootic circulation of YFV in the state. Next, using data from 781 NHPs carcasses collected in 2017-18, we used generalized additive mixed models (GAMMs) to identify the spatiotemporal and host-level drivers of YFV infection and intensity (an estimation of genomic viral load in the liver of infected NHP). Our GAMMs explained 65% and 68% of variation in virus infection and intensity, respectively, and uncovered strong temporal and spatial patterns for YFV infection and intensity. NHP infection was higher in the eastern part of Minas Gerais state, where 2017-2018 outbreaks affecting humans and NHPs were concentrated. The odds of YFV infection were significantly lower in NHPs from urban areas than from urban-rural or rural areas, while infection intensity was significantly lower in NHPs from urban areas or the urban-rural interface relative to rural areas. Both YFV infection and intensity were higher during the warm/rainy season compared to the cold/dry season. The higher YFV intensity in NHPs in warm/rainy periods could be a result of higher exposure to vectors and/or higher virus titers in vectors during this time resulting in the delivery of a higher virus dose and higher viral replication levels within NHPs. Further studies are needed to better test this hypothesis and further compare the dynamics of YFV enzootic cycles between different seasons. Author SummaryIn 2017 and 2018 massive sylvatic yellow fever (YF) outbreaks took place in Minas Gerais Brazil. To investigate yellow fever virus (YFV) circulation following these massive outbreaks, we investigated samples from 187 free-living non-human primate (NHPs) collected between January 2019 and June 2021. One sample belonging to a Callithrix, collected in June 2020 was positive for YFV. This virus was closely related to YFV from previous outbreaks (2017-2018) showing the continued enzootic circulation of YFV in the state. Next, we investigated the drivers of YFV infection and intensity (an estimation of viral load in each infected NHP) during the 2017-18 outbreaks. The odds of YFV infection in NHPs were lower in urban areas compared to rural ones as expected in sylvatic cycles. There were strong temporal and spatial patterns were observed for YFV infection and intensity, especially in the eastern part of Minas Gerais state. The higher YFV infection and intensity observed during the warm/rainy season (as opposed to the cold/dry one) could be related to higher exposure to vectors and/or higher virus titers in vectors during this time. The possible delivery of a higher virus dose in NHPs could lead to higher viral replication levels within NHPs explaining the higher intensity of infection during warm/rainy season. Further studies are needed to better test this hypothesis and further compare the dynamics of YFV enzootic cycles between different seasons.

microbiology↗

bioRxiv2022

Viral diversity and zoonotic risk in endangered species

A growing body of evidence links zoonotic disease risk, including pandemic threats, to biodiversity loss and other upstream anthropogenic impacts on ecosystem health. However, there is little current research assessing viral diversity in endangered species. Here, combining IUCN Red List data on 5,876 mammal species with data on host-virus associations for a subset of 1,273 extant species, we examine the relationship between endangered species status and viral diversity, including the subset of viruses that can infect humans (zoonotic viruses). We show that fewer total viruses and fewer zoonotic viruses are known to infect more threatened species. After correcting for sampling effort, zoonotic virus diversity is mostly independent of threat status, but endangered species--despite a higher apparent research effort--have a significantly lower diversity of viruses, a property that is not explained by collinearity with host phylogeography or life history variation. Although this pattern could be generated by real biological processes, we suspect instead that endangered species may be subject to additional sampling biases not captured by the total volume of scientific literature (e.g., lower rates of invasive sampling may decrease viral discovery). Overall, our findings suggest that endangered species are no more or less likely to host viruses that pose a threat to humans, but future zoonotic threats might remain undiscovered in these species. This may be concerning, given that drivers of endangered species vulnerability such as habitat disturbance, wildlife trade, or climate vulnerability may increase virus prevalence in reservoirs and risk of spillover into humans.

ecology↗