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1,994 results for “Tailings”
Population Dynamics of a Subpopulation of Lion-tailed Macaques in a Rainforest Fragment, in the southern Western Ghats of India
<p>The dataset includes absolute group counts of five groups of lion-tailed macaques inhabiting the Puthuthottam forest fragment of Valparai, Tamil Nadu, India. The counts were conducted over a period of three years between 2018-2020 at six-monthly intervals. </p>
Pigs feeding behaviours from two different farms, including behaviours during a tail biting event
<p>These data are linked to the article from Ollagnier et al, 2021 (https://doi.org/10.1101/2021.05.11.443554)</p> <p><strong>Data desription</strong></p> <p>This data set comprises the feeding behaviours of two herds of grower-finisher pigs weighing between 25 and 100 kilograms. One data set originates from a testing boar station in Sweden and contains data collected from October 2004 to July 2007. The data set comes from a previous retrospective study that Wallenbeck and Keeling published in 2013. The second data set contains data from the experimental pig farm of Agroscope and comprises recordings from November 2018 to April 2020. As tail docking is prohibited in Sweden and in Switzerland, the data are from pigs with intact tails.</p> <p>The Swedish data set includes data from 42 pens (21 TB and 21 CTL ) of boars (purebred Yorkshire, Landrace or Hampshire) recorded 70 days before and after the TB date. Boars were housed in groups of 7 to 14 animals per pen. Each pen measured 15.7 m<sup>2 </sup>and had a slatted floor and plain resting area. All pigs had <em>ad libitum</em> access to the pelleted feed, which was optimised according to the Swedish nutrition norms for fattening pigs [25]. Water was provided <em>ad libitum</em> and straw was offered daily.</p> <p>The Swiss data set consisted of 23 pens (six TB and 17 CTL) of females and castrated male pigs (Swiss Large White), recorded 100 days before and after the TB date. Twenty pens (18 m<sup>2</sup>) contained 11 to 15 pigs each and were equipped with two automatic feeders; three pens (78 m<sup>2</sup>) were equipped with eight automatic feeders for 31 to 55 pigs each. All pens had straw in racks and sawdust on the floor. Water was available <em>ad libitum</em> through nipple drinkers. The pelleted finisher diet was formulated to have 20% lower dietary crude protein and essential amino acids compared to a standard diet formulated according to the Swiss feeding recommendations for pigs.</p> <p><strong>Data structure:</strong></p> <p>Three observations were considered to describe the feeding behaviours of pigs. </p> <p><strong>DFV: </strong>Number of visits to the feeder (from 0:00 to 23:59:59 that date), unit=n, </p> <p><strong>DFC: </strong>Total feed consumption (from 0:00 to 23:59:59 that date), unit=g</p> <p><strong>StdFC</strong>: Daily standard deviation of the feed consumption at each visit, unit=g</p> <p>The data set also contains the following information:</p> <p><strong>Farm:</strong> origin of the feeding behavior data (Swiss or Swedish farm)</p> <p><strong>ID: </strong>unique identification of the pig</p> <p><strong>date:</strong> date at which the feeding behavior is recorded, numerical format.</p> <p><strong>TBSTART:</strong> date at which the tail biting event started in tail biting pens. An arbitrary date has been taken for control pens, numerical format.</p> <p><strong>PenID: </strong>unique identification of the pen.</p> <p><strong>PenType: </strong>control (K) or tail biting (TB). A pen was assigned to the TB category if at least one pig had to be treated for tail damages.</p> <p> </p> <p> </p>
Data from: Telemetry tails: A practical method for attaching animal-borne devices to small vertebrates in the field
<p><b><i>Context.</i></b> Continued miniaturisation of tracking technology increases its utility in animal applications. However, species morphology often dictates the type of animal-borne device (ABD) that can be used, and how it is attached. The morphology of species within Peramelemorphia preclude them from the standard collar attachment of ABDs for terrestrial mammals.</p> <p><b><i>Aims.</i></b> This paper describes a method for the tail-mount attachment of ABDs, and deployment results for Peramelemorphia across arid, semi-arid, and temperate Australia to <b>(a)</b> test the performance of attachments and ABDs in the field, and, <b>(b) </b>discuss the animal welfare considerations for this attachment method. </p> <p><b><i>Methods.</i></b> Tail-mount attachment of ABDs were field-tested on a total of 80 greater bilbies (<i>Macrotis lagotis</i>), and 14 long-nosed bandicoots (<i>Perameles nasuta</i>). </p> <p><b><i>Key results.</i></b> Time to natural detachment (TTND) was between 2 and 52 days with 65.74% (142 of 216) remaining on until manual removal. For ABDs that were manually removed, attachments were retained for up to 94 days. The method used for tail-mount attachment of ABDs to long-nosed bandicoots resulted in significantly shorter TTND compared to the method used for bilbies, and environmental factors (high temperatures and rainfall) had a negative effect on TTND. Tail-mount attached global positioning system (GPS) sensors collected large quantities of accurate data with a maximum fix success rate of 83.38%. Damage to GPS (antenna breakage and water ingress) during deployment, however, impacted performance. In environments with frequent rainfall and waterlogged soils, the tape on a small proportion (6.25%) of (n = 192) attachments to bilbies caused tail injury. All injuries were resolvable with most requiring minimal to no veterinary intervention. </p> <p><b><i>Key conclusions. </i></b>Attachment longevity can be affected by how the ABD is mounted to the tail, the species, and the deployment environment. The environment can also affect which adhesive tapes are suitable for ABD attachment. However, this method is highly modifiable, practical for field application, and can have long retention times relative to other temporary methods.</p> <p><b><i>Implications. </i></b>This ABD tail-mount attachment method adds another tool to the telemetry tool-kit, with all the benefits of a low-tech, low-cost, passive drop-off type attachment. This method has demonstrated practicality for Peramelemorphia, with potential application to other suitable small vertebrates.</p>
Pin-tailed whydah and Cape robin-chat calls for passive acoustic monitoring
<p>We provide the audio data (.wav) used to train neural network classifiers along with the corresponding labelled files (.svl). The .svl files are natively read using Sonic Visualiser (https://www.sonicvisualiser.org/) but can directly be read using Python as these are XML files.</p> <p>This is a three class classification dataset. The recordings were obtained using an AudioMoth which was placed at one location in Intaka Island Nature Reserve, Cape Town, South Africa. The recorder was attached to a tree at approximately 1.5 meters from the ground. The sampling rate was set to 48000Hz with a bit rate of 768kbps. The recordings took place in January 2021. While further recordings exist we only provide a small subset here. Additional data can be requested.</p> <p><strong>Files provided</strong></p> <p>Audio.zip - contains audio files (.wav)</p> <p>Annotations.zip - contains the corresponding labels (.svl) for Sonic Visualiser</p> <p><strong>Class description</strong></p> <p>CRC: calls of the Cape robin-chat (Cossypha caffra)</p> <p>PTW: calls of the pin-tailed whydah (Vidua macroura)</p> <p>NOISE: any sound event that does not contain a Cape robin-chat or pin-tailed whydah call</p> <p> </p> <p>Parts of this data was used in two MSc dissertations:</p> <ul> <li>"Acoustic Data Augmentation for Small Passive Acoustic Monitoring Datasets", Aime Nshimiyimana, African Centre of Excellence in Data Science (ACE-DS) of the University of Rwanda, College of Business and Economics</li> <li>"Pre-training neural networks on Xeno-Canto and eBird for bioacoustic classification models", Mikwa Boris Tamanjong, African Centre of Excellence in Data Science (ACE-DS) of the University of Rwanda, College of Business and Economics</li> </ul>
Influence of the haemosporidian Leucocytozoon spp. over reproductive output in a wild Neotropical passerine, the Thorn-tailed Rayadito Aphrastura spinicauda
<p>Life-history theory predicts that hosts may adjust the costs of parasites by altering their reproductive effort. Haemosporidian parasites can affect the reproductive output of wild birds in multiple ways.<b> </b>Thorn-tailed Rayaditos <i>Aphrastura spinicauda</i> breeding in Navarino Island, Southern Chile (55°-40° S) experience high prevalence of the haemosporidian <i>Leucocytozoon </i>spp., which opens the possibility of exploring how these parasites may affect reproductive output in a Neotropical bird species. We compared several variables describing reproductive output (laying date, clutch size, incubation period, brood size, nestling body condition and early-life telomere length) of infected and non-infected parents (individually and as breeding pairs). We found that infected-females and breeding pairs with both parents infected showed significantly shorter incubation periods than un-infected Thorn-tailed Rayaditos. Furthermore, breeding pairs with both parents infected raised nestlings with higher body condition than nestlings for which infection was present in only one or in none of the parents. Our results suggest that the higher the parental investment, the higher the risk of relapse of chronic infection by <i>Leucocytozoon </i>spp<i>. </i>Thorn-tailed Rayaditos that decrease their incubation period pay the cost of infection to take advantage of early breeding through a greater more availability of resources, producing nestlings with higher body condition.</p>
Codes: A new approach to interspecific synchrony in population ecology using tail association
<p>Standard methods for studying the association between two ecologically important variables provide only a small slice of the information content of the association, but statistical approaches are available that provide comprehensive information. In particular, available approaches can reveal<em> tail associations</em>, i.e., accentuated or reduced associations between the more extreme values of variables. We here study the nature and causes of tail associations between phenological or population-density variables of co-located species, and their ecological importance. We employ a simple method of measuring tail associations which we call the <em>partial Spearman correlation.</em> Using multidecadal, multi-species spatiotemporal datasets on aphid first flights and marine phytoplankton population densities, we assess the potential for tail association to illuminate two major topics of study in community ecology: the stability or instability of aggregate community measures such as total community biomass and its<br> relationship with the synchronous or compensatory dynamics of the community's constituent species; and the potential for fluctuations and trends in species phenology to result in trophic mismatches. We find that positively associated fluctuations in the population densities of co-located species commonly show asymmetric tail associations, i.e., it is common for two species' densities to be more correlated when large than when small, or vice versa. Ordinary measures of association such as correlation do not take this asymmetry into account. Likewise, positively associated fluctuations in the phenology of co-located species also commonly show asymmetric tail associations. We provide evidence that tail associations between two or more species' population density or phenology time series can be inherited from mutual tail associations of these quantities with an environmental driver. We argue that our understanding of community dynamics and stability, and of phenologies of interacting species, can be meaningfully improved in future work by taking into account tail associations.</p>
Seasonal variation in age, sex, and reproductive status of Mexican free-tailed bats
<p>In North America, Mexican free-tailed bats (Tadarida brasiliensis mexicana) consume vast numbers of insects contributing to the economic well-being of society. Mexican free-tailed bats have declined due to historic guano mining, roost destruction, and bioaccumulation of organochlorine pesticides. Long-distance migrations and dense congregations at roosts exacerbate these declines. Wind energy development further threatens bat communities worldwide and presents emerging challenges to bat conservation. Effective mitigation of bat mortality at wind energy facilities requires baseline data on the biology of affected populations. We collected data on age, sex, and reproductive condition of Mexican free-tailed bats at a cave roost in eastern Nevada located six km from a 152-megawatt industrial wind energy facility. Over five years, we captured 46,353 Mexican free-tailed bats. Although just over half of the caught individuals were non-reproductive adult males (53.6%), 826 pregnant, 892 lactating, 10,101 post-lactating, and 4,327 non-reproductive adult females were captured. Juveniles comprised 11.5% of captures. Female reproductive phenology was delayed relative to conspecific roosts at lower latitudes, likely due to cooler temperatures. Roost use by reproductive females and juvenile bats demonstrates this site is a maternity roost, with significant ecological and conservation value. To our knowledge, no other industrial scale wind energy facilities exist in such close proximity to a heavily used bat roost in North America. Given the susceptibility of Mexican free-tailed bats to wind turbine mortality and the proximity of this roost to a wind energy facility, these data provide a foundation from which differential impacts on demographic groups can be assessed.</p>
Multilocus phylogeography, population genetics and niche evolution of Australian Brown and Black-tailed Treecreepers (Aves: Climacteris)
<p>The Carpentarian barrier across northeastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modeling of Brown and Black-tailed Treecreepers (<em>Climacteris picumnus</em> and <em>C</em>. <em>melanurus</em>), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (<em>F</em><sub>st</sub> = 0.91), and reveals a signature of a recent selective sweep in <em>C. picumnus. </em>No loci among 14 anonymous autosomal markers exhibited reciprocal monophyly between species, and a variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7 – 2.8 MYA, depending on the model and assumptions about generation time. Paleo-ecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the last ~600 kyr and that the area of range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.</p>
Data from: Top-down control of a marine mesopredator: Increase in native white-tailed eagles accelerates the extinction of an endangered seabird population
<p><span>1. </span><span>Bottom-up control is an important regulator of marine mesopredators such as seabirds. The prevalence of top-down control on these species is however less well understood. In particular, how native predators affect seabird populations has rarely been quantified. </span></p> <p><span>2. </span><span>Here, we investigate how an increase in white-tailed eagles in northern Norway, a stronghold for the species, affected a local population of 25,000 pairs of black-legged kittiwakes, a red-listed seabird, during a 42-year period ending with colony extinction. We use a natural experiment of two neighbouring colonies with/without eagle predation to disentangle the effects of eagles from local kittiwake foraging conditions (using size of young herring as a proxy). </span></p> <p><span>3. </span><span>At the colony where eagle predation occurred, and in contrast to the eagle-free colony, kittiwake breeding success and population size declined with increased eagle abundance, the latter more strongly under poor foraging conditions. Breeding success increased with foraging conditions at both colonies. </span></p> <p><span>4. </span><span>Simple population modelling shows that although conditions were insufficient to sustain the eagle-exposed colony, the increased abundance of eagles sped up its extirpation by many years.</span></p> <p><span>5. </span><span>Policy implications</span><span>. Our study shows that top-down effects from avian predators can be significant regulators of seabird populations, challenging their conservation where native, often protected, predators are rising. Such effects, and their possible interaction with other factors, must also be accounted for when using seabird demographic traits as environmental indicators and when developing more flexible and effective management and action plans. </span></p>
Post-translocation dynamics of black-tailed prairie dogs (Cynomys ludovicianus): A successful conservation and human-wildlife conflict mitigation tool
<p>Prairie dogs have declined by 98% throughout their range in the grasslands of North America. Translocations have been used as a conservation tool to reestablish colonies of this keystone species and to mitigate human-wildlife conflict. Understanding the behavioral responses of prairie dogs to translocation is of utmost importance to enhance the persistence of the species and for species that depend on them, including the critically endangered black-footed ferret. In 2017 and 2018, we translocated 658 black-tailed prairie dogs on the Lower Brule Indian Reservation in central South Dakota, USA, a black-footed ferret recovery site. Here, we describe and evaluate the effectiveness of translocating prairie dogs into augered burrows and soft released within presumed coteries to reestablish colonies in previously occupied habitat. We released prairie dogs implanted with passive integrated transponders (PIT tags) and conducted recapture events approximately 1-month and 1-year post-release. We hypothesized that these methods would result in a successful translocation and that prairie dogs released as coteries would remain close to where they were released because of their highly social structure. In support of these methods leading to a successful translocation, 69% of marked individuals were captured 1-month post-release, and 39% were captured 1-year post-release. Furthermore, considerable recruitment was observed with 495 unmarked juveniles captured during the 1-year post-release trapping event, and the reestablished colony had more than doubled in area by 2021. Contrary to our hypothesis, yet to our knowledge a novel finding, there was greater initial movement within the colony 1-month post-release than expected based on recapture locations compared to published average territory size; however, 1-year after release most recaptured individuals were captured within the expected territory size when compared to capture locations 1-month post-release. This research demonstrates that while translocating prairie dogs may be socially disruptive initially, it is an important conservation tool.</p>
Genomic diversity and differentiation between island and mainland populations of White‐tailed Eagles (Haliaeetus albicilla)
<p>Using whole genome shotgun sequences from 92 white-tailed eagles (<em>Haliaeetus albicilla</em>) sampled from Greenland, Iceland, Norway, Denmark, Estonia, and Turkey between 1885–1950 and after 1990, we investigate the genomic variation within countries over time, and between countries. Clear signatures of ancient biogeographic substructure across Europe and the North‐East Atlantic are observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110‐115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.</p>
Population cytogenetics of the spiny-tailed goanna
<p>Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting geneflow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, <em>Varanus acanthurus</em>. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at geneflow within and between populations with rearrangements. We found that geneflow was present between individuals with chromosome rearrangements within populations, but there was no geneflow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.</p>
Data from: Social disappointment and partner presence affect long-tailed macaque refusal behaviour in an "inequity aversion" experiment
<p><span>Protest in response to unequal reward distribution is thought to have played a central role in the evolution of human cooperation. Some animals refuse food and become demotivated when rewarded more poorly than a conspecific, and this has been taken as evidence that non-human animals, like humans, protest in the face of inequity. An alternative explanation - social disappointment – shifts the cause of this discontent away from the unequal reward, to the human experimenter who could – but elects not to – treat the subject well. This study investigates whether social disappointment could explain frustration behaviour in long-tailed macaques, <em>Macaca</em> <em>fascicularis</em>. We tested 12 monkeys in a novel `inequity aversion' paradigm. Subjects had to pull a lever and were rewarded with low-value food; in half of the trials, a partner worked alongside the subjects receiving high-value food. Rewards were distributed either by a human or a machine. In line with the social disappointment hypothesis, monkeys rewarded by the human refused food more often than monkeys rewarded by the machine. </span>Our study extends previous findings in chimpanzees and suggests that social disappointment plus social facilitation or food competition effects drive food refusal patterns.</p>
Sexual selection does not drive hindwing tail elaboration in a moon moth, Actias luna
<p>The most emblematic animal traits are often attributed to sexual selection. While this pressure is an important force, elaborated traits that have been driven solely by natural selection are less enumerated. Here, we test an elaborate trait that has been studied in an anti-predator context, but that remains unstudied for its role in mating. We gave female <em>Actias</em> <em>luna</em> (Saturniidae) moths a choice between two males of differing hindwing tail treatments. In our primary experiment, males with intact tails garnered more matings than males with tails removed, but this difference appears to result from damage incurred by tail removal. We verified this with a series of additional experiments: we created a tail/no-tail dyad where we removed tails from both males, then reglued tails to one and applied glue to the hindwings of the other. We found no difference in mating success. To ensure that this no-difference result was not due to the glue itself, we offered females two intact males, with glue added to the wings of one. This dyad also had equal mating success. We therefore find no evidence that tails play a role in sexual selection. These results, in combination with previous research on bat-moth battles using <em>A. luna</em>, leads us to conclude that hindwing tail elaboration was likely driven by natural selection alone. We suggest that future research testing multiple selective forces on animal traits is needed to reveal the prevalence of natural versus sexual selection as the primary force driving trait elaboration in diverse animal taxa.</p>
Tail-Wave-Assisted Positron Acceleration in Nonlinear Laser Plasma Wakefields
<p>The data and vector diagrams of the results of positron trapping and acceleration when the initial parameters are modified.</p>
Giant Tidal Tails of Helium Escaping the Hot Jupiter HAT-P-32 b
<p>This dataset contains materials presented in the paper ``Giant Tidal Tails of Helium Escaping the Hot Jupiter HAT-P-32 b'' (Zhang et al. 2023) accepted for publication by Science Advances. Please cite this paper and the Zenodo repository if these data are used in your work.</p> <p>Description of these files: </p> <ul> <li><strong>HPF_data.zip</strong> includes all 77 observed HPF spectral data of HAT-P-32 A+b.</li> <li><strong>HAT-P-32b_properties.csv</strong> includes our measured spectroscopic and physical properties of the planetary system. Columns of this file are explained in a README file <strong>README_HAT-P-32b_properties.dat</strong></li> <li><strong>3d_simulation_EW_vs_orbital_phase.dat</strong> includes the helium excess equivalent widths as a function of the planet's orbital phase, as predicted by our 3D hydrodynamic simulations</li> <li><strong>3d_simulation_orbital_phase_vs_helium_central_wavelength.dat</strong> includes the central wavelength of helium excess spectral feature (in the stellar restframe) as a function of the planet's orbital phase, as predicted by our 3D hydrodynamic simulations. </li> </ul>
Root trait values of 11 trees and shrubs grown on mine tailings
<ol> <li>Root traits play significant roles in plant resource-use strategies, and are good predictors of plant growth and survival. However, their predicting role in phytoremediation remains poorly understood and we know much less about the functional covariation of root traits with soil heavy metal (HM) contamination.</li> <li>The objective of this study was to assess the importance of root traits to predict phytoremediation services and to quantify biomass cost (BC) for HM accumulation in eleven woody species grown on a Pb-Zn mine tailing of Southeastern China. Sixteen traits associated with root morphological and chemical features, as well as HM accumulation characteristics, were measured to examine whether there is a RES under HM stressors and whether the covariation among root traits was related to individual or multiple heavy metal translocation and bioconcentration.</li> <li>Our findings provide evidence for a multidimensional RES including one main trend of 'slow-fast' strategy, and a trend representing a trade-off between root system size and root tissue density, indicating root proliferation strategy in a metal-contaminated soil. Another trade-off between root cadmium concentration and root dry matter content implied the existence of a presumable biomass cost for HM accumulation, which was proved to be constrained by RES.</li> <li>Root traits were good predictors of individual or multiple HM translocation and bioconcentration, and linked with phytoremediation services: roots with more acquisitive traits promote HM translocation, whilst conservative roots fostered bioconcentration.</li> <li>This study demonstrates that woody species grown on HM-contaminated soils exhibit different capacities for accumulating or translocating HMs depending on their root system shapes, and their position on the RES. Our results highlighted the importance of root size-related traits in the framework of RES when plants face unfavorable soil conditions and narrow the gap in trait-based ecology. We, for the first time, define and quantify the biomass cost for HM accumulation, providing a better understanding of the resource-allocation theory.</li> </ol>
Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence
<p>Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 Cterminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis.</p>
Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence
<p><sup>* </sup>To whom correspondence may be addressed: g.j.l.wuite@vu.nl<br> <sup># </sup>The first three authors should be regarded as joint first authors</p> <p><strong>Abstract</strong><br> Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 C-terminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis.</p> <p><strong>Data Set Description</strong><br> This data set contains the raw data and analysis code for the single-molecule study of the binding dynamics of T7 gp2.5 and its interactions with single-stranded DNA (ssDNA). The experiments utilized a custom-built setup combining dual optical trapping, confocal microscopy, and microfluidics.</p> <p><strong>Methodology</strong><br> The single-molecule experiments were performed at room temperature in a 5-channel microfluidic flow cell using a custom-built experimental setup that combines dual optical trapping, confocal microscopy, and microfluidics for single-molecule assays. Data analysis was conducted using Python, Origin, and MATLAB. Detailed methodology and instrument specifications are provided in the associated publication.</p> <p><strong>Data Set Structure</strong><br> - `Raw_Data/`: Contains raw data files in TDMS format.<br> - `Data_Analysis_Code/`: Contains the code used for data analysis and figure generation.</p> <p><strong>File Formats</strong><br> - Raw data files are in TDMS format.</p> <p><strong>Usage Notes</strong><br> Along with the raw data, we also provided the analysis code which generates the figures. Users should be aware of the required citations, license terms, and ethical considerations when using this data set.</p> <p><strong>Acknowledgments</strong><br> This work was financially supported by: ‘Crowd management: The physics of genome processing in complex environments’ of Stichting voor Fundamenteel Onderzoek der Materie, China Scholarship Council (funding No. 201704910912) and the European Union H2020 Marie-Sklowdowska Curie International Training Network AntiHelix, Grant Agreement n. 859853.</p> <p><strong>Author Contributions</strong><br> J.C-D., L X., M.T.J.H., and G.J.L.W. conceptualized the research; J.C-D., and L.X. collected data; I.H. built the combined optical trapping and confocal microscope instrument and developed the MATLAB code for the analysis of kymograph data; S.A.S. and A.v.O. provided purified wild type T7 gp2.5 and tested their biochemical activity; S-J L. provided purified gp2.5-Δ21C and tested their biochemical activity; L X. J.C-D., and M.T.J.H. analyzed the data; J.C-D., L X., M.T.J.H., and G.J.L.W. wrote the manuscript; G.J.L.W. supervised the project; the manuscript is read, revised and confirmed by all the<br> </p>
Spiny tails and clades: A fully sampled phylogeny of hoplocercine lizards (Iguanidae/Hoplocercinae) and its taxonomic and nomenclatural implications
<p>Hoplocercine lizards (<em>Enyalioides</em>, <em>Morunasaurus</em>, and <em>Hoplocercus</em>) form a clade of ca. 20 currently recognized species. The phylogenetic relationships among hoplocercine lizards, whose members exhibit striking differences in morphology (e.g., spiny vs. non-spiny tails), have not been clearly resolved by previous molecular phylogenetic studies. We generated a considerably larger dataset including 130 new DNA sequences from one mitochondrial and four nuclear loci for all named and two unnamed species of Hoplocercinae. We analyzed the data under concatenated maximum likelihood (RAxML) and Bayesian (MrBayes) as well as summary coalescent (ASTRAL) approaches. While our phylogenetic hypotheses strongly supported the monophyly of Hoplocercinae, neither <em>Enyalioides</em> nor <em>Morunasaurus</em> was supported as monophyletic. Instead, <em>M. groi </em>was inferred with strong support to form a clade with<em> E. heterolepis </em>and<em> E. laticep</em>s. This clade was in turn the sister taxon to other species of <em>Morunasaurus</em> (<em>M. annularis, M. peruvianus</em>). The remaining species of Enyalioides formed a separate clade with a basal split between western (3 species) and eastern (13 species) subclades. Tree topology tests rejected the monophyly of <em>Enyalioides</em> but failed to reject monophyly of <em>Morunasaurus</em>, suggesting that further study is needed to resolve its taxonomic status. Based on our results, we establish the converted clade names Hoplocercinae, <em>Hoplocercus</em>, <em>Enyalioides</em>, and <em>Morunasaurus</em>, as well as the new clade name <em>Zimiamviasaurus</em>. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.