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opencc-by-4.0May 2024View details →

Conditioning, short-term and long-term memory tests of Drosophila melanogaster grown with and without predators

Conditioning (i.e., associative learning) and memory tests were performed following the methods of previous studies. We used samples of 10 adult flies (males only), raised in standard conditions and aged 6-7 days. The conditioning procedure consisted of 5 training sessions separated by 20-minute intervals (i.e., spaced protocol). During associative conditioning, flies were first exposed for 30 seconds (s) to one odorant simultaneously with a mechanical shock of 2000 rpm vibration pulses of 1 s duration, delivered every 5 s by a test tube shaker (Heidolph Instruments, Schwabach, Germany). This period was followed by a 60 s rest period (no odor and no shock). Then, for 30 s, another odorant was delivered without shock. The training session ended with a second rest period of 60 s. 3-octanol and 4-methylcyclohexanol (both 0.6 mL/L of paraffin) were used as odorants. Each fly group was chosen to be conditioned randomly to either 3-octanol or 4-methylcyclohexanol. The results of the final trial (the fifth out of 5 trials, referred to as the “conditioning” group hereafter) of associative conditioning were used to characterize the learning of fruit flies.  We tested 1 h (short-term memory, STM) and 24 h memory (LTM) retention after associative conditioning. During the memory retention assay, the flies walked to the choice point of a T-maze, in which they were exposed to two converging currents of air, one carrying 3-octanol and the other 4-methylcyclohexanol, and then allowed to choose between the two odors for 60 s. The memory score was calculated as the difference in the proportion of individuals choosing 3-octanol between flies conditioned to avoid 4-methylcyclohexanol and those conditioned to avoid 3-octanol.

opencc-by-4.0May 2024View details →

Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: a valuable addition to COVID-19 surveillance

Datasets used for the manuscript: Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: a valuable addition to COVID-19 surveillance pandemic_daily_passenger_counts.tsv: An overview of daily passenger arrival counts at Amsterdam Schiphol Airport per continent of origin during the study period 16-02-2020 - 04-09-2022 pre-pandemic_daily_passenger_averages.tsv: An overview of mean daily passenger arrival counts at Amsterdam Schiphol Airport in the pre-pandemic period 2017-2019. viral_load_data.tsv: Sample metadata (sample identifier, sampling date, flow, average # particles per ml, and flow-corrected viral-load) for samples taken at the wastewater treatment plant of Amsterdam Schiphol Airport. wastewater_variant_frequencies.tsv: SARS-CoV-2 lineage estimates in samples taken at the wastewater treatment plant of Amsterdam Schiphol Airport, analyzed using whole-genome tiled amplicon sequencing.

opencc-zeroMay 2024View details →

Data from: Tireless travellers: Sea turtles swim continuously during long-distance movements

While rest and sleep are crucial to animals, our understanding of whether and how long-distance migrants rest has been thwarted by the inability to relay high-resolution data from multi-channel loggers via satellite. We overcame these obstacles for an iconic long-distance migrator by equipping five loggerhead sea turtles (Caretta caretta) with satellite tags and data-loggers providing depth and 3-D acceleration measurements. Turtles were translocated to open-sea locations and induced to complete oceanic migrations of tens of km to return to their nesting beach performing active, oriented movements. Across a total of >600 hours of high-resolution data, we observed (i) constant flipper frequency (ca. 0.5 Hz) indicating that turtles never ceased movement, (ii) intense subsurface swimming (mostly around 1 m) for about 50% of time and (iii) deeper, less active dives up to 80 m, which were made day and night and more frequently in offshore waters. Flipper beat amplitude was much smaller in deep dives; hence the estimated energy expenditure was 37% lower on deep dives compared to subsurface swimming. These findings suggest that turtles, which can complete migrations of >2000 km, alternate between phases of intense near-surface swimming and periods of lower activity at depth, without fully resting during migration.

opencc-by-4.0Oct 2023View details →

Effect of long-term physical disability and aging on extracellular matrix biogenesis in human skeletal muscle

Supplemental Table for a study Effect of long-term physical disability and aging on extracellular matrix biogenesis in human skeletal muscle

Data from: Socio-ecological drivers of long-term ecosystem carbon stock trend: An assessment with the LUCCA model of the French case

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opencc-by-4.0Mar 2024View details →

Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing

Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has significant advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the cohort. We identified 20 distinct pathogenic variants, including three novel small variants and five somatic SVs. Furthermore, our analysis shows that the vast majority (93.8%) of RB1-disrupted patients fit the two-hit hypothesis through diverse types, including the biallelic hypermethylated promoter as well as small and large compound heterozygous mutations which were missing in SRS analysis. By constructing the evolutionary history of all genetic variants, we reveal the evolution trends that RB1 disruption early and followed by copy number changes, including amplifications of Chr2p, and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data.  We took IGV screenshots of SV and SNV/indels. The IGV naming conventions for SV is: sample name, chromosome 1, start, chromosome 2, end, SV type, SV length, SV breakpoint. The IGV naming convention for SNV/indels is: sample name, chromosome, position, reference allele, alternate allele.

opencc-zeroJun 2024View details →

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subjected to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12 to 171), the population has been able to maintain high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest underpinning the island adders' ability to maintain a high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

opencc-zeroJun 2024View details →

Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments

Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species-level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ('mitoenrichment'). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA ('targeted mitosequencing'). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38 to 2123-fold mean coverage. This produced complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible and can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.

opencc-by-4.0Jul 2024View details →

Long-term triaxial testing of Opalinus Clay, P-orientation, sandy facies

This data set describes a long-term (> 4 yr) rock mechanics experiment of Opalinus Clay (sandy facies) using a triaxial apparatus. The sample is consolidated and fully saturated. The bedding orientation is parallel to the main axis of the sample (P-orientation). Confining stress, axial stress and pore pressure are changed multiple times in order to investigate dilatancy, pressure diffusion coefficients and Young's modulus.

opencc-zeroJul 2024View details →

Long-term data reveal fitness costs of anthropogenic prey depletion for a subordinate competitor, the African wild dog (Lycaon pictus

Within carnivore guilds, dominant competitors (e.g., lions, Panthera leo) are limited primarily by the density of prey, while subordinate competitors (e.g., African wild dogs, Lycaon pictus) have been limited by the density of dominant competitors. Historically, the fitness and population density of subordinate competitors have not been tightly linked to prey density. However, populations of large herbivores have declined substantially across sub-Saharan Africa due to human impacts, and where prey depletion is severe, fitness costs for competitive subordinates may begin to outweigh the benefits of competitive release. Using long-term intensive monitoring of African wild dogs in Zambia's Luangwa Valley Ecosystem (LVE), we tested the effects of prey depletion on survival and reproduction. Our study area included four contiguous regions that varied in protection, prey density, and lion density. We fit Bayesian Cormack-Jolly-Seber and closed-capture models to estimate effects on survival and population density, and generalized linear models to estimate effects on reproductive success. We found that the LVE is a stronghold for wild dogs, with an estimated median density of 4.0 individuals/100 km2. Despite this high density, survival and reproduction differed among regions, and both components of fitness were substantially reduced in the region with the lowest prey density. Anthropogenic prey depletion is becoming an important limiting factor for African wild dogs. If prey depletion (or any other form of habitat degradation) becomes severe enough that its fitness costs outweigh the benefits of competitive release, such changes can fundamentally alter the balance between limiting factors for competitively subordinate species.

opencc-zeroJul 2024View details →

Long-term ecological studies' practices and goals for trainees

We created a survey for the other authors in the 2024 Ecology Letters special issue on very long-term ecological studies about their practices and goals for trainees. We received 27 responses from researchers around the world studying a broad range of organisms across ecosystems. In more than half of the responding programs, undergraduate students collect, curate, and analyze data, as well as develop research questions, present at conferences, and contribute to writing scientific papers. Unlike our program, which primarily recruits from one university, other long-term studies often target a variety of institutions (79% of respondents). About half reported targeted recruitment of students from marginalized identities and a similar proportion paid students for their work. Students were slightly more likely to collaborate with a cohort of other students (3.8 in 1-5 Likert scale) and have peer cohort building activities (3.6 in 1-5 Likert scale). When asked to rank the helpful characteristics of long-term studies to undergraduate students, top choices included "links between research, internship, classes", "extensive professional networks", "rich data", and "robust logistics". The rank of "paid salaries" was split, with about a third of the programs ranking it least helpful to students but the other third of programs ranking it either as the first or second most helpful attribute of long-term programs. Based on comments related to funding, the low salary ranking might be associated with student funding opportunities available through university grants or independent fellowships. Overall, this suggests the most impactful transformation long-term studies can make is to advocate for paying trainees in future grant proposals.

Fig. 10 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 10. Pelargoderus rubropunctatus (GuerinMeneville, 1833).

Fig. 8. Eupromus ruber Dalman, 1817 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 8. Eupromus ruber Dalman, 1817

Fig. 7. Eupromus laosensis Breuning, 1968 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 7. Eupromus laosensis Breuning, 1968

Fig. 5 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 5. Dolichoprosopus lethalis (Pascoe, 1866)

Fig. 1. Cornuscoparia annulicornis Heller, 1897 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 1. Cornuscoparia annulicornis Heller, 1897

Fig. 2. Cornuscoparia barsevskisi Votsekhovskii, 2020 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 2. Cornuscoparia barsevskisi Votsekhovskii, 2020

Fig. 4 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 4. Cornuscoparia schlaginhaufeni (Heller, 1910)

Fig. 9. Thermonotus pasteuri Ritsema, 1890 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 9. Thermonotus pasteuri Ritsema, 1890.

Fig. 12 in To The Knowledge Of Long-Horned Beetles (Coleoptera: Cerambycidae) Of The Oriental Region. Part 3.

Fig. 12. Pseudonemophas versteegi (Ritsema, 1881).