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BMJ (Clinical Research Ed.) May 2024
PubMed: 38806186
DOI: 10.1136/bmj.q1149 -
BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Social Media; Smartphone; Adolescent; Mental Health; Mental Disorders; Adolescent Health
PubMed: 38806185
DOI: 10.1136/bmj-2024-079828 -
PloS One 2024Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and...
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
Topics: Plasmids; Genetic Engineering; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Mutation; Base Sequence; Sequence Analysis, DNA
PubMed: 38805426
DOI: 10.1371/journal.pone.0304164 -
Astrobiology Jun 2024Geological evidence and atmospheric and climate models suggest habitable conditions occurred on early Mars, including in a lake in Gale crater. Instruments aboard the...
Geological evidence and atmospheric and climate models suggest habitable conditions occurred on early Mars, including in a lake in Gale crater. Instruments aboard the Curiosity rover measured organic compounds of unknown provenance in sedimentary mudstones at Gale crater. Additionally, Curiosity measured nitrates in Gale crater sediments, which suggests that nitrate-dependent Fe oxidation (NDFO) may have been a viable metabolism for putative martian life. Here, we perform the first quantitative assessment of an NDFO community that could have existed in an ancient Gale crater lake and quantify the long-term preservation of biological necromass in lakebed mudstones. We find that an NDFO community would have the capacity to produce cell concentrations of up to 10 cells mL, which is comparable to microbes in Earth's oceans. However, only a concentration of <10 cells mL, due to organisms that inefficiently consume less than 10% of precipitating nitrate, would be consistent with the abundance of organics found at Gale. We also find that meteoritic sources of organics would likely be insufficient as a sole source for the Gale crater organics, which would require a separate source, such as abiotic hydrothermal or atmospheric production or possibly biological production from a slowly turning over chemotrophic community.
Topics: Mars; Nitrates; Oxidation-Reduction; Iron; Extraterrestrial Environment; Geologic Sediments; Exobiology; Organic Chemicals; Lakes
PubMed: 38805190
DOI: 10.1089/ast.2023.0109 -
Plants (Basel, Switzerland) May 2024The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative...
The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative field trial in Central Italy, including provenances from Spain, Italy, and Greece, was screened for ACGW infestation over consecutive years. The Greek provenance Hortiatis expressed a high proportion of immune plants and was used to perform a genome-wide association study based on DNA pool sequencing (Pool-GWAS) by comparing two DNA pools from 25 susceptible and 25 resistant plants. DNA pools were sequenced with 50X coverage depth. Sequence reads were aligned to a reference genome and the pools were compared to identify SNPs associated with resistance. Twenty-one significant SNPs were identified and highlighted a small genomic region on pseudochromosome 3 (Chr 3), containing 12 candidate genes of three gene families: , , and . Functional analyses revealed a putative metabolic gene cluster related to saccharide biosynthesis in the genomic regions associated with resistance that could be involved in the production of a toxic metabolite against parasites. The comparison with previous genetic studies confirmed the involvement of Chr 3 in the control of resistance to ACGW.
PubMed: 38794426
DOI: 10.3390/plants13101355 -
PloS One 2024The exchange of information and social interactions on broad spatial scales between human groups in the past can be studied through the provenance of key indicators of...
Middle through late Holocene long-distance transport of exotic shell personal adornments in Central West Patagonia (southern South America). The archaeomalacological assemblage of Baño Nuevo 1.
The exchange of information and social interactions on broad spatial scales between human groups in the past can be studied through the provenance of key indicators of distant origin recorded at archaeological sites. The remains of shells of mollusk species, especially when crafted as elements of personal ornaments, express aspects of the behaviors and valuations for the populations that selected, transformed, and exchanged such items. In the southern cone of South America, past hunter-gatherer groups traveled long distances and interacted with communities distributed throughout the territory to acquire goods for technological use, visual display or considered highly valued materials. When recorded at distant locations, these goods of extra local origin are very informative regarding the differences between commonly used home ranges and the occasional access to remote spaces. We present the results of the analysis of the archaeomalacological assemblage of the Baño Nuevo 1 site, a cave with exceptional preservation conditions in Central West Patagonia. This site has yielded a diverse group of artifacts made of shells with origins from multiple distances, as well as evidence of the use of marine, freshwater, and terrestrial species. Its deposits, which extend over the last 11,000 years, reveal an antiquity of at least the middle Holocene for the acquisition, manufacture, use and transport of goods as personal ornaments from shells in the macroregion.
Topics: Archaeology; Humans; Animals; History, Ancient; Animal Shells; South America; Caves; Fossils; Argentina
PubMed: 38787897
DOI: 10.1371/journal.pone.0304454 -
Journal of Human Evolution Jun 2024The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of...
The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of the right and left parietal and left and right parts of the frontal bone. The fossil was assumed to belong to the Homo erectus s.l. hypodigm by some authors, whereas others see similarities with Middle Pleistocene fossils (Broken Hill 1/Kabwe, Bodo, or Ceprano). Here, we present the first attempt to make a complete reconstruction of the missing medial portion of the frontal bone and a comprehensive geometric morphometric analysis of this bone. We restored the calotte by aligning and mirroring the three preserved fragments. Afterward, we restored the missing portion by applying the thin-plate spline interpolation algorithm of target fossils onto the reconstructed Kocabaş specimen. For the geometric morphometric analyses, we collected 80 landmarks on the frontal bone (11 osteometric points, 14 bilateral curve semilandmarks, and 41 surface semilandmarks). The comparative sample includes 21 fossils from different chronological periods and geographical areas and 30 adult modern humans from different populations. Shape analyses highlighted the presence in Kocabaş of features usually related to Middle Pleistocene Homo, such as a developed supraorbital torus associated with a relatively short frontal squama and reduced post-toral sulcus. Cluster analysis and linear discriminant analysis classification procedure suggest Kocabaş being part of the same taxonomic unit of Eurasian and African Middle Pleistocene Homo. In light of our results, we consider that attributing the Kocabaş hominin to H. erectus s.l. may be unwarranted. Results of our analyses are compatible with different evolutionary scenarios, but a more precise chronological framework is needed for a thorough discussion of the evolutionary significance of this specimen. Future work should clarify its geological age, given uncertainties regarding its stratigraphic provenance.
Topics: Fossils; Hominidae; Animals; Turkey; Biological Evolution; Frontal Bone
PubMed: 38781712
DOI: 10.1016/j.jhevol.2024.103517 -
ENeuro Jun 2024Scientific research demands reproducibility and transparency, particularly in data-intensive fields like electrophysiology. Electrophysiology data are typically analyzed...
Scientific research demands reproducibility and transparency, particularly in data-intensive fields like electrophysiology. Electrophysiology data are typically analyzed using scripts that generate output files, including figures. Handling these results poses several challenges due to the complexity and iterative nature of the analysis process. These stem from the difficulty to discern the analysis steps, parameters, and data flow from the results, making knowledge transfer and findability challenging in collaborative settings. Provenance information tracks data lineage and processes applied to it, and provenance capture during the execution of an analysis script can address those challenges. We present Alpaca (Automated Lightweight Provenance Capture), a tool that captures fine-grained provenance information with minimal user intervention when running data analysis pipelines implemented in Python scripts. Alpaca records inputs, outputs, and function parameters and structures information according to the W3C PROV standard. We demonstrate the tool using a realistic use case involving multichannel local field potential recordings of a neurophysiological experiment, highlighting how the tool makes result details known in a standardized manner in order to address the challenges of the analysis process. Ultimately, using Alpaca will help to represent results according to the FAIR principles, which will improve research reproducibility and facilitate sharing the results of data analyses.
Topics: Animals; Electrophysiology; Electrophysiological Phenomena; Information Dissemination; Software; Humans; Data Analysis
PubMed: 38777610
DOI: 10.1523/ENEURO.0476-23.2024 -
Systematic and Applied Microbiology May 2024Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise...
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov.
Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 and Flavobacterium bizetiae, 99.0 % for strain F-65 and Flavobacterium branchiarum, 98.7 % for strain F-126 and Flavobacterium tructae, 98.2 % for strain F-323 and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 shared 100 % identical 16S rRNA genes, while strains F-323 and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 , F-65 , F-70 , F126 and F-323 represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 (=JCM 34194 = KCTC 82254 ), Flavobacterium pisciphilum sp. nov. F-65 (=JCM 34197 = KCTC 82257 ), Flavobacterium flavipigmentatum sp. nov. F-70 (Fl-33 = Fl-77 = JCM 34198 = KCTC 82258 ), Flavobacterium lipolyticum sp. nov. F-126 (JCM 34199 = KCTC 82259 ) and Flavobacterium cupriresistens sp. nov. F-323 (Fl-318 = JCM 34200 = KCTC 82260 ), are proposed.
PubMed: 38761464
DOI: 10.1016/j.syapm.2024.126518 -
The Science of the Total Environment Jul 2024Although seaweeds rank among the most productive vegetated habitats globally, their inclusion within Blue Carbon frameworks is at its onset, partially because they...
Although seaweeds rank among the most productive vegetated habitats globally, their inclusion within Blue Carbon frameworks is at its onset, partially because they usually grow in rocky substrates and their organic carbon (C) is mostly exported and stored beyond their habitat and thus, demonstrating its long-term storage is challenging. Here, we studied the sedimentary C storage in macroalgal forests dominated by Gongolaria barbata and in adjacent seagrass Cymodocea nodosa mixed with Caulerpa prolifera algae meadows, and bare sand habitats in Mediterranean shallow coastal embayments. We characterized the biogeochemistry of top 30 cm sedimentary deposits, including sediment grain-size, organic matter and C contents, C burial rates and the provenance of sedimentary C throughout stable carbon isotopes (δC) and pyrolysis analyses. Sediment C stocks and burial rates (since 1950) in G. barbata forests (mean ± SE, 3.5 ± 0.2 kg C m accumulated at 15.5 ± 1.6 g C m y) fall within the range of those reported for traditional Blue Carbon Ecosystems. Although the main species contributing to sedimentary C stocks in all vegetated habitats examined was C. nodosa (36 ± 2 %), macroalgae contributed 49 % (19 ± 2 % by G. barbata and 30 ± 3 % by C. prolifera) based on isotope mixing model results. Analytical pyrolysis confirmed the presence of macroalgae-derived compounds in the sediments, including N-compounds and α-tocopherol linked to G. barbata and C. prolifera, respectively. The sedimentary C burial rate linked to macroalgae within the macroalgal forests examined ranged from 5.4 to 9.5 g C m y (7.4 ± 2 g C m y). This study provides empirical evidence for the long-term (∼70 years) sequestration of macroalgae-derived C within and beyond seaweed forests in Mediterranean shallow coastal embayments and thereby, supports the inclusion of macroalgae in Blue Carbon frameworks.
Topics: Seaweed; Forests; Carbon Sequestration; Carbon; Mediterranean Sea; Environmental Monitoring; Ecosystem; Geologic Sediments
PubMed: 38750738
DOI: 10.1016/j.scitotenv.2024.173219