keyword
https://read.qxmd.com/read/38496948/topological-characteristics-of-the-pore-network-in-the-tight-sandstone-using-persistent-homology
#1
JOURNAL ARTICLE
Wei Wang, Zhiyong Yan, Lina Wang, Shuang Xu
Tight sandstone reservoirs have become important areas for unconventional reservoir development, and their pore network is a key feature for identifying tight sandstone, which affects fluid migration path and reservoir development efficiency. However, the connectivity characteristics of the pore network at different scales have remained unclear owing to the numerous pores and uneven pore shape. Here, using pore size distributions from many hundreds of tight sandstone samples and subsequent topological data analysis, we construct the topological structure of the pore network in the Yanchang Formation tight sandstone of the Ordos Basin in China and visualize the topological characteristics of the pore network with distances...
March 12, 2024: ACS Omega
https://read.qxmd.com/read/38496800/%C3%AF-a-new-north-american-species-of-etainia-lepidoptera-nepticulidae-feeding-on-arbutus-and-arctostaphylos-species-ericaceae
#2
JOURNAL ARTICLE
Erik J van Nieukerken, Donald R Davis, Steven V Swain, Marc E Epstein
Etainiathoraceleuca van Nieukerken, Epstein & Davis, sp. nov. is the second native American species of Etainia Beirne, 1945, and the second known Etainia species feeding on Ericaceae. The species is known from light-collected adults in the USA (California, Arizona) and Canada (Ontario). These were linked via DNA barcodes to larvae that make short leafmines on Arbutus and Arctostaphylos species, then continue feeding in stems and branches, causing damage in nurseries and planted trees in Sonoma and Marin Counties, California...
2024: ZooKeys
https://read.qxmd.com/read/38496577/high-throughput-sequencing-based-neutralization-assay-reveals-how-repeated-vaccinations-impact-titers-to-recent-human-h1n1-influenza-strains
#3
Andrea N Loes, Rosario Araceli L Tarabi, John Huddleston, Lisa Touyon, Sook San Wong, Samuel M S Cheng, Nancy H L Leung, William W Hannon, Trevor Bedford, Sarah Cobey, Benjamin J Cowling, Jesse D Bloom
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing...
March 9, 2024: bioRxiv
https://read.qxmd.com/read/38496486/highly-multiplexed-design-of-an-allosteric-transcription-factor-to-sense-novel-ligands
#4
Kyle K Nishikawa, Jackie Chen, Justin F Acheson, Svetlana V Harbaugh, Phil Huss, Max Frenkel, Nathan Novy, Hailey R Sieren, Ella C Lodewyk, Daniel H Lee, Jorge L Chávez, Brian G Fox, Srivatsan Raman
Designing biosensors to detect novel molecules is important in biotechnology. Allosteric transcription factors (aTF), which are widely used as biosensors, have proven challenging to design because mutating ligand-binding residues often disrupt allostery. Moreover, existing screening methods lack the sensitivity to identify rare, functional variants amidst a large pool of non-functional designs. We introduce Sensor-seq, a platform for designing and screening aTF biosensors with non-native ligand specificity...
March 8, 2024: bioRxiv
https://read.qxmd.com/read/38496463/modeling-the-genomic-complexity-of-human-cancer-using-cas12a-mice
#5
Jess D Hebert, Haiqing Xu, Yuning J Tang, Paloma A Ruiz, Colin Detrick, Jing Wang, Nicholas W Hughes, Oscar Donosa, Laura Andrejka, Saswati Karmakar, Irenosen Aboiralor, Le Cong, Julien Sage, Dmitri A Petrov, Monte M Winslow
Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models have been restricted in their ability to create multiple targeted edits, which has limited investigations into complex genetic interactions that underlie development, homeostasis, and disease. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp...
March 8, 2024: bioRxiv
https://read.qxmd.com/read/38495438/single-cell-lineage-tracing-with-endogenous-markers
#6
REVIEW
Yan Xue, Zezhuo Su, Xinyi Lin, Mun Kay Ho, Ken H O Yu
Resolving lineage relationships between cells in an organism provides key insights into the fate of individual cells and drives a fundamental understanding of the process of development and disease. A recent rapid increase in experimental and computational advances for detecting naturally occurring somatic nuclear and mitochondrial mutation at single-cell resolution has expanded lineage tracing from model organisms to humans. This review discusses the advantages and challenges of experimental and computational techniques for cell lineage tracing using somatic mutation as endogenous DNA barcodes to decipher the relationships between cells during development and tumour evolution...
February 2024: Biophysical Reviews
https://read.qxmd.com/read/38495311/an-alien-intermediate-snail-host-in-malawi-orientogalba-viridis-quoy-and-gaimard-1832-a-new-concern-for-schistosomiasis-transmission-in-africa
#7
JOURNAL ARTICLE
A Juhász, C Nkolokosa, E Kambewa, S Jones, L J Cunningham, P Chammudzi, D Kapira, G Namacha, D Lally, S A Kayuni, P Makaula, J Musaya, J R Stothard
The freshwater amphibious snail Orientogalba viridis commonly occurs in eastern Asia, on certain Pacific islands and more importantly has recently dispersed into Europe. Since this snail is now considered an invasive species, its distribution is of growing parasitological interest as an alien intermediate host for various trematodes, particularly liver flukes. As part of ongoing surveillance for snail-borne diseases in Malawi, a population of O. viridis was first observed in May 2023, alongside an alarming presence of a human schistosome cercaria...
April 2024: International Journal for Parasitology. Parasites and Wildlife
https://read.qxmd.com/read/38494250/phylogenetic-and-genetic-variation-of-common-mudskippers-periophthalmus-kalolo-lesson-1831-from-the-southern-coast-of-java-indonesia-inferred-from-the-coi-mitochondrial-gene
#8
JOURNAL ARTICLE
Tuty Arisuryanti, Katon Waskito Aji, Faizah Nur Shabrina, Diana Febriyanti, Budi Setiadi Daryono, Dwi Sendi Priyono
BACKGROUND: The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java...
March 2024: Journal, Genetic Engineering & Biotechnology
https://read.qxmd.com/read/38493661/surveillance-and-screening-of-stomoxyinae-flies-from-mallorca-island-spain-reveal-the-absence-of-selected-pathogens-but-confirm-the-presence-of-the-endosymbiotic-bacterium-wolbachia-pipientis
#9
JOURNAL ARTICLE
Mikel A González, Ignacio Ruiz-Arrondo, Daniel Bravo-Barriga, Cristina Cervera-Acedo, Paula Santibáñez, José A Oteo, Miguel Á Miranda, Carlos Barceló
Adult brachycera biting flies can significantly impact livestock through both direct effects (reduction of food intake, disturbance, painful bites, and blood loss) and indirect effects (pathogen transmission), leading to substantial economic losses and production damage. This study aimed to assess the presence of blood-sucking flies in six mixed-animal farm environments on the island of Mallorca (Balearic Islands, Spain) by employing multiple trapping methods. Additionally, distribution maps of brachycera biting fly species recorded in Spain were created, based on data extracted thorough review of scientific literature and citizen digital databases...
March 8, 2024: Research in Veterinary Science
https://read.qxmd.com/read/38491512/ethnopharmacology-of-five-flowers-herbal-tea-a-popular-traditional-beverage-in-hong-kong-and-south-china
#10
JOURNAL ARTICLE
Kwun-Tin Chan, Hoi-Yan Wu, Wing-Yee Tin, Paul Pui-Hay But, Sidney Chin-Hung Cheung, Pang-Chui Shaw
BACKGROUND: It has been a long-standing tradition of using herbal tea for preventive and therapeutic healthcare in Hong Kong and South China and Five Flowers Tea is one of the most popular herbal teas. Based on the principle of traditional Chinese medicine, the pharmacological functions are to clear heat and dispel dampness in the body. Heat and dampness are thought to contribute to a range of health problems, especially during the hot and humid season in South China and Hong Kong. The most prevalent herbs in the formula contain bioactive compounds including flavonoids, alkaloids and terpenoids, which have a wide range of pharmacological properties including anti-inflammation, antivirus, antidiarrhoea, antibacteria, and antioxidation...
March 15, 2024: Journal of Ethnobiology and Ethnomedicine
https://read.qxmd.com/read/38491157/a-comprehensive-dna-barcoding-reference-database-for-plecoptera-of-switzerland
#11
JOURNAL ARTICLE
Laurent Vuataz, Jean-Paul Reding, Alexis Reding, Christian Roesti, Céline Stoffel, Gilles Vinçon, Jean-Luc Gattolliat
DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys...
March 15, 2024: Scientific Reports
https://read.qxmd.com/read/38489863/dna-melting-analysis
#12
REVIEW
Carl T Wittwer, Andrew C Hemmert, Jana O Kent, Nick A Rejali
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting...
March 14, 2024: Molecular Aspects of Medicine
https://read.qxmd.com/read/38489348/bayesian-inference-of-relative-fitness-on-high-throughput-pooled-competition-assays
#13
JOURNAL ARTICLE
Manuel Razo-Mejia, Madhav Mani, Dmitri Petrov
The tracking of lineage frequencies via DNA barcode sequencing enables the quantification of microbial fitness. However, experimental noise coming from biotic and abiotic sources complicates the computation of a reliable inference. We present a Bayesian pipeline to infer relative microbial fitness from high-throughput lineage tracking assays. Our model accounts for multiple sources of noise and propagates uncertainties throughout all parameters in a systematic way. Furthermore, using modern variational inference methods based on automatic differentiation, we are able to scale the inference to a large number of unique barcodes...
March 15, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38487668/%C3%AF-a-new-species-of-svistella-gorochov-1987-from-xizang-china-orthoptera-trigonidiidae-trigonidiinae
#14
JOURNAL ARTICLE
Jing-Wen Hou, Yue Xu, Tian-Hao Hu, Zi-Heng Zhang, Shi-Yang Wu, Pu Gong, Zhu-Qing He
The genus Svistella Gorochov, 1987 includes 10 species from Asia, with nine documented in China. In this study, a new species, Svistellayayun He, sp. nov. , is described from Xizang, China. Morphologically, it resembles S.rufonotata (Chopard, 1932) but can be distinguished by a smaller inner tympanum, dark-brown setae on the 5th segment of the maxillary palp, and a rounded apex on the ectoparamere. To validate our morphological inferences and support the description of S.yayun sp. nov. as a new species, we performed a PCA based on bioacoustics parameters and molecular analysis...
2024: ZooKeys
https://read.qxmd.com/read/38485107/machine-learning-approaches-delimit-cryptic-taxa-in-a-previously-intractable-species-complex
#15
JOURNAL ARTICLE
Haley L A Heine, Shahan Derkarabetian, Rina Morisawa, Phoebe A Fu, Nathaniel H W Moyes, Sarah L Boyer
Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs)...
March 12, 2024: Molecular Phylogenetics and Evolution
https://read.qxmd.com/read/38484921/transcriptional-landscape-of-human-keratinocyte-models-exposed-to-60-ghz-millimeter-waves
#16
JOURNAL ARTICLE
Catherine Martin, Bertrand Evrard, Frederic Percevault, Kate Ryder, Thomas Darde, Aurélie Lardenois, Maxim Zhadobov, Ronan Sauleau, Frédéric Chalmel, Yves Le Dréan, Denis Habauzit
The use of millimeter waves (MMW) will exponentially grow in the coming years due to their future utilization in 5G/6G networks. The question of possible biological effects at these frequencies has been raised. In this present study, we aimed to investigate gene expression changes under exposure to MMW using the Bulk RNA Barcoding and sequencing (BRB-seq) technology. To address this issue, three exposure scenarios were performed aiming at: i) comparing the cellular response of two primary culture of keratinocytes (HEK and NHEK) and one keratinocyte derivate cell line (HaCaT) exposed to MMW; ii) exploring the incident power density dose-effect on gene expression in HaCaT cell line; and, iii) studying the exposure duration at the new ICNIRP exposure limit for the general population...
March 12, 2024: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://read.qxmd.com/read/38484189/a-temporal-developmental-map-separates-human-nk-cells-from-non-cytotoxic-ilcs-through-clonal-and-single-cell-analysis
#17
JOURNAL ARTICLE
Dang Nghiem Vo, Ouyang Yuan, Minoru Kanaya, Gladys Telliam-Dushime, Hongzhe Li, Olga Kotova, Emel Caglar, Kristian Honnens de Lichtenberg, Shamim Herbert Rahman, Shamit Soneji, Stefan Scheding, David Bryder, Karl-Johan Malmberg, Ewa Sitnicka
Natural Killer (NK) cells represent the cytotoxic member within the innate lymphoid cell (ILC) family that are important against viral infections and cancer. While the NK cell emergence from hematopoietic stem and progenitor cells through multiple intermediate stages and the underlying regulatory gene network has been extensively studied in mouse, this process is not well characterized in human. Here, using a temporal in vitro model to reconstruct the developmental trajectory of NK lineage, we identified an ILC-restricted oligo-potent Stage 3a CD34-CD117+CD161+CD45RA+CD56- progenitor population, that exclusively gave rise to CD56-expressing ILCs in vitro...
March 14, 2024: Blood Advances
https://read.qxmd.com/read/38484036/antibacterial-activity-of-nonantibiotics-is-orthogonal-to-standard-antibiotics
#18
JOURNAL ARTICLE
Mariana Noto Guillen, Carmen Li, Brittany Rosener, Amir Mitchell
Numerous nonantibiotic drugs have potent antibacterial activity and can adversely impact the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules consistent with the mode of action of their established classes, while nonantibiotics remained unconnected...
March 14, 2024: Science
https://read.qxmd.com/read/38482159/-alcyonidium-kuklinskii-sp-nov-a-new-species-of-antarctic-ctenostome-bryozoan-with-a-key-to-all-antarctic-species-of-the-genus
#19
JOURNAL ARTICLE
Thomas Schwaha, Valentina Cometti, Ahmed J Saadi, Matteo Cecchetto, Stefano Schiaparelli
UNLABELLED: Recent surveys of Antarctic waters in the Terra Nova Bay (Ross Sea) revealed numerous bryozoan species including ctenostome bryozoans. Whereas cheilostome bryozoans are well-studied in these latitudes, ctenostomes remain highly neglected. Large ctenostomes are easily recognized by their lack of calcified skeletons, but this lack also renders them difficult and tedious to identify. As a result, histology and reconstructions of internal soft tissues are required to classify this group of bryozoans...
2024: Organisms, Diversity & Evolution
https://read.qxmd.com/read/38481855/the-inbio-barcoding-initiative-database-dna-barcodes-of-iberian-bees
#20
JOURNAL ARTICLE
Thomas James Wood, Hugo Gaspar, Romain Le Divelec, Andreia Penado, Teresa Luísa Silva, Vanessa A Mata, Joana Veríssimo, Denis Michez, Sílvia Castro, João Loureiro, Pedro Beja, Sónia Ferreira
BACKGROUND: Bees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing 514 Iberian species, was constructed. The "InBIO Barcoding Initiative Database: DNA Barcodes of Iberian bees" dataset contains records of 1,059 sequenced specimens...
2024: Biodiversity Data Journal
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