keyword
https://read.qxmd.com/read/38543771/-xanthomonas-phage-pbr31-classifying-the-unclassifiable
#1
JOURNAL ARTICLE
Rashit I Tarakanov, Peter V Evseev, Ha T N Vo, Konstantin S Troshin, Daria I Gutnik, Aleksandr N Ignatov, Stepan V Toshchakov, Konstantin A Miroshnikov, Ibrahim H Jafarov, Fevzi S-U Dzhalilov
The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis and, especially, the taxonomic description of bacteriophages are often difficult due to the peculiarities of the evolution of bacteriophages, which often includes the horizontal transfer of genes and genomic modules. The latter is particularly pronounced for temperate bacteriophages, which are capable of integration into the bacterial chromosome...
March 6, 2024: Viruses
https://read.qxmd.com/read/38538616/raman-time-delay-in-attosecond-transient-absorption-of-strong-field-created-krypton-vacancy
#2
JOURNAL ARTICLE
Li Wang, Guangru Bai, Xiaowei Wang, Jing Zhao, Cheng Gao, Jiacan Wang, Fan Xiao, Wenkai Tao, Pan Song, Qianyu Qiu, Jinlei Liu, Zengxiu Zhao
Strong field ionization injects a transient vacancy in the atom which is entangled to the outgoing photoelectron. When the electron is finally detached, the ion is populated at different excited states with part of coherence information lost. The preserved coherence of matter after interacting with intense short pulses has important consequences on the subsequent nonequilibrium evolution and energy relaxation. Here we employ attosecond transient absorption spectroscopy to measure the time-delay of resonant transitions of krypton vacancy during their creation...
March 27, 2024: Nature Communications
https://read.qxmd.com/read/38538194/does-intensity-matter-a-randomized-crossover-study-of-the-role-of-acute-exercise-intensity-on-cognitive-performance-and-motor-speed-and-accuracy
#3
JOURNAL ARTICLE
Michael J Larson, Alexandra M Muir, Reilly O Reid, Kaylie A Carbine, Harrison Marsh, Hunter LaCouture, Chance McCutcheon, Bruce W Bailey
There is a well-recognized, yet nuanced, positive relationship between acute physical activity and cognitive function. However, the precise impact of exercise intensity remains ambiguous. We tested learning and memory, working memory and processing speed, and motor speed and accuracy across three distinct exercise intensities. A sample of 207 participants (100 female) between 18 and 44 years (mean age: 22.5±3.7years) completed all study procedures. Utilizing a within-subjects, cross-over design, participants completed moderate (35% VO2 Max), vigorous (70% VO2 Max), and sedentary (no exercise) conditions...
2024: Progress in Brain Research
https://read.qxmd.com/read/38527900/navigating-the-landscapes-of-spatial-transcriptomics-how-computational-methods-guide-the-way
#4
REVIEW
Runze Li, Xu Chen, Xuerui Yang
Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining...
2024: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/38527443/translating-the-timing-of-developmental-benchmarks-in-short-tailed-opossums-monodelphis-domestica-to-facilitate-comparisons-with-commonly-used-rodent-models
#5
JOURNAL ARTICLE
Chris Bresee, Jules Litman-Cleper, Cindy J Clayton, Leah Krubitzer
INTRODUCTION: The gray short-tailed opossum, Monodelhis domestica (M. domestica) is a widely used marsupial model species that presents unique advantages for neurodevelopmental studies. Notably their extremely altricial birth allows manipulation of postnatal pups at timepoints equivalent to embryonic stages of placental mammals. A robust literature exists on the development of short-tailed opossums, but many researchers working in the more conventional model species of mice and rats may find it daunting to identify the appropriate age at which to conduct experiments...
March 25, 2024: Brain, Behavior and Evolution
https://read.qxmd.com/read/38526948/phosphorylation-disorder-and-phase-separation-govern-the-behavior-of-frequency-in-the-fungal-circadian-clock
#6
JOURNAL ARTICLE
Daniyal Tariq, Nicole Maurici, Bradley M Bartholomai, Siddarth Chandrasekaran, Jay C Dunlap, Alaji Bah, Brian R Crane
Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms of gene expression to the diurnal cycle. In the filamentous fungus Neurospora crassa, the proteins F requency ( F RQ), the F RQ-interacting RNA helicase (FRH), and C asein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the white-collar complex (WCC). FRQ orchestrates key molecular interactions of the clock despite containing little predicted tertiary structure. Spin labeling and pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into the 989-residue intrinsically disordered FRQ and the FFC...
March 25, 2024: ELife
https://read.qxmd.com/read/38526535/repulsive-sema3e-plexin-d1-signaling-coordinates-both-axonal-extension-and-steering-via-activating-an-autoregulatory-factor-mtss1
#7
JOURNAL ARTICLE
Namsuk Kim, Yan Li, Ri Yu, Hyo-Shin Kwon, Anji Song, Mi-Hee Jun, Jin-Young Jeong, Ji Hyun Lee, Hyun-Ho Lim, Mi-Jin Kim, Jung-Woong Kim, Won-Jong Oh
Axon guidance molecules are critical for neuronal pathfinding because they regulate directionality and growth pace during nervous system development. However, the molecular mechanisms coordinating proper axonal extension and turning are poorly understood. Here, Metastasis Suppressor 1 (Mtss1), a membrane protrusion protein, ensured axonal extension while sensitizing axons to the Semaphorin 3E (Sema3E)-Plexin-D1 repulsive cue. Sema3E-Plexin-D1 signaling enhanced Mtss1 expression in projecting striatonigral neurons...
March 25, 2024: ELife
https://read.qxmd.com/read/38526072/applications-of-liquid-chromatography-tandem-mass-spectrometry-in-natural-products-research-tropane-alkaloids-as-a-case-study
#8
JOURNAL ARTICLE
Maris A Cinelli, Jill Cline, Tyler Watson
Although many drugs utilized today are synthetic in origin, natural products still provide a rich source of novel chemical diversity and bioactivity, and can yield promising leads for resistant or emerging diseases. The challenge, however, is twofold: not only must researchers find natural products and elucidate their structures, but they must also identify what is worth isolating and assaying (and what is already known - a process known as dereplication). With the advent of modern analytical instrumentation, the pace of natural product discovery and dereplication has accelerated...
March 8, 2024: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/38518155/efficacy-of-botulinum-toxin-in-the-treatment-of-facial-and-cervical-hypertrophic-scar-a-meta-analysis
#9
JOURNAL ARTICLE
Dong Yin, Mingfan Xi, Lifan Jiang, Mingqiu Du, Jun Qi
OBJECTIVE: Maxillofacial-neck hyperplastic scars have long been a persistent concern among individuals in both Western and Eastern countries. These scars exhibit rapid growth within 3-6 months following wound healing, subsequently receding at a slower pace, leading to skin redness, tension, and potential itching. The lack of comprehensive understanding regarding the formation mechanism and biological attributes of these scars has made them a prominent subject of research both domestically and internationally...
March 22, 2024: Alternative Therapies in Health and Medicine
https://read.qxmd.com/read/38518085/association-of-plasma-n-3-polyunsaturated-fatty-acid-levels-and-the-prevalence-of-frailty-in-older-adults-a-cross-sectional-analysis-of-uk-biobank
#10
JOURNAL ARTICLE
Junghyun Kim, Jason Westra, Nathan Tintle, William S Harris, Yongsoon Park
BACKGROUND: Circulating levels of n-3 polyunsaturated fatty acids (PUFAs) have been associated with frailty among Koreans (a population with a high intake of fish), but whether this association exists in Western populations with low fish intake is unknown. The present study examined the hypothesis that the prevalence of frailty was inversely associated with plasma levels of n-3 PUFAs, with the intake of oily fish, and with fish oil supplementation in older adults in the UK. METHODS: UK Biobank including 79,330 adults aged ≥ 65 years with dietary data, and 18,802 participants with plasma fatty acid data were used...
March 22, 2024: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://read.qxmd.com/read/38515765/potential-sources-of-time-lags-in-calibrating-species-distribution-models
#11
JOURNAL ARTICLE
Franz Essl, Adrián García-Rodríguez, Bernd Lenzner, Jake M Alexander, César Capinha, Pierre Gaüzère, Antoine Guisan, Ingolf Kühn, Jonathan Lenoir, David M Richardson, Sabine B Rumpf, Jens-Christian Svenning, Wilfried Thuiller, Damaris Zurell, Stefan Dullinger
The Anthropocene is characterized by a rapid pace of environmental change and is causing a multitude of biotic responses, including those that affect the spatial distribution of species. Lagged responses are frequent and species distributions and assemblages are consequently pushed into a disequilibrium state. How the characteristics of environmental change-for example, gradual 'press' disturbances such as rising temperatures due to climate change versus infrequent 'pulse' disturbances such as extreme events-affect the magnitude of responses and the relaxation times of biota has been insufficiently explored...
January 2024: Journal of Biogeography
https://read.qxmd.com/read/38509146/utilizing-epigenetics-to-study-the-shared-nature-of-development-and-biological-aging-across-the-lifespan
#12
REVIEW
Laurel Raffington
Recently, biological aging has been quantified in DNA-methylation samples of older adults and applied as so-called "methylation profile scores" (MPSs) in separate target samples, including samples of children. This nascent research indicates that (1) biological aging can be quantified early in the life course, decades before the onset of aging-related disease, (2) is affected by common environmental predictors of childhood development, and (3) shows overlap with "developmental processes" (e.g., puberty). Because the MPSs were computed using algorithms developed in adults, these studies indicate a molecular link between childhood environments, development, and adult biological aging...
March 21, 2024: NPJ Science of Learning
https://read.qxmd.com/read/38507255/metabolic-profiling-of-aortic-stenosis-and-hypertrophic-cardiomyopathy-identifies-mechanistic-contrasts-in-substrate-utilization
#13
JOURNAL ARTICLE
Nikhil Pal, Animesh Acharjee, Zsuzsanna Ament, Tim Dent, Arash Yavari, Masliza Mahmod, Rina Ariga, James West, Violetta Steeples, Mark Cassar, Neil J Howell, Helen Lockstone, Kate Elliott, Parisa Yavari, William Briggs, Michael Frenneaux, Bernard Prendergast, Jeremy S Dwight, Rajesh Kharbanda, Hugh Watkins, Houman Ashrafian, Julian L Griffin
Aortic stenosis (AS) and hypertrophic cardiomyopathy (HCM) are distinct disorders leading to left ventricular hypertrophy (LVH), but whether cardiac metabolism substantially differs between these in humans remains to be elucidated. We undertook an invasive (aortic root, coronary sinus) metabolic profiling in patients with severe AS and HCM in comparison with non-LVH controls to investigate cardiac fuel selection and metabolic remodeling. These patients were assessed under different physiological states (at rest, during stress induced by pacing)...
March 31, 2024: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://read.qxmd.com/read/38503508/how-does-selfing-affect-the-pace-and-process-of-speciation
#14
JOURNAL ARTICLE
Lucas Marie-Orleach, Sylvain Glémin, Marie K Brandrud, Anne K Brysting, Abel Gizaw, A Lovisa S Gustafsson, Loren H Rieseberg, Christian Brochmann, Siri Birkeland
Surprisingly little attention has been given to the impact of selfing on speciation, even though selfing reduces gene flow between populations and affects other key population genetics parameters. Here we review recent theoretical work and compile empirical data from crossing experiments and genomic and phylogenetic studies to assess the effect of mating systems on the speciation process. In accordance with theoretical predictions, we find that accumulation of hybrid incompatibilities seems to be accelerated in selfers, but there is so far limited empirical support for a predicted bias toward underdominant loci...
March 19, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38502013/-the-self-identity-of-psychiatry-in-the-21st-century
#15
JOURNAL ARTICLE
László Tringer
The relationship of mentally ill patients and the relational society has constantly changed during the course of history. The changes are true reflexions of the given society. In the management of behaviours disturbing community life medical treatment, law enforcement and religious measures change periodically, sometimes one, sometimes the other comes to the fore. One of the most influential spiritual currents of the 20th century has been the dismantling of large institutions, called deinstitutionalisation, which process could be experienced by the currently active professional generations...
2024: Psychiatria Hungarica: A Magyar Pszichiátriai Társaság Tudományos Folyóirata
https://read.qxmd.com/read/38500272/boltzmann-s-theorem-revisited-inaccurate-time-to-action-clocks-in-affective-disorders
#16
JOURNAL ARTICLE
Sari Goldstein Ferber, Aron Weller, Hermona Soreq
Timely goal-oriented behavior is essential for survival and is shaped by experience. In this paper, a multileveled approach was employed, ranging from the polymorphic level through thermodynamic molecular, cellular, intracellular, extracellular, non-neuronal organelles and electrophysiological waves, attesting for signal variability. By adopting Boltzmann's theorem as a thermodynamic conceptualization of brain work, we found deviations from excitation-inhibition balance and wave decoupling, leading to wider signal variability in affective disorders compared to healthy individuals...
March 18, 2024: Current Neuropharmacology
https://read.qxmd.com/read/38497525/wetness-severity-increases-abrupt-shifts-in-ecosystem-functioning-in-arid-savannas
#17
JOURNAL ARTICLE
L M Vermeulen, B Verbist, K Van Meerbeek, J Slingsby, P N Bernardino, B Somers
The accelerating pace of climate change has led to unprecedented shifts in surface temperature and precipitation patterns worldwide, with African savannas being among the most vulnerable regions. Understanding the impacts of these extreme changes on ecosystem health, functioning and stability is crucial. This paper focuses on the detection of breakpoints, indicative of shifts in ecosystem functioning, while also determining relevant ecosystem characteristics and climatic drivers that increase susceptibility to these shifts within the semi-arid to arid savanna biome...
March 2024: Global Change Biology
https://read.qxmd.com/read/38497258/a-new-lexicon-in-the-age-of-microbiome-research
#18
REVIEW
Thomas C G Bosch, Martin J Blaser, Edward Ruby, Margaret McFall-Ngai
At a rapid pace, biologists are learning the many ways in which resident microbes influence, and sometimes even control, their hosts to shape both health and disease. Understanding the biochemistry behind these interactions promises to reveal completely novel and targeted ways of counteracting disease processes. However, in our protocols and publications, we continue to describe these new results using a language that originated in a completely different context. This language developed when microbial interactions with hosts were perceived to be primarily pathogenic, as threats that had to be vanquished...
May 6, 2024: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://read.qxmd.com/read/38496213/julearn-an-easy-to-use-library-for-leakage-free-evaluation-and-inspection-of-ml-models
#19
JOURNAL ARTICLE
Sami Hamdan, Shammi More, Leonard Sasse, Vera Komeyer, Kaustubh R Patil, Federico Raimondo
The fast-paced development of machine learning (ML) and its increasing adoption in research challenge researchers without extensive training in ML. In neuroscience, ML can help understand brain-behavior relationships, diagnose diseases and develop biomarkers using data from sources like magnetic resonance imaging and electroencephalography. Primarily, ML builds models to make accurate predictions on unseen data. Researchers evaluate models' performance and generalizability using techniques such as cross-validation (CV)...
2024: GigaByte
https://read.qxmd.com/read/38482631/dna-methylation-clocks-for-estimating-biological-age-in-chinese-cohorts
#20
JOURNAL ARTICLE
Zikai Zheng, Jiaming Li, Tianzi Liu, Yanling Fan, Qiao-Cheng Zhai, Muzhao Xiong, Qiao-Ran Wang, Xiaoyan Sun, Qi-Wen Zheng, Shanshan Che, Beier Jiang, Quan Zheng, Cui Wang, Lixiao Liu, Jiale Ping, Si Wang, Dan-Dan Gao, Jinlin Ye, Kuan Yang, Yuesheng Zuo, Shuai Ma, Yun-Gui Yang, Jing Qu, Feng Zhang, Peilin Jia, Guang-Hui Liu, Weiqi Zhang
Epigenetic clocks are accurate predictors of human chronological age based on the analysis of DNA methylation at specific CpG sites. However, available DNA methylation (DNAm) age predictors are based on datasets with limited ethnic representation. Moreover, a systematic comparison between DNAm data and other omics datasets has not yet been performed. To address these knowledge gaps, we generated and analyzed DNA methylation datasets from two independent Chinese cohorts, revealing age-related DNAm changes. Additionally, a DNA methylation (DNAm) aging clock (iCAS-DNAmAge) and a group of DNAm-based multi-modal clocks for Chinese individuals were developed, with most of them demonstrating strong predictive capabilities for chronological age...
March 14, 2024: Protein & Cell
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