Article
Multidisciplinary Sciences
Ting-Ting Li, Tian Xia, Jia-Qi Wu, Hao Hong, Zhao-Lin Sun, Ming Wang, Fang-Rong Ding, Jing Wang, Shuai Jiang, Jin Li, Jie Pan, Guang Yang, Jian-Nan Feng, Yun-Ping Dai, Xue-Min Zhang, Tao Zhou, Tao Li
Summary: This study reports the de novo assembly of a cattle genome and provides a detailed annotation of the immunogenomic loci. The immunogenomic regions, including immunoglobulin (IG) loci, T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. The characterization of immune genes in cattle reveals their diversity and the MHC gene structures are also revealed with properly phased haplotypes.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Guizhen Zhu, Wenmei Zhang, Yaoyao Zhao, Tian Chen, Hanyu Yuan, Yuanxing Liu, Guangsheng Guo, Zhihong Liu, Xiayan Wang
Summary: Studying the mechanisms of drug antitumor activity at the single-cell level is crucial for accurate cancer treatment. However, current metabolomics-based approaches are limited due to the small size and low metabolite contents of single cells. In this study, we develop a label-free platform, sMDA-scM, which combines intact living-cell electro-launching ionization mass spectrometry with metabolomics analysis, to investigate the drug action mechanisms. Using this platform, we identify different metabolic responses in subpopulations of non-small-cell lung cancer cells treated with gefitinib, providing insights for evaluating therapeutic effects and overcoming drug resistance.
ANALYTICAL CHEMISTRY
(2023)
Article
Computer Science, Hardware & Architecture
Ding Li, Xuebing Yang, Yongqiang Tang, Chenyang Zhang, Wensheng Zhang, Lizhuang Ma
Summary: This paper introduces an active learning method called AL-STAL to address the issue of high labeling cost in action localization tasks. By selecting video samples with high informativeness and training the localization model, AL-STAL achieves superior performance compared to existing methods and demonstrates satisfying performance compared to fully-supervised learning on three benchmark datasets.
Article
Psychology, Multidisciplinary
Camille Gasser, Lila Davachi
Summary: Our behavior has a central role in real-world experiences, but it is unclear how engaging in a familiar sequence of actions influences memory for unrelated nonmotor information. In our study, we found that engaging in a predictable and well-learned action sequence enhances temporal order memory for novel items, but does not affect item memory. These findings suggest that familiar behaviors during novel learning scaffold within-event temporal memory.
PSYCHOLOGICAL SCIENCE
(2023)
Article
Geochemistry & Geophysics
Martin Gal, Ernest Lotter, Gerrit Olivier, Mark Green, Stephen Meyer, Phil Dales, Anya M. Reading
Summary: The article introduces a modular cross-correlation location algorithm for induced seismicity, which uses automated procedures to enhance data processing efficiency and includes using cross-correlation values as quality constraints for outlier detection. The algorithm includes cross pairs of P and S arrivals as well as autocorrelations to add distance constraints to hypocenter estimation, successfully inferring 92% of source information.
SEISMOLOGICAL RESEARCH LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Shunhua Han, Guilherme B. Dias, Preston J. Basting, Raghuvir Viswanatha, Norbert Perrimon, Casey M. Bergman
Summary: Animal cell lines often undergo extreme genome restructuring events that hinder de novo whole-genome assembly. This study used long-read and linked-read technologies to sequence the genome of a tetraploid Drosophila cell line and developed a novel method called TELR for TE analysis. The results shed light on the role and mechanism of transposable elements in animal cell culture genome evolution.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Adam J. Stevens, Andrew R. Harris, Josiah Gerdts, Ki H. Kim, Coralie Trentesaux, Jonathan T. Ramirez, Wesley L. McKeithan, Faranak Fattahi, Ophir D. Klein, Daniel A. Fletcher, Wendell A. Lim
Summary: Cell adhesion molecules play a crucial role in various cellular processes, and their synthetic counterparts can be generated by combining extracellular interactions with intracellular domains. These synthetic molecules allow for customized cell-cell interactions with properties similar to native interactions. The intracellular domains determine the interface morphology and mechanics, while the extracellular interaction domains specify the connectivity between cells. This toolkit of synthetic cell adhesion molecules enables the assembly of multicellular architectures and the systematic remodeling of native tissues, providing insights into the evolution of different classes of cell-cell interfaces. Overall, these tools have significant implications for cell and tissue engineering and the study of multicellular organization.
Article
Biochemistry & Molecular Biology
Lin Lin, Raffaella Capozzoli, Alexia Ferrand, Miro Plum, Andrea Vettiger, Marek Basler
Summary: The spatiotemporal regulation of T6SS assembly remains poorly understood. This study identifies a class of periplasmic proteins (TslA) that is required for the precise localization of T6SS to the site of contact between neighboring bacteria. The localization is dependent on the outer membrane porin OmpA.
Article
Mathematics, Applied
Jaka Smrekar
Summary: We study spaces of continuous functions and sections with domain a paracompact Hausdorff k-space $X$ and range a nilpotent CW complex $Y$, with emphasis on localization at a set of primes. For $\mathop {\rm map}\nolimits _\phi (X,\,Y)$, the space of maps with prescribed restriction $\phi$ on a suitable subspace $A\subset X$, we construct a natural spectral sequence of groups that converges to $\pi _*(\mathop {\rm map}\nolimits _\phi (X,\,Y))$ and allows for detection of localization on the level of $E<^>2$. Our applications extend and unify the previously known results.
PROCEEDINGS OF THE ROYAL SOCIETY OF EDINBURGH SECTION A-MATHEMATICS
(2023)
Article
Chemistry, Multidisciplinary
Supraja S. Chittari, Allie C. Obermeyer, Abigail S. Knight
Summary: Through studying thermoresponsive copolymers, it is found that the nonequilibrium thermal hysteretic behavior is influenced by composition and stimulus path. Analysis of heat-cool cycles reveals that hysteresis in copolymers varies based on side chain length and hydrophobicity. The temperature ramp rate also affects hysteresis, as optimized temperature protocols can trap the material in insoluble states. This study uncovers fundamental principles for harnessing out-of-equilibrium effects in synthetic soft materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Astronomy & Astrophysics
Belinda Damian, Jessy Jose, Manash R. Samal, Estelle Moraux, Swagat R. Das, Sudeshna Patra
Summary: Through observational analysis of eight young clusters, we conclude that there is no strong evidence for an environmental effect in the underlying form of the IMF.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Biology
Pavan Vedula, Satoshi Kurosaka, Brittany MacTaggart, Qin Ni, Garegin Papoian, Yi Jiang, Dawei W. Dong, Anna Kashina
Summary: The study investigates the role of coding sequence in beta- and gamma-cytoplasmic actins' intracellular functions, revealing that differences in translation rates between the two actins affect their dynamics at focal adhesions, actin bundle formation, and cell migration. This coding sequence-mediated difference in actin translation plays a key role in cell migration.
Article
Astronomy & Astrophysics
David Guszejnov, Carleen Markey, Stella S. R. Offner, Michael Y. Grudic, Claude-Andre Faucher-Giguere, Anna L. Rosen, Philip F. Hopkins
Summary: Stars form in dense, clustered environments, and feedback from newly formed stars ejects gas, leaving behind star clusters. Clusters are assembled through mergers, while still accreting gas. During this process, a small proportion of stars are ejected, with no significant difference in mass distribution compared to stars inside clusters. The initial mass segregation of star formation sites is maintained in merged clusters, which eventually relax to a centrally condensed configuration through dynamical interactions. However, this process is not complete before feedback expels remaining gas, causing the clusters to become unbound and breakup. Turbulent driving and periodic cloud geometry can reduce clustering and prevent gas expulsion.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Kazuya Tsujita, Reiko Satow, Shinobu Asada, Yoshikazu Nakamura, Luis Arnes, Keisuke Sako, Yasuyuki Fujita, Kiyoko Fukami, Toshiki Itoh
Summary: Changes in cell mechanics contribute to cancer cell dissemination. High plasma membrane (PM) tension inhibits cancer dissemination by counteracting mechanosensitive BAR family protein assembly, while restoration of PM tension phenotypically convert malignant cells into a non-motile epithelial cell state.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Vera Kleene, Valentina Corvaglia, Erika Chacin, Ignasi Forne, David B. Konrad, Pardis Khosravani, Celine Douat, Christoph F. Kurat, Ivan Huc, Axel Imhof
Summary: The use of synthetic foldamers that mimic double-stranded DNA has shown potential for interfering with protein-DNA interactions and disrupting the chromatin-bound proteome. These foldamers have been found to efficiently interfere with the association of the origin recognition complex with chromatin, leading to disruption of the cell cycle. This interaction is mediated by a direct interaction between the foldamers and the origin recognition complex, resulting in a failure to organize chromatin around replication origins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Neurosciences
James R. Engle, Christopher J. Machado, Michele R. Permenter, Julie A. Vogt, Andrew P. Maurer, Alicia M. Bulleri, Carol A. Barnes
JOURNAL OF NEUROSCIENCE
(2016)
Article
Neurosciences
Andrew P. Maurer, Sara N. Burke, Kamran Diba, Carol A. Barnes
JOURNAL OF NEUROSCIENCE
(2017)
Article
Behavioral Sciences
M. A. Kreher, S. A. Johnson, J. -M. Mizell, D. K. Chetram, D. T. Guenther, S. D. Lovett, B. Setlow, J. L. Bizon, S. N. Burke, A. P. Maurer
NEUROBIOLOGY OF LEARNING AND MEMORY
(2019)
Article
Neurosciences
Sarah A. Johnson, Sabrina Zequeira, Sean M. Turner, Andrew P. Maurer, Jennifer L. Bizon, Sara N. Burke
Summary: The prefrontal cortex plays a critical role in mnemonic similarity task performance, but the time course of its involvement is distinct from that of the hippocampus.
Article
Neurosciences
Douglas R. Miller, Dylan T. Guenther, Andrew P. Maurer, Carissa A. Hansen, Andrew Zalesky, Habibeh Khoshbouei
Summary: The dopaminergic neurons in the substantia nigra pars compacta (SNC) and ventral tegmental area (VTA) exhibit regional differences in network connectivity, with a higher incidence of hub-like neurons in the VTA compared to the SNC. Neuronal loss in the SNC increases network clustering, whereas the VTA compensates by decreasing network clustering due to a larger number of hub-neurons. Network properties in these dopaminergic brain regions can be regulated via a dopamine transporter mechanism, demonstrating novel regulatory mechanisms of functional network topology.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Neurosciences
Jack P. Kennedy, Yuchen Zhou, Y. Qin, Sarah D. Lovett, A. Sheremet, S. N. Burke, A. P. Maurer
Summary: This study explores the relationship between theta rhythm and voluntary movement in hippocampal neurophysiology research, highlighting the impact of running speed on theta frequency and power compared to acceleration. The results suggest that speed plays a more significant role in influencing theta frequency, contradicting previous findings that acceleration is the dominant factor. Caution is advised in interpreting absolute claims about hippocampal physiology from single behavioral repertoires, emphasizing the need to consider multiple sensory inputs in navigation tasks.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Neurosciences
Yu Qin, Alex Sheremet, Tara L. Cooper, Sara N. Burke, Andrew P. Maurer
Summary: The hippocampal theta rhythm is strongly associated with awake behavior and is believed to represent a cognitive state of the brain. It has been theorized that theta activity propagates reentrantly across regions of the Papez circuit. This observation complements the energy cascade hypothesis, which suggests that large-amplitude, slow-frequency oscillations reflect activity propagating across a large population of neurons. Higher frequency oscillations, like gamma, are related to the interaction and distribution of inhibitory and excitatory neurons on a local level. The data support models of how activity moves across the nervous system, indicating that the brain utilizes large-scale activity patterns to support higher cognitive processes.
Article
Neurosciences
Leslie S. Gaynor, Meena Ravi, Sabrina Zequeira, Andreina M. Hampton, Wonn S. Pyon, Samantha Smith, Luis M. Colon-Perez, Marjory Pompilus, Jennifer L. Bizon, Andrew P. Maurer, Marcelo Febo, Sara N. Burke
Summary: This study aimed to determine whether cognitive training in aged rats resulted in changes in global resting-state functional connectivity. The results showed an increase in global functional connectivity between baseline and post-training resting state scans in aged rats that underwent cognitive training. Additionally, there was an increase in connectivity between hippocampal cortex, perirhinal cortex, and frontal cortical areas, as well as a reduced reciprocal connectivity within the retrosplenial cortex in the trained aged rats.
Article
Neurosciences
Y. Zhou, A. Sheremet, Y. Qin, J. P. Kennedy, N. M. DiCola, S. N. Burke, A. P. Maurer
