bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inherited myogenic abilities in muscle precursor cells defined by the mitochondrial complex I-encoding protein
Authors: Motohashi Norio , Minegishi Katsura , Aoki Yoshitsugu 
Published: October 2023

AbstractSkeletal muscle comprises different muscle fibers, including slow- and fast-type muscles, and satellite cells (SCs), which exist in individual muscle fibers and possess different myogenic properties. Previously, we reported that myoblasts (MBs) from slow-type enriched soleus (SOL) had a high potential to self-renew compared with cells derived from fast-type enriched tibialis anterior (TA). However, whether the functionality of myogenic cells in adult muscles is attributed to the muscle fiber in which they reside and whether the characteristics of myogenic cells derived from slow- and fast-type fibers can be distinguished at the genetic level remain unknown. Global gene expression analysis revealed that the myogenic potential of MBs was independent of the muscle fiber type they reside in but dependent on the region of muscles they are derived from. Thus, in this study, proteomic analysis was conducted to clarify the molecular differences between MBs derived from TA and SOL. NADH dehydrogenase (ubiquinone) iron-sulfur protein 8 (Ndufs8), a subunit of NADH dehydrogenase in mitochondrial complex I, significantly increased in SOL-derived MBs compared with that in TA-derived cells. Moreover, the expression level of Ndufs8 in MBs significantly decreased with age. Gain- and loss-of-function experiments revealed that Ndufs8 expression in MBs promoted differentiation, self-renewal, and apoptosis resistance. In particular, Ndufs8 suppression in MBs increased p53 acetylation, followed by a decline in NAD/NADH ratio. Nicotinamide mononucleotide treatment, which restores the intracellular NAD+ level, could decrease p53 acetylation and increase myogenic cell self-renewal ability in vivo. These results suggested that the functional differences in MBs derived from SOL and TA governed by the mitochondrial complex I-encoding gene reflect the magnitude of the decline in SC number observed with aging, indicating that the replenishment of NAD+ is a possible approach for improving impaired cellular functions caused by aging or diseases.
Frontal cortex activity during the production of diverse social communication calls in marmoset monkeys
Authors: Zhao Lingyun , Wang Xiaoqin 
Published: October 2023

AbstractVocal communication is essential for social behaviors in humans and non-human primates. While the frontal cortex is crucial to human speech production, its role in vocal production in non-human primates has long been questioned. It is unclear whether activities in the frontal cortex represent diverse vocal signals used in non-human primate communication. Here we studied single neuron activities and local field potentials (LFP) in the frontal cortex of male marmoset monkeys while the animal engaged in vocal exchanges with conspecifics in a social environment. We found that both single neuron activities and LFP were modulated by the production of each of the four major call types. Moreover, neural activities showed distinct patterns for different call types and theta-band LFP oscillations showed phase-locking to the phrases of twitter calls, suggesting a neural representation of vocalization features. Our results suggest important functions of the marmoset frontal cortex in supporting the production of diverse vocalizations in communication.
De novo genome assembly depicts the immune genomic characteristics of cattle
Authors: Li Ting-Ting , Xia Tian , Wu Jia-Qi , Hong Hao , Sun Zhao-Lin , Wang Ming , Ding Fang-Rong , Wang Jing , Jiang Shuai , Li Jin , Pan Jie , Yang Guang , Feng Jian-Nan , Dai Yun-Ping , Zhang Xue-Min , Zhou Tao , Li Tao 
Published: October 2023

AbstractImmunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.
A silicon transporter gene required for healthy growth of rice on land
Authors: Mitani-Ueno Namiki , Yamaji Naoki , Huang Sheng , Yoshioka Yuma , Miyaji Takaaki , Ma Jian Feng 
Published: October 2023

AbstractSilicon (Si) is the most abundant mineral element in the earth’s crust. Some plants actively accumulate Si as amorphous silica (phytoliths), which can protect plants from stresses. Here, we report a gene (SIET4) that is required for the proper accumulation and cell-specific deposition of Si in rice and show that it is essential for normal growth. SIET4 is constitutively expressed in leaves and encodes a Si transporter. SlET4 polarly localizes at the distal side of epidermal cells and cells surrounding the bulliform cells (motor cells) of the leaf blade, where Si is deposited. Knockout of SIET4 leads to the death of rice in the presence but not absence of Si. Further analysis shows that SIET4 knockout induces abnormal Si deposition in mesophyll cells and the induction of hundreds of genes related to various stress responses. These results indicate that SIET4 is required for the proper export of Si from leaf cells to the leaf surface and for the healthy growth of rice on land.
Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in Kinshasa Province, Democratic Republic of Congo
Authors: Sendor Rachel , Banek Kristin , Kashamuka Melchior M. , Mvuama Nono , Bala Joseph A. , Nkalani Marthe , Kihuma Georges , Atibu Joseph , Thwai Kyaw L. , Svec W. Matthew , Goel Varun , Nseka Tommy , Lin Jessica T. , Bailey Jeffrey A. , Emch Michael , Carrel Margaret , Juliano Jonathan J. , Tshefu Antoinette , Parr Jonathan B. 
Published: October 2023

AbstractReports suggest non-falciparum species are an underappreciated cause of malaria in sub-Saharan Africa but their epidemiology is ill-defined, particularly in highly malaria-endemic regions. We estimated incidence and prevalence of PCR-confirmed non-falciparum and Plasmodium falciparum malaria infections within a longitudinal study conducted in Kinshasa, Democratic Republic of Congo (DRC) between 2015-2017. Children and adults were sampled at biannual household surveys and routine clinic visits. Among 9,089 samples from 1,565 participants, incidences of P. malariae, P. ovale spp., and P. falciparum infections by 1-year were 7.8% (95% CI: 6.4%-9.1%), 4.8% (95% CI: 3.7%-5.9%) and 57.5% (95% CI: 54.4%-60.5%), respectively. Non-falciparum prevalences were higher in school-age children, rural and peri-urban sites, and P. falciparum co-infections. P. falciparum remains the primary driver of malaria in the DRC, though non-falciparum species also pose an infection risk. As P. falciparum interventions gain traction in high-burden settings, continued surveillance and improved understanding of non-falciparum infections are warranted.
Kinetics of the xanthophyll cycle and its role in photoprotective memory and response
Authors: Short Audrey , Fay Thomas P. , Crisanto Thien , Mangal Ratul , Niyogi Krishna K. , Limmer David T. , Fleming Graham R. 
Published: October 2023

AbstractEfficiently balancing photochemistry and photoprotection is crucial for survival and productivity of photosynthetic organisms in the rapidly fluctuating light levels found in natural environments. The ability to respond quickly to sudden changes in light level is clearly advantageous. In the alga Nannochloropsis oceanica we observed an ability to respond rapidly to sudden increases in light level which occur soon after a previous high-light exposure. This ability implies a kind of memory. In this work, we explore the xanthophyll cycle in N. oceanica as a short-term photoprotective memory system. By combining snapshot fluorescence lifetime measurements with a biochemistry-based quantitative model, we show that short-term memory arises from the xanthophyll cycle. In addition, the model enables us to characterize the relative quenching abilities of the three xanthophyll cycle components. Given the ubiquity of the xanthophyll cycle in photosynthetic organisms the model described here will be of utility in improving our understanding of vascular plant and algal photoprotection with important implications for crop productivity.
Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field
Authors: Bouidghaghen Jugurta , Moreau Laurence , Beauchêne Katia , Chapuis Romain , Mangel Nathalie , Cabrera‐Bosquet Llorenç , Welcker Claude , Bogard Matthieu , Tardieu François 
Published: October 2023

AbstractBreeding for resilience to climate change requires considering adaptive traits such as plant architecture, stomatal conductance and growth, beyond the current selection for yield. Robotized indoor phenotyping allows measuring such traits at high throughput for speed breeding, but is often considered as non-relevant for field conditions. Here, we show that maize adaptive traits can be inferred in different fields, based on genotypic values obtained indoor and on environmental conditions in each considered field. The modelling of environmental effects allows translation from indoor to fields, but also from one field to another field. Furthermore, genotypic values of considered traits match between indoor and field conditions. Genomic prediction results in adequate ranking of genotypes for the tested traits, although with lesser precision for elite varieties presenting reduced phenotypic variability. Hence, it distinguishes genotypes with high or low values for adaptive traits, conferring either spender or conservative strategies for water use under future climates.
Adrenergic modulation of melanocortin pathway by hunger signals
Authors: Sayar-Atasoy Nilufer , Laule Connor , Aklan Iltan , Kim Hyojin , Yavuz Yavuz , Ates Tayfun , Coban Ilknur , Koksalar-Alkan Fulya , Rysted Jacob , Davis Debbie , Singh Uday , Alp Muhammed Ikbal , Yilmaz Bayram , Cui Huxing , Atasoy Deniz 
Published: October 2023

AbstractNorepinephrine (NE) is a well-known appetite regulator, and the nor/adrenergic system is targeted by several anti-obesity drugs. To better understand the circuitry underlying adrenergic appetite control, here we investigated the paraventricular hypothalamic nucleus (PVN), a key brain region that integrates energy signals and receives dense nor/adrenergic input, using a mouse model. We found that PVN NE level increases with signals of energy deficit and decreases with food access. This pattern is recapitulated by the innervating catecholaminergic axon terminals originating from NTSTH-neurons. Optogenetic activation of rostral-NTSTH → PVN projection elicited strong motivation to eat comparable to overnight fasting whereas its inhibition attenuated both fasting-induced & hypoglycemic feeding. We found that NTSTH-axons functionally targeted PVNMC4R-neurons by predominantly inhibiting them, in part, through α1-AR mediated potentiation of GABA release from ARCAgRP presynaptic terminals. Furthermore, glucoprivation suppressed PVNMC4R activity, which was required for hypoglycemic feeding response. These results define an ascending nor/adrenergic circuit, NTSTH → PVNMC4R, that conveys peripheral hunger signals to melanocortin pathway.
Adaptive design of mRNA-loaded extracellular vesicles for targeted immunotherapy of cancer
Authors: Dong Shiyan , Liu Xuan , Bi Ye , Wang Yifan , Antony Abin , Lee DaeYong , Huntoon Kristin , Jeong Seongdong , Ma Yifan , Li Xuefeng , Deng Weiye , Schrank Benjamin R. , Grippin Adam J. , Ha JongHoon , Kang Minjeong , Chang Mengyu , Zhao Yarong , Sun Rongze , Sun Xiangshi , Yang Jie , Chen Jiayi , Tang Sarah K. , Lee L. James , Lee Andrew S. , Teng Lirong , Wang Shengnian , Teng Lesheng , Kim Betty Y. S. , Yang Zhaogang , Jiang Wen 
Published: October 2023

AbstractThe recent success of mRNA therapeutics against pathogenic infections has increased interest in their use for other human diseases including cancer. However, the precise delivery of the genetic cargo to cells and tissues of interest remains challenging. Here, we show an adaptive strategy that enables the docking of different targeting ligands onto the surface of mRNA-loaded small extracellular vesicles (sEVs). This is achieved by using a microfluidic electroporation approach in which a combination of nano- and milli-second pulses produces large amounts of IFN-γ mRNA-loaded sEVs with CD64 overexpressed on their surface. The CD64 molecule serves as an adaptor to dock targeting ligands, such as anti-CD71 and anti-programmed cell death-ligand 1 (PD-L1) antibodies. The resulting immunogenic sEVs (imsEV) preferentially target glioblastoma cells and generate potent antitumour activities in vivo, including against tumours intrinsically resistant to immunotherapy. Together, these results provide an adaptive approach to engineering mRNA-loaded sEVs with targeting functionality and pave the way for their adoption in cancer immunotherapy applications.
Biosynthesis and engineering of the nonribosomal peptides with a C-terminal putrescine
Authors: Chen Hanna , Zhong Lin , Zhou Haibo , Bai Xianping , Sun Tao , Wang Xingyan , Zhao Yiming , Ji Xiaoqi , Tu Qiang , Zhang Youming , Bian Xiaoying 
Published: October 2023

AbstractThe broad bioactivities of nonribosomal peptides rely on increasing structural diversity. Genome mining of the Burkholderiales strain Schlegelella brevitalea DSM 7029 leads to the identification of a class of dodecapeptides, glidonins, that feature diverse N-terminal modifications and a uniform putrescine moiety at the C-terminus. The N-terminal diversity originates from the wide substrate selectivity of the initiation module. The C-terminal putrescine moiety is introduced by the unusual termination module 13, the condensation domain directly catalyzes the assembly of putrescine into the peptidyl backbone, and other domains are essential for stabilizing the protein structure. Swapping of this module to another two nonribosomal peptide synthetases leads to the addition of a putrescine to the C-terminus of related nonribosomal peptides, improving their hydrophilicity and bioactivity. This study elucidates the mechanism for putrescine addition and provides further insights to generate diverse and improved nonribosomal peptides by introducing a C-terminal putrescine.
Automatic correction of performance drift under acquisition shift in medical image classification
Authors: Roschewitz Mélanie , Khara Galvin , Yearsley Joe , Sharma Nisha , James Jonathan J. , Ambrózay Éva , Heroux Adam , Kecskemethy Peter , Rijken Tobias , Glocker Ben 
Published: October 2023

AbstractImage-based prediction models for disease detection are sensitive to changes in data acquisition such as the replacement of scanner hardware or updates to the image processing software. The resulting differences in image characteristics may lead to drifts in clinically relevant performance metrics which could cause harm in clinical decision making, even for models that generalise in terms of area under the receiver-operating characteristic curve. We propose Unsupervised Prediction Alignment, a generic automatic recalibration method that requires no ground truth annotations and only limited amounts of unlabelled example images from the shifted data distribution. We illustrate the effectiveness of the proposed method to detect and correct performance drift in mammography-based breast cancer screening and on publicly available histopathology data. We show that the proposed method can preserve the expected performance in terms of sensitivity/specificity under various realistic scenarios of image acquisition shift, thus offering an important safeguard for clinical deployment.
Deterministic full-scenario analysis for maximum credible earthquake hazards
Authors: Wang Xiang-Chao , Wang Jin-Ting , Zhang Chu-Han 
Published: October 2023

AbstractGreat earthquakes are one of the major threats to modern society due to their great destructive power and unpredictability. The maximum credible earthquake (MCE) for a specific fault, i.e., the largest magnitude earthquake that may occur there, has numerous potential scenarios with different source processes, making the future seismic hazard highly uncertain. We propose a full-scenario analysis method to evaluate the MCE hazards with deterministic broadband simulations of numerous scenarios. The full-scenario analysis is achieved by considering all uncertainties of potential future earthquakes with sufficient scenarios. Here we show an application of this method in the seismic hazard analysis for the Xiluodu dam in China by simulating 22,000,000 MCE scenarios in 0–10 Hz. The proposed method can provide arbitrary intensity measures, ground-motion time series, and spatial ground-motion fields for all hazard levels, which enables more realistic and accurate MCE hazard evaluations, and thus has great application potential in earthquake engineering.
Ligand activation mechanisms of human KCNQ2 channel
Authors: Ma Demin , Zheng Yueming , Li Xiaoxiao , Zhou Xiaoyu , Yang Zhenni , Zhang Yan , Wang Long , Zhang Wenbo , Fang Jiajia , Zhao Guohua , Hou Panpan , Nan Fajun , Yang Wei , Su Nannan , Gao Zhaobing , Guo Jiangtao 
Published: October 2023

AbstractThe human voltage-gated potassium channel KCNQ2/KCNQ3 carries the neuronal M-current, which helps to stabilize the membrane potential. KCNQ2 can be activated by analgesics and antiepileptic drugs but their activation mechanisms remain unclear. Here we report cryo-electron microscopy (cryo-EM) structures of human KCNQ2-CaM in complex with three activators, namely the antiepileptic drug cannabidiol (CBD), the lipid phosphatidylinositol 4,5-bisphosphate (PIP2), and HN37 (pynegabine), an antiepileptic drug in the clinical trial, in an either closed or open conformation. The activator-bound structures, along with electrophysiology analyses, reveal the binding modes of two CBD, one PIP2, and two HN37 molecules in each KCNQ2 subunit, and elucidate their activation mechanisms on the KCNQ2 channel. These structures may guide the development of antiepileptic drugs and analgesics that target KCNQ2.
Obesity dysregulates the pulmonary antiviral immune response
Authors: Almond Mark , Farne Hugo A. , Jackson Millie M. , Jha Akhilesh , Katsoulis Orestis , Pitts Oliver , Tunstall Tanushree , Regis Eteri , Dunning Jake , Byrne Adam J. , Mallia Patrick , Kon Onn Min , Saunders Ken A. , Simpson Karen D. , Snelgrove Robert J. , Openshaw Peter J. M. , Edwards Michael R. , Barclay Wendy S. , Heaney Liam M. , Johnston Sebastian L. , Singanayagam Aran 
Published: October 2023

AbstractObesity is a well-recognized risk factor for severe influenza infections but the mechanisms underlying susceptibility are poorly understood. Here, we identify that obese individuals have deficient pulmonary antiviral immune responses in bronchoalveolar lavage cells but not in bronchial epithelial cells or peripheral blood dendritic cells. We show that the obese human airway metabolome is perturbed with associated increases in the airway concentrations of the adipokine leptin which correlated negatively with the magnitude of ex vivo antiviral responses. Exogenous pulmonary leptin administration in mice directly impaired antiviral type I interferon responses in vivo and ex vivo in cultured airway macrophages. Obese individuals hospitalised with influenza showed dysregulated upper airway immune responses. These studies provide insight into mechanisms driving propensity to severe influenza infections in obesity and raise the potential for development of leptin manipulation or interferon administration as novel strategies for conferring protection from severe infections in obese higher risk individuals.
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite
Authors: Cordisco Estefanía , Zanor María Inés , Moreno Diego Martín , Serra Diego Omar 
Published: October 2023

AbstractThe propensity of bacteria to grow collectively in communities known as biofilms and their ability to overcome clinical treatments in this condition has become a major medical problem, emphasizing the need for anti-biofilm strategies. Antagonistic microbial interactions have extensively served as searching platforms for antibiotics, but their potential as sources for anti-biofilm compounds has barely been exploited. By screening for microorganisms that in agar-set pairwise interactions could antagonize Escherichia coli’s ability to form macrocolony biofilms, we found that the soil bacterium Bacillus subtilis strongly inhibits the synthesis of amyloid fibers –known as curli-, which are the primary extracellular matrix (ECM) components of E. coli biofilms. We identified bacillaene, a B. subtilis hybrid non-ribosomal peptide/polyketide metabolite, previously described as a bacteriostatic antibiotic, as the effector molecule. We found that bacillaene combines both antibiotic and anti-curli functions in a concentration-dependent order that potentiates the ecological competitiveness of B. subtilis, highlighting bacillaene as a metabolite naturally optimized for microbial inhibition. Our studies revealed that bacillaene inhibits curli by directly impeding the assembly of the CsgB and CsgA curli subunits into amyloid fibers. Moreover, we found that curli inhibition occurs despite E. coli attempts to reinforce its protective ECM by inducing curli genes via a RpoS-mediated competition sensing response trigged by the threatening presence of B. subtilis. Overall, our findings illustrate the relevance of exploring microbial interactions not only for finding compounds with unknown and unique activities, but for uncovering additional functions of compounds previously categorized as antibiotics.
Extracting quantum dynamical resources: consumption of non-Markovianity for noise reduction
Authors: Berk Graeme D. , Milz Simon , Pollock Felix A. , Modi Kavan 
Published: October 2023

AbstractA great many efforts are dedicated to developing noise reduction and mitigation methods. One remarkable achievement in this direction is dynamical decoupling (DD), although its applicability remains limited because fast control is required. Using resource theoretic tools, we show that non-Markovianity is a resource for noise reduction, raising the possibility that it can be leveraged for noise reduction where traditional DD methods fail. We propose a non-Markovian optimisation technique for finding DD pulses. Using a prototypical noise model, we numerically demonstrate that our optimisation-based methods are capable of drastically improving the exploitation of temporal correlations, extending the timescales at which noise suppression is viable by at least two orders of magnitude, compared to traditional DD which does not use any knowledge of the non-Markovian environment. Importantly, the corresponding tools are built on operational grounds and can be easily implemented to reduce noise in the current generation of quantum devices.