bluuebunny/crossref_metadata_2025 huggingface dataset:
Cerebellar Hypermetabolism in a Hodgkin Lymphoma Leads to Diagnosis of Paucisymptomatic Cryptococcus neoformans Meningitis
Authors: Vanerwegen Eef , Ahmadi Bidakhvidi Niloefar , Vergote Vibeke K. J. , Janssens Ann , Deroose Christophe M.
Published: May 2023

Malignancy-associated cerebellar hypermetabolism on [18F]FDG PET/CT has 2 major causes: paraneoplastic autoimmune encephalitis and neoplasias (leptomeningeal/cerebellar metastases and primary cerebellar tumors). We present the case of a 33-year-old man with a newly diagnosed Hodgkin lymphoma and mere episodical headache, unexpectedly displaying intense cerebellar hypermetabolism on his staging [18F]FDG PET/CT. Both neurolymphomatosis and paraneoplastic subacute cerebellar degeneration were ruled out by clinical presentation, MR, and repeated lumbar punctures. Instead, cerebrospinal fluid analysis unveiled aCryptococcus neoformansmeningitis, highlighting the possibility of paucisymptomatic central nervous system infections as differential diagnosis in malignancy-related cerebellar hypermetabolism in addition to (para)neoplastic causes.
Orbital Radioiodine Uptake in Epithelial Conjunctival Inclusion Cyst on Scintigraphy in a Patient With Differentiated Thyroid Cancer
Authors: Makarewicz Maciej , Skierkowski Witold , Makarewicz Jacek
Published: May 2023

Abnormal focal accumulation of 131I is generally a reliable indicator of differentiated thyroid cancer metastases. However, many examples of false-positive 131I uptake were reported but only a few with orbital accumulation of radioiodine. We report the case of a 68-year-old woman with differentiated thyroid cancer who underwent thyroid remnants ablation with radioiodine. A focus of considerable 131I uptake corresponding to a small, periorbital tumor was detected on posttherapy whole-body 131I scan and head SPECT/CT. The tumor was surgically removed, and pathology revealed a conjunctival inclusion cyst with no features of thyroid tissue. Orbital 131I uptake was not detected on follow-up scans.
Application of Auricular Cartilage Scaffold Combined With L-Shaped Prosthesis in Asian Rhinoplasty
Authors: Li Yi , Guo Hao , Tang Dongsheng , Xin Zengtao , Yang Weiyuan , Yao Ping
Published: May 2023

Rhinoplasty is a common surgical procedure in medical cosmetology. From patients with saddle nose deformity to beauty seekers with low and short noses, this surgery is mainly sought to improve the nose’s appearance. To investigate the effect of modified auricular cartilage scaffold combined with L-shaped prosthesis in rhinoplasty. This retrospective study included 54 patients who underwent auricular cartilage augmentation rhinoplasty with L-shaped implants in our hospital from July 2018 to July 2021. The function of nasal ventilation and olfaction was inspected. As a result, the degree of nasal tip protrusion and the changes in the superior lip angle of columella were improved. The patients’ satisfaction was measured a year after the surgery. Patients who underwent auricular cartilage augmentation rhinoplasty with L-shaped prosthesis were satisfied with the surgery outcomes. Using a protective auricular cartilage scaffold combined with an L-shaped implant for augmentation rhinoplasty reduced the shortage of the application and reinforced the stability of the auricular cartilage augmentation rhinoplasty. At >12 months follow-up, there were no serious adverse effects on nasal ventilation and olfactory function in any of the patients. The presented method made full use of auricular cartilage so that it reduced the harvest of the cartilage. Besides, it achieved the remarkable lift of the nose tip, thus simulating the appearance of costal cartilage rhinoplasty. Furthermore, the risk of implant exposure was efficiently reduced, making it worthy of clinical application.
Reconstruction of Rapidly Growing Merkel Cell Carcinoma of the Cheek With Multidisciplinary Cooperation
Authors: Park Tae Jun , Ki Sae Hwi , Yoon Jin Myung
Published: May 2023

Merkel cell carcinoma (MCC) is a rare and very aggressive skin cancer. An 83-year-old female presented with a 1.5 cm-sized non-tender mass on her left cheek and was diagnosed with MCC. The margin of MCC was well-defined and there was no cervical node metastasis on pre-operative computed tomography. Three weeks after the first visit, the mass rapidly increased in size. We checked the magnetic resonance imaging, a rapid-growing 2.5 cm sized nodular region and metastatic cervical lymph node were found. We performed wide excision of the MCC and neck lymph need dissection with multidisciplinary cooperation. The soft tissue defect was about 6.0×5.0 cm2 in size and reconstructed with radial forearm free flap. On permanent biopsy, the size of MCC was 3.0×2.3 cm2. There was no recurrence of MCC with radiation therapy during an 18-month follow-up. We experienced an older patient with a rapid-growing MCC and cervical lymph node metastasis in a brief time. With our experience, we discuss the evaluation and treatment plan of the rapid-growing MCC for good results.
Lessons Learned From Using Silicone Implants in Clean-Contaminated Regions of the Face
Authors: Edwards Elise , Policherla Rohan , Thaller Seth R.
Published: May 2023

Augmentation rhinoplasty changes the shape of the nose using implanted material. In the 1980s, nasal implantology began to favor silicone over traditional autologous grafts because the synthetic material presented exciting benefits. However, long-term complications of nasal silicone implants have since emerged. This has necessitated the introduction of safe and effective materials. Despite an overwhelming transition to the use of improved implants, craniofacial surgeons will likely continue to see the consequences of silicone implant use as long-term complications arise in the innumerable patients who have had this procedure worldwide.
HEART RATE VARIABILITY PARAMETERS WERE NOT ASSOCIATED WITH 30-DAY ALL-CAUSE MORTALITY IN INTENSIVE CARE UNIT PATIENTS WITH OR WITHOUT ATRIAL FIBRILLATION: A RETROSPECTIVE STUDY OF THE MIMIC-IV DATABASE
Authors: Li Sheran , Yang Qiyu , Wu Peiyu , Lu Yujing , Yang Zhengfei , Jiang Longyuan
Published: May 2023

Objective: Our study aims to evaluate the association between heart rate variability (HRV) and short- and long-term prognosis in patients admitted to intensive care unit (ICU). Methods and Results: Adult patients continuously monitored for over 24 h in ICUs from the the American Medical Information Mart for Intensive Care (MIMIC)-IV Waveform Database were recruited in our study. Twenty HRV-related variables (8 time domain, 6 frequency domain, and 6 nonlinear variables) were calculated based on RR intervals. The association between HRV and all-cause mortality was assessed. Ninety-three patients met the inclusion criteria and were classified into atrial fibrillation (AF) and sinus rhythm (SR) groups, which were further divided into 30-day survivor group and nonsurvivor\groups based on their survival status. The 30-day all-cause mortality rates in AF and SR groups were 36.3% and 14.6%, respectively. All the time domain, frequency domain, and nonlinear HRV parameters did not differ significantly between survivors and nonsurvivors with or without AF (all P > 0.05). Presence of renal failure, malignancy, and elevated blood urea nitrogen level were associated with increased 30-day all-cause mortality in SR patients, while presence of sepsis, infection, higher platelet count, and magnesium level were associated with increased 30-day all-cause mortality in AF patients. Conclusions: Heart rate variability variables were not associated with increased 30-day all-cause mortality in ICU patients with or without AF.
Identification of secondary metabolites containing a diketopiperazine core in extracts from myxobacterial strains with growth inhibition activity against a range of prey species
Authors: Radford Emily Jade , Whitworth David , Allison Gordon
Published: May 2023

Myxobacteria produce a variety of bioactive secondary metabolites, and with a wealth of under-researched species they hold vast potential for undiscovered compounds. With the ever-increasing need for new antibiotics, the development of novel therapeutics is vitally important. Therefore, this study aimed to extract and elucidate antimicrobial metabolites from the following myxobacteria: Myxococcus xanthus CA010 and AB022; Corallococcus exiguus DSM14696T; Myxococcus stipitatus DSM14675T; Corallococcus aberystwythensis AB050AT. Metabolite mixtures were extracted in acetone from XAD-16 resin incubated in liquid cultures and analysed using GC-MS. Bioactivity was identified using a growth inhibition assay against a panel of clinically relevant prey species including Gram-positive and Gram-negative bacteria and a fungus. The growth of Klebsiella pneumoniae and Enterococcus faecalis was most affected by the metabolite mixtures and the mixtures from AB022 and AB050AT were effective against the most prey. GC-MS analysis revealed metabolites with roles in synthesis and degradation of amino acids and fatty acids, but also identified compounds A and B with a diketopiperazine (DKP) core. With previously confirmed bioactivity of compound A, it is suggested that these DKP compounds are contributing to the antimicrobial activity observed.  Furthermore, many compounds could not be identified and so these unknowns present further potential for novel bioactive compounds.
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms
Authors: Xiao Sian , Alshahrani Mohammed , Gupta Grace , Tao Peng , Verkhivker Gennady
Published: May 2023

The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and the increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, extensive microsecond MD simulations and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant which is contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of conformational states. The results suggested that variant-specific changes of conformational mobility in the functional interfacial loops of the spike receptor binding domain can be fine-tuned through cross-talk between convergent mutations thereby providing an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulating conformational plasticity at the binding interface and regulating allosteric responses. This study also characterized the dynamics-induced evolution of allosteric pockets in the Omicron complexes that revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions. Through integrative computational approaches, this investigation provides a systematic analysis and comparison of the effects of Omicron subvariants on conformational dynamics and allosteric signaling in the complexes with the ACE2 receptor.

For Table of Contents Use Only
Discovery of new deaminase functions by structure-based protein clustering
Authors: Huang Jiaying , Lin Qiupeng , Fei Hongyuan , He Zixin , Xu Hu , Li Yunjia , Qu Kunli , Han Peng , Gao Qiang , Li Boshu , Liu Guanwen , Zhang Lixiao , Hu Jiacheng , Zhang Rui , Zuo Erwei , Luo Yonglun , Ran Yidong , Qiu Jin-Long , Zhao Kevin Tianmeng , Gao Caixia
Published: May 2023

The elucidation of protein function and its exploitation in bioengineering have greatly contributed to the development of the life sciences. Existing protein mining efforts generally rely on amino acid sequences rather than protein structures due to technical difficulties in structural elucidation. We describe here for the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected the deaminase family of proteins to analyze and through this approach identified many previously unknown deaminase properties. We applied these new deaminases to the development of new cytosine base editors with distinct features. Although we found many new double-stranded DNA deaminases from the DddA-like protein clade, we were surprised to find that most of the proteins in this family were not actually double-stranded DNA cytidine deaminases. From this protein clade, we engineered the smallest single-strand specific cytidine deaminase, which facilitates the first efficient cytosine base editor to be packaged into a single AAV vector. Importantly, we also profiled a deaminase from this clade that edits robustly in soybean plants, which previously suffered from poor editing by cytosine base editors. These newly discovered deaminases based on AI-assisted structural predictions greatly expand the utility of base editors for therapeutic and agricultural applications.
High-resolution kinetics of herbivore-induced plant volatile transfer reveal clocked response patterns in neighboring plants
Authors: Waterman Jamie M. , Cofer Tristan M. , Wang Lei , Glauser Gaétan , Erb Matthias
Published: May 2023

Volatiles emitted by herbivore-attacked plants (senders) can enhance defenses in neighboring plants (receivers), with important consequences for community dynamics. However, the temporal dynamics of this phenomenon remain poorly studied. Using a custom-built, high- throughput proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) system, we explored temporal patterns of volatile transfer and responses between herbivore-attacked and undamaged maize plants. We found that continuous exposure to natural blends of herbivore-induced volatiles results in clocked temporal response patterns in neighboring plants, characterized by an induced terpene burst at the onset of the second day of exposure. This delayed burst is not explained by terpene accumulation during the night, but coincides with delayed jasmonate accumulation in receiver plants. The delayed burst occurs independent of day : night light transitions and cannot be fully explained by sender volatile dynamics. Instead, it is the result of a stress memory from volatile exposure during the first day and secondary exposure to bioactive volatiles on the second day. Our study reveals that prolonged exposure to natural blends of stress-induced volatiles results in a response that integrates priming and direct induction into a distinct and predictable temporal response pattern. This provides an answer to the long-standing question of whether stress volatiles predominantly induce or prime plant defenses in neighboring plants, by revealing that they can do both in sequence.
Physiological Responses of The Leaves of a High-Altitude PlantPicrorhiza kurroato Cold Stress
Authors: Agrawal Shreya , Saklani Pooja
Published: May 2023

There are various plants that grow in high elevations and experience various environmental stresses, cold stress being the most prevalent one. Plants undergo biochemical, metabolic, molecular, and physiological changes under cold stress hence, they adopt various mechanisms to tolerate it. The antioxidant defense system, osmotic regulators and photosynthetic pigments in the plant provide them stress tolerance. The present study is conducted on a high-altitude plant,Picrorhiza kurroawhich grows in such environmental conditions, to study the physiological parameters that provides it the coping mechanism against the cold stress. For this study, the leaves were collected from Pothivasa (2200 m asl) and Tungnath (3600 m asl) in Rudraprayag, Uttarakhand, India. The photosynthetic pigments, lipid peroxidation, antioxidant enzymes, and osmoprotectants present in the leaves were determined to visualize the impact of cold stress. It was revealed that the concentration of chlorophyll a, chlorophyll b, and carotenoids increased with increase in elevation. The activity of SOD, CAT, POD, APOX and GR were analyzed and they were observed to decrease with altitude. The MDA concentration which is an indicator of lipid peroxidation is higher in Pothivasa (2.214 μmol L-1) and lower in Tungnath (1.697 μmol L-1). There is a significant increase in the total protein content, total soluble sugar content and total proline content along the altitudinal gradient. Therefore, the leaves from both the sampling locations revealed the physiological changes occurred in them to adapt to the cold stress conditions.
Machine-learning guided Venom Induced Dermonecrosis Analysis tooL: VIDAL
Authors: Laprade William , Bartlett Keirah E. , Christensen Charlotte R. , Kazandjian Taline D. , Patel Rohit N. , Crittenden Edouard , Dawson Charlotte A. , Mansourvar Marjan , Wolff Darian S. , Fryer Thomas J. , Laustsen Andreas H. , Casewell Nicholas R. , Gutiérrez José María , Hall Steven R. , Jenkins Timothy P.
Published: May 2023

Snakebite envenoming is a global public health issue that causes significant morbidity and mortality, particularly in low-income regions of the world. The clinical manifestations of envenomings vary depending on the snake’s venom, with paralysis, haemorrhage, and necrosis being the most common and medically relevant effects. To assess the efficacy of antivenoms against dermonecrosis, a preclinical testing approach involvesin vivomouse models that mimic local tissue effects of cytotoxic snakebites in humans. However, current methods for assessing necrosis severity are time-consuming and susceptible to human error. To address this, we present the Venom Induced Dermonecrosis Analysis tool (VIDAL), a machine-learning-guided image-based solution that can automatically identify dermonecrotic lesions in mice, adjust for lighting biases, scale the image, extract lesion area and discolouration, and calculate the severity of dermonecrosis. We also introduce a new unit, the dermonecrotic unit (DnU), to better capture the complexity of dermonecrosis severity. Our tool is comparable to the performance of state-of-the-art histopathological analysis, making it an accessible, accurate, and reproducible method for assessing dermonecrosis. Given the urgent need to address the neglected tropical disease that is snakebite, high-throughput technologies such as VIDAL are crucial in developing and validating new and existing therapeutics for this debilitating disease.
Large-scale genomic rearrangements boost SCRaMbLE inSaccharomyces cerevisiae
Authors: Li Tianyi , Zhao Shijun , Cheng Li , Hou Sha , Luo Zhouqing , Xu Jinsheng , Yu Wenfei , Jiang Shuangying , Monti Marco , Schindler Daniel , Zhang Weimin , Hou Chunhui , Ma Yingxin , Cai Yizhi , Boeke Jef D. , Dai Junbiao
Published: May 2023

Genomic rearrangements contribute to gene copy number alterations, disruption of protein-coding sequences and/or perturbation of cis-regulatory networks. SCRaMbLE, a Cre/loxP-based system implanted in synthetic yeast chromosomes, can effectively introduce genomic rearrangements, and is thus a potential tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we constructed a yeast strain, SparLox83, containing 83 loxPsym sites distributed across all 16 chromosomes, with at least two sites per chromosome. Inducing Cre recombinase expression in SparLox83 produced versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, SCRaMbLE of the hetero-diploid strains derived from crossing SparLox83 with strains possessing synthetic chromosome III (synIII) from the Sc2.0 project led to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to a strain with only synIII. Analysis of these evolved strains demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and can consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool to study the consequence of genomic rearrangements and help accelerate strain engineering in Saccharomyces cerevisiae.
PENet: A phenotype encoding network for automatic extraction and representation of morphological discriminative features
Authors: Zhao Zhengyu , Lu Yuanyuan , Tong Yijie , Chen Xin , Bai Ming
Published: May 2023

Discriminative traits are important in biodiversity and macroevolution, but extracting and representing these features from huge natural history collections using traditional methods can be challenging and time-consuming. To fully utilize the collections and their associated metadata, it is urgent now to increase the efficiency of automatic feature extraction and sample retrieval. We developed a Phenotype Encoding Network (PENet), a deep learning-based model that combines hashing methods to automatically extract and encode discriminative features into hash codes. We tested the performance of PENet on six datasets, including a newly constructed beetle dataset with six subfamilies and 6566 images, which covers more than 60% of the genera in the family Scarabaeidae. PENet showed excellent performance in feature extraction and image retrieval. Two visualization methods, t-SNE, and Grad-CAM, were used to evaluate the representation ability of the hash codes. Further, by using the hash codes generated from PENet, a phenetic distance tree was constructed based on the beetle dataset. The result indicated the hash codes could reveal the phenetic distances and relationships among categories to a certain extent. PENet provides an automatic way to extract and represent morphological discriminative features with higher efficiency, and the generated hash codes serve as a low-dimensional carrier of discriminative features and phenotypic distance information, allowing for broader applications in systematics and ecology.
Massive invasion of organellar DNA drives nuclear genome evolution inToxoplasma
Authors: Namasivayam Sivaranjani , Sun Cheng , Bah Assiatu B , Oberstaller Jenna , Pierre-Louis Edwin , Etheridge Ronald Drew , Feschotte Cedric , Pritham Ellen J. , Kissinger Jessica C.
Published: May 2023

Toxoplasma gondiiis a zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extantT. gondiiME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but notku80mutant,Toxoplasmaparasites. Comparisons withNeospora caninum, a species that diverged fromToxoplasma∼28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.

Significance Statement

This study reveals how DNA located in cellular compartments called organelles can be transferred to the nucleus of the cell and inserted into the nuclear genome of apicomplexan parasiteToxoplasma. Insertions alter the DNA sequence and may lead to significant changes in how genes function. Unexpectedly, we found that the human protist pathogen,Toxoplasma gondiiand closely-related species have the largest observed organellar genome fragment content (>11,000 insertion comprising over 1 Mb of DNA) inserted into their nuclear genome sequence despite their compact 65 Mb nuclear genome. Insertions are occurring at a rate that makes them a significant mutational force that deserves further investigation when examining causes of adaptation and virulence of these parasites.
Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation
Authors: An Luye , Kim Dahihm , Donahue Leanne , Mejooli Menansili Abraham , Eom Chi-Yong , Nishimura Nozomi , White Andrew C
Published: May 2023

Vitiligo is an autoimmune skin disease caused by cutaneous melanocyte loss. Although phototherapy and T cell suppression therapy have been widely used to induce epidermal re-pigmentation, full pigmentation recovery is rarely achieved due to our poor understanding of the cellular and molecular mechanisms governing this process. Here, we identify unique melanocyte stem cell (McSC) epidermal migration rates between male and female mice, which is due to sexually dimorphic cutaneous inflammatory responses generated by ultra-violet B exposure. Using genetically engineered mouse models, and unbiased bulk and single-cell mRNA sequencing approaches, we determine that manipulating the inflammatory response through cyclooxygenase and its downstream prostaglandin product regulates McSC proliferation and epidermal migration in response to UVB exposure. Furthermore, we demonstrate that a combinational therapy that manipulates both macrophages and T cells (or innate and adaptive immunity) significantly promotes epidermal melanocyte re-population. With these findings, we propose a novel therapeutic strategy for repigmentation in patients with depigmentation conditions such as vitiligo.
N4-acetylcytidine (ac4C) promotes mRNA localization to stress granules
Authors: Kudrin Pavel , Singh Ankita , Meierhofer David , Kuśnierczyk Anna , Vang Ørom Ulf Andersson
Published: May 2023

Stress granules are an integral part of the stress response that are formed from non-translating mRNAs aggregated with proteins. While much is known about stress granules, the factors that drive their mRNA localization are incompletely described. Modification of mRNA can alter the properties of the nucleobases and affect processes as translation, splicing and localization of individual transcript. Here, we show that the RNA modification N4-acetylcytidine (ac4C) on mRNA associates with transcripts enriched in stress granules and that stress granule localized transcripts with ac4C are particularly translationally regulated. In addition, we show that ac4C on mRNA can mediate co-localization of the protein NOP58 to stress granules. Our results show that acetylation of mRNA regulates localization of both stress-sensitive transcripts and RNA-binding proteins to stress granules and adds to our understanding of the molecular mechanisms responsible for stress granule formation.
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Authors: Mishra Rishi Kumar , Sharma Prafful , Khaja Faisal Tarique , Uday Adwaith B. , Hussain Tanweer
Published: May 2023

Ribosomes from plants have unique plant-specific features that may aid in rapid gene expression and regulation in response to changing environmental conditions due to their sessile nature. Here, we present high-resolution cryo-electron microscopy structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). We compare wheat ribosome with closely related ribosomes from a dicot plant and other eukaryotes from yeast to humans. While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in peptide exit tunnel, Zinc-finger motif in eL34 is absent and uL4 is extended making an exclusive interaction network. We note striking differences in eL15-Helix 11 (25S) interaction network, eL6-Expansion segment 7 assembly and certain rRNA chemical modifications between monocot and dicot ribosomes. Among eukaryotic ribosomes, we observe that rRNA modification (Gm75) in 5.8S rRNA is highly conserved and a base flipping (G1506) in peptide exit tunnel, and these features are likely involved in sensing nascent peptide. Finally, we discuss importance of universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs
Authors: Hochstoeger Tobias , Papasaikas Panagiotis , Piskadlo Ewa , Chao Jeffrey A.
Published: May 2023

A central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation of ribosomal protein and translation factor mRNAs mediated by the 5′-terminal oligopyrimidine motif (5′TOP). Recently, La-related protein 1 (LARP1) has been proposed to be the specific regulator of 5′TOP mRNA translation downstream of mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested to have a general role in repression. Here, we employ single-molecule translation site imaging of 5′TOP and canonical mRNAs to study the translational dynamics of single mRNAs in living cells. Our data reveals that 4EBP1/2 has a dominant role in translation repression of both 5′TOP and canonical mRNAs during pharmacological inhibition of mTOR. In contrast, we find that LARP1 selectively protects 5′TOP mRNAs from degradation in a transcriptome-wide analysis of mRNA half-lives. Our results clarify the roles of 4EBP1/2 and LARP1 in regulating 5′TOP mRNAs and provides a framework to further study how these factors control cell growth during development and disease.
Vimentin filaments integrate low complexity domains in a highly complex helical structure
Authors: Eibauer Matthias , Weber Miriam S. , Kronenberg-Tenga Rafael , Beales Charlie T. , Boujemaa-Paterski Rajaa , Turgay Yagmur , Sivagurunathan Suganya , Kraxner Julia , Köster Sarah , Goldman Robert D. , Medalia Ohad
Published: May 2023

Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion beam milling, cryo-electron microscopy and tomography, to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, densely-packed and highly-ordered helical symmetric structure of 40 α-helices in cross-section, organized into 5 protofibrils. Surprisingly, the intrinsically disordered head domains form an amyloid-like fiber in the center of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking strength and stretchability.
Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1
Authors: Kupke Janina , Klimmt Julien , Mudlaff Franziska , Schwab Maximilian , Lutsik Pavlo , Plass Christoph , Sticht Carsten , Oliveira Ana M.M.
Published: May 2023

Epigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA-sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
Changes of Cd content in chloroplasts are mirrored by the activity of photosystem I, but not by photosystem II
Authors: Lysenko Eugene A. , Kusnetsov Victor V.
Published: May 2023

Cd is one of the most toxic heavy metals and widespread pollutant. We searched for a direct Cd action on the photosynthetic electron transport chain using induced chlorophyll fluorescence and P700light absorption. Young barley and maize plants were treated with Cd in toxic (80 μM) and nearly lethal (250 μM) concentrations. The maximal and relative photochemical activities of PSI, its major limitation at the donor side, and partially acceptor-side limitation of PSII changed in agreement with Cd accumulation in the corresponding chloroplasts. Probably, acceptor-side limitation of PSII increased with a direct Cd action under 80 μM that was overcome with an indirect Cd action under 250 μM. These alterations can be explained by Cd/Cu substitution in plastocyanin. The photochemical and non-photochemical quenching by PSII varied diversely that cannot be explained unambiguously by any mechanism. The limitations of PSI (Y(ND), Y(NA)) and PSII (qC) were compared for the first time. They were ranged as follows: Y(NA) < qC < Y(ND). Short segments of qC and Y(ND) dynamics varied proportionally to each other. This implies the existence of an unknown mechanism adjusting limitations at the acceptor side of PSII (qC) and at the donor side of PSI (Y(ND)).

Highlights

PSI activity changed in agreement with the changes of Cd content in chloroplasts

The data on PSII activity cannot be clearly explained by Cd action

PSII acceptor-side limitation qC was governed by opposed direct and indirect Cd actions

PSI and qC changes can be explained by Cd/Cu substitution in plastocyanin

Limitations qC of PSII and Y(ND) of PSI changed proportionally for a short time
Identifying cellular markers of focal cortical dysplasia type II with cell-type deconvolution and single-cell signatures
Authors: Galvão Isabella C. , Kandratavicius Ludmyla , Messias Lauana A. , Athié Maria C. P. , Assis-Mendonça Guilherme R. , Alvim Marina K. M. , Ghizoni Enrico , Tedeschi Helder , Yasuda Clarissa L. , Cendes Fernando , Vieira André S. , Rogerio Fabio , Lopes-Cendes Iscia , Veiga Diogo F. T.
Published: May 2023

Focal cortical dysplasia (FCD) is a brain malformation that causes medically refractory epilepsy. FCD is classified into three categories based on structural and cellular abnormalities, with FCD type II being the most common and characterized by disrupted organization of the cortex and abnormal neuronal development. In this study, we employed cell-type deconvolution and single-cell signatures to analyze bulk RNA-seq from multiple transcriptomic studies, aiming to characterize the cellular composition of brain lesions in patients with FCD IIa and IIb subtypes. Our deconvolution analyses revealed specific cellular changes in FCD IIb, including neuronal loss and an increase in reactive astrocytes (astrogliosis) when compared to FCD IIa. Astrogliosis in FCD IIb was further supported by a gene signature analysis and histologically confirmed by glia fibrilla acidic protein (GAP) immunostaining. Overall, our findings demonstrate that FCD II subtypes exhibit differential neuronal and glial compositions, with astrogliosis emerging as a hallmark of FCD IIb. These observations, validated in independent patient cohorts and confirmed using immunohistochemistry, offer novel insights into the involvement of glial cells in FCD type II pathophysiology and may contribute to the development of targeted therapies for this condition.
Stem cells tightly regulate dead cell clearance to maintain tissue fitness
Authors: Stewart Katherine S , Gonzales Kevin AU , Yuan Shaopeng , Tierney Matthew T , Bonny Alain R , Yang Yihao , Infarinato Nicole R , Cowley Christopher J , Levorse John M , Pasolli Hilda Amalia , Ghosh Sourav , Rothlin Carla V , Fuchs Elaine
Published: May 2023

Summary Paragraph

Macrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial number of these dying cells are cleared by ‘non-professional phagocytes’, local epithelial cells that are critical to organismal fitness. How non-professional phagocytes sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying their multifunctionality. Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires both local lipids produced by apoptotic corpses to activate RXRα, and tissue-specific retinoids for RARγ activation. This dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an effective mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.
Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system inClostridioides difficile
Authors: Muzyukina Polina , Shkaruta Anton , Guzman Noemi M. , Andreani Jessica , Borges Adair L. , Bondy-Denomy Joseph , Maikova Anna , Semenova Ekaterina , Severinov Konstantin , Soutourina Olga
Published: May 2023

CRISPR-Cas systems provide their prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. The identification of Acr proteins is challenging due to their small size and high sequence diversity, and only a limited number has been characterized to date. In this study, we report the discovery of a novel Acr protein, AcrIB2, encoded by the φCD38-2Clostridioides difficilephage that efficiently inhibits interference by the type I-B CRISPR-Cas system of the host and likely acts as a DNA mimic. MostC. difficilestrains contain twocasoperons, one encoding a full set of interference and adaptation proteins and another encoding interference proteins only. Unexpectedly, we show that only the partial operon is required for interference and is subject to inhibition by AcrIB2.
The medial prefrontal cortex during flexible decisions: Evidence for its role in distinct working memory processes
Authors: Kidder Kevan , Gillis Ryan , Miles Jesse , Mizumori Sheri
Published: May 2023

During decisions that involve working memory, task-related information must be encoded, maintained across delays, and retrieved. Few studies have attempted to causally disambiguate how different brain structures contribute to each of these components of working memory. In the present study, we used transient optogenetic disruptions of rat medial prefrontal cortex (mPFC) during a serial spatial reversal learning (SSRL) task to test its role in these specific working memory processes. By analyzing numerous performance metrics, we found: 1) mPFC disruption impaired performance during only the choice epoch of initial discrimination learning of the SSRL task, 2) mPFC disruption impaired performance in dissociable ways across all task epochs (delay, choice, return) during flexible decision-making, 3) mPFC disruption resulted in a reduction of the typical vicarious-trial-and-error (VTE) rate modulation that was related to changes in task demands. Taken together, these findings suggest that the mPFC plays an outsized role in working memory retrieval, becomes involved in encoding and maintenance when recent memories conflict with task demands, and enables animals to flexibly utilize working memory to update behavior as environments change.
Distinctive cellular and junctional dynamics independently regulate the rotation and elongation of the internal organ
Authors: Inaki Mikiko , Higashi Takamasa , Okuda Satoru , Matsuno Kenji
Published: May 2023

Complex structures of organs are formed at high reproducibility, and deformations of epithelia play major roles in these processes. To acquire the intricate morphology, an epithelium simultaneously suffers multiple structural changes. For example, to form the left-right asymmetric structure ofDrosophilaembryonic hindgut, its epithelial tube concurrently rotates and elongates, which are driven by cell sliding and convergent extension, respectively. However, how an epithelium simultaneously accomplishes multiple structural changes remains unclear. To address this issue, we here studied the relevancy between these two mechanisms in the hindgut morphogenesis. Our live imaging analysis revealed thatMyosin1DandE-cadherin, orPar-3are required only for cell sliding or convergent extension, respectively, while Myosin II is essential for both. Mathematical models showed that these cellular dynamics share a single mechanical system in the same time window. Such specificity and universality of the machineries controlling epithelial dynamics might be a general strategy adopted in complex tissue morphogenesis.
p90RSK2, a new MLCK, rescues contractility in myosin light chain kinase null smooth muscle
Authors: Kalra Jaspreet , Artamonov Mykhaylo , Wang Hua , Franke Aaron , Markowska Zaneta , Jin Li , Derewenda Zygmunt S. , Ayon Ramon , Somlyo Avril
Published: May 2023

Background

Phosphorylation of smooth muscle (SM) myosin regulatory light chain (RLC20) is a critical switch leading to contraction or cell migration. The canonical view held that the only kinase catalyzing this reaction is the short isoform of myosin light chain kinase (MLCK1). Auxiliary kinases may be involved and play a vital role in blood pressure homeostasis. We have previously reported that p90 ribosomal S6 kinase (RSK2) functions as such a kinase, in parallel with the classical MLCK1, contributing ∼25% of the maximal myogenic force in resistance arteries and regulating blood pressure. Here, we take advantage of a MLCK1 null mouse to further test our hypothesis that RSK2 can function as an MLCK, playing a significant physiological role in SM contractility.

Methods

Fetal (E14.5-18.5) SM tissues were used as embryos die at birth. We investigated the necessity of MLCK for contractility, cell migration and fetal development and determined the ability of RSK2 kinase to compensate for the lack of MLCK and characterized it’s signaling pathway in SM.

Results

Agonists induced contraction and RLC20phosphorylation inmylk1-/-SM, that was inhibited by RSK2 inhibitors. Embryos developed and cells migrated in the absence of MLCK. The pCa-tension relationships in WT vsmylk1-/-muscles demonstrated a Ca2+-dependency due to the Ca2+-dependent tyrosine kinase Pyk2, known to activate PDK1 that phosphorylates and fully activates RSK2. The magnitude of contractile responses was similar upon addition of GTPγS to activate the RhoA/ROCK pathway. The Ca2+-independent component was through activation of Erk1/2/PDK1/RSK2 leading to direct phosphorylation of RLC20, to increase contraction. RSK2, PDK1, Erk1/2 and MLCK formed a signaling complex on the actin filament, optimally positioning them for interaction with adjacent myosin heads.

Conclusions

RSK2 signaling constitutes a new third signaling pathway, in addition to the established Ca2+/CAM/MLCK and RhoA/ROCK pathways to regulate SM contractility and cell migration.
Artificial cerebellum on FPGA: Realistic real-time cerebellar spiking neural network model capable of real-world adaptive motor control
Authors: Shinji Yusuke , Okuno Hirotsugu , Hirata Yutaka
Published: May 2023

The cerebellum plays a central role in motor control and learning. Its neuronal network architecture, firing characteristics of component neurons, and learning rules at their synapses have been well understood in terms of anatomy and physiology. A realistic artificial cerebellum with mimetic network architecture and synaptic plasticity mechanisms may allow us to analyze cerebellar information processing in real world by applying it to adaptive control of actual machines. Several artificial cerebellums have previously been constructed, but they required a high-performance hardware to run in real time for real-world machine control. Presently, we implemented an artificial cerebellum with the size of 104spiking neuron models on a field-programmable gate array (FPGA) which is compact, lightweight, portable, and low-power-consumption. In the implementation three novel techniques are employed: 1) 16-bit fixed-point operation with randomized rounding, 2) fully connected spike information transmission, 3) alternative memory that uses pseudo-random number generators. We demonstrate that the FPGA artificial cerebellum runs in real time, and its component neuron models behave as those in the corresponding artificial cerebellum configured on a personal computer in Python. We applied the FPGA artificial cerebellum to adaptive control of a machine in real-world and demonstrate that the artificial cerebellum is capable of adaptively reducing control error after sudden load changes. This is the first implementation and demonstration of a spiking artificial cerebellum on an FPGA applicable to real-world adaptive control. The FPGA artificial cerebellum may provide neuroscientific insights into cerebellar information processing in adaptive motor control and may be applied to various neuro-devices to augment and extend human motor control capabilities.