bluuebunny/crossref_metadata_2025 huggingface dataset:
Brief Report: Trends in HIV Mortality in the Context of the COVID-19 Pandemic
Authors: Patterson Wendy , Rosenthal Mark , Rajulu Deepa T.
Published: May 2023

Background:

The COVID-19 pandemic led to an increase in the number of deaths among all populations, including people with diagnosed HIV (PWDH). The aim of this study was to analyze the top causes of death (COD) among PWDH before the start of the COVID-19 pandemic, during the start of the COVID-19 pandemic, and a year later; to determine changes in the leading COD among PWDH; and to determine whether the historical trend of decreasing deaths related to HIV continued through the pandemic.

Methods:

To examine mortality among PWDH in New York State (NYS), records for PWDH who died from 2015 to 2021 were extracted from the NYS HIV registry and Vital Statistics Death Data.

Results:

The number of deaths among PWDH in NYS increased 32% from 2019 to 2020 and continued in 2021. COVID-19 was one of the most common underlying COD among PWDH in 2020. In 2021, COVID-19–related deaths decreased while HIV and diseases of the circulatory system remained the top COD. HIV listed as either the underlying or contributing COD showed a consistent downward trend in the percentage of HIV-related deaths among PWDH, from 45% in 2015 to 32% in 2021.

Conclusions:

There was a large increase in deaths among PWDH in 2020, with a substantial percentage related to COVID-19. However, even with the introduction of COVID-19 in 2020, the percentage of deaths related to HIV—one of the goals of the Ending the Epidemic Initiative in NYS—continued to decrease.
Real-Time Identification of Nodal Metastases With 99mTc–Prostate-Specific Membrane Antigen–Based Radioguidance and Indocyanine Green Fluorescence Imaging in Primary Prostate Cancer Surgery—On the Road to Hybrid Image-Guided Surgery
Authors: de Barros Hilda A. , van Oosterom Matthias N. , van Leeuwen Fijs W.B. , van der Poel Henk G. , van Leeuwen Pim J.
Published: May 2023

Recent developments in image-guided prostate cancer surgery focus on extending prostate-specific membrane antigen–directed radioguidance with optical tumor detection using fluorescence, as radio- and fluorescence signals complement each other with in-depth detection and real-time visualization, respectively. As a step in this direction, we report here the integration of indocyanine green fluorescence imaging into a 99mTc–prostate-specific membrane antigen–targeted radioguided surgery workflow.
Peritoneal and Nodal Gliomatosis Mimicking Metastasis on FDG PET/CT in a Patient With Ovarian Immature Teratoma
Authors: Lee Sang Mi , Choi Min Chul , Lee Jeong Won , Kim Taehoen , Jang Su Jin
Published: May 2023

Peritoneal and nodal gliomatosis is a rare disease condition characterized by implants of mature glial tissue on the peritoneum and lymph nodes. It is typically associated with teratoma and has no adverse effect on prognosis. We present a case of 22-year-old woman who underwent FDG PET/CT for the staging of ovarian immature teratoma. PET/CT revealed mildly increased FDG uptake in the peritoneal cavity and increased FDG uptake in the internal mammary and cardiophrenic angle lymph nodes, which were histopathologically diagnosed as peritoneal and nodal gliomatosis. This case suggests that PET/CT findings of peritoneal and nodal gliomatosis could mimic metastasis.
Generalized Muscular Uptake of 99mTc-MDP on Bone Scan in a Patient With Scleromyxedema-Associated Myopathy
Authors: Chen Jinzhi , Zhang Xi , Li Qian , Liu Meng , Fu Zhanli
Published: May 2023

A 62-year-old man presented with a 5-year history of progressive myasthenia, myalgia, and skin changes. Upon laboratory testing, elevated serum creatine kinase and lactate dehydrogenase, as well as monoclonal immunoglobulin Gκ, were observed. A bone scan revealed generalized muscular uptake of 99mTc-MDP, whereas 18F-FDG PET/CT demonstrated only mild hypermetabolism of the muscles. A muscle biopsy showed myofibrillary vacuolar degeneration, and a skin biopsy indicated scleromyxedema. Based on these findings, the patient was diagnosed with scleromyxedema-associated myopathy.
Primary Hepatic Gastrointestinal Stromal Tumor on 18F-FDG PET/CT Images
Authors: Jiang Yang , Lu Qingqing , Lou Cen , Huang Zhongke
Published: May 2023

Primary hepatic gastrointestinal stromal tumor is an extremely rare type of liver tumor with an unknown origin and poor prognosis and usually lacking specific symptoms. This makes it difficult to make an accurate diagnosis. We report the case of a 56-year-old man with primary hepatic gastrointestinal stromal tumor demonstrating multiple heterogeneous lesions with intense FDG uptake in the liver on PET/CT mimicking hepatocellular carcinoma or sarcoma. Primary hepatic gastrointestinal stromal tumor should be considered among the differential diagnoses when multiple FDG-avid primary liver neoplasms are found in patients with malignant characteristic on PET/CT imaging.
Clinical Characteristics and Prognostic Analysis of Osteolytic and Hyperostosis Sphenoid Orbital Meningiomas: A Single-Center Experience
Authors: He Haiyong , Li Manting , Luo Lun , Guo Ying , Li Wensheng
Published: May 2023

Reactive hyperostosis of spheno-orbital meningiomas (SOMs) often occurred in the sphenoid wing, while osteolytic SOMs (O-SOMs) were rarely discussed. This study preliminarily evaluated the clinical characteristics of O-SOMs and analyzed prognostic factors affecting the recurrence of SOMs. We retrospectively analyzed the medical records of consecutive patients who underwent surgery for a SOM between 2015 and 2020. According to the bone changes of sphenoid wing, SOMs were divided into O-SOMs and hyperostosis SOMs (H-SOMs). A total of 31 procedures were performed in 28 patients. All cases were treated by pterional-orbital approach. It was confirmed that 8 cases were O-SOMs and the other 20 cases were H-SOMs. Total tumor resection was performed in 21 cases. There were 19 cases with Ki 67 ≥3%. The patients were followed up for 3 to 87 months. Proptosis improved in all patients. All O-SOMs had no visual deterioration, while 4 H-SOMs cases had visual deterioration. There was no significant difference in clinical outcomes between the two types of SOM. The recurrence of SOM was related to the degree of resection, but not to the type of bone lesions, invasion of cavernous sinus and Ki 67.
A Patient With Exophytic Primary Optic Nerve Sheath Meningioma: Stratified Risk of Surgery Based on the Morphology
Authors: Yamashiro Kei , Sadato Akiyo , Hirose Yuichi
Published: May 2023

Primary optic nerve sheath meningioma (pONSM) is one of the most challenging tumors to manage. Although surgical excision may be considered a treatment option to maintain visual function, the safety of surgery remains debatable due to the non-negligible risk of optic nerve injury. pONSM often grows concentrically around the optic nerve; however, it can also demonstrate an exophytic growth from the optic nerve. The risk of surgical excision of pONSM may vary based on the tumor’s growth pattern and area of contact with the optic nerve; however, there has been no detailed report on risk stratification to date. The authors present an illustrative case of an exophytic pONSM which was removed surgically without complications, suggesting that tumor morphology may also influence the surgical risk. In this report, the imaging and intraoperative features of exophytic pONSM are presented in detail, and the risk factors for complications are discussed.
Cricoid chondronecrosis: a serious complication of prolonged endotracheal intubation
Authors: Bijou Walid , Oukessou Youssef , Mohamed Laachoubi , Rouadi Sami , Abada Reda , Roubal Mohamed , Mahtar Mohamed
Published: May 2023

Chondronecrosis is a rare life-threatening complication of endotracheal intubation. This case is a patient with a history of severe brain injury, who developed a cricoid chondronecrosis after prolonged intubation. The complication was suspected when decannulation led to upper airway obstruction and was confirmed by laryngoscopy and computed tomography. We discuss the diagnosis of the condition, the causative factors, treatment through a literature review.
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance
Authors: Anzai Takumi , Kijima Kaede , Fujimori Miki , Nakamoto Soma , Ishihama Akira , Shimada Tomohiro
Published: May 2023

LldR is a lactate-responsive transcription factor (TF) that transcriptionally regulates the lldPRD operon consisting of lactate permease and lactate dehydrogenase. The lldPRD operon facilitates the utilisation of lactic acid in bacteria. However, the role of LldR in whole genomic transcriptional regulation, and the mechanism involved in adaptation to lactate remains unclear. We used genomic SELEX (gSELEX) to comprehensively analyse the genomic regulatory network of LldR to understand the overall regulatory mechanism of lactic acid adaptation of the model intestinal bacterium

Escherichia coli

. In addition to the involvement of the lldPRD operon in utilising lactate as a carbon source, genes related to glutamate-dependent acid resistance and altering the composition of membrane lipids were identified as novel targets of LldR. A series of in vitro and in vivo regulatory analyses led to the identification of LldR as an activator of these genes. Furthermore, the results of lactic acid tolerance tests and co-culture experiments with lactic acid bacteria suggested that LldR plays a significant role in adapting to the acid stress induced by lactic acid. Therefore, we propose that LldR is an l-/d-lactate sensing TF for utilising lactate as a carbon source and for resistance to lactate-induced acid stress in intestinal bacteria.
CXCL4-induced PBMCs Modulate Vascular Extracellular Matrix through Wnt5a-CaMKII-dependent Release of Calcific Extracellular Vesicles and Matrix Metalloproteinase-7
Authors: Krohn Jona B. , Sicklinger Florian , Spieler Anja , Dihlmann Susanne , Gleissner Christian A. , Katus Hugo A. , Frey Norbert , Leuschner Florian
Published: May 2023

Background

Macrophage heterogeneity plays an increasing role in the study of vascular inflammatory responses. The CXCL4-induced monocyte/macrophage phenotype has previously been implicated with atherosclerotic plaque destabilization, a key process preceding plaque rupture. Monocyte-derived macrophages were found to exhibit a unique transcriptome in the presence of CXCL4 characterized by upregulation of S100A8 and MMP7. However, the mechanisms involved in CXCL4-induced monocyte-mediated vascular inflammation are unknown.

Methods

Single-cell RNA sequencing data were examined for CXCL4-dependent gene expression signatures in plaque macrophages. Human PBMCs were differentiated with CXCL4 and subsequently characterized in terms of osteogenic gene and protein expression signatures and calcific extracellular vesicle release. Association of the CXCL4-induced phenotype with the Wnt pathway was investigated, and CXCL4-induced PBMC-derived EV were analyzed for their potential to elicit an inflammatory response in vSMC. In-vitro findings were verified histologically in calcified human carotid artery plaques.

Results

In human plaque macrophages, single-cell sequencing revealed a CXCL4-susceptible subpopulation bearing a distinct proinflammatory gene expression profile. CXCL4-differentiated PBMCs exhibited a marked induction of S100A8, MMP7 and osteogenic marker transcription concomitant with augmented release of calcific EVs enriched with MMP7, S100A8 and alkaline phosphatase. Under osteogenic conditions, increased overt calcification of the extracellular matrix was observedin vitro. Analysis of inflammatory pathway activation identified the paracrine Wnt5a-CaMKII signaling axis to be causally linked to the CXCL4-induced osteogenic PBMC phenotype, S100A8 and MMP7 enrichment as well as calcific potential of secreted EV. Additionally, CXCL4-polarized PBMC-derived EV differentially stimulated osteogenic/inflammatory genotype transition in vSMC. In human carotid artery plaques, occurrence of CXCL4-induced mononuclear cells coincided with Wnt5a-CaMKII pathway activation and progressive plaque calcification.

Conclusions

This study introduces a novel mechanism driving monocyte/macrophage-mediated extracellular matrix remodeling in calcific inflammatory responses through Wnt5a-CaMKII-activated secretion of MMP7+S100A8+calcifying EV by CXCL4-induced pro-inflammatory monocytes.

Graphical Abstract
Targeted Sequencing of the 9p21.3 Region Reveals Association with Reduced Disease risks in Ashkenazi Jewish Centenarians
Authors: Zhu Yizhou , Ryu Seungjin , Tare Archana , Barzilai Nir , Atzmon Gil , Suh Yousin
Published: May 2023

Genome-wide association studies (GWAS) have pinpointed the chromosomal locus 9p21.3 as a genetic hotspot for various age-related disorders. Common genetic variants in this locus are linked to multiple traits, including coronary artery diseases, cancers, and diabetes. Centenarians are known for their reduced risk and delayed onset of these conditions. To investigate whether this evasion of disease risks involves diminished genetic risks in the 9p21.3 locus, we sequenced this region in an Ashkenazi Jewish centenarian cohort (centenarians: n=450, healthy controls: n=500). Risk alleles associated with cancers, glaucoma, CAD, and T2D showed a significant depletion in centenarians. Furthermore, the risk- and non-risk genotypes are linked to two distinct low-frequency variant profiles, enriched in controls and centenarians, respectively. Our findings provide evidence that the extreme longevity cohort is associated with collectively lower risks of multiple age-related diseases in the 9p21.3 locus.
TARANIS interacts with VRILLE and PDP1 to modulate the circadian transcriptional feedback mechanism inDrosophila
Authors: Akpoghiran Oghenerukevwe , Afonso Dinis J.S. , Zhang Yanan , Koh Kyunghee
Published: May 2023

The molecular clock that generates daily rhythms of behavior and physiology consists of interlocked transcription-translation feedback loops. InDrosophila, the primary feedback loop involving the CLOCK-CYCLE transcriptional activators and the PERIOD-TIMELESS transcriptional repressors is interlocked with a secondary loop involving VRILLE (VRI) and PAR DOMAIN PROTEIN 1 (PDP1), a repressor and activator ofClocktranscription, respectively. Whereas extensive studies have found numerous transcriptional, translational, and post-translational modulators of the primary loop, relatively little is known about the secondary loop. In this study, using male and female flies as well as cultured cells, we demonstrate that TARANIS (TARA), aDrosophilahomolog of the TRIP-Br/SERTAD family of transcriptional coregulators, functions with VRI and PDP1 to modulate the circadian period and rhythm strength. Knocking downtarareduces rhythm amplitude and can shorten the period length, while overexpressing TARA lengthens the circadian period. Additionally,taramutants exhibit reduced rhythmicity and lower expression of the PDF neuropeptide. We find that TARA can form a physical complex with VRI and PDP1, enhancing their repressor and activator functions, respectively. The conserved SERTA domain of TARA is required to regulate the transcriptional activity of VRI and PDP1, and its deletion leads to reduced locomotor rhythmicity. Consistent with TARA’s role in enhancing VRI and PDP1 activity, overexpressingtarahas a similar effect on the circadian period and rhythm strength as simultaneously overexpressingvriandPdp1. Together, our results suggest that TARA modulates circadian behavior by enhancing the transcriptional activity of VRI and PDP1.

Statement of Significance

Internal molecular clocks generating circadian rhythms of around 24 hours broadly impact behavior and physiology, and circadian dysfunction is associated with various neurological and metabolic diseases. TheDrosophilacircadian clock is a valuable model for understanding the molecular mechanisms underlying daily rhythms as many components of the clock are highly conserved. In this study, we identify a conserved gene,taranis, as a novel regulator of theDrosophilamolecular clock. We show that TARANIS modulates circadian behavior by physically interacting with and enhancing the transcriptional activity of clock proteins VRILLE and PDP1. Since mammalian homologs of VRILLE and PDP1 also function in the molecular clock, our results have implications for understanding the mammalian circadian clock.
Neuronal Synchrony and Critical Bistability: Mechanistic Biomarkers for Localizing the Epileptogenic Network
Authors: Wang Sheng H , Arnulfo Gabriele , Nobili Lino , Myrov Vladislav , Ferrari Paul , Ciuciu Philippe , Palva Satu , Palva J Matias
Published: May 2023

Objective

Post-surgical seizure freedom in drug-resistant epilepsy (DRE) patients varies from 30 to 80%, implying that in many cases the current approaches fail to fully map the epileptogenic zone (EZ). This suggests that the EZ entails a broader epileptogenic brain network (EpiNet) beyond the seizure-zone (SZ) that show seizure activity.

Methods

We first used computational modeling to identify putative complex-systems- and systems-neuroscience-driven mechanistic biomarkers for epileptogenicity. We then extracted these epileptogenicity biomarkers from stereo-EEG (SEEG) resting-state data from DRE patients and trained supervised classifiers to localize the SZ with these biomarkers against gold-standard clinical localization. To further explore the prevalence of these pathological biomarkers in an extended network outside of the clinically-identified SZ, we also used unsupervised classification.

Results

Supervised SZ-classification trained on individual features achieved accuracies of 0.6–0.7 areaunder-the-receiver-operating-characteristics curve (AUC). However, combining all criticality and synchrony features improved the AUC up to 0.85.

Unsupervised classification uncovered an EpiNet-like cluster of brain regions with 51% of regions outside of SZ. Brain regions in this cluster engaged in inter-areal hypersynchrony and locally exhibited high amplitude bistability and excessive inhibition, which was strikingly similar to the high seizure-risk regime revealed by computational modeling.

Significance

The finding that combining biomarkers improves EZ localization shows that the different mechanistic biomarkers of epileptogenicity assessed here yield synergistic information. On the other hand, the discovery of SZ-like pathophysiological brain dynamics outside of the clinically-defined EZ provides experimental localization of an extended EpiNet.

Key points

We advanced novel complex-systems- and systems-neuroscience-driven biomarkers for epileptogenicity

Increased bistability, inhibition, and power-low scaling exponents characterized our model operating in a high seizure-risk regime and SEEG oscillations in the seizure-zone (SZ)

Combining all biomarkers yielded more accurate supervised SZ-classification than using any individual biomarker alone

Unsupervised classification revealed more extended pathological brain networks including the SZ and many non-seizure-zone areas that were previously considered healthy
Microplastics clog reproduction in a monkeyflower species
Authors: Carvallo Gastón O. , Muñoz-Michea Valeska
Published: May 2023

Plastic debris is a widespread and significant marker of global change, found in all ecosystems and overpassing the total animal biomass on the whole planet. Despite its ubiquity, our knowledge of its potential effects on terrestrial organisms and ecological processes is still limited.

Recently, a study showed that honey beeApis melliferatransport microplastics (MP; plastic fragments <5 mm) that are added to their bodies. Additionally, a report showed that MP has the potential to reach plant ovules. These findings suggest that pollinators may inadvertently deposit MP on flower stigmas, which could impact the reproductive output of plants.

We assessed whether small polypropylene fragments (<63 μm) deposited on the stigmas decrease pollen tube development, seed production, seed mass, and germination in the Andean-yellow monkeyflowerErythranthe lutea(Phrymaceae).

Using a mix of hand-pollination treatments and ultrastructure observation, we showed that the MP deposit has a negative impact on seed production and the number of pollen tubes that reached ovaries. However, mass per seed and germination of the resulting seeds were not affected.

Our findings warn about the deleterious effects of synthetic plastic on a critical ecosystem process, pollination, and suggest that MP could have significant consequences for angiosperms and crop production.
A Wireless Optoelectronic Probe Monitors Tissue Oxygenation in the Deep Brain
Authors: Cai Xue , Zhang Haijian , Wei Penghu , Liu Quanlei , Sheng Dawid , Li Zhen , Zhao Wenxin , Ye Zhongyin , Xue Zhao , Xie Yang , Dai Yang , Wang Changming , Wang Yuqi , Fu Xin , Zhang Bozhen , Yin Lan , Peng Hongshang , Ding He , Zhao Guoguang , Sheng Xing
Published: May 2023

Real-time detection of tissue oxygenation in the nervous system is crucial for neuroscience exploration and clinical diagnostics. Compared to blood oxygenation, the partial pressure of oxygen in brain tissue (PbtO2) possesses more direct relevance to local neural activities and metabolic conditions. In this paper, we present an implantable optoelectronic probe that wirelessly and continuously monitors PbtO2signals in the deep brain of living animals. The thin-film, microscale implant integrates a light-emitting diode and a photodetector coated with oxygen sensitive dyes. Powered by a battery or an inductive coil, a miniaturized circuit is capable of recording and wirelessly transmitting PbtO2signals, which allows for simultaneous monitoring of PbtO2levels in multiple freely moving rodents. The wireless micro-probe captures cerebral hypoxia states of mice in various scenarios, including altered inspired oxygen concentration, acute ischemia. Particularly, in mouse models with seizures, the micro-probe associates temporal PbtO2variations in multiple brain regions with electrical stimulations imposed in the hippocampus. These materials and device strategies overcome the limits of existing oxygen sensing approaches and provide important insights into neurometabolic coupling.
Metabolite Profiling and Cytotoxic Investigation ofSenecio biafraeOliv. & Hiern (Compositae) on Nauplii Brine Shrimps and Cancer Cell Lines
Authors: Akinola Funke Toyin , Oriyomi Olumayowa Vincent , Ogundele Seun Bayonle , Adekola Mukaila Babatunde , Agbedahunsi Morounfolu Joseph , Babalola Olusegun Olubunmi
Published: May 2023

The study investigated the cytoactivities of methanolic leaf extract (MLE) and fractions ofSenecio biafrae, profiled, and elucidated their metabolites. Hydromethanolic extract ofS. biafraeobtained by maceration was partitioned and subjected to cytotoxicity using brine shrimp lethality assay (BSLA), human cervical adenocarcinoma (HeLa) and prostate cancer cell (PC3) lines. The bioactive principles of most active fractions were profiled using GC-MS. The dichloromethane fraction (DMF) was purified using column and high-performance liquid chromatography to afford compounds 1 and 2 identified by 1H and 13C, DEPT-90, DEPT-135, COSY, NOESY and EIMS spectra. The MLE and its fractions exhibited good toxicity on nauplii brine shrimp. The HF exhibited a pronounced cytoactivity on PC-3 cell line with 92.8% followed by DMF. The GC-MS profiling of HF and DMF identified 17 and 6 constituents respectively comprising saturated and unsaturated fatty acids, diterpenoidal alcohol, phytol and aromatic compounds. Hexadecanoic acid, cis, cis, cis-9, 12, 15-octadecatrienoic acid, and phytol accounted for the highest percentage of the constituents in both fractions. Structure elucidation confirmed compounds 1 and 2 as stigmasterol and ergosterol with cytoactivity which compared favourably with doxorubicin. The study revealed thatS.biafraecontains cytotoconstituents evidenced by proliferation inhibition of HeLa and PC-3 cell lines. The cyto-activities and bioconstituents indicate thatS.biafraehas the potential to be considered as a candidate for drug development in the management of cancer-related conditions. Further investigation into the specific bioactive compounds and their mechanisms of action could provide valuable insights into the therapeutic potential ofS.biafraein cancer treatment.
Similarity and dissimilarity in alteration of gene expression profile associated with inhalational anesthesia between sevoflurane and desflurane
Authors: Nogi Takehiro , Uranishi Kousuke , Suzuki Ayumu , Hirasaki Masataka , Nakamura Tina , Kazama Tomiei , Nagasaka Hiroshi , Okuda Akihiko , Mieda Tsutomu
Published: May 2023

Although sevoflurane is the most commonly used inhalational anesthetic agent, the popularity of desflurane is increasing to a similar level. The main beneficial property of desflurane is the relatively fast emergence of the patient from the anesthetic state after halting its supply compared with anesthesia using other anesthetic agents. However, there has been no comprehensive comparison of the effects of these two anesthetic agents on alterations in liver gene expression profiles in animals, including humans, to assess the levels of hepatotoxicity that is induced at least in some extent by inhalational anesthesia. Thus, we compared alterations in the global gene expression profiles in the livers of rats subjected to inhalational anesthesia by sevoflurane or desflurane by a next-generation sequencing method. Our data revealed that both anesthetic agents significantly activated a similar set of genes including those related to drug metabolism and circadian rhythm. Furthermore, many genes downregulated by sevoflurane were also downregulated by desflurane. However, many of the genes related to the cholesterol biosynthetic process were specifically repressed by sevoflurane, but not by desflurane.
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
Authors: Ermshaus Arik , Piechotta Michael , Rüter Gina , Keilholz Ulrich , Leser Ulf , Benary Manuela
Published: May 2023

Motivation

In precision oncology, clinicians are aiming to find the best treatment for any patient based on their molecular characterization. A major bottleneck is the annotation and evaluation of individual variants, for which usually a range of knowledge bases are manually screened. To incorporate and integrate the vast information of different databases, fast and accurate methods for harmonization are necessary.

preon is a fast and accurate library for the normalization of drug names and cancer types in large-scale data integration.

Availability and Implementation

preon is implemented in Python and freely available via the PyPI repository. Source code and gold standard data sets are available athttps://github.com/ermshaua/preon/.

Contact

manuela.benary@bih-charite.de

Supplementary information

Supplementary data are available online.
Shigellagenerates distinct IAM subpopulations during epithelial cell invasion to promote efficient intracellular niche formation
Authors: Sanchez Lisa , Connor Michael G. , Hamon Mélanie , Valenzuela Camila , Enninga Jost
Published: May 2023

The facultative intracellular pathogenShigella flexneriinvades non-phagocytic epithelial gut cells. Through a syringe-like apparatus called type 3 secretion system, it injects effector proteins into the host cell triggering actin rearrangements leading to its uptake within a tight vacuole, termed the bacterial-containing vacuole (BCV). Simultaneously,Shigellainduces the formation of large vesicles around the entry site, which we refer to as infection- associated macropinosomes (IAMs). After entry,Shigellaruptures the BCV and escapes into the host cytosol by disassembling the BCV remnants. Previously, IAM formation has been shown to be required for efficient BCV escape, but the molecular events associated with BCV disassembly have remained unclear. To identify host components required for BCV disassembly, we performed a microscopy-based screen to monitor the recruitment of BAR domain-containing proteins, which are a family of host proteins involved in membrane shaping and sensing (e.g. endocytosis and recycling) duringShigellaepithelial cell invasion. We identified endosomal recycling BAR protein Sorting Nexin-8 (SNX8) localized to IAMs in a PI(3)P-dependent manner before BCV disassembly. At least two distinct IAM subpopulations around the BCV were found, either being recycled back to cellular compartments such as the plasma membrane or transitioning to become RAB11A positive “contact-IAMs” involved in promoting BCV rupture. The IAM subpopulation duality was marked by the exclusive recruitment of either SNX8 or RAB11A. Finally, hindering PI(3)P production at the IAMs led to an inhibition of SNX8 recruitment at these compartments and delayed both, the step of BCV rupture time and successive BCV disassembly. Overall, our work sheds light on howShigellaestablishes its intracellular niche through the subversion of a specific set of IAMs.
Nanoparticle-induced biomembrane fusion: unraveling the effect of core size on stalk formation
Authors: Brosio Giorgia , Rossi Giulia , Bochicchio Davide
Published: May 2023

Membrane fusionin vitrois a strategy to load model or cell-derived vesicles with proteins, drugs, and genetic materials for theranostic applications. It is thus crucial to develop strategies to control the fusion process, also through synthetic fusogenic agents. Ligand-protected, membrane-penetrating gold nanoparticles (Au NPs) can facilitate membrane fusion, but the molecular mechanisms remain unresolved. Here, we tackle NP-induced stalk formation using a coarse-grained Molecular Dynamics approach and enhanced sampling techniques. We show that smaller (2 nm in diameter) NPs lead to a lower free energy barrier and higher stalk stability than larger NPs (4 nm). We demonstrate that this difference is due to a different ligand conformational freedom, which in turn depends on the Au core curvature. Our study provides precious insights into the mechanisms underlying NP-mediated membrane fusion, while our computational approach is general and applicable to studying stalk formation caused by other fusogenic agents.

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The cell walls of differentCharaspecies (Charophyceae) are characterized by branched galactans rich in 3-O-methylgalactose and absence of arabinogalactan-proteins
Authors: Pfeifer Lukas , Mueller Kim-Kristine , Utermöhlen Jon , Erdt Felicitas , Zehge Jean Bastian Just , Schubert Hendrik , Classen Birgit
Published: May 2023

Streptophyte algae are the closest relatives of land plants and their latest common ancestor performed the most drastic adaptation that happened in plant evolution around 500 million years ago: the conquest of land. Beside other adaptations, this step required changes in cell wall composition. Today knowledge on cell walls of streptophyte algae and especially presence of arabinogalactan-proteins (AGPs), which are important signaling molecules of all land plants, is limited. To get deeper insights in cell walls of streptophyte algae, especially of the Charophyceae, we performed sequential cell wall extractions of fourCharaspecies. The three speciesChara globularis,Chara subspinosaandChara tomentosarevealed comparable cell wall compositions with pectins, xylans and xyloglucans, whereasChara asperawas outstanding with higher amounts of uronic acids in the pectic fractions and lack of reactivity with antibodies binding to xylan- and xyloglucan epitopes. Search for AGPs in the fourCharaspecies and alsoNitellopsis obtusarevealed presence of galactans with pyranosidic galactose in 1,3-, 1,6- and 1,3,6-linkage, which are typical galactan motifs of land plant AGPs. A unique feature of these branched galactans were high portions of 3-O-methylgalactose. OnlyNitellopsiscontained substantial amounts of Ara. Bioinformatic search for prolyl-4-hydroxylase necessary for biosynthesis of AGPs revealed one possible functional sequence in the genome ofChara braunii, but no hydroxyproline could be detected in the fourCharaspecies andNitellopsis obtusa. We conclude that AGPs typical for land plants are absent at least in these members of the Charophyceae.
Phytocystatin 6 is a context-dependent, tight-binding inhibitor ofArabidopsis thalianalegumain isoform β
Authors: Santos Naiá P. , Soh Wai T. , Demir Fatih , Tenhaken Raimund , Briza Peter , Huesgen Pitter F. , Brandstetter Hans , Dall Elfriede
Published: May 2023

Plant legumains are crucial for processing seed storage proteins and are critical regulators of plant programmed cell death. Although research on legumains boosted recently, little is known about their activity regulation. In our study, we used pull-down experiments to identify AtCYT6 as a natural inhibitor of legumain isoform β (AtLEGβ) inArabidopsis thaliana. Biochemical analysis revealed that AtCYT6 inhibits both AtLEGβ and papain-like cysteine proteases through two cystatin domains. The N-terminal domain inhibits papain-like proteases, while the C-terminal domain inhibits AtLEGβ. Furthermore, we showed that AtCYT6 interacts with legumain in a substrate-like manner, facilitated by a conserved asparagine residue in its reactive center loop. Complex formation was additionally stabilized by charged exosite interactions, contributing to pH-dependent inhibition. Processing of AtCYT6 by AtLEGβ suggests a context-specific regulatory mechanism with implications for plant physiology, development, and programmed cell death. These findings enhance our understanding of AtLEGβ regulation and its broader physiological significance.
Extracellular G-quadruplex and Z-DNA protect biofilms from DNase I and forms a DNAzyme with peroxidase activity
Authors: Minero Gabriel Antonio S. , Møllebjerg Andreas , Thiesen Celine , Johansen Mikkel Illemann , Jørgensen Nis Pedersen , Birkedal Victoria , Otzen Daniel , Meyer Rikke L.
Published: May 2023

Many bacteria form biofilms to protect themselves from predators or stressful environmental conditions. In the biofilm, bacteria are embedded in a protective extracellular matrix composed of polysaccharides, proteins and extracellular DNA (eDNA). eDNA most often arises from lysed cells, and it is the only matrix component most biofilms appear to have in common. However, little is known about the form DNA takes in the extracellular space, and how different non-canonical DNA structures such as Z-DNA or G-quadruplex formation might contribute to its function in the biofilm.

The aim of this study was to determine if non-canonical DNA structures form in eDNA-rich staphylococcal biofilms, and if these structures protect the biofilm from degradation by nucleases. We grewStaphylococcus epidermidisbiofilms in laboratory media amended with hemin and NaCl to stabilize secondary DNA structures and visualized their location by immunolabelling and fluorescence microscopy. We furthermore visualized the macroscopic biofilm structure by optical coherence tomography. We developed assays to quantify degradation of Z-DNA and G-quadruplex DNA oligos by different nucleases, and subsequently investigated how these enzymes affected eDNA in the biofilms.

Z-DNA and G-quadruplex DNA were abundant in the biofilm matrix, and were often present in a web-like structure in biofilms grownin vitroandin vivousing a murine implant-associated osteomyelitis model.In vitro, the structures did not form in the absence of NaCl or mechanical shaking during biofilm growth, or in bacterial strains deficient in eDNA or exopolysaccharide production. We thus infer that eDNA and polysaccharides interact, leading to non-canonical DNA structures under mechanical stress when stabilized by salt, and we confirmed that G-quadruplex DNA and Z-DNA was also present in biofilms from infected implants. Mammalian DNase I lacked activity against Z-DNA and G-quadruplex DNA, while Micrococcal nuclease could degrade G-quadruplex DNA and S1 Aspergillus nuclease could degrade Z-DNA. Micrococcal nuclease, which originates fromStaphylococcus aureus, may thus be key for dispersal of biofilm in staphylococci. In addition to its structural role, we show for the first time that the eDNA in biofilms forms a DNAzyme with peroxidase-like activity in the presence of hemin. While peroxidases are part of host defenses against pathogens, we now show that biofilms can possess intrinsic peroxidase activity in the extracellular matrix.

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Development of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic strategy for Alzheimer’s disease
Authors: Du Yuhong , Bradshaw William J. , Leisner Tina M. , Annor-Gyamfi Joel K. , Qian Kun , Bashore Frances M. , Sikdar Arunima , Nwogbo Felix O. , Ivanov Andrey A. , Frye Stephen V. , Gileadi Opher , Brennan Paul E. , Levey Allan I. ,   the Emory-Sage-SGC TREAT-AD Center, Axtman Alison D. , Pearce Kenneth H. , Fu Haian , Katis Vittorio L.
Published: May 2023

Recent genome-wide association studies have revealed genetic risk factors for Alzheimer’s disease (AD) that are exclusively expressed in microglia within the brain. A proteomics approach identified moesin (MSN), a FERM (four-point-one ezrin radixin moesin) domain protein, and the receptor CD44 as hub proteins found within a co-expression module strongly linked to AD clinical and pathological traits as well as microglia. The FERM domain of MSN interacts with the phospholipid PIP2and the cytoplasmic tails of receptors such as CD44. This study explored the feasibility of developing protein-protein interaction inhibitors that target the MSN–CD44 interaction. Structural and mutational analyses revealed that the FERM domain of MSN binds to CD44 by incorporating a beta strand within the F3 lobe. Phage-display studies identified an allosteric site located close to the PIP2binding site in the FERM domain that affects CD44 binding within the F3 lobe. These findings support a model in which PIP2binding to the FERM domain stimulates receptor tail binding through an allosteric mechanism that causes the F3 lobe to adopt an open conformation permissive for binding. High-throughput screening of a chemical library identified two compounds that disrupt the MSN–CD44 interaction, and one compound series was further optimized for biochemical activity, specificity, and solubility. The results suggest that the FERM domain holds potential as a drug development target. The small molecule preliminary leads generated from the study could serve as a foundation for additional medicinal chemistry effort with the goal of controlling microglial activity in AD by modifying the MSN–CD44 interaction.
Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing
Authors: Franco-Echevarría Elsa , Nielsen Mathias , Schulten Anna , Cheema Jitender , Morgan Tomos E , Bienz Mariann , Dean Caroline
Published: May 2023

Polycomb Repressive Complex 2 (PRC2) mediates epigenetic silencing of target genes in animals and plants. In Arabidopsis, PRC2 is required for the cold-induced epigenetic silencing of theFLCfloral repressor locus to align flowering with spring. During this process, PRC2 relies on VEL accessory factors, including the constitutively expressed VRN5 and the cold-induced VIN3. The VEL proteins are physically associated with PRC2, but their individual functions remain unclear. Here, we show an intimate association between recombinant VRN5 and multiple components within a reconstituted PRC2, dependent on a compact conformation of VRN5 central domains. Key residues mediating this compact conformation are conserved amongst VRN5 orthologs across the plant kingdom. By contrast, VIN3 interacts with VAL1, a transcriptional repressor that binds directly toFLC. These associations differentially affect their role in H3K27me deposition: both proteins are required for H3K27me3, but only VRN5 is necessary for H3K27me2. Although originally defined as vernalization regulators, VIN3 and VRN5 co-associate with many targets in the Arabidopsis genome that are modified with H3K27me3. Our work, therefore, reveals the distinct accessory roles for VEL proteins in conferring cold-induced silencing onFLC, with broad relevance for PRC2 targets generally.
Soybean-SCN duel: Novel insight into Soybean’s Resistant Responses toHeterodera glycines
Authors: Torabi Sepideh , Seifi Soren , Geddes-McAlister Jennifer , Tenuta Albert , Wally Owen , Torkamaneh Davoud , Eskandari Milad
Published: May 2023

Soybean cyst nematodes (SCN,Heterodera glycinesIchinohe) are a significant threat to soybean production globally, causing severe yield losses and necessitating the development of effective strategies to combat this devastating nematode disease. This study presents dual RNA-seq analyses of the three most common SCN-resistant lines (Plant Introduction (PI) 437654, 548402, and 88788) and the susceptible line Lee74 against the SCN HG type 1.2.5.7 to identify the mechanisms of resistance and virulence genes involved in resistance breakdown. Transcriptomic and pathway analyses reveal the activation of the phenylpropanoid pathway, MAPK signaling pathway, plant hormone signal transduction, and secondary metabolite pathways in the resistance mechanisms. PI 437654, which exhibited robust resistance (female index, FI=0%), demonstrated unique gene expression associated with cell wall reinforcement, oxidative enzymes, ROS scavengers, and Ca+2 sensors governing the salicylic acid (SA) biosynthesis process, indicating its key defense mechanism. Moreover, using different hosts with varying levels of immunity and a susceptible line provided insights into SCN pathogenesis and howH. glycineovercomes different layers of host immunity by modulating its virulence genes. This research provides novel insights into the molecular mechanisms underlying soybean-SCN interactions and identifies potential targets for developing strategies to manage this devastating nematode disease.
Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements
Authors: Kharytonchyk Siarhei , Burnett Cleo , GC Keshav , Telesnitsky Alice
Published: May 2023

HIV-1 uses heterogeneous transcription start sites (TSSs) to generate two RNA 5’ isoforms that adopt radically different structures and perform distinct replication functions. Although these RNAs differ in length by only two bases, exclusively the shorter RNA is encapsidated while the longer RNA is excluded from virions and provides intracellular functions. The current study examined TSS usage and packaging selectivity for a broad range of retroviruses and found that heterogenous TSS usage was a conserved feature of all tested HIV-1 strains, but all other retroviruses examined displayed unique TSSs. Phylogenetic csomparisons and chimeric viruses’ properties provided evidence that this mechanism of RNA fate determination was an innovation of the HIV-1 lineage, with determinants mapping to core promoter elements. Fine-tuning differences between HIV-1 and HIV-2, which uses a unique TSS, implicated purine residue positioning plus a specific TSS-adjacent dinucleotide in specifying multiplicity of TSS usage. Based on these findings, HIV-1 expression constructs were generated that differed from the parental strain by only two point mutations yet each expressed only one of HIV-1’s two RNAs. Replication defects of the variant with only the presumptive founder TSS were less severe than those for the virus with only the secondary start site.
“Epidermal Eg5 promotes X-ROS dependent paclitaxel neurotoxicity”
Authors: Diaz Antonio Cadiz , Cirrincione Anthony M , Schmidt Natalie A , Ugo Marie J , Amaya Sanchez Maria Celina , Reimonn Cassandra A. , Wuchty Stefan , Pellegrini Adriana D , Rude Leah RK , Pappalardo Leah G , Regan Daniel P , Howell Caitlin , Hrstka Sybil , Dasari Surendra , Lisse Thomas S , Harrison Benjamin J , Xu Mike Xiangxi , Staff Nathan P , Rieger Sandra
Published: May 2023

Taxanes are chemotherapeutic agents that induce microtubule modifications in cancer cells, resulting in cell cycle modifications and tumor remission. Here we show that paclitaxel, a widely used taxane, also induces microtubule modifications in healthy epidermal keratinocytes leading to chemotherapy-induced peripheral neuropathy (CIPN). Paclitaxel activates the cell cycle regulator, Kinesin-5 (Eg5), which promotes microtubule detyrosination and fasciculation (dfMT). Eg5 loss protects neurons from paclitaxel neurotoxicity, whereas keratinocyte-specific overexpression promotes axon degeneration.In vivoimaging and 3D reconstructions of dfMTs and nuclei, combined with mechanotransduction studies further show that dfMTs constrict keratinocyte nuclei, leading to nuclear Nox-dependent reactive oxygen species (X-ROS) formation upstream of MMP-13 and cutaneous sensory axon degeneration. This new insight facilitates our understanding of chemotherapy side effects and highlights the need for targeted therapies.
SLC12A9 is a lysosome-detoxifying ammonium – chloride co-transporter
Authors: Levin-Konigsberg Roni , Mitra Koushambi , Nigam AkshatKumar , Spees Kaitlyn , Hivare Pravin , Liu Katherine , Kundaje Anshul , Krishnan Yamuna , Bassik Michael C.
Published: May 2023

Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity causes ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH4+). Ammonium buildup compromises lysosomal function, suggesting the existence of mechanisms that protect cells from ammonium toxicity. Here, we identified SLC12A9 as a lysosomal ammonium exporter that preserves lysosomal homeostasis. SLC12A9 knockout cells showed grossly enlarged lysosomes and elevated ammonium content. These phenotypes were reversed upon removal of the metabolic source of ammonium or dissipation of the lysosomal pH gradient. Lysosomal chloride increased in SLC12A9 knockout cells and chloride binding by SLC12A9 was required for ammonium transport. Our data indicate that SLC12A9 is a chloride-driven ammonium co-transporter that is central in an unappreciated, fundamental mechanism of lysosomal physiology that may have special relevance in tissues with elevated ammonia, such as tumors.
Reinforcement-based option competition in human dorsal stream during exploration/exploitation of a continuous space
Authors: Hallquist Michael N. , Hwang Kai , Luna Beatriz , Dombrovski Alexandre Y.
Published: May 2023

Primates exploring and exploiting a continuous sensorimotor space rely on maps in the dorsal stream that guide visual search, locomotion, and grasp. For example, an animal swinging from one tree limb to the next uses rapidly evolving sensorimotor representations to decide when to harvest a reward. We show that such exploration/exploitation depends on dynamic maps of competing option values in the human dorsal stream. Using a reinforcement learning (RL) model capable of rapid learning and efficient exploration and exploitation, we show that preferred options are selectively maintained on the map while the values of spatiotemporally distant alternatives are compressed. Consistent with biophysical models of cortical option competition, dorsal stream BOLD signal increased and posterior cortical β1/α oscillations desynchronized as the number of potentially valuable options grew, matching predictions of information-compressing RL rather than traditional RL that caches long-term values. BOLD and β1/α responses were correlated and predicted the successful transition from exploration to exploitation. These option competition dynamics were observed across parietal and frontal dorsal stream regions, but not in the occipito-temporal MT+ sensitive to the average reward rate. Our results also illustrate that models’ diverging predictions about information dynamics can help to adjudicate between them based on population activity.

Graphical abstract