bluuebunny/crossref_metadata_2025 huggingface dataset:
A case report of anastomosing hemangioma of the ovary
Authors: Wang Zhen , Hu Junbo
Published: May 2023

Rationale:

Anastomosing hemangioma (AH) is a rare benign neoplastic vascular lesion that histologically resembles a well-differentiated angiosarcoma. AH commonly involves the urinary system and testes. However, these tumors can also involve the ovaries in some rare cases. This manuscript presents the case of a 28-year-old Chinese woman diagnosed with ovarian AH.

Patient concerns:

The woman was admitted to the hospital with a 4-month history of a right ovarian mass discovered by ultrasound (US) after a spontaneous abortion. The US examination showed a 4 cm × 4 cm irregularly shaped mass with a rich blood supply.

Diagnoses:

AH of the right ovar.

Intervention:

The patient underwent laparoscopic surgery to remove the mass. The postoperative pathological examination revealed that the mass contained capillaries arranged in a characteristic anastomotic or confluent pattern commonly seen in AHs.

Outcomes:

The mass was successfully removed. The follow-up examination at 7 months post-surgery showed that the patient recovered well, and no recurrence or metastasis was found.

Lessons:

AH of the ovary is a rare benign vascular tumor. On imaging examinations, AHs appear as mostly well-defined, heterogeneous nodules with peripheral enhancement as other benign nodules. However, a definitive diagnosis can only be achieved through histopathological examination.
“The Platysma Contraction Pattern in Healthy Adults: A Vector Analysis Study.”
Authors: Ohana Oded , Fezza John P. , Sykes Jonathan , Yoelin Steve G. , Lee James H. , Fezza Reed M. , Lee Wendy W.
Published: May 2023

Background:

The platysma muscle’s role in lower face dynamics is complex. Multiple insertion points to soft-tissue structures at various levels in the lower face create make for a multi-faceted contraction pattern. To avoid adverse effects in cosmetic procedures when targeting the platysma, its anatomy and physiology must be understood. Clinical observations hint to a bi-directional contraction pattern.

Methods:

Eighteen healthy volunteers (13 women and 5 men) with a mean age of 44.2 ± 10.1 years were enrolled. Skin displacement vector analysis was used upon maximal platysma contraction to characterize and calculate the movement of the neck and lower-face skin.

Results:

In all of the participants a bidirectional movement of the skin was observed: the skin of the lower face and inferior to the jaw-line moved caudally, while the skin of the lower neck moved cephalad. Both movements converged at a line situated at 54±10 percent and 55±8 percent of the length between the clavicle and the inferior base of the ear lobe in men and women respectively (p = 0.70).

Conclusions:

The platysma is a bidirectional muscle with a line-of convergence. While the superior portion acts as lip depressor, the lower portion elevates the skin of the upper chest and lower neck. This transition can explain some of the clinically observed adverse effects of neuromodulation of the neck area. It can potentially direct neuromodulation injections to focus above the convergence line to better address lower-face descent.
Combined use of autologous sustained-release scaffold of adipokines and acellular adipose matrix to construct highly vascularized, mature, engineered adipose tissue
Authors: Xu Mimi , He Yunfan , Li Yibao , Liu Kaiyang , Zhang Yuchen , Su Ting , Yao Yao , Jin Xiaoxuan , Zhang Xiangdong , Lu Feng
Published: May 2023

Background:

Adipose tissue engineering plays a key role in the reconstruction of soft tissue defects. The acellular adipose matrix (AAM) is a promising biomaterial for the construction of engineered adipose tissue. However, AAM lacks sufficient adipo-induction potency owing to the abundant loss of matrix-bound adipokines during decellularization.

Methods:

An adipose-derived extracellular matrix (ECM) collagen scaffold, “adipose collagen fragment” (ACF), was prepared using a novel mechanical method that provides sustained release of adipokines. Here, we used label-free proteomics methods to detect the protein components in AAM and ACF. In vivo, ACF was incorporated into AAM or acellular dermal matrix (ADM) and implanted into nude mice to evaluate adipogenesis. Neo-adipocytes, neo-vessels and corresponding gene expression were evaluated. The effects of ACF on adipogenic differentiation of human adipose-derived stem cells (ADSCs) and tube formation by human umbilical vein endothelial cells were tested in vitro.

Results:

Proteomics analysis showed that ACF contains diverse adipogenic and angiogenic proteins. ACF can release diverse adipokines and induce highly vascularized, mature adipose tissue in AAM, and even in non-adipogenic ADM. Higher expression of adipogenic markers PPAR-γ and CEBP-α and greater numbers of tubule structures were observed in ACF-treated groups in vitro.

Conclusion:

The combination of ACF and AAM could serve as a novel and promising strategy to construct mature, vascularized adipose tissue for soft tissue reconstruction.
Ocular Torsional Instability—A Neurodiagnostic Sign of Prenuclear Disease
Authors: Brodsky Michael C.
Published: May 2023

Background:

Accurate diagnosis of efferent visual system disease in neuro-ophthalmology involves the classification of clinical signs as prenuclear, nuclear, or infranuclear in origin. Over many years, I have come to recognize ocular torsional instability as a clinical sign of prenuclear disease.

Methods:

Retrospective chart review of patients in whom ocular torsional instability was diagnosed using indirect ophthalmoscopy.

Results:

Twenty patients were diagnosed as having ocular torsional instability (OTI). Eight had neuro-ophthalmologic disease caused by structural injury to prenuclear ocular motor areas. Six of these had structural lesions primarily involving the cerebellum, one had a midbrain glioma, and one had traumatic encephalomalacia. Eight additional patients had infantile strabismus (esotropia in 7, exotropia in 1) associated with various combinations of monocular nasotemporal optokinetic asymmetry, latent nystagmus, and dissociated vertical divergence (DVD), indicating prenuclear involvement of subcortical visuovestibular pathways within the brain. Three additional patients presented with intermittent exotropia with DVD signifying early onset, while 2 had acquired esotropia that was noninfantile in origin. One had partially accommodative esotropia with bilateral inferior oblique overaction, and one presented with acquired esotropia followed by spontaneous secondary exotropia.

Conclusions:

OTI provides a useful clinical sign of prenuclear ocular motor dysfunction. When detected in patients without any signs of infantile or early-onset strabismus, OTI signifies the need for neuroimaging to rule out neurovestibular or cerebellar causes of prenuclear disease.
Determining the Minimum Clinically Important Difference for the European Hernia Society Quality of Life Instrument in Inguinal Hernia Repair Patients
Authors: Shukla Priya , Huang Li-Ching , Zhao Alison , Sharew Betemariam , Miller Ben , Beffa Lucas , Petro Clayton C , Krpata David M , Prabhu Ajita S , Rosen Michael J
Published: May 2023

BACKGROUND:

Patient-reported outcomes in clinical research allow for a more comprehensive and meaningful assessment of interventions but are subjective and difficult to interpret. European Registry for Abdominal Wall Hernias-Quality of Life (EuraHS-QoL) is a tool designed to assess perioperative quality of life for patients undergoing inguinal hernia repair, one of the most performed operations worldwide. Defining the minimum clinically important difference (MCID) for EuraHS-QoL tool can help standardize its interpretation for research purposes and facilitate improved shared decision making in clinical settings.

STUDY DESIGN:

A combination of 3 approaches for estimating MCIDs was used in this study. First, 2 distribution-based approaches were used that based estimates on statistical parameters of the data. The SEM provided a minimum value for the MCID, and one-half of the SD provided a point estimate of the MCID. Second, anchor-based approaches integrated patient perceptions of their overall well-being before and after surgery to provide benchmarks for the MCID. Last, iterative surveys of expert hernia surgeons were used to yield the final MCIDs for each domain and the composite EuraHS-QoL score.

RESULTS:

The overall range of EuraHS-QoL is 0 to 90, with subdomain ranges of 0 to 30 for the pain domain, 0 to 40 for the restriction of activities domain, and 0 to 20 for the cosmesis domain, with higher scores representing worse outcomes. The overall MCID for EuraHS-QoL is 10. Domain-specific MCIDs are 3 for the pain domain, 5 for the restriction of activities domain, and 2 for the cosmesis domain.

CONCLUSIONS:

In this study, we define overall and domain-specific MCIDs for the EuraHS-QoL instrument using statistical methods, patient-based methods, and clinical expertise, providing estimates that are both statistically and clinically significant.
Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.
Authors: Mahoney-Kurpe Sam C. , Palevich Nikola , Noel Samantha J. , Gagic Dragana , Biggs Patrick J. , Soni Priya , Reid Peter M. , Koike Satoshi , Kobayashi Yasuo , Janssen Peter H. , Attwood Graeme T. , Moon Christina D.
Published: May 2023

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ‘Christensenellales’, were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6–99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other

Christensenellaceae

strains and had <88.1 % sequence identity to the closest type-strain sequence from

Luoshenia tenuis

NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order ‘Christensenellales’. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.
The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage
Authors: Snaith Ann E. , Dunn Steven J. , Moran Robert A. , Newton Paul N. , Dance David A. B. , Davong Viengmon , Kuenzli Esther , Kantele Anu , Corander Jukka , McNally Alan
Published: May 2023

Increased colonization by antimicrobial-resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL)-producing

Escherichia coli

that colonized travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 48 isolates obtained from the daily stool samples of 23 travellers over a 3 week period. This method revealed a collection of 105 distinct plasmids, 38.1 % (n=40) of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=23) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasized the importance of IS elements, specifically members of the IS6/IS26 family, in the evolution of complex multidrug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying bla
CTX-M and mcr genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in

E. coli

populations that can disseminate internationally through travel networks.
The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate
Authors: Prity Farzana T. , Tobin Liam A. , Maharajan Ram , Paulsen Ian T. , Cain Amy K. , Hamidian Mehrad
Published: May 2023

Acinetobacter baumannii

is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although

A. baumannii

is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant

A. baumannii

(strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus

Acinetobacter

beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.
The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Feasibility Phase
Authors: Mendez Luque Laura F. , Avelar-Barragan Julio , Nguyen Hellen , Nguyen Jenny , Soyfer Eli M. , Liu Jiarui , Chen Jane H. , Mehrotra Nitya , Kosiorek Heidi E. , Dueck Amylou , Himstead Alexander , Heide Elena , Lem Melinda , El Alaoui Kenza , Mas Marin Eduard , Scherber Robyn M. , Mesa Ruben A. , Whiteson Katrine L. , Odegaard Andrew , Fleischman Angela G.
Published: May 2023

Purpose

Chronic inflammation is integral to Myeloproliferative Neoplasm (MPN) pathogenesis. JAK inhibitors reduce cytokine levels, but not without significant side effects. Nutrition is a low-risk approach to reduce inflammation and ameliorate symptoms in MPN. We performed a randomized, parallel-arm study to determine the feasibility of an education-focused Mediterranean diet intervention among MPN patients.

Experimental Design

We randomly assigned participants to either a Mediterranean diet or standard US Dietary Guidelines for Americans (USDA). Groups received equal but separate education with registered dietician counseling and written dietary resources. Patients were prospectively followed for feasibility, adherence, and symptom burden assessments. Biological samples were collected at four time points during the 15-week study to explore changes in inflammatory biomarkers and gut microbiome.

Results

The Mediterranean diet was as easy to follow for MPN patients as the standard USDA diet. Over 80% of the patients in the Mediterranean diet group achieved a Mediterranean Diet Adherence Score of ≥8 throughout the entire active intervention period, whereas less than 50% of the USDA group achieved a score of ≥8 at any time point. Improvement in symptom burden was observed in both diet groups. No significant changes were observed in inflammatory cytokines. The diversity and composition of the gut microbiome remained stable throughout the duration of the intervention.

Conclusions

With dietician counseling and written education MPN patients can adhere to a Mediterranean eating pattern. Diet interventions may be further developed as a component of MPN care, and potentially even be incorporated into the management of other chronic clonal hematologic conditions.

STATEMENT OF TRANSLATIONAL RELEVANCE

Chronic clonal hematologic disorders, such as myeloproliferative neoplasm (MPN), lie at the intersection between malignancy and chronic inflammatory disease. Chronic inflammation is responsible for many of the clinical consequences of MPN. Diet is a central tenant of management of chronic conditions characterized by subclinical inflammation, such as cardiovascular disease, but has not entered the treatment algorithm for clonal hematologic disorders. Here, we establish that a Mediterranean diet intervention is feasible in the MPN patient population and can improve symptom burden. These findings warrant large dietary interventions in patients with clonal hematologic disorders to test the utility of diet in improvement of clinical outcomes.
Intercomparison of growth models for Antarctic krill (Euphausia superba): towards a generalised understanding
Authors: Bahlburg Dominik , Thorpe Sally , Meyer Bettina , Berger Uta , Murphy Eugene
Published: May 2023

Antarctic krill is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, which provide alternative perspectives and cross-validation of analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.
Human hnRNPA1 reorganizes telomere-bound Replication Protein A
Authors: Granger Sophie L. , Sharma Richa , Kaushik Vikas , Razzaghi Mortezaali , Honda Masayoshi , Gaur Paras , Bhat Divya S. , Labenz Sabryn M. , Heinen Jenna E. , Williams Blaine A. , Tabei S. M. Ali , Wlodarski Marcin W. , Antony Edwin , Spies Maria
Published: May 2023

Human replication protein A (RPA) is a heterotrimeric ssDNA binding protein responsible for many aspects of cellular DNA metabolism. Dynamic interactions of the four RPA DNA binding domains (DBDs) with DNA control replacement of RPA by downstream proteins in various cellular metabolic pathways. RPA plays several important functions at telomeres where it binds to and melts telomeric G-quadruplexes, non-canonical DNA structures formed at the G-rich telomeric ssDNA overhangs. Here, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM) and mass photometry (MP) with biophysical and biochemical analyses to demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) specifically remodels RPA bound to telomeric ssDNA by dampening the RPA configurational dynamics and forming a ternary complex. Uniquely, among hnRNPA1 target RNAs, telomeric repeat-containing RNA (TERRA) is selectively capable of releasing hnRNPA1 from the RPA-telomeric DNA complex. We speculate that this telomere specific RPA-DNA-hnRNPA1 complex is an important structure in telomere protection.

One Sentence Summary

At the single-stranded ends of human telomeres, the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) binds to and modulates conformational dynamics of the ssDNA binding protein RPA forming a ternary complex which is controlled by telomeric repeat-containing RNA (TERRA).
Metabolic alterations unravel the materno–fetal immune responses with disease severity in pregnant women infected with SARS-CoV-2
Authors: Hora Sandhya , Pahwa Prabhjyoti , Siddiqui Hamda , Saxena Anoushka , Kashyap Minal , Sevak Jayesh Kumar , Singh Ravinder , Javed Maryam , Yadav Pushpa , Kale Pratibha , Ramakrishna Gayatri , Rathore Asmita , Maras Jaswinder Singh , Tyagi Shakun , Sarin Shiv kumar , Trehanpati Nirupama
Published: May 2023

Background

Pregnancy being immune compromised state, COVID-19 disease poses high risk of premature delivery and threat to fetus. Plasma metabolome regulates immune cellular responses and we aimed to analyze the plasma secretome, metabolome and immune cells in COVID-19 positive pregnant mother and cord blood.

Methods

COVID-19 RT-PCR positive pregnant females (n=112) asymptomatic (n=82), or with mild (n=21) or moderate (n=9) disease and control healthy pregnant (n=10) females were included. Mother’s blood and cord blood (n=80) was analysed for untargeted metabolome profiling and plasma cytokines by high-resolution mass spectrometry (MS) and multiplex cytokine bead array. Immune scan in mothers was done using flow cytometry.

Results

In asymptomatic SARS-CoV-2 infection, --the amino acid metabolic pathways such as glycine, serine, L-lactate and threonine metabolism was upregulated, riboflavin and tyrosine metabolism, downregulated. In mild to moderate disease, the pyruvate and NAD+metabolism (energy metabolic pathways) were mostly altered. In addition to raised TNF-α, IFN-α, IFN-γ, IL-6 cytokine storm, IL-9 was increased in both mothers and neonates. Pyruvate and NAD+metabolic pathways along with IL-9 and IFN-γ had impact on non-classical monocytes, increased CD4 T cells and B cells but depleted CD8+T cells. Cord blood mimicked the mother’s metabolomic profiles by showing altered valine, leucine, isoleucine, glycine, serine, threonine in asymptomatic and NAD+and riboflavin metabolism in mild and moderate disease subjects.

Conclusions

Our results demonstrate a graduated immune-metabolomic interplay in mother and fetus in pregnant females with different degrees of severity of COVID-19 disease. IL-9 and IFN- γ regulated pyruvate, lactate TCA metabolism and riboflavin metabolism with context to disease severity are hall marks of this materno-fetal metabolome.

Highlights

SARS-CoV-2 infection alters energy consumption metabolic pathways during pregnancy.

Pregnant women with mild to moderate COVID-19 show increased energy demands, and consume stored glucose by upregulating pyruvate and NAD+metabolism.

Increased TNF-α and IL-9 in mild COVID-19 disease involve TCA cycle to produce lactate and consume stored glucose by up regulating pyruvate and nicotinamide and nicotinate metabolism.

With mild to moderate disease, raised IL-9 and TNF-α, decreased riboflavin pathway, exhaustion of T and B cells cause pathogenesis.

Cord blood mimics the metabolic profile of mother’s peripheral blood, SARS- CoV-2 infection reshapes immune-metabolic profiles of mother-infant dyad.

Graphical Abstract
Identification and mapping ofRpi-blb4in diploid wild potato speciesSolanum bulbocastanum
Authors: Li Jie , Kaur Amanpreet , Harrower Brian , Armstrong Miles , Dou Daolong , Wang Xiaodan , Hein Ingo
Published: May 2023

More than 170 years after causing the potato famine in Ireland, late blight is still considered one of the most devastating crop diseases. Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen,Phytophthora infestans. We have identified and mapped a novel broad-spectrum disease resistance gene effective againstP. infestansfrom the wild, diploid potato speciesSolanum bulbocastanum. Diagnostic resistance gene enrichment sequencing (dRenSeq) was used to confirm the uniqueness of the identified resistance. RenSeq and GenSeq-based mapping of the resistance, referred to asRpi-blb4, alongside recombinant screening, positioned the locus responsible for the resistance to potato Chromosome 5. The interval spans approximately 2.3 MB and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.
In-section Click-iT detection and super-resolution CLEM: Shedding light on nucleolar ultrastructure and S-phase progression in plants
Authors: Franek M , Koptasikova L , Miksatko J , Pospisil J , Liebl D , Esner M , Macickova E , Dvorackova M , Fajkus J
Published: May 2023

Correlative light and electron microscopy (CLEM) is an essential tool that allows for localisation of a particular target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometer scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of serial sections by both, single-molecule localization microscopy and transmission electron microscopy for correlative analysis. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows a dramatic improvement in fluorophore blinking behavior relative to the whole-mount approaches. Here we used commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-typeArabidopsis thalianaseedlings, as well as FASCIATA1 and NUCLEOLIN1 mutants and applied our on-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.
KLIPP - a precision CRISPR approach to target structural variant junctions in cancer
Authors: Yang Huibin , Hulbatte Radhika Suhas , Kelleher Alan , Gratsch Natalie , Wang Yin , Palmbos Philip L. , Ljungman Mats
Published: May 2023

Current cancer therapies typically give rise to dose-limiting normal tissue toxicity. We have developed KLIPP, a precision cancer approach that specifically kills cancer cells using CRISPR/Cas9 technology. The approach consists of guide RNAs that target cancer-specific structural variant junctions to nucleate two parts of a dCas9-conjugated endonuclease, Fok1, leading to its activation. We show that KLIPP causes induction of DNA double strand breaks (DSBs) at the targeted junctions and cell death. When cancer cells were grown orthotopically in mice, activation of Fok1 at only two junctions led to the disappearance of tumor cells in 7/11 mice. This therapeutic approach has high specificity for tumor cells and is independent of tumor-specific drivers. Individualized translation of KLIPP to patients would be transformative and lead to consistent and simplified cancer treatment decisions.
Thrombocytopenia Independently Leads to Monocyte Immune Dysfunction
Authors: Li Chen , Ture Sara K. , Nieves-Lopez Benjamin , Blick-Nitko Sara K. , Maurya Preeti , Livada Alison C. , Stahl Tyler J. , Kim Minsoo , Pietropaoli Anthony P. , Morrell Craig N.
Published: May 2023

In addition to their well-studied hemostatic functions, platelets are immune cells. Platelets circulate at the interface between the vascular wall and leukocytes, and transient platelet-leukocyte complexes are found in both healthy and disease states, positioning platelets to provide physiologic cues of vascular health and injury. Roles for activated platelets in inducing and amplifying immune responses have received an increasing amount of research attention, but our past studies also showed that normal platelet counts are needed in healthy conditions to maintain immune homeostasis. We have now found that thrombocytopenia (a low platelet count) leads to monocyte dysfunction, independent of the cause of thrombocytopenia, in a manner that is dependent on direct platelet-monocyte CD47 interactions that regulate monocyte immunometabolism and gene expression. Compared to monocytes from mice with normal platelet counts, monocytes from thrombocytopenic mice had increased toll-like receptor (TLR) responses, including increased IL-6 production. Furthermore,ex vivoco-incubation of resting platelets with platelet naïve bone marrow monocytes, induced monocyte metabolic programming and durable changes in TLR agonist responses. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) on monocytes from thrombocytopenic mice showed persistently open chromatin at LPS response genes and resting platelet interactions with monocytes induced histone methylation in a CD47 dependent manner. Using mouse models of thrombocytopenia and sepsis, normal platelet numbers were needed to limit monocyte immune dysregulation andIL6expression in monocytes from human patients with sepsis also inversely correlated with patient platelet counts. Our studies demonstrate that in healthy conditions, resting platelets maintain monocyte immune tolerance by regulating monocyte immunometabolic processes that lead to epigenetic changes in TLR-related genes. This is also the first demonstration of sterile cell interactions that regulate of innate immune-metabolism and monocyte pathogen responses.
GRK2 Kinases in the Primary Cilium Initiate SMOOTHENED-PKA Signaling in the Hedgehog Cascade
Authors: Walker Madison F. , Zhang Jingyi , Steiner William , Ku Pei-I , Zhu Ju-Fen , Michaelson Zachary , Yen Yu-Chen , Lee Annabel , Long Alyssa B. , Casey Mattie J. , Poddar Abhishek , Nelson Isaac B. , Arveseth Corvin D. , Nagel Falko , Clough Ryan , LaPotin Sarah , Kwan Kristen M. , Schulz Stefan , Stewart Rodney A. , Tesmer John J. G. , Caspary Tamara , Subramanian Radhika , Ge Xuecai , Myers Benjamin R.
Published: May 2023

During Hedgehog (Hh) signal transduction in development and disease, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by binding the protein kinase A catalytic subunit (PKA-C) and physically blocking its enzymatic activity. Here we show that GPCR kinase 2 (GRK2) orchestrates this process during endogenous Hh pathway activation in the vertebrate primary cilium. Upon SMO activation, GRK2 rapidly relocalizes from the ciliary base to the shaft, triggering SMO phosphorylation and PKA-C interaction. Reconstitution studies reveal that GRK2 phosphorylation enables active SMO to bind PKA-C directly. Lastly, the SMO-GRK2-PKA pathway underlies Hh signal transduction in a range of cellular andin vivomodels. Thus, GRK2 phosphorylation of ciliary SMO, and the ensuing PKA-C binding and inactivation, are critical initiating events for the intracellular steps in Hh signaling. More broadly, our study suggests an expanded role for GRKs in enabling direct GPCR interactions with diverse intracellular effectors.
Improving xylose consumption inRhodotorula toruloidesthrough heterologous expression of xylose reductase and xylulokinase
Authors: de Oliveira Paola Monteiro , Pinheiro Marina Julio , De Biaggi Juliano Sabedotti , Tšitšerin Artjom , Tammekivi Eliise , Herodes Koit , Bonturi Nemailla , Lahtvee Petri-Jaan
Published: May 2023

The oleaginous yeastRhodotorula toruloidesis a promising host for sustainable bioproduction due to its capacity to naturally utilize xylose present in lignocellulosic biomass, an abundant and renewable resource. However, its xylose consumption pathway is still not completely understood. To better understand the potential limitations in xylose utilization inR. toruloides, heterologous xylose reductase fromScheffersomyces stipitis, together with the native and heterologous xylulokinases from three different microorganisms (Scheffersomyces stipitis, Candida intermedia, andEscherichia coli) were overexpressed solely and in combination. The overexpression of xylulokinases showed more significant improvements in terms of xylose consumption rate compared to the single overexpression of xylose reductase. When the heterologous xylulokinase fromEscherichia coliwas overexpressed, the specific xylose consumption rate was improved by 66% and the maximum specific growth rate by 30% compared to the parental strain. The xylose specific consumption rate increased by 146% and the maximum specific growth rate increased by 118% when heterologous genes for xylose reductase and xylulokinase fromE. coliwere overexpressed together. These results suggest that the low expression of xylulokinase inR. toruloides, which has been reported previously, could limit its sugar consumption, while supporting higher lipid accumulation in this yeast.
The marine natural microbiome mediates physiological outcomes in host nematodes
Authors: Xue Yiming , Xie Yusu , Cao Xuwen , Zhang Liusuo
Published: May 2023

Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores, however how habitat bacteria effects physiological outcomes in marine nematodes remains largely unknown. Here, we used aLitoditis marinainbred line to assess how native bacteria modulates host nematode physiology. We characterized seasonal dynamic bacterial compositions inL. marinahabitats, and examined the impacts of 448 habitat bacteria isolates onL. marinadevelopment, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development ofL. marinaand its terrestrial relativeCaenorhabditis eleganswere significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated withL. marinadevelopment (e.g., ubiquinol and hemebbiosynthesis), while pyridoxal 5’-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ10, hemeb, Acetyl-CoA, and acetaldehyde promotedL. marinadevelopment, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared betweenL. marinaandC. elegans. Furthermore, we identified two bacterial metabolic pathways correlated withL. marinalifespan, while a distinct one inC. elegans. Strikingly, we found that glycerol supplementation significantly extendedL. marinabut notC. eleganslongevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects onL. marinaandC. elegansphysiology. Our integrative approach will provide a microbe–nematodes framework for microbiome mediated effects on host animal fitness.
Perceived Clinical Readiness of Senior Medical Students as Outcomes of Online Clerkship in the Philippines: New Normal in Medical Education
Authors: Abear Adam James A. , Benitez Marie Bernice P. , Cabrillos Krissha Marie S. , Casaña Adrian V. , Doctora Ma. Theresa Mae P. , Ellema Joan Marie D. , Fuentes Bianca Louise U. , Lam Justin Riley Y. , Mendoza John Emmanuel C. , Tan Shairah P. , Tan Shannon D.
Published: May 2023

TITLE

Perceived Clinical Readiness of Senior Medical Students as Outcomes 0f Online Clerkship in the Philippines: New Normal in Medical Education

INTRODUCTION

COVID-19 formed new challenges to the medical institutions; it resulted in the transition from the usual face-to-face classes and direct clerkship training within the hospital to a new remote learning with online lectures and virtual clinical experience. Given the new online interactive setting, problems were raised given the limited patient care and interaction as well as restricted bedside teaching opportunities and its impact on how medical students can acquire and hone their clinical skills.

OBJECTIVE

To determine the perceived clinical readiness of the medical clerks in the new normal setting in the Philippines.

METHODOLOGY

Convenience sampling was used to gather respondents who were asked to answer an online survey questionnaire. The questions pertained to: academic training profile, clinical skills, patient management, communication, understanding clinical guidelines, and personal development. After analyzing the data, the scales of readiness from these subjects were gathered.

RESULTS

The medical clerks in the Philippines perceived that they were ready with regards to understanding clinical guidelines, communication, personal development, and patient management. They were moderately ready in the different clinical skills in the departments of Family and Community Medicine, Internal Medicine, Pediatrics, Surgery and Obstetrics and Gynecology with some specific skills in Surgery and Obstetrics and Gynecology being perceived as less ready than the rest.

CONCLUSION

The impact of the pandemic has disrupted the student’s confidence and readiness. This shows that online clerkship in this time of pandemic may have provided learning to a certain degree but it is not enough to replace what face-to-face training could offer.
Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters
Authors: Zahm Adam M. , Owens William S. , Himes Samuel R. , Rondem Kathleen E. , Fallon Braden S. , Gormick Alexa N. , Bloom Joshua S. , Kosuri Sriram , Chan Henry , English Justin G.
Published: May 2023

Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. However, a reliable and precise method for selecting minimally-sized synthetic promoters with desired background, amplitude, and stimulation response profiles has been elusive. In this study, we introduce a massively parallel reporter assay library containing 6184 synthetic promoters, each less than 250 bp in length. This comprehensive library allows for rapid identification of promoters with optimal transcriptional output parameters across multiple cell lines and stimuli. We showcase this library’s utility to identify promoters activated in unique cell types, and in response to metabolites, mitogens, cellular toxins, and agonism of both aminergic and non-aminergic GPCRs. We further show these promoters can be used in luciferase reporter assays, eliciting 50-100 fold dynamic ranges in response to stimuli. Our platform is effective, easily implemented, and provides a solution for selecting short-length promoters with precise performance for a multitude of applications.
Transcriptional changes consistent with impaired neuronal differentiation, angiogenesis, and tumor plasticity induced in human subpallial telencephalic organoid-glioblastoma chimeras
Authors: Chiola Simone , Yang Jingye , Ullah H M Arif , Napan Kandy , Huang Qiju , Gamboa Nicholas , Youssef Osama , Colman Howard , Cheshier Samuel H. , Shcheglovitov Alex
Published: May 2023

Glioblastoma multiforme (GBM) is one of the most aggressive and therapy-resistant brain tumors prevalent in both adults and children. Despite extensive research to understand GBM pathology, it remains unclear how neural cells in the human brain interact with GBM cells to support their brain propagation and therapy resistance and whether GBM cells exert any influence on the properties of human neural cells. In this study, we co-culture human stem cell-derived subpallial telencephalic organoids with patient-derived proneural or mesenchymal GBM spheroids to investigate their reciprocal interactions. We show that both proneural and mesenchymal GBM spheroids readily fuse and propagate with human organoids, forming organoid-GBM chimeras, without the need for exogenous growth factors. GBM cells within the chimeras adapt by modulating gene expression profiles consistent with diminished proliferation, heightened hypoxia, increased angiogenesis, and proneural-to-mesenchymal transition in proneural GBM. Both proneural or mesenchymal GBMs also exert an impact on the properties of neural cells in the chimeras, leading to the suppression of neuronal genes and an upregulation expression of genes associated with hypoxia and angiogenesis. Collectively, this study identifies specific genes and molecular pathways that can be altered in GBM and neural cells by reciprocal interactions in a human developing brain-like environment for an increased understanding of GBM pathology and future therapy development.
Treacle’s ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair
Authors: Velichko Artem K. , Petrova Nadezhda V. , Deriglazov Dmitry A. , Kovina Anastasia P. , Luzhin Artem V. , Kazakov Eugene P. , Kireev Igor I. , Razin Sergey V. , Kantidze Omar L.
Published: May 2023

We investigated the role of the nucleolar protein Treacle in organizing and regulating the nucleolus in human cells. Our results support Treacle’s ability to form liquid-like phase condensates through electrostatic interactions among molecules. The formation of these biomolecular condensates is crucial for segregating nucleolar fibrillar centers from the dense fibrillar component and ensuring high levels of rRNA gene transcription and accurate rRNA processing. Both the central and C-terminal domains of Treacle are required to form liquid-like condensates. The initiation of phase separation is attributed to the C-terminal domain. The central domain is characterized by repeated stretches of alternatively charged amino-acid residues and is vital for condensate stability. Overexpression of mutant forms of Treacle that cannot form liquid-like phase condensates compromises the assembly of fibrillar centers, suppressing rRNA gene transcription and disrupting rRNA processing. These mutant forms also fail to recruit DNA topoisomerase II binding protein 1 (TOPBP1), suppressing the DNA damage response in the nucleolus.
Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs
Authors: Olsen Johan G. , Prestel Andreas , Kassem Noah , Broendum Sebastian S. , Shamim Hossain Mohammad , Simonsen Signe , Grysbæk Martin , Mortensen Josefine , Rytkjær Louise Lund , Haxholm Gitte W. , Marabini Riccardo , Carr Antony M. , Crehuet Ramon , Nielsen Olaf , Kragelund Birthe B.
Published: May 2023

DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) fromS. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy,in vivoassays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
Phage activity againstStaphylococcus aureusis impaired in plasma and synovial fluid
Authors: Mutti Michele , Moreno David Sáez , Restrepo-Córdoba Marcela , Visram Zehra , Resch Grégory , Corsini Lorenzo
Published: May 2023

S. aureus is a pathogen that frequently causes severe morbidity and phage therapy is being discussed as an alternative to antibiotics for the treatment of S. aureus infections. In this in vitro and animal study, we demonstrated that the activity of anti-staphylococcal phages is severely impaired in plasma and synovial fluid. Despite phage replication in these matrices, lysis of the bacteria was slower than phage propagation, and no reduction of the bacterial population was observed. This phage inhibition is due to a 99% reduction of phage adsorption, already at 10% plasma concentration. Coagulation factors bind S. aureus resulting in the formation of aggregates and blood clots that protect the bacterium from the phages. This was confirmed by the finding that purified fibrinogen is sufficient to impair phage activity. In contrast, dissolution of the clots by tissue plasminogen activator (tPA) partially restored phage activity. Consistent with these in vitro findings, phage treatment did not reduce bacterial burdens in a neutropenic mouse S. aureus thigh infection model. In summary, phage treatment of S. aureus infections may be fundamentally challenging, and more investigation is needed prior to proceeding to in-human trials.
PI(3,4,5)P3 allosteric regulation of repressor activator protein 1 controls antigenic variation in trypanosomes
Authors: Touray Abdoulie O. , Rajesh Rishi , Isebe Tony , Sternlieb Tamara , Loock Mira , Kutova Oksana , Cestari Igor
Published: May 2023

African trypanosomes evade host immune clearance by antigenic variation, causing persistent infections in humans and animals. These parasites express a homogeneous surface coat of variant surface glycoproteins (VSGs). They transcribe one out of hundreds of VSG genes at a time from telomeric expression sites (ESs) and periodically change the VSG expressed by transcriptional switching or recombination. The mechanisms underlying the control of VSG switching and its developmental silencing remain elusive. We report that telomeric ES activation and silencing entail an on/off genetic switch controlled by a nuclear phosphoinositide signaling system. This system includes a nuclear phosphatidylinositol 5-phosphatase (PIP5Pase), its substrate PI(3,4,5)P3, and the repressor-activator protein 1 (RAP1). RAP1 binds to ES sequences flanking VSG genes via its DNA binding domains and represses VSG transcription. In contrast, PI(3,4,5)P3 binds to the N-terminus of RAP1 and controls its DNA binding activity. Transient inactivation of PIP5Pase results in the accumulation of nuclear PI(3,4,5)P3, which binds RAP1 and displaces it from ESs, activating transcription of silent ESs and VSG switching. The system is also required for the developmental silencing of VSG genes. The data provides a mechanism controlling reversible telomere silencing essential for the periodic switching in VSG expression and its developmental regulation.