bluuebunny/crossref_metadata_2025 huggingface dataset:
Detrimental Effect ofTrypanosoma brucei bruceiInfection on Memory B Cells and Host Ability to Recall Protective B-cell Responses
Authors: Moon Sangphil , Janssens Ibo , Kim Kyung Hyun , Stijlemans Benoit , Magez Stefan , Radwanska Magdalena
Published: March 2022

Background

Trypanosoma brucei brucei evades host immune responses by multiple means, including the disruption of B-cell homeostasis. This hampers anti-trypanosome vaccine development. Because the cellular mechanism underlying this pathology has never been addressed, our study focuses on the fate of memory B cells (MBCs) in vaccinated mice upon trypanosome challenge.

Methods

A trypanosome variant surface glycoprotein (VSG) and fluorescent phycoerythrin were used as immunization antigens. Functional and cellular characteristics of antigen-specific MBCs were studied after homologous and heterologous parasite challenge.

Results

Immunization with AnTat1.1 VSG triggers a specific antibody response and isotype-switched CD73+CD273+CD80+ MBCs, delivering 90% sterile protection against a homologous parasite challenge. As expected, AnTat1.1 VSG immunization does not protect against infection with heterologous VSG-switched parasites. After successful curative drug treatment, mice were shown to have completely lost their previously induced protective immunity against the homologous parasites, coinciding with the loss of vaccine-induced MBCs. A phycoerythrin immunization approach confirmed that trypanosome infections cause the general loss of antigen-specific splenic and bone marrow MBCs and a reduction in antigen-specific immunoglobulin G.

Conclusions

Trypanosomosis induces general immunological memory loss. This benefits the parasites by reducing the stringency for antigenic variation requirements.
Overview of the ethical guidelines for medical and biological research involving human subjects in Japan
Authors: Eba Junko , Nakamura Kenichi
Published: March 2022

The new national guidelines for clinical research, the Ethical Guidelines for Medical and Biological Research Involving Human Subjects, were implemented in Japan in June 2021. The guidelines were developed by integrating two ethical guidelines: Ethical Guidelines for Medical and Health Research Involving Human Subjects and Ethical Guidelines for Human Genome/Gene Analysis Research. The Ethical Guidelines for Clinical Research were originally developed as three separate guidelines: Ethical Guidelines for Human Genome/Gene Analysis Research formulated in 2001, Ethical Guidelines for Epidemiological Research in 2002 and Ethical Guidelines for Clinical Research in 2003. They have undergone several amendments and integration in response to the government’s policy changes, such as the protection of personal information, conflicts of interest and reliability of clinical research. The three major changes introduced in the New Integrated Guidelines in 2021 are centralized review, electromagnetic informed consent and research cooperating organization. These are expected to be used as tools to facilitate the conduct of research. This review discusses the regulations of academic clinical research in Japan, the history of ethical guidelines and the three major changes introduced in the New Integrated Guidelines.
Deacetylation of MTHFD2 by SIRT4 senses stress signal to inhibit cancer cell growth by remodeling folate metabolism
Authors: Zhang Fan , Wang Di , Li Jintao , Su Ying , Liu Suling , Lei Qun-Ying , Yin Miao
Published: March 2022

Folate metabolism plays an essential role in tumor development. Various cancers display therapeutic response to reagents targeting key enzymes of the folate cycle, but obtain chemoresistance later. Therefore, novel targets in folate metabolism are highly demanded. Methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase 2 (MTHFD2) is one of the key enzymes in folate metabolism and its expression is highly increased in multiple human cancers. However, the underlying mechanism that regulates MTHFD2 expression remains unknown. Here, we elucidate that SIRT4 deacetylates the conserved lysine 50 (K50) residue in MTHFD2. K50 deacetylation destabilizes MTHFD2 by elevating cullin 3 E3 ligase-mediated proteasomal degradation in response to stressful stimuli of folate deprivation, leading to suppression of nicotinamide adenine dinucleotide phosphate production in tumor cells and accumulation of intracellular reactive oxygen species, which in turn inhibits the growth of breast cancer cells. Collectively, our study reveals that SIRT4 senses folate availability to control MTHFD2 K50 acetylation and its protein stability, bridging nutrient/folate stress and cellular redox to act on cancer cell growth.
Effects of aging on basement membrane of tibialis anterior muscle during recovery following muscle injury in rats
Authors: Kanazawa Yuji , Nagano Mamoru , Koinuma Satoshi , Sugiyo Shinichi , Shigeyoshi Yasufumi
Published: March 2022

We investigated the effect of aging on the basement membrane (BM) during postinjury muscle recovery. Using a rat model, we found that aging delayed muscle fiber and BM recovery. In addition, expression of BM-related factors peaked 7 days after muscle injury among both young and older rats. Peak expression of collagen IV synthetic factors decreased with age, whereas expression of the degradative factor was unaffected by age. These results suggest that age-related delays in postinjury muscle fiber and BM recovery may be related to the suppression of collagen IV synthetic factors.
SEED LIPID DROPLET PROTEIN1, SEED LIPID DROPLET PROTEIN2, and LIPID DROPLET PLASMA MEMBRANE ADAPTOR mediate lipid droplet–plasma membrane tethering
Authors: Krawczyk Hannah Elisa , Sun Siqi , Doner Nathan M , Yan Qiqi , Lim Magdiel Sheng Satha , Scholz Patricia , Niemeyer Philipp William , Schmitt Kerstin , Valerius Oliver , Pleskot Roman , Hillmer Stefan , Braus Gerhard H , Wiermer Marcel , Mullen Robert T , Ischebeck Till
Published: March 2022

Membrane contact sites (MCSs) are interorganellar connections that allow for the direct exchange of molecules, such as lipids or Ca2+ between organelles, but can also serve to tether organelles at specific locations within cells. Here, we identified and characterized three proteins of Arabidopsis thaliana that form a lipid droplet (LD)–plasma membrane (PM) tethering complex in plant cells, namely LD-localized SEED LD PROTEIN (SLDP) 1 and SLDP2 and PM-localized LD-PLASMA MEMBRANE ADAPTOR (LIPA). Using proteomics and different protein–protein interaction assays, we show that both SLDPs associate with LIPA. Disruption of either SLDP1 and SLDP2 expression, or that of LIPA, leads to an aberrant clustering of LDs in Arabidopsis seedlings. Ectopic co-expression of one of the SLDPs with LIPA is sufficient to reconstitute LD–PM tethering in Nicotiana tabacum pollen tubes, a cell type characterized by dynamically moving LDs in the cytosolic streaming. Furthermore, confocal laser scanning microscopy revealed both SLDP2.1 and LIPA to be enriched at LD–PM contact sites in seedlings. These and other results suggest that SLDP and LIPA interact to form a tethering complex that anchors a subset of LDs to the PM during post-germinative seedling growth in Arabidopsis.
SNARE SYP132 mediates divergent traffic of plasma membrane H+-ATPase AHA1 and antimicrobial PR1 during bacterial pathogenesis
Authors: Baena Guillermo , Xia Lingfeng , Waghmare Sakharam , Karnik Rucha
Published: March 2022

The vesicle trafficking SYNTAXIN OF PLANTS132 (SYP132) drives hormone-regulated endocytic traffic to suppress the density and function of plasma membrane (PM) H+-ATPases. In response to bacterial pathogens, it also promotes secretory traffic of antimicrobial pathogenesis-related (PR) proteins. These seemingly opposite actions of SYP132 raise questions about the mechanistic connections between the two, likely independent, membrane trafficking pathways intersecting plant growth and immunity. To study SYP132 and associated trafficking of PM H+-ATPase 1 (AHA1) and PATHOGENESIS-RELATED PROTEIN1 (PR1) during pathogenesis, we used the virulent Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) bacteria for infection of Arabidopsis (Arabidopsis thaliana) plants. SYP132 overexpression suppressed bacterial infection in plants through the stomatal route. However, bacterial infection was enhanced when bacteria were infiltrated into leaf tissue to bypass stomatal defenses. Tracking time-dependent changes in native AHA1 and SYP132 abundance, cellular distribution, and function, we discovered that bacterial pathogen infection triggers AHA1 and SYP132 internalization from the plasma membrane. AHA1 bound to SYP132 through its regulatory SNARE Habc domain, and these interactions affected PM H+-ATPase traffic. Remarkably, using the Arabidopsis aha1 mutant, we discovered that AHA1 is essential for moderating SYP132 abundance and associated secretion of PR1 at the plasma membrane for pathogen defense. Thus, we show that during pathogenesis SYP132 coordinates AHA1 with opposing effects on the traffic of AHA1 and PR1.
Scurvy in Children: The Silent Masquerader
Authors: Subhash Swathy , Santosh Sanuja Titus
Published: March 2022

In modern society, scurvy is well known in its historical perspective rather than clinical relevance. Scurvy is classically thought to manifest with signs of ‘bleeding painful gums’ in the undernourished. Little is known regarding its ability to mimic a wide range of rheumatological, orthopaedic, neurological and haematological illnesses. Due to the rarity of its occurrence, there is a poor understanding among present-day clinicians, and so scurvy can easily deceive the uninitiated. We report a school-aged boy with normal neurodevelopment who presented with lower limb pain and difficulty in walking. He was seen by multiple specialist doctors before the clinical diagnosis of scurvy was made by a general paediatrician. Investigations showed that this child had X-ray changes typical of scurvy with low serum ascorbic acid levels. On supplementation with vitamin C, he showed dramatic improvement in symptoms and gradually achieved complete recovery.
Involvement ofArabidopsisAcyl Carrier Protein 1 in PAMP-Triggered Immunity
Authors: Zhao Zhenzhen , Fan Jiangbo , Yang Piao , Wang Zonghua , Opiyo Stephen Obol , Mackey David , Xia Ye
Published: March 2022

Plant fatty acids (FAs) and lipids are essential in storing energy and act as structural components for cell membranes and signaling molecules for plant growth and stress responses. Acyl carrier proteins (ACPs) are small acidic proteins that covalently bind the fatty acyl intermediates during the elongation of FAs. The Arabidopsis thaliana ACP family has eight members. Through reverse genetic, molecular, and biochemical approaches, we have discovered that ACP1 localizes to the chloroplast and limits the magnitude of pattern-triggered immunity (PTI) against the bacterial pathogen Pseudomonas syringae pv. tomato. Mutant acp1 plants have reduced levels of linolenic acid (18:3), which is the primary precursor for biosynthesis of the phytohormone jasmonic acid (JA), and a corresponding decrease in the abundance of JA. Consistent with the known antagonistic relationship between JA and salicylic acid (SA), acp1 mutant plants also accumulate a higher level of SA and display corresponding shifts in JA- and SA-regulated transcriptional outputs. Moreover, methyl JA and linolenic acid treatments cause an apparently enhanced decrease of resistance against P. syringae pv. tomato in acp1 mutants than that in WT plants. The ability of ACP1 to prevent this hormone imbalance likely underlies its negative impact on PTI in plant defense. Thus, ACP1 links FA metabolism to stress hormone homeostasis to be negatively involved in PTI in Arabidopsis plant defense.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The CYCLOPS Response Element in the NIN Promoter Is Important but Not Essential for Infection Thread Formation During Lotus japonicus–Rhizobia Symbiosis
Authors: Akamatsu Akira , Nagae Miwa , Takeda Naoya
Published: March 2022

The establishment of the legume-rhizobia symbiosis, termed the root-nodule symbiosis (RNS), requires elaborate interactions at the molecular level. The host plant–derived transcription factor NODULE INCEPTION (NIN) is known to be crucial for RNS, regulating associated processes such as alteration of root hair morphology, infection thread formation, and cell division during nodulation. This emphasizes the importance of the precise spatiotemporal regulation of NIN expression for the establishment of RNS; however, the detailed role of NIN promoter sequences in this process remains unclear. The daphne mutant, a nin mutant allele containing a chromosomal translocation approximately 7 kb upstream of the start codon, does not form nodules but does form infection threads, indicating that the region within 7 kb of the NIN start codon contributes to NIN expression during infection thread formation. CYCLOPS binds to a CYCLOPS response element ( CYC-RE) in the NIN promoter, and cyclops mutants are defective in infection thread formation. Here, we performed complementation analysis in nin mutants, using various truncated forms of the NIN promoter, and found that the CYC-RE is important for infection thread formation. Additionally, the CYC-RE deletion mutant, generated through CRISPR/Cas9 technology, displayed a significant reduction in infection thread formation, indicating that the CYC-RE is important for the fine-tuning of NIN expression during this process. However, the fact that infection thread formation is not completely abolished in the CYC-RE deletion mutant suggests that cis and trans factors other than CYCLOPS and the CYC-RE may cooperatively regulate NIN expression for the induction of infection thread formation.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
RNA-Seq Analysis Discovers the Critical Role of Rel in ppGpp Synthesis, Pathogenicity, and the VBNC State of Clavibacter michiganensis
Authors: Bai Kaihong , Jiang Na , Chen Xing , Xu Xiaoli , Li Jianqiang , Luo Laixin
Published: March 2022

The viable but nonculturable (VBNC) state is a unique survival strategy of bacteria in response to stress conditions. It was confirmed that Clavibacter michiganensis, the causal agent of bacterial canker in tomato, could be induced into the VBNC state by exposure to CuSO4 in an oligotrophic solution. RNA-sequencing analysis was used to monitor the mechanisms of the VBNC state during CuSO4 induction in C. michiganensis. The results identified that numerous genes involved in stringent response, copper resistance, and stress resistance were upregulated, and some involved in cell division were downregulated significantly. The study investigated the importance of Rel, which is an essential enzyme in the synthesis of the molecular alarmone ppGpp, via the generation of a Δrel mutant and its complementation strain. Biological characterization revealed that deficiency of rel reduced the bacterial growth, production of exopolysaccharides, and pathogenicity as well as ppGpp production. The Δrel mutant increased the sensitivity to environmental stress, exhibiting reduced growth on minimal media and a propensity to enter the VBNC state in response to CuSO4. These findings have important implications for the understanding of survival mechanism and management of C. michiganensis and other phytopathogenic bacteria.
Prognostic Stratification of Diffuse Large B-cell Lymphoma Using Clinico-genomic Models: Validation and Improvement of the LymForest-25 Model
Authors: Mosquera Orgueira Adrián , Díaz Arías Jose Ángel , Cid López Miguel , Peleteiro Raíndo Andrés , López García Alberto , Abal García Rosanna , González Pérez Marta Sonia , Antelo Rodríguez Beatriz , Aliste Santos Carlos , Pérez Encinas Manuel Mateo , Fraga Rodríguez Máximo Francisco , Bello López José Luis
Published: March 2022

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Despite notable therapeutic advances in the last decades, 30%–40% of affected patients develop relapsed or refractory disease that frequently precludes an infamous outcome. With the advent of new therapeutic options, it becomes necessary to predict responses to the standard treatment based on rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). In a recent communication, we presented a new machine learning model (LymForest-25) that was based on 25 clinical, biochemical, and gene expression variables. LymForest-25 achieved high survival prediction accuracy in patients with DLBCL treated with upfront immunochemotherapy. In this study, we aimed to evaluate the performance of the different features that compose LymForest-25 in a new UK-based cohort, which contained 481 patients treated with upfront R-CHOP for whom clinical, biochemical and gene expression information for 17 out of 19 transcripts were available. Additionally, we explored potential improvements based on the integration of other gene expression signatures and mutational clusters. The validity of the LymForest-25 gene expression signature was confirmed, and indeed it achieved a substantially greater precision in the estimation of mortality at 6 months and 1, 2, and 5 years compared with the cell-of-origin (COO) plus molecular high-grade (MHG) classification. Indeed, this signature was predictive of survival within the MHG and all COO subgroups, with a particularly high accuracy in the “unclassified” group. Integration of this signature with the International Prognostic Index (IPI) score provided the best survival predictions. However, the increased performance of molecular models with the IPI score was almost exclusively restricted to younger patients (<70 y). Finally, we observed a tendency towards an improved performance by combining LymForest-25 with the LymphGen mutation-based classification. In summary, we have validated the predictive capacity of LymForest-25 and expanded the potential for improvement with mutation-based prognostic classifications.
Optimized infection control practices augment the robust protective effect of vaccination for ESRD patients during a hemodialysis facility SARS-CoV-2 outbreak
Authors: Meller Megan E. , Pfaff Bridget L. , Borgert Andrew J. , Richmond Craig S. , Athas Deena M. , Kenny Paraic A. , Sabin Arick P.
Published: March 2022

Background

While dialysis patients are at greater risk of serious SARS-CoV-2 complications, stringent infection prevention measures can help mitigate the risk of infection and transmission within dialysis facilities. We describe an outbreak of 14 cases diagnosed in a 13-day period in the second quarter of 2021 in a hospital-based ESRD facility, and our coordinated use of epidemiology, viral genome sequencing, and infection control practices to quickly end the cycle of transmission.

Methods

Symptomatic patients and staff members were diagnosed via RT-PCR tests. Facility-wide screening was conducted using rapid SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic PCR specimens.

Results

Of the 106 patients who received dialysis in the facility, 10 were diagnosed with SARS-CoV-2 infection, as was one patient support person. Of three positive staff members, two were unvaccinated and had provided care for six and four of the affected patients, respectively. Sequencing demonstrated that all the cases in the cluster shared an identical B.1.1.7./Alpha substrain. Attack rates were greatest among unvaccinated patients and staff. Vaccine effectiveness was 88% among patients.

Conclusions

Prompt recognition of an infection cluster and rapid intervention efforts successfully ended the outbreak. Alongside consistent adherence to core infection prevention measures, vaccination was highly effective in reducing disease incidence and morbidity in this vulnerable population.
Trivalent NDV-HXP-S vaccine protects against phylogenetically distant SARS-CoV-2 variants of concern in mice
Authors: González-Domínguez Irene , Martínez Jose Luis , Slamanig Stefan , Lemus Nicholas , Liu Yonghong , Lai Tsoi Ying , Carreño Juan Manuel , Singh Gagandeep , Singh Gagandeep , Schotsaert Michael , Mena Ignacio , McCroskery Stephen , Coughlan Lynda , Krammer Florian , García-Sastre Adolfo , Palese Peter , Sun Weina
Published: March 2022

Equitable access to vaccines is necessary to limit the global impact of the coronavirus disease 2019 (COVID-19) pandemic and the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. In previous studies, we described the development of a low-cost vaccine based on a Newcastle Disease virus (NDV) expressing the prefusion stabilized spike protein from SARS-CoV-2, named NDV-HXP-S. Here, we present the development of next-generation NDV-HXP-S variant vaccines, which express the stabilized spike protein of the Beta, Gamma and Delta variants of concerns (VOC). Combinations of variant vaccines in bivalent, trivalent and tetravalent formulations were tested for immunogenicity and protection in mice. We show that the trivalent preparation, composed of the ancestral Wuhan, Beta and Delta vaccines, substantially increases the levels of protection and of cross-neutralizing antibodies against mismatched, phylogenetically distant variants, including the currently circulating Omicron variant.
Acupuncture with or without acupoint application for primary dysmenorrhea: protocol for a systematic review and meta-analysis
Authors: Zhao Xuewei , Tian Yu , Zhao Jinying , Jiang Hailin , Sun Jiabao , Zhi Xiaoyu , Liu Baiyan , Liu Wu , Liu Yanze , Li Tie , Wang Fuchun
Published: March 2022

Introduction

Dysmenorrhea is the most common gynaecological symptom reported by women. Ninety percent of women presenting for primary care experience some menstrual pain. Population surveys suggest that, although prevalence rates vary considerably by geographic al location, complaints of dysmenorrhea are widespread in diverse populations. This study will evaluate the results of randomized controlled trials to determine the efficacy and safety of acupuncture with or without acupoint application for the treatment of dysmenorrhea.

Methods

Eight databases, including China National Knowledge Infrastructure, Chinese Scientific Journal Database, Cochrane Central Register of Controlled Trials, Embase, MEDLINE, PubMed, Wanfang Database, and Web of Science, will be searched using English and Chinese search strategies. In addition, manual retrieval of research papers, conference papers, ongoing experiments, and internal reports, among others, will supplement electronic retrieval. All eligible studies published on or before December 12, 2021 will be selected. To enhance the effectiveness of the study, only clinical randomized controlled trials related to the use of acupuncture with or without acupoint application for the treatment of dysmenorrhea will be included.

Analysis

The Visual Analog Scale will be the primary outcome measure, whereas the McGill pain questionnaire, SF-36 Scale, Self-Rating Anxiety, and Self-Rating Depression scale will be the secondary outcomes. Side effects and adverse events will be included as safety evaluations. To ensure the quality of the systematic evaluation, study selection, data extraction, and quality assessment will be independently performed by two authors, and a third author will resolve any disagreement.

Ethics and dissemination

This systematic review will evaluate the efficacy and safety of acupuncture with or without acupoint application for the treatment of dysmenorrhea. Since all included data will be obtained from published articles, it does not require ethical approval and will be published in a peer-reviewed journal.

INPLASY registration number

INPLASY202230051.
Inference of B cell clonal families using heavy/light chain pairing information
Authors: Ralph Duncan K. , Matsen Frederick A.
Published: March 2022

Abstract

Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically im-prove clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to thepartissoftware package (https://github.com/psathyrella/partis).

AuthorSummary

Antibodies form part of the adaptive immune response, and are critical to immunity acquired by both vaccination and infection. Next generation sequencing of the B cell receptor (BCR) repertoire provides a broad and highly informative view of the DNA sequences from which antibodies arise. Until recently, however, this sequencing data was not able to pair together the two domains (from separate chromosomes) that make up a functional antibody. In this paper we present several methods to improve analysis of the newpaireddata that does pair together sequence data for complete antibodies. We first show a method that better groups together sequences stemming from the same ancestral cell, solving a problem called “clonal family inference.” We then show two methods that can correct for various imperfections in the data’s identification of which sequences pair together to form complete antibodies, which together may allow for significantly simplified experimental methods.
An integrative analysis of the biological clock hypothesis in human gut microbiome
Authors: Moss Anh D. , Sun Shan , Blakley Ivory C. , Fodor Anthony A.
Published: March 2022

Background

While previous studies have explored the relationship between aging and the gut microbiome, it remains unclear how consistent and reproducible this association is across different cultures and groups. We performed an integrative analysis with 11 independent datasets from nine different countries to test the idea that the aging gut microbiome can be viewed as a biological clock, in which microbial changes associated with age are consistent and measurable across distinct datasets.

Results

As expected, our Principal Coordinate Analysis found strong batch effects with study ID by far the strongest signal across datasets. Despite this large batch effect, we found a consistent signal across studies that was largely driven by sample size with only our larger cohorts showing taxa in common associated with age. Likewise, Shannon diversity and richness were not consistently associated with age across the 11 datasets, but some positive correlations with richness and host age were observed among the four largest cohorts. The taxon with the most potential as a biomarker for the aging human gut microbiome is genus Bifidobacterium, with significantly negative associations with host age in three out of the four datasets that had more than 200 samples.

Conclusion

The driving force behind low reproducibility of association of age with the microbiome in previous studies appears to be inadequate sample size rather than structural differences in the microbial community based on cohort characteristics. Results from a power analysis suggest that future studies on the aging human gut microbiome consider on the order of 100-300 samples to consistently observe an age signal. With these larger sample sizes, parametric and non-parametric model yield broadly similar power.
High-throughput and high-sensitivity biomarker monitoring in body fluid by FAIMS-enhanced fast LC SureQuant™ IS targeted quantitation
Authors: Kalogeropoulos Konstantinos , Savickas Simonas , Haack Aleksander M. , Larsen Cathrine A. , Mikosiński Jacek , Schoof Erwin M. , Smola Hans , Bundgaard Louise , auf dem Keller Ulrich
Published: March 2022

The authors have withdrawn their manuscript whilst they perform additional analyses to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (uadk@dtu.dk).
Sensory neuron-associated macrophages proliferate in the sensory ganglia after peripheral nerve injury in a CX3CR1 signaling dependent manner
Authors: Guimarães Rafaela M. , da Silva Conceição E. A. , Davoli-Ferreira Marcela , Gomes Francisco Isaac F. , Mendes Atlante , Fonseca Miriam M. , Damasceno Samara , Andrade Larissa P. , Cunha Fernando Q. , Alves-Filho José C. , Cunha Thiago M.
Published: March 2022

Resident macrophages are distributed across all tissues and are highly heterogeneous as a consequence of adaptation to different tissue-specific environments. The resident macrophages of the sensory ganglia (sensory neuron-associated macrophages, sNAMs) are in close contact with the cell body of primary sensory neurons and might play physiological and pathophysiological roles. After peripheral nerve injury, there is an increase in the population of macrophages in the sensory ganglia which have been involved in different conditions, especially in neuropathic pain development and nerve regeneration. However, it is still under debate whether macrophages accumulation in the sensor ganglia after peripheral nerve injury is due to the local proliferation of resident macrophages or as a result of blood monocytes infiltration. Here, we confirmed that the number of macrophages increased in the DRGs after spared nerve injury (SNI) model in mice. By using different approaches, we found that the increase in the number of macrophages in the DRGs after SNI is mainly in consequence of the proliferation of resident CX3CR1+ macrophages but not due to infiltration of CCR2+ blood monocytes. These proliferating macrophages are the source of the production of pro-inflammatory cytokines such as TNF and IL-1b. In addition, we found that CX3CR1 signaling is involved in the sNAMs proliferation after peripheral nerve injury. In summary, these results indicated that peripheral nerve injury leads to sNAMs proliferation in the sensory ganglia in a CX3CR1-dependent manner. In conclusion, sNAMs proliferation could be modulated to change pathophysiological conditions such as chronic neuropathic pain and/or nerve regeneration.
Semaphorin3F reduces vascular endothelial and smooth muscle cell PI3K activation and decreases neointimal plaque formation
Authors: Rattanasopa Chutima , Castano-Mayan David , Su Chengxun , Farrugia Aaron J. , Corlianò Maria , Nilcham Pakhwan , Pang Crystal , Hota Monalisa , Mei Koh Ser , Lee Wendy , Cibi Dasan Mary , Aiba Atsu , Singh Manvendra K. , Wong Siew Cheng , Rotzschke Olaf , Bershadsky Alexander , Hou Han Wei , Liehn Elisa A. , Ghosh Sujoy , Singaraja Roshni R.
Published: March 2022

We previously conducted genetic analyses, and identified semaphorin signaling as associating with coronary artery disease. Of the semaphorins, human vascular expression profiling suggestedSEMA3Fas potentially linked to atherogenesis. In hyperlipidemic mice, SEMA3F reduced aortic lesion area, and increased fibrous cap endothelial content, leading to plaque stability. In a disturbed-flow-mediated endothelial dysfunction-driven lesion model, the absence ofSema3fincreased plaques, further implicating SEMA3F in endothelial function. Monocyte adhesion toSema3f-/-vascular endothelial cells (VECs) was elevated, driven by increased PI3K activity, leading to increased NF-κB-mediated elevation in VCAM1 and ICAM1 expression, suggesting that SEMA3F reduces VEC PI3K activity. Increased permeability led to increased monocyte transmigration throughSema3f-/-VECs, and mTOR phosphorylation was decreased, suppressing VE-cadherin expression and cell-cell adherens junction stability. Actomyosin fiber formation was decreased inSema3f-/-VECs, which was reversed by PI3K inhibition, further implicating SEMA3F in adherens junction stability. InSema3f-/-vascular smooth muscle cells (VSMCs), active PI3K was also increased. PI3K facilitates VSMC proliferation, migration, and pro-atherogenic phenotype switching, which were reduced by SEMA3F. In agreement, in a model of VSMC proliferation and migration-induced neointima formation, SEMA3F reduced plaques. Semaphorin3F is causally atheroprotective. SEMA3F’s suppression of VEC and VSMC PI3K activation may contribute to its atheroprotection.
MRSCloud: a Cloud-based MR Spectroscopy Tool for Basis Set Simulation
Authors: Hui Steve C.N. , Saleh Muhammad G. , Zöllner Helge J. , Oeltzschner Georg , Fan Hongli , Li Yue , Song Yulu , Jiang Hangyi , Near Jamie , Lu Hanzhang , Mori Susumu , Edden Richard A. E.
Published: March 2022

Background

Accurate quantification of in vivo proton magnetic resonance spectra involves modeling with a linear combination of known metabolite basis functions. Basis sets can be generated by numerical simulation using the quantum mechanical density-matrix formalism. Accurate simulations for a basis set require correct sequence timings, and pulse shapes and durations.

Purpose

To present a cloud-based spectral simulation tool ‘MRSCloud’. It allows community users of MRS to simulate a vendor- and sequence-specific basis set online in a convenient and timeefficient manner. This tool can simulate basis sets for 3 major MR scanner vendors (GE, Philips, Siemens), including conventional acquisitions and spectral editing schemes (MEGA, HERMES, HERCULES) with PRESS and semi-LASER localization.

Study Type

Prospective.

Specimen

N/A

Field Strength/Sequence

Simulations of 3T basis sets for conventional and spectral-editing sequences (MEGA, HERMES, HERCULES) with PRESS and sLASER localizations.

Assessment

Simulated metabolite basis functions generated by MRSCloud are compared to those generated by FID-A and MARSS, and a phantom-acquired basis-set from LCModel.

Statistical Tests

Intraclass correlation coefficients (ICC) were calculated to measure the agreement between individual metabolite basis functions generated using different packages. Statistical analysis was performed using R in RStudio.

Results

Simulation time for a full basis set is approximately 1 hour. ICCs between MRSCloud and FID-A were at least 0.98 and ICCs between MRSCloud and MARSS were at least 0.96. ICCs between simulated MRSCloud basis spectra and acquired LCModel basis spectra were lowest for Gln at 0.68 and highest for NAA at 0.96.

Data Conclusion

Substantial reductions in runtime have been achieved by implementing the 1D projection method, coherence-order filtering, and pre-calculation of propagators. High ICC values indicated that the accelerating features are running correctly and produce comparable and accurate basis sets. The generated basis set has been successfully used with LCModel.
flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits
Authors: Zhou Feng , Butterworth Adam S , Asimit Jennifer L
Published: March 2022

flashfm-ivis provides a suite of interactive visualisation plots to view potential causal genetic variants that underlie associations that are shared or distinct between multiple quantitative traits and compares results between single- and multi-trait fine-mapping. Unique features include network diagrams that show joint effects between variants for each trait and regional association plots that integrate fine-mapping results, all with user-controlled zoom features for an interactive exploration of potential causal variants across traits.

Availability and Implementation

flashfm-ivis is an open-source software under the MIT license. It is available as an interactive web-based tool (http://shiny.mrc-bsu.cam.ac.uk/apps/flashfm-ivis/) and as an R package format. Code and documentation are available at https://github.com/fz-cambridge/flashfm-ivis and https://zenodo.org/record/6376244#.YjnarC-l2X0. Additional features can be downloaded as standalone R libraries to encourage reuse.

Contact

feng.zhou@mrc-bsu.cam.ac.uk or jennifer.asimit@mrc-bsu.cam.ac.uk
Cellular Mechanisms Underlying Central Sensitization in a Mouse Model of Chronic Muscle Pain
Authors: Lin Yu-Ling , Yang Zhu-Sen , Wong Wai-Yi , Lin Shih-Che , Wang Shuu-Jiun , Chen Shih-Pin , Cheng Jen-Kun , Lu Hui , Lien Cheng-Chang
Published: March 2022

Chronic pain disorders are often associated with psychiatric symptoms. The central nucleus of the amygdala (CeA) has emerged as an integrative hub for nociceptive and affective components during the development of central pain. Although the exact cause for this process remains unknown, prior adverse injuries are precipitating factors and thought to transform nociceptors into a primed state for chronic pain. However, the cellular basis underlying the primed state and the subsequent pain chronification remains unknown. Here, we investigated cellular and synaptic alterations of the CeA in a mouse model of chronic muscle pain. In these mice, local infusion of pregabalin, a clinically approved drug for fibromyalgia and other chronic pain disorders, into the CeA or selective inactivation of somatostatin-expressing CeA (CeA-SST) neurons during the priming phase prevented pain chronification. Further, electrophysiological recording revealed that CeA-SST neurons received increased excitatory transmission and showed enhanced excitability in chronic pain states. In line with the possible role of CeA-SST neurons in central sensitization, chemogenetic inactivation of CeA-SST neurons or pharmacological suppression of nociceptive afferents from the brainstem to CeA-SST neurons by pregabalin after the development of chronic muscle pain alleviated pain and negative emotions.
Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue
Authors: Ziemski Michal , Adamov Anja , Kim Lina , Flörl Lena , Bokulich Nicholas A.
Published: March 2022

The volume of public nucleotide sequence data has blossomed over the past two decades, enabling novel discoveries via re-analysis, meta-analyses, and comparative studies for uncovering general biological trends. However, reproducible re-use and management of sequence datasets remains a challenge. We created the software pluginq2-fondueto enable user-friendly acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles. The software allows fully provenance-tracked programmatic access to and management of data from the Sequence Read Archive (SRA). Sequence data and accompanying metadata retrieved withq2-fonduefollow a validated format, which is interoperable with the QIIME 2 ecosystem and its multiple user interfaces. To highlight the manifold capabilities ofq2-fondue, we present several demonstration analyses using amplicon, whole genome, and shotgun metagenome datasets. These use cases demonstrate howq2-fondueincreases analysis reproducibility and transparency from data download to final visualizations by including source details in the integrated provenance graph. We believeq2-fonduewill lower existing barriers to comparative analyses of nucleotide sequence data, enabling more transparent, open, and reproducible conduct of meta-analyses.q2-fondueis a Python 3 package released under the BSD 3-clause license athttps://github.com/bokulich-lab/q2-fondue.
An in-silico analysis of experimental designs to study right ventricular function and pulmonary hypertension
Authors: Colebank M. J. , Chesler N.C.
Published: March 2022

In-vivostudies of pulmonary hypertension (PH) have provided key insight into the progression of the disease and right ventricular (RV) dysfunction. Additionalin-silicoexperiments using multiscale computational models have provided further details into biventricular mechanics and hemodynamic function in the presence of PH, yet few have assessed whether model parameters are identifiable prior to data collection. Moreover, none have used modeling to devise synergistic experimental designs. To address this knowledge gap, we conduct an identifiability analysis of a multiscale cardiovascular model across four simulated experimental designs. We determine a set of parameters using a combination of Morris screening and local sensitivity analysis, and test for identifiability using profile likelihood based confidence intervals. We employ Markov chain Monte Carlo (MCMC) techniques to quantify parameter and model forecast uncertainty in the presence of noise corrupted data. Our results show that model calibration to only RV pressure suffers from identifiability issues and suffers from large forecast uncertainty in output space. In contrast, parameter and model forecast uncertainty is substantially reduced once additional left ventricular (LV) pressure and volume data is included. A comparison between single point systolic and diastolic LV data and continuous, time-dependent LV pressure volume data reveals that even basic, functional data from the LV remedies identifiability issues and provides substantial insight into biventricular interactions.

Author Summary

Computational models of cardiac dynamics are becoming increasingly useful in understanding the underlying mechanisms of disease.In-silicoanalyses are especially insightful in understanding PH and eventual RV dysfunction, as these conditions are diagnosed months to years after disease onset. Many researchers couple computational models within-vivoexperimental models of PH, yet few ever assess what data might be necessary or sufficient for parameter inference prior to designing their experiments. Here, we considered a multiscale computational model including sarcomere dynamics, biventricular interactions, and vascular hemodynamics, and assessed whether parameters could be inferred accurately given limited cardiac data. We utilized sensitivity analyses, profile likelihood confidence intervals, and MCMC to quantify parameter influence and uncertainty. We observed that RV pressure alone is not sufficient to infer the influential parameters in the model, whereas combined pressure and volume data in both the RV and LV reduced uncertainty in model parameters and in model forecasts. We conclude that synergistic PH studies utilizing computational modeling include these data to reduce issues with parameter identifiability and minimize uncertainty.
Enhanced intrathecal drug dispersion achieved by high volume injection and natural micromixing
Authors: Ayansiji Ayankola O. , Gehrke Daniel S. , Baralle Bastien , Nozain Ariel , Singh Meenesh R. , Linninger Andreas A.
Published: March 2022

Background

Traditionally, there is a widely held belief that drug dispersion after intrathecal (IT) delivery is confined locally near the injection site. We posit that high volume infusions can overcome this perceived limitation of IT administration.

Methods

To test our hypothesis, subject-specific deformable phantom models of the human central nervous system were manufactured so that tracer infusion could be realistically replicated in vitro over the entire physiological range of pulsating cerebrospinal fluid (CSF) amplitudes and frequencies. Dispersion of IT injected tracers was studied systematically with high-speed optical methods to determine the relative impact of injection parameters including infusion volume, flow rate, catheter configurations and natural CSF oscillations.

Results

Optical imaging analysis of high-volume infusion experiments showed that tracer spreads quickly throughout the spinal subarachnoid space (SAS), reaching the cervical region in less than ten minutes. The experimentally observed biodispersion is much faster than suggested by prior theories (Taylor-Aris-Watson TAW dispersion). Our experiments indicate that micro-mixing patterns induced by oscillatory CSF flow around microanatomical features such as nerve roots significantly accelerate solute transport. Strong micro mixing effects due to anatomical features in the spinal subarachnoid space were found to be active in intrathecal drug administration but were not considered in prior dispersion theories. Their omission explains why prior models developed in the engineering community are poor predictors for IT delivery.

Conclusion

Our experiments support the feasibility of targeting large sections of the neuroaxis or brain utilizing high-volume IT injection protocols. The experimental tracer dispersion profiles acquired with an in vitro human CNS analog informed a new predictive model of tracer dispersion as a function of physiological CSF pulsations and adjustable infusion parameters. The ability to predict spatiotemporal dispersion patterns is an essential prerequisite for exploring new indications of IT drug delivery that targets specific regions in the central nervous system (CNS) or the brain.
Quadripulse Stimulation: A Replication Study with A Newly Developed Stimulator
Authors: Kimura Ikko , Ugawa Yoshikazu , Hayashi Masamichi J , Amano Kaoru
Published: March 2022

Quadripulse stimulation (QPS) is a promising patterned repetitive transcranial magnetic stimulation protocol, which allows the modulation of brain activity for over one hour after the stimulation. Recently, Deymed Diagnostic developed a new stimulator specifically designed to deliver QPS (DuoMAG MP-Quad, https://deymed.com/duomag-qps). The properties of the after-effect with this new stimulator were expected to parallel those obtained with another stimulator, the Magstim stimulator, which is currently used in the psychological and clinical research but not commercially available anymore. Nevertheless, experimental validation of DuoMAG MP-Quad was still warranted. We thus studied the QPS after-effect induced by this stimulator. As a result, motor evoked potentials were found to be bidirectionally modulated by the QPS for more than one hour, consistent with previous studies using the Magstim stimulator. Moreover, the degree of the after-effect was comparable to the after-effect induced by the other stimulator. Taken together, we conclude that the newly developed QPS stimulator is as effective as the Magstim stimulator.