bluuebunny/crossref_metadata_2025 huggingface dataset:
Causal relationship between gut microbiota and immune thrombocytopenia: a Mendelian randomization study of two samples
Authors: Guo Dongmei , Chen Qian , Wang Guojun , Li ChunPu ,   FinnGen consortium
Published: November 2023

Background

Some observational studies have shown that immune thrombocytopenia (ITP) is highly associated with the alteration-composition of gut microbiota. However, the causality of gut microbiota on ITP has not yet been determined.

Methods

Based on accessible summary statistics of the genome-wide union, the latent connection between ITP and gut microbiota was estimated using bi-directional Mendelian randomization (MR) and multivariable MR (MVMR) analyses. Inverse variance weighted (IVW), weighted median analyses, and MR-Egger regression methods were performed to examine the causal correlation between ITP and the gut microbiota. Several sensitivity analyses verified the MR results. The strength of causal relationships was evaluated using the MR-Steiger test. MVMR analysis was undertaken to test the independent causal effect. MR analyses of reverse direction were made to exclude the potential of reverse correlations. Finally, GO enrichment analyses were carried out to explore the biological functions.

Results

After FDR adjustment, two microbial taxa were identified to be causally associated with ITP (PFDR < 0.10), namely Alcaligenaceae (PFDR = 7.31 × 10–2) and Methanobacteriaceae (PFDR = 7.31 × 10–2). In addition, eight microbial taxa were considered as potentially causal features under the nominal significance (P < 0.05): Actinobacteria, Lachnospiraceae, Methanobacteria, Bacillales, Methanobacteriales, Coprococcus2, Gordonibacter, and Veillonella. According to the reverse-direction MR study findings, the gut microbiota was not significantly affected by ITP. There was no discernible horizontal pleiotropy or instrument heterogeneity. Finally, GO enrichment analyses showed how the identified microbial taxa participate in ITP through their underlying biological mechanisms.

Conclusion

Several microbial taxa were discovered to be causally linked to ITP in this MR investigation. The findings improve our understanding of the gut microbiome in the risk of ITP.
Does pre-enrichment of anodes with acetate to select for Geobacter spp. enhance performance of microbial fuel cells when switched to more complex substrates?
Authors: Christgen Beate , Spurr Martin , Milner Edward M. , Izadi Paniz , McCann Clare , Yu Eileen , Curtis Tom , Scott Keith , Head Ian M.
Published: November 2023

Many factors affect the performance of microbial fuel cells (MFCs). Considerable attention has been given to the impact of cell configuration and materials on MFC performance. Much less work has been done on the impact of the anode microbiota, particularly in the context of using complex substrates as fuel. One strategy to improve MFC performance on complex substrates such as wastewater, is to pre-enrich the anode with known, efficient electrogens, such as Geobacter spp. The implication of this strategy is that the electrogens are the limiting factor in MFCs fed complex substrates and the organisms feeding the electrogens through hydrolysis and fermentation are not limiting. We conducted a systematic test of this strategy and the assumptions associated with it. Microbial fuel cells were enriched using three different substrates (acetate, synthetic wastewater and real domestic wastewater) and three different inocula (Activated Sludge, Tyne River sediment, effluent from an MFC). Reactors were either enriched on complex substrates from the start or were initially fed acetate to enrich for Geobacter spp. before switching to synthetic or real wastewater. Pre-enrichment on acetate increased the relative abundance of Geobacter spp. in MFCs that were switched to complex substrates compared to MFCs that had been fed the complex substrates from the beginning of the experiment (wastewater-fed MFCs - 21.9 ± 1.7% Geobacter spp.; acetate-enriched MFCs, fed wastewater - 34.9 ± 6.7% Geobacter spp.; Synthetic wastewater fed MFCs – 42.5 ± 3.7% Geobacter spp.; acetate-enriched synthetic wastewater-fed MFCs - 47.3 ± 3.9% Geobacter spp.). However, acetate pre-enrichment did not translate into significant improvements in cell voltage, maximum current density, maximum power density or substrate removal efficiency. Nevertheless, coulombic efficiency (CE) was higher in MFCs pre-enriched on acetate when complex substrates were fed following acetate enrichment (wastewater-fed MFCs – CE = 22.0 ± 6.2%; acetate-enriched MFCs, fed wastewater – CE =58.5 ± 3.5%; Synthetic wastewater fed MFCs – CE = 22.0 ± 3.2%; acetate-enriched synthetic wastewater-fed MFCs – 28.7 ± 4.2%.) The relative abundance of Geobacter ssp. and CE represents the average of the nine replicate reactors inoculated with three different inocula for each substrate. Efforts to improve the performance of anodic microbial communities in MFCs utilizing complex organic substrates should therefore focus on enhancing the activity of organisms driving hydrolysis and fermentation rather the terminal-oxidizing electrogens.
Research progress and management strategies of fungal diseases in Camellia oleifera
Authors: Chen Xingzhou , He Yuan , Wang Zhikai , Niu Anqi , Xue Yi , Zhou Diao , Zhou Guoying , Liu Junang
Published: November 2023

Camellia oleifera Abel, a woody oil plant, that is endemic to China. Tea oil, also referred to as “oriental olive oil,” is a superior quality plant-based cooking oil. The production of tea oil accounts for 8% of the total edible vegetable oil production in the country. Since 2022, the annual output value of C. oleifera industry has exceeded 100 billion yuan, making it one of the major economic contributors to China’s rural revitalization development strategy. In recent years, demand and production have grown in parallel. However, this has led to an increase in the incidence levels of pest and diseases. Pests and diseases significantly reduce the quality and yield of C. oleifera. C. oleifera diseases are mainly caused by pathogenic fungi. C. oleifera anthracnose, soft rot, leaf spot, coal stain, leaf gall disease, and root rot are the most important fungal diseases affecting the C. oleifera industry. However, the same disease may be caused by different pathogenic fungi. C. oleifera can be found in half of China and is found in several climatic zones. The geographical distribution of woody plant diseases is consistent with the distribution of the tree species and the ecology of the range, which also results in a highly complex distribution of fungal diseases of C. oleifera. The management of fungal diseases in C. oleifera is extremely challenging due to the variety of pathogenic fungal species, multiple routes of transmission, the lack of resistant plants, and the environmental safety of chemical measures. The optimal strategy for addressing fungal diseases in C. oleifera is to develop and apply an integrated disease management plan. This review provides a brief overview of the pathogenic species, pathogenesis, pathogenesis, geographical distribution, current management strategies, and potentially new methods of C. oleifera fungal diseases, to provide direction for the development of comprehensive management measures for C. oleifera fungal diseases in the future.
Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia
Authors: Kauter Anne , Brombach Julian , Lübke-Becker Antina , Kannapin Dania , Bang Corinna , Franzenburg Sören , Stoeckle Sabita D. , Mellmann Alexander , Scherff Natalie , Köck Robin , Guenther Sebastian , Wieler Lothar H. , Gehlen Heidrun , Semmler Torsten , Wolf Silver A. , Walther Birgit
Published: November 2023

Introduction

Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum β-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited.

Methods

We collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and 10 (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1–V2 gene sequencing.

Results

We included 48 samples in the SSG (n = 16 horses), 45 in the 5DG (n = 15), and 20 in the CG (for t0 and t1, n = 10). Two samples of equine patients receiving antibiotic prophylaxis (6.5%) were positive for ESBL-producing Enterobacterales at t0, while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing there was no significant difference between horses suffering from acute colic (5DG, SDImean of 5.90, SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1.

Conclusion

Colic surgery and PAP drive the equine gut microbiome towards dysbiosis and reduced biodiversity that is accompanied by an increase of samples positive for ESBL-producing Enterobacterales. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.
An overview of molecular markers for identification of non-human fecal pollution sources
Authors: Zlender Tanja , Rupnik Maja
Published: November 2023

Identifying primary sources of fecal pollution is important for assessing public health risks and implementing effective remediation strategies. To date, one of the main molecular approaches for identifying sources of fecal pollution relies on detecting molecular markers within bacterial, viral, or mitochondrial nucleic acids, that are indicative of a particular host. With a primary focus on identifying fecal pollution originating from humans, the field of fecal source tracking often places less emphasis on livestock sources, frequently leaving the problem of wildlife fecal pollution unaddressed. In this review, we summarize 55 previously published and validated molecular assays and describe methods for the detection of molecular markers that are indicative of non-human hosts. They cover a range of 15 animal species/groups with a primary focus on domestic animals including cattle, pigs, dogs, and poultry. Among assays associated with wild animals, the majority are designed to detect bird feces, while the availability of assays for detecting feces of other wild animals is limited. Both domestic and wild animals can represent a zoonotic reservoir of human enteropathogens, emphasizing the importance of their role in public health. This review highlights the need to address the complexity of fecal contamination and to include a broader range of animal species into assay validation and marker identification.
Supplementation with postbiotic from Bifidobacterium Breve BB091109 improves inflammatory status and endocrine function in healthy females: a randomized, double-blind, placebo-controlled, parallel-groups study
Authors: Motei Diana Elena , Beteri Beyda , Hepsomali Piril , Tzortzis George , Vulevic Jelena , Costabile Adele
Published: November 2023

This study evaluated the effects of dietary supplementation with a postbiotic extract of Bifidobacterium breve BB091109 on pro-inflammatory cytokines levels and markers of endocrine function. A prospective, double-blind, placebo-controlled, randomized, single-centered, parallel study was conducted on a group of 40–55-year-old females. The study included 30 healthy females, divided into two groups: a supplement (n = 20) and a placebo (n = 10) groups. Blood and saliva samples were collected at baseline (wk0), after 4 weeks (wk 4) and 12 weeks (12wk) of daily supplementation (500 mg), and 4 weeks (wk 16) after termination of supplementation. The levels of fasting CRP, IL-6, IL-10, TNF-α, IFN-γ, DHEA, estradiol, estriol, progesterone, cortisol and human growth hormone were analysed. The results revealed a significant effect of the 90-day supplementation with B. breve postbiotic extract on changes in CRP, IL-6 levels, DHEA, estradiol and estriol. In conclusion, the supplementation with the B. breve postbiotic extract improved endocrine function in females over 40 years old and induced protective changes in inflammatory markers. These findings highlight the potential health benefits of this supplementation in promoting hormonal balance and reducing inflammation in this population.
A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth
Authors: Yang Nan , Zhang Wenbin , Wang Dan , Cao Dingding , Cao Yanyu , He Weihong , Lin Ziting , Chen Xiaofeng , Ye Guiping , Chen Zhiming , Chen Jianjun , Wei Xiangying
Published: November 2023

Introduction

Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect.

Methods

Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses.

Results

Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes.

Discussion

Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.
A global bibliometric and visualized analysis of bacterial biofilm eradication from 2012 to 2022
Authors: Wang Tao , Zhang Rui , Chen Zhiling , Cao Peipei , Zhou Qionglin , Wu Qiang
Published: November 2023

Background

To deeply explore the dynamic trends, focal points and emerging topics of bacterial biofilm eradication field and provide novel insights for prospective research endeavors, the first global bibliometric and visualized analysis of the field was employed in this study.

Methods

The study meticulously curated articles and reviews concentrating on biofilm eradication from the Web of Science Core Collection (WoSCC) and identified literature published in 2012–2022 for further analysis, and the bibliometric and visualized analysis was performed to elucidate a clustering pattern in the domain with tools mainly including CiteSpace and VOSviewer.

Results

15,503 authors affiliated with 2,397 institutions spanning 96 countries or regions contributed to a corpus of 3,201 articles, containing 7,005 keywords. The USA emerged as a commanding vanguard in exploring the antibiofilm strategies and displaying pioneering initiatives within this sphere. The Chinese Academy of Sciences (CAS) emerged as the most prolific source of publications. Noteworthy among authors, Pandian Shunmugiah Karutha secured the lead in article contributions as well as co-citations while Deng Le with his team is poised to become a dominant influence in the future. Despite that, the extent of collaborative engagement across different institutions and authors appeared to fall short of its potential. Frontiers in Microbiology led the discourse by publishing a substantial body of articles and standing as the most recurrently co-cited publication. The most influential research domains encompassed “bacterial biofilm formation, “photodynamic therapy” and “phage therapy.” Recent trends and forefronts concentrate on intensifying research into facilitating the shift of multiple strategies for biofilm eradication from controlled lab settings or animal studies to real-world clinical environments.

Conclusion

Fundamentally, this study presents a comprehensive scrutiny and reveals that the realm of bacterial biofilm eradication is undergoing rapid evolution, with even greater expansion anticipated in the times ahead. Subsequent scholars should emphasize the augmentation of collaborative efforts and focus their energies on emerging topics, thus contributing to break through current barriers in transitioning biofilm eradication strategies from the “fundamental” stage to “practical” application.
Responses of soil microbial biomass, microbial entropy and soil-microorganism stoichiometry imbalance to different utilization patterns in the artificial grassland of karst desertification area
Authors: Chi Yongkuan , Song Shuzhen , Xiong Kangning , Albasher Gadah , Fang Jinzhong
Published: November 2023

Different utilization patterns can alter the C, N, P cycles and their ecological stoichiometry characteristics in grassland soils. However, the effects of different utilization patterns on soil microbial biomass, microbial entropy and soil-microorganism stoichiometry imbalance of artificial grassland are not clear. So this study was took different utilization patterns of artificial grassland [i.e., grazing grassland (GG), mowing grassland (MG), enclosed grassland (EG)] as the research object to investigate responses of soil microbial biomass, microbial entropy and soil-microorganism stoichiometry imbalance to different utilization patterns in the karst rocky desertification control area. We found that the contents of microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) were highest in GG, and the content of microbial biomass phosphorus (MBP) was highest in EG. Soil microbial biomass entropy carbon (qMBC) and soil microbial biomass entropy nitrogen (qMBN) of GG and MG were higher than those of EG, but soil microbial biomass entropy phosphorus (qMBP) was opposite. C:N stoichiometry imbalance (C:Nimb) was EG > GG > MG, C:P stoichiometry imbalance (C:Pimb) was EG > MG > GG, N:P stoichiometry imbalance (N:Pimb) was MG > EG > GG. MBN was significantly positive correlated with C:Nimb and C:Pimb, MBC was significantly negative correlated with C:Pimb, MBP was significantly negative correlated with N:Pimb. The redundancy analysis (RDA) results showed that N:Pimb (p = 0.014), C:Nimb (p = 0.014), and C:P in the soil (C:Psoil, p = 0.028) had the most significant effect on microbial entropy. EG had a significant effect on soil microbial biomass and microbial entropy. The results of this study can directly or indirectly reflect the grassland soil quality under different utilization patterns in the karst rocky desertification area, which has a certain reference value for the degraded ecosystem restoration.
Leaf, root, and soil microbiomes of an invasive plant, Ardisia crenata, differ between its native and exotic ranges
Authors: Nakamura Naoto , Toju Hirokazu , Kitajima Kaoru
Published: November 2023

Introduction

Ecological underpinnings of the invasion success of exotic plants may be found in their interactions with microbes, either through the enemy release hypothesis and the enhanced mutualism hypothesis. Whereas recent high-throughput sequencing techniques have significantly expanded our understanding of plant-associated microbiomes and their functional guilds, few studies to date have used these techniques to compare the microbiome associated with invasive plants between their native and exotic ranges.

Methods

We extracted fungal and bacterial DNA within leaf endosphere, root endosphere and soil of an invasive plant, Ardisia crenata, sampled from their native range Japan and exotic range Florida, USA. Using Illumina sequencing data, we compared microbial community compositions and diversity between the native and exotic ranges, and tested whether abundance of pathogenic or mutualistic microbes differ between the native or exotic ranges in accordance to the enemy release hypothesis or the enhanced mutualism hypothesis.

Results

Fungal and bacterial community compositions differed among leaves, roots and soil, and between the native and exotic ranges. Despite a higher microbial diversity in the soil in the exotic range than in the native range, the microbial diversity within leaf and root was lower in the exotic range compared to the native range. In addition, leaves in the native range harbored a greater number of plant pathogenic fungi compared to those in the exotic range.

Discussion

These patterns suggest plant controls over what microbes become associated with leaves and roots. The higher abundance of leaf pathogenic fungi, including the pathogen which is known to cause specific disease in A. crenata in the exotic range than in the native range, support the enemy release hypothesis and highlighted potential importance of examining microbial communities both above- and below-ground.
The Pseudomonas syringae pv. tomato DC3000 effector HopD1 interferes with cellular dynamics associated with the function of the plant immune protein AtNHR2B
Authors: Marín-Ponce Luis Francisco , Rodríguez-Puerto Catalina , Rocha-Loyola Perla , Rojas Clemencia M.
Published: November 2023

The plant pathogenic bacterium Pseudomonas syringae pv tomato DC3000 (Pst DC3000) causes disease in tomato, in the model plant Arabidopsis thaliana, and conditionally in Nicotiana benthamiana. The pathogenicity of Pst DC3000 is mostly due to bacterial virulence proteins, known as effectors, that are translocated into the plant cytoplasm through the type III secretion system (T3SS). Bacterial type III secreted effectors (T3SEs) target plants physiological processes and suppress defense responses to enable and support bacterial proliferation. The Pst DC3000 T3SE HopD1 interferes with plant defense responses by targeting the transcription factor NTL9. This work shows that HopD1 also targets the immune protein AtNHR2B (Arabidopsis thaliana nonhost resistance 2B), a protein that localizes to dynamic vesicles of the plant endomembrane system. Live-cell imaging of Nicotiana benthamiana plants transiently co-expressing HopD1 fused to the epitope haemagglutinin (HopD1-HA) with AtNHR2B fused to the red fluorescent protein (AtNHR2B-RFP), revealed that HopD1-HA interferes with the abundance and cellular dynamics of AtNHR2B-RFP-containing vesicles. The results from this study shed light into an additional function of HopD1 while contributing to understanding how T3SEs also target vesicle trafficking-mediated processes in plants.
Paralog-specific TTC30 regulation of Sonic hedgehog signaling
Authors: Hoffmann Felix , Bolz Sylvia , Junger Katrin , Klose Franziska , Stehle Isabel F. , Ueffing Marius , Boldt Karsten , Beyer Tina
Published: November 2023

The intraflagellar transport (IFT) machinery is essential for cilia assembly, maintenance, and trans-localization of signaling proteins. The IFT machinery consists of two large multiprotein complexes, one of which is the IFT-B. TTC30A and TTC30B are integral components of this complex and were previously shown to have redundant functions in the context of IFT, preventing the disruption of IFT-B and, thus, having a severe ciliogenesis defect upon loss of one paralog. In this study, we re-analyzed the paralog-specific protein complexes and discovered a potential involvement of TTC30A or TTC30B in ciliary signaling. Specifically, we investigated a TTC30A-specific interaction with protein kinase A catalytic subunit α, a negative regulator of Sonic hedgehog (Shh) signaling. Defects in this ciliary signaling pathway are often correlated to synpolydactyly, which, intriguingly, is also linked to a rare TTC30 variant. For an in-depth analysis of this unique interaction and the influence on Shh, TTC30A or B single- and double-knockout hTERT-RPE1 were employed, as well as rescue cells harboring wildtype TTC30 or the corresponding mutation. We could show that mutant TTC30A inhibits the ciliary localization of Smoothened. This observed effect is independent of Patched1 but associated with a distinct phosphorylated PKA substrate accumulation upon treatment with forskolin. This rather prominent phenotype was attenuated in mutant TTC30B. Mass spectrometry analysis of wildtype versus mutated TTC30A or TTC30B uncovered differences in protein complex patterns and identified an impaired TTC30A–IFT57 interaction as the possible link leading to synpolydactyly. We could observe no impact on cilia assembly, leading to the hypothesis that a slight decrease in IFT-B binding can be compensated, but mild phenotypes, like synpolydactyly, can be induced by subtle signaling changes. Our systematic approach revealed the paralog-specific influence of TTC30A KO and mutated TTC30A on the activity of PRKACA and the uptake of Smoothened into the cilium, resulting in a downregulation of Shh. This downregulation, combined with interactome alterations, suggests a potential mechanism of how mutant TTC30A is linked to synpolydactyly.
Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico and in vitro approaches
Authors: Gorostiola González Marina , Sijben Hubert J. , Dall’ Acqua Laura , Liu Rongfang , IJzerman Adriaan P. , Heitman Laura H. , van Westen Gerard J. P.
Published: November 2023

Glutamate is an essential excitatory neurotransmitter and an intermediate for energy metabolism. Depending on the tumor site, cancer cells have increased or decreased expression of excitatory amino acid transporter 1 or 2 (EAAT1/2, SLC1A3/2) to regulate glutamate uptake for the benefit of tumor growth. Thus, EAAT1/2 may be an attractive target for therapeutic intervention in oncology. Genetic variation of EAAT1 has been associated with rare cases of episodic ataxia, but the occurrence and functional contribution of EAAT1 mutants in other diseases, such as cancer, is poorly understood. Here, 105 unique somatic EAAT1 mutations were identified in cancer patients from the Genomic Data Commons dataset. Using EAAT1 crystal structures and in silico studies, eight mutations were selected based on their close proximity to the orthosteric or allosteric ligand binding sites and the predicted change in ligand binding affinity. In vitro functional assessment in a live-cell, impedance-based phenotypic assay demonstrated that these mutants differentially affect L-glutamate and L-aspartate transport, as well as the inhibitory potency of an orthosteric (TFB-TBOA) and allosteric (UCPH-101) inhibitor. Moreover, two episodic ataxia-related mutants displayed functional responses that were in line with literature, which confirmed the validity of our assay. Of note, ataxia-related mutant M128R displayed inhibitor-induced functional responses never described before. Finally, molecular dynamics (MD) simulations were performed to gain mechanistic insights into the observed functional effects. Taken together, the results in this work demonstrate 1) the suitability of the label-free phenotypic method to assess functional variation of EAAT1 mutants and 2) the opportunity and challenges of using in silico techniques to rationalize the in vitro phenotype of disease-relevant mutants.
Structure and computation-guided yeast surface display for the evolution of TIMP-based matrix metalloproteinase inhibitors
Authors: Shoari Alireza , Khalili-Tanha Ghazaleh , Coban Mathew A. , Radisky Evette S.
Published: November 2023

The study of protein-protein interactions (PPIs) and the engineering of protein-based inhibitors often employ two distinct strategies. One approach leverages the power of combinatorial libraries, displaying large ensembles of mutant proteins, for example, on the yeast cell surface, to select binders. Another approach harnesses computational modeling, sifting through an astronomically large number of protein sequences and attempting to predict the impact of mutations on PPI binding energy. Individually, each approach has inherent limitations, but when combined, they generate superior outcomes across diverse protein engineering endeavors. This synergistic integration of approaches aids in identifying novel binders and inhibitors, fine-tuning specificity and affinity for known binding partners, and detailed mapping of binding epitopes. It can also provide insight into the specificity profiles of varied PPIs. Here, we outline strategies for directing the evolution of tissue inhibitors of metalloproteinases (TIMPs), which act as natural inhibitors of matrix metalloproteinases (MMPs). We highlight examples wherein design of combinatorial TIMP libraries using structural and computational insights and screening these libraries of variants using yeast surface display (YSD), has successfully optimized for MMP binding and selectivity, and conferred insight into the PPIs involved.
Unsupervised but not supervised gait parameters are related to fatigue in Parkinson’s disease: a pilot study
Authors: Pilotto Andrea , Rizzardi Andrea , Zatti Cinzia , Hansen Clint , Donini Antonio , Romijnders Robbin , Maetzler Walter , Padovani Alessandro
Published: November 2023

Introduction

Fatigue is a common and disabling symptom in Parkinson’s disease (PD), also affecting gait. Detection of fatigue-associated changes of gait using mobile health technologies (MHT) could become increasingly effective.

Methods

Cognitively unimpaired PD patients without fluctuations (UPDRS IV < 1) underwent a standard neurological assessment including the PD-Fatigue scale (PFS-16). PD patients with (PD-F) and without fatigue (PD-N) were matched for age, sex, cognitive function and disease severity. Each participant underwent MHT gait assessment under supervised condition (SC) and unsupervised condition (UC).

Results

Gait parameters of 21 PD-F and 21 PD-N did not significantly differ under SC. Under UC, PD-F showed higher step time, step time variability and asymmetry index compared to PD-N and the PFS-16 correlated with step time.

Conclusion

This is the first MHT-based study with PD patients showing a correlation between fatigue and gait parameters. In addition, the data collected suggest that UC is clearly superior to SC in addressing this question.
Functional maturation of human iPSC-derived pyramidal neurons in vivo is dependent on proximity with the host tissue
Authors: Raïs Célia , Gaspar Santos Daniela , Sansone Giulia , Blanchard Stéphane , Bourgeois Jean-Pierre , Jagla Bernd , Saudemont Baptiste , Schlick Laurène , Pons Stéphanie , Maskos Uwe
Published: November 2023

Human induced pluripotent stem cells (hiPSCs) have been used extensively in vitro to model early events in neurodevelopment. Because of a number of shortcomings, previous work has established a potential to use these cells in vivo after transplantation into the mouse brain. Here, we describe a systematic approach for the analysis of transplanted hiPSC-derived neurons and glial cells over time in the mouse brain. Using functional two-photon imaging of GCaMP6f- expressing human neural cells, we define and quantify the embryonic-like features of their spontaneous activity. This is substantiated by detailed electron microscopy (EM) of the graft. We relate this to the synaptic development the neurons undergo up to 7 months in vivo. This system can now be used further for the genetic or experimental manipulation of developing hiPSC-derived cells addressing neurodevelopmental diseases like schizophrenia or Autism Spectrum Disorder.
CD8+ T cells in brain injury and neurodegeneration
Authors: Zhang Zhaolong , Duan Zhongying , Cui Yu
Published: November 2023

The interaction between the peripheral immune system and the brain is increasingly being recognized as an important layer of neuroimmune regulation and plays vital roles in brain homeostasis as well as neurological disorders. As an important population of T-cell lymphocytes, the roles of CD8+ T cells in infectious diseases and tumor immunity have been well established. Recently, increasing number of complex functions of CD8+ T cells in brain disorders have been revealed. However, an advanced summary and discussion of the functions and mechanisms of CD8+ T cells in brain injury and neurodegeneration are still lacking. Here, we described the differentiation and function of CD8+ T cells, reviewed the involvement of CD8+ T cells in the regulation of brain injury including stroke and traumatic brain injury and neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), and discussed therapeutic prospects and future study goals. Understanding these processes will promote the investigation of T-cell immunity in brain disorders and provide new intervention strategies for the treatment of brain injury and neurodegeneration.
Inferring connectivity of an oscillatory network via the phase dynamics reconstruction
Authors: Rosenblum Michael , Pikovsky Arkady
Published: November 2023

We review an approach for reconstructing oscillatory networks’ undirected and directed connectivity from data. The technique relies on inferring the phase dynamics model. The central assumption is that we observe the outputs of all network nodes. We distinguish between two cases. In the first one, the observed signals represent smooth oscillations, while in the second one, the data are pulse-like and can be viewed as point processes. For the first case, we discuss estimating the true phase from a scalar signal, exploiting the protophase-to-phase transformation. With the phases at hand, pairwise and triplet synchronization indices can characterize the undirected connectivity. Next, we demonstrate how to infer the general form of the coupling functions for two or three oscillators and how to use these functions to quantify the directional links. We proceed with a different treatment of networks with more than three nodes. We discuss the difference between the structural and effective phase connectivity that emerges due to high-order terms in the coupling functions. For the second case of point-process data, we use the instants of spikes to infer the phase dynamics model in the Winfree form directly. This way, we obtain the network’s coupling matrix in the first approximation in the coupling strength.
Prevalence of non-neurological autoantibodies and related comorbidities in stiff person spectrum disorders
Authors: Balshi Alexandra , Taylor Elena , Huang Yishang , Obando Danielle , Miles Ashley , Comisac Michael , Wang Yujie , Newsome Scott D.
Published: November 2023

Background

Stiff Person Syndrome Spectrum Disorders (SPSD) are a group of rare neurological disorders that can present alongside other autoimmune conditions. However, not much is known about the breadth of non-neurological autoantibodies seen in SPSD nor the observed prevalence of co-existing autoimmune comorbidities and their impact on SPSD.

Objective

This study aimed to investigate the prevalence of non-neurological autoantibodies and associated conditions in a large cohort of people with SPSD.

Methods

A retrospective review of 205 patients with suspected/definitive SPSD seen at Johns Hopkins Hospital from 1997 to 2023 was performed as part of an ongoing, observational study. Relevant demographics, clinical data (e.g., SPSD phenotypes, comorbid conditions, and dates of diagnoses), and laboratory values were collected from electronic medical records. Lab values were excluded if completed within 6 months of receiving intravenous immunoglobin treatment. Summary statistics were performed and assessment for any associations between autoimmune comorbidities and disease burden (modified Rankin score [mRS] and ambulation status) was performed.

Results

The majority of participants had classic SPS (66%), followed by SPS-plus (18%) and PERM (6%) with less than 5% each of the remaining phenotypes and suspected SPS. The average age at symptom onset in this cohort was 44.1 ± 14.5 years (mean ± standard deviation). The majority of the cohort was white (66%) and female patients (75%). The mean mRS was 2.5, and over 70% required assistive devices for ambulation. The most commonly identified non-neurological autoantibodies were anti-nuclear (ANA) (31%), thyroperoxidase (30%), thyroglobulin (20%), and anti-parietal cell (18%) autoantibodies. The most common comorbid autoimmune conditions were autoimmune thyroiditis (38%), insulin-dependent diabetes mellitus (26%), and pernicious anemia (10%). Having more autoimmune comorbidities was weakly associated with higher mRS and a greater need for ambulatory assistance.

Conclusion

The results of this study will hopefully help promote awareness of which autoantibody and medical comorbidity clinicians should be aware of and monitor people with SPSD. Further research is needed to identify if poorly controlled non-neurological autoimmune disorders contribute to disease burden in SPSD and/or if the timing of being diagnosed with one of these conditions plays a role in future disability.
Cochlear inflammaging: cellular and molecular players of the innate and adaptive immune system in age-related hearing loss
Authors: Parekh Shailee , Kaur Tejbeer
Published: November 2023

Age-related hearing loss is the most common sensory disorder worldwide that contributes to numerous health conditions in the aging population. Despite its prevalence, current treatments, including hearing aids, are unsatisfactory in improving hearing deficits or slowing or reversing its pathophysiology. Immunosenescence is a key driver of neurodegenerative disease, and a similar mechanism has recently come to attention in age-related hearing loss. Imbalanced levels of cytokines and chemokines contribute to aberrant immune cell activity and a chronic pro-inflammatory microenvironment that may lead to degradation of inner ear structure and function. Macrophages, typically guardians of organ homeostasis, are found to develop dysregulated activity with aging due to unidentified factors, and they interact with other components of the innate immune system to damage sensory hair cells, synapses, neurons, and other structures of the inner ear critical to sensory signal transmission. They also increasingly trigger the inflammasome, a protein complex involved in inflammatory cell death, and the complement cascade, to perpetuate a cycle of inflammation and cellular damage in the cochlea, resulting in hearing loss. Senescence in certain T cell populations have indicated a role of adaptive immunity in age-related hearing loss as well. Deciphering the mechanisms of immune dysregulation is a critical first step in producing targeted therapies for hearing loss. This brief review describes the current and emerging research surrounding the dysregulation of the innate and adaptive immune systems in age-related hearing loss and its parallels with other neurodegenerative diseases.
Evidence for vibration coding of sliding tactile textures in auditory cortex
Authors: Roberts Roberta D. , Loomes Aldrin R. , Kwok Hoi Fei , Wing Alan M. , Allen Harriet A.
Published: November 2023

Introduction

Psychophysical studies suggest texture perception is mediated by spatial and vibration codes (duplex theory). Vibration coding, driven by relative motion between digit and stimulus, is involved in the perception of very fine gratings whereas coarse texture perception depends more on spatial coding, which does not require relative motion.

Methods

We examined cortical activation, using functional Magnetic Resonance Imaging associated with fine and coarse tactile spatial gratings applied by sliding or touching (sliding vs. static contact) on the index finger pad.

Results

We found regions, contralateral to the stimulated digit, in BA1 in S1, OP1, OP3, and OP4 in S2, and in auditory cortex, which were significantly more activated by sliding gratings but did not find this pattern in visual cortex. Regions in brain areas activated by vibrotactile stimuli (including auditory cortex) were also modulated by whether or not the gratings moved. In a control study we showed that this contrast persisted when the salience of the static condition was increased by using a double touch.

Discussion

These findings suggest that vibration from sliding touch invokes multisensory cortical mechanisms in tactile processing of roughness. However, we did not find evidence of a separate visual region activated by static touch nor was there a dissociation between cortical response to fine vs. coarse gratings as might have been expected from duplex theory.
rTMS regulates homotopic functional connectivity in the SCD and MCI patients
Authors: Ge Honglin , Chen ShanShan , Che Zigang , Wu Huimin , Yang Xinyi , Qiao Meizhao , Chi Lei , Fan Jia , Zhong Yeming , Zou Caiyun , Lin Xingjian , Chen Jiu
Published: November 2023

Objective

Impaired interhemispheric connectivity and corpus callosum atrophy have been linked to cognitive impairment in Alzheimer’s disease (AD). Existing evidence indicates that repetitive transcranial magnetic stimulation (rTMS) targeting the bilateral precuneus may enhance cognitive function in AD. This study aims to investigate the effects of precuneus rTMS on cognitive function, as well as alterations in interhemispheric functional connectivity (FC) and its structural basis in patients with subjective cognitive decline (SCD) and mild cognitive impairment (MCI).

Methods

A total of 14 patients with SCD and 16 patients with MCI were enrolled in this study and received 10 Hz rTMS intervention on the bilateral precuneus for 2 weeks. Neurocognitive scales, structural and functional magnetic resonance imaging were collected at enrollment and after the rTMS intervention. Interhemispheric FC was assessed using mirror homotopic functional connectivity (VMHC), while the structural equation modeling (SEM) was employed to analyze the relationship between corpus callosum volume, interhemispheric connectivity, and cognitive function after rTMS intervention.

Results

The precuneus rTMS not only enhanced episodic memory in SCD, but also improved multiple cognitive domains in MCI. Post-rTMS intervention, decreased VMHC values in the lingual cortex, middle occipital gyrus, putamen, and fusiform gyrus were observed in SCD, and an increased VMHC value in the postcentral gyrus along with reduced VMHC value in the cerebellum and putamen in MCI. After intervention, more brain regions show decreased FC in SCD and MCI patients, suggesting that precuneus rTMS may protect cerebral cortical plasticity by reducing excessive functional compensation, and thus improve cognitive function. The SEM indicated that the corpus callosum serves as the structural foundation for rTMS regulation of interhemispheric FC to further improve cognitive function.

Conclusion

10 Hz rTMS in the bilateral precuneus could be a promising strategy to improve cognitive function in patients with SCD and MCI. Our study implies that improvements in cognition brought about by precuneus rTMS may result from the remodeling of interhemispheric FC, with the corpus callosum possibly acting as the anatomical basis for functional modulation.
Asteroid impact: the potential of astrocytes to modulate human neural networks within organoids
Authors: Lavekar S. S. , Patel M. D. , Montalvo-Parra M. D. , Krencik R.
Published: November 2023

Astrocytes are a vital cellular component of the central nervous system that impact neuronal function in both healthy and pathological states. This includes intercellular signals to neurons and non-neuronal cells during development, maturation, and aging that can modulate neural network formation, plasticity, and maintenance. Recently, human pluripotent stem cell-derived neural aggregate cultures, known as neurospheres or organoids, have emerged as improved experimental platforms for basic and pre-clinical neuroscience compared to traditional approaches. Here, we summarize the potential capability of using organoids to further understand the mechanistic role of astrocytes upon neural networks, including the production of extracellular matrix components and reactive signaling cues. Additionally, we discuss the application of organoid models to investigate the astrocyte-dependent aspects of neuropathological diseases and to test astrocyte-inspired technologies. We examine the shortcomings of organoid-based experimental platforms and plausible improvements made possible by cutting-edge neuroengineering technologies. These advancements are expected to enable the development of improved diagnostic strategies and high-throughput translational applications regarding neuroregeneration.
Breast milk immune composition varies during the transition stage of lactation: characterization of immunotypes in the MAMI cohort
Authors: Rio-Aige Karla , Fernández-Bargalló Aina , Vegas-Lozano Esteban , Miñarro-Alonso Antonio , Castell Margarida , Selma-Royo Marta , Martínez-Costa Cecilia , Rodríguez-Lagunas Maria José , Collado Maria Carmen , Pérez-Cano Francisco José
Published: November 2023

Background

Breast milk is a complex and dynamic fluid needed for infant development and protection due to its content of bioactive factors such as immunoglobulins (Igs). Most studies focus primarily on IgA, but other types of Ig and even other immune components (cytokines and adipokines) may also play significant roles in neonatal health. As a first step, we aimed to characterize the Ig profile, many cytokines, and two adipokines (leptin and adiponectin) at two sampling time points within the transitional stage, which is the least studied phase in terms of these components. The secondary objective was to identify different breast milk immunotypes in the MAMI cohort substudy, and finally, we further aimed at analyzing maternal and infant characteristics to identify influencing factors of breast milk immune composition.

Methods

Breast milk samples from 75 mothers were studied between days 7 and 15 postpartum. The Igs, cytokines, and adipokine levels were determined by a multiplex approach, except for the IgA, IgM, and leptin that were evaluated by ELISA.

Results

IgA, IgM, IgE, IgG2, IL-1β, IL-5, IL-6, IL-10, and IL-17 were significantly higher on day 7 with respect to day 15. The multiple factor analysis (MFA) allowed us to identify two maternal clusters (immunotypes) depending on the breast milk immune profile evolution from day 7 to day 15, mainly due to the IgE and IgG subtypes, but not for IgA and IgM, which always presented higher levels early in time.

Conclusion

All these results demonstrated the importance of the dynamics of the breast milk composition in terms of immune factors because even in the same lactation stage, a difference of 1 week has induced changes in the breast milk immune profile. Moreover, this immune profile does not evolve in the same way for all women. The dynamic compositional changes may be maternal-specific, as we observed differences in parity and exclusive breastfeeding between the two BM immunotype groups, which could potentially impact infant health.