bluuebunny/crossref_metadata_2025 huggingface dataset:
Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model
Authors: Pallikkuth Suresh , Mendez Roberto , Russell Kyle , Sirupangi Tirupataiah , Kvistad Daniel , Pahwa Rajendra , Villinger Francois , Banerjee Santanu , Pahwa Savita
Published: October 2021

Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate the age associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 geriatric (age 19-24 years) and 4 young adult (age 3-4 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in peripheral blood mononuclear cells (PBMC) by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate, and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the gut microbiome in geriatric animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young adults. Highly abundant microbes in the geriatric animals showed a direct association with plasma biomarkers of inflammation and immune activation such as neopterin, CRP, TNF, IL-2, IL-6, IL-8 and IFN-γ. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of geriatric animals compared to the young adults. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile. Aging NHP can serve as a model for investigating the relationship of the gut microbiome to particular age-associated comorbidities and for strategies aimed at modulating the microbiome.
Mucosal-Associated Invariant T (MAIT) Cell Dysfunction and PD-1 Expression in Prostate Cancer: Implications for Immunotherapy
Authors: Jarvis Ellie-May , Collings Shaun , Authier-Hall Astrid , Dasyam Nathaniel , Luey Brendan , Nacey John , Painter Gavin F. , Delahunt Brett , Hermans Ian F. , Weinkove Robert
Published: October 2021

Prostate cancer is the second most common cancer in men worldwide. Despite an abundance of prostate-specific antigens, immunotherapies have yet to become a standard of care, potentially limited by T-cell dysfunction. Up to 10% of human circulating T-cells, and a significant fraction in the urogenital tract, are mucosal-associated invariant T (MAIT) cells. MAIT cells express stereotyped T-cell receptors that recognize riboflavin metabolites derived from microbes presented by MR-1. We evaluated the number, phenotype and function of circulating MAIT cells, alongside two other innate-like T (ILT) -cell subsets, in men with prostate cancer and age- and sex-matched controls. MAIT cells in men with prostate cancer circulated at similar frequencies to controls, but their cytokine production and proliferation was impaired. In contrast, the function of two other ILT-cell populations (natural killer T-cells and Vγ9Vδ2 T-cells) was not impaired. In both patients and controls, MAIT cells expressed high levels of the immune checkpoint molecule PD-1 at rest, while upregulation of PD-1 in response to the MR-1 ligand 5-amino-6D-ribitylaminouracil (5-A-RU) was greater in patients. 5-A-RU also induced upregulation of PD-L1 and -L2 RNA in primary mononuclear cells. We confirmed that circulating MAIT cell number and function were preserved before and during anti-PD1 therapy with pembrolizumab in a cohort of patients with melanoma. In vitro, 5-A-RU enhanced mononuclear cell cytotoxicity against the PD-L1 positive prostate cancer cell line PC3 in an MR-1-dependent manner. Addition of pembrolizumab enhanced this cytotoxicity, and was associated with increased MAIT cell expression of CD107a and IFN-γ. We conclude that prostate cancer is associated with MAIT-cell dysfunction, and that this might be overcome through the application of potent MR-1 ligands with PD-1 blockade. These findings may have implications for the development of cancer immunotherapies that exploit MAIT cells.
Immune Modulation of Metastatic Niche Formation in the Bone
Authors: Cheng Xinyu , Wang Zhan
Published: October 2021

Bone metastasis is commonly seen in patients with breast cancer, prostate cancer and lung cancer. Tumor-intrinsic factors and the tumor microenvironment cooperate to affect the formation of bone metastatic niche. Within the bone microenvironment, immune cells have been regarded as a major contributor to metastatic progression. In this review, we describe the dynamic roles of immune cells in regulating metastatic homing, seeding, dormancy, and outgrowth in the bone. We also summarize the diverse functions of immune molecules including chemokines, cytokines, and exosomes in remodeling the bone metastatic niche. Furthermore, we discuss the therapeutic and prognostic potential of these cellular and molecular players in bone metastasis.
MHC-Optimized Peptide Scaffold for Improved Antigen Presentation and Anti-Tumor Response
Authors: Tagliamonte Maria , Mauriello Angela , Cavalluzzo Beatrice , Ragone Concetta , Manolio Carmen , Luciano Antonio , Barbieri Antonio , Palma Giuseppe , Scognamiglio Giosuè , Di Mauro Annabella , Di Bonito Maurizio , Tornesello Maria Lina , Buonaguro Franco M. , Vitagliano Luigi , Caporale Andrea , Ruvo Menotti , Buonaguro Luigi
Published: October 2021

Tumor Associated Antigens (TAAs) may suffer from an immunological tolerance due to expression on normal cells. In order to potentiate their immunogenicity, heteroclitic peptides (htcPep) were designed according to prediction algorithms. In particular, specific modifications were introduced in peptide residues facing to TCR. Moreover, a MHC-optimized scaffold was designed for improved antigen presentation to TCR by H-2Db allele. The efficacy of such htcPep was assessed in C57BL/6 mice injected with syngeneic melanoma B16F10 or lung TC1 tumor cell lines, in combination with metronomic chemotherapy and immune checkpoint inhibitors. The immunogenicity of htcPep was significantly stronger than the corresponding wt peptide and the modification involving both MHC and TCR binding residues scored the strongest. In particular, the H-2Db-specific scaffold significantly potentiated the peptides’ immunogenicity and control of tumor growth was comparable to wt peptide in a therapeutic setting. Overall, we demonstrated that modified TAAs show higher immunogenicity compared to wt peptide. In particular, the MHC-optimized scaffold can present different antigen sequences to TCR, retaining the conformational characteristics of the corresponding wt. Cross-reacting CD8+T cells are elicited and efficiently kill tumor cells presenting the wild-type antigen. This novel approach can be of high clinical relevance in cancer vaccine development.
Vertical Nitrate Flux Induced by Kelvin–Helmholtz Billows Over a Seamount in the Kuroshio
Authors: Acabado Cristy S. , Cheng Yu-Hsin , Chang Ming-Huei , Chen Chung-Chi
Published: October 2021

Kelvin–Helmholtz (KH) billows can facilitate microscale turbulent mixing around seamounts in the Kuroshio. This study sought to describe the influence of billow intensity (i.e., “intermittent and small” and “steady and large” billows) on vertical nitrate fluxes. KH billows led to turbulent kinetic energy dissipation rates [ε = O (10–7 to 10–6) W kg–1] and eddy diffusivities [Kρ = O (10–4 to 10–3) m2 s–1] that were significantly stronger than those outside the billow depths. The mean nitrate flux estimated using Kρ in the billow depths had a maximal value of 10.0 mmol m–2 day–1, which was much higher than estimates for the open ocean. The nitrate flux associated with the shallow KH billows at two vertical levels contributed to enrich the subsurface phytoplankton maximum, while the deeper billows closer to the summit were found to induce a large amount of nitrate flux from the deeper to the subsurface water. This study showed that KH billows make important contributions to seamount ecosystems, particularly in the cycling and vertical mixing of nutrients to make them available for potential downstream transport.
Effects of Waves and Sediment Disturbance on Seed Bank Persistence at Tidal Flats
Authors: Zhu Zhenchang , Bouma Tjeerd J. , Zhu Qin , Cai Yanpeng , Yang Zhifeng
Published: October 2021

Coastal wetlands such as salt marshes have been increasingly valued for their capacity to buffer global climate change effects, yet their long-term persistence is threatened by environmental changes. Whereas, previous studies largely focused on lateral erosion risk induced by stressors like sea level rise, it remains poorly understood of the response of lateral expansion to changing environments. Seedling establishment is a key process governing lateral marsh expansion as seen in many coastal regions such as Europe and East Asia. Here, we evaluate mechanistically the response of seed bank dynamics to changing physical disturbance at tidal flats, using the globally common coastal foundation plant, cordgrass as a model. We conducted a large-scale field study in an estuary in Northwest Europe, where seed bank dynamics of cordgrass in the tidal flats was determined and linked to in situ hydrodynamics and sediment dynamics. The results revealed that wave disturbance reduced the persistence of seeds on the surface, whereas amplified sediment disturbance lowered the persistence of both surface and buried seeds. Overall, this indicates that increasing storminess and associated sediment variability under climate change threatens seed bank persistence in tidal flats, and hence need urgently be incorporated into models for long-term bio-geomorphological development of vegetated coastal ecosystems. The knowledge gained here provides a basis for more accurate predictions on how climatically driven environmental changes may alter the fitness, resilience and persistence of coastal foundation plants, with significant implications for nature-based solutions with coastal vegetation to mitigate climate change effects.
Inconsistencies in How Environmental Risk Is Evaluated in Sweden for Dumping Dredged Sediment at Sea
Authors: Bruce Peter , Bradshaw Clare , Ohlsson Yvonne , Sobek Anna , Christiernsson Anna
Published: October 2021

Millions of tons of dredged sediment are dumped at sea annually. International conventions limit dumping when there is a risk of adverse ecological effects, for example if the sediment is contaminated. However, the perception of risk differs substantially among stakeholders and in Sweden there is a lack of guidelines for how to address such risk. In the current study, we examined exemptions to the Swedish ban on dumping at sea, to explore the extent of dumping and how ecological aspects were considered in the evaluation of risks. We analyzed data from all cases granted exemption by county administrative boards and all court cases considering exemption to the ban from the beginning of 2015 to June 2020. We found that while dumping is the least common alternative management method for dredged sediment in total number of cases (98/792), dumping is the main method in terms of volume (30.8/38.2 million m3). When considering exemptions, the courts mainly evaluated the risk of exposure to contaminants and resuspended sediment for the environment adjacent to the dumpsite. The risks from contaminants were characterized based on various lines of reasoning, mainly relying on reference values not based on a scientific correlation to environmental risk. We argue that the evaluations were not in line with current regulations and international conventions as they insufficiently accounted for the ecotoxicological risk of the dumped sediment. These issues are potentially similar in other Baltic Sea countries, where there is a similar dependency on binary chemical limit values.
Synthesis of Different Sizes TiO2 and Photovoltaic Performance in Dye-Sensitized Solar Cells
Authors: Mahmoud Sawsan A. , Mohamed Basma S. , Killa H. M.
Published: October 2021

For more than 2 decades, extensive research has been done in the field of Dye-Sensitized Solar Cells (DSSCs) due to their low cost, easy preparation methodology, less toxicity, and ease of production. In this work, the performance of DSSCs containing different particle sizes is studied. N2-doped TiO2was prepared by the sol-gel method, controlling the particle size through the addition of different H2O/Ti mole ratios R = 0, 20, 30, and 40. The dried samples at 100°C were characterized by X-ray diffraction, Optical Properties, High-Resolution Transmission Electron Microscope, Scanning Electron Microscope, Fourier-Transform Infrared Spectroscopy, N2-Adsorption-Desorption Isotherm, Raman Spectroscopy, and Dynamic Light Scattering (DLS). DLS results show that the size of TiO2decreases as the H2O/TiO2content increases from 0 to 40. It is found that TiO2nanoparticles with smaller particle size distribution has the lowest conversion efficiency of 0.95% with H2O/Ti ratio = 40, and the photoelectrode with higher size has a conversion efficiency of 1.59% for the water-free sample. This could be explained as the larger particles have better dye adsorption, indicating that it has an effective surface area for greater photon absorption and electron-hole generation. The results also indicate that trimodal distribution with larger size also absorbs different wavelengths due to the broad distribution of the particle size.
Experimental Pulp-Capping Agent Radiopaque Dicalcium Silicate Cement Facilitates Dentinogenesis
Authors: Kuo Wei-Ting , Li Xin , Chen Fang-Yuan , Wang Yan-Jie , Chen Zhi , Ding Shinn-Jyh , Zhang Lu
Published: October 2021

This study was designed to comparatively evaluate an experimental pulp-capping agent radiopaque dicalcium silicate cement (RDSC), white-colored mineral trioxide aggregate (WMTA), iRoot BP Plus and Biodentine both ex vivo and in vivo. Fourier Transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) were utilized to analyze the phase composition of pulp-capping agents. The surface morphology and element analysis were finished by Scanning electron microscopy (SEM) and Energy Dispersive X-Ray Spectroscopy (EDX). Color stability of the cements and pulp responses induced by different cements were examined by ex-vivo human tooth culture model and in-vivo miniature pig model. Micro-computed tomography was used for quantitative evaluation of the newly formed mineralized tissue. RDSC exhibited discoloration in both models, while WMTA exhibited more visible discoloration. The occurrence of discoloration for WMTA was significantly higher than that of RDSC (p < 0.05), iRoot BP Plus and Biodentine on the 7th day, also higher (p < 0.05) than that of iRoot BP Plus and Biodentine on the 70th day. Mineralized foci were noted in all 7-days groups except the control group both ex vivo and in vivo. Intact and complete reparative dentin bridge formation which possessed tubular structures was noted in all 70-days groups in vivo. RDSC appeared to induce the thickest dentin bridge formation among all these pulp-capping agents which showed statistically significant difference to that of Biodentine (p < 0.05). With decent biological properties, RDSC may have the potential to be a pulp-capping agent recommended in the non-aesthetic area alternative to WMTA, Biodentine and iRoot BP Plus.
Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking
Authors: Linke Rita B. , Zeki Sibel , Mayer René , Keiblinger Katharina , Savio Domenico , Kirschner Alexander K. T. , Reischer Georg H. , Mach Robert L. , Sommer Regina , Farnleitner Andreas H.
Published: October 2021

Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g., adhesion of DNA to the sample matrix, inefficient precipitation of DNA, pipetting errors and (partial) loss of the DNA pellet during DNA isolation), quality control is essential at all processing levels. In soil microbiology, particular attention has been paid to the inorganic component of the sample matrix affecting DNA extractability. In water quality testing, however, this aspect has mostly been neglected so far, although it is conceivable that these mechanisms have a similar impact. The present study was therefore dedicated to investigate possible matrix effects on results of water quality analysis. Field testing in an aquatic environment with pronounced chemo-physical gradients [total suspended solids (TSS), inorganic turbidity, total organic carbon (TOC), and conductivity] indicated a negative association between DNA extractability (using a standard phenol/chloroform extraction procedure) and turbidity (spearman ρ = −0.72, p < 0.001, n = 21). Further detailed laboratory experiments on sediment suspensions confirmed the hypothesis of inorganic turbidity being the main driver for reduced DNA extractability. The observed effects, as known from soil samples, were also indicated to result from competitive effects for free charges on clay minerals, leading to adsorption of DNA to these inorganic particles. A protocol modification by supplementing the extraction buffer with salmon sperm DNA, to coat charged surfaces prior to cell lysis, was then applied on environmental water samples and compared to the standard protocol. At sites characterized by high inorganic turbidity, DNA extractability was significantly improved or made possible in the first place by applying the adapted protocol. This became apparent from intestinal enterococci and microbial source tracking (MST)-marker levels measured by quantitative polymerase chain reaction (qPCR) (100 to 10,000-fold median increase in target concentrations). The present study emphasizes the need to consider inorganic turbidity as a potential loss factor in DNA extraction from water-matrices. Negligence of these effects can lead to a massive bias, by up to several orders of magnitude, in the results of molecular MST and fecal pollution diagnostics.
Electroporation as an Efficacy Potentiator for Antibiotics With Different Target Sites
Authors: Lovšin Žana , Klančnik Anja , Kotnik Tadej
Published: October 2021

Antibiotic resistance is a global health threat, and there is ample motivation for development of novel antibacterial approaches combining multiple strategies. Electroporation is among the promising complementary techniques – highly optimizable, effective against a broad range of bacteria, and largely impervious to development of resistance. To date, most studies investigating electroporation as an efficacy potentiator for antibacterials used substances permissible in food industry, and only few used clinical antibiotics, as acceptable applications are largely limited to treatment of wastewaters inherently contaminated with such antibiotics. Moreover, most studies have focused mainly on maximal achievable effect, and less on underlying mechanisms. Here, we compare Escherichia coli inactivation potentiation rates for three antibiotics with different modes of action: ampicillin (inhibits cell wall synthesis), ciprofloxacin (inhibits DNA replication), and tetracycline (inhibits protein synthesis). We used concentrations for each antibiotic from 0 to 30× its minimum inhibitory concentration, a single 1-ms electric pulse with amplitude from 0 to 20 kV/cm, and post-pulse pre-dilution incubation either absent (≲1 min) or lasting 60 min, 160 min, or 24 h. Our data show that with incubation, potentiation is significant for all three antibiotics, increases consistently with pulse amplitude, and generally also with antibiotic concentration and incubation time. With incubation, potentiation for ampicillin was rather consistently (although with weak statistical significance) superior to both ciprofloxacin and tetracycline: ampicillin was superior to both in 42 of 48 data points, including 7 with significance with respect to both, while at 60- and 160-min incubation, it was superior in 31 of 32 data points, including 6 with significance with respect to both. This suggests that electroporation potentiates wall-targeting antibiotics more than those with intracellular targets, providing motivation for in-depth studies of the relationship between the mode of action of an antibiotic and its potentiation by electroporation. Identification of substances permissible in foods and targeting the cell wall of both Gram-negative and Gram-positive bacteria might provide candidate antibacterials for broad and strong potentiation by electroporation applicable also for food preservation.
Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination
Authors: Lyautey Emilie , Bonnineau Chloé , Billard Patrick , Loizeau Jean-Luc , Naffrechoux Emmanuel , Tlili Ahmed , Topp Edward , Ferrari Benoît J.D. , Pesce Stéphane
Published: October 2021

Lake sediments are natural receptors for a wide range of anthropogenic contaminants including organic matter and toxicants such as trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls that accumulate over time. This contamination can impact benthic communities, including microorganisms which play a crucial role in biogeochemical cycling and food-webs. The present survey aimed at exploring whether anthropogenic contamination, at a large lake scale, can influence the diversity, structure and functions of microbial communities associated to surface sediment, as well as their genetic potential for resistance to metals and antibiotics. Changes in the characteristics of these communities were assessed in surface sediments collected in Lake Geneva from eight sampling sites in October 2017 and May 2018. These sampling sites were characterized by a large concentration range of metal and organic compound contamination. Variation between the two sampling periods were very limited for all sampling sites and measured microbial parameters. In contrast, spatial variations were observed, with two sites being distinct from each other, and from the other six sites. Benthic communities from the most contaminated sampling site (Vidy Bay, near the city of Lausanne) were characterized by the lowest bacterial and archaeal diversity, a distinct community composition, the highest abundance of antibiotic resistance genes and functional (respiration, denitrification, methanogenesis, phosphatase, and beta-glucosidase) activity levels. The second sampling site which is highly influenced by inputs from the Rhône River, exhibited low levels of diversity, a distinct community composition, high abundance of antibiotic resistance genes and the highest bacterial abundance. Overall, our results suggest that local anthropogenic contamination, including organic matter and toxicants, is a major driver of the diversity and functioning of sediment-microbial communities in Lake Geneva. This highlights the need to consider benthic microbial communities and a suite of complementary ecotoxicological endpoints for more effective environmental risk assessments of contaminants in lake sediments.
Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry
Authors: Susanti Dwi , Volland Alyssa , Tawari Nilesh , Baxter Nielson , Gangaiah Dharanesh , Plata Germán , Nagireddy Akshitha , Hawkins Troy , Mane Shrinivasrao P. , Kumar Arvind
Published: October 2021

Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming Bacillus spp. offer advantages over traditional probiotic strains as Bacillus spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal’s gastrointestinal tract. Despite numerous reports on the use of Bacillus spores as feed additives, detailed characterizations of Bacillus probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from Ba PTA84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.
Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation
Authors: Wallner Adrian , Moulin Lionel , Busset Nicolas , Rimbault Isabelle , Béna Gilles
Published: October 2021

Burkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia, Caballeronia, Trinickia, and Mycetohabitans. We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI (Burkholderia cepacia complex Injectisome) and PSI (Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto (s.s.) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity.
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing
Authors: Carroll Laura M. , Buehler Ariel J. , Gaballa Ahmed , Siler Julie D. , Cummings Kevin J. , Cheng Rachel A. , Wiedmann Martin
Published: October 2021

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, whole-genome sequencing (WGS) was used to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement among susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50–60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring blaCMY- and blaCTX–M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.
Immobilization of Antibodies by Genetic Fusion to a Fungal Self-Assembling Adhesive Protein
Authors: Stanzione Ilaria , Izquierdo-Bote Daniel , González García María Begoña , Giardina Paola , Piscitelli Alessandra
Published: October 2021

Although antibody immobilization on solid surfaces is extensively used in several applications, including immunoassays, biosensors, and affinity chromatography, some issues are still challenging. Self-assembling protein layers can be used to coat easily different surfaces by direct deposition. A specific biofunctional layer can be formed using genetic engineering techniques to express fused proteins acting as self-immobilizing antibodies. In this study, fusion proteins combining the self-assembling adhesive properties of a fungal hydrophobin and the functionality of the single chain fragment variables (ScFvs) of two antibodies were produced. The chosen ScFvs are able to recognize marine toxins associated with algal blooms, saxitoxin, and domoic acid, which can bioaccumulate in shellfish and herbivorous fish causing food poisoning. ScFvs fused to hydrophobin Vmh2 from Pleurotus ostreatus were produced in Escherichia coli and recovered from the inclusion bodies. The two fusion proteins retained the functionality of both moieties, being able to adhere on magnetic beads and to recognize and bind the two neurotoxins, even with different performances. Our immobilization procedure is innovative and very easy to implement because it allows the direct functionalization of magnetic beads with ScFvs, without any surface modification. Two different detection principles, electrochemical and optical, were adopted, thus achieving a versatile platform suitable for different antigen detection methods. The sensitivity of the saxitoxin optical biosensor [limit of detection (LOD) 1.7 pg/ml] is comparable to the most sensitive saxitoxin immunosensors developed until now.
Connectivity-Based Topographical Changes of the Corpus Callosum During Aging
Authors: Liu Yuchen , Hsu Chih-Chin Heather , Huang Chu-Chung , Zhang Yajuan , Zhao Jiajia , Tsai Shih-Jen , Chen Liang-Kung , Lin Ching-Po , Lo Chun-Yi Zac
Published: October 2021

Background: The corpus callosum (CC) is the most prominent white matter connection for interhemispheric information transfer. It is implicated in a variety of cognitive functions, which tend to decline with age. The region-specific projections of the fiber bundles with microstructural heterogeneity of the CC are associated with cognitive functions and diseases. However, how the CC is associated with the information transfer within functional networks and the connectivity changes during aging remain unclear. Studying the CC topography helps to understand the functional specialization and age-related changes of CC subregions.

Methods: Diffusion tractography was used to subdivide the CC into seven subregions from 1,086 healthy volunteers within a wide age range (21–90 years), based on the connections to the cortical parcellations of the functional networks. Quantitative diffusion indices and connection probability were calculated to study the microstructure differences and age-related changes in the CC subregions.

Results: According to the population-based probabilistic topography of the CC, part of the default mode network (DMN) and limbic network (LN) projected fibers through the genu and rostrum; the frontoparietal network (FPN), ventral attention network (VA) and somatomotor networks (SM) were interconnected by the CC body; callosal fibers arising from the part of the default mode network (DMN), dorsal attention network (DA) and visual network (VIS) passed through the splenium. Anterior CC subregions interconnecting DMN, LN, FPN, VA, and SM showed lower fractional anisotropy (FA) and higher mean diffusivity (MD) and radial diffusivity (RD) than posterior CC subregions interconnecting DA and VIS. All the CC subregions showed slightly increasing FA and decreasing MD, RD, and axial diffusivity (AD) at younger ages and opposite trends at older ages. Besides, the anterior CC subregions exhibited larger microstructural and connectivity changes compared with the posterior CC subregions during aging.

Conclusion: This study revealed the callosal subregions related to functional networks and uncovered an overall “anterior-to-posterior” region-specific changing trend during aging, which provides a baseline to identify the presence and timing of callosal connection states.
Can Levodopa Challenge Testing Predict the Effect of Deep Brain Stimulation? One-Year Outcomes in a Chinese Cohort
Authors: Lin Wei , Shi Dongliang , Wang Dan , Yang Likun , Wang Yuhai , Jin Lingjing
Published: October 2021

Objective: Our study examined whether levodopa challenge test (LCT) results could predict quality of life (QoL) outcomes after surgery to implant subthalamic nucleus deep brain stimulation (STN-DBS) electrodes to treat advanced Parkinson’s disease (PD).

Methods: Forty patients with STN-DBS underwent a follow-up 1 year after implantation surgery to analyze the correlation between preoperative levodopa impact test results and postoperative Unified Parkinson’s Disease Rating Scale (UPDRS) III motor score, postoperative PD Questionnaire-39 (PDQ-39) score, and PDQ-39 improvement.

Results: Improvements in QoL were associated with several preoperative characteristics including preoperative UPDRS-III tremor, UPDRS-III tremor (off-60) (p = 0.049), UPDRS-III tremor (off-120) (p = 0.012), Mini-Mental State Examination (p = 0.012), and PDQ-39 (p = 0.012) before surgery. Multiple linear regression model using preoperative MMSE [odds ratio (OR) = 0.342, 95% confidence interval (CI) = 0.051–2.297], preoperative UPDRS-III tremor (OR = 2.099, 95% CI = 0.585–7.535), UPDRS-III tremor (off-60) [OR = 1.316, 95% CI = 0.804–2.154, UPDRS-III tremor (off-120) OR = 0.913, 95% CI = 0.691–1.207], correctly classified 88.5% of patients.

Conclusion: Levodopa challenge test results cannot predict the effect of DBS. However, the test can be incorporated into a regression prediction model to the quality of life of PD patients after DBS with other preoperative factors.
Patterned Feeding of a Hyper-Palatable Food (Oreo Cookies) Reduces Alcohol Drinking in Rats
Authors: Leon Zoela , Shah Krishna , Bailey Lauren S. , Karkhanis Anushree N. , Sirohi Sunil
Published: October 2021

While a bidirectional positive link between palatable food intake and alcohol drinking has been suggested, several rodents studies report reduced alcohol drinking following palatable diets exposure. These studies utilized purified rodents’ diets high in sugar/fat; however, the effects of hyper-palatable food (HPF) rich in fat and sugar on alcohol drinking remain unclear. Furthermore, neural substrates involved in HPF-mediated changes in alcohol consumption are poorly understood. Therefore, the present study evaluated the effects of patterned feeding of a hyper-palatable food (Oreo cookies) on alcohol drinking as well as dopamine (DA) and serotonin (5-HT) content in rat’s mesocorticolimbic (medial-prefrontal cortex, orbitofrontal cortex, amygdala, and nucleus accumbens) circuitry. Male Long Evans rats received 8-weeks of intermittent (Mon, Tue, Wed) Oreo cookies access, which induced a patterned feeding, in which rats in the Oreo group overconsumed calories on HPF days whereas underconsumption was observed on chow only (Thu, Fri) days. Following HPF exposure, alcohol consumption was evaluated while patterned feeding continued. Alcohol intake in the Oreo group was significantly lower as compared to the chow controls. However, alcohol intake in the Oreo group increased to the levels seen in the group receiving chow following the suspension of patterned HPF feeding. Finally, DA levels in the nucleus accumbens were significantly greater, whereas its metabolite (DOPAC) levels were lower in the Oreo group compared to the chow controls. Surprisingly, 5-HT levels remained unaltered in all tested brain areas. Together, these data suggest that HPF-associated increased DA availability and reduced DA turnover within mesocorticolimbic circuitry may regulate alcohol drinking following patterned HPF feeding.
Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains
Authors: Li Ye , Walker Logan A. , Zhao Yimeng , Edwards Erica M. , Michki Nigel S. , Cheng Hon Pong Jimmy , Ghazzi Marya , Chen Tiffany Y. , Chen Maggie , Roossien Douglas H. , Cai Dawen
Published: October 2021

Identifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Current Brainbow based transgenic animals take the advantage of multispectral labeling to differentiate neighboring cells or lineages, however, their applications are limited by the color capacity. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing, and data analysis pipelines to conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with unprecedented speed, scale, and resolution.
Low Ankle-Brachial Index Is Associated With Stroke Recurrence in Ischemic Stroke Patients With Atrial Fibrillation
Authors: Han Minho , Baik Minyoul , Kim Young Dae , Choi Junghye , Seo Kangsik , Park Eunjeong , Heo Ji Hoe , Nam Hyo Suk
Published: October 2021

Introduction: Cardioembolic stroke (CE) has poor outcomes and high recurrence rates. A low ankle-brachial index (ABI <0.9) is associated with atrial fibrillation (AF) and poor stroke outcomes. We investigated whether a low ABI is associated with stroke recurrence, major adverse cardiovascular events (MACE), and mortality in patients with CE and whether this association is affected by AF.

Methods: We enrolled patients with CE who underwent ABI measurements during hospitalization. Recurrent stroke was defined based on newly developed neurologic symptoms with relevant lesions 7 days after the index stroke. MACE comprised stroke recurrence, myocardial infarction, or death.

Results: Of 775 patients, 427 (55.1%) were AF patients and 348 (44.9%) were non-AF patients. Patients were followed up for a median of 33.6 (IQR, 18.0–51.6) months. In total, 194 (25.0%) patients experienced MACE, including 77 (9.9%) patients with stroke recurrence and 101 (13.0%) patients with mortality, during the study period. Multivariable Cox regression analysis showed that an ABI <0.9 was independently associated with MACE (AF patients: hazard ratio [HR] = 2.327, 95% confidence interval [CI] = 1.371–3.949, non-AF patients: HR = 3.116, 95% CI = 1.465–6.629) and mortality (AF patients: HR = 2.659, 95% CI = 1.483–4.767, non-AF patients: HR = 3.645, 95% CI = 1.623–8.187). Stroke recurrence was independently associated with an ABI <0.9 in AF patients (HR = 3.559, 95% CI = 1.570–8.066), but not in non-AF patients (HR = 1.186, 95% CI = 0.156–8.989).

Conclusions: We found that a low ABI is associated with stroke recurrence, MACE, and mortality in patients with CE. In particular, the association between ABI and recurrent stroke is only present in AF patients. A low ABI may be a useful prognostic marker in patients with CE, especially in AF patients.
The Genetic Basis of Phenotypic Heterogeneity in the Neuronal Ceroid Lipofuscinoses
Authors: Gardner Emily , Mole Sara E.
Published: October 2021

The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that affect children and adults. They share some similar clinical features and the accumulation of autofluorescent storage material. Since the discovery of the first causative genes, more than 530 mutations have been identified across 13 genes in cases diagnosed with NCL. These genes encode a variety of proteins whose functions have not been fully defined; most are lysosomal enzymes, or transmembrane proteins of the lysosome or other organelles. Many mutations in these genes are associated with a typical NCL disease phenotype. However, increasing numbers of variant disease phenotypes are being described, affecting age of onset, severity or progression, and including some distinct clinical phenotypes. This data is collated by the NCL Mutation Database which allows analysis from many perspectives. This article will summarise and interpret current knowledge and understanding of their genetic basis and phenotypic heterogeneity.
Vitamin D in Multiple Sclerosis—Lessons From Animal Studies
Authors: Haindl Michaela Tanja , Hochmeister Sonja
Published: October 2021

Multiple sclerosis is a multifactorial disease of the central nervous system with both genetic and environmental causes. The exact disease mechanisms are still unclear. Consequently, studies of possible treatment and preventive measures cover a large setting of heterogeneous approaches. Vitamin D is one of these approaches, and in many trials the relation of vitamin D serum levels and multiple sclerosis disease risk and activity describes different effects with sometimes inconsistent findings. Animal models are substantial for the research of disease mechanisms, and many of the drugs that are currently in use in multiple sclerosis have been developed, tested, or validated via animal studies. Especially when clinical studies show contradicting findings, the use of standardized settings and information about the mechanistic background is necessary. For this purpose, animal models are an essential tool. There is a variety of different experimental settings and types of animal models available, each of them with own strengths but also weaknesses. This mini-review aims to overview results of vitamin D studies in different animal models and sums up the most important recent findings.
Effectiveness of Natalizumab in Achieving No Evidence of Disease Activity (NEDA-3)—Data From a Local Norwegian Cohort
Authors: Jaklin Andreas K. , Benjaminsen Espen , Alstadhaug Karl B.
Published: October 2021

Objective: We aimed to determine the effectiveness of natalizumab (NTZ) by assessing overall No Evidence of Disease Activity 3 (NEDA-3) in a local Norwegian cohort.

Background: NTZ is an immunomodulating drug used in the treatment of multiple sclerosis (MS). It has typically been used as a second-line treatment, but certain patients with high disease activity have started directly with NTZ.

Methods: This retrospective cohort study includes all patients who received NTZ for relapsing–remitting MS at Nordland Hospital in the period 2008–2018. In June 2019, status for every patient was assessed, and a survival curve was used to show the cumulative probability of achieving NEDA-3 over time.

Results: The cohort consisted of 66 patients, 49 women and 17 men with a mean age of 40.0 ± 10.8 years. Each patient received on average 45.8 ± 36.4 NTZ infusions. Mean age and Expanded Disability Status Scale (EDSS) at first infusion was 34.8 ± 10.5 and 3.2 ± 1.9, respectively. Prior to NTZ treatment, 83% had used other disease modulating drugs and 65% were anti-JC virus (JCV) seronegative. During the study period, seven patients converted to seropositive. In 2019, 40 patients had switched or stopped treatment: 19 due to positive JCV serostatus, 9 due to disease activity, 7 due to adverse effects or complications (1 progressive multifocal leukoencephalopathy), 2 due to pregnancy, and 3 due to autologous hematopoietic cell transplantation abroad. Three patients experienced rebound in the wake of discontinuation (7.5%). Of the patients receiving NTZ for more than 3 years (n = 33), 50% had achieved NEDA-3 after 3 years. Compared to those with evidence of disease activity (EDA), these NEDA-3 patients had significant lower EDSS score before first NTZ treatment (p = 0.04). They were also slightly, but not significantly, younger at debut of their MS, at the diagnosis and at first NTZ treatment. Of all the patients who ever started on NTZ, 23% had achieved NEDA-3 5 years later. The mean EDSS in 2019 was 3.6 ± 2.5.

Conclusion: Despite the high rate of treatment switch, mainly due to the risk of PML, almost one in four who started on NTZ achieved NEDA-3 after 5 years, and the overall disease progression was low in the total cohort. Treating less advanced disease seems to predict better long-term stability.