scholarly journals Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence

2020 ◽  
Vol 9 (11) ◽  
pp. 3700
Author(s):  
Garrit Koller ◽  
Federico Foschi ◽  
Philip Mitchell ◽  
Elizabeth Witherden ◽  
Kenneth Bruce ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Inflammatory Responses ◽  
Clinical Signs ◽  
Signs And Symptoms ◽  
Resistant Bacteria ◽  
Low Grade ◽  
Taxonomic Assignment ◽  
Microbial Composition ◽  
Endodontic Infections

Background: Infections of the root canal space involve polymicrobial biofilms and lead to chronic, low grade inflammatory responses arising from the seeding of microbes and by-products. Acute exacerbation and/or disseminating infections occur when established microbial communities undergo sudden changes in phenotypic behaviour. Methods: Within clinical endodontic infections, we assessedcategorical determinants comprising, and changing microbial composition of, chronic polymicrobial infections and their association with amoebae. After standardised assessment, primary or secondary infections underwent sampling and DNA processing, targeting bacteria, fungi and amoebae, including 16S high-throughput sequencing. After taxonomic assignment, community composition was correlated with clinical signs and symptoms. Diversity and abundance analyses were carried out in relation to the presence of non-bacterial amplicons. Results: Clinical specimens revealed two distinct community clusters, where specific changes correlated with clinical signs. An association between the compositions of microbiomes was found between these groups and the presence of Entamoeba gingivalis in 44% of cases. When amoebae were present in endodontic infections, we demonstrate changes in microbial community structure that mirror those observed in treatment-resistant or recurrent infections. Conclusions: Amoeba are present in endodontic infections at a high prevalence, and may promote increased virulence by enrichment for phagocytosis-resistant bacteria.

scholarly journals Muscle damage and inflammation during recovery from exercise

2017 ◽  
Vol 122 (3) ◽  
pp. 559-570 ◽  
Author(s):  
Jonathan M. Peake ◽  
Oliver Neubauer ◽  
Paul A. Della Gatta ◽  
Kazunori Nosaka
Keyword(s):  
Muscle Strength ◽  
Muscle Damage ◽  
Muscle Tissue ◽  
Time Course ◽  
Inflammatory Responses ◽  
Large Body ◽  
Clinical Signs ◽  
Muscle Length ◽  
Signs And Symptoms ◽  
Exercise Induced

Unaccustomed exercise consisting of eccentric (i.e., lengthening) muscle contractions often results in muscle damage characterized by ultrastructural alterations in muscle tissue, clinical signs, and symptoms (e.g., reduced muscle strength and range of motion, increased muscle soreness and swelling, efflux of myocellular proteins). The time course of recovery following exercise-induced muscle damage depends on the extent of initial muscle damage, which in turn is influenced by the intensity and duration of exercise, joint angle/muscle length, and muscle groups used during exercise. The effects of these factors on muscle strength, soreness, and swelling are well characterized. By contrast, much less is known about how they affect intramuscular inflammation and molecular aspects of muscle adaptation/remodeling. Although inflammation has historically been viewed as detrimental for recovery from exercise, it is now generally accepted that inflammatory responses, if tightly regulated, are integral to muscle repair and regeneration. Animal studies have revealed that various cell types, including neutrophils, macrophages, mast cells, eosinophils, CD8 and T-regulatory lymphocytes, fibro-adipogenic progenitors, and pericytes help to facilitate muscle tissue regeneration. However, more research is required to determine whether these cells respond to exercise-induced muscle damage. A large body of research has investigated the efficacy of physicotherapeutic, pharmacological, and nutritional interventions for reducing the signs and symptoms of exercise-induced muscle damage, with mixed results. More research is needed to examine if/how these treatments influence inflammation and muscle remodeling during recovery from exercise.

scholarly journals Physicochemical Characteristics and Microbial Communities in Gochujang, a Traditional Korean Fermented Hot Pepper Paste

2021 ◽  
Vol 11 ◽  
Author(s):  
Jung-A Ryu ◽  
Eiseul Kim ◽  
Mi-Ju Kim ◽  
Shinyoung Lee ◽  
Sung-Ran Yoon ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Salt Concentration ◽  
High Throughput Sequencing ◽  
Sugar Content ◽  
Physicochemical Characteristics ◽  
Reducing Sugar ◽  
Hot Pepper ◽  
Microbial Composition ◽  
Factors Affecting ◽  
High Level

Gochujang is a Korean fermented hot pepper paste beneficial to human health by providing various nutrients. In this study, its physicochemical characteristics were identified, and its microbial communities were analyzed by high-throughput sequencing. The interrelationship between physicochemical characteristics and microbial composition was investigated to reveal the properties of gochujang before and after fermentation. After fermentation, all samples showed decreased salt concentration, pH, and reducing sugar content, while the acidity and amino-type nitrogen increased. The water content, salt concentration, amino-type nitrogen, and reducing sugar differed according to the batches of samples. Bacillus, Aerosakkonema, and Enterococcus were identified as the predominant bacterial genera. Furthermore, Aerosakkonema was the most abundant genus before fermentation; however, it was replaced by Bacillus as it decreased after fermentation. For the fungi, Aspergillus dominated before fermentation, whereas Zygosaccharomyces and Millerozyma dominated after fermentation. The high level of amino-type nitrogen in gochujang was related to the relative abundance of B. haynesii/B. licheniformis before fermentation. Additionally, the high abundance of Z. rouxii after fermentation was related to the flavor of gochujang. This comprehensive analysis of the microbial community associated with the physicochemical properties of gochujang could help in understanding the factors affecting the quality of the product.

Diversity and function of microbial communities in the sand sheath of Agropyron cristatum by metagenomic analysis

2021 ◽  
pp. 1-13
Author(s):  
Yuehua Wang ◽  
Meixiao Wu ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Polyketide Synthase ◽  
Phosphorus Uptake ◽  
Agropyron Cristatum ◽  
Bulk Soil ◽  
Phosphorus Cycle ◽  
Mannitol Dehydrogenase ◽  
Microbial Composition ◽  
Illumina Hiseq

The roots of most gramineous plants are surrounded by a variety of microorganisms; however, few studies have focused on the rhizosheath of psammophytes. Therefore, in this study, we used Illumina HiSeq high-throughput sequencing technology to analyse the composition and functional diversity of microbial communities in the rhizosheath of sand-grown Agropyron cristatum (L.) Gaertn. We found that the number of species and functions of microbial communities gradually decreased from the rhizosheath to the bulk soil. Thus, the microbial composition of the rhizosheath was richer and more diverse, and the abundance of bacteria, including Sphingosinicella, Rhizorhabdus, Friedmanniella, Geodermatophilus, Blastococcus, and Oscillatoria, was higher, and the abundance of fungi, such as Mycothermus, was higher. The abundance of CO2 fixation-related genes (acsA, Pcc, and cbbL) in the carbon cycle; NO3–, NO2–, NH2OH, and N2 transformation genes (nrtP, nirS, hao, and nifK) in the nitrogen cycle; soxB/A/C, Sat, and dsrB genes in the sulphur cycle; and 1-phosphate mannitol dehydrogenase (MtlD) gene and polyketide synthase gene (pks) were higher in the rhizosheath than in the bulk soil, as well as genes related to phosphorus uptake in the phosphorus cycle. Our findings showed that the rhizosheath may host the predominant microbial species related to the formation of a rhizosheath.

scholarly journals Histopathological study of cystoscopic bladder biopsies

2015 ◽  
Vol 5 (9) ◽  
pp. 717-719
Author(s):  
R Baidya ◽  
B Sigdel ◽  
NL Baidhya
Keyword(s):  
Urinary Bladder ◽  
Transitional Cell ◽  
Clinical Signs ◽  
Signs And Symptoms ◽  
Developed Countries ◽  
Histopathological Study ◽  
Low Grade ◽  
Neoplastic Lesions ◽  
Clinical Signs And Symptoms ◽  
Hematoxylin And Eosin Stain

Background: Urinary bladder diseases constitute an important source of clinical signs and symptoms which are more disabling than lethal. The prevalence of bladder tumor in developed countries is approximately six times higher compared with that in developing countries. The aim of this study was to find out various lesions in urinary bladder biopsies and its frequencies.Materials and Methods: This was a five year retrospective study from January 2008 to December 2013, carried out at B&B Hospital, Lalitpur. All the relevant data of 324 patients who had undergone cystoscopic biopsy of urinary bladder were included in the study. All blocks were retrieved and stained with Hematoxylin and Eosin stain and examined under light microscope.Results: The spectrum of pathological lesions included inflammations and tumors. Non-neoplastic lesions were predominant (61.11%) followed by Transitional cell tumors accounted for 124 cases (38.27%). Non-neoplastic lesions comprises of cystitis and tuberculosis. Papillary urothelial neoplasms was the most common tumors seen in this study with 55 low grade, and 54 high grade Papillary urothelial carcinoma according to recent WHO grading. Single cases each of adenocarcinoma and paraganglioma were diagnosed.Conclusion: Cystoscopic biopsies help in the early diagnosis and treatment of various bladder lesions. Analysis of cystoscopic biopsies was done to ascertain the type of urinary bladder lesions in our country.Journal of Pathology of Nepal (2015) Vol. 5, 717-719

Are there clinical signs and symptoms of infection to indicate the presence of multidrug-resistant bacteria in venous ulcers?

2017 ◽  
Vol 35 (4) ◽  
pp. 178-186
Author(s):  
Silvana de Lima Vieira dos Santos ◽  
Marlene Andrade Martins ◽  
Marinésia Aparecida do Prado ◽  
José Verdú Soriano ◽  
Maria Márcia Bachion
Keyword(s):  
Clinical Signs ◽  
Signs And Symptoms ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Multidrug Resistant Bacteria ◽  
Venous Ulcers ◽  
Clinical Signs And Symptoms

scholarly journals NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

F1000Research ◽  
2018 ◽  
Vol 5 ◽  
pp. 1791 ◽  
Author(s):  
Javier Ramiro-Garcia ◽  
Gerben D. A. Hermes ◽  
Christos Giatsis ◽  
Detmer Sipkema ◽  
Erwin G. Zoetendal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Read Length ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Microbial Composition ◽  
Sample Composition ◽  
Mock Communities

Background: Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises meta-analyses, although this fact is often disregarded. Results: To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as a frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed for the evaluation of important causes of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 97.78%. On average 99.95% and 88.43% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.21% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not achieved with QIIME. Conclusions: Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.

scholarly journals NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1791 ◽  
Author(s):  
Javier Ramiro-Garcia ◽  
Gerben D. A. Hermes ◽  
Christos Giatsis ◽  
Detmer Sipkema ◽  
Erwin G. Zoetendal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Read Length ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Microbial Composition ◽  
Sample Composition ◽  
Mock Communities

Background Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded. Results To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME. Conclusions Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.

scholarly journals Primary intracranial germ cell tumour originating from right brachium Pontis with hypertrophic Olivary degeneration: a case report

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanong Li ◽  
Peng Wang ◽  
Jin Feng ◽  
Jiayi Wang ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Preoperative Diagnosis ◽  
Demyelinating Disease ◽  
Germ Cell Tumour ◽  
Clinical Signs ◽  
Signs And Symptoms ◽  
Neurological Deficits ◽  
Low Grade ◽  
Ataxic Gait ◽  
Intracranial Germinoma ◽  
Hypertrophic Olivary Degeneration

Abstract Background Primary right brachium pontis germinoma with hypertrophic olivary degeneration (HOD) is extremely rare. A preoperative diagnosis is challenging due to the absence of characterized clinical and neuroimaging features, and biopsy should be considered. Case presentation A 20-year-old male patient presented with a case of primary intracranial germinoma originating from right brachium pontis with HOD manifesting as ocular myoclonus, nystagmus in both eyes, ataxic gait and incoordination of the limbs. Magnetic resonance imaging (MRI) revealed an irregular patchy lesion with hyperintensity on T2-weighted images (T2WI) and T2 fluid-attenuated inversion recovery (FLAIR) without enhancement by gadolinium (Gd). Furthermore, a focal hyperintense nodule on T2WI in the left inferior olive nucleus (ION) of the medulla oblongata was considered hypertrophic olivary degeneration (HOD) based on the patient’s symptoms and neuroimaging findings. Due to suspected demyelinating disease and low-grade glioma (LGG), a biopsy was planned. The pathological diagnosis was germinoma. Subsequently, he received chemoradiation therapy, resulting in the improvement of neurological deficits and the disappearance of the lesion on MRI. Conclusion A case of “Primary right brachium pontis germinoma with HOD” is reported for the first time. A preoperative diagnosis is challenging due to the fact of absence of clinical signs and symptoms and neuroimaging characteristics. However, patients can have favourable prognoses with appropriate evaluation and treatment.

Neuroleptic malignant syndrome: risk factors, pathophysiology, and treatment

2004 ◽  
Vol 16 (4) ◽  
pp. 219-228 ◽  
Author(s):  
Jambur Ananth ◽  
Kamala Aduri ◽  
Sharath Parameswaran ◽  
Sarath Gunatilake
Keyword(s):  
Neuroleptic Malignant Syndrome ◽  
Heat Stroke ◽  
Clinical Signs ◽  
Signs And Symptoms ◽  
Active Phase ◽  
Initial Step ◽  
Antipsychotic Agents ◽  
Patient Treatment ◽  
Low Grade ◽  
Dopamine Receptor Antagonists

Neuroleptic malignant syndrome (NMS) is associated with the administration of antipsychotic agents and other drugs such as l-dopa, antidepressants, and antihistaminic agents. Unexpected changes in mental status, new-onset catatonia, episodic tachycardia, tachypnea, hypertension, dysarthria, dysphagia, diaphoresis, sialorrhea, incontinence, low-grade temperature elevations, and rigidity should arouse suspicion. Several lines of evidence provide support for the involvement of dopamine. Most of the drugs implicated in NMS are D2 dopamine receptor antagonists. Central noradrenergic activity is also possibly related to the disorder, as sympathetic hyperactivity is associated with the active phase of NMS. Currently, the definitive role of GABA deficiency in NMS is yet to be established. Differential diagnosis should include malignant hyperthermia, lethal catatonia, lithium toxicity, serotonin syndrome, and heat stroke. A high degree of suspicion and the discontinuation of antipsychotic agents even if the diagnosis is not established are essential for the safety of the patient. Treatment of NMS should be individualized and be based empirically on the character, duration, and severity of the clinical signs and symptoms noted. The initial step in the treatment of NMS is the removal of the offending agent. Full-blown NMS is a serious condition and requires immediate supportive, nutritive, and electrolyte therapies. The administration of drugs that can improve NMS, such as IV dantrolene and/or oral bromocriptine, may also be taken into consideration, based on the severity and nature of the NMS.

scholarly journals Loss of a Single Plant Functional Group in Litter Had Marginal Impacts on Microbial Community Diversity and Composition in a Tibet Fir Forest

2021 ◽  
Author(s):  
Qianwei Li ◽  
Lifeng Wang ◽  
Yamei Chen ◽  
Li Guo ◽  
Chengming You ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Driving Forces ◽  
Community Diversity ◽  
Plant Functional Groups ◽  
Plant Residues ◽  
Microbial Composition ◽  
Ecological Processes ◽  
And Function

Abstract Aim The decomposition of plant residues is a fundamental process of soil organic matter accumulation. The loss of plant functional groups (PFGs) could affect this process by producing litter of different qualities in the soil. Microorganisms are one of the indispensable driving forces of ecological processes, but the mechanisms by microbial communities respond to aboveground PFG changes are still unclear, which limits our understanding of biogeochemical cycle changes under PFG loss.Methods We assessed the microbial taxonomic and functional composition of six typical single PFGs (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern), random loss of a single PFG (SPFG) from litter mixtures and total mixture of six PFGs in a Tibetan fir forest by a high-throughput sequencing method.Results The microbial composition and function did not change with loss of a SPFG in litter, and microbial communities were mainly determined by the carbon and nitrogen ratio (C:N), carbon and phosphorus ratio (C:P), N and lignin, and bacterial functional pathways and fungal functional guilds were both determined by N, C:N and C:P ratios. Bacterial diversity was positively related while fungal diversity was negatively related to N and cellulose concentrations.Conclusion We speculated that the difference in initial litter qualities (especially C:N) between different PFGs, rather than a decreased number of PFGs, is a determinant of microbial composition and function. As the loss of PFG does not change litter quality, the microbial community can resist the loss of PFG, which maintains alpine ecosystem carbon and nutrient cycling stability.

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