scholarly journals Role of Exposure on the Microbial Consortiums on Historical Rural Granite Buildings

2021 ◽  
Vol 11 (9) ◽  
pp. 3786
Author(s):  
Elsa Fuentes ◽  
Rafael Carballeira ◽  
Beatriz Prieto
Keyword(s):  
Environmental Factors ◽  
Green Algae ◽  
Abundant Species ◽  
Lichenized Fungi ◽  
Factors Associated ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Local granite has been used throughout history in Galicia (NW Spain), forming the basis of much of the region’s architecture. Like any other rock, granite provides an ecological niche for a multitude of organisms that form biofilms that can affect the physical integrity of the stone. In this study, for the first time, characterization of the microbial consortium forming biofilms that developed on historical rural granite buildings is carried out using a combination of culture-dependent and next generation sequencing (NGS) techniques. Results pointed to differences in biofilm composition on the studied rural granite buildings and that of previously analyzed urban granite buildings, especially in terms of abundance of cyanobacteria and lichenized fungi. Exposure was corroborated as an important factor, controlling both the diversity and abundance of microorganisms on walls, with environmental factors associated with a northern orientation favoring a higher diversity of fungi and green algae, and environmental factors associated with the west orientation determining the abundance of lichenized fungi. The orientation also affected the distribution of green algae, with one of the two most abundant species, Trentepohlia cf. umbrina, colonizing north-facing walls, while the other, Desmococcus olivaceus, predominated on west-facing walls.

scholarly journals CSF3R T618I, SETBP1 G870S, SRSF2 P95H, and ASXL1 Q780* tetramutation co-contribute to myeloblast transformation in a chronic neutrophilic leukemia

2021 ◽  
Author(s):  
Yi Qian ◽  
Yan Chen ◽  
Xiaoming Li
Keyword(s):  
Alpha Interferon ◽  
Past Medical History ◽  
Variant Allele Frequency ◽  
Significant Past Medical History ◽  
Chronic Neutrophilic Leukemia ◽  
Hypercellular Marrow ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Stat Pathway

AbstractChronic neutrophilic leukemia (CNL) is a rare but serious myeloid malignancy. In a review of reported cases for WHO-defined CNL, CSF3R mutation is found in about 90% cases and confirmed as the molecular basis of CNL. Concurrent mutations are observed in CSF3R-mutated CNL patients, including ASXL1, SETBP1, SRSF2, JAK2, CALR, TET2, NRAS, U2AF1, and CBL. Both ASXL1 and SETBP1 mutations in CNL have been associated with a poor prognosis, whereas, SRSF2 mutation was undetermined. Our patient was a 77-year-old man and had no significant past medical history and symptoms with leukocytosis. Bone marrow (BM) aspirate and biopsy revealed a markedly hypercellular marrow with prominent left-shifted granulopoiesis. Next-generation sequencing (NGS) of DNA from the BM aspirate of a panel of 28 genes, known to be pathogenic in MDS/MPN, detected mutations in CSF3R, SETBP1, and SRSF2, and a diagnosis of CNL was made. The patient did not use a JAK-STAT pathway inhibitor (ruxolitinib) but started on hydroxyurea and alpha-interferon and developed pruritus after 4 months of diagnosis and nasal hemorrhage 1 month later. Then, the patient was diagnosed with CNL with AML transformation and developed intracranial hemorrhage and died. We repeated NGS and found that three additional mutations were detected: ASXL1, PRKDC, MYOM2; variant allele frequency (VAF) of the prior mutations in CSF3R, SETBP1, and SRSF2 increased. The concurrence of CSF3RT618I, ASXL1, SETBP1, and SRSF2 mutation may be a mutationally detrimental combination and contribute to disease progression and AML transformation, as well as the nonspecific treatment of hydroxyurea and alpha-interferon, but the significance and role of PRKDC and MYOM2 mutations were not undetermined.

scholarly journals Molecular analysis of the microflora in chronic venous leg ulceration

2003 ◽  
Vol 52 (4) ◽  
pp. 365-369 ◽  
Author(s):  
K.E. Hill ◽  
C.E. Davies ◽  
M.J. Wilson ◽  
P. Stephens ◽  
K.G. Harding ◽  
...  
Keyword(s):  
Individual Species ◽  
Venous Leg Ulcer ◽  
Bacterial Populations ◽  
Cultural Methods ◽  
Rdna Sequences ◽  
Oral Microflora ◽  
16S Rdna Sequences ◽  
First Time

There is growing evidence to suggest that the resident microflora of chronic venous leg ulcers impairs cellular wound-healing responses, thereby playing an important role in maintaining the non-healing phenotype of many of these wounds. The significance of individual species of bacteria will remain unclear until it is possible to characterize fully the microflora of such lesions. The limitations and biases of culture-based microbiology are being realized and the subsequent application of molecular methods is revealing greater diversity within mixed bacterial populations than that demonstrated by culture alone. To date, this approach has been limited to a small number of systems, including the oral microflora. Here, for the first time, the comprehensive characterization of the microflora present in the tissue of a chronic venous leg ulcer is described by the comparison of 16S rDNA sequences amplified directly from the wound tissue with sequences obtained from bacteria that were isolated by culture. The molecular approach demonstrated significantly greater bacterial diversity than that revealed by culture. Furthermore, sequences were retrieved that may possibly represent novel species of bacteria. It is only by the comprehensive analysis of the wound microflora by both molecular and cultural methods that it will be possible to further our understanding of the role of bacteria in this important condition.

scholarly journals Characterization of Unknown Orthobunya-Like Viruses from India

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 451 ◽  
Author(s):  
Shannon Whitmer ◽  
Pragya Yadav ◽  
Prasad Sarkale ◽  
Gouri Chaubal ◽  
Alicia Francis ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Febrile Illness ◽  
Geographic Region ◽  
Emerging Viruses ◽  
Simbu Serogroup ◽  
Isolation And Characterization ◽  
Karnataka State ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.

Phonons in deformable microporous crystalline solids

2019 ◽  
Vol 234 (7-8) ◽  
pp. 513-527 ◽  
Author(s):  
Bogdan Kuchta ◽  
Filip Formalik ◽  
Justyna Rogacka ◽  
Alexander V. Neimark ◽  
Lucyna Firlej
Keyword(s):  
Periodic Structures ◽  
Structural Transformations ◽  
Crystalline Solids ◽  
Predictive Tool ◽  
Crystalline Materials ◽  
Numerical Tools ◽  
Collective Vibrations ◽  
First Time

Abstract Phonons are quantum elastic excitations of crystalline solids. Classically, they correspond to the collective vibrations of atoms in ordered periodic structures. They determine the thermodynamic properties of solids and their stability in the case of structural transformations. Here we review for the first time the existing examples of the phonon analysis of adsorption-induced transformations occurring in microporous crystalline materials. We discuss the role of phonons in determining the mechanism of the deformations. We point out that phonon-based methodology may be used as a predictive tool in characterization of flexible microporous structures; therefore, relevant numerical tools must be developed.

Adipocyte-rich CTNNB1-mutated Intramuscular Gardner Fibroma Progressing to Desmoid Fibromatosis

2020 ◽  
pp. 109352662096880
Author(s):  
Andrea Bakker ◽  
Jonathan C Slack ◽  
Mara Caragea ◽  
Kyle C Kurek ◽  
Marie-Anne Bründler
Keyword(s):  
Soft Tissue ◽  
Soft Tissue Tumor ◽  
Soft Tissue Tumors ◽  
Molecular Testing ◽  
Tissue Mass ◽  
Desmoid Fibromatosis ◽  
Benign Soft Tissue Tumor ◽  
First Time ◽  
Generation Sequencing

Gardner fibroma (GF) is a benign soft-tissue tumor that is associated with Gardner syndrome and can progress to, or co-occur with, desmoid fibromatosis (DF). Herein, we report a unique case of an 11-year-old boy who presented with a rapidly growing soft-tissue mass after biopsy of a stable fat-rich lesion present in the calf muscles since infancy, with Magnetic resonance imaging findings suggesting an intramuscular adipocytic tumor. The resection showed GF and DF. DF arising from a preexisting GF (the so-called “GF-DF sequence”) is a well-documented phenomenon. Although immunohistochemistry was negative for nuclear β-catenin expression, a CTTNB1 S45F mutation, which has been associated with aggressive behavior in DF, was identified in both components using a next-generation sequencing-based molecular assay. This is the first time a mutation in CTNNB1 has been identified in GF and the GF–DF sequence, thus expanding our knowledge of the molecular pathogenesis of the GF–DF sequence and highlighting the role of molecular testing in pediatric soft-tissue tumors. The histologic findings of an adipocyte-rich intramuscular GF also are unique, expanding the morphological spectrum of GF and adding GF to the differential diagnosis of intramuscular lesions with an adipocytic component.

scholarly journals Traumatic glioblastoma: commentary and suggested mechanism

2018 ◽  
Vol 46 (6) ◽  
pp. 2170-2176
Author(s):  
Nissim Ohana ◽  
Daniel Benharroch ◽  
Dimitri Sheinis ◽  
Abraham Cohen
Keyword(s):  
Traumatic Brain Injury ◽  
Transcription Factors ◽  
Brain Injury ◽  
Brain Injuries ◽  
Hypoxia Inducible Factor ◽  
Subsequent Development ◽  
Factors Associated ◽  
The Relationship

The role of head trauma in the development of glioblastoma is highly controversial and has been minimized since first put forward. This is not unexpected because skull injuries are overwhelmingly more common than glioblastoma. This paper presents a commentary based on the contributions of James Ewing, who established a major set of criteria for the recognition of an official relationship between trauma and cancer. Ewing’s criteria were very stringent. The scholars who succeeded Ewing have facilitated the characterization of traumatic brain injuries since the introduction of computed tomography and magnetic resonance imaging. Discussions of the various criteria that have since developed are now being conducted, and those of an unnecessarily limiting nature are being highlighted. Three transcription factors associated with traumatic brain injury have been identified: p53, hypoxia-inducible factor-1α, and c-MYC. A role for these three transcription factors in the relationship between traumatic brain injury and glioblastoma is suggested; this role may support a cause-and-effect link with the subsequent development of glioblastoma.

scholarly journals Molecular Genetics and Interferon Signature in the Italian Aicardi Goutières Syndrome Cohort: Report of 12 New Cases and Literature Review

2019 ◽  
Vol 8 (5) ◽  
pp. 750 ◽  
Author(s):  
Jessica Garau ◽  
Vanessa Cavallera ◽  
Marialuisa Valente ◽  
Davide Tonduti ◽  
Daisy Sproviero ◽  
...  
Keyword(s):  
Interferon Signaling ◽  
Cerebral Calcification ◽  
Interferon Signature ◽  
Interferon Stimulated Genes ◽  
Functional Investigation ◽  
Genetically Determined ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing ◽  
Italian Cohort

Aicardi-Goutières syndrome (AGS) is a genetically determined early onset encephalopathy characterized by cerebral calcification, leukodystrophy, and increased expression of interferon-stimulated genes (ISGs). Up to now, seven genes (TREX1, RNASEH2B, RNASEH2C, RNASEH2A, ADAR1, SAMHD1, IFIH1) have been associated with an AGS phenotype. Next Generation Sequencing (NGS) analysis was performed on 51 AGS patients and interferon signature (IS) was investigated in 18 AGS patients and 31 healthy controls. NGS identified mutations in 48 of 51 subjects, with three patients demonstrating a typical AGS phenotype but not carrying mutations in known AGS-related genes. Five mutations, in RNASEH2B, SAMHD1 and IFIH1 gene, were not previously reported. Eleven patients were positive and seven negatives for the upregulation of interferon signaling (IS > 2.216). This work presents, for the first time, the genetic data of an Italian cohort of AGS patients, with a higher percentage of mutations in RNASEH2B and a lower frequency of mutations in TREX1 than those seen in international series. RNASEH2B mutated patients showed a prevalence of negative IS consistent with data reported in the literature. We also identified five novel pathogenic mutations that warrant further functional investigation. Exome/genome sequencing will be performed in future studies in patients without a mutation in AGS-related genes.

Role of Ancillary Techniques in Biliary Cytopathology Specimens

2019 ◽  
Vol 64 (1-2) ◽  
pp. 175-181 ◽  
Author(s):  
Lester Layfield
Keyword(s):  
Mutational Analysis ◽  
Diagnostic Sensitivity ◽  
Individual Gene ◽  
Duct Systems ◽  
Brushing Cytology ◽  
Standard Of Practice ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Biliary brushing cytology has become the standard of practice for the investigation of strictures of the biliary and pancreatic duct systems. The methodology however has a limitation in that it has low diagnostic sensitivity when only cytologic evaluation is used. A number of testing methodologies have been applied to brushing specimens in an attempt to improve overall sensitivity without loss of specificity. These have included DNA ploidy analysis, immunocytochemistry, individual gene mutational analysis, fluorescence in-situ hybridization (FISH), and next generation sequencing (NGS). Currently, FISH coupled with routine cytology appears to be the method of choice for improving diagnostic sensitivity. NGS shows significant promise for improvement of diagnostic sensitivity.

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