scholarly journals The Ubiquity and Development-Related Abundance Dynamics of Ophiocordyceps Fungi in Soft Scale Insects

2021 ◽  
Vol 9 (2) ◽  
pp. 404
Author(s):  
Jun Deng ◽  
Yuhua Yu ◽  
Xu Wang ◽  
Qian Liu ◽  
Xiaolei Huang
Keyword(s):  
Relative Abundance ◽  
Growth And Development ◽  
Developmental Stages ◽  
Scale Insects ◽  
Plant Feeding ◽  
Its Gene ◽  
Next Generation Sequencing Ngs ◽  
New Evidence ◽  
Generation Sequencing

Mutual relationships with symbionts play a crucial role in the evolution and ecology of plant-feeding hemipteran insects. However, there was no specific dominant bacterium observed in soft scales (Coccidae) in the previous studies, it is still unclear whether soft scales have specific primary symbionts. In this study, a nuclear ribosomal internal transcribed spacer (ITS)gene fragment was used to analyze the diversity of fungal communities in 28 Coccidae species based on next-generation sequencing (NGS). Furthermore, samples from different developmental stages of Ceroplastes japonicus were sequenced to illustrate the dynamics of fungal community. Our results showed that Coccidae-associated Ophiocordyceps fungi (COF) were prevalent in all 28 tested species with high relative abundance. Meanwhile, the first and second instars of C. japonicus, two important stages for growth and development, had high relative abundance of COF, while the relative abundances in other stages were low, ranging from 0.68% to 2.07%. The result of fluorescent in situ hybridization showed that the COF were widely present in hemolymph and vertically transmitted from mother to offspring. Our study confirms that the COF have intimate associations with the growth and development of soft scales, and provides new evidence to support that COF are primary fungal symbionts for Coccidae.

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.

scholarly journals Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

2016 ◽  
Vol 82 (7) ◽  
pp. 2227-2237 ◽  
Author(s):  
Daiana Lima-Morales ◽  
Ruy Jáuregui ◽  
Amelia Camarinha-Silva ◽  
Robert Geffers ◽  
Dietmar H. Pieper ◽  
...  
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Contaminated Soils ◽  
Catabolic Gene ◽  
The Czech Republic ◽  
Its Gene ◽  
Benzene Toluene ◽  
Gene Structures

ABSTRACTThree types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensivein situbioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.

scholarly journals Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum

2015 ◽  
Vol 9 ◽  
pp. BBI.S20751 ◽  
Author(s):  
Stefan Simm ◽  
Sotirios Fragkostefanakis ◽  
Puneet Paul ◽  
Mario Keller ◽  
Jens Einloft ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Ribosome Biogenesis ◽  
Developmental Stages ◽  
Male Gametophyte ◽  
Expression Profiles ◽  
Transcript Abundance ◽  
Rrna Processing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.

scholarly journals Gastrointestinal Pathology in Samples from Coronavirus Disease 2019 (COVID-19)-Positive Patients

2021 ◽  
Author(s):  
Maria Westerhoff ◽  
Dan Jones ◽  
Steven M. Hrycaj ◽  
May P. Chan ◽  
Liron Pantanowitz ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
In Situ Hybridization ◽  
Respiratory Illness ◽  
Inclusion Criteria ◽  
Gastrointestinal Pathology ◽  
Gastrointestinal Tissue ◽  
Tissue Specimens ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACT CONTEXT.–Although primarily considered a respiratory illness, coronavirus disease 2019 (COVID-19) can cause gastrointestinal manifestations. OBJECTIVE.–To evaluate histopathology and in situ hybridization for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in gastrointestinal samples from patients with recent and remote COVID-19. DESIGN.–Patients with positive SARS-CoV-2 nasopharyngeal tests and a gastrointestinal tissue specimen were included. SARS-CoV-2 in situ hybridization (ISH) was performed on each sample. A subset had SARS-CoV-2 next generation sequencing (NGS) performed. RESULTS.–Twenty-five patients met inclusion criteria. Five had positive SARS-CoV-2 nasopharyngeal tests within 7 days of their gastrointestinal procedure. Two were ulcerative colitis patients on steroid therapy who lacked typical COVID-19 symptoms. Their colectomies showed severe ulcerative colitis; one demonstrated SARS-CoV-2 by NGS but a negative ISH. Another had an ischemic colon resected as a complication of the COVID-19 course; however, both ISH and NGS were negative. A fourth had a normal-appearing terminal ileum but positive ISH and NGS. The fifth patient had ileal ulcers with SARS-CoV-2 negativity by both modalities. The remaining 20 patients had positive nasopharyngeal tests an average of 53 days prior to procedure. None of their samples demonstrated SARS-CoV-2 ISH positivity, but one was positive on NGS despite a negative nasopharyngeal test. CONCLUSIONS.–Gastrointestinal findings from SARS-CoV-2-infected patients ranged from normal with virus detected by ISH and NGS, to bowel ischemia secondary to systemic viral effects, without evidence of virus in the tissue. No distinct histologic finding was identified in those with gastrointestinal tissue specimens demonstrating SARS-CoV-2 positivity in this cohort.

scholarly journals Antenatal Microbial Colonization of Mammalian Gut

2018 ◽  
Vol 26 (8) ◽  
pp. 1045-1053 ◽  
Author(s):  
Elisa Borghi ◽  
Valentina Massa ◽  
Marco Severgnini ◽  
Grazia Fazio ◽  
Laura Avagliano ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Amniotic Fluid ◽  
Fluorescent In Situ Hybridization ◽  
Microbial Colonization ◽  
Bacterial Dna ◽  
Commensal Microbiota ◽  
High Interindividual Variability ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The widely accepted dogma of intrauterine sterility and initial colonization of the newborn during birth has been blurred by recent observations of microbial presence in meconium, placenta, and amniotic fluid. Given the importance of a maternal-derived in utero infant seeding, it is crucial to exclude potential environmental or procedural contaminations and to assess fetal colonization before parturition. To this end, we analyzed sterilely collected intestinal tissues, placenta, and amniotic fluid from rodent fetuses and tissues from autoptic human fetuses. Total bacterial DNA was extracted from collected samples and analyzed by Next Generation Sequencing (NGS) techniques using hypervariable 16S ribosomal RNA (rRNA) regions (V3-V4). Colonizing microbes were visualized in situ, using labeled probes targeting 16S ribosomal DNA by fluorescent in situ hybridization. The NGS analysis showed the presence of pioneer microbes in both rat and human intestines as well as in rodent placentas and amniotic fluids. Microbial communities showed fetus- and dam-dependent clustering, confirming the high interindividual variability of commensal microbiota even in the antenatal period. Fluorescent in situ hybridization analysis confirmed the microbes’ presence in the lumen of the developing gut. These findings suggest a possible antenatal colonization of the developing mammalian gut.

scholarly journals Primary renal NUT carcinoma identified by next-generation sequencing: A case report and literature review

2020 ◽  
Author(s):  
Fei Yang ◽  
Danhua Shen ◽  
Junping Shi
Keyword(s):  
Next Generation Sequencing ◽  
Ewing Sarcoma ◽  
Undifferentiated Carcinoma ◽  
Next Generation ◽  
Advanced Neoplasm ◽  
Poorly Differentiated ◽  
Nut Carcinoma ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background NUT carcinoma is a rare aggressive squamous cell carcinoma subtype genetically defined by NUTM1 rearrangements. NUT carcinoma usually has a primitive differentiation state and can be easily misdiagnosed as an undifferentiated carcinoma or Ewing sarcoma. Case presentation We report a case of NUT carcinoma of renal origin initially diagnosed as a malignant small round-cell tumor, likely to be Ewing sarcoma/primitive neuroectodermal tumor. Based on next-generation sequencing (NGS), the diagnosis was revised to NUT carcinoma with a characteristic NUTM1 rearrangement. The patient relapsed after surgery and received a standard NUT carcinoma treatment. However, due to advanced neoplasm progression, first-line chemotherapy failed and the patient died. Conclusion Routine NUT immunohistochemistry staining, NGS, and/or fluorescent in situ hybridization for poorly differentiated carcinoma and sarcoma tumors can help avoid misdiagnosis of NUT carcinoma-related tumors, allowing patients to benefit from bromodomain and extra-terminal motif inhibitor therapy.

scholarly journals Antenatal microbial colonisation of mammalian gut

2017 ◽  
Author(s):  
Elisa Borghi ◽  
Valentina Massa ◽  
Marco Severgnini ◽  
Grazia Fazio ◽  
Laura Avagliano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Amniotic Fluid ◽  
Interindividual Variability ◽  
High Interindividual Variability ◽  
Hybridisation Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Culture Dependent ◽  
Human Foetuses

ABSTRACTThe widely accepted dogma of intrauterine sterility and initial colonisation of the newborn during birth has been blurred by recent observations of microbial presence in meconium, placenta and amniotic fluid. Given the importance of a maternal-derived in utero infant seeding, it is crucial to exclude potential environmental or procedural contaminations, and to assess foetal colonisation before parturition. To ascertain antenatal microbial colonisation in mammals, we analysed sterilely collected intestinal tissues from rodent foetuses in parallel with experimental controls, and tissues from autoptic human foetuses. Next generation sequencing (NGS) showed the presence of pioneer microbes in both rat and human intestines, as well as in rodent placentas and amniotic fluids. Live microbes were isolated from culture-dependent analyses from homogenized rat foetal intestines.Microbial communities showed foetus- and dam-dependent clustering, confirming the high interindividual variability of microbiota even in the antenatal period. Fluorescent in situ hybridisation analysis confirmed the microbes’ existence in the lumen of the developing gut.These findings have vast implications for an emerging field of enhancing the management of healthy pregnancies, and for understanding how the infant microbiome starts and it is thus shaped.

Correlated Studies of Cellular Interactions Using TEM, Freeze Etching, and SEM

1974 ◽  
Vol 32 ◽  
pp. 320-321
Author(s):  
J. P. Revel
Keyword(s):  
Developmental Stages ◽  
Three Dimensional ◽  
Cell Movement ◽  
Cellular Interactions ◽  
Serial Sections ◽  
Cell Sheets ◽  
Freeze Etching ◽  
Early Developmental

Movement of individual cells or of cell sheets and complex patterns of folding play a prominent role in the early developmental stages of the embryo. Our understanding of these processes is based on three- dimensional reconstructions laboriously prepared from serial sections, and from autoradiographic and other studies. Many concepts have also evolved from extrapolation of investigations of cell movement carried out in vitro. The scanning electron microscope now allows us to examine some of these events in situ. It is possible to prepare dissections of embryos and even of tissues of adult animals which reveal existing relationships between various structures more readily than used to be possible vithout an SEM.

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