Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae

Background: Coinfection of Hepatitis C virus (HCV) with human immunodeficiency virus (HIV) has a higher risk of mortality than HCV or HIV monoinfection. HCV and HIV infections are specified by systemic inflammation, but the inflammation process in HCV/HIV coinfection is much complicated and is not well characterized. Objective: The aim of this study was to analyze the expression of TLR-3, TLR-7, IL-10, IFN-1 (IFN-α, IFN-β), and TNF-α in HIV, HCV and HIV/HCV co-infected patients. Methods: Forty-five patients including HIV group (n=15), HCV group (n=15), HIV/HCV coinfection group (n=15) and healthy control group (n=15) participated. Peripheral blood mononuclear cells (PBMCs) were obtained. PBMC-RNA, HCV and HIV RNA were extracted from all subjects and cDNA was synthesized. The viral load analyzed by reverse transcription-quantitative PCR (RT-qPCR), and the expression levels of IFN-α, IFN-β, TLR-3, TLR-7, TNF, and IL-10 mRNA were quantified in PBMCs. Results: The levels of IFN-I, IL-10, and TNF-α were overexpressed in all patients’ groups (P<0.05), TLR-7 was upregulated in all groups, but this upregulation was not statistically significant (p>0.05). TLR-3 showed a decrease in all patient groups (P<0.05). The statistical analysis demonstrated that TLR-3 has a negative correlation with HIV load, whereas other genes positively correlated with HIV load. In addition, TLR-3, TNF-α, and IFN-I were negatively correlated with HCV load, whereas TLR-7 and IL-10 s were positively correlated with HCV load. Conclusion: Our results showed a significant relationship between the expression level of innate immunity genes and inflammation in HCV, HIV, and HIV/HCV coinfected patients.

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Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Microorganisms ◽

10.3390/microorganisms9010064 ◽

2020 ◽

Vol 9 (1) ◽

pp. 64

Author(s):

Maija Nuppunen-Puputti ◽

Riikka Kietäväinen ◽

Lotta Purkamo ◽

Pauliina Rajala ◽

Merja Itävaara ◽

...

Keyword(s):

Significant Proportion ◽

Debaryomyces Hansenii ◽

Fungal Communities ◽

Fungal Colonization ◽

Rock Surface ◽

Mica Schist ◽

Deep Subsurface ◽

Bacterial Phyla ◽

In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

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Discrete element analysis of the punching behaviour of a secured drapery system: from laboratory characterization to idealized in situ conditions

Acta Geotechnica ◽

10.1007/s11440-020-01119-z ◽

2021 ◽

Author(s):

Antonio Pol ◽

Fabio Gabrieli ◽

Lorenzo Brezzi

Keyword(s):

Mechanical Response ◽

Steel Wire ◽

Discrete Element ◽

Wire Mesh ◽

Steel Plates ◽

Loading Conditions ◽

Element Analysis ◽

In Situ Conditions ◽

Wire Meshes

AbstractIn this work, the mechanical response of a steel wire mesh panel against a punching load is studied starting from laboratory test conditions and extending the results to field applications. Wire meshes anchored with bolts and steel plates are extensively used in rockfall protection and slope stabilization. Their performances are evaluated through laboratory tests, but the mechanical constraints, the geometry and the loading conditions may strongly differ from the in situ conditions leading to incorrect estimations of the strength of the mesh. In this work, the discrete element method is used to simulate a wire mesh. After validation of the numerical mesh model against experimental data, the punching behaviour of an anchored mesh panel is investigated in order to obtain a more realistic characterization of the mesh mechanical response in field conditions. The dimension of the punching element, its position, the anchor plate size and the anchor spacing are varied, providing analytical relationships able to predict the panel response in different loading conditions. Furthermore, the mesh panel aspect ratio is analysed showing the existence of an optimal value. The results of this study can provide useful information to practitioners for designing secured drapery systems, as well as for the assessment of their safety conditions.

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Development of an Easy-to-Operate Underwater Raman System for Deep-Sea Cold Seep and Hydrothermal Vent In Situ Detection

Sensors ◽

10.3390/s21155090 ◽

2021 ◽

Vol 21 (15) ◽

pp. 5090

Author(s):

Qingsheng Liu ◽

Jinjia Guo ◽

Wangquan Ye ◽

Kai Cheng ◽

Fujun Qi ◽

...

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Methane Hydrate ◽

Sulfur Cycle ◽

Cold Seep ◽

Remotely Operated Vehicle ◽

Bacterial Mats ◽

Optical Module ◽

In Situ Detection

As a powerful in situ detection technique, Raman spectroscopy is becoming a popular underwater investigation method, especially in deep-sea research. In this paper, an easy-to-operate underwater Raman system with a compact design and competitive sensitivity is introduced. All the components, including the optical module and the electronic module, were packaged in an L362 × Φ172 mm titanium capsule with a weight of 20 kg in the air (about 12 kg in water). By optimising the laser coupling mode and focusing lens parameters, a competitive sensitivity was achieved with the detection limit of SO42− being 0.7 mmol/L. The first sea trial was carried out with the aid of a 3000 m grade remotely operated vehicle (ROV) “FCV3000” in October 2018. Over 20,000 spectra were captured from the targets interested, including methane hydrate, clamshell in the area of cold seep, and bacterial mats around a hydrothermal vent, with a maximum depth of 1038 m. A Raman peak at 2592 cm−1 was found in the methane hydrate spectra, which revealed the presence of hydrogen sulfide in the seeping gas. In addition, we also found sulfur in the bacterial mats, confirming the involvement of micro-organisms in the sulfur cycle in the hydrothermal field. It is expected that the system can be developed as a universal deep-sea survey and detection equipment in the near future.

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Identification of innate immunity genes and pathways using a comparative genomics approach

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0802405105 ◽

2008 ◽

Vol 105 (19) ◽

pp. 7016-7021 ◽

Cited By ~ 53

Author(s):

S. Alper ◽

R. Laws ◽

B. Lackford ◽

W. A. Boyd ◽

P. Dunlap ◽

...

Keyword(s):

Innate Immunity ◽

Comparative Genomics ◽

Immunity Genes

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Discovering innate immunity genes using differential display: A story of RNA helicases

Journal of Cellular Physiology ◽

10.1002/jcp.20797 ◽

2006 ◽

Vol 209 (3) ◽

pp. 636-644 ◽

Cited By ~ 8

Author(s):

Zaida G. Ramirez-Ortiz ◽

Rajas V. Warke ◽

Laura Pacheco ◽

Kris Xhaja ◽

Devanand Sarkar ◽

...

Keyword(s):

Innate Immunity ◽

Differential Display ◽

Rna Helicases ◽

Immunity Genes

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Relating Induced in Situ Conditions of Raw Chicken Breast Meat to Pinking

Poultry Science ◽

10.1093/ps/83.1.109 ◽

2004 ◽

Vol 83 (1) ◽

pp. 109-118 ◽

Cited By ~ 6

Author(s):

K. Holownia ◽

M.S. Chinnan ◽

A.E. Reynolds ◽

JW Davis

Keyword(s):

Chicken Breast ◽

Breast Meat ◽

In Situ Conditions ◽

Chicken Breast Meat

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A microscopic approach to investigate bacteria under in situ conditions in sea-ice samples

Annals of Glaciology ◽

10.3189/172756401781818275 ◽

2001 ◽

Vol 33 ◽

pp. 304-310 ◽

Cited By ~ 76

Author(s):

Karen Junge ◽

Christopher Krembs ◽

Jody Deming ◽

Aaron Stierle ◽

Hajo Eicken

Keyword(s):

Sea Ice ◽

Pore Space ◽

Three Dimensional ◽

Epifluorescence Microscopy ◽

Microbial Populations ◽

Microbial Life ◽

Dimensional Network ◽

In Situ Conditions ◽

Fluorescent Stain

AbstractMicrobial populations and activity within sea ice have been well described based on bulk measurements from melted sea-ice samples. However, melting destroys the micro-environments within the ice matrix and does not allow for examination of microbial populations at a spatial scale relevant to the organism. Here, we describe the development of a new method allowing for microscopic observations of bacteria localized within the three-dimensional network of brine inclusions in sea ice under in situ conditions. Conventional bacterial staining procedures, using the DNA-specific fluorescent stain DAPI, epifluorescence microscopy and image analysis, were adapted to examine bacteria and their associations with various surfaces within microtomed sections of sea ice at temperatures from −2° to −15°C. The utility and sensitivity of the method were demonstrated by analyzing artificial sea-ice preparations of decimal dilutions of a known bacterial culture. When applied to natural, particle-rich sea ice, the method allowed distinction between bacteria and particles at high magnification. At lower magnifications, observations of bacteria could be combined with those of other organisms and with morphology and particle content of the pore space. The method described here may ultimately aid in discerning constraints on microbial life at extremely low temperatures.

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Trial applications at gymnasiums of in-situ sound absorption measurement method by ensemble averaging technique

INTER-NOISE and NOISE-CON Congress and Conference Proceedings ◽

10.3397/in-2021-2729 ◽

2021 ◽

Vol 263 (2) ◽

pp. 4532-4537

Author(s):

Toru Otsuru ◽

Reiji Tomiku ◽

Noriko Okamoto ◽

Siwat Lawanwadeekul

Keyword(s):

Measurement Method ◽

Sound Absorption ◽

Glass Wool ◽

Absorption Measurement ◽

Ensemble Averaging ◽

Averaging Technique ◽

In Situ Conditions ◽

Measurement Consistency ◽

Absorption Characteristics

The authors have been published a series of papers on a measurement method for sound absorption characteristics of materials using ensemble averaging technique, i.e., EA method. The papers' results included measurement mechanisms, measurement uncertainty, and so on. Herein, to examine adaptability, especially in in-situ conditions, the EA method is applied to measure absorption characteristics of materials installed in two gymnasiums. A glass-wool panel with the dimension of 0.5 m by 0.5 m by 0.05 m and with the density of 32 kg m^-3 was brought around and measured to check the measurement consistency. Several measurements were conducted during badminton plays were undergoing. Measured sound absorption coefficients revealed that most results agree well with those measured in reverberation rooms. Certain improvement is necessary for the specimen brought to the in-situ measurement to keep the consistency. The inconsistency is considered to originate from unstable conditions between the specimen and floor.

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