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Anoxia

Anoxia: A condition characterized by a complete lack of oxygen supply to tissues, which can lead to severe tissue damage and organ failure.
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Most cited protocols related to «Anoxia»

The strains and plasmids used in this study are listed in Additional file 4: Table S3. E. coli strains were grown in Luria–Bertani medium at 37°C with shaking (180 rpm) or on solid growth medium, which contained 1.6% (w/v) agar. R. sphaeroides strains were cultivated at 32°C in 50-ml Erlenmeyer flasks containing 40 ml malate minimal medium (Additional file 4: Table S4) with continuous shaking at 140 rpm, resulting in a constant dissolved oxygen concentration of approximately 25–30 μM during the exponential phase. These growth conditions are designated as oxic growth. To achieve anoxic conditions, we used completely filled screw-cap Meplat bottles for liquid cultures, which were sealed with Parafilm and cultivated in the dark. The remaining oxygen was used up by the cultures within 60 seconds, as confirmed using an oxygen sensor. To allow anaerobic respiration, dimethyl sulphoxide (DMSO) was added as electron acceptor at a final concentration of 60 mM. Anoxic incubation over several days resulted in a final OD660 of approximately 0.5. Conditions of iron limitation were achieved by transferring R. sphaeroides into iron-limited malate minimal medium containing the iron chelator 2,2′-dipyridyl (30 μM; Merck KGaA) three times. Inductively coupled plasma mass spectrometry (ICP-MS) using an Agilent 7500ce spectrometer confirmed that the iron content was drastically reduced in iron-limited medium (from 140 mg l-1 to 16 mg l-1) [22 (link)]. When required, antibiotics were added to liquid or solid growth media at the following concentrations: spectinomycin (10 μg ml-1); kanamycin (25 μg ml-1); tetracycline (2 μg ml-1) (for R. sphaeroides); kanamycin (25 μg ml-1); and tetracycline (20 μg ml-1) (for E. coli).
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Publication 2014
Agar Anoxia Antibiotics, Antitubercular Chelating Agents Culture Media Escherichia coli Growth Disorders Iron Iron Metabolism Disorders Kanamycin malate Mass Spectrometry Neoplasm Metastasis Oxidants Oxygen Oxygen-25 Plasma Plasmids Respiration Spectinomycin Strains Sulfoxide, Dimethyl Tetracycline
For all respiration experiments, mitochondria were incubated in RM at 37°C in the presence of sodium and in the absence of exogenous substrates or energy phosphates in order to deplete endogenous Ca2+ from the mitochondrial matrix (5 (link), 6 (link), 9 (link)). After the depletion step, 10 mM Pi and 0.13 mM ADP were added, followed by glutamate (G, 10 mM) and malate (M, 1 mM) ± Ca2+. Addition of fuel (G+M) initiated a submaximal increase in Jo followed by a subsequent transition to State 4 Jo. For experiments designed to measure maximal Jo, State 3 was then elicited with a bolus of 1.3 mM ADP which resulted in consumption of all the oxygen in the chamber providing the fully reduced state (anoxia). Free Ca2+ concentrations were made using the calculator programs of Fabiato and Fabiato (26 (link)) translated to Labview VIs (National Instruments Corp, Austin, TX) by Reitz and Pollack (27 (link)).
Steady-state, intermediate Jo was attained using a progressive creatine kinase (CK) energetic clamp (28 (link)), we have recently modified (29 (link)). Briefly, by utilizing a large total creatine pool, excess CK, a known [ATP], and the CK equilibrium constant (KCK, 150 (30 (link))), the extramitochondrial ATP/ADP ratio, and thus, free energy of ATP hydrolysis (ΔGATPe) can be calculated from the added phosphocreatine (PCr)/creatine (Cr) ratio:
where ΔGATP° is the standard ΔGATP (-7.592 kcal/mol), R is the gas constant (1.987 cal·K-1·mol-1), and T is temperature (310°K). Mitochondria oxidizing G+M at State 4 were given 2.5 mM PCr, 5 mM Cr, 5 mM ATP, and 75 U/ml CK, resulting in a Jo of ∼2/3 of State 3. Subsequent additions of PCr (to 3.75, 5, 7.5, and 10 mM) were made to slow Jo to ∼1/3 of State 3.
Additional experiments with pyruvate were conducted similar to those from Messer et al. (28 (link)). Briefly, mitochondria in the presence of saturating M were exposed to the CK clamp as described above with a PCr/Cr ratio of 0.25. Pyruvate was then titrated in stepwise at 10, 25, 50, 100, and 500 μM to increase respiration. The novel aspect of this experiment was that upon reaching a steady state with 500 μM pyruvate, stepwise additions of PCr were then made to slow Jo. Thus, in a single experiment, Jo was changed by both “Push” (pyruvate titration) and “Pull” (CK clamp) mechanisms.
Publication 2013
Anoxia austin Cell Respiration Creatine Creatine Kinase Glutamates Hydrolysis malate Mitochondria Oxygen Phosphates Phosphocreatine Pyruvate Sodium Titrimetry

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Publication 2016
Adult Anoxia Biological Assay Chromatin Immunoprecipitation Sequencing Diabetes Mellitus Donor, Organ Donors Ethics Committees, Research Homo sapiens Insulin Pancreas RNA-Seq secretion Tissues Wounds and Injuries
The materials and methods used in this work are described in detail in SI Appendix, Materials and Methods. The Bilophila and Desulfovibrio strains were grown in carbonate-buffered mineral salts medium reduced with Ti(III)-nitrilotriacetate. Cell-free extracts were prepared by French press disruption followed by centrifugation to remove unbroken cells; these extracts were used for proteomics analysis and measurement of Tpa, SarD, and IslAB activity. Sulfite was detected by a colorimetric (fuchsin) assay as well as by HPLC after derivatization, and acetaldehyde was detected by HPLC after derivatization. A hydrophilic interaction liquid chromatography column and HPLC-MS system was used to detect taurine, alanine, sulfoacetaldehyde, and isethionate. His-tagged Tpa and SarD were produced using E. coli Rosetta 2 DE3 and the His-tagged GREs, AdhE, and DctP using E. coli BL21. The His-tagged GRE activating enzymes were overexpressed in E. coli BL21(DE3) ΔiscR::kan. Before induction, these cultures were rendered anoxic by sparging with argon. Cell lysis and enzyme purification were also done under anoxic conditions. The recombinant GREs were rendered anoxic after purification and activated by incubation in the presence of the GRE-activating enzyme, SAM, and acriflavine as a photosensitizer in Hepes-bicine buffer under ambient light. Kinetics and substrate ranges of the GREs were measured spectrophotometrically using a coupled assay with alcohol dehydrogenase, reducing the acetaldehyde to ethanol concomitant with NADH formation.
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Publication 2019
2'-deoxycytidine 5'-triphosphate Acetaldehyde Acriflavine Alanine Anoxia Argon Bilophila Biological Assay Buffers Carbonates Cell Extracts Cells Centrifugation Colorimetry Dehydrogenase, Alcohol Desulfovibrio Enzymes Escherichia coli Ethanol HEPES High-Performance Liquid Chromatographies Hydrophilic Interactions Kinetics Light Liquid Chromatography Minerals N,N-bis(2-hydroxyethyl)glycine NADH Photosensitizing Agents Rosaniline Dyes Salts Strains Sulfites sulfoacetaldehyde Taurine
Three extremophilic microbes, previously isolated from the deep-sea anoxic brine lakes, were selected as part of a genome-sequencing project due to their phylogenetic position, peculiar features and unique biotope. Analysis of their draft genomes provides us with a first glimpse on some of their unusual characteristics and the ways they cope with living in such a harsh environment [11 (link)-13 (link)].
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Publication 2013
Anoxia brine Extremophiles Genome

Most recents protocols related to «Anoxia»

Gordonibacter urolithinfaciens DSM
27213T, Ellagibacter isourolithinifaciens DSM 104140T obtained from the DSMZ culture collection,
and the isolated strain E. bolteae CEBAS
S4A9 were cultivated anaerobically in 5 mL WAM tubes. First, 2 mL
of a diluted aliquot of G. urolithinfaciens DSM 27213T and E. bolteae CEBAS S4A9 strains was transferred to WAM (100 mL). Similarly, 2
mL of diluted aliquots of E. isourolithinifaciens DSM 104140T and E. bolteae CEBAS S4A9 strains was transferred to WAM (100 mL). Finally, EA
dissolved in propylene glycol was added to the 100 mL cultures to
obtain a final concentration of 25 μM. During incubation in
an anoxic environment at 37 °C, aliquots (5 mL) were taken for
HPLC analyses as described below. Incubations were made in triplicate,
and the experiment was repeated twice.
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Publication 2023
Anoxia Ellagibacter isourolithinifaciens Gordonibacter urolithinfaciens Propylene Glycol Strains
The
isolated strain E. bolteae CEBAS S4A9
and representative strains of the closest relatives (E. bolteae DSM 29485, DSM 15670T, Enterocloster asparagiformis DSM 15981T, Enterocloster citroniae DSM 19261T, and Enterocloster clostridioformis DSM 933T) obtained from the DSMZ culture collection were
used to investigate their capacity to produce final Uros in the presence
of EA and other Uro intermediaries. Briefly, isolated and DSMZ strains
were separately incubated on a WAM agar plate for 6 days. A single
colony was cultivated in a 5 mL WAM tube. Diluted inoculum (2 mL)
was transferred to WAM (20 mL), obtaining an initial load of 104 CFU mL–1. EA, Uro-M6, Uro-D, Uro-C, Uro-A,
IsoUro-A, and Uro-B were dissolved in propylene glycol and added to
the 20 mL cultures to obtain a final concentration of 15 μM
each. After incubation in an anoxic environment at 37 °C, aliquots
(5 mL) were taken periodically for high-performance liquid chromatography
(HPLC) analyses as described below.
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Publication 2023
Agar Anoxia Clostridium asparagiforme Clostridium citroniae Clostridium clostridioforme High-Performance Liquid Chromatographies Propylene Glycol Strains
Black freshwater sediment was retrieved, in June 2019 (TS1) and October 2020 (TS2), from a pond at Aarhus University campus (Vennelyst Park), Denmark (56.164672, 10.207908) at a water depth of 0.5–1 m. The sediment was stored with overlying water at 15°C for 2 weeks.
Before inoculation, sediment was homogenized, sieved (pore size: 0.5 mm) and autoclaved in 2 L bottles for 20 min as described in Thorup et al. (2021) (link) and Marzocchi et al. (2022) (link). Cooled down sediment (15°C) was distributed into 20 and 10 ethanol-cleaned Plexiglas core liners that were closed with a rubber stopper at the bottom. After 24 h settling time, the stoppers were pushed upwards to align the sediment surface with the core liner edge. The cores were inoculated by transferring a clump of sediment from a two-week-old, pre-grown single-strain enrichment culture of Ca. Electronema aureum GS (Thorup et al., 2021 (link)) and submerged in an aquarium with autoclaved tap water. The aquarium was covered with aluminum foil to prevent algae formation, equipped with aeration and a lid to prevent excessive evaporation, and kept at 15°C. Overlying water was replenished and refreshed several times during the incubation periods.
During the first time series (TS1), O2, pH, and EP profiles were measured combined with 16S rRNA sequencing and microscopy observations over 80 days, due to technical issues, the videos could not be used for flocking observations. The sequencing and microscopy observations were repeated in the second time series (TS2) with O2 and EP measurements over 81 days, and additionally the pH was measured on day 81. Following microsensor measurements (of both TS1 and TS2), 1–2 of the measured cores were sliced based on geochemical zone: the oxic layer (determined by the oxygen penetration depth) and the anoxic layer (below the oxygen penetration depth). Samples for light microscopy and 16S rRNA amplicon sequencing were taken from the anoxic layer of each core, of which the latter were frozen at −80°C until RNA extraction.
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Publication 2023
Aluminum Anoxia Dental Cavity Liner Ethanol Freezing Light Microscopy Microscopy Oxygen Plexiglas RNA, Ribosomal, 16S Rubber Strains Vaccination
At each time point, profiles were made of 1–3 randomly chosen core(s). Microprofiles were measured, with the aeration turned off, by moving in-house made O2, pH and EP microsensors (Revsbech and Jørgensen, 1986 ; Revsbech, 1989 (link); Damgaard et al., 2014 (link)) stepwise (100–500 μm) downwards from ~3,000 μm above the sediment–water interface (SWI) to a depth of ~35,000 μm using a motorized micromanipulator (Unisense A/S, Denmark). At each step there was a 2 s waiting time before measuring a value for 2 s. All profiles were acquired using a four-channel multimeter with built-in A/D converter (Unisense). For the EP and pH sensors an in-house made millivoltmeter (resistance >1014 Ω,), and for the O2 sensor a picoamperemeter (Unisense) that was digitized with a 16-bit A/D converter (ADC-216, Unisense), was used. The software SensorTrace PRO (Unisense) was used to control the micromanipulator and acquire measurements.
EP was used as a proxy for cable bacteria activity (Damgaard et al., 2014 (link)) and was measured downwards combined with an upwards profile. EP and pH profiles were measured against a general-purpose reference electrode (REF201 Radiometer Analytical, Denmark).
O2 profiles were calibrated using Na-ascorbate in alkaline anoxic tap water and air-saturated (15°C) overlying water. The pH sensor was calibrated by a 3-point calibration (pH 4.0, 7.0, 10.0) with AVS TITRINORM buffers (VWR Chemicals, Denmark), and pH profiles were always measured in the dark. The reach of the anoxic zones was derived by determining the oxygen penetration depth from the O2 measurements after the profiles were adjusted to the SWI. Two EP profiles (downwards and upwards) were made for each core, and were drift corrected, using the measurements from the overlying water and the time between the up and down profiles. Current densities were calculated per core and averaged per time point (1–3 profile pairs/cores), as showcased in Risgaard-Petersen et al. (2015) (link), using a sediment conductivity of 0.04 S m−1 (water conductivity of 0.05 S m−1 and sediment porosity of 0.87).
The cathodic oxygen consumption (COC) of cable bacteria, which is the contribution of the cable bacterial cathodic cells to the total oxygen consumption performed in the sediment, and the (electric) current density (mA m−2) in the sediment generated by the cable bacteria, used for this purpose were calculated as described in Risgaard-Petersen et al. (2015) (link) from the EP and O2 microsensor measurements of the exact cores that were subsequently sampled for flocking observations.
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Publication 2023
Anoxia Bacteria Buffers Electric Conductivity Electricity Oxygen Consumption
As a part of routine clinical evaluation, patients were repeatedly evaluated with various neurobehavioural tests during their stay in the acute neurorehabilitation unit. In our analyses we used the total CRS-R score (0 = absence of any response, 23 = cognitively mediated behaviors) and the Disability rating scale (DRS) (Williams and Smith, 2017 (link)) scores (0 = no disability, 29 = extreme vegetative state) at discharge. The items in this scale correspond to the three original World Health Organization categories of impairment, disability, and handicap, and track a patient's functional and cognitive progress from coma to the community. In addition, the patients were also assessed with the Motor Behavior Tool – revised (MBT-r) (Jöhr et al., 2020 , Pincherle et al., 2019 (link)), a clinical evaluation tool for detecting subtle motor behavior that might reflect residual cognition in unresponsive patients. The patients with detected signs of motor behaviour are identified as patients with clinical cognitive motor dissociation. Experienced clinicians or neuropsychologists carried out the neurobehavioral evaluations. Patients’ demographic and clinical data are presented in Table 1.

Demographic and clinical data.

SubjectSexAge (years)Interval Injury to MRI (days)Interval MRI to discharge (days)EtiologyCRS-R intitialDRS at disch. (days)CRS-R at disch. (days)
1f671434CVAVS/UWS523
2m24845CVAVS/UWS2213
3m644528CVAVS/UWS224
4f57911CVAMCS1715
5f7210128CVAMCS255
6m731641CVAVS/UWS1916
7f67420TBIVS/UWS923
8m37142ANOXCOMA274
9f353333TBIVS/UWS217
10m602110TBIVS/UWS923
11m631963CVAMCS422
12m551941CVAMCS1511
13m423114TBICOMA1520
14f65438ANOXCOMA723
15m2728716TBIVS/UWS2011
16m28428TBIMCS223
17f373060TBICOMA239
18m471644TBIVS/UWS722
19f663028TBICOMA1123
20f393420CVACOMA1121
21f522327CVAMCS1521
22m613527CVACOMA1418
23m613434CVACOMA1123
24m785041ENCCOMA1513
25m442826TBICOMA1121
26f602649CVACOMA2211
27f694159ENCMCS1811
28f543025TBIVS/UWS265
29m50963ANOXMCS822
30f842614TBICOMA2113
31m162012TBIMCS623
32m351925LEUCOVS/UWS1813
33m492915CVAMCS-621
34m722213CVAMCS-722
35m554147CVACOMA2922
36f5863−5CVAVS/UWS920
37f25387TBIVS/UWS1111
38m732037TBIVS/UWS722
39m603820CVAVS/UWS1122
40m59433ANOXVS/UWS238

CVA = cardiovascular accident, TBI = traumatic brain injury, ANOX = anoxia, ENC = encephalopathy, LEUCO = leucoencephalopathy, VS/UWS = vegetative state or unresponsive wakefulness syndrome, MCS = minimally conscious state, DRS = Disability Rating Scale, CRS-R = Coma Recovery Scale – Revised.

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Publication 2023
Accidents Anoxia Cardiovascular System Cognition Comatose Disabled Persons Encephalopathies Injuries Leukoencephalopathy Minimally Conscious State Neurological Rehabilitation Patient Discharge Patients Syndrome Traumatic Brain Injury Vegetative State Wakefulness

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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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The C57BL/6 mouse is a widely used inbred mouse strain. It is a common laboratory mouse model utilized for a variety of research applications.
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The Hypoxia Incubator Chamber is a laboratory equipment designed to provide a controlled low-oxygen environment for cell culture and experimentation. It maintains a specified oxygen concentration within the chamber, allowing researchers to study cellular responses to hypoxic conditions.
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H9c2 cells are a subclone of cells derived from embryonic rat heart tissue. They are commonly used as an in vitro model to study cardiomyocyte biology and function.
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Phosphate-buffered saline (PBS) is a widely used buffer solution in biological research and laboratory procedures. It is a balanced salt solution that maintains a physiological pH and osmolarity, making it suitable for a variety of applications. PBS is primarily used to maintain the viability and integrity of cells, tissues, and other biological samples during various experimental protocols.

More about "Anoxia"

Anoxia, also known as hypoxia, is a condition characterized by a complete lack of oxygen supply to tissues, leading to severe tissue damage and organ failure.
Researchers can leverage PubCompare.ai, an AI-powered platform, to enhance the reproducibility and accuracy of their anoxia studies.
The platform helps researchers locate the best protocols and products from literature, pre-prints, and patents, enabling them to optimize their anoxia research and drive scientific discovery.
Advanced comparisons provided by PubCompare.ai can enhance the accuracy and reproducibility of anoxia studies.
When studying anoxia, researchers often employ various cell lines and animal models, such as H9c2 cells and C57BL/6 mice.
Maintaining optimal cell culture conditions, including the use of Fetal Bovine Serum (FBS), Dulbecco's Modified Eagle's Medium (DMEM), and antibiotics like Penicillin/Streptomycin, is crucial for maintaining cell viability and ensuring the reliability of experimental results.
Additionally, specialized equipment like anaerobic chambers and hypoxia incubator chambers can be utilized to simulate and study the effects of oxygen deprivation on cells and tissues.
Centrifugation techniques, such as the JA-10 Fixed-Angle Rotor, may also be employed to isolate and purify cellular components for further analysis.
By leveraging the insights and tools provided by PubCompare.ai, researchers can enhance the reproducibility and accuracy of their anoxia studies, ultimately leading to more robust scientific discoveries and advancing our understanding of this critical condition.