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A comparative study for petroleum removal capacities of the bacterial consortia entrapped in sodium alginate,sodium alginate/poly(vinyl alcohol),and bushnell haas agar

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Petroleum Science 2024年第1期21卷 705-715页

作者： Sezen Bilen Ozyurek department of biology(biotechnology) Faculty of ScienceHacettepe UniversityAnkaraBeytepe06800Turkey

The purpose of this study was to identify and compare the degradation efficiencies of free and entrapped bacterial consortia(Staphylococcus capitis CP053957.1 and Achromobacter marplatensis MT078618.1)to different polymers such as Sodium Alginate(SA),Sodium Alginate/Poly(Vinyl Alcohol)(SA/PVA),and Bushnell Haas Agar(BHA).In addition to SA and SA/PVA,which are cost-effective,non-toxic and have different functional groups,BHA,which is frequently encountered in laboratory-scale studies but has not been used as an entrapment material until now.Based on these,the polymers with different surface morphologies and chemical compositions were analyzed by SEM and FT-IR.While the petroleum removal efficiency was higher with the entrapped bacterial consortia than with the free one,BHA-entrapped bacterial consortium enhanced the petroleum removal more than SA and SA/PVA.Accordingly,the degradation rate of bacterial consortia entrapped with BHA was 2.039 day^(-1),SA/PVA was 1.560,SA was 0.993,the half-life period of BHA-entrapped bacterial consortia is quite low(t_(1/2)=0.339)compared with SA(t_(1/2)=0.444)and SA/PVA(t_(1/2)=0.697).The effects of the four main factors such as:amount of BHA(0.5,1,1.5,2,2.5,3 g),disc size(4,5,6,7,8 mm),inoculum concentration(1,2.5,5,7.5,10 mL),and incubation period on petroleum removal were also investigated.The maximum petroleum removal(94.5%)was obtained at≥2.5 mL of bacterial consortium entrapped in 2 g BHA with a 7 mm disc size at 168 h and the results were also confirmed by statistical analysis.Although a decrease was observed during the reuse of bacterial consortium entrapped in BHA,the petroleum removal was still above 50%at 10th cycle.Based on GC-MS analysis,the removal capacity of BHA-entrapped consortium was over 90%for short-chain n-alkanes and 80%for medium-chain n-alkanes.Overall,the obtained data are expected to provide a potential guideline in cleaning up the large-scale oil pollution in the future.Since there has been no similar study investigating petroleum removal with the bacte

关键词： Entrapment of bacterial consortia Petroleum RemovalBushnell Haas agar Sodium alginate Sodium alginate/poly(vinyl alcohol)

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Assessment of the ecological state of haplic chernozem contaminated by oil,fuel oil and gasoline after remediation

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Petroleum Research 2024年第1期9卷 155-164页

作者： Anna Ruseva Tatiana Minnikova Sergey Kolesnikov Dmitry Trufanov Nikita Minin Sofya Revina Vladimir Gayvoronsky Southern Federal University Academy of Biology and Biotechnology344090Rostov-on-DonRussia

The intensive use of petroleum hydrocarbon products has made them priority environmental pollutants.When petroleum hydrocarbons enter the soil,a change in physical,chemical,and biological properties is observed.The natural restoration of oil-contaminated soils is a lengthy process;therefore,remediation is often required.The aim of this study is to assess the change in the ecological state of haplic chernozem soil contaminated with oil,fuel oil,and gasoline after remediation.The indicators of soil biological activity,such as phytotoxicity(germination,length of shoots and roots),the activity of oxidoreductase enzymes(catalase and dehydrogenases),and the total number of bacteria were studied.The effects of nitroammophoska fertilizer,sodium humate,biochar,and the biofertilizer“Baikal EM-1”on the ecological state of soils contaminated with oil,fuel oil,and gasoline were studied.Pollution with oil,fuel oil,and gasoline decreased the values of all biological indicators.The most sensitive indicator was the length of radish roots in soils polluted with oil,gasoline,and fuel oil after remediation with nitroammophoska and Baikal EM-1 addition.The length of roots was the most sensitive indicator when remediation was performed with biochar and sodium humate added to soil contaminated with oil and gasoline,and with contamination of haplic chernozem soil with fuel oil,the total number of bacteria was the most sensitive indicator.The most effective ameliorant to phytotoxicity indicators for oil pollution was a 1 D dose of biochar,for fuel oil it was 1 D biochar and 2 D sodium humate,and for gasoline it was a 2 D dose of biochar and Baikal EM-1.All ameliorants at most of the studied doses increased dehydrogenase activity,but increased catalase activity only in some cases.An increase in the total number of bacteria in oil-contaminated soils was promoted by biochar and nitroammophoska at a dose of 2 D.Nitroammophoska was the most effective in ameliorant in soils contaminated with fuel oil;in soils polluted with gasoline,all doses o

关键词： Pollution Petroleum hydrocarbons Haplic chernozem Ameliorant dose Biological indicators Soil properties

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Oxygen is an essential gasotransmitter directly sensed via protein gasoreceptors

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Animal Models and Experimental Medicine 2024年第2期7卷 189-193页

作者： Savani Anbalagan Faculty of biology Institute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityPoznańPoland

The current restrictive criteria for gasotransmitters exclude oxygen(O_(2))as a gasotransmitter in vertebrates.In this manuscript,I propose a revision of gasotransmitter criteria to include O_(2) per se as a signaling molecule and'essential gasotransmitter'for vertebrates.This revision would enable us to search for protein-based O_(2)-binding sensors(gasoreceptors)in all cells in the brain or other tissues rather than specialized tissues such as the carotid body or gills.If microorganisms have protein-based O_(2)-binding sensors or gasoreceptors such as DosP or FixL or FNR with diverse signaling domains,then eukaryotic cells must also have O_(2)-binding sensors or gasoreceptors.Just as there are proteinbased receptor(s)for nitric oxide(GUCY1A,GUCY1B,CLOCK,NR1D2)in cells of diverse tissues,it is reasonable to consider that there are protein-based receptors for O_(2) in cells of diverse tissues as well.In mammals,O_(2) must be acting as a gasotransmitter or gaseous signaling molecule via protein-based gasoreceptors such as androglobin that very likely mediate acute sensing of O_(2).Accepting O_(2) as an essential gasotransmitter will enable us to search for gasoreceptors not only for O_(2) but also for other nonessential gasotransmitters such as hydrogen sulfide,ammonia,methane,and ethylene.It will also allow us to investigate the role of environment-derived metal ions in acute gas(or solute)sensing within and between organisms.Finally,accepting O_(2) per se as a signaling molecule acting via gasoreceptors will open up the field of gasocrinology.

关键词： essential gasotransmitter gasocrine gasoreceptor gasocrinology

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Phytochemical analysis, antioxidant, acetylcholinesterase, and α-amylase inhibitors from Hippeastrum hybridum extract

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Journal of Traditional Chinese Medicine 2024年第3期44卷 496-504页

作者： Naila Sher Mushtaq Ahmed Nadia Mushtaq department of biotechnology University of Science and Technology department of Botany University of Science and Technology

OBJECTIVE:To investigate the effects of Hippeastrum hybridum（HH） as a free radical scavenger,and an inhibitor of the two enzymes i-e Alpha-amylase（α-amylase） and acetylcholinesterase（AChE）.METHODS:In this study,HH plant was preliminary analyzed for phytochemical screening and then tested for its antioxidant,anti-α-amylase,and anti-AChE efficiency via standard procedures.RESULTS:Phytochemical analysis shows the existence of different compounds;while Coumarins and quinones were absent.The total phenolic,flavonoid,and tannins content were found to be（78.52±0.69） mg GAE/g,（2.01±0.04） mg RUE/g,and（58.12±0.23） mg TAE/g of plant extract respectively.28.02%±0.02% alkaloid and 2.02%±0.05% saponins were present in the HH extract.The HH extract showed the anti-oxidant property with IC50（50%inhibition） of（151.01±0.13）(HH),（79.01±0.04）(Ascorbic acid) for ferric reducing,（91.48±0.13）(HH),（48.02±0.11）(Ascorbic acid) against Ammonium molybdenum,（156.02±0.31）(HH),（52.38±0.21）(Ascorbic acid) against DPPH,136.01±0.21（HH）,52.02±0.31（Ascorbic acid） against H2O2,and 154.12±0.03（HH）,（40.05±0.15）(Ascorbic acid)μg/mL against ABTS respectively.Statistical analysis indicated that HH caused a competitive type of inhibition of α-amylase(Vmaxremained constant and Km increases from 10.65 to84.37%) while Glucophage caused the un-competitive type of inhibition i-e both Km and Vmaxdecreased from40.49 to 69.15%and 38.86 to 69.61%respectively.The Ki,（inhibition constant）;KI,（dissociation constant）,Km,（Michaelis-Menten constant）,and IC50 were found to be62,364,68.1,and 38.08±0.22 for HH and 12,101.05,195,34.01±0.21 for Glucophage.Similarly,HH causes an anon-competitive type of inhibition of AChE i-e Km remains constant while Vmaxdecreases from 60.5%to74.1%.The calculated Ki,KI,Km,and IC50 were found to be 32,36.2,0.05,and 18.117±0.018.CONCLUSION:From the current results,it is concluded that HH extract contains bioactive compounds,and could be a good alternative to controlling oxidants,Alzheimer‘s and Type-Ⅱ diabetic diseases.

关键词： Hippeastrum hybridum acetylcholinesterase alpha-amylase antioxidant phytochemicals

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RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

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Virologica Sinica 2024年第1期39卷 156-168页

作者： Changqiao You Shuai Jiang Yunyun Ding Shunxing Ye Xiaoxiao Zou Hongming Zhang Zeqi Li Fenglin Chen Yongliang Li Xingyi Ge Xinhong Guo College of biology Hunan UniversityChangsha410082China College of Bioscience and biotechnology Hunan Agricultural UniversityChangsha410128China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

关键词： RNA barcode segments SARS-CoV-2 variants and related lineages HCoVs Genetic tests Complete genome sequences

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Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

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Animal Models and Experimental Medicine 2024年第1期7卷 36-47页

作者： Roa'a H.S.Yosief Iqbal M.Lone Aharon Nachshon Heinz Himmelbauer Irit Gat-Viks Fuad A.Iraqi department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael School of Molecular Cell biology and biotechnology George S.Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael Institute of Computational biology Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 181190 ViennaAustria

Background:Aspergillus fumigatus(Af)is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic back-ground.The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus(Af)using an RNAseq approach in CC lines and hepatic gene expression.Methods:We studied 31 male mice from 25 CC lines at 8 weeks old;the mice were infected with Af.Liver tissues were extracted from these mice 5 days post-infection,and next-generation RNA-sequencing(RNAseq)was performed.The GENE-E analysis platform was used to generate a clustered heat map matrix.Results:Significant variation in body weight changes between CC lines was ob-served.Hepatic gene expression revealed 12 top prioritized candidate genes differ-entially expressed in resistant versus susceptible mice based on body weight changes.Interestingly,three candidate genes are located within genomic intervals of the previ-ously mapped quantitative trait loci(QTL),including Gm16270 and Stox1 on chromo-some 10 and Gm11033 on chromosome 8.Conclusions:Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af.As a next step,eQTL analysis will be performed for our RNA-Seq data.Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

关键词： aspergillus fumigatus infection collaborative cross(CC)mice gene expression profile gene-network host susceptibility quantitative trait loci(QTL)mapping RNA-Seq

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A Cocktail of Natural Compounds Holds Promise for New Immunotherapeutic Potential in Head and Neck Cancer

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Chinese Journal of Integrative Medicine 2024年第1期30卷 42-51页

作者： Sunil Kumar Asmita Das department of biotechnology Delhi Technological UniversityDelhi(110042)India

Objective: To obtain detailed understanding on the gene regulation of natural compounds in altering prognosis of head and neck squamous cell carcinomas(HNSC). Methods: Gene expression data of HNSC samples and peripheral blood mononuclear cells(PBMCs) of HNSC patients were collected from Gene Expression Omnibus(GEO). Differential gene expression analysis of GEO datasets were achieved by the GEO2R tool. Common differentially expressed gerres(DEGs) were screened by comparing DEGs of HNSC with those of PBMCs. The combination was further analyzed for regulating pathways and biological processes that were affected. Results: Totally 110 DEGs were retrieved and identified to be involved in biological processes related to tumor regulation. Then 102 natural compounds were screened for a combination such that the expressions of all 110 commonly DEGs were altered. A combination of salidroside, ginsenoside Rd, oridonin, britanin, and scutellarein was chosen. A multifaceted, multi-dimensional tumor regression was showed by altering autophagy, apoptosis, inhibiting cell proliferation, angiogenesis, metastasis and inflammatory cytokines production. Conclusions: This study has helped develop a unique combination of natural compounds that will markedly reduce the propensity of development of drug resistance in tumors and immune evasion by tumors. The result is crucial to developing a combinatorial natural therapeutic cocktail with accentuated immunotherapeutic potential.

关键词： natural compounds chemopreventive gene expression head and neck cancer immunomodulator salidroside ginsenoside Rd oridonin britanin scutellarein

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RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila

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Marine Life Science & Technology 2024年第2期6卷 183-197页

作者： Huijuan Hao Yinjie Lian Chenhui Ren Sitong Yang Min Zhao Tao Bo Jing Xu Wei Wang Key Laboratory of Chemical biology and Molecular Engineering of Ministry of Education Institute of BiotechnologyShanxi UniversityTaiyuan 030006China School of Life Science Shanxi UniversityTaiyuan 030006China Shanxi Key Laboratory of biotechnology Taiyuan 030006China

Histone modification and nucleosome assembly play important roles in chromatin-related processes.Histone chaperones form different complexes and coordinate histone transportation and assembly.Various histone chaperone complexes have been identified in different organisms.The ciliate protozoa(ciliates)have various chromatin structures and different nuclear morphology.However,histone chaperone components and functions of different subunits remain unclear in ciliates.Tet-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental stages.Here,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental stages.REBL1 knockdown inhibited cellular proliferation.The macronuclear morphology became bigger in growing mutants.The abnormal macronuclear structure also occurred in the starvation stage.Furthermore,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic nuclei.RebL1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental stages.REBL1 knockdown affected expression levels of the genes involved in chromatin organization and transcription.Taken together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in T.thermophila.

关键词： Gametogenesis Histone chaperone Macronuclear structure RebL1 Tetrahymena thermophilaIntroduction

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Electrobiocorrosion by microbes without outer-surface cytochromes

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mLife 2024年第1期3卷 110-118页

作者： Dawn E.Holmes Trevor L.Woodard Jessica A.Smith Florin Musat Derek R.Lovley department of Microbiology University of Massachusetts AmherstAmherstMassachusettsUSA department of Physical and Biological Science Western New England UniversitySpringfieldMassachusettsUSA department of Biomolecular Sciences Central Connecticut State UniversityNew BritainConnecticutUSA department of biology Section for MicrobiologyAarhus UniversityAarhusDenmark department of Molecular biology and biotechnology Facuity of Biology and GeologyBabes-Bolyai UniversityCluj-NapocaRomania

Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage.Some microbes are capable of direct metal-to-microbe electron transfer(electrobiocorrosion),but the prevalence of electrobiocorrosion among diverse methanogens and acetogens is poorly understood because of a lack of tools for their genetic manipulation.Previous studies have suggested that respiration with 316L stainless steel as the electron donor is indicative of electrobiocorrosion,because,unlike pure Fe^(0),316L stainless steel does not abiotically generate H2 as an intermediary electron carrier.Here,we report that all of the methanogens(Methanosarcina vacuolata,Methanothrix soehngenii,and Methanobacterium strain IM1)and acetogens(Sporomusa ovata and Clostridium ljungdahli)evaluated respired with pure Fe^(0)as the electron donor,but only M.vacuolata,Mx.soehngeni,and S.ovata were capable of stainless steel electrobiocorrosion.The electrobiocorrosive methanogens re-quired acetate as an additional energy source in order to produce methane from stainless steel.Cocultures of S.ovata and Mx.soehngeni demonstrated how acetogens can provide acetate to methanogens during corrosion.Not only was Meth-anobacterium strain IM1 not capable of electrobiocorrosion,but it also did not accept electrons from Geobacter metal-lireducens,an effective electron-donating partner for direct interspecies electron transfer to all methanogens that can directly accept electrons from Fe^(0).The finding that M.vacuolata,Mx.soehngeni,and S.ovata are capable of electrobiocorrosion,despite a lack of the outer-surface c-type cytochromes previously found to be important in other electrobiocorrosive microbes,demonstrates that there are multiple microbial strategies for making electrical contact with Fe^(0).

关键词： acetogen corrosion Fe^(0) methanogen stainless steel

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Immune response to inactivated bacterial vector carrying the recombinant K39 antigen of Leishmania infantum in mice

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Asian Pacific Journal of Tropical Biomedicine 2024年第5期14卷 199-206页

作者： Lucelina S.Araújo Bruno B.Silva Eduarda N.F.N.Santos Arnaldo S.Bezerra Samuel S.Frota Assis R.Montenegro Eridan O.P.T.Florean Maurício Fvan Tilburg Maria Izabel F.Guedes Laboratory of biotechnology and Molecular biology Northeast Biotechnology NetworkState University of CearáFortalezaBrazil Faculty of Veterinary Medicine State University of CearáFortalezaBrazil

Objective:To evaluate the immunological response elicited by an inactivated bacterial vector carrying the K39 antigen of Leishmania infantum,and a purified antigen.Methods:Mice were subjected to the following treatments:(1)Purified recombinant K39(rK39)protein at a 20μg dose with complete Freund’s adjuvant;(2)Inactivated Escherichia coli(BL21 DE3)carrying the K39 protein at an equivalent total protein content of 200μg;(3)Inactivated bacteria lacking the K39 protein;(4)Non-immunized control animals.Serological monitoring was performed.All groups were challenged by intraperitoneal injection of 10^(7) Leishmania infantum promastigotes.After euthanasia,the liver and spleen were collected to analyze the levels of TNF,IFN-γ,IL-12,IL-4,and IL-10.Results:Mice immunized with purified rK39 or the inactivated bacterial vector carrying the K39 antigen of Leishmania infantum showed a long-lasting immune response with high levels of polyclonal antibodies specifically recognizing the recombinant proteins.The IgG1 subclass was the predominant immunoglobulin;however,the induction of IgG2a and the profile of cytokines produced were indicative of the induction of a mixed-type response.Conclusions:The inactivated bacterial vector carrying the K39 antigen,as well as the purified antigen can induce a long-lasting immune response in immunized mice,predominantly favouring a Th2 profile response.

关键词： Visceral leishmaniasis K39 Inactivated bacterial vector Vaccine Immune response Th1 Th2 Leishmania infantum

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