Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf.

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth's climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

Evaluation of clinical and laboratory findings in severe group COVID-19 pregnants without comorbidity.

BACKGROUND: COVID - 19 disease may be seen with different clinical presentations in pregnant women. Comorbid diseases are important factors affecting the progression of this disease. In this study, we aimed to evaluate the clinical and laboratory findings in pregnant women with COVID - 19 who had no comorbid disease. METHODS: This retrospective designed study included 217 patients with Covid PCR positive in typically COVID - 19 clinic. The patients were classified into asymptomatic, nonsevere, and severe disease groups. The symptoms, laboratory results, hospital followups and intensive care records of the patients and the findings of new borns are presented. RESULTS: Most of the patients (78%) were in the third trimester of pregnancy, and 103 patients in the study group had severe disease. Fever in the non-severe group and respiratory distress in the severe group were the most common symptoms in the patients. The severe clinical manifestations were specifically observed in the third trimester patients. In the severe group, neutrophil, lactat dehydrogenase, ferritin, CK - MB, IL - 6, and hospital stay were statistically higher than those in other groups (p < 0.05). Increase in BUN and creatine were the most predictive parameters in intensive care admission. While the intensive care unit (ICU) requirement was higher in patients in the severe group, premature birth was observed more frequently in the severe group (p < 0.05) .

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing.

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural 13C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [13C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [13C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with 13C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from "dark" primary production.IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ "dark" primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community.

Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.

First molecular characterization of a Turkish orf virus strain from a human based on a partial B2L sequence.

Cases of orf virus infection in human in Turkey have been reported for many years. Scab material from a man was found positive by PCR using pan-parapox-specific primers for parapoxvirus infection. The amplicon was purified and sequenced. The present study provides for the first time a phylogenetic analysis of parapoxviruses from Turkey. The partial B2L gene sequence of a Turkish orf virus from a human presented here may be useful for characterization of parapoxvirus infections in Turkey based on the phylogenetic analysis studies.

Evaluating the outcome after center of rotation of angulation (CORA)-based leveling osteotomy (CBLO) technique to repair unilateral cranial cruciate ligament deficiency using a pressure-sensitive walkway system.

The objective of this study was to evaluate the mid-term outcome of center of rotation of angulation (CORA)-based leveling osteotomy (CBLO) in dogs with cranial cruciate ligament (CrCL) deficiency using a pressure-sensitive walkway system. Fifteen dogs with unilateral CrCL deficiency were treated with CBLO for an average of 50 wk (median 46 wk, range: 38 to 91) prior to the evaluation. The contralateral hind limb was confirmed free of any signs of pathology by clinical examination and lateral stifle radiography. A control group of 20 healthy dogs was included to establish reference values for comparison purposes. Spatiotemporal parameters and peak vertical force (PVF) were measured and symmetry index (SI) was calculated between the left and right pelvic limb and between thoracic and pelvic limbs, in both groups. The mean hind limb SI for the 15 CBLO-treated dogs and the 20 dogs in the control group was 1.02 ± 0.1 and 1.03 ± 0.07, respectively, the difference being not significant (P = 0.75). There was no significant difference in the thoracic limb/pelvic limb ratio between the 2 groups (P = 0.42). The dogs' recovery was objectively measured on a pressure-sensitive walkway and the CrCL-deficient dogs had returned to full functioning within 6 to 12 mo. Center of rotation of angulation-based leveling osteotomy provided normal function of the operated hind limb and should be considered as an option for treating canine CrCL deficiency.

L'objectif de cette étude était d'évaluer les résultats à moyen terme de l'ostéotomie de nivellement basée sur le centre de rotation de l'angulation (CORA) (CBLO) chez les chiens présentant une déficience du ligament croisé crânien (CrCL) mesurée par une plaque sensible à la pression. Quinze chiens présentant un déficit unilatéral du CrCL ont été traités par CBLO pendant une moyenne de 50 semaines (médiane 46 semaines, plage de 38 à 91) avant l'évaluation. Le membre postérieur controlatéral a été confirmé exempt de tout signe de pathologie par un examen clinique et une radiographie du grasset latéral. Un groupe témoin de 20 chiens sains a été inclus pour établir des valeurs de référence à des fins de comparaison. Les paramètres spatio-temporels et la force verticale maximale (PVF) ont été mesurés, et l'indice de symétrie (SI) a été calculé entre les membres pelviens gauche et droit et entre les membres thoracique et pelvien, dans les deux groupes. L'IS moyen des membres postérieurs pour les 15 chiens traités au CBLO et les 20 chiens du groupe témoin était de 1,02 ± 0,1 et 1,03 ± 0,07, respectivement, la différence n'étant pas significative (P = 0,75). Il n'y avait pas de différence significative dans le rapport membre thoracique/membre pelvien entre les deux groupes (P = 0,42). La récupération des chiens a été objectivement mesurée sur une plaque sensible à la pression et les chiens avec une déficience du CrCL étaient revenus à un fonctionnement complet en 6 à 12 mois. Le centre de rotation de l'ostéotomie de nivellement basée sur l'angulation a fourni une fonction normale du membre postérieur opéré et doit être considérée comme une option pour le traitement du déficit du CrCL canin.(Traduit par Docteur Serge Messier).

Carbon metabolism and biogeography of candidate phylum "Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey.

Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.

Comparison of hybrid machine learning methods for the prediction of short-term meteorological droughts of Sakarya Meteorological Station in Turkey.

Drought is a harmful natural disaster with various negative effects on many aspects of life. In this research, short-term meteorological droughts were predicted with hybrid machine learning models using monthly precipitation data (1960-2020 period) of Sakarya Meteorological Station, located in the northwest of Turkey. Standardized precipitation index (SPI), depending only on precipitation data, was used as the drought index, and 1-, 3-, and 6-month time scales for short-term droughts were considered. In the prediction models, drought index was predicted at t + 1 output variable by using t, t - 1, t - 2, and t - 3 input variables. Artificial neural networks (ANNs), adaptive neuro-fuzzy inference system (ANFIS), Gaussian process regression (GPR), support vector machine regression (SVMR), k-nearest neighbors (KNN) algorithms were employed as stand-alone machine learning methods. Variation mode decomposition (VMD), discrete wavelet transform (DWT), and empirical mode decomposition (EMD) were utilized as pre-processing techniques to create hybrid models. Six different performance criteria were used to assess model performance. The hybrid models used together with the pre-processing techniques were found to be more successful than the stand-alone models. Hybrid VMD-GPR model yielded the best results (NSE = 0.9345, OI = 0.9438, R2 = 0.9367) for 1-month time scale, hybrid VMD-GPR model (NSE = 0.9528, OI = 0.9559, R2 = 0.9565) for 3-month time scale, and hybrid DWT-ANN model (NSE = 0.9398, OI = 0.9483, R2 = 0.9450) for 6-month time scale. Considering the entire performance criteria, it was determined that the decomposition success of VMD was higher than DWT and EMD.

Chlorhexidine shampooing of dogs the night before elective surgery: Are human recommendations applicable to veterinary medicine?

The objective of this study was to investigate the effect of the night before surgery chlorhexidine shampooing on skin bacterial colony-forming units (CFU) in dogs. Twenty-five dogs had the right hindleg washed with chlorhexidine gluconate solution the night before sampling, the untreated left hindleg was used as a control. Colony-forming units were counted from 150 agar plates, 75 from each side. Median CFU on the treated side and the control side after clipping was 11 and 50, respectively (P = 0.01). Samples obtained after scrubbing the skin with CHXG, and after the final disinfection with alcohol showed no difference in CFU between sides. The "night before" chlorhexidine wash effectively decimated the skin surface bacterial CFU, but this effect was only evident after clipping. After the routine preoperative chlorhexidine scrubbing and alcohol disinfection no beneficial effects were proven.

L'objectif de cette étude était d'étudier l'effet du shampooing à la chlorhexidine la nuit précédant la chirurgie sur les unités formatrices de colonies (UFC) de la peau chez le chien. Vingt-cinq chiens ont eu la patte arrière droite lavée avec une solution de gluconate de chlorhexidine (CHXG) la nuit avant l'échantillonnage, la patte arrière gauche non traitée a été utilisée comme témoin. Les unités formatrices de colonies ont été comptées à partir de 150 gélose, 75 de chaque côté. La médiane des UFC du côté traité et du côté témoin après la tonte était de 11 et 50 respectivement (P = 0,01). Les échantillons obtenus après avoir frotté la peau avec du CHXG et après la désinfection finale avec de l'alcool n'ont montré aucune différence d'UFC entre les côtés. Le lavage à la chlorhexidine « la veille ¼ a effectivement décimé les UFC de la surface de la peau, mais cet effet n'était évident qu'après la tonte. Après le lavage préopératoire de routine à la chlorhexidine et la désinfection à l'alcool, aucun effet bénéfique n'a été prouvé.(Traduit par Docteur Serge Messier).

Morphological and molecular characterization of garlic (Allium sativum L.) genotypes sampled from Turkey.

Garlic is a vegetable widely used both in food and as a pharmaceutical raw material in the world due to its contents. Although morphological differences are observed in garlic, which is obligatory apomictically propagated, clonal propagation causes narrowing variation, a genetic bottleneck. This situation complicates breeding programs aiming improvements in preferred agronomic characteristics. For this reason, determining the morphological and molecular differences between garlic genotypes originating from Turkey is important for breeding studies. In this study, morphological and molecular characteristics of 39 garlic genotypes, which are widely cultivated in Turkey, were determined. Kahramanmaras4 genotype was different from other genotypes in terms of some morphological features (fresh weight, dry weight, and bulb diameter). In the molecular characterization study, 10 Inter-Simple Sequence Repeats (ISSR) primers were used, and it was determined that the genotype TekDis31 of Tunceli region was different from other garlic genotypes. Genetic similarity coefficient was found to be high (0.85-1.0) in genotypes except for TekDis31 garlic genotype. In general, some garlic clones (Maras3 and Kayseri30, Urfa33 and Topakli35, Kastamonu22 and Kastamonu28, Urfa10 and Kastamonu14, Kastamonu29 and Bademci23) were completely similar to each other, while few differences were found among others. In conclusion, this study revealed that the garlic plant, despite its clonal propagation, consisted of some level of morphological and partially molecular variation. Due to its mode of reproduction (vegetative), this variation may largely be due to point or chromosomal mutation. Furthermore, the 10 identified ISSR primers can generate valuable information for genetic diversity for use by garlic breeders.

Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks.

Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.

Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis.

Fungi are ubiquitous in the ocean and hypothesized to be important members of marine ecosystems, but their roles in the marine carbon cycle are poorly understood. Here, we use 13C DNA stable isotope probing coupled with phylogenetic analyses to investigate carbon assimilation within diverse communities of planktonic and benthic fungi in the Benguela Upwelling System (Namibia). Across the redox stratified water column and in the underlying sediments, assimilation of 13C-labeled carbon from diatom extracellular polymeric substances (13C-dEPS) by fungi correlated with the expression of fungal genes encoding carbohydrate-active enzymes. Phylogenetic analysis of genes from 13C-labeled metagenomes revealed saprotrophic lineages related to the facultative yeast Malassezia were the main fungal foragers of pelagic dEPS. In contrast, fungi living in the underlying sulfidic sediments assimilated more 13C-labeled carbon from chemosynthetic bacteria compared to dEPS. This coincided with a unique seafloor fungal community and dissolved organic matter composition compared to the water column, and a 100-fold increased fungal abundance within the subseafloor sulfide-nitrate transition zone. The subseafloor fungi feeding on 13C-labeled chemolithoautotrophs under anoxic conditions were affiliated with Chytridiomycota and Mucoromycota that encode cellulolytic and proteolytic enzymes, revealing polysaccharide and protein-degrading fungi that can anaerobically decompose chemosynthetic necromass. These subseafloor fungi, therefore, appear to be specialized in organic matter that is produced in the sediments. Our findings reveal that the phylogenetic diversity of fungi across redox stratified marine ecosystems translates into functionally relevant mechanisms helping to structure carbon flow from primary producers in marine microbiomes from the surface ocean to the subseafloor.

War and infection in the pre-antibiotic era: the Third Ottoman Army in 1915.

BACKGROUND: The aim of this study, which evaluated historical data, was to delineate the probable impacts of infectious diseases on human populations under extraordinary circumstances. The second goal was to disclose the mortality rates for infectious diseases in the absence of antibiotics. METHODS: The Third Ottoman Army records at the Turkish General Staff Military History and Strategic Study Directorate were studied retrospectively for the period between March 1915 and February 1916. RESULTS: For the Third Ottoman Army, the number of infection-related deaths over the single-year period was 23,601. Malaria, relapsing fever and dysentery were the most common infections. In that pre-antibiotic era, the highest mortality rates were seen for cholera (80%), pulmonary tuberculosis (58%) and typhoid fever (51%). However, typhus had the maximum share in soldier deaths (6053 soldiers). The rate of vector-borne infections peaked in the summer of 1915, while the frequency of respiratory tract infections was highest in the colder months. In contrast, gastrointestinal tract infections appeared to maintain a steady state throughout the year. CONCLUSIONS: If the wartime data for 1915 are accepted to provide a model for extraordinary circumstances in the 21st century, vector-borne, respiratory tract and gastrointestinal infections can be accepted as the challenging issues with significant mortality.

Ozone therapy and hyperbaric oxygen treatment in lung injury in septic rats.

Various therapeutic protocols were used for the management of sepsis including hyperbaric oxygen (HBO) therapy. It has been shown that ozone therapy (OT) reduced inflammation in several entities and exhibits some similarity with HBO in regard to mechanisms of action. We designed a study to evaluate the efficacy of OT in an experimental rat model of sepsis to compare with HBO. Male Wistar rats were divided into sham, sepsis+cefepime, sepsis+cefepime+HBO, and sepsis+cefepime+OT groups. Sepsis was induced by an intraperitoneal injection of Escherichia coli; HBO was administered twice daily; OT was set as intraperitoneal injections once a day. The treatments were continued for 5 days after the induction of sepsis. At the end of experiment, the lung tissues and blood samples were harvested for biochemical and histological analysis. Myeloperoxidase activities and oxidative stress parameters, and serum proinflammatory cytokine levels, IL-1ß and TNF-α, were found to be ameliorated by the adjuvant use of HBO and OT in the lung tissue when compared with the antibiotherapy only group. Histologic evaluation of the lung tissue samples confirmed the biochemical outcome. Our data presented that both HBO and OT reduced inflammation and injury in the septic rats' lungs; a greater benefit was obtained for OT. The current study demonstrated that the administration of OT as well as HBO as adjuvant therapy may support antibiotherapy in protecting the lung against septic injury. HBO and OT reduced tissue oxidative stress, regulated the systemic inflammatory response, and abated cellular infiltration to the lung demonstrated by findings of MPO activity and histopathologic examination. These findings indicated that OT tended to be more effective than HBO, in particular regarding serum IL-1ß, lung GSH-Px and histologic outcome.

Predictive hematological and immunological parameters associated with postpartum progressed Covid-19 disease.

Background: In pregnancy, Coronavirus disease-2019 (COVID-19) infection disease may be more severe due to existing physiological changes. Similarly, changes during and after birth can make the patient more subceptible. Objective: To investigate possible laboratory findings that was related to postpartum progression of COVID-19 disease. Methods: Pregnant women who are pregnant at 28 weeks or more and who are COVID-19 positive at the time of delivery were investigated in this study. Progressed post- delivery and non-progressed COVID-19 positive pregnants' laboratory findings were analyzed. Hematological and immunological parameters associated with postpartum progressed COVID-19 disease were evaluated. Results: Totally 151 individuals were conducted to the study. In the prenatal analysis, higher BMI and lower albumin levels were detected in the progressed group (p<0.05). In the postpartum analysis; White Blood Cell, lymphocyte and albumin were increased, while neutrophil, NLR, LDH, CK, D-DIMER, Ferritin, CRP and IL-6 were decreased in the non-progressed group as opposite of the progressed group (p<005). Conclusion: We observed that prenatal low albumin and high BMI may be related to progression of the COVID-19 disease after delivery. In progressed group, inflammatory markers were increased after delivery while in non-progressed group they were improved. These markers may be warning for the postpartum progression of COVID-19 disease.

Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment.

Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.

Stability of hepatitis C virus RNA in blood samples by TaqMan real-time PCR.

The storage conditions of blood samples for reliable results are very important in hepatitis C virus (HCV) RNA amplification tests used in routine HCV analyses. According to many studies, storage conditions could affect the RNA stability for HCV RNA detection. We have studied HCV RNA stability in blood samples stored at 4 degrees C. Nineteen blood samples containing different HCV RNA levels were stored at 4 degrees C and they were then analyzed by TaqMAN real-time PCR method. HCV RNA levels remained almost stable (100%) at least for five weeks at this storage condition. However, among them, the stability period was up to 11 weeks in two of the samples. As with these findings, there was a slightly significant correlation between the positivity time and the beginning HCV RNA levels (r=0.474, P=0.040). We conclude that, blood samples can be stored at 4 degrees C for five weeks without any significant difference in detected HCV RNA level by using TaqMan real-time PCR.

[Progressive multifocal leukoencephalopathy in an elderly patient with no obvious immunosuppression]. / Belirlenebilen bir immünyetmezligi olmayan yasli bir hastada gelisen progresif multifokal lökoensefalopati.

Progressive multifocal leukoencephalopathy (PML) which is a severe demyelinating disease of the central nervous system (CNS), is caused by a human polyomavirus known as JC virus (JCV). PML is seen primarily in immunosuppressed (AIDS, organ transplant or malignancy) patients. In this report, a case of PML that developed in a 75-years-old female patient with no known immunosuppression was presented. The patient was admitted to the emergency department with complaints of headache and burning sensation in head. Cerebrospinal fluid (CSF) examination revealed increase in lymphocytic cells. Since lesions compatible with tuberculoma were detected in brain tissue by magnetic resonance imaging, antituberculous therapy initiated empirically. The disease exhibited a progressive course and all the serological, molecular, microbiological and biochemical tests performed in blood and CSF failed to identify the causative agent. Pathological and immunohistochemical examination of the brain biopsy specimens demonstrated demyelinating disease. Brain biopsy, CSF, serum and urine specimens were investigated by real-time polymerase chain reaction specific for JCV and JCV-DNA was detected in the urine samples. Follow-up visits of the patient indicated a progressive course. In conclusion, after ruling out the other primary causes, JCV should be investigated in patients with demyelinating CNS disease even in the absence of significant immunosuppressive condition. Elderly patients should be considered in the risk group for demyelinating disease of CNS due to JCV.

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments.

The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation5-7, but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor. Lokiarchaeon gene expression was significantly different across a hypoxic-sulfidic redox gradient, whereby genes involved in growth, fermentation and H2-dependent carbon fixation had the highest expression under the most reducing (sulfidic) conditions. Quantitative stable isotope probing revealed that anaerobic utilization of CO2 and diatomaceous extracellular polymeric substances by Lokiarchaeon was higher than the bacterial average, consistent with higher expression of Lokiarchaeon genes, including those involved in transport and fermentation of sugars and amino acids. The quantitative stable isotope probing and gene expression data demonstrate homoacetogenic activity of Candidatus Lokiarchaeota, whereby fermentative H2 production from organic substrates is coupled with the Wood-Ljungdahl carbon fixation pathway8. The high energetic efficiency provided by homoacetogenesis8 helps to explain the elevated metabolic activity of Lokiarchaeon in this anoxic, energy-limited setting.

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor.

How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD+ Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.