scholarly journals Biphenyl/PCB Degrading bph Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs)

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 404 ◽  
Author(s):  
Jun Hirose ◽  
Hidehiko Fujihara ◽  
Takahito Watanabe ◽  
Nobutada Kimura ◽  
Hikaru Suenaga ◽  
...  

We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic bph gene cluster as integrative conjugative elements (ICEs), and they were classified into four groups based on the structural features of the bph genes. Group I (five strains) possessed bph genes that were very similar to the ones in Pseudomonas furukawaii KF707 (formerly Pseudomonas pseudoalcaligenes KF707), which is one of the best characterized biphenyl-utilizing strains. This group of strains carried salicylate catabolic sal genes that were approximately 6-kb downstream of the bph genes. Group II (two strains) possessed bph and sal genes similar to the ones in KF707, but these strains lacked the bphX region between bphC and bphD, which is involved in the downstream catabolism of biphenyl. These bph-sal clusters in groups I and II were located on an integrative conjugative element that was larger than 110 kb, and they were named ICEbph-sal. Our previous study demonstrated that the ICEbph-sal of Pseudomonas putida KF715 in group II existed both in an integrated form in the chromosome (referred to as ICEbph-salKF715 (integrated)) and in a extrachromosomal circular form (referred to as ICEbph-sal (circular)) (previously called pKF715A, 483 kb) in the stationary culture. The ICEbph-sal was transferred from KF715 into P. putida AC30 and P. putida KT2440 with high frequency, and it was maintained stably as an extrachromosomal circular form. The ICEbph-salKF715 (circular) in these transconjugants was further transferred to P. putida F39/D and then integrated into the chromosome in one or two copies. Meanwhile, group III (one strain) possessed bph genes, but not sal genes. The nucleotide sequences of the bph genes in this group were less conserved compared to the genes of the strains belonging to groups I and II. Currently, there is no evidence to indicate that the bph genes in group III are carried by a mobile element. Group IV (two strains) carried bph genes as ICEs (59–61 kb) that were similar to the genes found in Tn4371 from Cupriavidus oxalacticus A5 and ICEKKS1024677 from the Acidovorax sp. strain KKS102. Our study found that bph gene islands have integrative functions, are transferred among soil bacteria, and are diversified through modification.

2021 ◽  
Author(s):  
M. Shaminur Rahman ◽  
M. Nazmul Hoque ◽  
Joynob Akter Puspo ◽  
M. Rafiul Islam ◽  
Niloy Das ◽  
...  

The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome dysbiosis in different stages of anaerobic digestion, we analyzed 16 samples dividing into four groups (Group-I = 2; Group-II = 5; Group-III = 5 and Group-IV = 4) through whole metagenome sequencing (WMS). The physicochemical analysis revealed that highest CH 4 production (74.1%, on Day 35 of digestion) was associated with decreased amount of non-metal (phosphorus and sulfur) and heavy metals (chromium, lead and nickel). The WMS generated 380.04 million reads mapped to ~ 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. The PS analysis detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively which were represented by Firmicutes , Bacteroidetes , Proteobacteria , Actinobacteria , Spirochaetes and Fibrobacteres (> 93.0% of the total abundances). The archaeal fraction of the AD microbiomes was represented by 343 strains, of which 95.90% strains shared across these metagenomes. The indicator species analysis showed that Methanosarcina vacuolate , Dehalococcoides mccartyi , Methanosarcina sp. Kolksee and Methanosarcina barkeri were the highly specific for energy production in Group-III and Group-IV. However, most of the indicator phylotypes displayed reduced abundance in the initial stage of biogas production (Group-I and Group-II) compared to their increased relative abundances in Group-IV (Day 35). The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla were associated with highest level (74.1%) of energy production (Group-IV). In addition to taxonomic dysbiosis, top CH 4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, MT1-MMP pericellular network, acetyl-CoA production, motility and chemotaxis. This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.


1988 ◽  
Vol 34 (8) ◽  
pp. 938-946 ◽  
Author(s):  
G. Fonty ◽  
P. Gouet ◽  
Harinirina Ratefiarivelo ◽  
J. P. Jouany

We attempted to determine the degree of diversification of the microflora that allow the establishment of Bacteroides succinogenes S85 in the rumen of gnotoxenic lambs. Four lambs (group I) received an inoculum orally, composed of 182 noncellulolytic bacterial strains (inoculum 1) previously isolated from the rumen of conventional young lambs. Two lambs (group II) were inoculated with 32 strains (inoculum 2) selected among the 182 strains of inoculum 1. Two lambs (group III) received an inoculum (inoculum 3) composed of 106 noncellulolytic bacterial strains previously isolated from the rumen of meroxenic lambs. Two lambs (group IV) were inoculated with 16 strains (inoculum 4) chosen among the 106 strains of inoculum 3. All lambs were inoculated from birth except two lambs of group I, which were inoculated from 1 month of age. Each lamb then received orally a pure culture of B. succinogenes. This strain became established more easily in the rumen of lambs that had received complex inocula (group I). Its population reached a level close to that generally observed in conventional lambs (107–108 bacteria mL−1). In contrast, B. succinogenes became established in only one lamb of group II, but bacterial numbers varied considerably. In group III, repeated inoculations were necessary to obtain its definitive establishment (107–108 bacteria mL−1 after weaning). In spite of several inoculations, this cellulolytic species failed to establish in the rumen of lambs of group IV, which had received the less complex inoculum. The volatile fatty acid levels were very different from one lamb group to another. The more complex the inoculum administered to the animals, the higher the concentration. In those that received inoculum 1, the volatile fatty acid concentration was similar to that measured in conventional lambs fed the same diet (approximately 80 mmol L−1 after feeding). In lambs inoculated with only 16 strains there were almost no fermentations (30 mmol L−1 of volatile fatty acid). These results demonstrate that the establishment of cellulolytic bacteria, functions of the rumen, and the stability of the ecosystem depend on the complexity and diversity of the microflora. In the light of present knowledge, it is not possible to determine accurately the operative composition of the minimum flora enabling rumen development and function.


Author(s):  
K.K. SEKHRI ◽  
C.S. ALEXANDER ◽  
H.T. NAGASAWA

C57BL male mice (Jackson Lab., Bar Harbor, Maine) weighing about 18 gms were randomly divided into three groups: group I was fed sweetened liquid alcohol diet (modified Schenkl) in which 36% of the calories were derived from alcohol; group II was maintained on a similar diet but alcohol was isocalorically substituted by sucrose; group III was fed regular mouse chow ad lib for five months. Liver and heart tissues were fixed in 2.5% cacodylate buffered glutaraldehyde, post-fixed in 2% osmium tetroxide and embedded in Epon-araldite.


1998 ◽  
Vol 80 (09) ◽  
pp. 393-398 ◽  
Author(s):  
V. Regnault ◽  
E. Hachulla ◽  
L. Darnige ◽  
B. Roussel ◽  
J. C. Bensa ◽  
...  

SummaryMost anticardiolipin antibodies (ACA) associated with antiphospholipid syndrome (APS) are directed against epitopes expressed on β2-glycoprotein I (β2GPI). Despite a good correlation between standard ACA assays and those using purified human β2GPI as the sole antigen, some sera from APS patients only react in the latter. This is indicative of heterogeneity in anti-β2GPI antibodies. To characterize their reactivity profiles, human and bovine β2GPI were immobilized on γ-irradiated plates (β2GPI-ELISA), plain polystyrene precoated with increasing cardiolipin concentrations (CL/β2GPI-ELISA), and affinity columns. Fluid-phase inhibition experiments were also carried out with both proteins. Of 56 selected sera, restricted recognition of bovine or human β2GPI occurred respectively in 10/29 IgA-positive and 9/22 IgM-positive samples, and most of the latter (8/9) were missed by the standard ACA assay, as expected from a previous study. Based on species specificity and ACA results, IgG-positive samples (53/56) were categorized into three groups: antibodies reactive to bovine β2GPI only (group I) or to bovine and human β2GPI, group II being ACA-negative, and group III being ACA-positive. The most important group, group III (n = 33) was characterized by (i) binding when β2GPI was immobilized on γ-irradiated polystyrene or cardiolipin at sufficient concentration (regardless of β2GPI density, as assessed using 125I-β2GPI); (ii) and low avidity binding to fluid-phase β2GPI (Kd in the range 10–5 M). In contrast, all six group II samples showed (i) ability to bind human and bovine β2GPI immobilized on non-irradiated plates; (ii) concentration-dependent blockade of binding by cardiolipin, suggesting epitope location in the vicinity of the phospholipid binding site on native β2GPI; (iii) and relative avidities approximately 100-fold higher than in group III. Group I patients were heterogeneous with respect to CL/β2GPI-ELISA and ACA results (6/14 scored negative), possibly reflecting antibody differences in terms of avidity and epitope specificity. Affinity fractionation of 23 sera showed the existence, in individual patients, of various combinations of antibody subsets solely reactive to human or bovine β2GPI, together with cross-species reactive subsets present in all samples with dual reactivity namely groups III and II, although the latter antibodies were poorly purified on either column. Therefore, the mode of presentation of β2GPI greatly influences its recognition by anti-β2GPI antibodies with marked inter-individual heterogeneity, in relation to ACA quantitation and, possibly, disease presentation and pathogenesis.


2015 ◽  
Vol 18 (3) ◽  
pp. 098
Author(s):  
Cem Arıtürk ◽  
Serpil Ustalar Özgen ◽  
Behiç Danışan ◽  
Hasan Karabulut ◽  
Fevzi Toraman

<p class="p1"><span class="s1"><strong>Background:</strong> The inspiratory oxygen fraction (FiO<sub>2</sub>) is usually set between 60% and 100% during conventional extracorporeal circulation (ECC). However, this strategy causes partial oxygen pressure (PaO<sub>2</sub>) to reach hyperoxemic levels (&gt;180 mmHg). During anesthetic management of cardiothoracic surgery it is important to keep PaO<sub>2</sub> levels between 80-180 mmHg. The aim of this study was to assess whether adjusting FiO<sub>2</sub> levels in accordance with body temperature and body surface area (BSA) during ECC is an effective method for maintaining normoxemic PaO<sub>2</sub> during cardiac surgery.</span></p><p class="p1"><span class="s1"><strong>Methods:</strong> After approval from the Ethics Committee of the University of Acıbadem, informed consent was given from 60 patients. FiO<sub>2</sub> adjustment strategies applied to the patients in the groups were as follows: FiO<sub>2</sub> levels were set as 0.21 × BSA during hypothermia and 0.21 × BSA + 10 during rewarming in Group I; 0.18 × BSA during hypothermia and 0.18 × BSA + 15 during rewarming in Group II; and 0.18 × BSA during hypothermia and variable with body temperature during rewarming in Group III. Arterial blood gas values and hemodynamic parameters were recorded before ECC (T1); at the 10th minute of cross clamp (T2); when the esophageal temperature (OT) reached 34°C (T3); when OT reached 36°C (T4); and just before the cessation of ECC (T5).</span></p><p class="p1"><span class="s1"><strong>Results:</strong> Mean PaO<sub>2</sub> was significantly higher in Group I than in Group II at T2 and T3 (<em>P</em> = .0001 and <em>P</em> = .0001, respectively); in Group I than in Group III at T1 (<em>P</em> = .02); and in Group II than in Group III at T2, T3, and T4 <br /> (<em>P</em> = .0001 for all). </span></p><p class="p1"><span class="s1"><strong>Conclusion: </strong>Adjustment of FiO<sub>2</sub> according to BSA rather than keeping it at a constant level is more appropriate for keeping PaO<sub>2</sub> between safe level limits. However, since oxygen consumption of cells vary with body temperature, it would be appropriate to set FiO<sub>2</sub> levels in concordance with the body temperature in the <br /> rewarming period.</span></p>


2016 ◽  
pp. 108-111
Author(s):  
T.F. Tatarchuk ◽  
◽  
D.G. German ◽  

The article presents the comparative analysis of the state of the cervix in women with endometrial polyps and micropolyps. Patients and methods. The study involved 130 patients aged 18-35 years: 70 patients with endometrial polyps (group I), 30 patients with micropolyps (group II) and 30 patients of the control group (group III). Results. According to the anamnesis of women in the I group were significantly more frequent diseases of the cervix, which corrected physical surgery methods, in particular cryodestruction. In group II, the representatives of these indicators were similar to healthy. Normal colposcopic picture met significantly less frequently in patients and I, and II group. The differences in the incidence of HPV high oncogenic risk in all groups were not statistically significant. Conclusion. Destructive methods used in the detection of any changes in the cervix are often overly aggressive, form scars and contributing to inflamaciones process. In the chain of events leading to the formation of PE, cervical pathology and its correction can take the basic place. Key words: endometrial polyp, micropolyps, chronic endometritis, uterine cervix, colposcopy.


Author(s):  
Г.В. ШИРЯЕВ ◽  
Ю.Г. ТУРЛОВА ◽  
Г.С. НИКИТИН

Изучено влияние кормовой добавки в форме индивидуальных болюсов Метраболь на возможность снижения негативного влияния субклинического кетоза (СКК) и результативность искусственного осеменения высокопродуктивных молочных коров в посттранзитный период. Животные были подобраны по принципу условных аналогов и разделены на 3 группы в зависимости от концентрации β-оксимасляной кислоты в их крови. В I группе (n=18) у коров не было СКК, концентрация кислоты составляла <1,0 ммоль/л, во II группе (n=21) у животных зарегистрирован СКК, концентрация кислоты — 1,0…1,4 ммоль/л. С целью поиска решения по снижению негативного влияния СКК на репродуктивные показатели была сформирована III группа коров, переболевших СКК (n=24) с концентрацией β-оксимасляной кислоты в крови 1,0…1,4 ммоль/л, но с использованием болюсов, применяемых для ускоренного восстановления репродуктивной функции коров после отела. Важной составляющей опыта явилось то, что к моменту гормональной синхронизации у коров всех 3 групп фиксировалось отсутствие СКК (снижение β-оксимасляной кислоты до уровня <1,0 ммоль/л). Для синхронизации полового цикла выбрана схема Пресинх-овсинх. Установлено, что гормональная синхронизация животных, перенесших СКК, в сравнении со здоровыми, не позволяет снизить негативное влияние данного нарушения обмена веществ. Во II группе у животных зафиксированы самые низкие репродуктивные показатели (количество использованных доз; индекс осеменения, сервис-период; время от первого до успешного осеменения; результат первичного осеменения; количество животных, осемененных 3 и более раз). В III группе применение болюсов позволило, в сравнении с животными II группы, не только избежать отрицательного воздействия СКК, но и превзойти по изучаемым параметрам животных из I группы. The effect of the feed additive in the form of individual boluses Metrabol on the possibility of reducing the negative effect of subclinical ketosis (CCK) and the effectiveness of artificial insemination of highly productive dairy cows in the post-transit period was studied. The animals were selected according to the principle of conditional analogs and divided into 3 groups depending on the concentration of β-hydroxybutyric acid in their blood. In group I (n=18), the cows did not have SSC, the acid concentration was <1.0 mmol/L, in group II (n=21), SSC was registered in animals — 1.0...1.4 mmol / L. In order to find a solution to reduce the negative effect of CCB on reproductive indices, a group III of cows was formed who had CCB (n = 24) with a concentration of β-hydroxybutyric acid in their blood of 1.0...1.4 mmol/L, but using boluses, used to accelerate the restoration of the reproductive function of cows after calving. An important component of the experiment was that by the time of hormonal synchronization, cows of all 3 groups had no SSC (decrease in β-hydroxybutyric acid to a level of <1.0 mmol/L). To synchronize the sexual cycle, the Pressinh-ovsinh scheme was chosen. It was found that hormonal synchronization of animals that underwent SSC, in comparison with healthy ones, does not allow reducing the negative effect of this metabolic disorder. In group II, animals had the lowest reproductive indices (number of doses used; insemination index, service period; time from first to successful insemination; result of primary insemination; number of animals inseminated 3 or more times). In group III, the use of boluses made it possible, in comparison with animals of group II, not only to avoid the negative effect of SSC, but also to surpass the animals from group I in terms of the studied parameters.


Author(s):  
M. M. Chaudhary ◽  
C. T. Khasatiya ◽  
S. B. Patel ◽  
S. S. Chaudhary ◽  
V. B. Atara ◽  
...  

The serum progesterone and estradiol profiles during synchronization of estrus by buck effect and PGF2α treatments were monitored in Surti does. Total eighteen non-pregnant does selected were evenly divided into 3 groups, 6 does in each group. The does of Group I were teased with a sexuallyactive- apronized buck; and those of Group II were treated with PGF2α, i.e., Inj. Lutalyse® @ 7.5 mg/doe IM twice 11 days apart, while the Group III served as untreated control. Blood samples were collected from all the animals on day 0 (before 1st PGF2α injection), 3rd day (during treatment), 11th day (before 2nd PGF2α injection), 14th day (after treatment) and 40th day (post-service) by jugular vein puncture. The serum separated was stored at -20°C till further analysis. In all the three groups, 83.33% does, conceived at first service in the sampling cycle. The overall mean serum progesterone concentration of Group I does (5.82±0.72 ng/ml) was significantly higher (p less than 0.01) as compared to Group II (2.93±0.38 ng/ml) and III (2.88±0.30 ng/ml). Similarly, the overall mean serum progesterone concentration of Surti does on day 0 (2.65±0.46 ng/ml), 3rd (2.56±0.80 ng/ml), 11th (4.45±0.84 ng/ml) and 14th (3.40±0.63 ng/ml) did not differ significantly, but the overall mean level at day 40 (6.31±0.45 ng/ml) was significantly (p less than 0.01) higher, because most of animals became pregnant at that time. The overall mean serum oestradiol-17β levels of Group I (24.40±2.98 pg/ ml) was significantly higher (p less than 0.01) than in Group II (15.77±1.77 pg/ml) and III (12.21±1.45 pg/ ml). On the other hand, the overall mean serum oestradiol-17β levels of Surti does on day 0 (12.89±1.21 pg/ml), 3rd (15.84±1.74 pg/ml), 11th (14.81±1.96 pg/ml), 14th (22.15±2.97 pg/ml) and 40th (21.64±5.16 pg/ml) did not differ significantly (p>0.05) and the slightly higher overall mean level found at 40th day might be the influence of the non-pregnant does at first service in the cumulative animals. The hormonal profile reflected the initiation of cyclicity and establishment of pregnancy in treated and control animals.


2020 ◽  
Author(s):  
Jan Niclas Mumm ◽  
Lucas Bohn ◽  
Lennert Eismann ◽  
Alexander Buchner ◽  
Theresa Vilsmaier ◽  
...  

BACKGROUND Pelvic floor training (PFT) is the gold standard for conservative treatment of male stress urinary incontinence. OBJECTIVE To evaluate patients´ perspective at risk of incontinence on PFT and application of digital technologies for PFT. METHODS Patients undergoing transurethral surgery of the prostate (group I), radical prostatectomy (group II) or treatment at a specialized incontinence outpatient clinic (group III) were surveyed anonymously. Chi-Square test and Kruskal-Wallis-analysis were used for statistical analysis. RESULTS 180 patients were included in the final analysis. In group I (n=35) no patient underwent PFT prior to transurethral surgery. 23.5% of patients in group II (n=51) and 95.7% of patients in group III (n=94) performed PFT. 11.4% in group I, 80.4% in group II and 91.5% in group III have been advised to perform PFT by their urologist. Regarding the information level on PFT, patients from group I (median 1, range 0-5) are less satisfied than patients from group II (median 3, 0-9) or group III (median 5, range 0-10, p<0.001). 88.6% of patients from group I are willing to perform PFT as preventive treatment or to avoid incontinence surgery, 100% from group II and 68.4% from group III (p<0.001). The likelihood to use digital PFT is higher in group I (median: 9, range 0-10) and II (median: 9, range 0-10) than in group III (median: 4, range 0-10, p<0.001). CONCLUSIONS Patients at risk of incontinence currently have limited access to PFT, although they are willing to perform PFT. Digital PFT is highly accepted by patients preoperatively and might be a valuable tool to increase PFT participation.


Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 471
Author(s):  
Jongmin Lee ◽  
Sung-Soo Park ◽  
Tong Yoon Kim ◽  
Dong-Gun Lee ◽  
Dong-Wook Kim

We aimed to identify whether lymphopenia is a reliable prognostic marker for COVID-19. Using data derived from a Korean nationwide longitudinal cohort of 5628 COVID-19 patients, we identified propensity-matched cohorts (n = 770) with group I of severe lymphopenia (absolute lymphocyte counts [ALC]: <500/mm3, n = 110), group II of mild-to-moderate lymphopenia (ALC: ≥500–<1000/mm3, n = 330), and group III, no lymphopenia (ALC: ≥1000/mm3, n = 330). A significantly higher mortality rate was associated with lymphopenia severity: 40% in group I, 22.7% in group II, and 13.0% in group III (p < 0.001). At 28 days, the estimated inferior overall survival associated with intensified lymphopenia: 62.7% in group I, 79.9% in group II, and 89.0% in group III (p < 0.001). Lymphopenia contributed significantly toward a greater need for interventions in all groups but at varying degrees: requirements of invasive ventilation, intensive oxygen supply, or adequate oxygen supply, respectively (p < 0.001). The lymphopenia intensity was independently associated with higher COVID-19 mortality in multivariable analysis; adjusted odds ratios of 5.63 (95% CI, 3.0–10.72), and 2.47 (95% CI, 1.5–4.13) for group I and group II, respectively. Lymphopenia and its severity levels may serve as reliable predictive factors for COVID-19 clinical outcomes; thus, lymphopenia may provide the prognostic granularity required for clinical use in the management of patients with COVID-19.


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