scholarly journals Pangenomics reveal diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria

2019 ◽  
Author(s):  
Jimmy H.W. Saw ◽  
Takuro Nunoura ◽  
Miho Hirai ◽  
Yoshihiro Takaki ◽  
Rachel Parsons ◽  
...  

AbstractIt has been hypothesized that abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylumChloroflexievolved specialized metabolism for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the metabolic schemes proposed, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore this question, we reconstructed SAR202 single amplified genomes and metagenome-assembled genomes from locations around the world, including the deepest ocean trenches. In analyses of 122 SAR202 genomes that included six subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, and further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the Group III SAR202, in the proposed classMonstramariaand expansions of dioxygenase enzymes were prevalent in Group IV. We found that Group I SAR202 encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescencein situhybridization with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 in stratified water columns.ImportanceThe oceans contain an estimated 662 Pg C of dissolved organic carbon (DOC). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolism and classes of compounds that could be important for understanding of the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them, but until then they provide a perspective that directs our attention to the biochemistry of resistant DOM metabolism. Our findings also fundamentally change our understanding of the ecology of SAR202, showing that metabolically diverse variants of these cells occupy niches spanning all depths, and are not relegated to the dark ocean.

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jimmy H. W. Saw ◽  
Takuro Nunoura ◽  
Miho Hirai ◽  
Yoshihiro Takaki ◽  
Rachel Parsons ◽  
...  

ABSTRACT It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns. IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.


1998 ◽  
Vol 36 (6) ◽  
pp. 1733-1736 ◽  
Author(s):  
Ana María Calcagno ◽  
Gustavo Niño-Vega ◽  
Felipe San-Blas ◽  
Gioconda San-Blas

Randomly amplified polymorphic DNA (RAPD) analysis of 33Paracoccidioides brasiliensis strains from Argentina, Brazil, Colombia, Peru, and Venezuela produced reproducible amplification products which were sufficiently polymorphic to allow differentiation of the strains. Types generated with five primers (OPG 03, OPG 05, OPG 14, OPG 16, and OPG 18) resulted in a high discriminatory index (0.956). The discriminatory index was slightly reduced (0.940) when only two primers (OPG 3 and OPG 14) were used. A dendrogram based on these results showed a high degree of similarity among the strains, and genetic differences were expressed in clusters related to geographical regions but not to pathological features of the disease. With a few exceptions, strains were sorted into five groups by geographical origin as follows: group I, Venezuelan strains; group II, Brazilian strains; group III, Peruvian strains; group IV, Colombian strains; and group V, Argentinian strains. The group containing the most disparate strains was group V (discriminatory index, 0.633); the discriminatory index for the other four groups was 0.824. The use of primer OPG 18 by itself was sufficient to discriminate species specificity, and the use of primer OPG 14 by itself was sufficient to discriminate among the geographical locations of the strains in the sample. This method may be helpful for epidemiological studies ofP. brasiliensis.


2021 ◽  
Vol 664 ◽  
pp. 23-42
Author(s):  
AK Shantharam ◽  
CL Wei ◽  
M Silva ◽  
AR Baco

Northern Gulf of Mexico canyons are centers of organic matter accumulation and biodiversity, but studies of their finer-scale (sub-100 km) ecological patterns are scarce. Detailed sampling of macrofauna within the DeSoto Canyon was undertaken along 3 depth transects on the canyon wall, axis, and adjacent slope. Sediment, terrain, and water mass parameters were also compiled for the same stations. Within the canyon, macrofaunal abundance decreased, evenness increased, and richness followed the expected parabolic curve with depth, peaking at 1100 m. Cluster analysis identified 3 canyon depth groups that conformed to established bathymetric boundaries for the non-canyon Gulf of Mexico slope: Group I at <500 m, Group II at 669-1834 m, and Group III at >2000 m. Explanatory environmental models indicate that canyon community structure was strongly correlated with oxygen concentration and fluorescence, with a weaker potential influence from any of salinity, particulate organic carbon, sediment organic carbon, or slope. Comparisons of the habitats indicated that abundances were highest on the canyon wall. Slope community structure differed from that of either of the canyon habitats. Environmental models consisted of single variables including oxygen concentration, sediment organic carbon, slope, and temperature with similar explanatory values. Community differences within the canyon and between the canyon and adjoining slope contradict previous findings of a single faunal zone for the whole study area. Factors that may contribute to inter-habitat heterogeneity include potential hydrocarbon seepage, organically enriched sediment deposits along channels, or remnant influence from the Deepwater Horizon spill, warranting more research into this dynamic ecosystem.


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.


Author(s):  
Anton Bózner ◽  
Mikuláš Gažo ◽  
Jozef Dostál

It is anticipated that Japanese quail /Coturnix coturnix japonica/ will provide animal proteins in long term space flights. Consequently this species of birds is of research interest of international space program INTERCOSMOS. In the year 1987 we reported on an experiment /2/ in which the effect of chronic acceleration of 2 G hypergravitation, the hypodynamy and the simultaneous effect of chronic acceleration and the location in the centre of the turntable of the centrifuge on the protein fractions in skeletal muscles was studied. The ultrastructure of the heart muscle was now in this experiments examined as well.Japanese quail cockerels, aged 48 days were exposed to 2 G hypergravitation /group IV/ in a 6,4 m diameter centrifuge, to hypodynamy /group III/ and their combination /group V/, respectively for 6 days / Fig.1/. The hypodynamy in group III was achieved by suspending the birds in jackets without contact the floor. The group II was located in the centre ofthe turntable of the centrifuge. The control group I. was kept under normal conditions. The quantitative ultrastructure of myocard was evaluated by the methods of Weibel/3/ - this enables to determine the number, relative size and volume of mitochondria volume of single mitochondria, defficiency of mitochondrial cristae and volume of myofibrils.


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.


Author(s):  
Ahmed Mousa ◽  
Ossama M. Zakaria ◽  
Mai A. Elkalla ◽  
Lotfy A. Abdelsattar ◽  
Hamad Al-Game'a

AbstractThis study was aimed to evaluate different management modalities for peripheral vascular trauma in children, with the aid of the Mangled Extremity Severity Score (MESS). A single-center retrospective analysis took place between 2010 and 2017 at University Hospitals, having emergencies and critical care centers. Different types of vascular repair were adopted by skillful vascular experts and highly trained pediatric surgeons. Patients were divided into three different age groups. Group I included those children between 5 and 10 years; group II involved pediatrics between 11 and 15 years; while children between 16 and 21 years participated in group III. We recruited 183 children with peripheral vascular injuries. They were 87% males and 13% females, with the mean age of 14.72 ± 04. Arteriorrhaphy was performed in 32%; end-to-end anastomosis and natural vein graft were adopted in 40.5 and 49%, respectively. On the other hand, 10.5% underwent bypass surgery. The age groups I and II are highly susceptible to penetrating trauma (p = 0.001), while patients with an extreme age (i.e., group III) are more susceptible to blunt injury (p = 0.001). The MESS has a significant correlation to both age groups I and II (p = 0.001). Vein patch angioplasty and end-to-end primary repair should be adopted as the main treatment options for the repair of extremity vascular injuries in children. Moreover, other treatment modalities, such as repair with autologous vein graft/bypass surgery, may be adopted whenever possible. They are cost-effective, reliable, and simple techniques with fewer postoperative complication, especially in poor/limited resources.


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.


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