Antarctica is covered by multiple larger glaciers with diverse extreme conditions. Microorganisms in Antarctic regions are primarily responsible for diverse biogeochemical processes. The identity and ...functionality of microorganisms from polar glaciers are defined. However, little is known about microbial communities from the high elevation glaciers. The Union Glacier, located in the inland of West Antarctica at 79°S, is a challenging environment for life to survive due to the high irradiance and low temperatures. Here, soil and rock samples were obtained from three high mountains (Rossman Cove, Charles Peak, and Elephant Head) adjacent to the Union Glacier. Using metagenomic analyses, the functional microbial ecosystem was analyzed through the reconstruction of carbon, nitrogen and sulfur metabolic pathways. A low biomass but diverse microbial community was found. Although archaea were detected, bacteria were dominant. Taxa responsible for carbon fixation were comprised of photoautotrophs (Cyanobacteria) and chemoautotrophs (mainly Alphaproteobacterial clades:
Bradyrhizobium
,
Sphingopyxis
, and
Nitrobacter
). The main nitrogen fixation taxa were
Halothece
(Cyanobacteria),
Methyloversatilis
, and
Leptothrix
(Betaproteobacteria). Diverse sulfide-oxidizing and sulfate-reducing bacteria, fermenters, denitrifying microbes, methanogens, and methane oxidizers were also found. Putative producers provide organic carbon and nitrogen for the growth of other heterotrophic microbes. In the biogeochemical pathways, assimilation and mineralization of organic compounds were the dominant processes. Besides, a range of metabolic pathways and genes related to high irradiance, low temperature and other stress adaptations were detected, which indicate that the microbial communities had adapted to and could survive in this harsh environment. These results provide a detailed perspective of the microbial functional ecology of the Union Glacier area and improve our understanding of linkages between microbial communities and biogeochemical cycling in high Antarctic ecosystems.
A Gram-reaction-negative, aerobic, oxidase- and catalase-positive, yellow-pigmented, non-flagellated, rod-shaped bacterium, designed strain SM1501T, was isolated from surface seawater of the South ...China Sea. SM1501T grew at 7-42 °C and with 0-11 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that SM1501T represented a member of the genus Erythrobacter, sharing the highest 16S rRNA gene sequence similarity (97.4 %) with Erythrobacter luteus and 94.2-96.5 % 16S rRNA gene sequence similarities to other species of the genus Erythrobacterwith validly published names. The average nucleotide identity (ANI) value and in silico DNA-DNA hybridization value between SM1501T and E. luteus were only 74.6 and 20.0 %, respectively. The predominant cellular fatty acids of SM1501T were C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, diphosphatidylglycerol and phosphatidylcholine and the main respiratory quinone of was Q-10. Polyphasic data presented in this paper support the notion that SM1501T represents a novel species in the genus Erythrobacter, for which the name Erythrobacter xanthus sp. nov. is proposed. The type strain of Erythrobacterxanthus is SM1501T (=KCTC 42669T=CCTCC AB 2015396T).
Abstract
Background
The anti-coagulation protocol of patients with hemorrhage risk primary disease who need extracorporeal membrane oxygenation (ECMO) supported is controversial. This study evaluated ...the feasibility of a new anti-coagulation strategy, that is heparin-free after 3000 IU heparin loaded in veno-venous ECMO (VV ECMO) supported acute respiratory failure patients with hemorrhage risk.
Methods
A retrospective study was performed in a series of hemorrhage risk patients supported with VV ECMO at the First Affiliated Hospital of Zhengzhou University, between June 2012 to Sept 2020. A total of 70 patients received a low heparin bolus of 3000 units for cannulation but without subsequent, ongoing heparin administration. Patients were divided into survival (
n
= 25) and non-survival group (
n
= 45). Data of coagulation, hemolysis and membrane lung function were calculated and analyzed. The complications of patients were recorded. Finally, the binary Logistic regression was conducted.
Results
The longest heparin-free time was 216 h, and the mean heparin-free time was 102 h. Compared with survivors, the non-survivors were showed higher baseline SOFA score and lower platelet counts in 0.5 h, 24 h, 48 h and 96 h after ECMO applied. However, there was no significant differences between survivors and non-survivors in ACT, APTT, INR, D-dimer, fibrinogen, LDH, blood flow rate, Δp and P
post-ML
O
2
(all
p
< 0.05) of all different time point. Moreover, only the baseline SOFA score was significantly associated with mortality (
p
< 0.001, OR(95%CI): 2.754 (1.486–5.103)) while the baseline levels of ACT, APTT, INR, platelet, D-dimer, fibrinogen and LDH have no association with mortality. The percentage of thrombosis complications was 54.3% (38/70) including 3 oxygenator changed but there was no significant difference of complications in survival and non-survival groups (
p
> 0.05).
Conclusions
The anticoagulation protocol that no heparin after a 3000 units heparin bolus in VV ECMO supported acute respiratory failure patients with hemorrhage risk is feasible.
Summary
Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and ...effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl‐CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate‐CoA ligase (PrpE) and acryloyl‐CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP‐catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl‐CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.
Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide and acrylate, is an important step in global sulfur cycling. Since acrylate is toxic to cells, it is important to understand how organisms utilize and detoxify acrylate. Through molecular and structural analyses, we provide the molecular mechanism for acrylate metabolism and detoxification in DMSP‐catabolizing Roseobacters and suggest an effective detoxification system which is likely relevant to many metabolic processes and environments beyond DMSP catabolism in Roseobacters.
Obesity is a growing epidemic around the world, and obese patients are generally regarded as high risk for surgery compared with normal weight patients. The purpose of this study was to evaluate the ...influence of obesity on the surgical outcomes of laparoscopic gastrectomy (LG) for gastric cancer.
We reviewed data for all patients undergoing LG for gastric cancer at our institute between October 2004 and December 2016. Patients were divided into non-obese and obese groups and the perioperative outcomes were compared. Furthermore, a subgroup analysis was conducted to evaluate which of the two commonly used methods of LG, laparoscopic-assisted gastrectomy (LAG) and totally laparoscopic gastrectomy (TLG), is more suitable for obese patients.
A total of 1691 patients, 1255 non-obese and 436 obese or overweight patients, underwent LG during the study period. The mean operation time was significantly longer in the obese group than in the non-obese group (209.9 ± 29.7 vs. 227.2 ± 25.7 min, P < 0.01), and intraoperative blood loss was significantly lower in the non-obese group (113.4 ± 34.1 vs. 136.9 ± 36.7 ml, P < 0.01). Time to first flatus, time to oral intake, and postoperative hospital stay were significantly shorter in the non-obese group than in the obese group (3.3 ± 0.8 vs. 3.6 ± 0.9 days; 4.3 ± 1.0 vs. 4.6 ± 1.0 days; and 9.0 ± 2.2 vs. 9.6 ± 2.2 days, respectively; P < 0.01). 119 (9.5%) of the non-obese patients had postoperative complications as compared to 44 (10.1%) of the obese patients (P = 0.71). In the subgroup analysis of all patients, TLG showed improved results for early surgical outcomes compared to LAG, mainly due to its advantages in obese patients.
Obesity is associated with long operation time, increased blood loss, and slow recovery after laparoscopic gastric resection but does not affect intraoperative security or effectiveness. TLG may have less negative results in obese patients than LAG due to a variety of reasons. Our analysis shows that TLG is more advantageous, with regard to early surgical outcomes, for obese patients.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Trimethylamine (TMA) and trimethylamine N‐oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin‐containing ...monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half‐reaction and an oxidative half‐reaction. In the reductive half‐reaction, FAD is reduced and a C4a‐hydroperoxyflavin intermediate forms. In the oxidative half‐reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP+ bends and interacts with D317, shutting off the entrance to create a protected micro‐environment for catalysis and exposing C4a‐hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP+ undergoes a conformational change in the oxidative half‐reaction of FMOs.
Trimethylamine (TMA) and trimethylamine N‐oxide (TMAO) are widespread in the ocean. TMA monooxygenase (Tmm), a bacterial flavin‐containing monooxygenase (FMO), is responsible for converting marine TMA to TMAO. In this study, we elucidated the catalytic mechanism of TMA oxidation by a marine bacterial Tmm. The catalytic process of Tmm consists of a reductive half‐reaction and an oxidative half‐reaction. Our findings first demonstrate that NADP+ undergoes a conformational change in the oxidative half‐reaction of FMOs.
As typical bacterial replicons, circular chromosomes replicate bidirectionally and circular plasmids replicate either bidirectionally or unidirectionally. Whereas the finding of chromids ...(plasmid-derived chromosomes) in multiple bacterial lineages provides circumstantial evidence that chromosomes likely evolved from plasmids, all experimentally assayed chromids were shown to use bidirectional replication. Here, we employed a model system, the marine bacterial genus
, members of which consistently carry a chromosome and a chromid. We provide experimental and bioinformatic evidence that while chromids in a few strains replicate bidirectionally, most replicate unidirectionally. This is the first experimental demonstration of the unidirectional replication mode in bacterial chromids. Phylogenomic and comparative genomic analyses showed that the bidirectional replication evolved only once from a unidirectional ancestor and that this transition was associated with insertions of exogenous DNA and relocation of the replication terminus region (
) from near the origin site (
) to a position roughly opposite it. This process enables a plasmid-derived chromosome to increase its size and expand the bacterium's metabolic versatility while keeping its replication synchronized with that of the main chromosome. A major implication of our study is that the uni- and bidirectionally replicating chromids may represent two stages on the evolutionary trajectory from unidirectionally replicating plasmids to bidirectionally replicating chromosomes in bacteria. Further bioinformatic analyses predicted unidirectionally replicating chromids in several unrelated bacterial phyla, suggesting that evolution from unidirectionally to bidirectionally replicating replicons occurred multiple times in bacteria.
Chromosome replication is an essential process for cell division. The mode of chromosome replication has important impacts on the structure of the chromosome and replication speed. Bidirectional replication is the rule for bacterial chromosomes, and unidirectional replication has been found only in plasmids. To date, no bacterial chromosomes have been experimentally demonstrated to replicate unidirectionally. Here, we showed that the chromids (plasmid-derived chromosomes) in
replicate either uni- or bidirectionally and that a single evolutionary transition from uni- to bidirectionality explains this diversity. These uni- and bidirectionally replicating chromids likely represent two stages during the evolution from a small and unidirectionally replicating plasmid to a large and bidirectionally replicating chromosome. This study provides insights into both the physiology of chromosome replication and the early evolutionary history of bacterial chromosomes.
Although the Escherichia coli expression system is the most commonly used expression system, some proteins are still difficult to be expressed by this system, such as proteins with high ...thermolability and enzymes that cannot mature by autoprocessing. Therefore, it is necessary to develop alternative expression systems. In this study, a cold-adapted Pseudoalteromonas expression system was developed. A shuttle vector was constructed, and a conjugational transfer system between E. coli and psychrophilic strain Pseudoalteromonas sp. SM20429 was established. Based on the shuttle vector, three reporter vectors were constructed to compare the strength of the cloned promoters at low temperature. The promoter of xylanase gene from Pseudoalteromonas sp. BSi20429 was chosen due to its high activity at 10-15°C. An expression vector pEV containing the chosen promoter, multiple cloning sites and a His tag was constructed for protein expression and purification. With pEV as expression vector and SM20429 as the host, a cold-adapted protease, pseudoalterin, which cannot be maturely expressed in E. coli, was successfully expressed as an active extracellular enzyme when induced by 2% oat spelt xylan at 15°C for 48 h. Recombinant pseudoalterin purified from the culture by Ni affinity chromatography had identical N-terminal sequence, similar molecular mass and substrate specificity as the native pseudoalterin. In addition, another two cold-adapted enzymes were also successfully expressed by this system. Our results indicate that this cold-adapted Pseudoalteromonas expression system will provide an alternative choice for protein expression, especially for the Pseudoalteromonas proteins intractable for the E. coli system.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Halotolerant enzymes are beneficial for industrial processes requiring high salt concentrations and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions ...on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolabile esterase, E40, by increasing intraprotein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl, and its
and substrate affinity were both significantly reduced in 0.5 M NaCl. By introducing hydrophobic residues in loop 1 of the CAP domain and/or α7 of the catalytic domain in E40, we obtained several mutants with improved halotolerance, and the M3 S202W I203F mutant was the most halotolerant. ("M3" represents a mutation in loop 1 of the CAP domain in which residues R22-K23-T24 of E40 are replaced by residues Y22-K23-H24-L25-S26 of Est2.) Then we solved the crystal structures of the S202W I203F and M3 S202W I203F mutants to reveal the structural basis for their improved halotolerance. Structural analysis revealed that the introduction of hydrophobic residues W202 and F203 in α7 significantly improved E40 halotolerance by strengthening intradomain hydrophobic interactions of F203 with W202 and other residues in the catalytic domain. By further introducing hydrophobic residues in loop 1, the M3 S202W I203F mutant became more rigid and halotolerant due to the formation of additional interdomain hydrophobic interactions between the introduced Y22 in loop 1 and W204 in α7. These results indicate that increasing intraprotein hydrophobic interactions is also a way to improve the halotolerance of enzymes with industrial potential under high-salt conditions.
Esterases and lipases for industrial application are often subjected to harsh conditions such as high salt concentrations, low water activity, and the presence of organic solvents. However, reports on halotolerant esterases and lipases are limited, and the underlying mechanism for their halotolerance is still unclear due to the lack of structures. In this study, we focused on the improvement of the halotolerance of a salt-sensitive esterase, E40, and the underlying mechanism. The halotolerance of E40 was significantly improved by introducing hydrophobic residues. Comparative structural analysis of E40 and its halotolerant mutants revealed that increased intraprotein hydrophobic interactions make these mutants more rigid and more stable than the wild type against high concentrations of salts. This study shows a new way to improve enzyme halotolerance, which is helpful for protein engineering of salt-sensitive enzymes.
A novel Gram-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative bacterium, designated strain SM1970
T
, was isolated from a seawater sample collected from the Mariana Trench. ...Strain SM1970
T
grew at 15-37
o
C and with 1–5% (w/v) NaCl. It hydrolyzed colloidal chitin, agar and casein but did not reduce nitrate to nitrite. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1970
T
formed a distinct lineage close to the genus
Catenovulum
within the family
Alteromonadaceae
, sharing the highest sequence similarity (93.6%) with type strain of
Catenovulum maritimum
but < 93.0% sequence similarity with those of other known species in the class
Gammaproteobacteria.
The major fatty acids of strain SM1970
T
were summed feature 3 (C
16: 1
ω
7
c
and/or C
16: 1
ω
6
c
), C
16: 0
and summed feature 8 (C
18: 1
ω
7
c
and/or C
18: 1
ω
6
c
). The major polar lipids of the strain included phosphatidylethanolamine and phosphatidylglycerol and its main respiratory quinone was ubiquinone 8. The draft genome of strain SM1970
T
consisted of 77 scaffolds and was 4,172,146 bp in length, containing a complete set of genes for chitin degradation. The average amino acid identity (AAI) values between SM1970
T
and type strains of known
Catenovulum
species were 56.6–57.1% while the percentage of conserved proteins (POCP) values between them were 28.5–31.5%. The genomic DNA G + C content of strain SM1970
T
was 40.1 mol%. On the basis of the polyphasic analysis, strain SM1970
T
is considered to represent a novel species in a novel genus of the family
Alteromonadaceae
, for which the name
Marinifaba aquimaris
is proposed with the type strain being SM1970
T
(= MCCC 1K04323
T
= KCTC 72844
T
).
PDF
