Caldomycin, a new guanidopolyamine produced by a novel agmatine homocoupling enzyme involved in homospermidine biosynthesis

An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus. Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus. The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus. Furthermore, it is shown that caldomycin is a novel compound existing in nature.

ThermusQ: Toward the cell simulation platform for Thermus thermophilus

ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.

Isolation and genomic analysis of a type IV pili-independent Thermus thermophilus phage, φMN1 from a Japanese hot spring

A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a contractile tail, suggesting that φMN1 belonged to Myoviridae. An EM analysis focused on φMN1 adsorption to the Thermus host cell showed that the receptor molecules for the phage were uniformly distributed on the outer surface of the cells. The circular double-stranded DNA of φMN1 was 76,659 base pairs in length, and the guanine and cytosine content was 61.8%. It was predicted to contain 99 open reading frames, and its putative distal tail fiber protein, which is essential for non-piliated host cell surface receptor recognition, was dissimilar in terms of sequence and length with its counterpart in the type IV pili-dependent φYS40. A phage proteomic tree revealed that φMN1 and φYS40 are in the same cluster, but many genes had low sequence similarities and some seemed to be derived from both mesophilic and thermophilic organisms. The gene organization suggested that φMN1 evolved from a non-Thermus phage through large-scale recombination events of the genes determining the host specificity, followed by gradual evolution by recombination of both the thermophilic and mesophilic DNAs assimilated by the host Thermus cells. This newly isolated phage will provide evolutionary insights into thermophilic phages.

Thermus thermophilus polyploid cells directly imaged by X-ray laser diffraction

Thermus thermophilus is reportedly polyploid and carries four to five identical genome copies per cell, based on molecular biological experiments. To directly detect polyploidy in this bacterium, we performed live cell imaging by X-ray free-electron laser (XFEL) diffraction and observed its internal structures. The use of femtosecond XFEL pulses enables snapshots of live, undamaged cells. For successful XFEL imaging, we developed a bacterial culture method using a starch- and casein-rich medium that produces a predominance of rod-shaped cells shorter than the focused XFEL beam size, which is slightly smaller than 2 µm. When cultured in the developed medium, the length of T. thermophilus cells, which is typically ~4 µm, was less than half its usual length. We placed living cells in a micro-liquid enclosure array and successively exposed each enclosure to a single XFEL pulse. A cell image was successfully obtained by the coherent diffractive imaging technique with iterative phase retrieval calculations. The reconstructed cell image revealed five peaks, which are most likely to be nucleoids, arranged in a row in the polyploid cell without gaps. This study demonstrates that XFELs offer a novel approach for visualizing the internal nanostructures of living, micrometer-sized, polyploid bacterial cells.

A new metabolic pathway for sym-homospermidine synthesis in an extreme thermophile, Thermus thermophilus

In an extreme thermophile, Thermus thermophilus, sym-homospermidine is synthesized by the actions of two enzymes. The first enzyme coded by dhs gene (annotated to be deoxyhypusine synthase gene) catalyzes synthesis of an intermediate, supposed to be 1,9-bis(guanidino)-5-aza-nonane (=N1, N11-bis(amidino)-sym-homospermidine), from two molecules of agmatine in the presence of NAD. The second enzyme (aminopropylagmatinase) coded by speB gene catalyzes hydrolysis of the intermediate compound to sym-homospermidine releasing two molecules of urea.

Putrescine Biosynthesis from Agmatine by Arginase (TtARG) in Thermus thermophilus

In the three domains of life, three biosynthetic pathways are known for putrescine. The first route is conversion of ornithine to putrescine by ornithine decarboxylase (ODC: SpeC), the second route is the conversion of arginine to agmatine by arginine decarboxylase (ADC: SpeA), followed by the conversion of agmatine to putrescine by agmatine ureohydrolase (AUH: SpeB), and the third route is the conversion of agmatine to N-carbamoylputrescine by agmatine deiminase (agmatine iminohydrolase, AIH), followed by the conversion of N-carbamoylputrescine to putrescine by N-carbamoylputrescine amidohydrolase (NCPAH). An extreme thermophile, Thermus thermophilus produces putrescine, although this bacterium lacks homologs for putrescine synthesizing pathways such as ODC, AUH, AIH and NCPAH. To identify genes involved in putrescine biosynthesis in T. thermophilus, putrescine biosynthesis was examined by disruption of a predicted gene for agmatinase (agmatine ureohydrolase), or by using purified enzyme. It was found that arginase (TTHA1496) showed an agmatinase activity utilizing agmatine as a substrate. These results indicate that this bacterium can use arginase for putrescine biosynthesis. Arginase is a major contributor to putrescine biosynthesis under physiological conditions. The presence of an alternative pathway for converting agmatine into putrescine is functionally important for polyamine metabolism supporting survival at extreme environments.

Polyamines produced by an extreme thermophile are essential for cell growth at high temperature

An extreme thermophile, Thermus thermophilus grows at an optimum temperature of around 70 oC and produces 16 different polyamines including long-chain and branched-chain polyamines. We found that the composition of polyamines in the thermophile cells changes with culture temperature. Long-chain and branched-chain polyamines (unusual polyamines) were increased in the cells grown at high temperature such as 80 oC, but they were minor components in the cells grown at relatively lower temperature such as 60 oC. The effects of polyamines on cell growth were studied using T. thermophilus HB8 ΔspeA deficient in arginine decarboxylase. Cell growth of this mutant strain was significantly decreased at 70 oC. This mutant strain cannot produce polyamines and grows poorly at 75 oC. It was also determined whether polyamines are directly involved in protecting DNA from DNA double-strand breaks induced by heat. Polyamines protected DNA against double-strand breaks. Therefore, polyamines play essential roles in cell growth at extremely high temperature through maintaining a functional conformation of DNA against DNA double-strand breaks and depurination.

Application and outcomes of a standardized lymphadenectomy in laparoscopic right hemicolectomy requiring ligation of the middle colic artery

BACKGROUND

Complete mesocolic excision with central vessel ligation may be important for accurate staging and improving the prognosis of right-sided colon cancer. Although the procedure is often performed laparoscopically, approaching the middle colic artery (MCA) is technically demanding, especially when complete ligation of arteries at their roots is desired. We standardized our laparoscopic approach by establishing the dissection boundary along the superior mesenteric artery to achieve D3 lymphadenectomy in the region of the MCA. The aim of the present study was to evaluate, on the basis of perioperative and short-term oncologic outcomes, the feasibility and safety of our technique METHODS: We conducted a retrospective study on consecutive patients with cancer located at the ascending colon and transverse colon who had laparoscopic right hemicolectomy requiring ligation of the MCA.

RESULTS

There were 41 patients (22 males, median age 71 years [range 49-86] years). The median operation time was 285 min, and blood loss volume was 40 mL. Conversion to open surgery was required in 1 case. Complications that were Clavien-Dindo grade III or above occurred in 3 patients (7.3%). There was no anastomotic leakage. The median number of lymph nodes harvested was 46.

CONCLUSIONS

Our technique was shown to be a safe, feasible, and useful strategy for performance of right hemicolectomy requiring ligation of the MCA in cases of colon cancer. The technique facilitates maximal lymph node dissection. Having obtained favorable outcomes, we look forward to investigation into long-term outcomes.

Uninterrupted twice-daily direct oral anticoagulants are safer than once-daily ones for atrial fibrillation catheter ablation

Background

In patients undergoing AF catheter ablation (CA), uninterpreted DOACs reduced bleeding events without increasing ischemic events compared with vitamin K antagonist, and the continuation of anticoagulants is recommended for AF ablation. However, in the past studies, patients received once-daily DOACs in the evening, not in the morning of the procedure day. Moreover, there has been no study comparing uninterrupted 4 DOACs; therefore, the safety and effect of uninterpreted DOACs taken just in the morning of AF ablation is unknown.

Objective

The purpose of this study was to compare bleeding complications and thromboembolism events between 4 DOACs in patients undergoing AF ablation.

Method

This study was the retrospective single-center cohort study of consecutive patients who underwent AF ablation between April 2014 to July 2019. All patients continued DOAC uninterruptedly including just in the morning of the procedure. The primary endpoint included major bleeding events within the first 30 days after CA. The secondary endpoints included the composite events of ischemic stroke, systemic embolism, myocardial infarction, and vascular death.

Result

A total of 713 patients (mean age 64±12 years, 72% male) were included in this analysis; enrolled patients were 88, 238, 218, and 169 respectively in dabigatran, rivaroxaban, apixaban and edoxaban group. At the baseline, the ratio of age ≥75 years and CHADS2 score was higher in apixaban group, though all other baseline variables were similar between them.

The primary endpoint was observed 0%, 2.1%, 0.45%, and 4.7% respectively in dabigatran, rivaroxaban, apixaban, and edoxaban group (P=0.013) without significant difference about secondary endpoint between them (P=0.3).

Comparing twice-daily vs once-daily DOACs, the primary endpoint was observed significantly lower in the twice-daily group than in once-daily group (0.32% and 3.2% respectively, P=0.0054), without any significant difference about secondary endpoint (0% and 0.73% respectively, P=0.26).

Conclusion

Taking DOACs also in the morning of AF ablation, uninterrupted twice-daily DOACs are safer than once-daily DOACs without increasing ischemic event, although twice-daily DOACs, especially apixaban, were used in higher aged patients.

Figure 1

Funding Acknowledgement

Type of funding source: None

Micro-liquid enclosure array and its semi-automated assembling system for x-ray free-electron laser diffractive imaging of samples in solution

We developed micro-liquid enclosure arrays (MLEAs) for holding solution samples in coherent diffractive imaging (CDI) using x-ray free-electron lasers (XFELs). Hundreds of fully isolated micro-liquid enclosures are arranged in a single MLEA chip for efficient measurement, where each enclosure is destroyed after exposure to a single XFEL pulse. A semi-automated MLEA assembling system was also developed to enclose solution samples into MLEAs efficiently at high precision. We performed XFEL-based CDI experiments using MLEAs and imaged in-solution structures of self-assembled gold nanoparticles. The sample hit rate can be optimized by adjusting solution concentration, and we achieved a single-particle hit rate of 31%, which is not far from the theoretical upper limit of 37% derived from the Poisson statistics. MELAs allow us to perform CDI measurement under controlled solution conditions and will help reveal the nanostructures and dynamics of particles in solution.

Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (k_cat/K_m) of TTHA1643 toward d- and l-Glu was comparable; however, the k_cat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.

Atacama sub-millimeter telescope experiment polarimeter (APol) I: design and lab-test result: publisher's note

This publisher's note corrects errors in the author affiliations, abstract and the Funding sections in Appl. Opt.59, 2593 (2020).APOPAI0003-693510.1364/AO.378008.

Atacama sub-millimeter telescope experiment polarimeter (APol) I: design and lab-test result

In this paper, the Atacama Submillimeter Telescope Experiment (ASTE) is presented. A 10-m aperture telescope hosts a camera equipped with a transition edge sensor (TES). We developed a fore-optics module-"APol," to convert the 271 pixels of the TES working at 350 GHz into a sensitive imaging polarimeter without sacrificing the image quality and the ${7.5}^\prime$7.5^' field of view. Here, we describe the detailed optical design of APol and present the results of the preliminary test in a laboratory.

P1354 Prognostic value of the left ventricular longitudinal and circumferential function in patients with takotsubo syndrome during the acute phase

Background

Takotsubo syndrome is generally considered a benign disease with a reversible condition; however, hemodynamic and electrical instability during the acute phase exposes patients to the risk of serious adverse in-hospital events. The purpose of this study was to investigate the prognostic value of the left ventricular longitudinal and circumferential function in patients with TTS during the acute phase.

Methods

We divided the 27 patients with TTS (77.4 ± 10.2 years old, 21 females) into two groups; the severe group (SG) of 9 patients (in-hospital death, mechanical assist devices such as IABP or ECMO, oozing rupture) and non-severe group (NSG) of 18 patients. The echocardiographic examination on admission, catheter hemodynamic assessment, and laboratory data, and ST-T change in electrocardiogram were compared between two groups.

Results

There were no differences in age, laboratory data, electrocardiogram findings between the two groups. The LVEF was lower in SG (35.3 ± 6.1% vs. 45.9 ± 13.5%, p = 0.03). The index of Ballooning, the ratio of the systolic left ventricular diameter of ballooning segments to that of basal segments, was higher in SG (2.07 ± 0.61% vs.1.60 ± 0.32%, p = 0.016). The circumferential fractional shortening (CFS) of ballooning segments was lower in SG (4.6 ± 3.2% vs. 18.2 ± 8.2%, p = 0.00007), CFS of basal segments was not different between the two groups, and the ratio of CFS of ballooning segments to CFS of basal segments (CFS imbalance index) was lower in SG (5.60 ± 3.84 vs. 10.83 ± 3.92, p = 0.00003). The left ventricular longitudinal fractional shortening was lower in SG (0.12 ± 0.09 vs. 0.46 ± 0.19, p = 0.00003). The absolute value of GLS was lower in SG (7.6 ± 4.3% vs. 13.0 ± 3.6%, p = 0.002). In all three cases of in-hospital death, the CFS imbalance index was lower than 0.14.

Conclusion

In patients with TTS, left ventricular longitudinal and circumferential function could be related to serious adverse in-hospital events.

Design of a liquid cell toward three-dimensional imaging of unidirectionally-aligned particles in solution using X-ray free-electron lasers

A liquid cell was designed for coherent diffractive imaging measurements at high tilt angles and tested at SACLA.

Mucin expression in gastric- and gastro-oesophageal signet-ring cell cancer: results from a comprehensive literature review and a large cohort study of Caucasian and Asian gastric cancer

BACKGROUND

The literature on the prognostic relevance of signet-ring cell (SRC) histology in gastric cancer (GC) is controversial which is most likely related to inconsistent SRC classification based on haematoxylin-eosin staining. We hypothesised that mucin stains can consistently identify SRC-GC and predict GC patient outcome.

METHODS

We performed a comprehensive literature review on mucin stains in SRC-GC and characterised the mucin expression in 851 Caucasian GC and 410 Asian GC using Alcian Blue (AB)-Periodic Acid-Schiff (PAS), MUC2 (intestinal-type mucin), and MUC5AC (gastric-type mucin). The relationship between mucin expression and histological phenotype [poorly cohesive (PC) including proportion of SRCs, non-poorly cohesive (non-PC), or mucinous (MC)], clinicopathological variables, and patient outcome was analysed.

RESULTS

Depending on mucin expression and cut-offs, the positivity rates of SRC-GC reported in the literature varied from 6 to 100%. Patients with MUC2 positive SRC-GC or SRC-GC with (gastro)intestinal phenotype had poorest outcome. In our cohort study, PC with ≥ 10% SRCs expressed more frequently MUC2, MUC5AC, and ABPAS (p < 0.001, p = 0.004 and p < 0.001, respectively). Caucasians with AB positive GC or combined ABPAS-MUC2 positive and MUC5AC negative had poorest outcome (all p = 0.002). This association was not seen in Asian patients.

CONCLUSIONS

This is the first study to suggest that mucin stains do not help to differentiate between SRC-GC and non-SRC-GC. However, mucin stains appear to be able to identify GC patients with different outcome. To our surprise, the relationship between outcome and mucin expression seems to differ between Caucasian and Asian GC patients which warrants further investigations.

P1959Impact of hemodialysis in patients undergoing bypass surgery for peripheral arterial disease - 10-year follow-up study

Background

Although lower extremities bypass surgery has been commonly performed as the standard option to treat peripheral artery disease (PAD) even in patients on hemodialysis (HD) as well as general population, poorer prognosis still remains major problems in this specific population. In this 10-year follow-up study, we investigated the impact of HD after surgical revascularization in patients with PAD.

Methods

A total of 660 patients undergoing successfully bypass surgery were enrolled. Patients with acute limb ischemia were excluded. We compared 392 HD patients with 428 limbs and 268 non-HD (NHD) patients with 296 limbs during 10 years follow-up period. Primary endpoint was defined as major adverse cardiovascular events (MACE) including all-cause death, non-fatal myocardial infarction and stroke. Second endpoint was major adverse limb events (MALE) including any revascularization and major amputation. To minimize the differences of clinical characteristics between the two groups, propensity score adjusting with all baseline variables was performed.

Results

Prevalence of diabetes (53.3% vs. 35.2%), critical limb ischemia (77.5% vs. 52.1%) and infra-popliteal artery (48.2% vs. 19.6%) were higher in HD group compared to NHD group (p<0.0001 in all), inversely, age was younger in HD group than in NHD group (67±9 years vs. 71±9 years, p<0.0001). The 30-day mortality rate was comparable (3.1% in HD group vs. 1.5% in NHD group, p=0.19). The 10-year event-free survival rate for MACE was significantly lower in HD group compared to NHD group (45.3% vs. 67.4%, p<0.0001) and for MALE (60.0% vs. 80.0%, p=0.0007), respectively. After propensity score adjustment, the freedom rate from MACE was still lower in HD group compared to NHD group [45.6% vs. 67.6%, hazard ratio (HR) 1.89, 95% confidence interval (CI) 1.33–2.72, p=0.0003], however, the rate from MALE was statistically comparable between the two group (65.7% vs. 76.9%, 1.27, 95% CI 0.87–1.90, p=0.21). Furthermore, although the 10-year limb salvage rate was crudely lower in HD group compared to NHD group (80.6% vs. 91.6%, HR 1.57, 95% CI 1.05–2.40, p=0.0027), it was comparable after propensity score adjustment (89.4% vs. 90.1%, HR 1.09, 95% CI 0.59–1.88, p=0.79). Also, the mortality rate was consistently lower in HD patients (adjusted HR 2.37, 95% CI 1.62–3.50, p<0.0001).

Conclusion

The long-term freedom rate from MACE and mortality was markedly lower in HD patients compared to non-HD patients. However, the rate from MALE, especially limb salvage rate was similar between HD and NHD after adjustment for clinical characteristics. These results suggest that detection at the early stage of PAD may potentially improve the poor outcomes in this high risk population.

P1582Prognostic value of C-reactive protein/albumin ratio for cardiovascular morbidity and mortality in end-stage renal disease patients with incident haemodialysis therapy

Background

Hypoalbuminemia, a manifestation of protein-energy wasting or malnutrition, is commonly observed in patients with end-stage renal disease (ESRD), and is associated with chronic inflammation and increasing cardiovascular (CV) risk. Recently, C-reactive protein (CRP)/albumin ratio at discharge is reportedly a well-predictor of mortality in severe sepsis or cancer patients.

We investigated prognostic value of the CRP/albumin ratio at just starting haemodialysis (HD) therapy for CV morbidity and mortality in patients with ESRD.

Methods

A total of 1,548 ESRD patients were enrolled and were divided into quartiles according to CRP/albumin levels at initiation of HD; quartile 1 (Q1): <0.22, Q2: 0.23–0.54, Q3: 0.55–1.83 and Q4: >1.84. They were followed up for 10-year after starting HD therapy. Primary endpoint was CV events defined as hospitalization due to CV events such as cardiac disease, stroke and peripheral artery disease and CV death. We also evaluated the incremental value with C-index when CRP alone, albumin alone and the CRP/albumin ratio were added into a model with established risk factors.

Results

During follow-up period (median: 59 months), 512 cases experienced CV events (33.1%) including 165 cases of CV deaths (10.7%). Kaplan-Meier analysis shows that CV event-free survival rates for 10 years were 63.5%, 53.8%, 47.5% and 31.9% in Q1, Q2, Q3 and Q4, and that CV survival rates were 90.4%, 83.9%, 77.2% and 64.6% in Q1, Q2, Q3 and Q4, respectively (p<0.0001 in both). After adjustment for all baseline variables, elevated CRP/albumin ratio was identified as an independent predictor for CV events [hazard ratio (HR) 1.51, 95% confidence interval (CI) 1.11–2.07, p=0.0093 for Q2 vs. Q1, HR 1.79, 95% CI 1.33–2.42, p<0.0001 for Q3 vs. Q1and HR 2.27, 95% CI 1.70–3.07, p<0.0001 for Q4 vs. Q1, respectively]. As to CV mortality, similar results were obtained (HR 1.80, 95% CI 0.98–3.44, p=0.056 for Q2 vs. Q1, HR 2.56, 95% CI 1.45–4.71, p=0.0009 for Q3 vs. Q1 and HR 2.66, 95% CI 1.53–4.86, p=0.0004 for Q4 vs. Q1, respectively). Furthermore, adding the CRP/albumin ratio to a baseline model with established risk factors improved the C-index greater than that of CRP alone or albumin alone, respectively (0.715 from 0.692, p=0.0095 and from 0.683, p=0.0019)

Conclusion

The CRP/albumin ratio, which easily available from daily practice, could strongly stratify the risk of future CV morbidity and mortality in ESRD patients who need HD therapy.