GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data

MOTIVATION

Motivated by the challenges of decentralized genetic data spread across multiple international organizations, GINSA leverages the Global Biodiversity Information Facility infrastructure to automatically retrieve and link small ribosomal subunit sequences with locality information.

RESULTS

Testing on taxa from major organism groups demonstrates broad applicability across taxonomic levels and dataset sizes.

AVAILABILITY AND IMPLEMENTATION

GINSA is a freely accessible Python program under the MIT License and can be installed from PyPI via pip.

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity

The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.

Potential application of the haematology analyser XN-31 prototype for field malaria surveillance in Kenya

Background

Simple and accurate diagnosis is a key component of malaria control programmes. Microscopy is the current gold standard, however it requires extensive training and the results largely rely on the skill of the microscopists. Malaria rapid diagnostic tests (RDT) can be performed with minimal training and offer timely diagnosis, but results are not quantitative. Moreover, some Plasmodium falciparum parasites have evolved and can no longer be detected by existing RDT. Developed by the Sysmex Corporation, the XN-31 prototype (XN-31p) is an automated haematology analyser capable of detecting Plasmodium-infected erythrocytes and providing species differentiation and stage specific parasite counts in venous blood samples without any preparation in approximately one minute. However, factors such as stable electricity supply in a temperature-controlled room, cost of the instrument and its initial set-up, and need for proprietary reagents limit the utility of the XN-31p across rural settings. To overcome some of these limitations, a hub and spoke diagnosis model was designed, in which peripheral health facilities were linked to a central hospital where detection of Plasmodium infections by the XN-31p would take place. To explore the feasibility of this concept, the applicability of capillary blood samples with the XN-31p was evaluated with respect to the effect of sample storage time and temperature on the stability of results.

Methods

Paired capillary and venous blood samples were collected from 169 malaria-suspected outpatients in Homa Bay County Referral Hospital, Kenya. Malaria infections were diagnosed with the XN-31p, microscopy, RDT, and PCR. Capillary blood samples were remeasured on the XN-31p after 24 h of storage at either room (15–25 °C) or chilled temperatures (2–8 °C).

Results

Identical results in malaria diagnosis were observed between venous and capillary blood samples processed immediately after collection with the XN-31p. Relative to PCR, the sensitivity and specificity of the XN-31p with capillary blood samples were 0.857 and 1.000, respectively. Short-term storage of capillary blood samples at chilled temperatures had no adverse impact on parasitaemia and complete blood counts (CBC) measured by the XN-31p.

Conclusion

These results demonstrate the potential of the XN-31p to improve routine malaria diagnosis across remote settings using a hub and spoke model.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-022-04259-7.

A bolus of saline injection leads to increase in coronary flow based on the viscosity reduction effect: the mechanism of saline induced Pd/Pa ratio

Background

In conjunction with fractional flow reserve (FFR), our previous study has shown the accuracy and utility of saline induced Pd/Pa ratio (SPR) for the assessment of myocardial ischemia. However, the potential mechanism how saline injection leads to increase in coronary flow remains speculative.

Purpose

This study aimed to clarify the underlying mechanism of SPR by using swine models.

Methods

The study was conducted in four swine models, and bolus of 25°C saline, 40°C saline, and 25°C dextran was injected at rates of 40mL/5sec through a catheter inserted into the superior mesenteric artery. Its peripheral arterioles were observed and recorded by a digital microscope, and transit time of each fluid and a luminal diameter of arterioles before and after injection were measured.

Results

The result from arterioles diameters of pre- and post-injection (0.049±0.016mm vs. 0.050±0.016mm; P=0.636) indicated that luminal diameters remained unchanged regardless of fluid administration. The transit time of 25°C saline was significantly shorter than 25°C dextran (3.19±0.68sec vs. 6.15±1.19sec; P<0.0001). Although the result showed no significance, the transit time of 40°C saline with lower viscosity was shorten compared to 25°C saline (3.1±0.43sec vs. 3.65±0.46sec; P=0.088).

Conclusions

Compared to 25°C dextran (viscosity of 4.991mPa·s) having the same viscosity as 37°C whole blood, 25°C saline (viscosity of 1.012mPa·s) caused increasing to double the intravascular flow volume without dilating arterioles. The results strongly suggested that the potential mechanism of SPR was viscosity reduction effect. Combined with FFR which is based on vasodilation-mediated hyperemia, these findings may contribute to clarifying the pathophysiology and especially the microcirculation in coronary artery diseases.

Funding Acknowledgement

Type of funding source: None

The developing mechanism of atherosclerotic lesion in coronary side branch on the ventricular free wall differs by the location of lesion

Background

The effective treating method of coronary side branch lesions such as ostial stenosis or thin arteries has not been established. On the other hand, tortuous side branch rarely has stenotic lesions.

Purpose

We focused on coronary side branches on the ventricular free wall, and examined coronary risk factors and bending and stretching motion of branch which can contribute to the development of atherosclerotic lesion.

Methods

In elective and first-time coronary angiograms, we included side branches on the ventricular free wall (>2mm in diameter) and excluded previously treated ones. Study A; we divided arteries into proximal, middle, and distal segment, and examined the presence of tortuosity and stenotic lesions exceeding 50% diameter stenosis (DS) for each segment. A score of 1 was assigned to tortuous segment, and 0 to non-tortuous one. Study B; we included stenotic lesion (>50% DS) in side branch ostium and excluded those extended across main coronary arteries. Relation between lesions and patients' characteristics was examined.

Results

Study A; in 1,828 side branches from 472 patients, middle and distal segments had significantly higher tortuosity score than proximal (0.68, 0.78 vs. 0.34; p<0.0001). On the contrary, proximal segments had more stenotic lesions except ostial stenosis (230 vs. 69, 5; p<0.0001). Study B; in 1,740 side branches from 465 patients, 122 ostial stenotic lesions were found (7.0%). Multivariate logistic regression analysis revealed diabetes mellitus and age as independent contributors to development of ostial stenosis (Table).

Conclusions

Side branch stenosis developed less frequently in middle and distal segments, where stronger ventricular wall motion reinforces bending and stretching motion and tortuosity of arteries. This fact indicates that those characteristics may prevent developing atherosclerosis through increasing shear stress. On the other hand, diabetes mellitus strongly contributes to the development of ostial stenosis. Thus, the developing mechanism of atherosclerotic lesion in side branch on the ventricular free wall differs by the location of lesion.

Funding Acknowledgement

Type of funding source: None

Effectiveness of Preceding Solo Kidney Transplantation for Type 1 Diabetes With End-Stage Renal Failure

Preceding solo kidney transplantation for type 1 diabetes with end-stage renal failure is controversial because of less pancreatic graft survival in pancreas transplantation after kidney transplantation (PAK) than in simultaneous pancreas and kidney transplantation (SPK).

METHODS

To study the effectiveness of preceding solo kidney transplantation for type 1 diabetes with end-stage renal failure, comparative retrospective analysis was performed between SPK (n = 232) and PAK (n = 39) that were performed until December 2016.

RESULTS

At 1, 3, and 5 years, pancreatic graft survival in SPK was 87.5%, 86.4%, and 82.8%, respectively, and 87.1%, 65.0%, and 49.1%, respectively, in PAK, which showed lesser long-term graft survival than SPK. Because 10 cases out of 16 (62.5%) failed into pancreatic graft loss with rejection in PAK, which was about 3 times more than in SPK, control of rejection is very important; rejection episodes were decreased by rabbit antithymocyte globulin induction resulting in improved graft survival. Five-year patient survival was 88.0% in SPK and 96.6% in PAK.

CONCLUSION

Considering patient survival, preceding solo kidney transplantation for type 1 diabetes with end-stage renal failure should be performed if a donor is available.

Laparoscopy-Assisted Spleen-Preserving Distal Pancreatectomy for Living-Donor Pancreas Transplantation

BACKGROUND

Living pancreas transplantation plays an important role in the treatment of patients with severe type 1 diabetes. However, pancreatectomy is very invasive for the donor, and less-invasive surgical procedures are needed. Although some reports have described hand-assisted laparoscopic surgery for distal pancreatectomy in living-donor operations, less-invasive laparoscopy-assisted (LA) procedures are expected to increase the donor pool. We herein report the outcomes of four cases of LA spleen-preserving distal pancreatectomy (Warshaw technique [WT]) in living pancreas donors.

PATIENTS AND METHODS

Four living pancreas donors underwent LA-WT at our institution from September 2010 to January 2013. All donors fulfilled the donor criteria established by the Japan Society for Pancreas and Islet Transplantation.

RESULTS

The median donor age was 54 years. Two donors underwent left nephrectomy in addition to LA-WT for simultaneous pancreas-kidney transplantation. The median donor operation time for pancreatectomy was 340.5 minutes. The median pancreas warm ischemic time was 3 minutes. The median donor blood loss was 246 g. All recipients immediately achieved insulin independence. One donor required reoperation because of obstructive ileus resulting from a port-site hernia. Another donor developed a pancreatic fistula (International Study Group of Pancreatic Fistula grade B), which was controlled with conservative management. After a maximum follow-up of 73 months, no clinically relevant adverse events had occurred. These results were comparable with those of previous studies concerning living-donor pancreas transplantation.

CONCLUSION

The LA-WT is a safe and acceptable operation for living-donor pancreas transplantation.

Outcome of renal transplantation in patients with type 2 diabetic nephropathy: a single-center experience

BACKGROUND

Renal transplantation has been established as a treatment for end-stage renal disease (ESRD) due to diabetic nephropathy. However, few studies have focused on the outcome after renal transplantation in patients with ESRD and type 2 diabetic nephropathy. To investigate the effect of renal transplantation on ESRD with type 2 diabetic nephropathy, we retrospectively analyzed patients who received renal transplantation at our facility. This study aimed to compare the outcome of renal transplantation for type 2 diabetic nephropathy with that for nondiabetic nephropathy.

METHODS

We studied 290 adult patients, including 65 with type 2 diabetic nephropathy (DM group) and 225 with nondiabetic nephropathy (NDM group), who underwent living-donor renal transplantation at our facility from February 2008 to March 2013. We compared the 2 groups retrospectively.

RESULTS

In the DM and NDM groups, the 5-year patient survival rates were 96.6% and 98.7%, and the 5-year graft survival rates were 96.8% and 98.0%, respectively, with no significant differences between the groups. There were no significant differences in the rates of surgical complications, rejection, and infection. The cumulative incidence of postoperative cardiovascular events was higher in the DM group than in the NDM group (8.5% vs 0.49% at 5 years; P = .002).

CONCLUSIONS

Patient and graft survival rates after renal transplantation for type 2 diabetic nephropathy are not inferior to those for recipients without diabetic nephropathy. Considering the poor prognosis of patients with diabetic nephropathy on dialysis, renal transplantation can provide significant benefits for these patients.

Impact of flow cytometry crossmatch B-cell positivity on living renal transplantation

BACKGROUND

Various studies have reported poorer graft survival among individuals displaying T-cell-positive flow cytometry crossmatches (FCXM). Good outcomes have been observed in immunologically high-risk patients with the use of rituximab, plasmapheresis, and γ-globulin. Because the relevance of FCXM B-cell-positivity (BCXM (+)) alone remains controversial, we examined its impact on living donor renal transplantations.

PATIENTS AND METHODS

We retrospectively studied 146 adult renal transplantation recipients from April 2007 to June 2012, dividing the patients into BCXM (+) (n = 31) versus BCXM (-) recipients (n = 115). We examined patient and graft survivals as well as rejection rates at 0 to 3, 3 to 12, and 12 to 24 months. We also determined the incidence of infectious diseases. We performed stepwise multivariate regression to identify risk factors contributing rejection episodes.

RESULTS

One-year patient and graft survivals were 100% in both groups. The BCXM (-) group have a 16.8% rejection probability whereas the BCXM (+) group, 33.2% (P = .201). There were no significantly differences in the incidence of infectious diseases. Only the rate of a sensitizing history was an independent risk factor for a rejection episode.

CONCLUSION

BCXM (+) showed only a tendency but not a significant impact on rejection episodes compared with BCXM (-); short-term graft survivals were similar.

Decontamination of outdoor school swimming pools in Fukushima after the nuclear accident in March 2011

Because of radioactive fallout resulting from the Fukushima Daiichi Nuclear Power Plant (NPP) accident, water discharge from many outdoor swimming pools in Fukushima was suspended out of concern that radiocesium in the pool water would flow into farmlands. The Japan Atomic Energy Agency has reviewed the existing flocculation method for decontaminating pool water and established a practical decontamination method by demonstrating the process at eight pools in Fukushima. In this method, zeolite powder and a flocculant are used for capturing radiocesium present in pool water. The supernatant is discharged if the radiocesium concentration is less than the targeted level. The radioactive residue is collected and stored in a temporary storage space. Radioactivity concentration in water is measured with a NaI(Tl) or Ge detector installed near the pool. The demonstration results showed that the pool water in which the radiocesium concentration was more than a few hundred Bq L was readily purified by the method, and the radiocesium concentration was reduced to less than 100 Bq L. The ambient dose rates around the temporary storage space were slightly elevated; however, the total increase was up to 30% of the background dose rates when the residue was shielded with sandbags.

Immunogenicity of repeated Sendai viral vector vaccination in macaques

Induction of durable cellular immune responses by vaccination is an important strategy for the control of persistent pathogen infection. Viral vectors are promising vaccine tools for eliciting antigen-specific T-cell responses. Repeated vaccination may contribute to durable memory T-cell induction, but anti-vector antibodies could be an obstacle to its efficacy. We previously developed a Sendai virus (SeV) vector vaccine and showed the potential of this vector for efficient T-cell induction in macaques. Here, we examined whether repeated SeV vector vaccination with short intervals can enhance antigen-specific CD8(+) T-cell responses. Four rhesus macaques possessing the MHC-I haplotype 90-120-Ia were immunized three times with intervals of three weeks. For the vaccination, we used replication-defective F-deleted SeV vectors inducing CD8(+) T-cell responses specific for simian immunodeficiency virus Gag(206-216) and Gag(241-249), which are dominant epitopes restricted by 90-120-Ia-derived MHC-I molecules. All four animals showed higher Gag(206-216)-specific and Gag(241-249)-specific CD8(+) T-cell responses after the third vaccination than those after the first vaccination, indicating enhancement of antigen-specific CD8(+) T-cell responses by the second/third SeV vector vaccination even with short intervals. These results suggest that repeated SeV vector vaccination can contribute to induction of efficient and durable T-cell responses.

Laparoscopic splenectomy using pneumoperitoneum or gasless abdominal wall lifting: a 15-year single institution experience

INTRODUCTION

Laparoscopic splenectomy using pneumoperitoneum has been performed since 1992. The gasless abdominal wall-lifting method for laparoscopic splenectomy was introduced as an alternative. This retrospective study was undertaken to compare results using the two techniques.

METHODS

Between 1995 and 2010, 54 patients underwent laparoscopic splenectomy at a single institution; 30 underwent the procedure using the gasless technique and 24 using pneumoperitoneum. There were no significant differences between the two groups regarding age, sex or BMI, but more patients underwent concurrent operations in the pneumoperitoneum group. The abdominal wall-lift system with subcutaneous K-wires was used for the gasless method.

RESULTS

Intraoperative blood loss was similar in the two groups (193.0 ± 196.7 mL gasless, 217.3 ± 296.6 mL pneumoperitoneum; P > 0.05), but operative time (182.1 ± 92.1 min, 135.1 ± 46.1 min; P < 0.05), and resected spleen weight (306.1 ± 297.7 g, 138 ± 81.0 g; P < 0.05) were significantly different. In the gasless group, additional procedures included conversion (n = 1), mini-laparotomy (n = 2), and CO(2) insufflation (n = 2). Excluding the concurrent living-related kidney donor patients, hospital stay was similar (6.9 ± 2.5 days, 6.3 ± 2.0 days, P > 0.05).

CONCLUSION

Although gasless laparoscopic splenectomy is feasible, there are disadvantages, particularly the restricted operative working space in some patients. These results suggest that either technique may be used on an individual basis in patients undergoing laparoscopic splenectomy.

Intranasal Sendai viral vector vaccination is more immunogenic than intramuscular under pre-existing anti-vector antibodies

Viral vectors are promising vaccine tools for eliciting potent cellular immune responses. Pre-existing anti-vector antibodies, however, can be an obstacle to their clinical use in humans. We previously developed a Sendai virus (SeV) vector vaccine and showed the potential of this vector for efficient CD8(+) T-cell induction in macaques. Here, we investigated the immunogenicity of SeV vector vaccination in the presence of anti-SeV antibodies. We compared antigen-specific CD8(+) T-cell responses after intranasal or intramuscular immunization with a lower dose (one-tenth of that in our previous studies) of SeV vector expressing simian immunodeficiency virus Gag antigen (SeV-Gag) between naive and pre-SeV-infected cynomolgus macaques. Intranasal SeV-Gag immunization efficiently elicited Gag-specific CD8(+) T-cell responses not only in naive but also in pre-SeV-infected animals. In contrast, intramuscular SeV-Gag immunization induced Gag-specific CD8(+) T-cell responses efficiently in naive but not in pre-SeV-infected animals. These results indicate that both intranasal and intramuscular SeV administrations are equivalently immunogenic in the absence of anti-SeV antibodies, whereas intranasal SeV vaccination is more immunogenic than intramuscular in the presence of anti-SeV antibodies. It is inferred from a recent report investigating the prevalence of anti-SeV antibodies in humans that SeV-specific neutralizing titers in more than 70% of people are no more than those at the SeV-Gag vaccination in pre-SeV-infected macaques in the present study. Taken together, this study implies the potential of intranasal SeV vector vaccination to induce CD8(+) T-cell responses even in humans, suggesting a rationale for proceeding to a vaccine clinical trial using this vector.

Effects of O2 Gas Addition on Diamond-Like Carbon Film Deposition

The role of 02 gas addition on the deposition of Diamond-like Carbon (DLC) film was studied for hard disk drive (HDD) media application. The influence of 02 gas mixing ratio on DLC film quality was investigated using the dc magnetron sputtering method with a solid graphite target and Ar, CH4 and 02 mixing gases. The 02 mixing ratio was varied between 0% and 50%. Film quality was evaluated using Raman spectroscopy and XPS. When 02 gas mixing ratio increased the peak in Raman spectra shifted gradually to higher wavenumbers and its bandwidth became narrower. This indicates graphite component increased in the DLC film. In addition, the lubricant coverage on oxygen-containing DLC was improved. Because adding oxygen increases the terminations of carbonyl group on DLC surface, this result suggests that the polar surface causes higher affinity for the lubricant

Whole-body FDG-PET/CT on rheumatoid arthritis of large joints

OBJECTIVE

Fluorodeoxyglucose (FDG) uptake in joint lesions in patients with rheumatoid arthritis (RA) reportedly represents the degree of synovial inflammation. Most previous studies have focused on small joints, and the application of whole-body positron emission tomography (PET) combined with computed tomography (CT) (PET/CT) for the evaluation of inflammatory activity in large joints has not been well studied.

METHODS

Eighteen patients with RA underwent FDG-PET/CT. FDG uptake in the knee, hip, carpal, wrist, elbow, shoulder, and atlanto-axial joint (total of 13 joints) and in the axillary lymph nodes was evaluated by calculating the maximum standardized uptake value (SUV(max)) and the visual uptake scores as follows: 0, no uptake; 1, slight uptake; 2, moderate uptake (same as in liver); 3, higher than in liver; 4, highest uptake. The number of painful/swollen joints, the white blood cell (WBC) count, and the C-reactive protein (CRP) level were also evaluated.

RESULTS

Whole-body FDG-PET/CT delineated large-joint lesions in patients with RA, and the metabolic activity of inflammation was accurately overlaid on the joint anatomy. The total FDG score for all 13 joints was significantly correlated with the CRP level (r = 0.653, p < 0.01, n = 18). The total SUV(max) and the CRP level were weakly, but not significantly, correlated (r = 0.377, p > 0.05). The WBC count was not correlated with any other parameter. The mean number of joints per patient with an FDG uptake score of 2 or more was significantly larger than the mean number of painful/swollen joints (6.2 +/- 3.3 vs. 3.1 +/- 2.7, n = 18, p < 0.01) and both parameters were strongly correlated (r = 0.588, p < 0.01, n = 18). Also, FDG uptake score and SUV of painful/swollen joints were significantly higher than these of not painful/swollen joints. FDG uptake was significantly different from patients of remission and patients of active arthritis. Uptake in the atlanto-axial joint was observed in five (mostly asymptomatic) patients (5/18, 28%), and the uptake score was significantly correlated with the total FDG score (r = 0.669, p < 0.01, n = 18). The axillary lymph nodes score was correlated with the arm joints score.

CONCLUSION

FDG-PET/CT represents the inflammatory activity in large joints in patients with RA accurately and sensitively and may be helpful for early evaluations of the extent of RA throughout the whole body including high risk lesion of atlanto-axial joint. Furthermore, the visual FDG uptake score may be useful for evaluating arthritis in large joints.

High resolution neutron protein crystallography. Hydrogen and hydration in proteins

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins, and the development of the neutron imaging plate (NIP) became a breakthrough event in neutron protein crystallography. The general features of the NIP are reviewed. A high resolution neutron diffractometer dedicated to biological macromolecules (BIX-3) with the NIP has been constructed at Japan Atomic Energy Research Institute and this has enabled 1.5 Å resolution structural analyses of several proteins to be carried out. The specifications of BIX-3 and LADI (a quasi-Laue type diffractometer installed in the Institut Laue-Langevin) are compared. The crystal structures of myoglobin, wild type rubredoxin and a mutant of rubredoxin have been carried out using BIX-3. From these studies, several topics, such as the location of hydrogen bonds and certain acidic hydrogen atoms, the identification of methyl hydrogen atoms, details of H/D exchange and dynamical behavior of hydration structures have been investigated, and important information has been extracted from the structural results. Finally, a systematic procedure to grow large single crystals of proteins or nucleic acids is described.

Fabrication and optical properties of Pb(Mg(1/3)Nb(2/3))O(3)-PbTiO(3) thin films on Si substrates using the PLD method

Epitaxial 0.67Pb(Mg(1/3)Nb(2/3))O(3)-PbTiO(3)-0.33PbTiO(3) (PMN-PT) thin films with electro-optic effects were fabricated on (PMN-PT) thin films with electro-optic effects were fabricated on (La0(0.5)Sr0(0.5))CoO(3) (LSCO)/CeO(2)/YSZ-buffered Si(001) substrates using double-pulse excitation pulsed laser deposition (PLD) method with a mask placed between the target and the substrate. Epitaxial growth of PMN-PT thin films was undertaken using the two-step growth method of PMN-PT film. The PMN-PT seed layer was deposited at 500 degrees C on the LSCO/CeO(2)/YSZ/Si, which temperature was the same as that used for LSCO deposition. The PMN-PT thin films were deposited on the PMN-PT seed layer at 600 degrees C, which enables growth of high-crystallinity PMN-PT films with smooth surfaces. We obtained optimum fabrication conditions of PMNPT film with micrometer-order thickness. Resultant films showed high crystallinity with full width at half maximum (FWHM) = 0.73 deg and 1.6 mum thickness. Electro-optic properties and the refractive index value were measured at 633 nm wavelength using the prism coupling method. The obtained refractive index was 2.59. The electro-optic coefficients r(13) and r(33) were determined by applying the electrical field between a semitransparent, thin top electrode of Pt and a bottom LSCO electrode. The electro-optic coefficient was r(13) = 17 pm/V at transverse electric field (TE) mode and r(33) = 55 pm/V at transverse magnetic field (TM) mode.