Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.

Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.

Identification of four genes responsible for antimicrobial resistance of MEL-B against S. aureus.

There is increasing interest in the antimicrobial activity of mannosylerythritol lipids-B (MEL-B) against Gram-positive bacteria such as Staphylococcus aureus (S. aureus). However, the specific molecules involved in MEL-B's antimicrobial action against S. aureus have not been identified. This study utilized the Nebraska transposon mutant library (NTML), which contains 1920 mutants, each lacking three-quarters of the genes found in S. aureus. The NTML was screened to identify mutants resistant to MEL-B. Four mutants (Accession Number: SAUSA300_0904, SAUSA300_0752, SAUSA300_0387, and SAUSA300_2311) largely unaffected by incubation with MEL-B, indicating MEL-B resistance. Despite the strong binding of MEL-B to these mutants, the four molecules encoded by the deleted genes (yjbI, clpP, pbuX, or brpS) in each mutant were not directly recognized by MEL-B. Given that these molecules are not localized on the outer surface of S. aureus and that the antibacterial activity of MEL-B against S. aureus is facilitated by the effective transfer of two antibacterial fatty acids (caprylic acid and myristoleic acid) to S. aureus via ME, the deletion of each of the four molecules may alter the peptidoglycan structure, potentially inhibiting the effective transfer of these antimicrobial fatty acids into S. aureus.

Egg Yolk Protein Homologs Identified in Live-Bearing Sharks: Co-Opted in the Lecithotrophy-to-Matrotrophy Shift?

Reproductive modes of vertebrates are classified into two major embryonic nutritional types: yolk deposits (i.e., lecithotrophy) and maternal investment (i.e., matrotrophy). Vitellogenin (VTG), a major egg yolk protein synthesized in the female liver, is one of the molecules relevant to the lecithotrophy-to-matrotrophy shift in bony vertebrates. In mammals, all VTG genes are lost following the lecithotrophy-to-matrotrophy shift, and it remains to be elucidated whether the lecithotrophy-to-matrotrophy shift in nonmammalians is also associated with VTG repertoire modification. In this study, we focused on chondrichthyans (cartilaginous fishes)-a vertebrate clade that underwent multiple lecithotrophy-to-matrotrophy shifts. For an exhaustive search of homologs, we performed tissue-by-tissue transcriptome sequencing for two viviparous chondrichthyans, the frilled shark Chlamydoselachus anguineus and the spotless smooth-hound Mustelus griseus, and inferred the molecular phylogeny of VTG and its receptor very low-density lipoprotein receptor (VLDLR), across diverse vertebrates. As a result, we identified either three or four VTG orthologs in chondrichthyans including viviparous species. We also showed that chondrichthyans had two additional VLDLR orthologs previously unrecognized in their unique lineage (designated as VLDLRc2 and VLDLRc3). Notably, VTG gene expression patterns differed in the species studied depending on their reproductive mode; VTGs are broadly expressed in multiple tissues, including the uterus, in the two viviparous sharks, and in addition to the liver. This finding suggests that the chondrichthyans VTGs do not only function as the yolk nutrient but also as the matrotrophic factor. Altogether, our study indicates that the lecithotrophy-to-matrotrophy shift in chondrichthyans was achieved through a distinct evolutionary process from mammals.

Squalomix: shark and ray genome analysis consortium and its data sharing platform.

The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.

Effects of vitamin E supplementation on serum oxidative stress biomarkers, antibody titer after live bovine respiratory syncytial virus vaccination, as well as serum and fecal immunoglobulin A in weaned Japanese Black calves.

The purpose of this study was to determine the effects of vitamin E supplementation on blood oxidative stress biomarker in weaned calves. Thirty clinically healthy 12 weeks of age Japanese Black calves were randomly assigned to two groups: 15 calves received 300 IU of vitamin E daily from 12 to 18 weeks of age (VE group), and the other 15 calves did not receive the vitamin E (control group). Blood samples were taken at 12, 14, 16, 18, and 20 weeks of age. The concentration of serum reactive oxygen metabolites at 20 weeks of age were significantly lower in the VE group than those in the control group. Vitamin E supplementation to weaned calves might affect blood oxidative stress.

Roles of mannosylerythritol lipid-B components in antimicrobial activity against bovine mastitis-causing Staphylococcus aureus.

Mannosylerythritol lipid-B (MEL-B), which comprises ester-bonded hydrophilic ME and hydrophobic fatty acids, is a bio-surfactant with various unique properties, including antimicrobial activity against most gram-positive bacteria. The gram-positive Staphylococcus aureus is a causative pathogen of dairy cattle mastitis, which results in considerable economic loss in the dairy industry. Here, we demonstrate the efficacy of MEL-B as a disinfectant against bovine-derived S. aureus and elucidate a mechanism of action of MEL-B in the inhibition of bacterial growth. The growth of bovine mastitis causative S. aureus BM1006 was inhibited when cultured with MEL-B above 10 ppm. The activity of MEL-B required fatty acids (i.e., caprylic and myristoleic acids) as ME, the component of MEL-B lacking fatty acids, did not inhibit the growth of S. aureus even at high concentrations. Importantly, ME-bound fatty acids effectively inhibited the growth of S. aureus when compared with free fatty acids. Specifically, the concentrations of ME-bound fatty acids and free caprylic and myristoleic acids required to inhibit the growth of S. aureus were 10, 1442, and 226 ppm, respectively. The involvement of ME in the antimicrobial activity of MEL-B was confirmed by digestion of MEL-B with alkali, which dissociated ME and fatty acids. These results indicated that a mechanism of action of MEL-B in inhibiting the growth of S. aureus could be explained by the effective transporting of antimicrobial fatty acids to the bacterial surface via hydrophilic ME.

Effects of heating on the physical properties of premixed calcium silicate-based root canal sealers.

The purpose of this study was to examine the effect of heating on the physical properties of four types of premixed calcium silicate-based root canal sealers. Endoseal MTA, Well-Root ST, EndoSequence BC Sealer, EndoSequence BC Sealer HiFlow, and AH Plus (epoxy resin root canal sealer) were heated at 100°C for 1 min, and changes in setting time, flow, and film thickness were evaluated in accordance with ISO 6876:2012 standards. In addition, pH measurement and scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) analyses of the set materials were performed. All root canal sealers heated at 100°C showed significant decreases in setting time and flow, particularly Endoseal MTA. In addition, the film thickness of Endoseal MTA increased significantly after heating at 100°C. The pH and SEM/EDS results were not affected by heating. Heating calcium silicate-based root canal sealers accelerated setting time, decreased flow, and increased film thickness. However, the degree of these changes varied among the products. The present findings indicate that heat-induced changes in the physical properties of calcium silicate-based root canal sealers could adversely affect the quality of warm vertical condensation technique.

Examination of the Relationship between Straight Leg Raising Repetition Count and both Knee Extension Strength and Walking Independence in Patients with Collagen Disease.

OBJECTIVE: The aim of the current study was to examine the relationship between the straight leg raising (SLR) repetition count and both the knee extension strength (KES) and walking independence. METHODS: We enrolled 106 inpatients aged ≥20 years with collagen disease in a cross-sectional study. We measured the SLR repetition count, KES, and walking independence of each participant. The correlations between the SLR repetition count and KES/walking independence were then examined. Furthermore, patients were divided into three groups depending on their SLR repetition count (low, medium, or high), and the differences among the groups were analyzed. RESULTS: A moderately significant correlation was found between the SLR repetition count and KES (right: r=0.46, P<0.01; left: r=0.55, P<0.01). Moreover, there was a strong correlation between the maximum SLR repetition count and walking independence (r=0.74, P<0.01). Differences in KES and walking independence were observed among the SLR repetition groups (P<0.01). KES and walking independence in the group with a low repetition count were 0.08±0.04 kgf/kg and 1 (1-4) point, whereas the values in the group with a medium repetition count were 0.25±0.08 kgf/kg and 5 (1-7) points and those in the group with a high repetition count were 0.40±0.13 kgf/kg and 7 (4-7) points. CONCLUSION: The SLR repetition count is related to KES and walking independence. SLR repetition counts can be used in the clinical setting for the assessment of lower limb strength and walking independence.

Examination of Simple Outcome Measures and Cut-off Values Related to Walking Independence of Inpatients with Medical Diseases in Acute Care Hospitals.

OBJECTIVE: The objective of the current study was to identify simple outcome measures to predict walking independence in inpatients with medical diseases in acute care hospitals and to identify the cut-off values of the relevant measures. METHODS: Two hundred inpatients aged 20 years or above who had a medical disease were enrolled in this cross-sectional study. The subjects' walking independence, physical characteristics, cognitive status, and blood test data were examined. Logistic regression analysis was performed, and cut-off values were calculated. RESULTS: The identified outcome measures and their respective cut-off values were as follows: the straight leg raising (SLR) repetition count, 27; the one-leg standing time (OLST), 3.6 s; and the orientation score of the mini-mental state examination (MMSE), 9/10. CONCLUSIONS: Our study findings suggest that the SLR repetition count, OLST, and the MMSE orientation score are simple outcome measures related to walking independence in inpatients with medical diseases in acute care hospitals.

The pectoral fin muscles of the coelacanth Latimeria chalumnae: Functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods.

To investigate the morphology and evolutionary origin of muscles in vertebrate limbs, we conducted anatomical dissections, computed tomography and kinematic analyses on the pectoral fin of the African coelacanth, Latimeria chalumnae. We discovered nine antagonistic pairs of pronators and supinators that are anatomically and functionally distinct from the abductor and adductor superficiales and profundi. In particular, the first pronator and supinator pair represents mono- and biarticular muscles; a portion of the muscle fibers is attached to ridges on the humerus and is separated into two monoarticular muscles, whereas, as a biarticular muscle, the main body is inserted into the radius by crossing two joints from the shoulder girdle. This pair, consisting of a pronator and supinator, constitutes a muscle arrangement equivalent to two human antagonistic pairs of monoarticular muscles and one antagonistic pair of biarticular muscles in the stylopod between the shoulder and elbow joints. Our recent kinesiological and biomechanical engineering studies on human limbs have demonstrated that two antagonistic pairs of monoarticular muscles and one antagonistic pair of biarticular muscles in the stylopod (1) coordinately control output force and force direction at the wrist and ankle and (2) achieve a contact task to carry out weight-bearing motion and maintain stable posture. Therefore, along with dissections of the pectoral fins in two lungfish species, Neoceratodus forsteri and Protopterus aethiopicus, we discuss the functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods. Anat Rec, 299:1203-1223, 2016. © 2016 Wiley Periodicals, Inc.

Balance function in patients who had undergone allogeneic hematopoietic stem cell transplantation.

A previous study reported a 45% incidence of falling among allogeneic haematopoietic stem cell transplantation (allo-HSCT) patients during hospitalisation. We investigated balance and physical function in allo-HSCT patients. Thirty patients (18 men and 12 women) who underwent allo-HSCT between February 2013 and September 2014 were included in this study. Patients were evaluated for up to 3 weeks before and 7 weeks after transplantation. Balance was evaluated using the Timed Up and Go test (TUG) and length of centre of pressure (CoP). Physical function was assessed using hand-grip strength, knee-extensor strength tests, and the 6 min walk test (6MWT). TUG and length of CoP were significantly increased following HSCT (P<0.01). Hand-grip strength, knee-extensor strength, and the 6MWT score decreased significantly after allo-HSCT (P<0.01). TUG and length of CoP were negatively correlated with hand grip and knee-extensor strength (P≤0.05). The allo-HSCT patients in this study had worsened dynamic and static movements of the CoP after transplantation as well as decline of physical function. Rehabilitation staff, nurses, and physicians should recognize the decreased balance function of patients who have undergone allo-HSCT.

Early-phase differences in health-related quality of life, psychological status, and physical function between human leucocyte antigen-haploidentical and other allogeneic haematopoietic stem cell transplantation recipients.

PURPOSE: This study investigated the differences between allogeneic haematopoietic stem cell transplantation (allo-HSCT) patients receiving HSC from human leucocyte antigen (HLA)-haploidentical donors (HID) and other donors that included HLA-matched sibling, matched unrelated, and unrelated umbilical cord blood donors in the 6 weeks after HSCT with respect to quality of life (QOL), psychological status, and physical function. METHODS: The study included 126 patients (HID group, n = 100; other donor group, n = 26) who underwent allo-HSCT between July 2007 and December 2012. Patients were evaluated for health-related QOL using the Medical Outcome Study 36-item Short Form Health Survey. Psychological status was measured by Hospital Anxiety and Depression Scale. Physical function was assessed using tests for handgrip strength, knee extensor strength, and the 6-min walk test. RESULTS: After HSCT, the HID group showed significantly greater improvements in the general health subscale and Mental Component Summary (MCS) of QOL than the other donor group (P < 0.01). Multivariate analysis confirmed that complete remission and age were associated with changes in the general health subscale before and after HSCT (P < 0.05). With regard to physical function, the HID group showed significantly more decline than the other donor group with respect to handgrip strength and knee extensor muscle strength after HSCT (P < 0.05). Total corticosteroid dose was associated with decreased handgrip strength before and after HSCT (P < 0.05). CONCLUSIONS: The donor type affects QOL, psychological status, and physical function in allo-HSCT recipients; these findings may provide insights for customised rehabilitation strategies for HSCT recipients.

A five-year follow-up of a patient with fulminant myocarditis who underwent a stepwise and goal-oriented individualized comprehensive cardiac rehabilitation program.

A 39-year-old man developed fulminant myocarditis and was transferred on mechanical ventilation and a ventricular-assist device to our hospital. On Hospital Day 10, he was weaned from all medical engineering devices, and bedside rehabilitation was initiated. Although a multidisciplinary cardiac rehabilitation team had intervened since Hospital Day 3, he could not be encouraged to begin ambulation because of hypotension and tachycardia. Moreover, he complained of loss of self-confidence and anxiety regarding physical strength, and expansion of activities was difficult. Exercises reflecting his immediate desires and daily activities were used as activity goals, and we developed an individualized exercise program with stepwise increase in load to motivate him to perform rehabilitation. At the time of discharge, his cardiac function recovered to nearly normal levels; however, muscle strength and respiratory function had not recovered. While the intervention was continued at the cardiac rehabilitation outpatient unit, improvement was observed in physical health and mental health-related scale scores. The patient returned to work 4 months after onset of his myocarditis. Moreover, the cardiac rehabilitation team provided support to him for his long-term overseas assignment in the fifth year after myocarditis onset. Long-term comprehensive support by the cardiac rehabilitation team was feasible and useful. .

Relationship between corticosteroid dose and declines in physical function among allogeneic hematopoietic stem cell transplantation patients.

PURPOSE: The aim of this study was to investigate the relationship between corticosteroid dose and degree of physical function decrease in allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients during the early stage of recovery. We further investigated the confounding factors affecting loss of physical function. METHODS: The study included 113 patients who underwent allo-HSCT between July 2007 and April 2012 at Hyogo College of Medicine Hospital in Japan. Physical function was assessed using tests for hand-grip strength, knee-extensor strength, and the 6-min walk test (6MWT). Fatigue was measured using the Piper Fatigue Scale. Total corticosteroid dose, frequency of physical therapy, body weight, and nutritional status were also collected from medical records. RESULTS: Total corticosteroid dose was correlated with decrease of hand-grip and knee-extensors strength (P < 0.01) but was not correlated with 6MWT performance. Results of multivariate analysis confirmed that low physical function was associated not only with high corticosteroid dose but also with low frequency of physical therapy, increase in fatigue, and body weight loss (P < 0.05). Also, hemoglobin levels were associated with 6MWT (P < 0.05). CONCLUSIONS: This study showed the relationship between corticosteroid dose and declines in physical function and also showed other clinical factors affecting loss of physical function among allo-HSCT patients. Our results indicate that the effectiveness of rehabilitation may be influenced by corticosteroid treatment.

Gender differences in health-related quality of life, physical function and psychological status among patients in the early phase following allogeneic haematopoietic stem cell transplantation.

OBJECTIVE: The aim of this study was to examine gender differences in quality of life (QOL), physical function and psychological status before and in the early phase after allogeneic haematopoietic stem cell transplantation (allo-HSCT). METHODS: One hundred patients (66 men, 34 women) who underwent allo-HSCT between July 2007 and June 2011 at Hyogo College of Medicine Hospital were included in this study. Patients were evaluated for health-related QOL using the Medical Outcome Study 36-item Short Form Health Survey; exercise capacity was measured with the 6-min walk test, hand grip strength and knee extensor strength. Fatigue and psychological status were measured by the Piper Fatigue Scale and Hospital Anxiety and Depression Scale, respectively. RESULTS: Women had significantly lower scores for physical function and general health on health-related QOL tests compared with men (p < 0.01). No difference between genders was found in decline of physical function. In women, exercise capacity was strongly associated with QOL (p < 0.01). In men, depression and anxiety were closely related to QOL (p < 0.01). CONCLUSIONS: Gender-appropriate rehabilitation in allo-HSCT patients is important. Women may need more endurance exercises and training for activities of daily life. Men may need rehabilitation including a psychological approach.