Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity.

Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.

Intake levels and main sources of nutrients for Japanese children with motor or intellectual disabilities.

Proper nutritional management is important for the growth and development of children with motor or intellectual disabilities; however, few studies have investigated the nutrient intake of children with disabilities. This study aimed to investigate the nutrient intake and food groups that are the main sources of nutrients for children with disabilities. This cross-sectional observational study included twenty-five children (mean age, 11⋅8 years) from five hospitals in Japan. Using a 3-d weighed dietary record, we estimated the daily nutrient intake and food and beverage sources that contributed to nutrient intake. The mean values of calcium, magnesium, iron, vitamin A, thiamine, riboflavin, and vitamin C intake were below the recommended dietary allowance, and those of dietary fiber and potassium were below the levels recommended by the Tentative Dietary Goal for Preventing Lifestyle-related Diseases (DG). In contrast, the mean intake values of fat, saturated fatty acids, and sodium were above the DG levels. Dairy products, meat, vegetables, and cereals were found to be the major contributors of nutrients. Increased intake of vegetables may help alleviate insufficient micronutrient intake in children with disabilities.

Aqueous breakdown of aspartate and glutamate to n-ω-amino acids on the parent bodies of carbonaceous chondrites and asteroid Ryugu.

Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, suggesting the potential of amino acid abundances as molecular descriptors of parent body geochemistry. However, the chemical mechanisms responsible for the amino acid distributions remain to be elucidated particularly at low temperatures (<50°C). Here, we report that two representative proteinogenic amino acids, aspartic acid and glutamic acid, decompose to ß-alanine and γ-aminobutyric acid, respectively, under simulated geoelectrochemical conditions at 25°C. This low-temperature conversion provides a plausible explanation for the enrichment of these two n-ω-amino acids compared to their precursors in heavily aqueously altered CI chondrites and Ryugu's return samples. The results suggest that these heavily aqueously altered samples originated from the water-rich mantle of their water/rock differentiated parent planetesimals where protein α-amino acids were decomposed.

Prognosis of primary pulmonary adenocarcinoma after surgical resection in small-breed dogs: 52 cases (2005-2021).

BACKGROUND: Tumor size is an important prognostic factor in lung cancer in dogs, and the canine lung carcinoma stage classification (CLCSC) recently has been proposed to subdivide tumor sizes. It is unclear if the same classification scheme can be used for small-breed dogs. OBJECTIVES: To investigate whether the tumor size classification of CLCS is prognostic for survival and progression outcomes in small-breed dogs with surgically resected pulmonary adenocarcinomas (PACs). ANIMALS: Fifty-two client-owned small-breed dogs with PAC. METHODS: Single-center retrospective cohort study conducted between 2005 and 2021. Medical records of dogs weighing <15 kg with surgically resected lung masses histologically diagnosed as PAC were examined. RESULTS: The numbers of dogs with tumor size ≤3 cm, >3 cm to ≤5 cm, >5 cm to ≤7 cm, or >7 cm were 15, 18, 14, and 5, respectively. The median progression-free interval (PFI) and overall survival time (OST) were 754 and 716 days, respectively. In univariable analysis, clinical signs, lymph node metastasis, margin, and histologic grade were associated with PFI, and age, clinical signs, margin, and lymph node metastasis were associated with OST. Tumor size classification of CLCS was associated with PFI in all categories, and tumor size >7 cm was associated with OST. In multivariable analysis, tumor size >5 cm to ≤7 cm and margin were associated with PFI, and age was associated with OST. CONCLUSIONS AND CLINICAL IMPORTANCE: The tumor size classification of CLCS would be an important prognostic factor in small-breed dogs with surgically resected PACs.

Molecular evolution of patristacin genes in teleosts based on the genome survey.

During the evolution of astacin metalloprotease family genes, gene duplication occurred, especially in the lineage of teleosts, in which several types of astacins containing six conserved cysteines (c6ast) emerged. One of them is patristacin, originally found in syngnathid fishes, such as pipefishes and seahorses. Patristacin is expressed in the brood pouch and is present on the same chromosome as other c6ast (pactacin and nephrosin) genes. We first surveyed all the genes from 33 teleost species using a genome database, and characterized the genes by phylogenetic analysis. Pactacin and nephrosin gene homologs were found from all the examined species with only few exceptions, while patristacin gene homologs were found from only several lineages. The patristacin gene homologs were found as multicopy genes in most species of Percomorpha, one of the diverged groups in teleosts. Further diversification of the gene occurred during the evolution of Atherinomorphae, one of the groups in Percomorpha. Fishes of Atherinomorphae possess two types of patristacin, belonging to subclades 1 and 2. Among the Atherinomorpha, we chose the southern platyfish to examine the patristacin gene expression. Platyfish possess eight patristacin gene homologs, called XmPastn1, 2, 3, 4, 5, 7, 10, and 11. Of these genes, only XmPastn2 belongs to subclade 1, while the other seven belong to subclade 2. Only XmPastn2 showed strong expression in several organs of adult platyfish, as observed in reverse-transcription polymerase chain reaction of RNA extracts. Cells expressing XmPastn2 were predominantly mucus-secreting cells found in epidermis around the jaw, as revealed by in-situ hybridization. This result suggests that XmPastn2 is secreted and may contribute to mucus formation or secretion.

Anterior knee pain post-multiple surgeries for tibia fracture effectively managed with infrapatellar fat pad injection: a case report.

BACKGROUND: The anterior knee compartment is filled by the infrapatellar fat pad (IFP) and has been emphasized as a source of anterior knee pain (AKP). CASE PRESENTATION: A 51-year-old woman sustained a right tibial plateau and open diaphyseal fracture 2 years earlier. She remained with chronic AKP after undergoing bone fixations. Increased anterior portion of the IFP brightness and decreased adipose tissue gliding with flexion and extension compared to the unaffected side was shown on ultrasonography. An injection of 0.2% lidocaine between the patellar tendon and IFP, and into the IFP under ultrasound guidance, immediately relieved the pain. The pain kept recurring although injections were effective for a while; thus, surgery was scheduled. Scar tissue on the IFP surface was endoscopically excised and her pain dramatically reduced. CONCLUSION: This is the first report in which the detection of increased brightness on ultrasound of IFP and the injections into the IFP triggered an additional surgical intervention. Ultrasound evaluation and injection may be beneficial in pain clinic patients presenting with AKP and may provide an opportunity for diagnosis.

tRNA methylation resolves codon usage bias at the limit of cell viability.

Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3'-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival.

Intravascular papillary endothelial hyperplasia in the cecum: a case report.

BACKGROUND:  Intravascular papillary endothelial hyperplasia (IPEH), also known as Masson's tumor, is a benign, non-neoplastic vascular lesion that is characterized by reactive proliferation of papillary endothelial cells associated with a thrombus. These lesions typically develop in the vascular regions of the head and neck, oral cavity, or extremities; however, other organ systems have been affected. IPEH in the gastrointestinal tract is rare, with only a few cases reported to date. Thus, the pathogenesis and clinical features of IPEH in the gastrointestinal tract are not entirely understood. Moreover, the local excision of certain subtypes of IPEH can be curative; this makes timely diagnosis essential. We present the case of a patient with IPEH in the cecum that was discovered while investigating the cause of severe anemia. CASE PRESENTATION: A 29-year-old woman visited a general practitioner (GP) with the complaint of abdominal pain. She was diagnosed with acute appendicitis and was prescribed antibiotics. After treatment, her abdominal pain disappeared. However, she was found to be severely anemic (hemoglobin level, 6.5 g/dl). To determine the cause of her anemia, the GP referred her to our hospital for further examination and treatment. Computed tomography scan revealed cecal wall thickening. Further, a lower gastrointestinal endoscopy revealed a 2-cm raised mass-like lesion in the cecum. This lesion was pathologically identified as an inflammatory granuloma. The cause of her anemia was determined to be bleeding from the lesion in the cecum. She underwent laparoscopic ileocecal resection. Histopathological examination of the surgical specimen revealed a spongy structure comprising many small papillary fibrous tissues lined by a typical monolayer endothelium. Further, immunohistochemical analysis showed that the cells of the endothelium monolayer expressed CD31, CD34. The Ki-67 labeling index was < 1%. Based on these findings, the lesion was identified as an IPEH in the cecum. The patient's postoperative course was uneventful, and there was no evidence of recurrence during the 1.3 years of follow-up. CONCLUSIONS:  IPEH rarely arises within the abdominal cavity. Surgery remains the only treatment for IPEH and is associated with an excellent prognosis and a low recurrence rate. More aggressive lesions such as angiosarcoma should be excluded when considering the histologic diagnoses of IPEH, and expert pathologic review is vital. This is the first report of IPEH occurring in the cecum and represents a novel cause of gastrointestinal bleeding which the clinician should consider when evaluating a patient with atypical or difficult gastrointestinal bleeding sources.

Geoelectrochemistry-driven alteration of amino acids to derivative organics in carbonaceous chondrite parent bodies.

A long-standing question regarding carbonaceous chondrites (CCs) is how the CCs' organics were sourced and converted before and after the accretion of their parent bodies. Growing evidence shows that amino acid abundances in CCs decrease with an elongated aqueous alteration. However, the underlying chemical processes are unclear. If CCs' parent bodies were water-rock differentiated, pH and redox gradients can drive electrochemical reactions by using H2 as an electron source. Here, we simulate such redox conditions and demonstrate that α-amino acids are electrochemically altered to monoamines and α-hydroxy acids on FeS and NiS catalysts at 25 °C. This conversion is consistent with their enrichment compared to amino acid analogs in heavily altered CCs. Our results thus suggest that H2 can be an important driver for organic evolution in water-rock differentiated CC parent bodies as well as the Solar System icy bodies that might possess similar pH and redox gradients.

Evaluation of adverse events in small-breed dogs treated with maropitant and a single dose of doxorubicin.

BACKGROUND: The recommended doxorubicin (DOX) dose for small dogs is 1 mg/kg. Recent data suggest that DOX-induced gastrointestinal (GI) toxicosis can be reduced with maropitant treatment. OBJECTIVES: To investigate the incidence of adverse events (AEs) in small-breed dogs administered a single 25 mg/m2 DOX followed by administration of maropitant (DOX25). The primary aim was to assess myelo- and GI toxicoses for 2 weeks after DOX administration. The secondary aim was to compare the incidence and grades of AEs found in the DOX25 group with a historical control group (DOX 1 mg/kg without administration of antiemetic or antidiarrheal medications). ANIMALS: Nineteen small-breed tumor-bearing dogs. METHODS: A prospective, observational study of tumor-bearing dogs, weighing 5 to 10 kg, administered a single 25 mg/m2 dose of DOX IV, followed by administration of maropitant for the next 5 days. RESULTS: Inappetence, vomiting, and diarrhea were found in 7/19, 2/19, and 6/19 of the DOX25 dogs, respectively. Neutropenia and thrombocytopenia was 12/19 and 3/19, respectively. Most AEs were grades 1 and 2, except for grades 3 and 4 inappetence and neutropenia in 3 and 4 dogs, respectively. Furthermore, febrile neutropenia occurred in 3/19 dogs in the DOX25 group. All AEs between the DOX25 and historical control groups were not significantly different. CONCLUSIONS AND CLINICAL IMPORTANCE: Vomiting and diarrhea were deemed acceptable with 25 mg/m2 DOX followed by maropitant treatment in 5 to 10 kg dogs; however, additional supportive care might be needed for dogs with inappetence and neutropenia.

Development of type 1 diabetes in a patient treated with anti-interleukin-6 receptor antibody for rheumatoid arthritis.

Interleukin-6 is a pleiotropic cytokine that plays a pathogenic role in type 1 diabetes. Therefore, anti-interleukin-6 receptor antibody, tocilizumab, used for the treatment of rheumatoid arthritis, is considered a candidate for immune intervention in type 1 diabetes. Here, we report the case of a 73-year-old woman (HLA-DR9-DQ3 homozygote) with well-controlled rheumatoid arthritis who developed type 1 diabetes while receiving tocilizumab treatment. At 57 years-of-age, the patient was diagnosed with rheumatoid arthritis, for which she underwent tocilizumab therapy that enabled complete suppression of her joint inflammation. A total of 17 months after starting tocilizumab therapy, she noticed polydipsia, polyuria, general fatigue and weight reduction (-2 kg/month), and was diagnosed with type 1 diabetes with diabetic ketoacidosis based on an arterial pH of 7.26, serum ketone body of 7,437 µmol/L, blood glucose level of 925 mg/dL, glycated hemoglobin of 13.2% and the presence of anti-islet autoantibodies. This case report shows valuable insight regarding the effect of anti-interleukin-6 receptor antibody therapy on type 1 diabetes prevention.

Outcome of appendicular or scapular osteosarcoma treated by limb amputation in cats: 67 cases (1997-2018).

OBJECTIVE: To evaluate the metastasis rate, survival time, and prognostic factors associated with appendicular or scapular osteosarcoma treated by limb amputation in cats. ANIMALS: 67 cats with histologically confirmed appendicular or scapular osteosarcoma treated by limb amputation. PROCEDURES: This retrospective cohort study included cats with histologically confirmed appendicular or scapular osteosarcoma between January 1997 and December 2018. A questionnaire survey was conducted at veterinary clinics where limb amputation was performed. Distant metastasis, local recurrence, and lymph node metastasis rates and survival time were determined. Factors associated with distant metastasis and survival were investigated. RESULTS: The distant metastasis rate after limb amputation was 41.9% (26/62). The overall distant metastasis rate was 46.3% (31/67), including 5 cats with distant metastasis at the time of amputation. Osteosarcoma of the humerus resulted in distant metastasis in 6 of 7 cases. Osteosarcoma of the humerus was significantly associated with distant metastasis in univariate and multivariate analyses (adjusted OR, 9.56). The rate of lymph node metastasis after limb amputation was 3.0% (2/66), and the local recurrence rate was 9.0% (6/67). The median survival time was 527 days. Age and tumor location were not significantly associated with survival time. CLINICAL RELEVANCE: Distant metastasis occurs in approximately 40% of cats with appendicular or scapular osteosarcoma after limb amputation. In addition, osteosarcoma of the humerus has a particularly high incidence of distant metastasis. Detailed follow-up is therefore necessary, even after limb amputation, especially in cases of osteosarcoma of the humerus.

Update on the SedLine® algorithm for calculating the Patient State Index of older individuals during general anesthesia: a randomized controlled trial.

BACKGROUND: The SedLine® sensor processes (Masimo Corporation; Irvine, CA, USA) raw electroencephalogram (EEG) signals and displays the depth of sedation as a Patient State Index (PSi). Reliance on standard processed EEG data and failure to recognize age-related effects can lead to an erroneous interpretation that low-amplitude EEG findings in an older patient signify an insufficient depth of anesthesia presented as abnormally high PSi values (AHPSi). We hypothesized that the incidence of AHPSi would decrease with the use of the recently-updated version of the SedLine® sensor, in which the Bispectral Index (BIS) values were used to titrate anesthesia. METHODS: Thirty-three patients undergoing sevoflurane-remifentanil anesthesia were randomized into two groups. SedLine® sensors designed based on an old (v.1203) or updated (v.2000) algorithms were used. The BIS (v.4.1) and absolute index of total EEG power (TP) were simultaneously recorded. The attending anesthesiologists titrated the anesthetics, and BIS was maintained at 40-60. The incidence of AHPSi (PSi>50 with BIS 40-60) was calculated during the first 30 min after the start of surgery. RESULTS: Compared to the old algorithm group, the incidence of AHPSi was significantly lower in the updated algorithm group (26.7% vs. 4.2%, P<0.001). Lower TP values and the use of the old algorithm have significant effect on increased PSi values (P<0.001). CONCLUSIONS: The incidence of AHPSi decreased with the use of the updated version of the SedLine® algorithm.

Pactacin is a novel digestive enzyme in teleosts.

Generally, animals extract nutrients from food by degradation using digestive enzymes. Trypsin and chymotrypsin, one of the major digestive enzymes in vertebrates, are pancreatic proenzymes secreted into the intestines. In this investigation, we report the identification of a digestive teleost enzyme, a pancreatic astacin that we termed pactacin. Pactacin, which belongs to the astacin metalloprotease family, emerged during the evolution of teleosts through gene duplication of astacin family enzymes containing six cysteine residues (C6astacin, or C6AST). In this study, we first cloned C6AST genes from pot-bellied seahorse (Hippocampus abdominalis) and analyzed their phylogenetic relationships using over 100 C6AST genes. Nearly all these genes belong to one of three clades: pactacin, nephrosin, and patristacin. Genes of the pactacin clade were further divided into three subclades. To compare the localization and functions of the three pactacin subclades, we studied pactacin enzymes in pot-bellied seahorse and medaka (Oryzias latipes). In situ hybridization revealed that genes of all three subclades were commonly expressed in the pancreas. Western blot analysis indicated storage of pactacin pro-enzyme form in the pancreas, and conversion to the active forms in the intestine. Finally, we partially purified the pactacin from digestive fluid, and found that pactacin is novel digestive enzyme that is specific in teleosts.

[A Successful Case of Treatment by Lymphangiography for Chylothorax after Robotic Esophagectomy-A Case of Report].

A 50-year-old woman diagnosed with clinical Stage Ⅲ esophageal squamous cell carcinoma, received 2 cycles of docetaxel, cisplatin, 5-fluorouracil(DCF)therapy followed by robotic esophagectomy. In the 15th postoperative day, she suddenly had difficulty in breathing and a chest CT finding showed a large amount of right pleural effusion. Thoracocentesis yield a 1 L of chylous fluid confirmed diagnosis with postoperative chylothorax and conservative treatment was initiated. However, chylothorax was not improved. Therefore, a lipiodol lymphangiography from the inguinal lymph node was performed at the 20th postoperative day. Although the site of leakage could not identify, amount of drained pleural effusion was gradually decreased after lymphangiography, and drain was decannulated in the 28th postoperative day. Lipiodol lymphangiography may be a useful modality for both diagnosis and treatment for chylothorax after esophagectomy.

Efficacy of omarigliptin, once-weekly dipeptidyl peptidase-4 inhibitor, in patients with type 2 diabetes.

BACKGROUND: Omarigliptin is one of several once-weekly dipeptidyl peptidase-4 inhibitors (DPP-4is). Despite the high frequency of switching from various daily DPP-4is to omarigliptin in actual clinical practice, data regarding its efficacy in patients with type 2 diabetes (T2D) after switching are limited. AIM: To analyze the efficacy of omarigliptin in Japanese patients with T2D who had previously received treatment with other glucose-lowering agents. METHODS: Forty-nine T2D patients treated for the first time with omarigliptin were recruited retrospectively and divided into four groups defined as either add-on or switched from daily DPP-4is: switched from linagliptin, switched from sitagliptin, and switched from vildagliptin. During a 3-mo follow-up, the clinical parameters among these groups were assessed and compared, with the impact of the switch on glycemic variability as measured by continuous glucose monitoring also being evaluated in the switched groups. RESULTS: Hemoglobin A1c levels saw a significant decrease of -0.32% ± 0.41% in the add-on group (P = 0.002). However, the other groups' variables depended on the pre-switch daily DPP-4i: switched from linagliptin, -0.05% ± 0.22%; switched from sitagliptin, -0.17% ± 0.33%; and switched from vildagliptin, 0.45% ± 0.42%, which saw significant worsening (P = 0.0007). Multivariate logistic regression analysis revealed that switching from vildagliptin to omarigliptin was independently associated with worsening glycemic control (P = 0.0013). The mean and standard deviation of sensor glucose value, the mean amplitude of glycemic excursions, and the mean of daily difference significantly improved when switching the patient from either linagliptin or sitagliptin to omarigliptin. However, in patients switched from vildagliptin, not only did the glucose variability indices see no improvements, the mean of daily difference even underwent significant worsening. CONCLUSION: Administering omarigliptin as add-on therapy or switching to it from sitagliptin and linagliptin, but not vildagliptin, improves glycemic control and thus should help in decision making when selecting DPP-4is for T2D patients.