Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources.

Carbon source-dependent control of bacterial growth is fundamental to bacterial physiology and survival. However, pinpointing the metabolic steps important for cell growth is challenging due to the complexity of cellular networks. Here, the elastic net model and multilayer perception model that integrated genome-wide gene-deletion data and simulated flux distributions were constructed to identify metabolic reactions beneficial or detrimental to Escherichia coli grown on 30 different carbon sources. Both models outperformed traditional in silico methods by identifying not just essential reactions but also nonessential ones that promote growth. They successfully predicted metabolic reactions beneficial to cell growth, with high convergence between the models. The models revealed that biosynthetic pathways generally promote growth across various carbon sources, whereas the impact of energy-generating pathways varies with the carbon source. Intriguing predictions were experimentally validated for findings beyond experimental training data and the impact of various carbon sources on the glyoxylate shunt, pyruvate dehydrogenase reaction, and redundant purine biosynthesis reactions. These highlight the practical significance and predictive power of the models for understanding and engineering microbial metabolism.

Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12.

BACKGROUND: Pseudomonas putida S12 is a gram-negative bacterium renowned for its high tolerance to organic solvents and metabolic versatility, making it attractive for various applications, including bioremediation and the production of aromatic compounds, bioplastics, biofuels, and value-added compounds. However, a metabolic model of S12 has yet to be developed. RESULTS: In this study, we present a comprehensive and highly curated genome-scale metabolic network model of S12 (iSH1474), containing 1,474 genes, 1,436 unique metabolites, and 2,938 metabolic reactions. The model was constructed by leveraging existing metabolic models and conducting comparative analyses of genomes and phenomes. Approximately 2,000 different phenotypes were measured for S12 and its closely related KT2440 strain under various nutritional and environmental conditions. These phenotypic data, combined with the reported experimental data, were used to refine and validate the reconstruction. Model predictions quantitatively agreed well with in vivo flux measurements and the batch cultivation of S12, which demonstrated that iSH1474 accurately represents the metabolic capabilities of S12. Furthermore, the model was simulated to investigate the maximum theoretical metabolic capacity of S12 growing on toxic organic solvents. CONCLUSIONS: iSH1474 represents a significant advancement in our understanding of the cellular metabolism of P. putida S12. The combined results of metabolic simulation and comparative genome and phenome analyses identified the genetic and metabolic determinants of the characteristic phenotypes of S12. This study could accelerate the development of this versatile organism as an efficient cell factory for various biotechnological applications.

Extreme Gradient Boosting to Predict Atomic Layer Deposition for Platinum Nano-Film Coating.

Extreme gradient boosting (XGBoost) is an artificial intelligence algorithm capable of high accuracy and low inference time. The current study applies this XGBoost to the production of platinum nano-film coating through atomic layer deposition (ALD). In order to generate a database for model development, platinum is coated on α-Al2O3 using a rotary-type ALD equipment. The process is controlled by four parameters: process temperature, stop valve time, precursor pulse time, and reactant pulse time. A total of 625 samples according to different process conditions are obtained. The ALD coating index is used as the Al/Pt component ratio through ICP-AES analysis during postprocessing. The four process parameters serve as the input data and produces the Al/Pt component ratio as the output data. The postprocessed data set is randomly divided into 500 training samples and 125 test samples. XGBoost demonstrates 99.9% accuracy and a coefficient of determination of 0.99. The inference time is lower than that of random forest regression, in addition to a higher prediction safety than that of the light gradient boosting machine.

Gold Nanoparticle and Polymerase Chain Reaction (PCR)-Based Colorimetric Assay for the Identification of Campylobacter spp. in Chicken Carcass.

Campylobacteriosis is a common cause of gastrointestinal disease. In this study, we suggest a general strategy of applying gold nanoparticles (AuNPs) in colorimetric biosensors to detect Campylobacter in chicken carcass. Polymerase chain reaction (PCR) was utilized for the amplification of the target genes, and the thiolated PCR products were collected. Following the blending of colloid AuNPs with PCR products, the thiol bound to the surface of AuNPs, forming AuNP-PCR products. The PCR products had a sufficient negative charge, which enabled AuNPs to maintain a dispersed formation under electrostatic repulsion. This platform presented a color change as AuNPs aggregate. It did not need additional time and optimization of pH for PCR amplicons to adhere to the AuNPs. The specificity of AuNPs of modified primer pairs for mapA from Campylobacter jejuni and ceuE from Campylobacter coli was activated perfectly (C. jejuni, p-value: 0.0085; C. coli, p-value: 0.0239) when compared to Salmonella Enteritidis and Escherichia coli as non-Campylobacter species. Likewise, C. jejuni was successfully detected from artificially contaminated chicken carcass samples. According to the sensitivity test, at least 15 ng/µL of Campylobacter PCR products or 1×103 CFU/mL of cells in the broth was needed for the detection using the optical method.

Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup.

D-Tagatose is a promising low-calorie sugar-substituting sweetener in the food industry. Most ingested D-tagatose is fermented by intestinal microorganisms. Until now, Escherichia coli has been considered incapable of growing on D-tagatose. Here, we discovered a gene cluster involved in D-tagatose utilization in E. coli. The chromosome of the intestinal probiotic E. coli Nissle 1917 contains a six-gene cluster encoding the ABC transporter, D-tagatose kinase, D-tagatose-bisphosphate aldolase, and putative aldose 1-epimerase. The functionality of the gene cluster was experimentally validated. Based on single-gene deletions, D-tagatose dissimilation occurs via D-tagatose 6-phosphate to D-tagatose 1,6-bisphosphate to D-glyceraldehyde 3-phosphate plus dihydroxyacetone phosphate. Remarkably, this gene cluster was located in 93% of the completely sequenced genomes of the E. coli B2 phylogroup, which contains the majority of extraintestinal pathogenic and adherent-invasive E. coli strains prevalent in patients with inflammatory bowel disease. This highlights the importance of understanding the clinical significance of D-tagatose in microbiota alterations.

Clinical association between serum cholesterol level and the size of xanthelasma palpebrarum.

BACKGROUND: Xanthelasma palpebrarum (XP) is a benign periorbital lesion. The relationship between xanthelasma lesion size and serum cholesterol levels has been poorly studied. In this study, we investigated this relationship in the context of the clinical etiology of XP. METHODS: We retrospectively reviewed medical records and pathology reports of all patients treated for XP at our hospital between June 2014 and June 2021; the data were used to analyze lesion size, underlying disease, serum cholesterol, and disease recurrence. RESULTS: The mean values for patient age, serum cholesterol, and lesion size were 53.0 years, 235.0 mg/dL, and 69.2 mm2, respectively. XP mainly occurred in women (64.7%); furthermore, the incidence of XP and lesion size was greatest among patients in their 5th decade of life (41.2%). There was no statistically significant relationship between xanthelasma lesion size and serum cholesterol level. CONCLUSION: This study compared lesion size with various clinical features in XP patients. In patients who underwent surgery for XP, serum cholesterol levels tended to be higher than those in the general population. However, the trend between the size of XP and serum cholesterol level was unclear. Therefore, if a patient with XP visits the hospital for surgery, it is recommended to check the lipid profile to confirm underlying dyslipidemia regardless of the size.

Comparison of intermaxillary fixation techniques for mandibular fractures with focus on patient experience.

BACKGROUND: Intermaxillary fixation (IMF) is a technique that allows for the reduction and stabilization of mandibular fractures. Several methods of IMF, such as self-tapping screws or arch bars, have been developed. This study aimed to validate the usefulness of IMF with a self-tapping screw compared to IMF with arch bars with focus on the patients' perspective. METHODS: We retrospectively reviewed the medical records of all patients who were treated for mandibular fractures at our hospital between August 2014 and February 2021. A total of 57 patients were enrolled in this study. Thirteen patients were excluded from the analysis: three patients were lost to follow-up, and 10 patients did not undergo IMF. Finally, 44 patients were analyzed, of which 31 belonged to the arch bar group, and 13 belonged to the screw group. Patient discomfort and pain during IMF application and removal were analyzed using a patient self-assessment questionnaire. The surgeon also assessed oral hygiene, IMF stability, and occlusion. RESULTS: We applied IMF to 34 men (77%) and 10 women (23%). The mean age of the patients was 37.3 years. The most common fracture site was the angle (30%), followed by the parasymphysis (25%), the body (23%), the condyle (11%), and the ramus (11%). Patient discomfort and oral hygiene were statistically favorable in the screw group. The IMF application time was statistically shorter in the screw group (p< 0.001). IMF stability was not statistically different between the two groups. The pain score during IMF removal was lower in the screw group (p< 0.001). CONCLUSION: Compared to arch bars, IMF screws provide more comfort during the IMF period, help maintain favorable oral hygiene, and have a shorter application time. From the patient's perspective, IMF screws are an excellent alternative to conventional arch bars when applicable.

Eosinophil-mediated lung inflammation associated with elevated natural killer T cell response in COVID-19 patients.

BACKGROUND/AIMS: Coronavirus disease 2019 (COVID-19) is associated with acute respiratory syndrome. The mechanisms underlying the different degrees of pneumonia severity in patients with COVID-19 remain elusive. This study provides evidence that COVID-19 is associated with eosinophil-mediated inflammation. METHODS: We performed a retrospective case series of three patients with laboratory and radiologically confirmed COVID-19 pneumonia admitted to Chosun University Hospital. Demographic and clinical data on inflammatory cell lung infiltration and cytokine levels in patients with COVID-19 were collected. RESULTS: Cytological analysis of sputum, tracheal aspirates, and bronchoalveolar lavage fluid (BALF) samples from all three patients revealed massive infiltration of polymorphonuclear cells (PMNs), such as eosinophils and neutrophils. All sputum and BALF specimens contained high levels of eosinophil cationic proteins. The infiltration of PMNs into the lungs, together with elevated levels of natural killer T (NKT) cells in BALF and peripheral blood samples from patients with severe pneumonia in the acute phase was confirmed by flow cytometry. CONCLUSION: These results suggest that the lungs of COVID-19 patients can exhibit eosinophil-mediated inflammation, together with an elevated NKT cell response, which is associated with COVID-19 pneumonia.

Enhanced eosinophil-mediated inflammation associated with antibody and complement-dependent pneumonic insults in critical COVID-19.

Despite the worldwide effect of the coronavirus disease 2019 (COVID-19) pandemic, the underlying mechanisms of fatal viral pneumonia remain elusive. Here, we show that critical COVID-19 is associated with enhanced eosinophil-mediated inflammation when compared to non-critical cases. In addition, we confirm increased T helper (Th)2-biased adaptive immune responses, accompanying overt complement activation, in the critical group. Moreover, enhanced antibody responses and complement activation are associated with disease pathogenesis as evidenced by formation of immune complexes and membrane attack complexes in airways and vasculature of lung biopsies from six fatal cases, as well as by enhanced hallmark gene set signatures of Fcγ receptor (FcγR) signaling and complement activation in myeloid cells of respiratory specimens from critical COVID-19 patients. These results suggest that SARS-CoV-2 infection may drive specific innate immune responses, including eosinophil-mediated inflammation, and subsequent pulmonary pathogenesis via enhanced Th2-biased immune responses, which might be crucial drivers of critical disease in COVID-19 patients.

Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917.

Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of Escherichia coli intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.

Optimal harvest and efficient use of septal cartilage in rhinoplasty.

BACKGROUND: Nasal septal cartilage is used to obtain favorable aesthetic and functional outcomes in rhinoplasty, but is often difficult to harvest or the harvested amount is insufficient. Therefore, the objective of this study is to introduce how to harvest septal cartilage optimally without losing and use harvested cartilage efficiently. METHODS: From March 2015 to January 2020, we tried to harvest as much septal cartilage as possible while maintaining the L-strut in 30 patients. A spreader flap and septal rotation suture were used instead of a spreader graft. Also in patients who needed a spreader graft and septal extension graft, a spreader graft was used on one side and a one-piece spreader graft combined with a septal extension graft was performed on the other side. For tip plasty, a columella septal suture was performed first. Postoperative patient satisfaction was assessed using the Rhinoplasty Outcome Examination questionnaire. RESULTS: No serious complications were observed. The patient satisfaction score was 50% or above in 27 patients (90%) and less than 50% in only three patients (10%). The average score was 81.5 points. CONCLUSION: For septal cartilage deficiency, a spreader flap, the septal rotation suture, or onepiece spreader graft combined with a septal extension graft was used. The nasal tip was sufficiently rotated using the columellar septal suture technique first. These techniques made it possible to obtain good aesthetic outcomes using only septal cartilage, without harvesting other cartilage.

Interstitial lung disease induced by the roots of Achyranthes japonica Nakai: Three case reports.

BACKGROUND: The roots of Achyranthes japonica Nakai (AJN), called "Useul-puli," has been traditionally used to control pain and improve dysfunction in osteoarthritis patients in South Korea. CASE SUMMARY: We described 3 patients diagnosed with herbal medicine induced interstitial lung disease after consuming boiled the roots of AJN. They were referred to our hospital because of the modified Medical Research Council grade 4 dyspnea. Chest computed tomography showed bilateral ground-glass opacities with patchy consolidation. After treatment with systemic glucocorticoid therapy and discontinuation of the roots of AJN, their symptoms improved, and almost all ground-glass opacities and patchy consolidations on chest radiography and chest computed tomography resolved. CONCLUSION: We present three cases of interstitial lung disease induced by the roots of AJN.

Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms.

Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.

Pulmonary pleomorphic carcinoma presenting as undifferentiated non-small cell carcinoma with giant cells: A case report and review of literature.

Pulmonary pleomorphic carcinoma (PPC) is a poorly differentiated non-small cell lung carcinoma, including squamous cell carcinoma, adenocarcinoma, or undifferentiated non-small cell lung carcinoma with at least 10% spindle and/or giant cells. Here, we report a case of PPC showing undifferentiated non-small cell lung carcinoma with giant cells. A 71-year-old man with dyspnea underwent right lobectomy because of a mass in the right upper lobe of the lung. A 5.0 × 3.0 × 1.5 cm-sized tumor was identified; microscopically, the tumor composed of undifferentiated large sized tumor cells admixed with syncytial tumor giant cells and emperipoletic giant cells. Immunohistochemically, the tumor cells were reactive for pan-cytokeratin, but negative for P40, thyroid transcription factor 1 (TTF-1), and vimentin. The tumor cells were also positive for 3 clones of programmed death-ligand 1 (PD-L1). The clinical and histologic findings supported the diagnosis of an undifferentiated non-small cell lung carcinoma with giant cells, which is a subtype of pulmonary pleomorphic carcinoma. Unfortunately, after surgery, multifocal lymph node metastasis was identified in radiologic examination. Only palliative chemotherapy was administered to the patient, although he was indicated for immunochemotherapy. Pulmonary pleomorphic carcinoma is known to have a poor prognosis, even in early stages of the disease, therefore, we should be careful in the diagnosis to ensure optimal treatment.

A single amino acid substitution in aromatic hydroxylase (HpaB) of Escherichia coli alters substrate specificity of the structural isomers of hydroxyphenylacetate.

BACKGROUND: A broad range of aromatic compounds can be degraded by enteric bacteria, and hydroxyphenylacetic acid (HPA) degrading bacteria are the most widespread. Majority of Escherichia coli strains can use both the structural isomers of HPA, 3HPA and 4HPA, as the sole carbon source, which are catabolized by the same pathway whose associated enzymes are encoded by hpa gene cluster. Previously, we observed that E. coli B REL606 grew only on 4HPA, while E. coli B BL21(DE3) grew on 3HPA as well as 4HPA. RESULTS: In this study, we report that a single amino acid in 4-hydroxyphenylacetate 3-hydroxylase (HpaB) of E. coli determines the substrate specificity of HPA isomers. Alignment of protein sequences encoded in hpa gene clusters of BL21(DE3) and REL606 showed that there was a difference of only one amino acid (position 379 in HpaB) between the two, viz., Arg in BL21(DE3) and Cys in REL606. REL606 cells expressing HpaB having Arg379 could grow on 3HPA, whereas those expressing HpaB with Gly379 or Ser379 could not. Structural analysis suggested that the amino acid residue at position 379 of HpaB is located not in the active site, but in the vicinity of the 4HPA binding site, and that it plays an important role in mediating the entrance and stable binding of substrates to the active site. CONCLUSIONS: The arginine residue at position 379 of HpaB is critical for 3HPA recognition. Information regarding the effect of amino acid residues on the substrate specificity of structural isomers can facilitate in designing hydoxylases with high catalytic efficiency and versatility.

Epidermoid cyst in temple area with skull perforation.

Epidermoid cysts are benign tumors that account for approximately 1% of intracranial tumors. In very rare cases, temporally located extradural intradiploic epidermoid cysts can cause neurological symptoms and skull perforation. Herein, we report the case of a 34-year-old woman who underwent successful treatment of an epidermoid cyst in the temporal region accompanied by neurological symptoms. Accurate radiological evaluation and complete removal of the tumor and capsule play a vital role in ensuring favorable long-term outcomes. Computed tomography and magnetic resonance imaging scans can provide an accurate assessment of the extent of intracranial expansion and invasion of the cerebral parenchyma, as well as enabling the precise localization and characterization of the bone defect and mass. In addition, collaborative surgery with a neurosurgeon is required for cases involving intracranial expansion and dural invasion.

Schwannoma on the nasal dorsum and tip with sensory changes.

Schwannomas, which originate from Schwann cells in the peripheral nervous system, are slowgrowing and uncommon benign tumors. Most schwannomas (90%) occur in isolation, and multiple occurrences are a characteristic feature of neurofibromas. Schwannomas of the nose and nasal tip are particularly unusual. Although a few cases of schwannomas of the sinusoidal tract and nasal septum have been reported, schwannomas arising from the nasal dorsum area and tip are extremely rare. Sensory abnormalities are also a very rare symptom. We excised a schwannoma on the nasal dorsum through direct incision and a schwannoma on the nasal tip through open rhinoplasty. No postoperative complications involving recurrence, hematoma, or infection occurred. The possibility of neurological changes should be considered in cases of an abnormality in the peripheral nervous system. Schwannoma must be kept in mind as a possible cause of neurological changes localized to a specific dermatome, and should always be considered in the differential diagnosis of a mass on the nose.

Algoriphagus aquimaris sp. nov., isolated from seashore sand.

Strain F21T, a marine, aerobic, Gram-negative, rod-shaped bacterium, was isolated from seashore sand sampled in Pohang, Republic of Korea. Cells of strain F21T were non-motile, catalase-positive, oxidase-positive, non-spore-forming and formed pinkish-red colonies on marine agar. The strain grew optimally at 37°C, pH 7 and in the presence of 2-3 % NaCl (w/v). Analysis of the 16S rRNA gene sequence of strain F21T revealed that it belonged to the genus Algoriphagus, family Cyclobacteriaceae, with similarity values of 98.1 and 96.8 % to Algoriphagus marincola DSM 16067T and Algoriphagus ornithinivorans IMSNU 14014T, respectively. When comparing the genome sequence of F21 T with those of the type strains of six species of the genus Algoriphagus, the values obtained were below the thresholds for analyses of average nucleotide identity (71.8-92.7 %) and in silico DNA-DNA hybridization using the Genome-to-Genome Distance Calculator (14.7-75.2 %). The DNA G+C content of strain F21T was 42.0 mol%. The chemotaxonomic characteristics of F21T included MK-7 as the predominant isoprenoid quinone, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as major cellular fatty acids, and phosphatidylcholine and phosphatidylethanolamine as major polar lipids. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness, and genomic data, we named strain F21T as Algoriphagus aquimaris sp. nov. and proposed that strain F21T (=KEMB 2250-007T= KCTC 72106T=JCM 33187T) in the genus Algoriphagus represents a novel species.

Erratum to: Nondestructive Estimation of Lean Meat Yield of South Korean Pig Carcasses Using Machine Vision Technique.

[This corrects the article DOI: 10.5851/kosfa.2018.e44.].

Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks.

BACKGROUND: Detection of central nodes in asymmetrically directed biological networks depends on centrality metrics quantifying individual nodes' importance in a network. In topological analyses on metabolic networks, various centrality metrics have been mostly applied to metabolite-centric graphs. However, centrality metrics including those not depending on high connections are largely unexplored for directed reaction-centric graphs. RESULTS: We applied directed versions of centrality metrics to directed reaction-centric graphs of microbial metabolic networks. To investigate the local role of a node, we developed a novel metric, cascade number, considering how many nodes are closed off from information flow when a particular node is removed. High modularity and scale-freeness were found in the directed reaction-centric graphs and betweenness centrality tended to belong to densely connected modules. Cascade number and bridging centrality identified cascade subnetworks controlling local information flow and irreplaceable bridging nodes between functional modules, respectively. Reactions highly ranked with bridging centrality and cascade number tended to be essential, compared to reactions that other central metrics detected. CONCLUSIONS: We demonstrate that cascade number and bridging centrality are useful to identify key reactions controlling local information flow in directed reaction-centric graphs of microbial metabolic networks. Knowledge about the local flow connectivity and connections between local modules will contribute to understand how metabolic pathways are assembled.