Engineering Bacillus subtilis for the formation of a durable living biocomposite material.

Engineered living materials (ELMs) are a fast-growing area of research that combine approaches in synthetic biology and material science. Here, we engineer B. subtilis to become a living component of a silica material composed of self-assembling protein scaffolds for functionalization and cross-linking of cells. B. subtilis is engineered to display SpyTags on polar flagella for cell attachment to SpyCatcher modified secreted scaffolds. We engineer endospore limited B. subtilis cells to become a structural component of the material with spores for long-term storage of genetic programming. Silica biomineralization peptides are screened and scaffolds designed for silica polymerization to fabricate biocomposite materials with enhanced mechanical properties. We show that the resulting ELM can be regenerated from a piece of cell containing silica material and that new functions can be incorporated by co-cultivation of engineered B. subtilis strains. We believe that this work will serve as a framework for the future design of resilient ELMs.

A dimeric α-helical cell penetrating peptide mounted with an HER2-selective affibody.

We have developed a cell penetrating peptide (CPP) system with high selectivity and penetrability at nanomolar concentrations with a combination of an HER2-selective affibody, ZHER2:342 (ZHER2), and a dimeric α-helical leucine- and lysine-rich peptide, LK-2. ZHER2 and LK-2 are linearly fused together and expressed in a prokaryotic system to create the LK-2-ZHER2 protein, which can successfully distinguish and penetrate HER2-overexpressing cancer cells at nanomolar concentrations. LK-2-ZHER2 has the ability to intracellularly deliver doxorubicin as a conjugate form to enhance its anti-cancer effect on HER2-overexpressing breast cancer cells with a great selectivity. The selective penetrability was confirmed in vitro, in 3D spheroids, and in in vivo models. LK-2-ZHER2 has the capability to overcome the weak points of current CPPs, such as poor penetrability at low concentrations and a lack of selectivity, by combining powerful CPP and affibody sequences.

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity.

Activation entropy (ΔS ‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ‡ of 16.02 cal·mol-1·K-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

A beneficial role of computer-aided diagnosis system for less experienced physicians in the diagnosis of thyroid nodule on ultrasound.

Ultrasonography (US) is the primary diagnostic tool for thyroid nodules, while the accuracy is operator-dependent. It is widely used not only by radiologists but also by physicians with different levels of experience. The aim of this study was to investigate whether US with computer-aided diagnosis (CAD) has assisting roles to physicians in the diagnosis of thyroid nodules. 451 thyroid nodules evaluated by fine-needle aspiration cytology following surgery were included. 300 (66.5%) of them were diagnosed as malignancy. Physicians with US experience less than 1 year (inexperienced, n = 10), or more than 5 years (experienced, n = 3) reviewed the US images of thyroid nodules with or without CAD assistance. The diagnostic performance of CAD was comparable to that of the experienced group, and better than those of the inexperienced group. The AUC of the CAD for conventional PTC was higher than that for FTC and follicular variant PTC (0.925 vs. 0.499), independent of tumor size. CAD assistance significantly improved diagnostic performance in the inexperienced group, but not in the experienced groups. In conclusion, the CAD system showed good performance in the diagnosis of conventional PTC. CAD assistance improved the diagnostic performance of less experienced physicians in US, especially in diagnosis of conventional PTC.

Comparison of Korean vs. American Thyroid Imaging Reporting and Data System in Malignancy Risk Assessment of Indeterminate Thyroid Nodules.

BACKGROUND: The management of cytologically indeterminate thyroid nodules is challenging for clinicians. This study aimed to compare the diagnostic performance of the Korean Thyroid Imaging Reporting and Data Systems (K-TIRADS) with that of the American College of Radiology (ACR)-TIRADS for predicting the malignancy risk of indeterminate thyroid nodules. METHODS: Thyroid nodules diagnosed by fine-needle aspiration (FNA) followed by surgery or core needle biopsy at a single referral hospital were enrolled. RESULTS: Among 200 thyroid nodules, 78 (39.0%) nodules were classified as indeterminate by FNA (Bethesda category III, IV, and V), and 114 (57.0%) nodules were finally diagnosed as malignancy by surgery or core needle biopsy. The area under the curve (AUC) was higher for FNA than for either TIRADS system in all nodules, while all three methods showed similar AUCs for indeterminate nodules. However, for Bethesda category III nodules, applying K-TIRADS 5 significantly increased the risk of malignancy compared to a cytological examination alone (50.0% vs. 26.5%, P=0.028), whereas applying ACR-TIRADS did not lead to a change. CONCLUSION: K-TIRADS and ACR-TIRADS showed similar diagnostic performance in assessing indeterminate thyroid nodules, and K-TIRADS had beneficial effects for malignancy prediction in Bethesda category III nodules.

Diagnosing thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance cytology with the deep convolutional neural network.

To compare the diagnostic performances of physicians and a deep convolutional neural network (CNN) predicting malignancy with ultrasonography images of thyroid nodules with atypia of undetermined significance (AUS)/follicular lesion of undetermined significance (FLUS) results on fine-needle aspiration (FNA). This study included 202 patients with 202 nodules ≥ 1 cm AUS/FLUS on FNA, and underwent surgery in one of 3 different institutions. Diagnostic performances were compared between 8 physicians (4 radiologists, 4 endocrinologists) with varying experience levels and CNN, and AUS/FLUS subgroups were analyzed. Interobserver variability was assessed among the 8 physicians. Of the 202 nodules, 158 were AUS, and 44 were FLUS; 86 were benign, and 116 were malignant. The area under the curves (AUCs) of the 8 physicians and CNN were 0.680-0.722 and 0.666, without significant differences (P > 0.05). In the subgroup analysis, the AUCs for the 8 physicians and CNN were 0.657-0.768 and 0.652 for AUS, 0.469-0.674 and 0.622 for FLUS. Interobserver agreements were moderate (k = 0.543), substantial (k = 0.652), and moderate (k = 0.455) among the 8 physicians, 4 radiologists, and 4 endocrinologists. For thyroid nodules with AUS/FLUS cytology, the diagnostic performance of CNN to differentiate malignancy with US images was comparable to that of physicians with variable experience levels.

Sequencing Cell-free Fetal DNA in Pregnant Women With GCK-MODY.

CONTEXT: Individuals with monogenic diabetes due to inactivating glucokinase (GCK) variants typically do not require treatment, except potentially during pregnancy. In pregnancy, fetal GCK genotype determines whether treatment is indicated, but noninvasive methods are not clinically available. OBJECTIVE: This work aims to develop a method to determine fetal GCK genotype noninvasively using maternal cell-free fetal DNA. METHODS: This was a proof-of-concept study involving 3 pregnant women with a causal GCK variant that used information from 1) massive parallel sequencing of maternal plasma cell-free DNA, 2) direct haplotype sequences of maternal genomic DNA, and 3) the paternal genotypes to estimate relative haplotype dosage of the pathogenic variant-linked haplotype. Statistical testing of variant inheritance was performed using a sequential probability ratio test (SPRT). RESULTS: In each of the 3 cases, plasma cell-free DNA was extracted once between gestational weeks 24 and 36. The fetal fraction of cell-free DNA ranged from 21.8% to 23.0%. Paternal homozygous alleles that were identical to the maternal GCK variant-linked allele were not overrepresented in the cell-free DNA. Paternal homozygous alleles that were identical to the maternal wild-type-linked allele were significantly overrepresented. Based on the SPRT, we predicted that all 3 cases did not inherit the GCK variant. Postnatal infant genotyping confirmed our prediction in each case. CONCLUSION: We have successfully implemented a noninvasive method to predict fetal GCK genotype using cell-free DNA in 3 pregnant women carrying an inactivating GCK variant. This method could guide tailoring of hyperglycemia treatment in pregnancies of women with GCK monogenic diabetes.

Use of serotonin reuptake inhibitors and risk of subsequent bone loss in a nationwide population-based cohort study.

This study examined whether the use of SRIs is associated with an increased risk of bone loss using a nested case-control design with a nationwide population-based cohort in Korea. Using the Korean National Health Screening Cohort, subjects newly diagnosed with osteoporosis or osteopenia (n = 55,799) were matched with controls (n = 278,995) at a ratio of 1:5. We stratified the participants by their time-dependent use of SRIs and sex and controlled for various confounders, including lifestyle habits, laboratory data, and comorbidities. Conditional logistic regression showed that both recent and former users of SRIs had an increased risk of subsequent bone loss compared with non-users: men [recent users: odds ratio (OR) 1.35, 95% confidential interval (CI) 1.20, 1.53; former-users: OR 1.10, 95% CI 1.01, 1.20]; women (recent users: OR 1.38, 95% CI 1.28-1.48; former-users: OR 1.07, 95% CI 1.02, 1.21). The use of SRIs was associated with an increased risk of bone loss in both men and women. In particular, the association was stronger in recent users. These findings provide population-level evidence for the risk of bone loss associated with SRI exposure and highlight the importance of monitoring the bone health of SRI users.

Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications.

Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.

Sex differences in sarcopenia and frailty among community-dwelling Korean older adults with diabetes: The Korean Frailty and Aging Cohort Study.

AIMS/INTRODUCTION: We aimed to examine the prevalence of sarcopenia and frailty in Korean older adults with diabetes compared with individuals without diabetes. MATERIALS AND METHODS: We analyzed the data of 2,403 participants aged 70-84 years enrolled in the Korean Frailty and Aging Cohort Study. Sarcopenia was defined using the Asian Working Group for Sarcopenia and the Foundation for the National Institutes of Health. Frailty was assessed by the Cardiovascular Health Study frailty phenotype criteria. RESULTS: The mean age of the participants was 76.0 ± 3.9 years, and 47.2% were men. The prevalence of diabetes was 30.2% in men and 25.8% in women. Adults with diabetes showed a lower muscle mass index (appendicular skeletal muscle mass/body mass index) and handgrip strength in both sexes, but only the women showed decreased physical performance. Women with diabetes presented a higher prevalence of sarcopenia diagnosed by the Foundation for the National Institutes of Health criteria, and frailty compared with participants without diabetes (sarcopenia 14.7% vs 8.5%, P = 0.001; frailty 9.5% vs 4.9%, P = 0.003). Men in the high and middle tertiles for homeostatic model assessment of insulin resistance presented a significantly higher prevalence of sarcopenia, compared with men in the low tertile homeostatic model assessment of insulin resistance (high tertile 16.6%, middle tertile 13.3%, low tertile 8.6%). CONCLUSIONS: In older adults with diabetes, muscle mass index and muscle strength were lower than in those without diabetes. However, the prevalence of sarcopenia and frailty was higher and physical performance was lower only in women with diabetes.

Helicity Control of Polymeric Backbones with Alternating cis-trans Double Bonds in Cyclopolymerized Dipropargyl Amides.

We report the synthesis of new helical polymeric structures having alternating cis and trans double bonds and chiral amino acid side chains by metathesis cyclopolymerization. The polymer helicity, which is generated by the interaction between fluorenylmethyloxycarbonyl (Fmoc) groups in the side chains, is dramatically affected by solvents. A thorough experimental and theoretical analysis including nuclear magnetic resonance, atomic force microscopy, and density functional theory and molecular mechanics calculations suggests that the helicity of both backbone and side chains are determined by anti-syn rotation of the carbamate groups and by the different interactions of the Fmoc groups with solvents.

Association between muscle strength and advanced fibrosis in non-alcoholic fatty liver disease: a Korean nationwide survey.

BACKGROUND: We investigated the association between muscle strength and the prevalence of advanced fibrosis among individuals with non-alcoholic fatty liver disease (NAFLD) using a nationwide cross-sectional survey. METHODS: Individuals, 20 to 79 years of age, from the Korean National Health and Nutrition Examination Surveys (KNHANES) from 2014 to 2016 were selected (N = 14 861), with sample weights applied. Muscle strength was quantified as the handgrip strength divided by the body mass index (BMI); low muscle strength (LMS) was defined as the lowest quartile (Q1 ) of the handgrip strength/BMI for our sample population. NAFLD was defined as hepatic steatosis index >36. Advanced fibrosis was defined as a fibrosis-4 index score ≥1.30 (FibrosisFIB4 ). RESULTS: The mean age of the study population was 45.6 ± 0.2 years, and 42.4% were male. As muscle strength increased, the mean BMI and age decreased accordingly, and the proportions of diabetes, dyslipidaemia, hypertension, and obesity decreased significantly (P < 0.001 for all). In a crude analysis, the LMS was associated with an increased prevalence of NAFLD (odds ratio [OR] 3.62, 95% confidence interval [CI] 3.25-4.03, P < 0.001), which remained significant even after adjustment for age, sex, obesity, insulin resistance, diabetes, hypertension, dyslipidaemia, and high-sensitivity C-reactive protein (OR 1.66, 95% CI 1.28-2.16, P < 0.001). In this logistic regression model, the prevalence of NAFLD decreased by 24% with each quartile increment in muscle strength (OR 0.76, 95% CI 0.68-0.85, P < 0.001). Among individuals with NAFLD (n = 2092), LMS was significantly associated with the presence of advanced fibrosis (FibrosisFIB4 ) independently of age, sex, obesity, diabetes, hypertension, dyslipidaemia, and high-sensitivity C-reactive protein (OR 1.66, 95% CI 1.01-2.49, P = 0.015), which lost its statistical significance after additional adjustment for insulin resistance. CONCLUSIONS: Low muscle strength is independently associated with NAFLD. The significant association between LMS and advanced fibrosis in NAFLD may be mediated through insulin resistance.

De novo formation of citrate-based fluorophores on N-termini of peptides and proteins in cells and tissues.

We developed a new method for the de novo formation of fluorophores based on citrate (DNFC) in biological samples. Use of an amide coupling reagent and microwave irradiation greatly facilitates the fluorophore formation on peptides and proteins with N-terminal cysteine or serine. Since N-terminal cysteine and serine can form thiazolopyridone- or oxazolopyridone-based fluorophores emitting blue and green fluorescence, respectively, by the DNFC staining, each organelle, cell and tissue exhibited a characteristic fluorescence distribution. The DNFC staining is able to provide a new potential protocol for future cell imaging, histology and diagnosis.

Metabolomic profiles of induced pluripotent stem cells derived from patients with rheumatoid arthritis and osteoarthritis.

BACKGROUND: Metabolomics is the systemic study of the unique fingerprints of metabolites involved in cellular processes and biochemical reactions. The metabolomic approach is useful in diagnosing and predicting the development of rheumatoid arthritis (RA) and osteoarthritis (OA) and is emerging as a useful tool for identifying disease biomarkers. The aim of this study was to compare the metabolic blueprint of fibroblast-like synoviocyte (FLS) cells and induced pluripotent stem cells (iPSCs) derived from RA and OA patients. METHODS: Somatic cells of RA patients (n = 3) and OA patients (n = 3) were isolated, transduced with a lentiviral plasmid, and reprogrammed into iPSCs displaying pluripotency. Metabolic profiling of RA and OA patient-derived FLS cells and iPSCs was performed using liquid chromatography/mass spectrometry and statistical analysis. After normalization by the sum of the peak intensities through LC/MS, 37 metabolites were detected across RA and OA patients. RESULTS: The metabolites of RA and OA were distinguishable according to the PLS-DA analysis. LysoPC (20:4), 4-methoxychalcone, phosphorylcholine, and nicotinamide (NAM) were significantly higher in RA iPSCs than in OA iPSCs (p < 0.05). The NMNAT-3 enzyme, which catalyzes an important step in the biosynthesis of NAD+ from adenosine triphosphate, was also upregulated in RA iPSCs. Interestingly, the proliferation of RA iPSCs was significantly greater than OA iPSC proliferation (p < 0.05). NAM played a critical role in the proliferation of RA iPSCs but not in OA iPSCs. When iPSCs were treated with 100 nM of the NAM inhibitor tannic acid (TA), the proliferation of RA iPSCs was significantly reduced (p < 0.001). CONCLUSIONS: The metabolites of RA and OA FLS cells and RA and OA iPSCs were all clearly distinguishable from each other. NAM played a critical role in the proliferation of RA iPSCs but not in OA iPSCs. TA effectively inhibited the expression of NAM in RA iPSCs and is a possible effective treatment for RA patients.

Guanidine cyclic diimides and their polymers.

We report the formation and degradation of a unique guanidine cyclic diimide (GCDI) structure and GCDI-based polymers. The GCDI structure is readily formed under mild conditions. The X-ray crystal structure showed that the delocalized π-orbitals in the guanidine plane are significantly disrupted in the GCDI structure. Unlike amine-based imides, the GCDI structure readily degrades into the initial guanidine in protic solvents at ambient temperatures. Furthermore, poly(GCDI)s, a new category of polymers with the GCDI backbones, can be synthesized from guanidines and dianhydrides. Similar to the monomeric GCDIs, poly(GCDI)s are degraded in protic solvents unlike polyimides with high chemical stability.

In Vitro and In Vivo Antimicrobial Activity of Antibiotic-Conjugated Carriers with Rapid pH-Responsive Release Kinetics.

Two representative antibiotics, cephradine (CP) and moxifloxacin (MX), are covalently conjugated with a ß-cyclodextrin (ß-CD)-based carrier via pH-responsive 1-methyl-2-(2'-carboxyethyl) maleic acid amide (MCM) linkers with excellent conjugation efficiency via simple mixing. At pH 5.5, 90% and 80% of the CP and MX, respectively, are released from the carriers within 30 min, in contrast with the much-delayed release profile at pH 7.4. The in vitro inhibitory effect of ß-CD-MCM-CP on the growth of Staphylococcus aureus is significantly lower than that of free CP at pH 7.4, but it reaches the level of free CP at pH 5.5. Moreover, S. aureus develops significant CP resistance after pretreatment with free CP, whereas the initial CP sensitivity is maintained after pretreatment with ß-CD-MCM-CP at pH 7.4. However, ß-CD-MCM-MX exhibits no such pH-responsive activity against Bacteroides fragilis, probably due to the insufficient stability of the MX conjugation at pH 7.4. In nondiabetic and diabetic mouse models, ß-CD-MCM-CP significantly reduces the subcutaneous abscess scores and the bacterial counts in the abscess, although this represents only a marginal improvement in antimicrobial activity compared to free CP.

Association between deterioration in muscle strength and peripheral neuropathy in people with diabetes.

AIMS: Diabetic peripheral neuropathy (DPN) is a major risk factor for sarcopenia or frailty in older patients with diabetes. In this study, we investigated the association between DPN and muscle strength in type 2 diabetes. METHODS: DPN was assessed using the Michigan Neuropathy Screening Instrument Questionnaire (MNSI-Q) and Physical Examination (MNSI-PE) in 230 subjects with type 2 diabetes. Handgrip strength (HGS) was measured using an electronic grip strength dynamometer. RESULTS: The prevalence of DPN was 26.4% in men and 34.7% in women. HGS was significantly lower in men with DPN compared with men without DPN (27.0 ±â€¯9.4 vs. 29.7 ±â€¯8.4 kg, p = 0.036). This effect was not seen in women. In men, multivariate regression analysis showed that HGS was negatively associated with the MNSI-Q (ß = -1.200, p = 0.003) and MNSI-PE scores (ß = -0.937, p = 0.046) and resulted in an abnormal 10-gram monofilament test score (ß = -10.895, p < 0.001). However, HGS was not significantly associated with neuropathy in women. CONCLUSIONS: Muscle strength was lower in men with DPN than in those without DPN. Assessment of muscle function may have clinical implications in the prevention of sarcopenia and frailty in men with DPN.

Progression to Gestational Diabetes Mellitus in Pregnant Women with One Abnormal Value in Repeated Oral Glucose Tolerance Tests.

BACKGROUND: Women with one abnormal value (OAV) in a 100 g oral glucose tolerance test (OGTT) during pregnancy are reported to have an increased risk of adverse pregnancy outcomes. However, there is limited data about whether women with OAV will progress to gestational diabetes mellitus (GDM) when the OGTT is repeated. METHODS: To identify clinical and metabolic predictors for GDM in women with OAV, we conducted a retrospective study and identified women with OAV in the OGTT done at 24 to 30 weeks gestational age (GA) and repeated the second OGTT between 32 and 34 weeks of GA. RESULTS: Among 137 women with OAV in the initial OGTT, 58 (42.3%) had normal, 40 (29.2%) had OAV and 39 (28.5%) had GDM in the second OGTT. Maternal age, prepregnancy body mass index, weight gain from prepregnancy to the second OGTT, GA at the time of the OGTT, and parity were similar among normal, OAV, and GDM groups. Plasma glucose levels in screening tests were different (151.8±15.7, 155.8±14.6, 162.5±20.3 mg/dL, P<0.05), but fasting, 1-, 2-, and 3-hour glucose levels in the initial OGTT were not. Compared to women with screen negative, women with untreated OAV had a higher frequency of macrosomia. CONCLUSION: We demonstrated that women with OAV in the initial OGTT significantly progressed to GDM in the second OGTT. Clinical parameters predicting progression to GDM were not found. Repeating the OGTT in women with OAV in the initial test may be helpful to detect GDM progression.

Development of microsatellite markers and the genetic diversity of Myocastor coypus introduced to South Korea.

The nutria (Myocastor coypus) was introduced to South Korea in 1987 for breeding of individuals for fur and meat industry, and was accidentally released into the wild. Here, we report the development of microsatellites for the nutria collected from South Korea using Illumina MiSeq genome sequencing to identify the genetic variability and demographic history of these introduced populations. A total of 626,282 microsatellite sequences were identified, and nine polymorphic loci were characterized. We used four novel loci developed and three previously known loci to investigate the genetic diversity of twelve South Korean populations. A low level of diversity was found, and no signature of genetic structuring was revealed among populations, indicating that Korean nutria individuals originated from a single population or a highly inbred reared herd.