Escherichia coli cryptic prophages sense nutrients to influence persister cell resuscitation.

Cryptic prophages are not genomic junk but instead enable cells to combat myriad stresses as an active stress response. How these phage fossils affect persister cell resuscitation has, however, not been explored. Persister cells form as a result of stresses such as starvation, antibiotics and oxidative conditions, and resuscitation of these persister cells likely causes recurring infections such as those associated with tuberculosis, cystic fibrosis and Lyme disease. Deletion of each of the nine Escherichia coli cryptic prophages has no effect on persister cell formation. Strikingly, elimination of each cryptic prophage results in an increase in persister cell resuscitation with a dramatic increase in resuscitation upon deleting all nine prophages. This increased resuscitation includes eliminating the need for a carbon source and is due to activation of the phosphate import system resulting from inactivating the transcriptional regulator AlpA of the CP4-57 cryptic prophage. Deletion of alpA increases persister resuscitation, and AlpA represses phosphate regulator PhoR. Both phosphate regulators PhoP and PhoB stimulate resuscitation. This suggests a novel cellular stress mechanism controlled by cryptic prophages: regulation of phosphate uptake which controls the exit of the cell from dormancy and prevents premature resuscitation in the absence of nutrients.

Evaluation of the Effects of Developmental Trauma on Neurotransmitter Systems Using Functional Molecular Imaging.

Early life stress (ELS) is strongly associated with psychiatric disorders such as anxiety, depression, and schizophrenia in adulthood. To date, biological, behavioral, and structural aspects of ELS have been studied extensively, but their functional effects remain unclear. Here, we examined NeuroPET studies of dopaminergic, glutamatergic, and serotonergic systems in ELS animal models. Maternal separation and restraint stress were used to generate single or complex developmental trauma. Body weights of animals exposed to single trauma were similar to those of control animals; however, animals exposed to complex trauma exhibited loss of body weight when compared to controls. In behavioral tests, the complex developmental trauma group exhibited a decrease in time spent in the open arm of the elevated plus-maze and an increase in immobility time in the forced swim test when compared to control animals. In NeuroPET studies, the complex trauma group displayed a reduction in brain uptake values when compared to single trauma and control groups. Of neurotransmitter systems analyzed, the rate of decrease in brain uptake was the highest in the serotonergic group. Collectively, our results indicate that developmental trauma events induce behavioral deficits, including anxiety- and depressive-like phenotypes and dysfunction in neurotransmitter systems.

mIoT: Metamorphic IoT Platform for On-Demand Hardware Replacement in Large-Scaled IoT Applications.

As the Internet of Things (IoT) is becoming more pervasive in our daily lives, the number of devices that connect to IoT edges and data generated at the edges are rapidly increasing. On account of the bottlenecks in servers, due to the increase in data, as well as security and privacy issues, the IoT paradigm has shifted from cloud computing to edge computing. Pursuant to this trend, embedded devices require complex computation capabilities. However, due to various constraints, edge devices cannot equip enough hardware to process data, so the flexibility of operation is reduced, because of the limitations of fixed hardware functions, relative to cloud computing. Recently, as application fields and collected data types diversify, and, in particular, applications requiring complex computation such as artificial intelligence (AI) and signal processing are applied to edges, flexible processing and computation capabilities based on hardware acceleration are required. In this paper, to meet these needs, we propose a new IoT platform, called a metamorphic IoT (mIoT) platform, which can various hardware acceleration with limited hardware platform resources, through on-demand transmission and reconfiguration of required hardware at edges instead of via transference of sensing data to a server. The proposed platform reconfigures the edge's hardware with minimal overhead, based on a probabilistic value, known as callability. The mIoT consists of reconfigurable edge devices based on RISC-V architecture and a server that manages the reconfiguration of edge devices based on callability. Through various experimental results, we confirmed that the callability-based mIoT platform can provide the hardware required by the edge device in real time. In addition, by performing various functions with small hardware, power consumption, which is a major constraint of IoT, can be reduced.

Improving feature selection performance using pairwise pre-evaluation.

BACKGROUND: Biological data such as microarrays contain a huge number of features. Thus, it is necessary to select a small number of novel features to characterize the entire dataset. All combinations of the features subset must be evaluated to produce an ideal feature subset, but this is impossible using currently available computing power. Feature selection or feature subset selection provides a sub-optimal solution within a reasonable amount of time. RESULTS: In this study, we propose an improved feature selection method that uses information based on all the pairwise evaluations for a given dataset. We modify the original feature selection algorithms to use pre-evaluation information. The pre-evaluation captures the quality and interactions between two features. The feature subset should be improved by using the top ranking pairs for two features in the selection process. CONCLUSIONS: Experimental results demonstrated that the proposed method improved the quality of the feature subset produced by modified feature selection algorithms. The proposed method can be applied to microarray and other high-dimensional data.

Whole Genome Re-Sequencing of Three Domesticated Chicken Breeds.

Chicken is one of the most popular domesticated species worldwide, as it can serve an important role in agricultural as well as biomedical research fields. Because it inhabits almost every continent and presents diverse morphology and traits, the need of genetic markers for distinguishing each breed for various purposes has increased. The whole genome sequencing of three different breeds (White Leghorn, Korean domestic, and Araucana) that show similar coloring patterns, with the exception of the White Leghorn breed, have confirmed previously reported genomic alterations and identified many novel variants. Additionally, the Whole Genome Re-Sequencing (WGRS) approach identified an approximately 4 kb insert within SLCO1B3 responsible for blue egg shell color. Targeted investigation of pigment-related genes corroborated previously reported non-synonymous mutations, and provided deeper insight into chicken coloring, where not a single but a combination of non-synonymous mutations in the MC1R gene is likely to be responsible for altered feather coloring.

Lactobacillus plantarum L67 glycoprotein protects against cadmium chloride toxicity in RAW 264.7 cells.

The food and water we consume may be contaminated with a range of chemicals and heavy metals, such as lead, cadmium, arsenic, chromium, and mercury by accumulation through the food chain. Cadmium is known to be one of the major components in cigarette smoke and can cause lesions in many organs. Some lactobacilli can bind and remove heavy metals such as cadmium, lead, and copper. However, the mechanisms of cadmium toxicity and inhibition by probiotics are not clear. In this study, we demonstrated that glycoprotein (18 kDa) isolated from Lactobacillus plantarum L67 protected RAW 264.7 cells from expression of inflammation-related factors stimulated by cadmium chloride (100 µM). Furthermore, we evaluated the cytotoxicity of cadmium using the MTT assay and intracellular Ca(2+) using fluorescence, and assessed activities of activator protein kinase C (PKC-α), inducible nitric oxide synthase, activator protein (AP)-1, and mitogen-activated protein kinases using immunoblot. Our results indicated that glycoprotein isolated from L. plantarum L67 inhibited intracellular Ca(2+) mobilization. It also significantly suppressed inflammatory factors such as AP-1 (c-Jun and c-Fos), mitogen-activated protein kinases (ERK, JNK, and p38), and inducible nitric oxide synthase. Our findings suggest that the 24-kDa glycoprotein isolated from L. plantarum L67 might be used as a food component for protection of inflammation caused by cadmium ion.

The anti-allergic activity of Lactobacillus plantarum L67 and its application to yogurt.

Recently, interest in the beneficial role of probiotics in the protection and management of allergic diseases caused by immune disorders has been increasing. This study investigated the inhibitory effect of Lactobacillus plantarum L67 on induced allergic inflammatory response in bisphenol A-treated rat basophilic leukemia 2H3 (RBL-2H3) cells and mouse splenocytes. We also evaluated the applicability of L. plantarum L67 as a yogurt starter culture. We measured the ability of Lactobacillus strains to induce the production of IL-12 and IFN- γ in cultured splenocytes by ELISA. Bisphenol A (50µM)-treated RBL-2H3 cells were cotreated with a glycoprotein (18kDa) isolated from L. plantarum L67 (5-100µg/mL) for 30min. We measured the expression of mitogen-activated protein kinase (ERK and p38), AP-1 (c-Fos and c-Jun), T-bet, and GATA-binding protein 3 (GATA-3) using Western blotting to examine the differentiation of T helper cells. Furthermore, we evaluated the gene expression of IL-1ß, IL-6, and IL-10 using real-time quantitative PCR. Finally, we evaluated the applicability of L. plantarum L67 as a yogurt starter by measuring pH, enumeration of bacteria, and sensory scores. Our results showed that L67 protein inhibited the phosphorylation of ERK and p38 mitogen-activated protein kinase through the transcriptional activation of AP-1 in bisphenol A-treated RBL-2H3 cells. During differentiation of T helper cells, the expression of transcription factor GATA-3 was significantly suppressed by L67 protein (100µg/mL) treatment, whereas expression of transcription factor T-bet was increased. In addition, the L67 protein significantly attenuated the expression of T helper 2-linked cytokines IL-1ß, IL-6, and IL-10. These results indicate that L. plantarum L67, made available as yogurt starters and dietary supplements, has the potential to prevent allergy-related immune disorders.

Antimicrobial activity of the synthesized non-allergenic urushiol derivatives.

Synthesized urushiol derivatives possessing different carbon atomic length in the alkyl side chain inhibited the growth of food spoilage and pathogenic microorganisms. Particularly, non-allergenic 3-pentylcatechol showed a broad antimicrobial spectrum on an agar plate. Most food spoilage and pathogenic microorganisms were sensitive to urushiol derivatives in the liquid culture. The morphologies of the microorganisms were changed after treatment of 3-pentylcatechol.

Development of fluorescence-based liposome immunoassay for detection of Cronobacter muytjensii in pure culture.

Cronobacter spp. are important foodborne pathogens that carry a very high risk of infection to neonates as well as immunocompromised individuals. In the present study, fluorescence-based liposome immunoassay was developed as a new sensitive and rapid diagnostic system for detection of Cronobacter muytjensii (C. muytjensii). Liposomes (size, 206 nm) used in this study were made from cholesterol, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)], and sulforhodamine B (SRB). The outer surface of liposome was conjugated with rabbit anti-C. muytjensii IgG in order to develop immunoliposome. The immunoliposome was incubated with C. muytjensii, which was coated on a 96-well plate. Immunoliposomes bound to C. muytjensii were lysed with 30 mM octyl ß-D-glucopyranoside, after which the SRB fluorescence signal was measured at an excitation wavelength of 550 nm and emission wavelength of 585 nm. The signal was directly proportional to the amount of bacterial cells in the test sample. The developed fluorescence-based liposome immunoassay was confirmed to be highly specific to C. muytjensii with a detection limit of 6.3 × 10(4) CFU ml(-1) in pure culture as well as sensitive, efficient, and rapid when compared to culture-based methods. Based on its rapid efficiency and low cost, this fluorescence-based liposome immunoassay may be used to develop diagnostic kits for C. muytjensii detection.

Inhibitory effects of the κ-casein macropeptide isolated from milk protein on the biofilm formation and virulence of Listeria monocytogenes.

We demonstrate the inhibitory effects of κ-casein macropeptide (CMP) on the biofilm formation and virulence of Listeria monocytogenes Scott A. The inhibition of biofilm formation by CMP was initially investigated by using the protocol applied for the 96-well microtiter plate assay. Low concentrations of CMP (0.1, 0.2, 0.3, 0.4, and 0.5 mg/mL) that were tested resulted in a profound inhibitory effect on biofilm formation at a concentration of 0.4 mg/mL. CMP also significantly repressed the transcription of inlA (encoding internalin A) that was responsible for the initial adhesion and invasion event, and prolonged the survival of Caenorhabditis elegans infected by L. monocytogenes. Two-dimensional gel electrophoresis showed that newly identified proteins in the presence of CMP were involved in the stress response and metabolic processes that have important roles in developing listerial biofilms. Our results suggest that CMP from milk protein would be capable of eliminating biofilm formation and virulence by L. monocytogenes in the food industry.

Lactobacillus Persisters Formation and Resuscitation.

Lactobacillus is a commonly used probiotic, and many researchers have focused on its stress response to improve its functionality and survival. However, studies on persister cells, dormant cells that aid bacteria in surviving general stress, have focused on pathogenic bacteria that cause infection, not Lactobacillus. Thus, understanding Lactobacillus persister cells will provide essential clues for understanding how Lactobacillus survives and maintains its function under various environmental conditions. We treated Lactobacillus strains with various antibiotics to determine the conditions required for persister formation using kill curves and transmission electron microscopy. In addition, we observed the resuscitation patterns of persister cells using single-cell analysis. Our results show that Lactobacillus creates a small population of persister cells (0.0001-1% of the bacterial population) in response to beta-lactam antibiotics such as ampicillin and amoxicillin. Moreover, only around 0.5-1% of persister cells are heterogeneously resuscitated by adding fresh media; the characteristics are typical of persister cells. This study provides a method for forming and verifying the persistence of Lactobacillus and demonstrates that antibiotic-induced Lactobacillus persister cells show characteristics of dormancy, sensitivity of antibiotics, same as exponential cells, multi-drug tolerance, and resuscitation, which are characteristics of general persister cells. This study suggests that the mechanisms of formation and resuscitation may vary depending on the characteristics, such as the membrane structure of the bacterial species.

Robust metabolic syndrome risk score based on triangular areal similarity.

One of the limitations of currently-used metabolic syndrome (MetS) risk calculations is that they often depend on sample characteristics. To address this, we introduced a novel sample-independent risk quantification method called 'triangular areal similarity' (TAS) that employs three-axis radar charts constructed from five MetS factors in order to assess the similarity between standard diagnostic thresholds and individual patient measurements. The method was evaluated using large datasets of Korean (n = 72,332) and American (n = 11,286) demographics further segmented by sex, age, and race. The risk score exhibited a strong positive correlation with the number of abnormal factors and was closely aligned with the current diagnostic paradigm. The proposed score demonstrated high diagnostic accuracy and robustness, surpassing previously reported risk scores. This method demonstrated superior performance and stability when tested on cross-national datasets. This novel sample-independent approach has the potential to enhance the precision of MetS risk prediction.

Lactobacillus amylovorus KU4 induces adipose browning in obese mice by regulating PP4C.

We previously reported that Lactobacillus amylovorus KU4 (LKU4) promotes adipocyte browning in mice fed a high-fat diet (HFD mice) in part by remodeling the PPARγ transcription complex. However, the mechanism through which LKU4 enables PPARγ to drive adipocyte browning remains elusive. Here, we report that LKU4 inhibits the expression of PP4C in inguinal white adipose tissue of HFD mice and in insulin-resistant 3T3-L1 adipocytes, which promotes SIRT1-dependent PPARγ deacetylation by activating AMPK, leading to the browning of adipocytes. Consistently, the silencing of PP4C further enhances this pathway. Furthermore, we observed that lactate, a key LKU4 metabolite, reduces insulin-induced PP4C expression and suppresses PP4C inhibition of PPARγ deacetylation and transcriptional activity via AMPK-SIRT1, thereby facilitating the browning of adipocytes. Together, these data demonstrate that LKU4 promotes the AMPK-SIRT1-PPARγ pathway by inhibiting PP4C, thereby facilitating adipocyte browning in HFD mice.

Inhibitory Effects of Latilactobacillus curvatus BYB3 Cell-Free Extract on Human Melanoma B16F10 Cells and Tumorigenic Mice.

Latilactobacillus curvatus BYB3 (BYB3) is a species of lactic acid bacteria, formerly named Lactobacillus curvatus, which is isolated from kimchi. In this study, the effect of BYB3, Lactobacillus rhamnosus GG, and Lactobacillus acidophilus GP1B strain extracts at various concentrations was examined on B16F10, a mouse melanoma cell line. Cell viability was examined via MTT assay, and the results indicated that compared to the other two probiotics, BYB3 significantly decreased the total percentages of viable cells. The effects of BYB3 on cell migration and proliferation in B16F10 cells were evaluated using wound healing mobility and proliferation assays, respectively; the results indicated that BYB3 inhibits cell migration and proliferation in a concentration-dependent manner. Using human dermal fibroblast cells to investigate BYB3 extract in vivo had no effect on skin-related cells. Nonetheless, the BYB3 extract inhibited tumor growth in a mouse model, as demonstrated by liver slices. Therefore, this suggests that using BYB3 extract to inhibit melanoma may be a novel approach.

Reprogramming of mouse fibroblasts into induced pluripotent stem cells with Nanog.

Oct4-Sox2-Nanog transcriptional networks are critical for the maintenance of embryonic stem (ES) cell self-renewal and induction of pluripotency. However, in transcription factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), Nanog is initially dispensable and Oct4 remains the sole factor that could not be substituted/omitted. Here, we show that mouse fibroblasts could be reprogrammed into iPSCs by Nanog and Bmi1, which replaces Sox2, Klf4, and c-Myc, in the absence of Oct4. Furthermore, we show that in the presence of shh agonists (oxysterol and purmophamine), which replaces the function of Bmi1, a single transcription factor, Nanog is sufficient to reprogram mouse fibroblasts into iPSCs. Nanog-induced iPSCs resemble mESCs in terms of morphology, global gene expression profiles, epigenetic status and pluripotency both in vitro and in vivo. These findings support that Nanog can replace the Oct4 for the somatic cell reprogramming and underlie the mechanisms of Nanog in reprogramming process.

Possible involvement of Mycoplasma hominis in inhibiting the formation of biofilms by uropathogenic Escherichia coli (UPEC).

Here we examined the involvement of Mycoplasma hominis in the formation of biofilms by uropathogenic Escherichia coli (UPEC) strain CFT073. Initially, we thought that M. hominis does not affect the fitness of UPEC, including the growth and production of signaling molecules, such as autoinducer-2 and indole. We found, however, that the presence of M. hominis significantly decreased the degree of biofilm formation by UPEC CFT073 (approximately a 60% reduction for 10(5) ccu/mL of M. hominis as compared with UPEC alone). We also found that it had a slight effect in inhibiting the attachment and cytotoxicity of UPEC CFT073. These findings are specific to these UPEC strains rather than to enterohemorrhagic E. coli (EHEC) strains, found in normal intestinal flora. In addition, we performed whole-transcriptome profiling and quantitative real-time polymerase chain reaction (qRT-PCR) analysis. This indicated that the PhoPQ system and the anti-termination protein (encoded by ybcQ) were involved in the reduction of biofilm formation by M. hominis (corroborated by qRT-PCR). Furthermore, our results indicate that M. hominis raises the degree of transcription of toxin genes, including hha and pasT. Hence, we suggest a possible role of M. hominis in affecting the formation of biofilms by UPEC in the urinary tract.

Machine learning-based predictive model for prevention of metabolic syndrome.

Metabolic syndrome (MetS) is a chronic disease caused by obesity, high blood pressure, high blood sugar, and dyslipidemia and may lead to cardiovascular disease or type 2 diabetes. Therefore, the detection and prevention of MetS at an early stage are imperative. Individuals can detect MetS early and manage it effectively if they can easily monitor their health status in their daily lives. In this study, a predictive model for MetS was developed utilizing solely noninvasive information, thereby facilitating its practical application in real-world scenarios. The model's construction deliberately excluded three features requiring blood testing, specifically those for triglycerides, blood sugar, and HDL cholesterol. We used a large-scale Korean health examination dataset (n = 70, 370; the prevalence of MetS = 13.6%) to develop the predictive model. To obtain informative features, we developed three novel synthetic features from four basic information: waist circumference, systolic and diastolic blood pressure, and gender. We tested several classification algorithms and confirmed that the decision tree model is the most appropriate for the practical prediction of MetS. The proposed model achieved good performance, with an AUC of 0.889, a recall of 0.855, and a specificity of 0.773. It uses only four base features, which results in simplicity and easy interpretability of the model. In addition, we performed calibrations on the prediction probability and calibrated the model. Therefore, the proposed model can provide MetS diagnosis and risk prediction results. We also proposed a MetS risk map such that individuals could easily determine whether they had metabolic syndrome.

The PKA-SREBP1c Pathway Plays a Key Role in the Protective Effects of Lactobacillus johnsonii JNU3402 Against Diet-Induced Fatty Liver in Mice.

SCOPE: The present study aims to assess the protective effect of Lactobacillus johnsonii JNU3402 (LJ3402) against diet-induced non-alcoholic fatty liver disease (NAFLD) and determine the mechanism underlying its beneficial effect on the liver in mice. METHODS AND RESULTS: Seven-week-old male mice are fed a high-fat diet (HFD) with or without oral supplementation of LJ3402 for 14 weeks. In mice fed an HFD, LJ3402 administration alleviates liver steatosis, diet-induced obesity, and insulin resistance with a decreased hepatic expression of sterol-regulatory element-binding protein-1c (SREBP-1c), fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC), and an increased phosphorylation of SREBP-1c. The mechanistic study shows that LJ3402 inhibits SREBP-1c transcriptional activity by enhancing protein kinase A (PKA)-mediated phosphorylation and reduces the expression of its lipogenic target genes in AML12 and HepG2 cells, thereby attenuating hepatic lipid accumulation. Moreover, silencing the PKA α catalytic subunit or the inhibition of PKA activity by H89 abolishes LJ3402 suppression of free fatty acid (FFA)-induced SREBP-1c activity in hepatocytes. In addition, LJ3402 administration elevates the plasma lactate levels in mice fed an HFD; this lactate increases PKA-mediated SREBP-1c phosphorylation in AML12 cells with a decreased expression of its target genes, reducing hepatic lipid accumulation. CONCLUSION: LJ3402 attenuates HFD-induced fatty liver in mice through the lactate-PKA-SREBP-1c pathway.

Complete genome sequence of Limosilactobacillus fermentum JNU532 as a probiotic candidate for the functional food and feed supplements.

Lactic acid bacteria (LAB) have been reported to possess various beneficial properties and are commonly used as probiotics. LAB play a crucial role in milk fermentation, industrial lactic acid fermentation, and health and medicine. Limosilactobacillus fermentum isolated from fermented dairy and food products is considered as 'Generally Recognized as Safe' by FDA. Limosilactobacillus fermentum plays an important role in modulation of the intestinal microbiota, enhancing the host immune system and improving feed digestibility. We isolated a probiotic candidate that was identified and named Limosilactobacillus fermentum JNU532. In a previous report, cell-free culture of L. fermentum JNU532 exhibited anti-melanogenic and antioxidant activities. In this study, we present the complete genome assembly of the bacterial strain JNU532. The final genome consists of one circular chromosome (2,077,416 base pairs) with a guanine + cytosine (GC) ratio of 51.5%.

Complete genome and two plasmids sequences of Lactiplantibacillus plantarum L55 for probiotic potentials.

In this study, we report the complete genome sequence of Lactiplantibacillus plantarum L55, a probiotic strain of lactic acid bacteria isolated from kimchi. The genome consists of one circular chromosome (2,077,416 base pair [bp]) with a guanine cytosine (GC) content of 44.5%, and two circular plasmid sequences (54,267 and 19,592 bp, respectively). We also conducted a comprehensive analysis of the genome, which identified the presence of functional genes, genomic islands, and antibiotic-resistance genes. The genome sequence data presented in this study provide insights into the genetic basis of L. plantarum L55, which could be beneficial for the future development of probiotic applications.