The RsfSR two-component system regulates SigF function by monitoring the state of the respiratory electron transport chain in Mycobacterium smegmatis.

In Mycobacterium smegmatis, the transcriptional activity of the alternative sigma factor SigF is posttranslationally regulated by the partner switching system consisting of SigF, the anti-SigF RsbW1, and three anti-SigF antagonists (RsfA, RsfB, and RsbW3). We previously demonstrated that expression of the SigF regulon is strongly induced in the Δaa3 mutant of M. smegmatis lacking the aa3 cytochrome c oxidase, the major terminal oxidase in the respiratory electron transport chain. Here, we identified and characterized the RsfSR two-component system involved in regulating the phosphorylation state of the major anti-SigF antagonist RsfB. RsfS (MSMEG_6130) is a histidine kinase with the cyclase/histidine kinase-associated sensing extracellular 3 domain at its N terminus, and RsfR (MSMEG_6131) is a receiver domain-containing protein phosphatase 2C-type phosphatase that can dephosphorylate phosphorylated RsfB. We demonstrated that phosphorylation of RsfR on Asp74 by RsfS reduces the phosphatase activity of RsfR toward phosphorylated RsfB and that the cellular abundance of the active unphosphorylated RsfB is increased in the Δaa3 mutant relative to the WT strain. We also demonstrated that the RsfSR two-component system is required for induction of the SigF regulon under respiration-inhibitory conditions such as inactivation of the cytochrome bcc1 complex and aa3 cytochrome c oxidase, as well as hypoxia, electron donor-limiting, high ionic strength, and low pH conditions. Collectively, our results reveal a key regulatory element involved in regulating the SigF signaling system by monitoring the state of the respiratory electron transport chain.

A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration.

The accumulation of misfolded and aggregated proteins is a hallmark of neurodegenerative proteinopathies. Although multiple genetic loci have been associated with specific neurodegenerative diseases (NDs), molecular mechanisms that may have a broader relevance for most or all proteinopathies remain poorly resolved. In this study, we developed a multi-layered network expansion (MLnet) model to predict protein modifiers that are common to a group of diseases and, therefore, may have broader pathophysiological relevance for that group. When applied to the four NDs Alzheimer's disease (AD), Huntington's disease, and spinocerebellar ataxia types 1 and 3, we predicted multiple members of the insulin pathway, including PDK1, Akt1, InR, and sgg (GSK-3ß), as common modifiers. We validated these modifiers with the help of four Drosophila ND models. Further evaluation of Akt1 in human cell-based ND models revealed that activation of Akt1 signaling by the small molecule SC79 increased cell viability in all models. Moreover, treatment of AD model mice with SC79 enhanced their long-term memory and ameliorated dysregulated anxiety levels, which are commonly affected in AD patients. These findings validate MLnet as a valuable tool to uncover molecular pathways and proteins involved in the pathophysiology of entire disease groups and identify potential therapeutic targets that have relevance across disease boundaries. MLnet can be used for any group of diseases and is available as a web tool at http://ssbio.cau.ac.kr/software/mlnet.

Long-wave infrared transparent sulfur polymers enabled by symmetric thiol cross-linker.

Infrared (IR) transmissive polymeric materials for optical elements require a balance between their optical properties, including refractive index (n) and IR transparency, and thermal properties such as glass transition temperature (Tg). Achieving both a high refractive index (n) and IR transparency in polymer materials is a very difficult challenge. In particular, there are significant complexities and considerations to obtaining organic materials that transmit in the long-wave infrared (LWIR) region, because of high optical losses due to the IR absorption of the organic molecules. Our differentiated strategy to extend the frontiers of LWIR transparency is to reduce the IR absorption of the organic moieties. The proposed approach synthesized a sulfur copolymer via the inverse vulcanization of 1,3,5-benzenetrithiol (BTT), which has a relatively simple IR absorption because of its symmetric structure, and elemental sulfur, which is mostly IR inactive. This strategy resulted in approximately 1 mm thick windows with an ultrahigh refractive index (nav > 1.9) and high mid-wave infrared (MWIR) and LWIR transmission, without any significant decline in thermal properties. Furthermore, we demonstrated that our IR transmissive material was sufficiently competitive with widely used optical inorganic and polymeric materials.

Effects on the Thermo-Mechanical and Interfacial Performance of Newly Developed PI-Sized Carbon Fiber-Polyether Ether Ketone Composites: Experiments and Molecular Dynamics Simulations.

In this study, polyether ether ketone (PEEK) composites reinforced with newly developed water-dispersible polyimide (PI)-sized carbon fibers (CFs) were developed to enhance the effects of the interfacial interaction between PI-sized CFs and a PEEK polymer on their thermo-mechanical properties. The PI sizing layers on these CFs may be induced to interact vigorously with the p-phenylene groups of PEEK polymer chains because of increased electron affinity. Therefore, these PI-sized CFs are effective for improving the interfacial adhesion of PEEK composites. PEEK composites were reinforced with C-CFs, de-CFs, and PI-sized CFs. The PI-sized CFs were prepared by spin-coating a water-dispersible PAS suspension onto the de-CFs, followed by heat treatment for imidization. The composites were cured using a compression molding machine at a constant temperature and pressure. Atomic force and scanning electron microscopy observations of the structures and morphologies of the carbon fiber surfaces verified the improvement of their thermo-mechanical properties. Molecular dynamics simulations were used to investigate the effects of PI sizing agents on the stronger interfacial interaction energy between the PI-sized CFs and the PEEK polymer. These results suggest that optimal amounts of PI sizing agents increased the interfacial properties between the CFs and the PEEK polymer.

Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions.

Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.

Analysis of the Structure and the Thermal Conductivity of Semi-Crystalline Polyetheretherketone/Boron Nitride Sheet Composites Using All-Atom Molecular Dynamics Simulation.

Thermal transport simulations were performed to investigate the important factors affecting the thermal conductivity based on the structure of semi-crystalline polyetheretherketone (PEEK), and the addition of boron nitride (BN) sheets. The molecular-level structural analysis facilitated the prediction of the thermal conductivity of the optimal structure of PEEK reflecting the best parameter value of the length of amorphous chains, and the ratio of linkage conformations, such as loops, tails, and bridges. It was found that the long heat transfer paths of polymer chains were induced by the addition of BN sheets, which led to the improvement of the thermal conductivities of the PEEK/BN composites. In addition, the convergence of the thermal conductivities of the PEEK/BN composites in relation to BN sheet size was verified by the disconnection of the heat transfer path due to aggregation of the BN sheets.

Adaptive autophagy reprogramming in Schwann cells during peripheral demyelination.

The myelin sheath is an essential structure for the rapid transmission of electrical impulses through axons, and peripheral myelination is a well-programmed postnatal process of Schwann cells (SCs), the myelin-forming peripheral glia. SCs transdifferentiate into demyelinating SCs (DSCs) to remove the myelin sheath during Wallerian degeneration after axonal injury and demyelinating neuropathies, and macrophages are responsible for the degradation of myelin under both conditions. In this study, the mechanism by which DSCs acquire the ability of myelin exocytosis was investigated. Using serial ultrastructural evaluation, we found that autophagy-related gene 7-dependent formation of a "secretory phagophore (SP)" and tubular phagophore was necessary for exocytosis of large myelin chambers by DSCs. DSCs seemed to utilize myelin membranes for SP formation and employed p62/sequestosome-1 (p62) as an autophagy receptor for myelin excretion. In addition, the acquisition of the myelin exocytosis ability of DSCs was associated with the decrease in canonical autolysosomal flux and was demonstrated by p62 secretion. Finally, this SC demyelination mechanism appeared to also function in inflammatory demyelinating neuropathies. Our findings show a novel autophagy-mediated myelin clearance mechanism by DSCs in response to nerve damage.

Assessment of acute and non-acute suicide crisis symptoms: Validation of the Korean version of the acute suicidal affective disturbance inventory.

Suicide risk assessment is predominantly based on assessing current/recent suicidal ideation and past suicidal behavior. However, suicidal ideation and lifetime suicide attempt are poor predictors of imminent suicide risk or crisis. The acute suicidal affective disturbance inventory-lifetime (ASADI-L) was developed to assess symptoms of acute suicidal affective disturbance, which includes a drastic increase in suicidal intent, perceptions of social and/or self-alienation, hopelessness, and overarousal. However, the ASADI-L has not yet been validated in a Korean population. Also, the ASADI-L has only been validated for people who experience a drastic increase in suicidal intention over the course of hours or days (i.e., the acute suicidal intention group) and not validated for those who experience suicidal intention for a longer period (i.e., the non-acute suicidal intention group). Thus, the aims of this study were to (1) validate the ASADI-L in a sample of Korean community adults; and (2) compare clinical characteristics of the acute and non-acute suicidal intention groups. Among 1,675 community adults, data from 682 participants who reported a lifetime drastic increase in suicidal intent were analyzed. Results indicated that the ASADI-L has relevant reliability, validity, and a unidimensional factor structure. The acute suicidal intention group had higher ASAD symptoms as well as clinical symptoms than the non-acute group, but the two groups did not differ in history of suicide attempt. Overall, these findings suggest that the ASADI-L is a valid measure of acute and non-acute suicidal affective disturbance among Korean adults. Further investigation of the differences in acute and non-acute suicide risk is warranted.

Negative regulation of the acsA1 gene encoding the major acetyl-CoA synthetase by cAMP receptor protein in Mycobacterium smegmatis.

Acetyl-CoA synthetase (ACS) is the enzyme that irreversibly catalyzes the synthesis of acetyl-CoA from acetate, CoA-SH, and ATP via acetyl-AMP as an intermediate. In this study, we demonstrated that AcsA1 (MSMEG_6179) is the predominantly expressed ACS among four ACSs (MSMEG_6179, MSMEG_0718, MSMEG_3986, and MSMEG_5650) found in Mycobacterium smegmatis and that a deletion mutation of acsA1 in M. smegmatis led to its compromised growth on acetate as the sole carbon source. Expression of acsA1 was demonstrated to be induced during growth on acetate as the sole carbon source. The acsA1 gene was shown to be negatively regulated by Crp1 (MSMEG_6189) that is the major cAMP receptor protein (CRP) in M. smegmatis. Using DNase I footprinting analysis and site-directed mutagenesis, a CRP-binding site (GGTGA-N6-TCACA) was identified in the upstream regulatory region of acsA1, which is important for repression of acsA1 expression. We also demonstrated that inhibition of the respiratory electron transport chain by inactivation of the major terminal oxidase, aa3 cytochrome c oxidase, led to a decrease in acsA1 expression probably through the activation of CRP. In conclusion, AcsA1 is the major ACS in M. smegmatis and its gene is under the negative regulation of Crp1, which contributes to some extent to the induction of acsA1 expression under acetate conditions. The growth of M. smegmatis is severely impaired on acetate as the sole carbon source under respiration-inhibitory conditions.

Multifunctional-high resolution imaging plate based on hydrophilic graphene for digital pathology.

In the present study, we showed that hydrophilic graphene can serve as an ideal imaging plate for biological specimens. Graphene being a single-atom-thick semi-metal with low secondary electron emission, array tomography analysis of serial sections of biological specimens on a graphene substrate showed excellent image quality with improvedz-axis resolution, without including any conductive surface coatings. However, the hydrophobic nature of graphene makes the placement of biological specimens difficult; graphene functionalized with polydimethylsiloxane oligomer was fabricated using a simple soft lithography technique and then processed with oxygen plasma to provide hydrophilic graphene with minimal damage to graphene. High-quality scanning electron microscopy images of biological specimens free from charging effects or distortion were obtained, and the optical transparency of graphene enabled fluorescence imaging of the specimen; high-resolution correlated electron and light microscopy analysis of the specimen became possible with the hydrophilic graphene plate.

Activation of the SigE-SigB signaling pathway by inhibition of the respiratory electron transport chain and its effect on rifampicin resistance in Mycobacterium smegmatis.

Using a mutant of Mycobacterium smegmatis lacking the major aa3 cytochrome c oxidase of the electron transport chain (Δaa3), we demonstrated that inhibition of the respiratory electron transport chain led to an increase in antibiotic resistance of M. smegmatis to isoniazid, rifampicin, ethambutol, and tetracycline. The alternative sigma factors SigB and SigE were shown to be involved in an increase in rifampicin resistance of M. smegmatis induced under respiration-inhibitory conditions. As in Mycobacterium tuberculosis, SigE and SigB form a hierarchical regulatory pathway in M. smegmatis through SigE-dependent transcription of sigB. Expression of sigB and sigE was demonstrated to increase in the Δaa3 mutant, leading to upregulation of the SigB-dependent genes in the mutant. The pho U2 (MSMEG_1605) gene implicated in a phosphate-signaling pathway and the MSMEG_1097 gene encoding a putative glycosyltransferase were identified to be involved in the SigB-dependent enhancement of rifampicin resistance observed for the Δaa3 mutant of M. smegmatis. The significance of this study is that the direct link between the functionality of the respiratory electron transport chain and antibiotic resistance in mycobacteria was demonstrated for the first time using an electron transport chain mutant rather than inhibitors of electron transport chain.

Ultrahigh strength, modulus, and conductivity of graphitic fibers by macromolecular coalescence.

Theoretical considerations suggest that the strength of carbon nanotube (CNT) fibers be exceptional; however, their mechanical performance values are much lower than the theoretical values. To achieve macroscopic fibers with ultrahigh performance, we developed a method to form multidimensional nanostructures by coalescence of individual nanotubes. The highly aligned wet-spun fibers of single- or double-walled nanotube bundles were graphitized to induce nanotube collapse and multi-inner walled structures. These advanced nanostructures formed a network of interconnected, close-packed graphitic domains. Their near-perfect alignment and high longitudinal crystallinity that increased the shear strength between CNTs while retaining notable flexibility. The resulting fibers have an exceptional combination of high tensile strength (6.57 GPa), modulus (629 GPa), thermal conductivity (482 W/m·K), and electrical conductivity (2.2 MS/m), thereby overcoming the limits associated with conventional synthetic fibers.

Surface Modification of Sulfur-Assisted Reduced Graphene Oxide with Poly(phenylene sulfide) for Multifunctional Nanocomposites.

The sulfur on the sulfur-assisted reduced graphene oxide (SrGO) surface provides the origin of poly(phenylene sulfide) PPS-grafting via SNAr mechanism. In-situ polymerization from sulfur on SrGO afforded surface modification of SrGO, resulting in enhanced dispersibility in PPS. The tensile strength, electrical and thermal conductivities, and flame retardancy of PPS-coated SrGO were efficiently enhanced using highly concentrated SrGO and masterbatch (MB) for industrial purposes. Three-dimensional X-ray microtomography scanning revealed that diluting MB in the PPS resin afforded finely distributed SrGO across the PPS resin, compared to the aggregated state of graphene oxide. For the samples after dilution, the thermal conductivity and flame retardancy of PPS/SrGO are preserved and typically enhanced by up to 20%. The proposed PPS/SrGO MB shows potential application as an additive for reinforced PPS due to the ease of addition during the extrusion process.

In vivo optical imaging-guided targeted sampling for precise diagnosis and molecular pathology.

Conventional tissue sampling can lead to misdiagnoses and repeated biopsies. Additionally, tissue processed for histopathology suffers from poor nucleic acid quality and/or quantity for downstream molecular profiling. Targeted micro-sampling of tissue can ensure accurate diagnosis and molecular profiling in the presence of spatial heterogeneity, especially in tumors, and facilitate acquisition of fresh tissue for molecular analysis. In this study, we explored the feasibility of performing 1-2 mm precision biopsies guided by high-resolution reflectance confocal microscopy (RCM) and optical coherence tomography (OCT), and reflective metallic grids for accurate spatial targeting. Accurate sampling was confirmed with either histopathology or molecular profiling through next generation sequencing (NGS) in 9 skin cancers in 7 patients. Imaging-guided 1-2 mm biopsies enabled spatial targeting for in vivo diagnosis, feature correlation and depth assessment, which were confirmed with histopathology. In vivo 1-mm targeted biopsies achieved adequate quantity and high quality of DNA for next-generation sequencing. Subsequent mutational profiling was confirmed on 1 melanoma in situ and 2 invasive melanomas, using a 505-gene mutational panel called Memorial Sloan Kettering-Integrated mutational profiling of actionable cancer targets (MSK-IMPACT). Differential mutational landscapes, in terms of number and types of mutations, were found between invasive and in situ melanomas in a single patient. Our findings demonstrate feasibility of accurate sampling of regions of interest for downstream histopathological diagnoses and molecular pathology in both in vivo and ex vivo settings with broad diagnostic, therapeutic and research potential in cutaneous diseases accessible by RCM-OCT imaging.

Primary cutaneous T-cell lymphomas other than mycosis fungoides and Sézary syndrome. Part I: Clinical and histologic features and diagnosis.

Primary cutaneous T-cell lymphomas (CTCLs) are defined as lymphomas with a T-cell phenotype that present in the skin without evidence of systemic or extracutaneous disease at initial presentation. CTCLs other than mycosis fungoides and Sézary syndrome (SS) account for approximately one third of CTCLs and encompass a heterogenous group of non-Hodgkin lymphomas, ranging from indolent lymphoproliferative disorders to aggressive malignancies with a poor prognosis. The spectrum of CTCLs continues to broaden as new provisional entities are classified. Given the morphologic and histologic overlap among CTCLs and other diagnoses, a thorough clinical history, physical evaluation, and clinicopathologic correlation are essential in the work up and diagnosis of these rare entities. This article will summarize the epidemiologic, clinical, pathologic, and diagnostic features of CTCLs other than mycosis fungoides and SS.

Primary cutaneous T-cell lymphomas other than mycosis fungoides and Sézary syndrome. Part II: Prognosis and management.

Primary cutaneous T-cell lymphomas (CTCLs) other than mycosis fungoides (MF) and Sézary syndrome (SS) encompass a heterogenous group of non-Hodgkin lymphomas with variable clinical courses, prognoses, and management approaches. Given the morphologic and histologic overlap among the CTCL subtypes and other T-cell lymphomas with cutaneous manifestations, thorough evaluation with clinicopathologic correlation and exclusion of systemic involvement are essential prior to initiating therapy. Staging and treatment recommendations vary, depending on the subtype, clinical behavior, and treatment response. Generally, for subtypes in which staging is recommended, Ann Arbor or tumor, node, metastasis staging specific to CTCL other than MF or SS are used. For many subtypes, there is no standard treatment to date. Available recommended treatments range widely, from no active or minimal intervention with skin-directed therapy to aggressive systemic therapies that include multi-agent chemotherapy with consideration for hematopoietic stem cell transplant. Emerging targeted therapies, such as brentuximab, a chimeric antibody targeting CD30, show promise in altering the disease course of non-MF/SS CTCLs.

Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology.

In bacterial biotechnology, instead of producing functional proteins from plasmids, it is often necessary to deliver functional proteins directly into live cells for genetic manipulation or physiological modification. We constructed a library of cell-penetrating peptides (CPPs) capable of delivering protein cargo into bacteria and developed an efficient delivery method for CPP-conjugated proteins. We screened the library for highly efficient CPPs with no significant cytotoxicity in Escherichia coli and developed a model for predicting the penetration efficiency of a query peptide, enabling the design of new and efficient CPPs. As a proof-of-concept, we used the CPPs for plasmid curing in E. coli and marker gene excision in Methylomonas sp. DH-1. In summary, we demonstrated the utility of CPPs in bacterial engineering. The use of CPPs would facilitate bacterial biotechnology such as genetic engineering, synthetic biology, metabolic engineering, and physiology studies.