Comparative In Vitro Dissolution Assessment of Calcined and Uncalcined Hydroxyapatite Using Differences in Bioresorbability and Biomineralization

This study reports the effect of the not-calcining process on the bioresorption and biomineralization of hydroxyapatite through in vitro dissolution assessment. The prepared calcined hydroxyapatite (c-HAp) and uncalcined hydroxyapatite (unc-HAp) have a particle size of 2 μm and 13 μm, surface areas of 4.47 m2/g and 108.08 m2/g, and a Ca/P ratio of 1.66 and 1.52, respectively. In vitro dissolution assessments of c-HAp and unc-HAp were performed for 20 days at 37 °C in a citric acid buffer according to ISO 10993-14. During the dissolution, the c-HAp and unc-HAp confirmed an increase in weight, and the calcium and phosphorous ions were rapidly released. The calcium ions released from c-HAp formed rod-shaped particles with a longer and thinner morphology, while in unc-HAp, they appeared thicker and shorter. In the ICP-OES results, the concentrations of calcium elements were initially increased and then decreased by this formation. The rod-shaped particles identified as calcium citrate (Ca-citrate) through the XRD pattern. The calcium content of Ca-citrate particles from unc-HAp was higher than that from c-HAp. The unc-HAp demonstrated non-toxic properties in a cytotoxicity evaluation. Therefore, due to its higher bioresorption and biomineralization, unc-HAp exhibits enhanced biocompatibility compared to c-HAp.

ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes

The function of the mitogen-activated protein kinase signaling pathway is required for the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth and proliferation. Recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at the EGR1 gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK2 delays TOP2B catalysis of negative DNA supercoiling. In addition, ERK1 may relax DNA supercoiling by itself. ERK2 catalytic inhibition or knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we present the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with the EGR1 transcriptional start site (-30 to +20) that has the strongest affinity to TOP2B within -423 to +332. The structure shows TOP2B-mediated breakage and dramatic bending of the DNA. Transcription is activated by etoposide, while it is inhibited by ICRF193 at EGR1 and FOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.

The Impact of TP53 Mutations and Use of the TP53-Mutation-Reactivating Agent APR-246 on Metastatic Castrate-Sensitive Prostate Cancer

PURPOSE/OBJECTIVE(S)

TP53 mutations appear to be enriched over the spectrum of metastatic castration-sensitive prostate cancer (mCSPC) and are associated with worse survival outcomes. We chose to further explore the impact of dominant negative (DN) TP53 mutations on mCSPC progression and pro-metastatic behaviors in addition to studying the ability of APR-246, a small molecule targeting TP53 mutants, to blunt pro-metastatic behaviors.

MATERIALS/METHODS

We retrospectively analyzed 531 mCSPC patients who underwent next-generation sequencing. Patients were stratified by metastasis timing (synchronous if metastasis present at diagnosis or metachronous if arising after definitive treatment of localized disease) and the number of metastatic lesions (oligometastatic ≤5 or polymetastatic >5 lesions). Tumors were classified based on TP53 mutation status (missense, truncating, or wild-type [WT]) and dominant negativity, which was defined as the production of a mutant protein that reduces the residual WT protein's transcriptional activity according to the World Health Organization TP53 database. Clinical outcomes were radiographic progression-free survival (rPFS) and overall survival (OS), evaluated with Kaplan-Meier and multivariable Cox regression. To verify the impact of TP53 mutation on metastasis, we created isogenic 22Rv1 prostate cancer cell lines that carried either TP53 WT or TP53 R175H and tested this mutation for migration, invasion, and anchorage-independent growth. APR-246 (25-80 µM) was tested for anti-metastatic properties in vitro and anti-tumor growth in 22Rv1 xenografted nude mice.

RESULTS

In our cohort, 155 (29.2%) had a TP53 mutation, which mostly occurred in the DNA-binding domain (85.16%). DN TP53 mutations were associated with more aggressive disease states: DN TP53 mutations were enriched in patients with synchronous (vs. metachronous: 20.7% vs. 6.3%, p < 0.01) and polymetastatic disease (vs. oligometastatic: 14.4% vs. 7.9%, p < 0.01). On multivariable analysis, DN TP53 mutations were correlated with shorter rPFS (HR = 1.97, 95% CI: 1.31-2.98, p < 0.01) and OS (HR = 2.05, 95% CI: 1.14-3.68, p = 0.02) compared to those with TP53 WT. In vitro, 22Rv1 cells with DN TP53 R175H mutation had increased abilities to migrate, invade, and form colonies compared to TP53 WT. APR-246 treatment of TP53 R175H mutants blunted the pro-metastatic effects of the cell line in vitro (p < 0.01 for all assays by unpaired t-test). Interestingly, APR-246 also inhibited xenograft tumor growth of 22Rv1 TP53 R175H mutants (p < 0.0001 by two-way ANOVA).

CONCLUSION

DN TP53 mutations were associated with poorer survival outcomes for mCSPC patients. DN TP53 mutations also promoted prostate cancer pro-metastatic behaviors in vitro, which was effectively counteracted by APR-246, making it a promising treatment option that should be explored further in early-phase clinical studies.

Whole Regional Lymph Node Area Delineation with Deep Learning Model for Total Marrow and Lymphoid Irradiation

PURPOSE/OBJECTIVE(S)

Total body irradiation (TBI) has been performed for conditioning before hematopoietic stem cell transplantation. However, TBI can be related to diverse adverse events including radiation pneumonitis and cataract. Efforts to reduce these events include the total marrow irradiation (TMI) and total marrow and lymphoid irradiation (TMLI). Compared to TMI, TMLI requires more target delineations with lymph nodes which can be labor-intensive and time-consuming. However, with the TMI plans, the coverage to lymph node might be lower than TMLI and its clinical significance is unknown. In the current study, we aimed to develop a deep learning model for automatic delineation of whole regional lymph nodes area and assess the dose coverage of lymph nodes with TMI plans.

MATERIALS/METHODS

Whole regional lymph nodes (cervical, axillary, mediastinal, para-aortic, common iliac, external iliac, internal iliac, obturator, presacral, inguinal lymph nodes) were manually contoured by 3 radiation oncologists in 26 patients having whole body computed tomography (CT) images. Twenty patients were designated as the training/validation set and 6 patients as the testing set, and model was developed using the 'nnUNET' framework. The trained model was evaluated with dice coefficient score (DCS), precision, and recall. In addition, dose coverage of the automatically or manually delineated lymph nodes in TMI plans was calculated.

RESULTS

The mean value of DCS, precision, and recall of the trained model was 0.76, 0.81, and 0.74, respectively. Dose parameters for manually delineated lymph nodes in previously treated TMI plans showed the mean value of V100% (the percentage of volume receiving 100% of the prescribed dose), V95%, and V90% to be 46.50%, 62.12%, and 73.68%, respectively. The highest V90% was observed in presacral (93.61%), axillary (90.40%), obturator (88.78%), and internal iliac lymph nodes (84.67%). In contrast, the lowest V90% was identified in inguinal (47.95%), cervical (61.69%), and para-aortic (65.75%) and external iliac lymph nodes (68.97%). For automatically delineated lymph nodes, the mean value of V100%, V95%, and V90% of TMI plan was 38.35%, 55.06%, and 67.84%, respectively. The difference with dose coverage of lymph node between delineated manually and automatically was not statistically significant.

CONCLUSION

Automatic delineation of lymph node using deep learning showed the potential to reduce the labor-intensive process of TMLI. When treated with TMI, the coverage of inguinal, cervical, para-aortic and external iliac lymph nodes was lower than expected.

Relationships between Microbiome and Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer

PURPOSE/OBJECTIVE(S)

Gut microbiome is known to be involved in antitumor immunotherapy and chemotherapy responses; however, few research has focused on the role of gut microbiome in the setting of concurrent chemoradiotherapy (CCRT). In this study, we investigated the tumor microbiome dynamics in patients undergoing neoadjuvant CCRT for locally advanced rectal cancer and sought to determine whether the diversity and composition of microbiome affect treatment response.

MATERIALS/METHODS

A total of 103 samples from 26 patients with locally advanced rectal cancer were collected and 16S ribosomal RNA amplicon sequencing was performed. All patients underwent neoadjuvant CCRT followed by surgical resection between 2008 and 2016. Samples were obtained from both tumor and normal rectal tissue at pre- and post-CCRT. According to the American Joint Committee on Cancer tumor regression grading (TRG) system, patients were divided into responders (TRG 0, 1) and non-responders (TRG 2, 3). We performed diversity, taxonomy, and network analyses to compare responders and non-responders. Then, we established the Bayesian network model to predict treatment response in patients with rectal cancer.

RESULTS

Overall, we detected 1260 microbial genera from 287 families, 132 orders, 56 classes, and 32 phyla in the bacteria kingdom. Between tumor and normal rectal tissues, there was no difference in microbial diversity and composition. On the other hand, there was a significant decrease in diversity and compositional alterations when comparing pre- and post-CCRT samples (all p<0.001). Ten patients (38.5%) were classified as responders and 16 patients (61.5%) were classified as non-responders. In both groups, CCRT significantly reduced microbial diversity and altered their composition, but it was more pronounced in non-responders. In taxonomic analysis of pre-CCRT samples, butyrate-producing bacteria were differentially enriched in responders. Meanwhile, in post-CCRT samples, opportunistic pathogen were overrepresented in non-responders. The network analysis revealed that butyrate-producing bacteria had strong interactions in responders, whereas opportunistic pathogen demonstrated strong interactions in non-responders (Pearson's coefficient>0.5). Finally, five microbes were selected as the optimal set for the response prediction model, which yielded an area under the curve value of 82.33%.

CONCLUSION

CCRT significantly changed the diversity and composition of microbiome, especially in non-responders. Several microbes might be related with treatment response. These findings highlight the potential of microbiome to play an important role as a biomarker in patients with rectal cancer. (NCT02533271).

Identifying Common Topics in Patient Portal Messages with Unsupervised Natural Language Processing

PURPOSE/OBJECTIVE(S)

Patient portal messaging is an increasingly important form of communication between patients and medical providers. This has become particularly relevant in oncology, where patients undergo intense longitudinal treatments that require frequent communication regarding symptoms, appointments, and diagnostic results. The rise in the volume of these messages has significantly increased the workload of medical providers and consequent physician burn-out. Natural language processing (NLP), particularly transformer-based models, may offer an automated approach to characterize the content of patient messages and improve message triage and routing. In this study, we employed a state-of-the-art language model (Bidirectional Encoder Representations from Transformers; BERT) to identify data-derived categories of representative topics from real-world data thereby providing basic information to build an appropriate routing system.

MATERIALS/METHODS

Patient-generated portal messages sent to a messaging pool for a single institution radiation oncology department from 2014 to 2023 were extracted. BERTopic, an NLP-based topic modeling technique based on BERT was optimized for topic modeling of patient messages. Uniform Manifold Approximation and Projection (UMAP) was used to reduce dimensionality and visualize topic relationships across messages. The BERTopic-identified topic categories were subsequently labeled manually by one of the physician investigators. Differences of number of messages over time were assessed using t-tests.

RESULTS

A total of 47,492 messages were retrieved. The average number of messages per month from a single patient ranged from 1 to 18 (median 1.67, interquartile range 1.0-2.4). The total volume of patient messages showed a ten-fold increase over the study period, with 101 messages per month sent in 2014 and 999 messages per month in 2022 (p<0.001). BERTopic initially identified 35 topics whose relationships and degrees of overlap were visualized by UMAP. Due to physician-identified similarities, these topics were reduced into 13 categories. The most frequent topic category was messages about laboratory tests or imaging studies: 24.3%, followed by messages expressing appreciation: 18.9%, scheduling discussions: 15.6%, symptom-related messages: 11%, and treatment-related messages: 10.7%.

CONCLUSION

Patient portal messages sent to a single institution radiation oncology department have increased dramatically in volume since implementation, corresponding to a broader national trend. NLP successfully identified common subject themes across patient messages, many of which are related to scheduling. This presents potential opportunities to apply NLP to automate message routing in the future.

Impact of the New ESTRO-ACROP Target Volume Delineation Guideline on Breast-Related Complications after Implant-Based Reconstruction and Postmastectomy Radiotherapy

PURPOSE/OBJECTIVE(S)

The European Society for Radiotherapy and Oncology Advisory Committee in Radiation Oncology Practice (ESTRO-ACROP) recently updated a new target volume delineation guideline for postmastectomy radiotherapy (PMRT) after implant-based reconstruction. This study aimed whether this change has impact on breast-related complications.

MATERIALS/METHODS

We retrospectively reviewed patients who underwent PMRT after mastectomy with tissue expander or permanent implant insertion from 2016 to 2021. In total, 412 patients were included; 277 received RT by the new ESTRO-ACROP target delineation (ESTRO-T), and 135 received RT by conventional target delineation (CONV-T). The primary endpoint was comparison between the target groups of major breast-related complication, including infection, capsular contracture, deformity and necrosis requiring re-operation or re-hospitalization during follow-up after RT or delayed implant replacement. Complications were evaluated according to the Common Terminology Criteria for Adverse Events (CTCAE) version 5.0., and capsular contracture was graded by the Baker Classification.

RESULTS

The median follow-up was 29.5 months (range, 0.3-76.8). The 1-, 2-, and 3-year incidence rates of major breast-related complication were 5.7%, 10.0%, and 11.6% in the ESTRO-T group, and 8.2%, 13.8%, and 14.7% in the CONV-T groups; it did not show a difference between the groups (P = 0.55). In multivariate analyses, target delineation is not significantly associated with the major complications (hazard ratio [HR] = 0.93; P = 0.83, Table 1). There was no significant difference between the ESTRO-T and CONV-T groups in the incidence of any breast-related complications (3-year cumulative incidence, 37.3% vs. 29.4%, respectively; P = 0.28). Symptomatic RT-induced pneumonitis rates were 2.7% in the ESTRO-T group (7 patients) and 2.2% in the CONV-T group (3 patients). Only one local recurrence event occurred in the ESTRO-T group, which was within the ESTRO-target volume.

CONCLUSION

Target volume delineation according to the new ESTRO-ACROP guideline did not reduce the risk of major or any breast-related complications. As the dosimetric benefits of heart and lung have been reported, further analyses with long-term follow-up are necessary to evaluate whether it could be connected to better clinical outcomes.

The Early and Late Effects of High-Dose Irradiation on Cardiac Injury in a Rat Model

PURPOSE/OBJECTIVE(S)

Radiation-induced heart disease is a critical concern after radiotherapy (RT) for thoracic and chest wall tumors; however, the biological effects and mechanisms are still unknown. In this study, we investigated dose-responsive functional and pathological changes in rat hearts at 1, 3, and 5 months after high-dose irradiation. Then, we sought to elucidate the underlying mechanisms of myocardial changes induced by high-dose irradiation.

MATERIALS/METHODS

Whole hearts of rats (N = 72) were irradiated with a single fraction of 0 (control), 10, 20, or 30 Gy and allocated into three groups according to the follow-up period after RT: baseline, one, three, and five months. During follow-up periods, rats underwent functional evaluation by electrocardiogram and echocardiography at 4-week intervals. If a rat's body weight decreased by 20% or more, it was considered premature death, and the heart was explanted immediately. Otherwise, all hearts were explanted when each group's follow-up period was completed. Pathological changes of cardiac structures were evaluated using a light microscope after staining with hematoxylin-eosin, Masson's trichrome, α-smooth muscle actin, desmin, and connexin-43.

RESULTS

All rats irradiated with 0 or 10 Gy completed their follow-up periods with continuously increasing body weight. However, among rats irradiated with 20 or 30 Gy, half of the rats died prematurely at 8-10 weeks after RT, and the remainder survived until 20 weeks. In echocardiography, increased wall thickness and E/E' ratio, and decreased end-diastolic volume were observed in 20-30 Gy groups compared to 0-10 Gy groups from 8 weeks after RT. Ejection fraction was preserved in all groups. In pathological review, 20-30 Gy groups demonstrated diffuse inflammation and vacuolization at 4 weeks. Then, at 8 weeks, prominent fibrotic changes and intercalated disc disruptions were observed. Notably, fibrotic changes were somewhat resolved at 20 weeks, but intercalated disc disruptions were not repaired until 20 weeks. The 0 and 10 Gy groups showed no significant changes in both functional and pathological analyses.

CONCLUSION

Rats irradiated with 20 or 30 Gy showed diastolic dysfunction in functional analysis and time-dependent myocardial changes in pathological analysis. Radiation-induced fibrosis might be a "reactive" fibrosis, which could proceed to either a profibrotic course (progressive fibrosis) or an anti-fibrotic course (recovery phase). Further studies are needed to identify whether high-dose irradiation-induced cardiac fibrosis could be reversible.

Pattern and Complication of Reconstructed Breast Cancer Patients Who Received Postmastectomy Radiotherapy in the National Health Insurance Service Cohort

PURPOSE/OBJECTIVE(S)

This study aimed to analyze the nationwide pattern of reconstruction after mastectomy in patients with breast cancer who received postmastectomy radiotherapy (PMRT) and to compare complications according to fractionation and reconstruction procedures.

MATERIALS/METHODS

By using claim data from the National Health Insurance Service (NHIS) database, we analyzed breast cancer patients who received PMRT and underwent reconstruction between 2015 and 2020. We defined the grade ≥ 3 complications as the primary endpoint which involved hospital admission to the plastic surgery department. The complication was identified by using the procedure code for debridement and the International Classification of Diseases 10th codes for wound infections, dehiscence, necrosis, and mechanical complication of breast prosthesis and implant. The propensity score matching method was adopted to constitute the matched cohort between the hypofractionated fractionation (HF) and the conventional fractionation (CF), adjusted for age, diabetes, hypertension, obesity, smoking history, PMRT technique, use of bolus, year of PMRT delivery, and reconstruction method. Logistic regression was performed to evaluate the association between complication and variables.

RESULTS

Altogether 4,553 patients were analyzed: 1,395 (30.6%) in the HF group and 3,158 (69.4.%) in the CF group. The use of HF has steadily increased from 20.1% in 2015 to 42.2% in 2020. Immediate implant reconstruction (36.8%) method was the most frequently used, followed by immediate autologous (33.3%) and two-stage implant reconstruction methods (19.6%). In the matched cohort (N = 2,052), the major complication rate was not significantly different between the HF group and the CF group (5.9% [60/1,026] vs. 5.4% [55/1,026], P = 0.568) with the median follow-up of 30.9 months (range, 6.0-82.1). Surgical debridement was performed in 3.3% [34/1026] of the HF group and 3.5% [36/1026] of the CF group (P = 0.808). HF was not associated with major complications (odds ratio (OR) 1.09, 95% CI 0.75-1.59, P = 0.128).

CONCLUSION

In a nationwide insurance cohort, the complication rate was not significantly different between the HF group and the CF group. Our data suggest HF for reconstructed breasts is comparable to CF. However, consultation for fractionation regimen for reconstructed breast cancer patients may be still required at time of consideration of PMRT.

Safety and Efficacy of Stereotactic Body Radiotherapy for Ultra-Central Thoracic Tumors

PURPOSE/OBJECTIVE(S)

Stereotactic body radiotherapy (SBRT) is increasingly utilized in the management of ultra-central thoracic tumors, although concerns regarding significant toxicity remain. We sought to evaluate the toxicity and efficacy of SBRT to these tumors at our institution.

MATERIALS/METHODS

Patients with ultra-central lung tumors or nodes treated at our institution with SBRT between 2009 and 2019 were retrospectively reviewed. Ultra-central was defined as having the planning target volume (PTV) overlapping or abutting the central bronchial tree and/or esophagus. All SBRT plans were generated with homogenous dose distributions using target coverage objectives of ITV V100% >99%, PTV V95% >99%, and an ideal PTV Dmax <105% (strict <120%). All plans were reviewed in quality assurance rounds by a team of dosimetrists, physicists, and radiation oncologists. The primary endpoint was incidence of severe toxicity (ST), defined as SBRT-related grade ≥3 toxicities, graded using the Common Terminology Criteria for Adverse Events V5.0. Secondary endpoints included local failure (LF), progression-free survival (PFS) and overall survival (OS). Competing risk analysis was used to estimate incidence and predictors of ST and LF, with death as a competing risk. Kaplan-Meier method was used to estimate PFS and OS.

RESULTS

A total of 154 patients who received 162 ultra-central courses of SBRT were included, with a median follow-up of 21.5 months. Treatment intent was most commonly for oligoprogression (46%), oligometastasis (30%), followed by curative (20%). The most frequent tumor histologies were NSCLC (41%) and RCC (26%). SBRT prescription doses ranged from 30-55 Gy in 5 fractions (BED10 range 48-115 Gy). The most common prescription was 50 Gy in 5 fractions (42%). The cumulative incidence of ST was 8.9% at 3-years. The most common ST was pneumonitis (n = 4). Notable toxicities included bronchopleural fistula (n = 2, grade 3 and 4), bronchial stricture (n = 1, grade 3), and esophagitis leading to bleeding (n = 1, grade 4). There were no esophageal strictures or perforations, and no bronchial bleeds. There was 1 possible treatment related death from pneumonitis/pneumonia. Predictors of any ST included increased lung V5 Gy, decreased PTV V95%, and not having prior radiation therapy to the chest. The cumulative incidence of LF was 4.8%, 11% and 14% at 1-, 2-, and 3-years respectively. Predictors of LF included younger age, and greater volume of overlap between the PTV and esophagus. Median PFS was 8.4 months, while median OS was 3.7 years.

CONCLUSION

In one of the largest case series of ultra-central thoracic SBRT reported to date, homogenously prescribed SBRT plans were associated with relatively low rates of ST and LF across a variety of treatment indications. Predictors of ST should be interpreted recognizing the heterogeneity in toxicities observed. Identified predictors of both ST and LF can contribute to future work to optimize the therapeutic ratio in treatment of ultra-central thoracic tumors.

Thermally Stable and Reusable Silica and Nano-Fructosome Encapsulated CalB Enzyme Particles for Rapid Enzymatic Hydrolysis and Acylation

This study reports the preparation of silica-coated and nano-fructosome encapsulated Candida antarctica lipase B particles (CalB@NF@SiO₂) and a demonstration of their enzymatic hydrolysis and acylation. CalB@NF@SiO₂ particles were prepared as a function of TEOS concentration (3-100 mM). Their mean particle size was 185 nm by TEM. Enzymatic hydrolysis was performed to compare catalytic efficiencies of CalB@NF and CalB@NF@SiO₂. The catalytic constants (K_m, V_max, and K_cat) of CalB@NF and CalB@NF@SiO₂ were calculated using the Michaelis-Menten equation and Lineweaver-Burk plot. Optimal stability of CalB@NF@SiO₂ was found at pH 8 and a temperature of 35 °C. Moreover, CalB@NF@SiO₂ particles were reused for seven cycles to evaluate their reusability. In addition, enzymatic synthesis of benzyl benzoate was demonstrated via an acylation reaction with benzoic anhydride. The efficiency of CalB@NF@SiO₂ for converting benzoic anhydride to benzyl benzoate by the acylation reaction was 97%, indicating that benzoic anhydride was almost completely converted to benzyl benzoate. Consequently, CalB@NF@SiO₂ particles are better than CalB@NF particles for enzymatic synthesis. In addition, they are reusable with high stability at optimal pH and temperature.

Structural Analysis of Spermidine Synthase from Kluyveromyces lactis

Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5'-deoxy-5'-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis (KlSpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species.

Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae

Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.

Effects of Hydrophobic Modification of Linear- and Branch-Structured Fluorinated and Nonfluorinated Silanes on Mesoporous Silica Particles

This work reports a comparison of hydrophobic surface modification on mesoporous silica particles (MSPs) obtained by large-scale production using a batch reactor with linear and branched fluorinated and nonfluorinated silanes. Fluorinated silanes were used with TDF-TMOS and TFP-TMOS as a linear and branched structure, respectively. Nonfluorinated silanes were used with OD-TEOS and HMDS as a linear and branched structure, respectively. These four silanes were grafted on the surface of the MSPs as the function of the concentrations, and then, the water contact angles (WCAs) were measured. The WCA of the four silane-grafted MSPs was higher in the branch-structured silanes, namely, TFP-TMOS@MSPs and HMDS@MSPs than in linear-structured silanes, namely, TDF-TMOS and OD-TEOS due to the higher hydrophobicity by a lot of -F and -CH₃ groups. Furthermore, the relationship between the WCA and BET parameters was demonstrated using the surface areas, pore volumes, and grafted amounts of the four silane-grafted MSPs. The structural characterization was demonstrated by solid-state ²⁹Si MAS NMR to determine the bonding environment of Si atoms between the grafted silane and the surfaces of MSPs using the T ³/T ² and Q ³/Q ⁴ ratios of the fluorinated and nonfluorinated silane-grafted MSPs. Among the four silanes, nonfluorinated HMDS@MSPs had a high contact angle of 135° as fluorinated TFP-TMOS@MSPs. When 5 wt % of HMDS@MSPs mixed with gravure ink was coated on a biodegradable polylactic acid (PLA) film, the contact angle was improved to 131.8 from 83.3° of the natural PLA film.

NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis

Accelerated glycolysis is the main metabolic change observed in cancer, but the underlying molecular mechanisms and their role in cancer progression remain poorly understood. Here, we show that the deletion of the long noncoding RNA (lncRNA) Neat1 in MMTV-PyVT mice profoundly impairs tumor initiation, growth, and metastasis, specifically switching off the penultimate step of glycolysis. Mechanistically, NEAT1 directly binds and forms a scaffold bridge for the assembly of PGK1/PGAM1/ENO1 complexes and thereby promotes substrate channeling for high and efficient glycolysis. Notably, NEAT1 is upregulated in cancer patients and correlates with high levels of these complexes, and genetic and pharmacological blockade of penultimate glycolysis ablates NEAT1-dependent tumorigenesis. Finally, we demonstrate that Pinin mediates glucose-stimulated nuclear export of NEAT1, through which it exerts isoform-specific and paraspeckle-independent functions. These findings establish a direct role for NEAT1 in regulating tumor metabolism, provide new insights into the Warburg effect, and identify potential targets for therapy.

Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria, respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children.

Hydrophobic Mesoporous Silica Particles Modified With Nonfluorinated Alkyl Silanes

This work reports the preparation of hydrophobic mesoporous silica particles (MSPs) modified with nonfluorinated alkyl silanes. Alkyl silanes were grafted onto the surface of the MSPs as a function of the length of nonfluorinated alkyl chains such as propyltriethoxysilane (C₃), octyltriethoxysilane (C₈), dodecyltriethoxysilane (C₁₂), and octadecyltriethoxysilane (C₁₈). Moreover, the grafting of the different alkyl silanes onto the surface of MSPs to make them hydrophobic was demonstrated using different conditions such as by changing the pH (0, 4, 6, 8, and 13), solvent type (protic and aprotic), concentration of silanes (0, 0.12, 0.24, 0.36, 0.48, and 0.60 M), reaction time (1, 2, 3, and 4 days), and reaction temperature (25 and 40 °C). The contact angles of the alkyl silane-modified MSPs were increased as a function of the alkyl chain lengths in the order of C₁₈ > C₁₂ > C₈ > C₃, and the contact angle of C₁₈-modified MSPs was 4 times wider than that of unmodified MSPs. The unmodified MSPs had a contact angle of 25.3°, but C₁₈-modified MSPs had a contact angle of 102.1°. Furthermore, the hydrophobicity of the nonfluorinated alkyl silane-modified MSPs was also demonstrated by the adsorption of a hydrophobic lecithin compound, which showed the increase of lecithin adsorption as a function of the alkyl chain lengths. The cross-linking ratios of the modified silanes on the MSPs were confirmed by solid-state ²⁹Si-MAS nuclear magnetic resonance (NMR) measurement. Consequently, the hydrophobic modification on MSPs using nonfluorinated alkyl silanes was best preferred in a protic solvent, with a reaction time of ∼24 h at 25 °C and at a high concentration of silanes.

MRI Features May Predict Molecular Features of Glioblastoma in Isocitrate Dehydrogenase Wild-Type Lower-Grade Gliomas

BACKGROUND AND PURPOSE

Isocitrate dehydrogenase (IDH) wild-type lower-grade gliomas (histologic grades II and III) with epidermal growth factor receptor (EGFR) amplification or telomerase reverse transcriptase (TERT) promoter mutation are reported to behave similar to glioblastoma. We aimed to evaluate whether MR imaging features could identify a subset of IDH wild-type lower-grade gliomas that carry molecular features of glioblastoma.

MATERIALS AND METHODS

In this multi-institutional retrospective study, pathologically confirmed IDH wild-type lower-grade gliomas from 2 tertiary institutions and The Cancer Genome Atlas constituted the training set (institution 1 and The Cancer Genome Atlas, 64 patients) and the independent test set (institution 2, 57 patients). Preoperative MRIs were analyzed using the Visually AcceSAble Rembrandt Images and radiomics. The molecular glioblastoma status was determined on the basis of the presence of EGFR amplification and TERT promoter mutation. Molecular glioblastoma was present in 73.4% and 56.1% in the training and test sets, respectively. Models using clinical, Visually AcceSAble Rembrandt Images, and radiomic features were built to predict the molecular glioblastoma status in the training set; then they were validated in the test set.

RESULTS

In the test set, a model using both Visually AcceSAble Rembrandt Images and radiomic features showed superior predictive performance (area under the curve = 0.854) than that with only clinical features or Visually AcceSAble Rembrandt Images (areas under the curve = 0.514 and 0.648, respectively; P < . 001, both). When both Visually AcceSAble Rembrandt Images and radiomics were added to clinical features, the predictive performance significantly increased (areas under the curve = 0.514 versus 0.863, P < .001).

CONCLUSIONS

MR imaging features integrated with machine learning classifiers may predict a subset of IDH wild-type lower-grade gliomas that carry molecular features of glioblastoma.

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Simple Summary

Antimicrobial resistance acquired an endemic status in the Pakistan poultry sector. A cross-sectional study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant Escherichia coli using next-generation sequencing. Results show the widespread presence of diverse antibiotic resistance genes, virulence-associated genes, plasmid replicon types, and dysbiotic fecal microbial communities. Results indicate that antibiotic resistance altered the fecal microbial community structure of broiler chickens. The use of next-generation sequencing in this study documents a robust and cost-effective approach to study the fecal microbiome and resistome diversities of broiler chickens.

Abstract

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

Ursolic acid inhibits pigmentation by increasing melanosomal autophagy in B16F1 cells

Melanosomes are specialized membrane-bound organelles that are involved in melanin synthesis. Unlike melanosome biogenesis, the melanosome degradation pathway is poorly understood. Among the cellular processes, autophagy controls degradation of intracellular components by cooperating with lysosomes. In this study, we showed that ursolic acid inhibits skin pigmentation by promoting melanosomal autophagy, or melanophagy, in melanocytes. We found that B16F1 cells treated with ursolic acid suppressed alpha-melanocyte stimulating hormone (α-MSH) stimulated increase in melanin content and activated autophagy. In addition, we found that treatment with ursolic acid promotes melanosomal degradation, and bafilomycin A1 inhibition of autophagosome-lysosome fusion blocked the removal of melanosomes in α-MSH-stimulated B16F1 cells. Furthermore, depletion of the autophagy-related gene 5 (ATG5) resulted in significant suppression of ursolic acid-mediated anti-pigmentation activity and autophagy in α-MSH-treated B16F1 cells. Taken together, our results suggest that ursolic acid inhibits skin pigmentation by increasing melanosomal degradation in melanocytes.

Melasolv induces melanosome autophagy to inhibit pigmentation in B16F1 cells

The melanosome is a specialized membrane-bound organelle that is involved in melanin synthesis, storage, and transportation. In contrast to melanosome biogenesis, the processes underlying melanosome degradation remain largely unknown. Autophagy is a process that promotes degradation of intracellular components' cooperative process between autophagosomes and lysosomes, and its role for process of melanosome degradation remains unclear. Here, we assessed the regulation of autophagy and its contributions to depigmentation associated with Melasolv (3,4,5-trimethoxycinnamate thymol ester). B16F1 cells-treated with Melasolv suppressed the α-MSH-stimulated increase of melanin content and resulted in the activation of autophagy. However, introduction of bafilomycin A1 strongly suppressed melanosome degradation in Melasolv-treated cells. Furthermore, inhibition of autophagy by ATG5 resulted in significant suppression of Melasolv-mediated depigmentation in α-MSH-treated cells. Taken together, our results suggest that treatment with Melasolv inhibits skin pigmentation by promoting melanosome degradation via autophagy activation.

Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop

In spore forming microbes, germination protease (GPR) plays a key role in the initiation of the germination process. A critical step during germination is the degradation of small acid-soluble proteins (SASPs), which protect spore DNA from external stresses (UV, heat, low temperature, etc.). Inactive zymogen GPR can be activated by autoprocessing of the N-terminal pro-sequence domain. Activated GPR initiates the degradation of SASPs; however, the detailed mechanisms underlying the activation, catalysis, regulation, and substrate recognition of GPR remain elusive. In this study, we determined the crystal structure of GPR from Paenisporosarcina sp. TG-20 (PaGPR) in its inactive form at a resolution of 2.5 A. Structural analysis showed that the active site of PaGPR is sterically occluded by an inhibitory loop region (residues 202-216). The N-terminal region interacts directly with the self-inhibitory loop region, suggesting that the removal of the N-terminal pro-sequence induces conformational changes, which lead to the release of the self-inhibitory loop region from the active site. In addition, comparative sequence and structural analyses revealed that PaGPR contains two highly conserved Asp residues (D123 and D182) in the active site, similar to the putative aspartic acid protease GPR from Bacillus megaterium. The catalytic domain structure of PaGPR also shares similarities with the sequentially non-homologous proteins HycI and HybD. HycI and HybD are metal-loproteases that also contain two Asp (or Glu) residues in their active site, playing a role in metal binding. In summary, our results provide useful insights into the activation process of PaGPR and its active conformation.

Transcriptional regulation of Salmochelin glucosyltransferase by Fur in Salmonella

Pathogenic bacteria acquire the acquisition of iron from the host to ensure their survival. Salmonella spp. utilizes siderophores, including salmochelin, for high affinity aggressive import of iron. Although the iroBCDEN operon is reportedly responsible for the production and the transport of salmochelin, the molecular mechanisms underlying the regulation of its gene expression have not yet been characterized. Here, we analyzed the expression pattern of iroB using the lacZY transcriptional reporter system and determined the transcription start site in response to iron availability using primer extension analysis. We further examined the regulation of iroB expression by the ferric uptake regulator (Fur), a key regulatory protein involved in the maintenance of iron homeostasis in various bacteria, including Salmonella. Using sequence analysis followed by a gel shift assay, we verified that the Fur box lies within the promoter region of iroBCDE. The Fur box contained the consensus sequence (GATATTGGTAATTATTATC) and overlapped with the -10-element region. The expression of iroB was repressed by Fur in the presence of iron, as determined using an in vitro transcription assay. Therefore, we found that the iron acquisition system is regulated in a Fur-dependent manner in Salmonella.

Characterization of Surface-Modified Halloysite Nanotubes by Thermal Treatment Under Reducing Atmosphere

In recent years, the halloysite (Al₂Si₂O₅(OH)₄ · 2H₂O) has been highlighted owing to its naturally occurring one-dimensionalmicrostructure that enables versatile applications. Due to the demand for enhancing surface interaction, several types of research such as acid/base treatments have been conducted on the halloysite nanotubes. The objective of this study is to investigate the structural and surface properties of thermally treated halloysites under reducing atmosphere. The heat treatment is carried out in a gas-flow furnace at 400-800 °C under various atmosphere, e.g., ambient air, 4% H₂-balanced Ar, and 99.99% H₂. The thermal treatment of halloysites under reducing atmosphere show a similar phase transition around 500 °C as the heating under air. However, the halloysite reduced in pure hydrogen shows a significant increase of the zeta-potential, -36.7 mV for a 600 °C-treated sample, compared to the other samples. The mechanisms of the zeta-potential increase for the halloysite was also explored.

Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli

In metabolic engineering and synthetic biology fields, there have been efforts to produce variable bioalcohol fuels, such as isobutanol and 2-phenylethanol, in order to meet industrial demands. YjgB is an aldehyde dehydrogenase from Escherichia coli that shows nicotinamide adenine dinucleotide phosphate (NADP)-dependent broad selectivity for aldehyde derivatives with an aromatic ring or small aliphatic chain. This could contribute to the design of industrial synthetic pathways. We determined the crystal structures of YjgB for both its apo-form and NADP-complexed form at resolutions of 1.55 and 2.00 Å, respectively, in order to understand the mechanism of broad substrate selectivity. The hydrophobic pocket of the active site and the nicotinamide ring of NADP(H) are both involved in conferring its broad specificity toward aldehyde substrates. In addition, based on docking-simulation data, we inferred that π–π stacking between substrates and aromatic side chains might play a crucial role in recognizing substrates. Our structural analysis of YjgB might provide insights into establishing frameworks to understand its broad substrate specificity and develop engineered enzymes for industrial biofuel synthesis.

High Oxygen and Water-Vapor Transmission Rate and In Vitro Cytotoxicity Assessment with Illite-Polyethylene Packaging Films

This work reports the preparation of a ceramic hybrid composite film with illite and polyethylene (illite-PE), and the evaluation of the freshness-maintaining properties such as oxygen transmission rate (OTR), water vapor transmission rate (WVTR), tensile strength, and in vitro cytotoxicity. The particle size of the illite material was controlled to within 10 μm. The illite-PE masterbatch and film were prepared using a twin-screw extruder and a blown film maker, respectively. The dispersity and contents of illite material in each masterbatch and composite film were analyzed using a scanning electron microscope (SEM) and thermogravimetric analyzer (TGA). In addition, the OTR and WVTR of the illite-PE composite film were 8315 mL/m2·day, and 13.271 g/m2·day, respectively. The in vitro cytotoxicity of the illite-PE composite film was evaluated using L929 cells, and showed a cell viability of more than 92%. Furthermore, the freshness-maintaining property was tested for a packaging application with bananas; it was found to be about 90%, as indicated by changes in the color of the banana peel, after 12 days.

Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe

L-aspartate aminotransferase is a pyridoxal 5'-phosphate-dependent transaminase that catalyzes reversible transfer of an α-amino group from aspartate to α-ketoglutarate or from glutamate to oxaloacetate. L-aspartate aminotransferase not only mediates amino acid and carbohydrate metabolism but also regulates the cellular level of amino acids by catalyzing amino acid degradation and biosynthesis. To expand our structural information, we determined the crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe at 2.1 Å resolution. A structural comparison between two yeast L-aspartate aminotransferases revealed conserved enzymatic mechanism mediated by the open-closed conformational change. Compared with higher eukaryotic species, L-aspartate aminotransferases showed distinguishable inter-subunit interaction between the N-terminal arm and a large domain of the opposite subunit. Interestingly, structural homology search showed varied conformation of the N-terminal arm among 71 structures of the family. Therefore, we classified pyridoxal 5'-phosphate-dependent enzymes into eight subclasses based on the structural feature of N-terminal arms. In addition, structure and sequence comparisons showed strong relationships among the eight subclasses. Our results may provide insights into structure-based evolutionary aspects of pyridoxal 5'-phosphate-dependent enzymes.

Biosynthesis of DDMP saponins in soybean is regulated by a distinct UDP-glycosyltransferase

2,3-Dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one (DDMP) saponins are one of the major saponin groups that are widely distributed in legumes such as pea, barrel medic, chickpea, and soybean. The steps involved in DDMP saponin biosynthesis remain uncharacterized at the molecular level. We isolated two recessive mutants that lack DDMP saponins from an ethyl methanesulfonate-induced mutant population of soybean cultivar Pungsannamul. Segregation analysis showed that the production of DDMP saponins is controlled by a single locus, named Sg-9. The locus was physically mapped to a 130-kb region on chromosome 16. Nucleotide sequence analysis of candidate genes in the region revealed that each mutant has a single-nucleotide polymorphism in the Glyma.16G033700 encoding a UDP-glycosyltransferase UGT73B4. Enzyme assays and mass spectrum-coupled chromatographic analysis reveal that the Sg-9 protein has glycosyltransferase activity, converting sapogenins and group B saponins to glycosylated products, and that mutant proteins had only partial activities. The tissue-specific expression profile of Sg-9 matches the accumulation pattern of DDMP saponins. This is the first report on a new gene and its function in the biosynthesis of DDMP saponins. Our findings indicate that Sg-9 encodes a putative DDMP transferase that plays a critical role in the biosynthesis of DDMP saponins.

Fine particulate matter (PM2.5) inhibits ciliogenesis by increasing SPRR3 expression via c-Jun activation in RPE cells and skin keratinocytes

Exposure to fine particulate matter (PM) with diameter <2.5 µm (PM2.5) causes epithelium injury and endothelial dysfunction. Primary cilia are sensory organelles that transmit extracellular signals into intracellular biochemical responses and have roles in physiology. To date, there have been no studies investigating whether PM2.5 affects primary cilia in skin. We addressed this in the present study using normal human epidermal keratinocytes (NHEKs) and retinal pigment epithelium (RPE) cells. We found that formation of primary cilium is increased in differentiated NHEKs. However, treatment with PM2.5 blocked increased ciliogenesis in NHEKs and RPE cells. Furthermore, PM2.5 transcriptionally upregulated small proline rich protein 3 (SPRR3) expression by activating c-Jun, and ectopic expression of SPRR3 inhibits suppressed the ciliogenesis. Accordingly, treatment with c-Jun activator (anisomycin) induced SPRR3 expression, whereas the inhibitor (SP600125) recovered the ciliated cells and cilium length in PM2.5-treated cells. Moreover, c-Jun inhibitor suppressed upregulation of SPRR3 in PM2.5-treated cells. Taken together, our finding suggested that PM2.5 inhibits ciliogenesis by increasing SPRR3 expression via c-Jun activation in RPE cells and keratinocytes.

Proportional subcellular localization of Arabidopsis thaliana RabA1a

Subcellular localization of trafficking proteins in a single cell affects the assembly of trafficking machinery between organelles and vesicles throughout the targeting pathway. RabGTPase is one of the regulators to direct specific targeting of cargo molecules depending on GDP/GTP bound status. We have recently determined the crystal structures of GDP-bound inactive and both GTP- and GppNHp-bound active forms of Arabidopsis RabA1a. It is notable that the switch regions of RabA1a exhibit conformational changes derived by GDP or GTP binding. However, it was not clear that where the GDP- or GTP-bound RabA1a is localized at the subcellular level in a cell. Here we demonstrate that the distinct proportion of subcellular localization of RabA1a depends on its site-specific mutation as the GDP- or GTP-bound form. RabA1a proteins located at the plasma membrane, endosomes, and cytosol. While the GDP-bound form of RabA1a^S27N located more at endosomes than the plasma membrane compared to the proportions of RabA1a wild-type, and the GTP-bound RabA1a^Q72L located mainly at the plasma membrane in comparison to RabA1a wild-type and RabA1a^S27N. These distinct proportional localizations of RabA1a enable a cognate interaction between inactive/active RabA1 and effector molecules to direct specific targeting of its cargo molecules.

Separation of Halloysite Nano Tubes (HNTs) by Homogenization of Quartz Contaminated Kaolins

Natural halloysite kaolin contains a lot of impurities such as quartz phases and varies in morphology and size during their formation in the earth. So to utilize as a new type of natural nano material, removing quartz impurities from kaolin clays without scathe the tube morphologies are necessary. So to remove quartz impurities from kaolin by forming a well deflocculated aqueous slip without fracturing the morphology of tubes, the slip of homogenized halloysite clay was recovered by adding polyvalent metallic cations and anionic polyelectrolyte flocculants simultaneously to selectively flocculate the mixture of quartz and halloysite, whereby the halloysite particles form floes and the tubular halloysite remains in suspensions. Then, the uniform size and tubular shape of halloysite was obtained which could be suitably used as a container or a carrier to encapsulate nanomaterials.

Crystal structure of Arabidopsis thaliana RabA1a

RabGTPase is a member of the Ras superfamily of small GTPases, which share a GTP-binding pocket containing highly conserved motifs that promote GTP hydrolysis. In Arabidopsis, the RabA group, which corresponds to the Rab11 group in animals, functions in the recycling of endosomes that control docking and fusion during vesicle transport. However, their molecular mechanisms remain unknown. In this study, we determined the crystal structures of the GDP-bound inactive form and both GppNHp- and GTP-bound active forms of RabA1a, at resolutions of 2.8, 2.6, and 2.6 Å, respectively. A bound sulfate ion in the active site of the GDP-bound structure stabilized Switch II by bridging the interaction between a magnesium ion and Arg74. Comparisons of the two states of RabA1a with Rab11 proteins revealed clear differences in the Switch I and II loops. These results suggested that conformational change of the Switch regions of RabA1a, derived by GTP or GDP binding, could maintain subcellular membrane traffic through the specific interaction of effector molecules.

Crystal Structure of Histidine Triad Nucleotide-Binding Protein from the Pathogenic Fungus Candida albicans

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of 2.5 Å. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (α1-β1) and with the α3 helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.

Crystal Structure of the Type VI Secretion System Accessory Protein TagF from Pseudomonas Aeruginosa

BACKGROUND

Type VI Secretion System (T6SS) has been found in approximately onequarter of the gram-negative bacterial species, and its structural characteristics appear to slightly differ from species to species. The genes encoding T6SS are designated as type six secretion A-M (tssA-M). The expression of the tss gene cluster is regulated by various accessory genes, designated as type VI-associated genes A-P (tagA-P). Tag family proteins have been commonly found in bacteria expressing T6SS but not in all bacterial species. For instance, the tag gene cluster is well-conserved in Pseudomonas aeruginosa (Pa). The PaTagF protein has large homology with ImpM in Rhizobium leguminosarum and SciT in Salmonella enterica. The overexpression of PaTagF represses T6SS complex accumulation and suppresses T6SS antibacterial activity. Thus, the functions of TagF are mediated through direct interactions with the forkhead-associated protein Fha, as evident from the results of the yeast-two hybrid assays. Fha is involved in recruiting a membrane-associated complex either in threonine phosphorylation pathway-dependent or - independent manner. However, functional reports of the tag gene cluster are still limited.

OBJECTIVE

In this article, our motivation is to understand the molecular mechanism underlying the regulation of expression of the type VI secretion system complex.

METHODS

In this article, we start with obtaining the gene encoding PaTagF protein by polymerase chain reaction (PCR). Subsequently, the cloned gene is applied to overexpress of PaTagF protein in Escherichia coli, then purify the recombinant PaTagF protein. Thereafter, the protein is crystallized in a condition of 2.5 M NaCl, 0.1 M imidazole (pH 8.0), 3.2 M NaCl, 0.1 M BIS-TRIS propane (pH 7.0) and diffraction datasets of the PaTagF crystals are collected at the Pohang Accelerator Laboratory (PAL). The molecular structure of PaTagF protein is determined by molecular replacement using the uncharacterized protein PA0076 (PDB code:2QNU) as an initial search model by PHENIX crystallographic software package. Model building of PaTagF structure is performed using Coot program. Finally, the structural model is validated using phenix.refine program.

RESULTS

PaTagF exists as a tetramer in the asymmetric unit, and the overall fold of each monomer is composed of continuous beta-sheets wrapped by alpha-helices. Each monomer has variable conformations and lengths of both the N- and C-termini. Twelve residues, including the His6 tag from the N-terminus of a symmetry-related molecule, have been found in two of the tetrameric PaTagF structures. A structural homology search revealed that PaTagF was similar to the α-β-α sandwichlike structure of the longin domain on the differentially expressed in normal and neoplastic (DENN) superfamily, which is commonly found in proteins related to trafficking.

CONCLUSION

The tetrameric structure of PaTagF comprises varied N- and C-terminal regions in each subunit and may be stabilized by a symmetry-related molecule. This feature was also shown in the TssL structure from V. cholerae. Furthermore, our study showed that the overall fold of PaTagF is homologous to the longin domain of the DENN family. Therefore, further studies are warranted to elucidate the structure-based evolutionary relationship between protein transport systems from the bacteria and eukaryotic cells.

Changes in Bone Mineral Density After Kidney Transplantation

BACKGROUND

Numerous studies have shown that osteoporosis is common in kidney transplant recipients. However, the change in bone mineral density after kidney transplantation (KT) is not fully understood.

METHODS

Thirty-nine kidney transplant recipients with bone densitometry at pretransplant and 24 months after KT were reviewed.

RESULTS

The recipients' median age (44.5 ± 10.7 years) and dialysis duration before KT (4.2 ± 3.4 years) were recorded. The T-scores of the lumbar spine and femur neck at 24 months after KT were positively associated with the respective pretransplant T-score (P < .001 in the lumbar spine and P < .001 in the femur neck). However, the T-score after KT did not show significant change (P = .680 in lumbar spine, P = .093 in femur neck). Changes in the T-scores of the lumbar spine and femur neck over 24 months (delta T-score) were negatively associated with the respective pretransplant T-scores (P = .001 in lumbar spine, P = .026 in femur neck). Changes in the T-scores of the lumbar spine and femur neck over 24 months (delta T-score) were also associated with the pretransplant T-scores after the adjustment of other variables.

CONCLUSION

The change of bone mineral density was related with pretransplant bone mineral density. Careful follow-up of bone densitometry for KT recipients was needed.

Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate

The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3'-NADP⁺. Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3', 5'-bisphosphate (pAp), a known inhibitor of the 5'-3' exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO-pAp-Mg²⁺ complex at 1.8 Å resolution. In comparison with the DXO-RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor.

Suspected Frequent Relapsing IgG4-related Lung Disease in Kidney Transplant Patient: A Case Report

Besides the initial description of IgG4-related pancreatic disease, other sites are now commonly involved. However, occurrence of IgG4-related disease is rare in organ transplanted patients. A 57-year-old man who received a kidney transplantation presented with recurrent dyspnea on exertion. A computed tomography scan of the chest revealed bilateral interlobular septal thickening and multiple tubular and branching small nodular lesions in the right upper lobe, and mass-like consolidation of the left middle lobe. Despite no elevation of serum IgG4 level, a percutaneous core needle biopsy on consolidative mass showed interstitial fibrosis and infiltration of IgG4-positive plasma cells to be more than > 20 per high power field. After treatment with glucocorticoids and rituximab, the consolidative mass of the left middle lobe disappeared.

Whole-Tumor Histogram and Texture Analyses of DTI for Evaluation of IDH1-Mutation and 1p/19q-Codeletion Status in World Health Organization Grade II Gliomas

BACKGROUND AND PURPOSE

Prediction of the isocitrate dehydrogenase 1 (IDH1)-mutation and 1p/19q-codeletion status of World Health Organization grade ll gliomas preoperatively may assist in predicting prognosis and planning treatment strategies. Our aim was to characterize the histogram and texture analyses of apparent diffusion coefficient and fractional anisotropy maps to determine IDH1-mutation and 1p/19q-codeletion status in World Health Organization grade II gliomas.

MATERIALS AND METHODS

Ninety-three patients with World Health Organization grade II gliomas with known IDH1-mutation and 1p/19q-codeletion status (18 IDH1 wild-type, 45 IDH1 mutant and no 1p/19q codeletion, 30 IDH1-mutant and 1p/19q codeleted tumors) underwent DTI. ROIs were drawn on every section of the T2-weighted images and transferred to the ADC and the fractional anisotropy maps to derive volume-based data of the entire tumor. Histogram and texture analyses were correlated with the IDH1-mutation and 1p/19q-codeletion status. The predictive powers of imaging features for IDH1 wild-type tumors and 1p/19q-codeletion status in IDH1-mutant subgroups were evaluated using the least absolute shrinkage and selection operator.

RESULTS

Various histogram and texture parameters differed significantly according to IDH1-mutation and 1p/19q-codeletion status. The skewness and energy of ADC, 10th and 25th percentiles, and correlation of fractional anisotropy were independent predictors of an IDH1 wild-type in the least absolute shrinkage and selection operator. The area under the receiver operating curve for the prediction model was 0.853. The skewness and cluster shade of ADC, energy, and correlation of fractional anisotropy were independent predictors of a 1p/19q codeletion in IDH1-mutant tumors in the least absolute shrinkage and selection operator. The area under the receiver operating curve was 0.807.

CONCLUSIONS

Whole-tumor histogram and texture features of the ADC and fractional anisotropy maps are useful for predicting the IDH1-mutation and 1p/19q-codeletion status in World Health Organization grade II gliomas.

O-GlcNAcylation of ATG4B positively regulates autophagy by increasing its hydroxylase activity

Autophagy is a catabolic degradation process and maintains cellular homeostasis. And autophagy is activated in response to various stress conditions. Although O-GlcNAcylation functions a sensor for nutrient and stress, the relationship between O-GlcNAcylation and autophagy is largely unknown. Here, we identified that ATG4B is novel target for O-GlcNAcylation under metabolic stress condition. Treatment with PugNAc, an O-GlcNAcase inhibitor increased activation of autophagy in SH-SY5Y cells. Both bimolecular fluorescence complementation and immunoprecipitation assay indicated that OGT directly interacts with ATG4B in SH-SY5Y cells. We also found that the O-GlcNAcylated ATG4B was increased in autophagy activation conditions, and down-regulation of OGT reduces O-GlcNAcylation of ATG4B under low glucose condition. Furthermore, the proteolytic activity of ATG4B for LC3 cleavage was enhanced in PugNAc-treated cells. Taken together, these results imply that O-GlcNAcylation of ATG4B regulates autophagy activation by increasing its proteolytic activity under metabolic stress condition.

Molecular elucidation of a new allelic variation at the Sg-5 gene associated with the absence of group A saponins in wild soybean

In soybean, triterpenoid saponin is one of the major secondary metabolites and is further classified into group A and DDMP saponins. Although they have known health benefits for humans and animals, acetylation of group A saponins causes bitterness and gives an astringent taste to soy products. Therefore, several studies are being conducted to eliminate acetylated group A saponins. Previous studies have isolated and characterized the Sg-5 (Glyma.15g243300) gene, which encodes the cytochrome P450 72A69 enzyme and is responsible for soyasapogenol A biosynthesis. In this study, we elucidated the molecular identity of a novel mutant of Glycine soja, 'CWS5095'. Phenotypic analysis using TLC and LC-PDA/MS/MS showed that the mutant 'CWS5095' did not produce any group A saponins. Segregation analysis showed that the absence of group A saponins is controlled by a single recessive allele. The locus was mapped on chromosome 15 (4.3 Mb) between Affx-89193969 and Affx-89134397 where the previously identified Glyma.15g243300 gene is positioned. Sequence analysis of the coding region for the Glyma.15g243300 gene revealed the presence of four SNPs in 'CWS5095' compared to the control lines. One of these four SNPs (G1127A) leads to the amino acid change Arg376Lys in the EXXR motif, which is invariably conserved among the CYP450 superfamily proteins. Co-segregation analysis showed that the missense mutation (Arg376Lys) was tightly linked with the absence of group A saponins in 'CWS5095'. Even though Arg and Lys have similar chemical features, the 3D modelled protein structure indicates that the replacement of Arg with Lys may cause a loss-of-function of the Sg-5 protein by inhibiting the stable binding of a heme cofactor to the CYP72A69 apoenzyme.

An injectable and physical levan-based hydrogel as a dermal filler for soft tissue augmentation

A novel levan-based injectable hydrogel was developed as a dermal filler having better in vivo stability and efficacy compared to HA-based hydrogel.

Prediction of IDH1-Mutation and 1p/19q-Codeletion Status Using Preoperative MR Imaging Phenotypes in Lower Grade Gliomas

BACKGROUND AND PURPOSE

WHO grade II gliomas are divided into three classes: isocitrate dehydrogenase (IDH)-wildtype, IDH-mutant and no 1p/19q codeletion, and IDH-mutant and 1p/19q-codeleted. Different molecular subtypes have been reported to have prognostic differences and different chemosensitivity. Our aim was to evaluate the predictive value of imaging phenotypes assessed with the Visually AcceSAble Rembrandt Images lexicon for molecular classification of lower grade gliomas.

MATERIALS AND METHODS

MR imaging scans of 175 patients with lower grade gliomas with known IDH1 mutation and 1p/19q-codeletion status were included (78 grade II and 97 grade III) in the discovery set. MR imaging features were reviewed by using Visually AcceSAble Rembrandt Images (VASARI); their associations with molecular markers were assessed. The predictive power of imaging features for IDH1-wild type tumors was evaluated using the Least Absolute Shrinkage and Selection Operator. We tested the model in a validation set (40 subjects).

RESULTS

Various imaging features were significantly different according to IDH1 mutation. Nonlobar location, larger proportion of enhancing tumors, multifocal/multicentric distribution, and poor definition of nonenhancing margins were independent predictors of an IDH1 wild type according to the Least Absolute Shrinkage and Selection Operator. The areas under the curve for the prediction model were 0.859 and 0.778 in the discovery and validation sets, respectively. The IDH1-mutant, 1p/19q-codeleted group frequently had mixed/restricted diffusion characteristics and showed more pial invasion compared with the IDH1-mutant, no codeletion group.

CONCLUSIONS

Preoperative MR imaging phenotypes are different according to the molecular markers of lower grade gliomas, and they may be helpful in predicting the IDH1-mutation status.

Highly efficient antibody purification with controlled orientation of protein A on magnetic nanoparticles

In this study, we prepared protein A grafted magnetic nanoparticles for the industrial large-scale purification of antibodies with enhancement of binding capacity and immobilization by controlled orientation with chlorophenylsilane (CPTMS) on the surface. For site-specific immobilization of protein A, genetically modified protein A with a cysteine residue was expressed in E. coli and purified by affinity chromatography. To improve the surface area to volume ratio and increase the immobilization amount of protein A, chlorophenylsilane functionalized magnetic nanoparticles (CPTMS@MNPs) were prepared, which are smaller nanoparticles with an average diameter of 20 nm compared to commercial magnetic microparticles (Dynabeads) with an average size of 2.8 μm. The CPTMS@MNPs showed the enhancement of protein A immobilization and binding capacity to antibodies, being 11.5-fold and 7-fold higher than those of commercial Dynabeads, respectively. In addition, the CPTMS@MNPs retained about 80% of the initial protein binding capacity until the third stage of recycling. Therefore, protein A grafted CPTMS@MNPs may be useful for the industrial large-scale purification of antibodies.

The Initial Area Under the Curve Derived from Dynamic Contrast-Enhanced MRI Improves Prognosis Prediction in Glioblastoma with Unmethylated MGMT Promoter

BACKGROUND AND PURPOSE

Although perfusion and permeability MR parameters have known to have prognostic value, they have reproducibility issues. Our aim was to evaluate whether the initial area under the time-to-signal intensity curve (IAUC) derived from dynamic contrast-enhanced MR imaging can improve prognosis prediction in patients with glioblastoma with known MGMT status.

MATERIALS AND METHODS

We retrospectively examined 88 patients with glioblastoma who underwent preoperative dynamic contrast-enhanced MR imaging. The means of IAUC values at 30 and 60 seconds (IAUC30_mean and IAUC60_mean) were extracted from enhancing tumors. The prognostic values of IAUC parameters for overall survival and progression-free survival were assessed with log-rank tests, according to the MGMT status. Multivariate overall survival and progression-free survival models before and after adding the IAUC parameters as covariates were explored by net reclassification improvement after receiver operating characteristic analysis for 1.5-year overall survival and 1-year progression-free survival and by random survival forest.

RESULTS

High IAUC parameters were associated with worse overall survival and progression-free survival in the unmethylated MGMT group, but not in the methylated group. In the unmethylated MGMT group, 1.5-year overall survival and 1-year progression-free survival prediction improved significantly after adding IAUC parameters (overall survival area under the receiver operating characteristic curve, 0.86; progression-free survival area under the receiver operating characteristic curve, 0.74-0.76) to the model with other prognostic factors (overall survival area under the receiver operating characteristic curve, 0.81; progression-free survival area under the receiver operating characteristic curve, 0.69; P < .05 for all) except in the case of IAUC60_mean for 1-year progression-free survival prediction (P = .059). Random survival forest models indicated that the IAUC parameters were the second or most important predictors in the unmethylated MGMT group, except in the case of the IAUC60_mean for progression-free survival.

CONCLUSIONS

IAUC can be a useful prognostic imaging biomarker in patients with glioblastoma with known MGMT status, improving prediction of glioblastoma prognosis with the unmethylated MGMT promoter status.