Wheat rhizosphere-derived bacteria protect soybean from soilborne diseases

Soybean [Glycine max (L.) Merr.] is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2) and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN susceptible soybean "Williams 82". Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Neural network for autonomous segmentation and volumetric assessment of clot and edema in acute and subacute intracerebral hemorrhages

INTRODUCTION

Minimally-invasive surgical techniques for intracerebral hemorrhage (ICH) evacuation use imaging to guide the suction, lysing and/or drainage from the hemorrhage site via various designs. A previous international surgical study has shown that reduction of hematoma volume below 15 ml is indicative of improved long term patient outcomes. The study noted a need for tools to periodically visualize remaining clot during intervention to increase the likelihood of evacuating sufficient clot volumes without endangering rebleeds. Robust segmentation of MRI could guide surgeons and radiologists regarding remaining regions and approaches for prudent evacuation. We thus propose a Convolutional Neural Network (CNN) to identify and autonomously segment clot and peripheral edema in MR images of the brain and generate an estimate of the remaining clot volume.

MATERIALS AND METHODS

We used a retrospective, locally-acquired dataset of ICH patient scans taken on 3 T MRI scanners. Three sets of ground truth manual segmentations were independently generated by two imaging scientists and one radiology fellow. Evaluation of clot age was determined based on relative contrast of hemorrhage components and reviewed by a neurosurgeon. Model accuracy was determined by pixel-wise Dice coefficient (DC) calculations between each ground truth manual segmentation and the machine-derived autonomous segmentations.

RESULTS

The model produced autonomous segmentations of clot core with an average DC of 0.75 ± 0.21 relative to manual segmentations of the same scans. For edema, it produced segmentations with an average DC of 0.68 ± 0.16 relative to manual. From these pixel-wise segmentations, clot volume can be calculated. Model-produced segmentations underestimated clot volumes by an average of 17% relative to ground-truth.

CONCLUSION

The machine learning models were able to identify and segment volumes of ICH components swiftly and accurately.

Evaluation of sarcopenia in patients receiving intravesical Bacillus Calmette-Guérin for non-muscle invasive bladder cancer

BACKGROUND

Sarcopenia is associated with adverse outcomes for patients with muscle invasive bladder cancer (MIBC), but less is known about its impact in the setting of non-muscle invasive bladder cancer (NMIBC). Sarcopenia, skeletal muscle density, and adipose tissue area have been studied as markers of malnutrition and can be determined radiographically. The purpose of this study is to characterize the prevalence of sarcopenia in patients with NMIBC receiving intravesical Bacillus Calmette-Guérin (BCG).

METHODS

Following institutional review board approval, patients with NMIBC having received intravesical BCG were identified using institutional pharmacy records. Patients having undergone computed tomography (CT) of the abdomen and pelvis within 90 days of treatment were included in the analysis. Using sliceOmatic 5.0 software, skeletal muscle area (cm2) was measured at the L3 level to calculate skeletal muscle index (SMI), a marker of sarcopenia. Subcutaneous, visceral, and intramuscular adipose tissue areas in addition to skeletal muscle density were also measured. Frailty was evaluated as a secondary aim using the 5-Item Modified Frailty Index (mFI-5). Using predefined cutoffs, the prevalence of sarcopenia was determined. Descriptive statistics were used to characterize frailty and secondary body composition characteristics. Statistical analysis was performed to evaluate the impact of sarcopenia on recurrence rate and progression.

RESULTS

A total of 308 patients having received BCG between 2015 and 2020 were identified, of which 90 met criteria for analysis. Nearly all (94%) patients completed at least 5 out of 6 BCG induction instillations. Median body mass index (kg/m2) was 27.64 (IQR 24.9, 30.5) for females and 27.7 (IQR 24.9, 30.66) for males. Median SMI (cm2/m2) was 49.44 (IQR 39.39, 55.17) for females and 49.58 (IQR 40.25, 55.58) for males. A majority (61%) of patients were found to be sarcopenic. High-risk frailty was identified 36% of patients. There was no association between sarcopenia and recurrence rate or progression.

CONCLUSIONS

Sarcopenia and frailty are highly prevalent amongst patients with NMIBC. A diagnosis of NMIBC represents a window of opportunity to identify and intervene on modifiable risk factors such as sarcopenia and frailty, which are associated with adverse outcomes in more advanced disease states.

Integrated Fluorescence Microscopy (iFLM) for Cryo-FIB-milling and In-situ Cryo-ET

Correlative cryo-FLM-FIB milling is a powerful sample preparation technique for in situ cryo-ET. However, correlative workflows that incorporate precise targeting remain challenging. Here, we demonstrate the development and use of an integrated Fluorescence Light Microscope (iFLM) module within a cryo-FIB-SEM to enable a coordinate-based two-point 3D correlative workflow. The iFLM guided targeting of regions of interest coupled with an automated milling process of the cryo-FIB-SEM instrument allows for the efficient preparation of 9-12 ∼200 nm thick lamellae within 24 hours. Using regular and montage-cryo-ET data collection schemes, we acquired data from FIB-milled lamellae of HeLa cells to examine cellular ultrastructure. Overall, this workflow facilitates on-the-fly targeting and automated FIB-milling of cryo-preserved cells, bacteria, and possibly high pressure frozen tissue, to produce lamellae for downstream cryo-ET data collection.

PET/MRI in Gynecologic Malignancy

Patients with gynecologic malignancies often require a multimodality imaging approach for initial staging, treatment response assessment, and surveillance. MRI imaging and PET are two well-established and widely accepted modalities in this setting. Although PET and MRI imaging are often acquired separately on two platforms (a PET/computed tomography [CT] and an MRI imaging scanner), hybrid PET/MRI scanners offer the potential for comprehensive disease assessment in one visit. Gynecologic malignancies have been one of the most successful areas for implementation of PET/MRI. This article provides an overview of the role of this platform in the care of patients with gynecologic malignancies.

Federated learning enables big data for rare cancer boundary detection

Although machine learning (ML) has shown promise across disciplines, out-of-sample generalizability is concerning. This is currently addressed by sharing multi-site data, but such centralization is challenging/infeasible to scale due to various limitations. Federated ML (FL) provides an alternative paradigm for accurate and generalizable ML, by only sharing numerical model updates. Here we present the largest FL study to-date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature (n = 6, 314). We demonstrate a 33% delineation improvement for the surgically targetable tumor, and 23% for the complete tumor extent, over a publicly trained model. We anticipate our study to: 1) enable more healthcare studies informed by large diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further analyses for glioblastoma by releasing our consensus model, and 3) demonstrate the FL effectiveness at such scale and task-complexity as a paradigm shift for multi-site collaborations, alleviating the need for data-sharing.

Exploratory study of how Cognitive Multisensory Rehabilitation restores parietal operculum connectivity and improves upper limb movements in chronic stroke

Cognitive Multisensory Rehabilitation (CMR) is a promising therapy for upper limb recovery in stroke, but the brain mechanisms are unknown. We previously demonstrated that the parietal operculum (parts OP1/OP4) is activated with CMR exercises. In this exploratory study, we assessed the baseline difference between OP1/OP4 functional connectivity (FC) at rest in stroke versus healthy adults to then explore whether CMR affects OP1/OP4 connectivity and sensorimotor recovery after stroke. We recruited 8 adults with chronic stroke and left hemiplegia/paresis and 22 healthy adults. Resting-state FC with the OP1/OP4 region-of-interest in the affected hemisphere was analysed before and after 6 weeks of CMR. We evaluated sensorimotor function and activities of daily life pre- and post-CMR, and at 1-year post-CMR. At baseline, we found decreased FC between the right OP1/OP4 and 34 areas distributed across all lobes in stroke versus healthy adults. After CMR, only four areas had decreased FC compared to healthy adults. Compared to baseline (pre-CMR), participants improved on motor function (MESUPES arm p = 0.02; MESUPES hand p = 0.03; MESUPES total score p = 0.006); on stereognosis (p = 0.03); and on the Frenchay Activities Index (p = 0.03) at post-CMR and at 1-year follow-up. These results suggest enhanced sensorimotor recovery post-stroke after CMR. Our results justify larger-scale studies.

Alignment-free filtering for cfNA fusion fragments

Motivation

Cell-free nucleic acid (cfNA) sequencing data require improvements to existing fusion detection methods along multiple axes: high depth of sequencing, low allele fractions, short fragment lengths and specialized barcodes, such as unique molecular identifiers.

Results

AF4 was developed to address these challenges. It uses a novel alignment-free kmer-based method to detect candidate fusion fragments with high sensitivity and orders of magnitude faster than existing tools. Candidate fragments are then filtered using a max-cover criterion that significantly reduces spurious matches while retaining authentic fusion fragments. This efficient first stage reduces the data sufficiently that commonly used criteria can process the remaining information, or sophisticated filtering policies that may not scale to the raw reads can be used. AF4 provides both targeted and de novo fusion detection modes. We demonstrate both modes in benchmark simulated and real RNA-seq data as well as clinical and cell-line cfNA data.

Availability and implementation

AF4 is open sourced, licensed under Apache License 2.0, and is available at: https://github.com/grailbio/bio/tree/master/fusion.

Ultra-simple wearable local sweat volume monitoring patch based on swellable hydrogels

Quantifiably monitoring sweat rate and volume is important to assess the stress level of individuals and/or prevent dehydration, but despite intense research, a convenient, continuous, and low-cost method to monitor sweat rate and total sweat volume loss remains an un-met need. We present here an ultra-simple wearable sensor capable of measuring sweat rate and volume accurately. The device continuously monitors sweat rate by wicking the produced sweat into hydrogels that measurably swell in their physical geometry. The device has been designed as a simple to fabricate, low-cost, disposable patch. This patch exhibits stable and predictable operation over the maximum variable chemistry expected for sweat (pH 4-9 and salinity 0-100 mM NaCl). Preliminary in vivo testing of the patch has been achieved during aerobic exercise, and the sweat rates measured via the patch accurately follow actual sweat rates.

Catastrophic Antiphospholipid Syndrome Presenting with Genitourinary Manifestations

Catastrophic antiphospholipid syndrome (CAPS) is a rare disorder characterized by acute, multi-system dysfunc- tion due to small-vessel thrombosis related to anti-phospholipid antibodies. Here we present an unusual case of CAPS presenting with genitourinary manifestations. A 72-year-old male developed a series of symptoms over the course of two weeks. His symptoms included testicular inflammation, scrotal edema, priapism, hematuria, penile eschar, elbow eschars, and acute kidney injury. He was found to have anti-phospholipid antibodies and treated with anticoagulation, high-dose steroids and plasma exchange. His symptoms resolved with minimal lasting effects. This case is unique to the literature because of the extensive genitourinary involvement.

The National Dental Practice-Based Research Network Adult Anterior Open Bite Study: Treatment recommendations and their association with patient and practitioner characteristics

INTRODUCTION

This aim of this paper is to describe and identify the practitioner and patient characteristics that are associated with treatment recommendations for adult anterior open bite patients across the United States.

METHODS

Practitioners and patients were recruited within the framework of the National Dental Practice-Based Research Network. Practitioners were asked about their demographic characteristics and their treatment recommendations for these patients. The practitioners also reported on their patients' dentofacial characteristics and provided initial cephalometric scans and intraoral photographs. Patients were asked about their demographic characteristics, previous orthodontic treatment, and goals for treatment. Four main treatment groups were evaluated: aligners, fixed appliances, temporary anchorage devices (TADs), and orthognathic surgery. Extractions were also investigated. Predictive multivariable models were created comparing various categories of treatment as well as extraction/nonextraction decisions.

RESULTS

Ninety-one practitioners (mostly orthodontists) and 347 patients were recruited from October 2015 to December 2016. Increased aligner recommendations were associated with white and Asian patients, the presence of tongue habits, and female practitioners. TADs were recommended more often in academic settings. Recommendations for orthognathic surgery were associated with demographic factors, such as availability of insurance coverage and practitioner race/ethnicity, and dentofacial characteristics, such as anteroposterior discrepancies, more severe open bites, and steeper mandibular plane angles. Extraction recommendations were largely associated with severe crowding and incisor proclination.

CONCLUSIONS

Both doctor and patient demographic factors, as well as dentofacial characteristics, were significantly associated with treatment recommendations for adult anterior open bite patients.

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Contaminated landslide runout deposits in rivers - Method for estimating long-term ecological risks

The potential catastrophic event of a landslide bringing contaminants to surface waters has been highlighted in public media, but there are still few scientific studies analyzing the risk of landslides with contaminated soil. The aim of this study is to present a method to estimate the risk of potential long-term ecological effects on water bodies due to contaminated soil released into a river through a landslide. The study constitutes further development of previous work focusing on the instantaneous (short-term) release of contaminants and associated effects. Risk is here defined as the probability of surface water failing to comply with environmental quality standards (EQS). The transport model formulation is kept simple enough to allow for a probabilistic analysis as a first assessment of the impact on the river water quality from a landslide runout deposit containing contaminated soil. The model is applied at a contaminated site located adjacent to the Göta Älv River that discharges into the Gothenburg estuary, in southwest Sweden. The results from the case study show that a contaminated runout deposit will likely cause contamination levels above EQSs in the near area for a long time and that it will take several years for the deposit to erode, with the greatest erosion at the beginning when water velocities are their highest above the deposit. A contaminated landslide runout deposit will thus act as a source of contamination to the downstream water system until all the contaminated deposit has been eroded away and the contaminants have been transported from the deposit to the river, and further to the river mouth - diluted but not necessarily negligible. Therefore, it is important to prevent landslides of contaminated soil or waste, and if such events were to occur, to remove the contaminated runout deposit as soon as possible.

Predictors of emotional and physical dating violence in a sample of serious juvenile offenders

AIM

We estimate group-based dating violence trajectories and identify the adolescent risk factors that explain membership in each trajectory group.

METHOD

Using longitudinal data from the Pathways to Desistance Study, which follows a sample of 1354 serious juvenile offenders from Philadelphia, Pennsylvania and Phoenix, Arizona between mid-adolescence and early adulthood, we estimate group-based trajectory models of both emotional dating violence and physical dating violence over a span of five years in young adulthood. We then estimate multinomial logistic regression models to identify theoretically motivated risk factors that predict membership in these groups.

RESULTS

We identified three developmental patterns of emotional dating violence: none (33%), low-level (59%) and high-level decreasing (8%). The best-fitting model for physical dating violence also had three groups: none (73%), low-level (24%) and high-level (3%). Race/ethnicity, family and psychosocial variables were among the strongest predictors of both emotional and physical dating violence. In addition, delinquency history variables predicted emotional dating violence and relationship variables predicted physical dating violence.

CONCLUSIONS

Dating violence is quite prevalent in young adulthood among serious juvenile offenders. Numerous predictors distinguish between chronic dating violence perpetrators and other groups. These may suggest points of intervention for reducing future violence. Copyright © 2016 John Wiley & Sons, Ltd.

Are immigrants more likely than native-born Americans to perpetrate intimate partner violence?

Despite an emerging body of research indicating that immigrants are less likely than native-born Americans to engage in crime and antisocial behavior, less attention has focused specifically on intimate partner violence (IPV) perpetration among immigrant populations. We address this gap by using data from Wave II of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) and compare immigrants from Asia, Africa, Europe, and Latin America to native-born Americans with respect to multiple forms of IPV. After controlling for an extensive array of confounds, results indicate that in the aggregate, immigrants are significantly more likely to perpetrate IPV. However, examination of major world regions indicates these results are driven by Latin American immigrants. Immigrants from Asia, Africa, and Europe report a lower prevalence of IPV perpetration than native-born Americans. This study extends prior research on the immigrant paradox and suggests that future studies take into account regional heterogeneity when examining IPV and other forms of violence in immigrant populations.

With or Without You? Contextualizing the Impact of Romantic Relationship Breakup on Crime Among Serious Adolescent Offenders

The decline and delay of marriage has prolonged adolescence and the transition to adulthood, and consequently fostered greater romantic relationship fluidity during a stage of the life course that is pivotal for both development and offending. Yet, despite a growing literature of the consequences of romantic relationships breakup, little is known about its connection with crime, especially among youth enmeshed in the criminal justice system. This article addresses this gap by examining the effects of relationship breakup on crime among justice-involved youth-a key policy-relevant group. We refer to data from the Pathways to Desistance Study, a longitudinal study of 1354 (14% female) adjudicated youth from the juvenile and adult court systems in Phoenix and Philadelphia, to assess the nature and complexity of this association. In general, our results support prior evidence of breakup's criminogenic influence. Specifically, they suggest that relationship breakup's effect on crime is particularly acute among this at-risk sample, contingent upon post-breakup relationship transitions, and more pronounced for relationships that involve cohabitation. Our results also extend prior work by demonstrating that breakup is attenuated by changes in psychosocial characteristics and peer associations/exposure. We close with a discussion of our findings, their policy implications, and what they mean for research on relationships and crime among serious adolescent offenders moving forward.

A genome-wide association study of saturated, mono- and polyunsaturated red blood cell fatty acids in the Framingham Heart Offspring Study

Most genome-wide association studies have explored relationships between genetic variants and plasma phospholipid fatty acid proportions, but few have examined apparent genetic influences on the membrane fatty acid profile of red blood cells (RBC). Using RBC fatty acid data from the Framingham Offspring Study, we analyzed over 2.5 million single nucleotide polymorphisms (SNPs) for association with 14 RBC fatty acids identifying 191 different SNPs associated with at least 1 fatty acid. Significant associations (p<1×10(-8)) were located within five distinct 1MB regions. Of particular interest were novel associations between (1) arachidonic acid and PCOLCE2 (regulates apoA-I maturation and modulates apoA-I levels), and (2) oleic and linoleic acid and LPCAT3 (mediates the transfer of fatty acids between glycerolipids). We also replicated previously identified strong associations between SNPs in the FADS (chromosome 11) and ELOVL (chromosome 6) regions. Multiple SNPs explained 8-14% of the variation in 3 high abundance (>11%) fatty acids, but only 1-3% in 4 low abundance (<3%) fatty acids, with the notable exception of dihomo-gamma linolenic acid with 53% of variance explained by SNPs. Further studies are needed to determine the extent to which variations in these genes influence tissue fatty acid content and pathways modulated by fatty acids.

Deliberate self-harm and the nexus of violence, victimization, and mental health problems in the United States

Deliberate self-harm (DSH) is associated with diverse psychiatric diagnoses and broad psychopathology but less is known about its association with other forms of interpersonal violence and crime. Using the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), the current study examined linkages between not only DSH and mental health and substance abuse comorbidity, but also childhood abuse, lifetime victimization, and a variety of violent behaviors. We identified a prevalence of 2.91% for DSH and found that DSH is associated with generalized and severe psychopathology, wide-ranging substance abuse, and adverse childhood experiences. Contrary to other studies, we found significant racial and ethnic differences in DSH. African-American, Latinos, and Asians, were substantially less likely than Whites to report DSH. Our hypothesis that DSH would be associated with a variety of violent behaviors including robbery, intimate partner violence, forced sex, cruelty to animals, and use of a weapon was supported even after adjusting for an array of covariates. We extend previous research on DSH by examining its prevalence in one the largest comorbidity surveys ever conducted and show that DSH is associated with multiple forms of violent behavior toward others, including animals.

Impact of suppressing retinoic acid-related orphan receptor gamma t (ROR)γt in ameliorating central nervous system autoimmunity

Multiple sclerosis (MS) is an immune-mediated chronic central nervous system (CNS) disease affecting more than 400 000 people in the United States. Myelin-reactive CD4 T cells play critical roles in the formation of acute inflammatory lesions and disease progression in MS and experimental autoimmune encephalomyelitis (EAE), a well-defined mouse model for MS. Current MS therapies are only partially effective, making it necessary to develop more effective therapies that specifically target pathogenic myelin-specific CD4 T cells for MS treatment. While suppressing T-bet, the key transcription factor in T helper type 1 (Th1) cells, has been demonstrated to be beneficial in prevention and treatment of EAE, the therapeutic potential of retinoic acid-related orphan receptor gamma t (ROR)γt, the key transcription factor for Th17 cells, has not been well-characterized. In this study, we characterized the correlation between RORγt expression and other factors affecting T cell encephalitogenicity and evaluated the therapeutic potential of targeting RORγt by siRNA inhibition of RORγt. Our data showed that RORγt expression correlates with interleukin (IL)-17 production, but not with the encephalitogenicity of myelin-specific CD4 T cells. IL-23, a cytokine that enhances encephalitogenicity, does not enhance RORγt expression significantly. Additionally, granulocyte-macrophage colony-stimulating factor (GM-CSF) levels, which correlate with the encephalitogenicity of different myelin-specific CD4 T cell populations, do not correlate with RORγt. More importantly, inhibiting RORγt expression in myelin-specific CD4 T cells with an siRNA does not reduce disease severity significantly in adoptively transferred EAE. Thus, RORγt is unlikely to be a more effective therapeutic target for ameliorating pathogenicity of encephalitogenic CD4 T cells.

Abstract 612: Endostatin is a novel inhibitor of androgen receptor function in prostate cancer

Abnormalities in androgen-androgen receptor (AR) axis have long been recognized for their roles in promoting prostate tumor growth and metastasis. Conventional therapies targeting androgen ablation show transient tumor regression, however, when the tumor recurs during castration-refractory metastatic stage, the current treatment options are very limited. Although the precise mechanism by which prostate cancer (PCa) cells circumvent the androgen deprivation is unclear, recurring tumors have been shown to retain AR activity and upregulation of AR-target gene expression such as prostate specific antigen (PSA), suggesting that targeting AR remains a key component of developing novel therapeutic strategies. Here, we show a profound effect of endostatin, an endogenous angiogenesis inhibitor, on proliferation and invasion of AR-positive PCa cells by targeting AR function. The present study identified that intracellular trafficking of endostatin and direct interaction with AR disrupts AR nuclear translocation and the consequent transcriptional activation of PSA gene. In addition, our structural modeling and site-directed mutagenesis studies suggest that the binding mechanism may include the interaction of bulky side chains (F31 and F34) present in endostatin with the co-activator binding interface (AF-2) in AR ligand-binding domain (LBD). Regarding drug resistance to the second-generation androgen antagonists in patients with metastatic PCa, recent studies revealed that a missense mutation in AR LBD (F876L) and the consequential antagonist-to-agonist switch confers continued AR activity. In this context, our study suggests that endostatin can be recognized as an endogenous AR inhibitor where its molecular interaction with AR may prevent from agonistic switch of AR function by fully masking the AF-2 subdomain. Overall, the current finding provides new insights into endostatin whose anti-cancer activity is not only limited to inhibiting angiogenesis, but can also be expanded to suppressing AR-mediated PCa progression by disrupting AR transactivation.

Citation Format: Joo Hyoung Lee, Tatyana Isayeva, Matthew Larson, Diptiman Chanda, Igor Chesnokov, Selvarangan Ponnazhagan. Endostatin is a novel inhibitor of androgen receptor function in prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 612. doi:10.1158/1538-7445.AM2014-612

Structure/Function studies on Glucan Binding Protein C of Streptococcus mutans

Streptococcus mutans is a known etiological agent in dental caries. In the past several years, we have taken a concerted effort toward understanding the adhesion mechanisms adopted by the surface proteins S. mutans. The Glucan Binding Protein C (GBPC) is a LPXTG anchored surface protein on S. mutans that has been widely implicated to play a significant role in biofilm formation. GBPC displays limited homology to the V-region of Antigen I/II (AgI/II), another surface protein of S. mutans (1,2). We undertook to crystallize and resolve the structure of GBPC. Recombinant GbpC111-552 (residues encompassing 111-552) was cloned into a pET23d vector, and thereafter expressed in E.coli BL21(DE3). GbpC111-552 purified initially using affinity chromatography (his-tag), followed by anion exchange (MonoQ) and finally polished with size exclusion (Superdex 75). GbpC111-552 was crystallized using the vapor diffusion method by scanning various commercial crystallization kits on a 96 well plate format through the Art Robbins Gryphon robot. Large crystals were obtained from a refined droplet condition that contained 1 μl of protein (43.3 mg/ml) mixed with 1 μl of reservoir made of 100 mM Bis-Tris pH 6.5 and 25% (w/v) PEG3350. The crystal structure could not be resolved by molecular replacement. Therefore crystals were soaked in Sodium Iodide (NaI) and thereafter flash frozen with 9% glycerol as crytoprotectant. MAD data sets were collected and the crystal structure was resolved. We will present the crystal structure, and how based on its structural homology we discovered similar functionalities among the surface proteins of S. mutans. The structural and functional studies of these surface proteins we hope would allow the identification of the adherence motifs, which would aid in development of inhibitors. The development of such anti-adhesive inhibitors would aid in disease preventative therapies.

A novel biomechanical model assessing continuous orthodontic archwire activation

INTRODUCTION

The biomechanics of a continuous archwire inserted into multiple orthodontic brackets is poorly understood. The purpose of this research was to apply the birth-death technique to simulate the insertion of an orthodontic wire and the consequent transfer of forces to the dentition in an anatomically accurate model.

METHODS

A digital model containing the maxillary dentition, periodontal ligament, and surrounding bone was constructed from computerized tomography data. Virtual brackets were placed on 4 teeth (central and lateral incisors, canine, and first premolar), and a steel archwire (0.019 × 0.025 in) with a 0.5-mm step bend to intrude the lateral incisor was virtually inserted into the bracket slots. Forces applied to the dentition and surrounding structures were simulated by using the birth-death technique.

RESULTS

The goal of simulating a complete bracket-wire system on accurate anatomy including multiple teeth was achieved. Orthodontic forces delivered by the wire-bracket interaction were 19.1 N on the central incisor, 21.9 N on the lateral incisor, and 19.9 N on the canine. Loading the model with equivalent point forces showed a different stress distribution in the periodontal ligament.

CONCLUSIONS

The birth-death technique proved to be a useful biomechanical simulation method for placement of a continuous archwire in orthodontic brackets. The ability to view the stress distribution with proper anatomy and appliances advances our understanding of orthodontic biomechanics.

Comparative functional genomic analysis of Solanum glandular trichome types

Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.

Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

Physiological fluctuation of (99m)Tc-sestamibi uptake in normal mammary glands: a systematic investigation in female rats

BACKGROUND

Scintimammography is an imaging tool for the diagnosis and management of primary breast tumors. There remains a significant knowledge gap regarding the physiological fluctuations in the basal level of (99m)Tc-sestamibi uptake in normal mammary tissues with respect to the female reproductive cycle.

PURPOSE

To systematically characterize (99m)Tc-sestamibi uptake in normal mammary tissues in female Sprague Dawley (SD) rats in different estrous phases.

MATERIAL AND METHODS

The exact phase of the reproductive cycle was determined in 18 female SD rats. Each rat was sacrificed at 20 min after (99m)Tc-sestamibi injection (14.8 MBq/kg). The mammary glands were dissected, and the radioactivity uptake was measured by gamma counting.

RESULTS

Tc-99m-sestamibi uptake oscillates by about twofold and reaches a maximum at the proestrous phase of the rat reproductive cycle.

CONCLUSION

Tc-99m-sestamibi uptake fluctuates significantly in normal mammary tissues in synchrony with the female reproductive cycle, and peaks in the proestrous phase in rats, which is equivalent to the early to mid-follicular phase in the human menstrual cycle. This finding will likely benefit the detection of breast lesions that may otherwise be obscured by fluctuating background signals in surrounding normal breast tissues.

Specialty care and education associated with greater disease-specific knowledge but not satisfaction with care for chronic hepatitis C

BACKGROUND

Little is known about differences among hepatitis C virus (HCV) patients managed by generalists vs. specialists with respect to patient-centred outcomes, such as disease-specific knowledge, health-related quality of life (HRQoL) and satisfaction with care.

AIM

To examine selected patient-centred outcomes of HCV-related care provided in primary care, specialty care or both.

METHODS

A total of 629 chronic HCV patients completed a survey including an HCV knowledge assessment and validated instruments for satisfaction and HRQoL. Multivariable linear regression was used to compare outcomes between groups.

RESULTS

Adjusted total HCV knowledge score was lower among patients who did not attend specialty care (P < 0.01). Primary care and specialty patients did not differ in adjusted general HRQoL or satisfaction. Sixty percent of specialty patients underwent formal HCV education, which was associated with 5% higher knowledge score (P = 0.01). General HRQoL and patient satisfaction did not differ between primary care and specialty groups. Disease-specific knowledge and care satisfaction were independent of mental illness, substance abuse, socio-economic variables, history of antiviral treatment, formal HCV education and duration of time between last visit and survey completion.

CONCLUSIONS

Primary care patients with chronic HCV have lower adjusted disease-specific knowledge than specialty patients, but no difference in general HRQoL or patient satisfaction.

Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate

We identified a cis-prenyltransferase gene, neryl diphosphate synthase 1 (NDPS1), that is expressed in cultivated tomato (Solanum lycopersicum) cultivar M82 type VI glandular trichomes and encodes an enzyme that catalyzes the formation of neryl diphosphate from isopentenyl diphosphate and dimethylallyl diphosphate. mRNA for a terpene synthase gene, phellandrene synthase 1 (PHS1), was also identified in these glands. It encodes an enzyme that uses neryl diphosphate to produce beta-phellandrene as the major product as well as a variety of other monoterpenes. The profile of monoterpenes produced by PHS1 is identical with the monoterpenes found in type VI glands. PHS1 and NDPS1 map to chromosome 8, and the presence of a segment of chromosome 8 derived from Solanum pennellii LA0716 causes conversion from the M82 gland monoterpene pattern to that characteristic of LA0716 plants. The data indicate that, contrary to the textbook view of geranyl diphosphate as the "universal" substrate of monoterpene synthases, in tomato glands neryl diphosphate serves as a precursor for the synthesis of monoterpenes.

Safety analysis of radioimmunotherapy (RIT) in patients with relapsed or refractory low grade, follicular or transformed non-Hodgkin's lymphoma and mantle cell lymphoma based on age at time of therapy

e19529

Background: Radioimmunotherapy is a therapeutic option for relapsed or refractory indolent, follicular and transformed non Hodgkin's lymphoma and mantle cell lymphoma. Although prolongued myelotoxicity has been described with use of iodine I 131 tositumomab (TOSI) and yttrium 90 ibritumomab tiuxetan (IBRI), analysis of toxicity according to patients’ age at therapy still lacks. Methods: Utilizing the Rush University Medical Center database 61 subjects who received RIT between November/2003 and June/2008, either with TOSI or IBRI were divided in 2 groups according to age at time of therapy. Group 1 included patients between 33 and 60 (51.8±6.5) years of age (N=29) and group 2 included patients 61 years old or older (70.1±7.8) (N=32). Parameters compared between groups were: Time to nadir of lowest absolute neutrophil count (ANC), time to recovery ANC above 1000/mcL, time to nadir of lowest hemoglobin levels, time to recovery to hemoglobin levels above 8g/dL, time to lowest platelet count and time to recovery to platelet count above 100,000/mcL. Incidence o myelodysplastic syndrome (MDS) was also compared between groups. Groups characteristics such as sex, type of RIT, presence of disease in bone marrow, FLIPI/IPI and use of G-CSF were noted. Results: There was no significant statistical difference between groups in time (number of days) to achieve nadir of ANC (group 1 85.3±208; group 2 50.3±19.9), nadir of hemoglobin levels (group 1 106±60.6; group 2 84±57.0) and time to nadir of platelet level (group 1 53.5±70.7; group 2 41.8±9.6). There was no statistical significant difference between groups in duration of cytopenias, except for time for platelet recovery which was significant longer in group 2 using the Pearson Correlation analysis. (p=0.008). (Days for platelets recovery to levels above 100,000/mcL group 1 29.4±27.7; group 2 108.8 ±207.3). One patient in group 1 and three patients on group 2 were diagnosed with MDS but were also treated with different chemotherapy regimens. Conclusions: RIT should be considered a safe therapeutic modality in patients with refractory or relapsed indolent, follicular, NHL, transformed and Mantle Cell lymphoma regardless of age.

[Table: see text]

Inguinal Lymph Node Biopsy in Patients Infected with the Human Immunodeficiency Virus Is Safe

BACKGROUND AND PURPOSE

The incidence of postoperative complications in human immunodeficiency virus (HIV)-infected patients remains controversial. Published data suggest that these patients are at higher risk for postoperative surgical site infections (SSIs) than are uninfected patients if the site is contaminated. To determine the incidence of postoperative SSI in HIV-infected patients undergoing aseptic surgery at uncontaminated sites, we performed a prospective case series analysis. We hypothesized that the rate of postoperative SSI would be low for this aseptic procedure, irrespective of CD4(+) lymphocyte counts. Additionally, we monitored the rates of other complications, namely, hematoma, dorsal vein thrombosis, epididymitis, lymphocele, and suture extrusion.

METHODS

From May 1, 2000, through January 31, 2006, we performed 137 sterile inguinal lymph node biopsies in 44 HIV-infected patients as part of a funded study evaluating the role of peripheral lymphatic tissue in the pathophysiology of HIV infection. Postoperatively, we followed all patients for a minimum of 30 days.

RESULTS

Postoperatively, we noted one instance each (0.7%) of infection, dorsal vein thrombosis with epididymitis (0.7%), and lymphocele and two cases each (1.4%) of hematoma and suture extrusion. The CD4(+) count at the time of biopsy did not correlate with postoperative complications.

CONCLUSIONS

Inguinal lymph node biopsy in HIV-infected patients is safe, irrespective of CD4(+) lymphocyte count.

Lymphatic tissue fibrosis is associated with reduced numbers of naive CD4+ T cells in human immunodeficiency virus type 1 infection

The organized structure of lymphatic tissues (LTs) constitutes a microenvironment referred to as a niche that plays a critical role in immune system homeostasis by promoting cellular interactions and providing access to cytokines and growth factors on which cells are dependent for survival, proliferation, and differentiation. In chronic human immunodeficiency virus type 1 (HIV-1) infection, immune activation and inflammation result in collagen deposition and disruption of this LT niche. We have previously shown that these fibrotic changes correlate with a reduction in the size of the total population of CD4+ T cells. We now show that this reduction is most substantial within the naïve CD4+ T-cell population and is in proportion to the extent of LT collagen deposition in HIV-1 infection. Thus, the previously documented depletion of naïve CD4+ T cells in LTs in HIV-1 infection may be a consequence not only of a decreased supply of thymic emigrants or chronic immune activation but also of the decreased ability of those cells to survive in a scarred LT niche. We speculate that LT collagen deposition might therefore limit repopulation of naïve CD4+ T cells with highly active antiretroviral therapy, and thus, additional treatments directed to limiting or reversing inflammatory damage to the LT niche could potentially improve immune reconstitution.

Amount of lymphatic tissue fibrosis in HIV infection predicts magnitude of HAART-associated change in peripheral CD4 cell count

The structure of lymphatic tissues is an important component of lymphatic tissue T-cell homeostasis. Collagen deposition in lymphatic tissues (common in HIV infection) disrupts the niche and limits the size of the resident CD4 cell population. In this report we show that a single measurement of lymphatic tissue collagen predicts the magnitude of recovery of the peripheral CD4 cell pool with HAART (P < 0.001). This suggests that collagen-targeted therapies might be of benefit.

A model system of oral HIV exposure, using human palatine tonsil, reveals extensive binding of HIV infectivity, with limited progression to primary infection

Oral exposure to human immunodeficiency virus (HIV) type 1 results in systemic infection, but many details surrounding virus transmission remain unresolved. We developed a mucosal model, using human palatine tonsil with intact external epithelium, to study events after oral exposure to HIV. When applied to the external epithelium, semen from an HIV-seropositive patient and cell-free virus both established HIV infection in individual tonsillar cells. However, clusters of infected tonsillar cells were detected where the epithelial surface was damaged. Investigation of the initial events in HIV transmission revealed extensive and stable binding of HIV virions and seminal cells to tonsil epithelium. In experiments modeling physiologically relevant events, the addition of seminal plasma resulted in enhanced virion binding to epithelial cells. These results indicate that, although extensive binding of HIV virions and seminal cells can be demonstrated at an exposed mucosal surface, there is only limited progression from binding to primary infection.

CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract

The mechanisms underlying CD4⁺ T cell depletion in human immunodeficiency virus (HIV) infection are not well understood. Comparative studies of lymphoid tissues, where the vast majority of T cells reside, and peripheral blood can potentially illuminate the pathogenesis of HIV-associated disease. Here, we studied the effect of HIV infection on the activation and depletion of defined subsets of CD4⁺ and CD8⁺ T cells in the blood, gastrointestinal (GI) tract, and lymph node (LN). We also measured HIV-specific T cell frequencies in LNs and blood, and LN collagen deposition to define architectural changes associated with chronic inflammation. The major findings to emerge are the following: the GI tract has the most substantial CD4⁺ T cell depletion at all stages of HIV disease; this depletion occurs preferentially within CCR5⁺ CD4⁺ T cells; HIV-associated immune activation results in abnormal accumulation of effector-type T cells within LNs; HIV-specific T cells in LNs do not account for all effector T cells; and T cell activation in LNs is associated with abnormal collagen deposition. Taken together, these findings define the nature and extent of CD4⁺ T cell depletion in lymphoid tissue and point to mechanisms of profound depletion of specific T cell subsets related to elimination of CCR5⁺ CD4⁺ T cell targets and disruption of T cell homeostasis that accompanies chronic immune activation.

Appearance of peristaltic reflex in isolated guinea pig ileum in response to boluses of air, water, oil, and cellulose

Distension of an isolated preparation of guinea pig ileum triggers the peristaltic reflex, a characteristic movement of the intestinal walls which generates luminal pressures and clearance of luminal contents. To determine how the reflex responds to properties of luminal contents, we compared the responses triggered by boluses of air, oil, and cellulose to boluses of Krebs' solution. We found that oil and cellulose increased pressures and contraction length and decreased outflow. Cellulose, but not oil, slowed the velocity with which the contraction propagated and increased the delay with which the end point (upstream edge) of the contraction started to propagate after the lead point (downstream edge). Air tended to produce short contraction segments and high velocity. We conclude that bolus properties such as viscosity determine the response that isolated intestinal segments generate to distension. Response patterns are reflected in contraction length, propagation velocity, and other visual parameters that define wall movements.

Collagen deposition in HIV-1 infected lymphatic tissues and T cell homeostasis

Lymphatic tissues (LTs) are structurally organized to promote interaction between antigens, chemokines, growth factors, and lymphocytes to generate an immunologic response and maintain normal-sized populations of CD4(+) and CD8(+) T cells. Inflammation and tissue remodeling that accompany local innate and adaptive immune responses to HIV-1 replication cause damage to the LT architecture. As a result, normal populations of CD4(+) and CD8(+) T cells cannot be supported and antigen-lymphocyte interactions are impaired. This conclusion is supported herein following LT sampling before and during anti-HIV therapy in persons with acute, chronic, and late-stage HIV-1 infection. Among seven individuals treated with anti-retroviral therapy (ART) and four individuals deferring therapy we found evidence of significant paracortical T cell zone damage associated with deposition of collagen, the extent of which was inversely correlated with both the size of the LT CD4(+) T cell population and the change in peripheral CD4(+) T cell count with anti-HIV therapy. The HIV-1-associated inflammatory changes and scarring in LT both limit the ability of the tissue to support and reestablish normal-sized populations of CD4(+) T cells and suggest a novel mechanism of T cell depletion that may explain the failure of ART to significantly increase CD4(+) T cell populations in some HIV-1-infected persons.

Immunization by particle-mediated transfer of the granulocyte-macrophage colony-stimulating factor gene into autologous tumor cells in melanoma or sarcoma patients: report of a phase I/IB study

The primary objective of this phase I study was to determine the safety of an autologous tumor vaccine given by intradermal injection of lethally irradiated granulocyte-macrophage colony-stimulating factor (GM-CSF) gene-transfected autologous melanoma and sarcoma cells. Secondary objectives included validation of the gene delivery technology (particle-mediated gene transfer), determining the host immune response to the tumor after vaccination, and monitoring patients for evidence of antitumor response. Sixteen patients were treated with either of two different doses of GM-CSF-treated tumor cells. One patient received treatment with both doses of tumor cells. No treatment-related local or systemic toxicity was noted in any patient. Patients administered 100% treated cells (i.e., with a preparation of tumor cells that had all been exposed to GM-CSF DNA transfection) had a more extensive lymphocytic infiltrate at the vaccine site than did patients given 10% treated cells (a preparation of tumor cells in which 10% had been exposed to GM-CSF transfection) or nontreated tumor. The generation of a systemic immune response to autologous tumor by a delayed-type hypersensitivity response to the intradermal placement of nontransfected tumor cells was noted in one patient. One patient had a transient partial response of metastatic tumor sites. The entire procedure, from tumor removal to vaccine placement, was accomplished in less than 6 hr in all patients. Four of 17 patient tumor preparations produced greater than 3.0 ng of GM-CSF per 10(6) cells per 24 hr in vitro. The one patient with greater than 30 ng of GM-CSF per 10(6) cells per 24 hr in vitro had positive DTH, a significant histologic inflammatory response, and clinically stable disease. This technique of gene transfer was safe and feasible, but resulted in clinically relevant levels of gene expression in only a minority of patients.