Microplastics contamination in aquaculture-rich regions: A case study in Gresik, East Java, Indonesia

The widespread use of plastic has resulted in the accumulation of plastic waste across a range of sizes, notably including microplastics (MPs). The introduction of MPs into aquatic ecosystems can lead to the contamination of organisms, mainly fish. This study reports for the first time a quantitative and qualitative analysis conducted on the abundance of MPs encountered in water and sediment of milkfish aquaculture ponds in Gresik, East Java, Indonesia. Water and sediment samples were collected at three stations between February to April 2021. The abundance of MPs was analyzed through the application of one-way ANOVA tests and Pearson's correlation analysis. The results identified four types of MPs: fragments, fibers, films, and pellets. The highest abundance of MPs in both water (10.40 particle/L) and sediment samples (1.15 particle/g) was observed in March. The predominant MPs size in the water samples is 100-500 μm, while it is below 100 μm in the sediment. The color of the MPs varied across eight colors: black, purple, red, blue, yellow, pink, green, and transparent. The identification of MPs polymers was found to be polypropylene (PP), Polyurethane (PU), Polycarbonate (PC), Polyethylene terephthalate (PETE), High-density polyethylene (HDPE), and low-density polyethylene (LDPE). The presence of MPs in the water column and sediments was correlated with human activities around the ponds. Hence, the abundance of MPs is a source of pollution that has the potential to damage the nutritional quality of farmed milkfish. This study provides important information for the local governments to develop waste management policies for a cleaner environment and improved human health.

Disposable surgical/medical face masks and filtering face pieces: Source of microplastics and chemical additives in the environment

The production and consumption of disposable face masks (DFMs) increased intensely during the COVID-19 pandemic, leading to a high amount of them being found in the terrestrial and aquatic environment. The main goal of this research study is to conduct a comparative evaluation of the water-leachability of microplastics (MPs) and chemical additives from various types of disposable surgical/medical face masks (MM DFMs) and filtering face pieces (FFPs). Fourier-Transform Infrared Spectroscopy was used for MPs analysis. Liquid Chromatography/High Resolution Mass Spectrometry was used to analyse analytes presented in the water-leachates of DFMs. FFPs released 3-4 times more microplastic particles compared to MM DFMs. The release of MPs into water from all tested DFMs without mechanical stress suggests potential MP contamination originating from the DFM production process. Our study for the first time identified bisphenol B (0.25-0.42 μg/L) and 1,4-bis(2-ethylhexyl) sulfosuccinate (163.9-115.0 μg/L) as leachables from MM DFMs. MPs in the water-leachates vary in size, with predominant particles <100 μm, and the release order from DFMs is MMIIR > MMII > FFP3>FFP2>MMI. The main type of microplastics identified in the water leachates of the investigated face masks was polypropylene, accounting for 93-97% for MM DFMs and 82-83% for FFPs. Other polymers such as polyethylene, polycarbonate, polyester/polyethylene terephthalate, polyamide/Nylon, polyvinylchloride, and ethylene-propylene copolymer were also identified, but in smaller amounts. FFPs released a wider variety and a higher percentage (17-18%) of other polymers compared to MM DFMs (3-7%). Fragments and fibres were identified in all water-leachate samples, and fragments, particularly debris of polypropylene fibres, were the most common MP morphotype. The findings in this study are important in contributing additional data to develop science-based policy recommendations on the health and environmental impacts of MPs and associated chemical additives originated from DFMs.

Novel purification platform based on multimodal preparative scale separation of mAb fragments and aggregates

Monoclonal antibodies (mAbs) continue to dominate the biopharmaceutical industry. Certain mAbs are prone to fragmentation and clipping and in these cases, adequate removal of these species is critical during manufacturing. Fragments can be generated during fermentation, purification, storage, formulation, and administration. Their addition to the acidic charge-variant of the purified mAb has been reported to decrease stability and potency of the final product. However, contrary to mAb aggregation, manufacturers have not given much attention to removal of fragments and clipped species and as a result most conventional mAb platforms offer at best limited capabilities for their removal. In this study, we propose a novel purification platform that uses multimodal chromatography and achieves complete removal of a range of mAb fragments and clipped products (25-120 kDa). The utility of the platform has been successfully demonstrated for 2 IgG1s and 2 IgG4s. Further, adequate removal of the various host cell impurities such as host cell proteins (<10 ppm) and host cell DNA (<5 ppb) has been achieved. Finally, the platform was able to deliver adequate removal of high molecular weight impurities (<1 %) and a 30 % clearance of the acidic charge variant. The proposed single step has been shown to deliver what the polishing chromatography and intermediate purification chromatography steps deliver in a traditional mAb platform.

Pulmonary toxicity assessment of polypropylene, polystyrene, and polyethylene microplastic fragments in mice

Polypropylene (PP), polystyrene (PS), and polyethylene (PE) plastics are commonly used in household items such as electronic housings, food packaging, bottles, bags, toys, and roofing membranes. The presence of inhalable microplastics in indoor air has become a topic of concern as many people spent extended periods of time indoors during the COVID-19 pandemic lockdown restrictions, however, the toxic effects on the respiratory system are not properly understood. We examined the toxicity of PP, PS, and PE microplastic fragments in the pulmonary system of C57BL/6 mice. For 14 days, mice were intratracheally instilled 5 mg/kg PP, PS, and PE daily. The number of inflammatory cells such as macrophages, neutrophils, and eosinophils in the bronchoalveolar lavage fluid (BALF) of PS-instilled mice was significantly higher than that in the vehicle control (VC). The levels of inflammatory cytokines and chemokines in BALF of PS-instilled mice increased compared to the VC. However, the inflammatory responses in PP- and PE-stimulated mice were not significantly different from those in the VC group. We observed elevated protein levels of toll-like receptor (TLR) 2 in the lung tissue of PP-instilled mice and TLR4 in the lung tissue of PS-instilled mice compared with those to the VC, while TLR1, TLR5, and TLR6 protein levels remained unchanged. Phosphorylation of nuclear factor kappa B (NF-κB) and IĸB-α increased significantly in PS-instilled mice compared with that in VC. Furthermore, Nucleotide‑binding oligomerization domain‑like receptor family pyrin domain‑containing 3 (NLRP3) inflammasome components including NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and Caspase-1 in the lung tissue of PS-instilled mice increased compared with that in the VC, but not in PP- and PE-instilled mice. These results suggest that PS microplastic fragment stimulation induces pulmonary inflammation due to NF-ĸB and NLRP3 inflammasome activation by the TLR4 pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43188-023-00224-x.

Periarticular blast wounds without fracture a prospective case series

BACKGROUND

During the wars in Afghanistan and Iraq most injuries to service members involved the musculoskeletal system. These wounds often occurred around joints, and in some cases result in traumatic arthrotomy-a diagnosis that is not always clear, especially when there is no concomitant articular fracture. The aim of the present study is to evaluate the diagnosis and treatment of peri-articular blast injuries without fracture.

METHODS

The study cohort included 12 consecutive patients (12 involved extremities) who sustained peri-articular blast wounds of the extremities without fractures. The diagnosis of penetrating articular injury was based on clinical examination, radiographic findings, or aspiration. A peri-articular wound was defined as any wound, or radio-opaque blast fragment, within 5 cm of a joint. The New Injury Severity Score (NISS) was calculated for each patient. Four patients had upper, and 8 patients had lower extremity injuries. Nine of 12 patients had joint capsular penetration and underwent joint irrigation and debridement.

RESULTS

Two patients had retained intra-articular metal fragments. One patient had soft tissue blast wounds within 5 cm of a joint but did not have joint capsule penetration. There were no significant differences (p = 0.23) between the distribution of wounds to upper versus lower extremities. However, there were a significantly greater number of blast injuries attributed to Improvised Explosive Devices (IEDs) than from other blast mechanisms (p = 0.01).

CONCLUSION

Extremity blast injuries in the vicinity of joints involving only soft tissues present a unique challenge in surgical management. A high index of suspicion should be maintained for joint capsular penetration so that intra-articular injuries may be appropriately treated.

Discovery of 14-3-3 PPI Stabilizers by Extension of an Amidine-Substituted Thiophene Fragment

Protein-protein interaction (PPI) modulation is a promising approach in drug discovery with the potential to expand the 'druggable' proteome and develop new therapeutic strategies. While there have been significant advancements in methodologies for developing PPI inhibitors, there is a relative scarcity of literature describing the 'bottom-up' development of PPI stabilizers (Molecular Glues). The hub protein 14-3-3 and its interactome provide an excellent platform for exploring conceptual approaches to PPI modulation, including evolution of chemical matter for Molecular Glues. In this study, we employed a fragment extension strategy to discover stabilizers for the complex of 14-3-3 protein and an Estrogen Receptor alpha-derived peptide (ERα). A focused library of analogues derived from an amidine-substituted thiophene fragment enhanced the affinity of the 14-3-3/ERα complex up to 6.2-fold. Structure-activity relationship (SAR) analysis underscored the importance of the newly added, aromatic side chain with a certain degree of rigidity. X-ray structural analysis revealed a unique intermolecular π-π stacking binding mode of the most active analogues, resulting in the simultaneous binding of two molecules to the PPI binding pocket. Notably, analogue 11 displayed selective stabilization of the 14-3-3/ERα complex.

Vegetative fragment production as a means of propagule dispersal for tropical seagrass meadows

BACKGROUND AND AIMS

Long distance dispersal (LDD) contributes to the replenishment and recovery of tropical seagrass habitats exposed to disturbance, such as cyclones and infrastructure development. However, our current knowledge regarding the physical attributes of seagrass fragments that influence LDD predominantly stems from temperate species and regions. The goal of this paper is to measure seagrass fragment density and viability in two tropical species, assessing various factors influencing their distribution.

METHODS

We measured the density and viability of floating seagrass fragments for two tropical seagrass species (Zostera muelleri and Halodule uninervis) in two coastal seagrass meadows in the central Great Barrier Reef World Heritage Area, Australia. We assessed the effect of wind speed, wind direction, seagrass growing/senescent season, seagrass meadow density, meadow location and dugong foraging intensity on fragment density. We also measured seagrass fragment structure and fragment viability; i.e., potential to establish into a new plant.

KEY RESULTS

We found that seagrass meadow density, season, wind direction and wind speed influenced total fragment density, while season and wind speed influenced the density of viable fragments. Dugong foraging intensity did not influence fragment density. Our results indicate that wave action from winds combined with high seagrass meadow density increases seagrass fragment creation, and that more fragments are produced during the growing than the senescent season. Seagrass fragments classified as viable for Z. muelleri and H. uninervis had significantly more shoots and leaves than non-viable fragments. We collected 0.63 (±0.08 SE) floating viable fragments 100 m-2 in the growing season, and 0.13 (±0.03 SE) viable fragments 100 m-2 in the senescent season. Over a third (38%) of all fragments collected were viable.

CONCLUSION

There is likely to be a large number of viable seagrass fragments available for long distance dispersal. This study's outputs can inform dispersal and connectivity models that are used to direct seagrass ecosystem management and conservation strategies.

Effect of different types and shapes of microplastics on the growth of lettuce

The presence of microplastics in agricultural soils has emerged as a significant environmental concern due to their persistent nature. Microplastics of different properties (i.e., types, shapes, size, concentration) are present in the environment, but the studies on the effect of microplastics having different properties are limited. Thus, this study investigated the effects of different microplastics (low-density polyethylene (LDPE) fragments, polyvinyl chloride (PVC) fragments, and LDPE fiber) in soil on the growth of lettuce (Lactuca sativa L.). Pot tests were carried out to study the effect of a range of microplastic concentrations and different shapes and types of microplastics in soil on the lettuce growth. The different growth parameters such as lettuce weight, lengths, and chlorophyll contents were measured and compared. The results showed that the adverse effects of the microplastics on the lettuce growth increased with increasing microplastic concentration. The effects of LDPE fragments and fibers on the root weights and the chlorophyll contents were microplastic shape-dependent. Also, the effects of LDPE fragments and PVC fragments on the shoot and root weights and the chlorophyll contents were microplastic type-dependent. Among the three microplastics studied, LDPE fragments tend to have greater effects on the lettuce growth than the other microplastics. Overall, the results show that the effects of microplastics on different growth parameters of lettuce can be shape- and/or type-dependent. The presence of microplastics having different properties make the understanding the effects of microplastics on plants difficult, and this necessitates further studies.

Crystallographic fragment screening in academic cancer drug discovery

Fragment-based drug discovery (FBDD) has brought several drugs to the clinic, notably to target proteins once considered to be challenging, or even undruggable. Screening in FBDD relies upon observing and/or measuring weak (millimolar-scale) binding events using biophysical techniques or crystallographic fragment screening. This latter structural approach provides no information about binding affinity but can reveal binding mode and atomic detail on protein-fragment interactions to accelerate hit-to-lead development. In recent years, high-throughput platforms have been developed at synchrotron facilities to screen thousands of fragment-soaked crystals. However, using accessible manual techniques it is possible to run informative, smaller-scale screens within an academic lab setting. This chapter describes general protocols for home laboratory-scale fragment screening, from fragment soaking through to structure solution and, where appropriate, signposts to background, protocols or alternatives elsewhere.

Abundance, characteristics, fate, and removal of microplastics during municipal wastewater treatment plant in the west of Iran: the case of Kermanshah city

The threat of microplastics (MPs) in aquatic systems is almost a new challenge in environmental management. The municipal wastewater treatment plants (WWTPs) act both as collectors of MPs from anthropic use and as a source to natural environments. This study is aimed to determine the abundance, characteristics, and removal of MPs in a municipal WWTP with conventional activated sludge process. Particle size/type, influent loads, and removal rate of MPs in bar screen, grit chamber, primary sedimentation, returned activated sludge, and secondary clarification units of this WWTP were studied by collecting composite samples from wastewater and sludge over a 3-month sampling campaign. Suspected MP particles were counted by light microscopy and characterized using SEM, EDS, FTIR, and TGA-DSC techniques. The mean total MPs, fibers, and fragment concentration after the grit chamber were 6608, 3594, and 3014 which were reduced to 1855, 802, and 1053 particles/L in the effluent, respectively. The sludge retention of total MPs, fibers, and fragments were 8001, 3277, and 4719 particles/L, respectively. The overall efficiency of WWTP with an activated sludge process to remove MPs was 64% and it removed 66.6% and 60% of fibers and fragments, respectively. Fibers were the dominant shape for the collected samples after the grit chamber and fragments were prevalent in the effluent. Polyethylene polymer was detected in most wastewater samples. Existing treatment processes are effective in the removal of MP particles but still act as a potential source to the aquatic ecosystem.

Experimental study on clinical and morphological determination of the optimal cannula diameter for lipoaspirate harvest from rabbit inguinal fat pad

Determining the most appropriate cannula diameter for lipoaspirate harvesting is important, both in terms of the quality and composition of the material obtained, and the ease of practical use of the cannula. The size of the cannula is one of the main factors affecting the qualitative characteristics of the obtained lipoaspirate sample for further use of adipose tissue. The purpose of the investigation was to clinically and histomorphometrically determine the optimal cannula diameter for lipoaspirate samples collection from rabbit inguinal fat pad in an experimental study. The methods of Animal models, Surgical procedures, Macroscopic examination, Histological examination, and Morphometric study were applied. There is a direct correlation between the percentage of connective tissue fibres in the lipoaspirate and the diameter of the cannula. The lack of clear criteria for selecting a lipoaspiration cannula is one of the limitations to obtaining generally accepted lipoaspiration protocols with subsequent use of adipose tissue. In this study, the animal experiment determined the most ideal cannula diameter suitable for collecting the largest amount of lipoaspirate for subsequent use.

Occurrence and characteristics of fibreglass-reinforced plastics and microplastics on a beach impacted by abandoned fishing boats: A case study from Chellanam, India

Plastics and microplastics have been quantified and characterised at disposal sites of abandoned fishing boats and along the high-water line (HWL) of a fish landing centre in Chellanam, India. Fibreglass-reinforced plastic (FRP) made a greater contribution to the plastic pool at the disposal sites (~ 4.5 n m^-2 and 18 g m^-2) than the HWL (~ 0.25 n m^-2 and < 1 g m^-2) and was an abundant component of the microplastic pool at the former. Infrared analysis of micro-sized FRPs revealed various resins (e.g., alkyd, polyester, epoxy), while X-ray fluorescence analysis of the painted surfaces of meso-sized FRPs returned variable concentrations of copper and lead. Concentrations of Pb were high enough to contaminate sand up to ~400 mg kg^-1. The relatively high density of FRP and its association with glass fibres and metal-bearing paints results in particles with potentially very different fates and toxicities to more "conventional" (non-composite) thermoplastics.

Characterization of Combined Blast- and Fragment-Induced Pelvic Injuries and Hemostatic Resuscitation in Rabbits

INTRODUCTION

To establish a blast- and fragment-induced pelvic injury animal model in rabbits, observe its injury characteristics, and explore the effects of hemostatic resuscitation combined with damage control surgery (DCS) with respect to this injury model.

METHODS

Forty-eight rabbits were randomly allocated to four groups: group A rabbits were subjected to pelvic injury, group B rabbits to pelvic injury + DCS, group C rabbits to pelvic injury + DCS + resuscitation with Hextend, and group D rabbits to pelvic injury + DCS + Hextend + hemostatic resuscitation with tranexamic acid, fibrinogen concentrate, and prothrombin complex concentrate. Simulated blast and fragment-induced pelvic injury was produced by a custom-made machine. We implemented CT scanning and necropsy to assess the injury state and calculated the coefficient of variation (CV) of the cumulative abbreviated injury scale (AIS) to assess the reproducibility of the animal model. Immediately after instrumentation (0 h), and 1 h, 2 h, 4 h, and 8 h after injury, blood samples were taken for laboratory tests.

RESULTS

We found that severe pelvic injury was produced with an AIS CV value of 10.32%, and the rabbits demonstrated severe physiologic impairment and coagulo-fibrinolytic derangements with high mortality. In rabbits of group D, however, physiologic and coagulo-fibrinolytic parameters were significantly enhanced with improved organ function and lowered mortality when compared with the other three groups.

CONCLUSIONS

We herein established in rabbits a blast- and fragment-induced pelvic injury animal model that exhibited high reproducibility, and we demonstrated that hemostatic resuscitation plus DCS was effective in improving the outcome.

BCM-DTI: A fragment-oriented method for drug-target interaction prediction using deep learning

The identification of drug-target interaction (DTI) is significant in drug discovery and development, which is usually of high cost in time and money due to large amount of molecule and protein space. The application of deep learning in predicting DTI pairs can overcome these limitations through feature engineering. However, most works do the features extraction using the whole drug and target, which do not take the theoretical basis of pharmacological reaction that the interaction is closely related to some substructure of molecule and protein into consideration, thus poor in performance. On the other hand, some substructure-oriented studies only consider a single type of fragment, e.g., functional group. To address these issues, we propose an end-to-end predicting framework for drug-target interaction named BCM-DTI that takes diverse fragment types into account, including branch chain, common substructure and motif/fragments, and applies a feature learning module based on CNN to learn the synergistic effect between these fragments. We implement BCM-DTI on four public datasets, and the results show that BCM-DTI outperforms state-of-the-art approaches and requires lower training cost.

Fragment-based drug discovery of small molecule ligands for the human chemokine CCL28

The mucosal chemokine CCL28 is a promising target for immunotherapy drug development due to its elevated expression level in epithelial cells and critical role in creating and maintaining an immunosuppressive tumor microenvironment. Using sulfotyrosine as a probe, NMR chemical shift mapping identified a potential receptor-binding hotspot on the human CCL28 surface. CCL28 was screened against 2,678 commercially available chemical fragments by 2D NMR, yielding thirteen verified hits. Computational docking predicted that two fragments could occupy adjoining subsites within the sulfotyrosine recognition cleft. Dual NMR titrations confirmed their ability to bind CCL28 simultaneously, thereby validating an initial fragment pair for linking and merging strategies to design high-potency CCL28 inhibitors.

Occurrence of Microplastics in the Gastrointestinal Tracts of Edible Fishes from South Indian Rivers

Microplastics (MPs) in the gastrointestinal (GI) tracts of the five fish species from the Kollidam and Vellar rivers of Tamil Nadu, Southern India were evaluated. A total of 315 MPs were isolated from GI tracts of 23 fishes (Chanos chanos, Chanda nama, Chelon macrolepis, Carangoides malabaricus and Gerrus filamentosus) sampled from both rivers. MPs ranged from 109 to 129 μm (119 ± 79.7) and 181 to 284 μm (122 ± 92.6) in size, with fibres (85.7%) and fragments (14.3%) being the most common ones in the fishes from Kollidam and Vellar river, respectively. The colour pattern of ingested MPs was dominated by blue, transparent, red, yellow and black in collected fishes from both rivers. In this study, MPs were higher in fishes with omnivore feeding habits due to their broad diet habits. Moreover, urban wastes, fishing and agricultural activities are the possible primary sources of MPs in both rivers.

Simultaneous screening of 239 synthetic cannabinoids and metabolites in blood and urine samples using liquid chromatography-high resolution mass spectrometry

Synthetic cannabinoids (SCs) are new psychoactive substances that function as endocannabinoid CB1 and CB2 receptor agonists. Abuse of SCs can lead to symptoms such as confusion, dizziness, and even death. At present, Synthetic cannabinoids constitute one of the largest groups of new psychoactive substances and become popular recreational drugs of abuse for their psychoactive properties. The continuous transformation of SCs also leads to an endless emergence of new types. An efficient, high-throughput screening method is therefore very important for their identification. This paper describes a liquid chromatography-high resolution mass spectrometry (LC-HRMS) method for simultaneously screening 179 SCs and 80 SC metabolites in blood and urine. Simple acetonitrile was used to precipitate the blood and urine proteins, and the supernatants obtained after centrifugation were analyzed. The LC-HRMS run time was 20 min. The mass spectrometer used an ESI source with a scanning range of m/z 100-1000. LC-HRMS provided accurate mass, retention time, and fragment ions for qualitative analysis. The method validation results showed that the limits of detection (LODs) for over 80% compounds were 5 ng/mL in blood and urine samples. At low concentrations (50 ng/mL), 229 compounds (95.8%) in the blood showed recoveries of more than 50%, and 232 compounds (97.1%) had matrix effects greater than 80%. In the urine, 219 compounds (91.6%) had recoveries above 50%, and the matrix effects of 234 compounds (97.9%) were greater than 80%. This method was successfully applied to actual forensic cases.

Silencing Specific Genes in Plants Using Virus-Induced Gene Silencing (VIGS) Vectors

As an efficient tool for functional genomics, VIGS (virus-induced gene silencing) has been widely used in reverse and forward genetics to identify genes involved in various biology processes in many plant species. Up to now, at least 50 VIGS vectors based on RNA viruses, DNA viruses or satellites have been developed for either dicots or monocots or both. Silencing specific genes using VIGS vector involves five major steps including, first, choosing an appropriate VIGS vector for the plant; second, selecting a fragment of targeted host gene; third, cloning the fragment into viral VIGS vector; forth, inoculating and infecting the appropriate plant; and fifth, quantifying silencing effects including recording silencing phenotypes and determining silencing efficiency of the target gene. In this chapter, we introduce these steps for VIGS assay in dicots and monocots, by taking a cucumber mosaic virus-based VIGS vector for Nicotiana benthamiana and maize plants as an example. Moreover, we list available VIGS vectors for monocots.

Airborne microplastics in indoor and outdoor environments of a coastal city in Eastern China

Microplastics (MPs) in marine and terrestrial environments have been intensively studied, but the dynamics of airborne MPs remains limited. Existing studies on atmospheric MPs are mostly derived from collection of atmospheric deposition, whereas direct measurements of airborne MPs are scarce. However, the abundance of airborne MPs is more relevant for evaluating human inhalation exposure risk. Herein, airborne MPs in indoor and outdoor environments from urban and rural areas of a coastal city in eastern China were investigated. MP concentrations (mean±SD) in indoor air (1583 ± 1180 n/m³) were an order of magnitude higher than outdoor air (189 ± 85 n/m³), and airborne MP concentrations in urban areas (224 ± 70 n/m³) were higher than rural areas (101 ± 47 n/m³). MPs smaller than 100 µm dominated airborne MPs, and the predominant shape of airborne MPs was fragments, as opposed to fibers. The larger MP size fractions contained a higher proportion of fibers, whereas the smaller size fractions were nearly exclusively composed of fragments. The health risk caused by ubiquitous airborne MPs should not be discounted as the maximum annual outdoor exposure of airborne MPs can reach 1 million/year, while indoor exposure may be even higher due to higher indoor airborne MP concentrations.

Microplastics in some fish species and their environs in Eastern Visayas, Philippines

Microplastics are a global concern, and yet, Philippine studies about it are still wanting. This study investigated microplastic ingestion among detritus-feeding mullet versus the herbivorous rabbitfish, and between freshwater and marine fishes. The first part aimed to compare microplastics in fishes' guts differing in feeding guilds, individual sizes, and body weights. The second part compared MPs in fishes' guts and their surrounding waters. Part one revealed that herbivores (58.57%) ingested more MPs than their detritivore-counterparts (30.0%). Pearson correlation, averaging 0.06, suggests a weak correlation between fish weight and MPs amount for both species. Part two showed marine fishes (66.0%) ingested more MPs than its freshwater counterparts (45.0%). A very weak correlation was observed between fish weight and amount of MPs ingested. Fish along the estuary ingested more MPs than those in other stations. No significant differences (p = 0.23) between the MPs in the water samples from each sampling stations was found.

Effect of chamfer design on load capacity of reattached incisors

OBJECTIVE

This study aimed to evaluate the effect of different chamfer preparations on the load capacity of reattached fractured incisors under lingual loading.

METHODS

Eighty #8 typodonts were randomly assigned to four groups (n = 20 each). They were sectioned to simulate crown fracture, and reattached with a self-etch adhesive and a resin composite. The preparation for each group was: (1) no chamfer; (2) buccal chamfer; (3) lingual chamfer; and (4) circumferential chamfer. Forty-eight human lower incisors were grouped and prepared similarly (n = 12 each). These teeth were tested for their load capacity under a lingual load on a universal testing machine. Finite element models were used to examine the stresses on the reattached surfaces to help interpret the experimental results.

RESULTS

The buccal chamfer did not increase the load capacity when compared with the no-chamfer group. Lingual and circumferential chamfers respectively increased the fracture load by 36.9% and 32.3% in typodonts, and 78.5% and 33.3% in human incisors. The increase was statistically significant (p < 0.05). A higher fracture load tended to be accompanied by a larger area of deflected cohesive fracture. Finite element analysis showed that lingual and circumferential chamfers reduced the fracture-causing tensile stress at the lingual margin of the reattachment interface by approximately 70% and 60%, respectively, in human upper incisors.

SIGNIFICANCE

It was the joint design, and not the size of the bond area, that affected the load capacity of reattached incisors. Among the preparations considered, only those with a lingual chamfer could increase the load capacity of reattached incisors under a lingual load.

Multi-target Drug Discovery via PTML Modeling: Applications to the Design of Virtual Dual Inhibitors of CDK4 and HER2

BACKGROUND

Cyclin-dependent kinase 4 (CDK4) and the human epidermal growth factor receptor 2 (HER2) are two of the most promising targets in oncology research. Thus, a series of computational approaches have been applied to the search for more potent inhibitors of these cancerrelated proteins. However, current approaches have focused on chemical analogs while predicting the inhibitory activity against only one of these targets, but never against both.

AIMS

We report the first perturbation model combined with machine learning (PTML) to enable the design and prediction of dual inhibitors of CDK4 and HER2.

METHODS

Inhibition data for CDK4 and HER2 were extracted from ChEMBL. The PTML model relied on artificial neural networks to allow the classification/prediction of molecules as active or inactive against CDK4 and/or HER2.

RESULTS

The PTML model displayed sensitivity and specificity higher than 80% in the training set. The same statistical metrics had values above 75% in the test set. We extracted several molecular fragments and estimated their quantitative contributions to the inhibitory activity against CDK4 and HER2. Guided by the physicochemical and structural interpretations of the molecular descriptors in the PTML model, we designed six molecules by assembling several fragments with positive contributions. Three of these molecules were predicted as potent dual inhibitors of CDK4 and HER2, while the other three were predicted as inhibitors of at least one of these proteins. All the molecules complied with Lipinski's rule of five and its variants.

CONCLUSION

The present work represents an encouraging alternative for future anticancer chemotherapies.

Intra-articular Fracture Pattern in Intercondylar Distal Femur Fractures: An Analysis of Frequency and Major Fracture Fragments

INTRODUCTION

The treatment of intercondylar distal femur fractures requires anatomic reduction of intra-articular fragments and absolute fixation. Preoperative planning is necessary to understand fracture morphology. All fracture lines need to be recognized as the primary implant may not capture all articular fragments, mainly when coronal plane fractures are present. Oftentimes, independent interfragmentary compression screws are necessary. No recent studies have visually mapped out the distal femur articular fracture fragments necessary for absolute fixation. The objectives of this study are to determine the frequency of coronal plane fractures in intercondylar distal femur fractures and describe the pattern of intra-articular fracture fragments.

MATERIALS AND METHODS

The hospital's trauma registry was queried for distal femur ORIF CPT codes logged in the past four years. A retrospective chart review was performed using the EMR and CT scans. Demographics and mechanisms of injury were analyzed. Fracture fragments were surveyed and drawn out by hand on a template for easy organization. Patients' fractures were categorized into the following groups: fractures with no intra-articular coronal plane fractures, those with medial coronal fractures, those with lateral coronal fractures, or those with both medial and lateral coronal fractures. Major fracture fragments were identified.

RESULTS

A total of 55 patients were included. 26 patients (47%) were found to have no intra-articular coronal plane fractures; 6 patients (11%) were found to have medial coronal plane fractures; 15 patients (27%) were found to have lateral coronal plane fractures, and 8 patients (15%) had medial and lateral coronal plane fractures. Collectively, intra-articular coronal plane fractures were identified in 29 patients (53%) with intercondylar distal femur fractures. Four major fracture fragments along with intercondylar and condylar comminution sites were identified.

DISCUSSION

Distal femur intra-articular coronal plane fractures can yield large anterior and posterior condylar fracture fragments of either the medial condyle, lateral condyle, or both condyles. Coronal plane fracture fragments must be identified to obtain absolute fixation. Our study found a higher coronal plane fracture line frequency (52.7%) than prior commonly cited studies. Surgeons must be on the lookout for anterior fracture fragments, posterior fracture fragments, and articular comminution when treating intercondylar femur fractures.

Spatial and temporal distribution of microplastic in surface water of tropical estuary: Case study in Benoa Bay, Bali, Indonesia

In 2010, Indonesia estimated as the second-largest country in the world that donates plastic to the sea. This study aims to investigate the spatial and temporal distribution of microplastics in tropical estuaries. The sampling was carried out in Benoa Bay with four repetitions representing the wet and dry seasons. Spatially it was found that the highest microplastic abundance around the Suwung landfill, while the lowest at Badung River Estuary, middle, and an inlet of the Benoa Bay. The highest percentage to the lowest microplastic based on the size was 500-1000 μm (37.9%), >1000 μm (35.7%), 300-500 μm (22.1%), and <300 μm (4.3%), while based on the shape were fragments (73.19%), foam (17.02%), fiber (6.38%), and granule (3.40%). No significant differences were found between the wet and dry seasons based on the abundance, but significantly varied based on size and shape. Polymers of microplastics were dominated by polystyrene, polypropylene, and polyethylene.

FDP avulsion: A washer technique

Background

Flexor digitorum profundus (FDP) avulsion injuries occur following forced hyperextension of the distal interphalangeal joint (DIPJ).

Methods

We highlight a case report of FDP avulsion injury fixed using a single hole of a plate in combination with a cortical screw to act as a washer. A search and discussion of the literature is included.

Profiling and targeting connective tissue remodeling in autoimmunity - A novel paradigm for diagnosing and treating chronic diseases

Connective tissue (ConT) remodeling is an essential process in tissue regeneration, where a balanced replacement of old tissue by new tissue occurs. This balance is disturbed in chronic diseases, often autoimmune diseases, usually resulting in the buld up of fibrosis and a gradual loss of organ function. During progression of liver, lung, skin, heart, joint, skeletal and kidney diseasesboth ConT formation and degradation are elevated, which is tightly linked to immune cell activation and a loss of specific cell types and extracellular matrix (ECM) structures that are required for normal organ function. Here, we address the balance of key general and organ specific components of the ECM during homeostasis and in disease, with a focus on collagens, which are emerging as both structural and signaling molecules harbouring neoepitopes and autoantigens that are released during ConT remodeling. Specific collagen molecular signatures of ConT remodeling are linked to disease activity and stage, and to prognosis across different organs. These signatures accompany and further drive disease progression, and often become detectable before clinical disease manifestation (illness). Recent advances allow to quantify and define the nature of ConT remodeling via blood-based assays that measure the levels of well-defined collagen fragments, reflecting different facets of ConT formation and degradation, and associated immunological processes. These novel serum assays are becoming important tools of precision medicine, to detect various chronic and autoimmune diseases before their clinical manifestation, and to non-invasively monitor the efficacy of a broad range of pharmacological interventions.

NMR quality control of fragment libraries for screening

Fragment-based screening has evolved as a remarkable approach within the drug discovery process both in the industry and academia. Fragment screening has become a more structure-based approach to inhibitor development, but also towards development of pathway-specific clinical probes. However, it is often witnessed that the availability, immediate and long-term, of a high quality fragment-screening library is still beyond the reach of most academic laboratories. Within iNEXT (Infrastructure for NMR, EM and X-rays for Translational research), a EU-funded Horizon 2020 program, a collection of 782 fragments were assembled utilizing the concept of "poised fragments" with the aim to facilitate downstream synthesis of ligands with high affinity by fragment ligation. Herein, we describe the analytical procedure to assess the quality of this purchased and assembled fragment library by NMR spectroscopy. This quality assessment requires buffer solubility screening, comparison with LC/MS quality control and is supported by state-of-the-art software for high throughput data acquisition and on-the-fly data analysis. Results from the analysis of the library are presented as a prototype of fragment progression through the quality control process.

Iced block method: An efficient method for preparation of micro-sized expanded polystyrene foams

Recently, numerous studies concerning dye-labeled microplastic beads have reported on the end-of-life, environmental effects of microplastics because of their ubiquitous commercial usage. Less is understood about the toxicity and bioaccumulation of plastics other than microplastic beads, which can also harm the environment (e.g., fragments, fibers, foams, and films). Expanded polystyrene (EPS) is widespread in the environment owing to its many uses, however, limited research has been conducted on EPS foams. This study focuses on developing an efficient method for the preparation of micro-sized EPS foams for research purposes and compares it with previous microplastics preparation methods reported in 68 previous studies. It was demonstrated that the iced EPS block method (iced EPS block + water) generated larger quantities of smaller-sized EPS foams (20-200 and 200-500 μm) compared to the EPS + ice + water and EPS + water methods. The optimal protocol includes 1) iced EPS block preparation, 2) grinding and sieving, and 3) collecting. Additionally, it was confirmed that the iced EPS block method requires less money, labor, and time compared to previously reported methods in the literature. The method proposed in this research can assist future investigations into the environmental effects of EPS foams.

Discovery of the first Mycobacterium tuberculosis MabA (FabG1) inhibitors through a fragment-based screening

Mycobacterium tuberculosis (M.tb), the etiologic agent of tuberculosis, remains the leading cause of death from a single infectious agent worldwide. The emergence of drug-resistant M.tb strains stresses the need for drugs acting on new targets. Mycolic acids are very long chain fatty acids playing an essential role in the architecture and permeability of the mycobacterial cell wall. Their biosynthesis involves two fatty acid synthase (FAS) systems. Among the four enzymes (MabA, HadAB/BC, InhA and KasA/B) of the FAS-II cycle, MabA (FabG1) remains the only one for which specific inhibitors have not been reported yet. The development of a new LC-MS/MS based enzymatic assay allowed the screening of a 1280 fragment-library and led to the discovery of the first small molecules that inhibit MabA activity. A fragment from the anthranilic acid series was optimized into more potent inhibitors and their binding to MabA was confirmed by ¹⁹F ligand-observed NMR experiments.

Occurrence of microplastics in the Han River and riverine fish in South Korea

Microplastic pollution has been paid attention due to the possibly global threat to human health and ecosystem in recent years. In this study, we investigated the distribution of microplastics in the Han River and its tributaries, South Korea, and in six species of inhabiting fish, namely carp (C. carpio), crucian carp (C. cuvieri), bluegill (L. macrochirus), bass (M. salmoides), catfish (S. asotus), and snakehead (C. argus). We found that the concentration of microplastics in the surface waters (0 m) was 0-42.9 particles/m³ (mean: 7.0 ± 12.9 particles/m³) compared to 20.0-180.0 particles/m³ (mean: 102.0 ± 50.3 particles/m³) at a depth of 2 m. Concentrations in the river tributaries ranged from 1.2 to 234.5 particles/m³ (mean: 91.1 ± 72.3 particles/m³). The most common types the plastic identified were polyethylene (PE), silicone, and polystyrene, while polytetrafluoroethylene (PTFE), polyethylene, and polyester dominated in the tributaries. With respect to shape, >73% of the recovered microplastics were fragments and the rest were fibers in the water. We also measured the concentration of microplastics in the intestines of fish, which ranged from 4 to 48 particles/fish (mean: 22.0 ± 16.0 particles/fish). The most common types of plastic found in the sampled fish were polytetrafluoroethylene (PFTE), polyethylene (PE), and rayon, and >94% of all the microplastic found in fish was in the form of fragments with the remainder being fibers. The concentrations of microplastic in the gills of fish ranged from 1 to 16 particles/fish (mean: 8.3 ± 6.0 particles/fish). In contrast, no microplastic was found in the flesh of the sampled fish. Our results imply that the ingestion of microplastics by fish is more closely related to habitat rather than feeding habits.

Fragments of drains retained during operations on the temporomandibular joint

Drains are robust and reports of breakages and retained fragments are rare. There is no consensus about the management of such cases and we know of no reported cases. We present the case of an 18-year-old man with a retained drain fragment after repair of an open condyle.

Quantifying Intermediary Metabolism and Lipogenesis in Cultured Mammalian Cells Using Stable Isotope Tracing and Mass Spectrometry

Metabolism plays a central role in virtually all diseases, including diabetes, cancer, and neurodegeneration. Detailed analysis is required to identify the specific metabolic pathways dysregulated in the context of a given disease or biological perturbation. Measurement of metabolite concentrations can provide some insights into altered pathway activity or enzyme function, but since most biochemicals are metabolized by various enzymes in distinct pathways within cells and tissues, these approaches are somewhat limited. By applying metabolic tracers to a biological system, one can visualize pathway-specific information depending on the tracer used and analytes measured. To this end, stable isotope tracers and mass spectrometry are emerging as important tools for the examination of metabolic pathways and fluxes in cultured mammalian cells and other systems. Here, we describe a detailed workflow for quantifying metabolic processes in mammalian cell cultures using stable isotopes and gas chromatography coupled to mass spectrometry (GC-MS). As a case study, we apply ¹³C isotopic labeled glucose and glutamine to a cancer cell line to quantify substrate utilization for TCA metabolism and lipogenesis. Guidelines are also provided for interpretation of data and considerations for application to other cell systems. Ultimately, this approach provides a robust and precise method for quantifying stable isotope labeling in metabolite pools that can be applied to diverse biological systems.

Discovery of a novel series of pyridine and pyrimidine carboxamides as potent and selective covalent inhibitors of Btk

Btk is an attractive target for the treatment of a range of Bcell malignancies as well as several autoimmune diseases such as murine lupus and rheumatoid arthritis. Several covalent irreversible inhibitors of Btk are currently in development including ibrutinib which was approved for treatment of B-cell malignancies. Herein, we describe our efforts using X-ray guided structure based design (SBD) to identify a novel chemical series of covalent Btk inhibitors. The resulting pyridine carboxamides were potent and selective inhibitors of Btk having excellent enzymatic and cellular inhibitory activity.

Design, synthesis and biological evaluation of novel 4-phenylisoquinolinone BET bromodomain inhibitors

The bromodomain and extra-terminal (BET) family of epigenetic proteins has attracted considerable attention in drug discovery given its involvement in regulating gene transcription. Screening a focused small molecule library based on the bromodomain pharmacophore resulted in the identification of 2-methylisoquinoline-1-one as a novel BET bromodomain-binding motif. Structure guided SAR exploration resulted in >10,000-fold potency improvement for the BRD4-BD1 bromodomain. Lead compounds exhibited excellent potencies in both biochemical and cellular assays in MYC-dependent cell lines. Compound 36 demonstrated good physicochemical properties and promising exposure levels in exploratory PK studies.

The good and the bad collagens of fibrosis - Their role in signaling and organ function

Usually the dense extracellular structure in fibrotic tissues is described as extracellular matrix (ECM) or simply as collagen. However, fibrosis is not just fibrosis, which is already exemplified by the variant morphological characteristics of fibrosis due to viral versus cholestatic, autoimmune or toxic liver injury, with reticular, chicken wire and bridging fibrosis. Importantly, the overall composition of the ECM, especially the relative amounts of the many types of collagens, which represent the most abundant ECM molecules and which centrally modulate cellular functions and physiological processes, changes dramatically during fibrosis progression. We hypothesize that there are good and bad collagens in fibrosis and that a change of location alone may change the function from good to bad. Whereas basement membrane collagen type IV anchors epithelial and other cells in a polarized manner, the interstitial fibroblast collagens type I and III do not provide directional information. In addition, feedback loops from biologically active degradation products of some collagens are examples of the importance of having the right collagen at the right place and at the right time controlling cell function, proliferation, matrix production and fate. Examples are the interstitial collagen type VI and basement membrane collagen type XVIII. Their carboxyterminal propeptides serve as an adipose tissue hormone, endotrophin, and as a regulator of angiogenesis, endostatin, respectively. We provide an overview of the 28 known collagen types and propose that the molecular composition of the ECM in fibrosis needs careful attention to assess its impact on organ function and its potential to progress or reverse. Consequently, to adequately assess fibrosis and to design optimal antifibrotic therapies, we need to dissect the molecular entity of fibrosis for the molecular composition and spatial distribution of collagens and the associated ECM.

Biomarker responses in zebrafish (Danio rerio) larvae exposed to pristine low-density polyethylene fragments

There are serious concerns over the adverse impacts of microplastics (MPs) on living organisms. The main objective of this study was to test the effects of MPs on the total length, weight, condition factor (CF), transcriptional level of antioxidant, anti and pro-apoptotic, and neurotransmitter genes, and the histopathology of the gill, liver, brain, kidney, and intestine in the larvae of zebrafish (Danio rerio). Fish were exposed to one of three levels of pristine low-density polyethylene (LDPE) fragments (5, 50, or 500 μg/L) for 10 or 20 days. No significant changes were observed in any of the selected biomarkers across MP concentrations at days 10 or 20. The expression of casp9 (caspase 9, apoptosis-related cysteine protease), casp3a (caspase 3, apoptosis-related cysteine protease a) and cat (catalase), however, were significantly lower in the larvae sampled at day 20 than day 10. We provide evidence that virgin short-term exposure to LDPE fragments has minimal impact on biomarker responses in D. rerio larvae.

Reproduction capacity of Potamogeton crispus fragments and its role in water purification and algae inhibition in eutrophic lakes

The role of fragments in restoring eutrophic lakes remains unclear despite the importance of re-establishing submerged macrophytes via fragments. This study established a manipulative experiment using different biomass fragments of Potamogeton crispus. This approach was adapted to study the reproductive capacity, nutrient removal efficiency, and algae inhibitory effect of fragments. Results showed that fragments could grow throughout a 49-day experiment by maintaining the stable photosynthesis efficiency of leaves and lengthening the stems. These floating fragments could regenerate by producing turions for the maintenance of their species. Moreover, the increasing removal efficiency of TP, TN, NH₄⁺-N, and NO₃^--N in water with the increase of fragment biomass indicates that the fragments could effectively purify water quality. Floating fragments competed with algae for nutrients, occupied a favorable ecological niche, and reduced algae biomass. They altered the structure of algae community and shifted the dominated green algae to cyanobacteria, the green algae of phytoplankton, and benthic algae. Findings imply that the postponable regulation of fragments is necessary for the ecological restoration of eutrophic lakes.

Recombinant Kinase Production and Fragment Screening by NMR Spectroscopy

During the past decade fragment-based drug discovery (FBDD) has rapidly evolved and several drugs or drug candidates developed by FBDD approach are clinically in use or in clinical trials. For example, vemurafenib, a V600E mutated BRAF inhibitor, was developed by utilizing FBDD approach and approved by FDA in 2011. In FBDD, screening of fragments is the starting step for identification of hits and lead generation. Fragment screening usually relies on biophysical techniques by which the protein-bound small molecules can be detected. NMR spectroscopy has been extensively used to study the molecular interaction between the protein and the ligand, and has many advantages in fragment screening over other biophysical techniques. This chapter describes the practical aspects of fragment screening by saturation transfer difference NMR.

Pressing fixation of mallet finger fractures with the end of a K-wire (a new fixation technique for mallet fractures)

AIM

The aim of this study was to describe and evaluate a surgical technique for the treatment of mallet finger fractures using a K-wire stabilization of the distal interphalangeal (DIP) joint and another K-wire pressing the bone fragment.

METHODS

Between June 2007 and March 2014, 41 patients (28 men, 13 women) with isolated closed mallet finger fracture were treated using two K-wires. In the cohort, the mean joint surface involvement was 44.3% (range: 28-62%). With a mean period of 23.6 months, patient follow-up lasted 13-34 months. The fingers were evaluated for loss of extension and flexion of the (DIP) joints. The results were graded using Crawford's criteria.

RESULTS

Union of all fractures took place at an average of 5.5 weeks after the surgical procedure. Average extension lag was 4°, and active flexion 71°. According to the Crawford rating scale, 35 fingers were excellent, four were good, one was fair, and one was poor.

CONCLUSIONS

Pressing fixation of the bone fragment with the end of a K-wire was a useful technique in the treatment of mallet finger fractures.

TYPE OF STUDY/LEVEL OF EVIDENCE

Therapeutic IV.

Delivering Transgenic DNA Exceeding the Carrying Capacity of AAV Vectors

Gene delivery using recombinant adeno-associated virus (rAAV) has emerged to the forefront demonstrating safe and effective phenotypic correction of diverse diseases including hemophilia B and Leber's congenital amaurosis. In addition to rAAV's high efficiency of transduction and the capacity for long-term transgene expression, the safety profile of rAAV remains unsoiled in humans with no deleterious vector-related consequences observed thus far. Despite these favorable attributes, rAAV vectors have a major disadvantage preventing widespread therapeutic applications; as the AAV capsid is the smallest described to date, it cannot package "large" genomes. Currently, the packaging capacity of rAAV has yet to be definitively defined but is approximately 5 kb, which has served as a limitation for large gene transfer. There are two main approaches that have been developed to overcome this limitation, split AAV vectors, and fragment AAV (fAAV) genome reassembly (Hirsch et al., Mol Ther 18(1):6-8, 2010). Split rAAV vector applications were developed based upon the finding that rAAV genomes naturally concatemerize in the cell post-transduction and are substrates for enhanced homologous recombination (HR) (Hirsch et al., Mol Ther 18(1):6-8, 2010; Duan et al., J Virol 73(1):161-169, 1999; Duan et al., J Virol 72(11):8568-8577, 1998; Duan et al., Mol Ther 4(4):383-391, 2001; Halbert et al., Nat Biotechnol 20(7):697-701, 2002). This method involves "splitting" the large transgene into two separate vectors and upon co-transduction, intracellular large gene reconstruction via vector genome concatemerization occurs via HR or nonhomologous end joining (NHEJ). Within the split rAAV approaches there currently exist three strategies: overlapping, trans-splicing, and hybrid trans-splicing (Duan et al., Mol Ther 4(4):383-391, 2001; Halbert et al., Nat Biotechnol 20(7):697-701, 2002; Ghosh et al., Mol Ther 16(1):124-130, 2008; Ghosh et al., Mol Ther 15(4):750-755, 2007). The other major strategy for AAV-mediated large gene delivery is the use of fragment AAV (fAAV) (Dong et al., Mol Ther 18(1):87-92, 2010; Hirsch et al., Mol Ther 21(12):2205-2216, 2013; Lai et al., Mol Ther 18(1):75-79, 2010; Wu et al., Mol Ther 18(1):80-86, 2010). This strategy developed following the observation that the attempted encapsidation of transgenic cassettes exceeding the packaging capacity of the AAV capsid results in the packaging of heterogeneous single-strand genome fragments (<5 kb) of both polarities (Dong et al., Mol Ther 18(1):87-92, 2010; Hirsch et al., Mol Ther 21(12):2205-2216, 2013; Lai et al., Mol Ther 18(1):75-79, 2010; Wu et al., Mol Ther 18(1):80-86, 2010). After transduction by multiple fAAV particles, the genome fragments can undergo opposite strand annealing, followed by host-mediated DNA synthesis to reconstruct the intended oversized genome within the cell. Although, there appears to be growing debate as to the most efficient method of rAAV-mediated large gene delivery, it remains possible that additional factors including the target tissue and the transgenomic sequence factor into the selection of a particular approach for a specific application (Duan et al., Mol Ther 4(4):383-391, 2001; Ghosh et al., Mol Ther 16(1):124-130, 2008; Hirsch et al., Mol Ther 21(12):2205-2216, 2013; Trapani et al., EMBO Mol Med 6(2):194-211, 2014; Ghosh et al., Hum Gene Ther 22(1):77-83, 2011). Herein we discuss the design, production, and verification of the leading rAAV large gene delivery strategies.

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

PubChem atom environments

BACKGROUND

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures?

RESULTS

For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased.

CONCLUSIONS

The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

The structural use of carbostyril in physiologically active substances

Carbostyril (2-quinolinone, 2-quinolone) is an important structural component frequently used in natural products and in physiologically active substances including drugs. It is a 2-ring condensed heterocyclic compound containing several positions that can be replaced by arbitrary substituent groups and is used as a chemical building block, scaffold, fragment, and pharmacophore in drug design or discovery. Since the number of compounds that can be designed using carbostyril is exceedingly large, the steric structures of carbostyril derivatives can be adjusted to the unique, spatially oriented shape of, for example, the active sites of pharmaceutical target molecules. Moreover, the internal amide of the carbostyril unit exhibits distinctive features because of the fixed cis form of the lactam amide group. Because carbostyril has been used as a component in drugs and other bioactive compounds over time, carbostyril derivatives may improve absorption, distribution, metabolism, excretion, and toxicity (ADMET). Therefore, carbostyril derivatives have enormous potential. In this review, the potential and advantages of the use of carbostyril and its related molecular skeletons, such as 3,4-dihydrocarbostyril, are discussed by focusing on the physiologically active substances in which they are incorporated.

Pullout wire fixation together with distal interphalangeal joint Kirschner wire stabilization for acute combined tendon and bone (double level) mallet finger injury

This article describes a previously unclassified type of combined tendon/bone mallet finger. This supplements the conventional Doyle classification. The article also describes the technique for surgical treatment of such mallet fingers, which involves the use of a pullout wire with K-wire stabilization of the distal interphalangeal joint.

Detection and phenotyping of circulating tumor cells in high-risk localized prostate cancer

BACKGROUND

In this study, we aimed to determine the feasibility of identifying CTCs in patients with HRLPC, using a modified isolation procedure using the CellSearch (Veridex) platform, and to assess the expression of stem cell and epithelial-mesenchymal transition (EMT) markers on the CTCs.

PATIENTS AND METHODS

Thirty-five patients with HRLPC who had chosen prostatectomy for definitive management were prospectively identified. After obtaining consent, four 30-mL blood draws were performed, 2 before surgery and 2 after surgery. The CTC-containing fraction was Ficoll-purified and transferred to a CellSave (Veridex) tube containing dilution buffer before standard enumeration using the CellSearch system. Loss of E-cadherin expression, a marker of EMT, and CD133, a putative prostate cancer stem cell marker, were characterized using the open channel of the CellSearch platform. CTC fragments were also enumerated.

RESULTS

Using the modified methodology, CTCs were detectable in 49% of patients before surgery. Although no correlation between CTC count and biochemical recurrence (BR) was observed, the percentages of CD133 and E-cadherin-positive CTC fragments were associated with BR at 1 year.

CONCLUSION

Our results suggest that further research into the development of CTCs as prognostic biomarkers in HRLPC is warranted.

Structure-based drug design for G protein-coupled receptors

Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.

A highly immunogenic fragment derived from Zaire Ebola virus glycoprotein elicits effective neutralizing antibody

In order to produce polyvalent vaccines based on single rVSV vector, we investigated the immunogenicity, antibody neutralizing activity, and antigenic determinant domain of Zaire Ebola's fragment MFL (aa 393-556) that contains furin site and internal fusion loop. Both the recombinant protein and the recombinant plasmid of fragment MFL elicited high levels of antibody, similar to those of Zaire Ebola GP (ZGP). The MFL fragment of ZGP also elicited high levels of neutralizing antibody and induced moderate cellular immune response in mice, as revealed by the proliferation and cytokine secretion of splenocytes. Through the analysis of the induction of neutralizing antibody by pVAX1-based recombinant plasmids that expressed truncated fragments of MFL, we found that the domain containing the internal fusion loop and the furin site was the major contributor of fragment MFL's immunogenicity. Furthermore, the rVSV-based bivalent vaccine expressing Sudan Ebola GP (SGP) and MFL fragment elicited efficient cross-immunity against ZGP and SGP with high levels of neutralizing antibody. Our results indicate that fragment MFL is an effective and novel antigen for the production of neutralizing antibody and polyvalent vaccines of Ebola virus.

Development of an oligonucleotide-based fluorescence assay for the identification of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors

Topoisomerase 1 (TOP1) generates transient nicks in the DNA to relieve torsional stress encountered during the cellular processes of transcription, replication, and recombination. At the site of the nick there is a covalent linkage of TOP1 with DNA via a tyrosine residue. This reversible TOP1-cleavage complex intermediate can become trapped on DNA by TOP1 poisons such as camptothecin, or by collision with replication or transcription machinery, thereby causing protein-linked DNA single- or double-strand breaks and resulting in cell death. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme involved in the repair of TOP1-associated DNA breaks via hydrolysis of 3'-phosphotyrosine bonds. Inhibition of TDP1 is therefore an attractive strategy for targeting cancer cells in conjunction with TOP1 poisons. Existing methods for monitoring the phosphodiesterase activity of TDP1 are generally gel based or of high cost. Here we report a novel, oligonucleotide-based fluorescence assay that is robust, sensitive, and suitable for high-throughput screening of both fragment and small compound libraries for the detection of TDP1 inhibitors. We further validated the assay using whole cell extracts, extending its potential application to determine of TDP1 activity in clinical samples from patients undergoing chemotherapy.

Strategies to stabilize compact folding and minimize aggregation of antibody-based fragments

Monoclonal antibodies (mAbs) have proven to be useful for development of new therapeutic drugs and diagnostic techniques. To overcome the difficulties posed by their complex structure and folding, reduce undesired immunogenicity, and improve pharmacokinetic properties, a plethora of different Ab fragments have been developed. These include recombinant Fab and Fv segments that can display improved properties over those of the original mAbs upon which they are based. Antibody (Ab) fragments such as Fabs, scFvs, diabodies, and nanobodies, all contain the variable Ig domains responsible for binding to specific antigenic epitopes, allowing for specific targeting of pathological cells and/or molecules. These fragments can be easier to produce, purify and refold than a full Ab, and due to their smaller size they can be well absorbed and distributed into target tissues. However, the physicochemical and structural properties of the immunoglobulin (Ig) domain, upon which the folding and conformation of all these Ab fragments is based, can limit the stability of Ab-based drugs. The Ig domain is fairly sensitive to unfolding and aggregation when produced out of the structural context of an intact Ab molecule. When unfolded, Ab fragments may lose their specificity as well as establish non-native interactions leading to protein aggregation. Aggregated antibody fragments display altered pharmacokinetic and immunogenic properties that can augment their toxicity. Therefore, much effort has been placed in understanding the factors impacting the stability of Ig folding at two different levels: 1) intrinsically, by studying the effects of the amino acid sequence on Ig folding; 2) extrinsically, by determining the environmental conditions that may influence the stability of Ig folding. In this review we will describe the structure of the Ig domain, and the factors that impact its stability, to set the context for the different approaches currently used to achieve stable recombinant Ig domains when pursuing the development of Ab fragment-based biotechnologies.

Indications for bullet removal: overview of the literature, and clinical practice guidelines for European trauma surgeons

PURPOSE

The incidence of gunshot wounds from civilian firearms is increasing. Despite this fact, guidelines on indications for bullet removal are scarce. In this analysis, we combine an overview of the available literature in these rare entities with our experiences in our own clinical practices.

METHODS

We conducted a systematic literature search of computerized bibliographic databases (Medline, EMBASE, and the Cochrane Central Register). The local experience of the authors was reviewed in light of the available literature.

RESULTS

145 full-text articles were suitable for further evaluation. Only six retrospective studies were available, and no prospective study could be retrieved. Most of the articles were case reports. In the South African co-author's own clinical practice, approximately 800 patients are treated per year with gunshot wounds.

CONCLUSIONS

In summary, there are only a few clear indications for bullet removal. These include bullets found in joints, CSF, or the globe of the eye. Fragments leading to impingement on a nerve or a nerve root, and bullets lying within the lumen of a vessel, resulting in a risk of ischemia or embolization, should be removed. Rare indications are lead poisoning caused by a fragment, and removal that is required for a medico-legal examination. In all other cases the indication should be critically reviewed.