Label-Free Techniques for Probing Biomolecular Condensates

Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.

WITHDRAWN: Trace metals translocation from soil to plants: Health risk assessment via consumption of vegetables in the urban sprawl of a developing country

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Contamination and ecological risk assessment of Cr, As, Cd and Pb in water and sediment of the southeastern Bay of Bengal coast in a developing country

Safe levels of heavy metals in the surface water and sediment of the eastern Bay of Bengal coast have not been universally established. Current study characterized heavy metals such as arsenic (As), chromium (Cr), cadmium (Cd) and lead (Pb) in surface water and sediments of the most important fishing resource at the eastern Bay of Bengal coast, Bangladesh. Both water and sediment samples were analyzed using inductively coupled plasma mass spectrometer. Considering both of the seasons, the mean concentrations of Cr, As, Cd, and Pb in water samples were 33.25, 8.14, 0.48, and 21.14 μg/L, respectively and in sediment were 30.47, 4.48, 0.20, and 19.98 mg/kg, respectively. Heavy metals concentration in water samples surpassed the acceptable limits of usable water quality, indicating that water from this water resource is not safe for drinking, cooking, bathing, and any other uses. Enrichment factors also directed minor enrichment of heavy metals in sediment of the coast. Other indexes for ecological risk assessment such as pollution load index (PLI), contamination factor (CF), geoaccumulation index (Igeo), modified contamination degree (mCd), and potential ecological risk index (PERI) also indicated that sediment of the coastal watershed was low contamination. In-depth inventorying of heavy metals in both water and sediment of the study area are required to determine ecosystem health for holistic risk assessment and management.

Label-free identification of protein aggregates using deep learning

Protein misfolding and aggregation play central roles in the pathogenesis of various neurodegenerative diseases (NDDs), including Huntington's disease, which is caused by a genetic mutation in exon 1 of the Huntingtin protein (Httex1). The fluorescent labels commonly used to visualize and monitor the dynamics of protein expression have been shown to alter the biophysical properties of proteins and the final ultrastructure, composition, and toxic properties of the formed aggregates. To overcome this limitation, we present a method for label-free identification of NDD-associated aggregates (LINA). Our approach utilizes deep learning to detect unlabeled and unaltered Httex1 aggregates in living cells from transmitted-light images, without the need for fluorescent labeling. Our models are robust across imaging conditions and on aggregates formed by different constructs of Httex1. LINA enables the dynamic identification of label-free aggregates and measurement of their dry mass and area changes during their growth process, offering high speed, specificity, and simplicity to analyze protein aggregation dynamics and obtain high-fidelity information.

Intravenous thrombolysis for multi-ethnic Asians with acute ischaemia stroke in Malaysian public primary stroke centres versus acute stroke ready hospitals: Comparison of real-world clinical outcomes

INTRODUCTION

Intravenous thrombolysis (IVT) with recombinant tissue plasminogen activator is beneficial in acute ischaemic stroke (AIS). We aim to compare the realworld clinical outcomes and service efficiency of IVT in Malaysian primary stroke centres (PSCs) versus acute stroke ready hospitals (ASRHs).

MATERIALS AND METHODS

We conducted a multi-centre cohort study involving 5 PSCs and 7 ASRHs in Malaysia. Through review of medical records of AIS patients who received IVT from 01 January 2014 to 30 June 2021, real-world data was extracted for analysis. Univariate and multivariate regression models were employed to evaluate the role of PSCs versus ASRHs in post-IVT outcomes and complications. Statistical significance was set at p<0.05.

RESULTS

A total of 313 multi-ethnic Asians, namely 231 from PSCs and 82 from ASRHs, were included. Both groups were comparable in baseline demographic, clinical, and stroke characteristics. The efficiency of IVT delivery (door-toneedle time), functional outcomes (mRS at 3 months post- IVT), and rates of adverse events (intracranial haemorrhages and mortality) following IVT were comparable between the 2 groups. Notably, 46.8% and 48.8% of patients in PSCs and ASRHs group respectively (p=0.752) achieved favourable functional outcome (mRS≤1 at 3 months post-IVT). Regression analyses demonstrated that post-IVT functional outcomes and adverse events were independent of the role of PSCs or ASRHs.

CONCLUSION

Our study provides real-world evidence which suggests that IVT can be equally safe, effective, and efficiently delivered in ASRHs. This may encourage the establishment of more ASRHs to extend the benefits of IVT to a greater proportion of stroke populations and enhance the regional stroke care.

Characterization of flat-fielding systems for quantitative microscopy

Optical flat-fielding systems, such as field-mapping or integration-based beam shapers, are used to transform nonuniform illumination into uniform illumination. Thus, flat-fielding paves the way for imaging that is independent of position within a field of view and enables more quantitative analysis. Here, we characterize and compare three systems for homogenizing both widefield and multifocal illumination. Our analysis includes two refractive field-mapping beam shapers: PiShaper and TopShape, as well as one integration-based: Köhler integrator. The comparison is based on figures of merit including ISO-standard values, such as the plateau uniformity and edge steepness, transmission efficiency, stability of the beams along propagation and multifocal intensity, pitch, and point width. By characterizing and comparing existing beam shapers, we facilitate the choice of the appropriate flat-fielding solution and increase their accessibility for different applications.

Homogeneous multifocal excitation for high-throughput super-resolution imaging

Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for field-independent imaging (mfFIFI). By integrating mfFIFI into an instant structured illumination microscope (iSIM), we extend the field of view (FOV) to >100 × 100 µm² while maintaining high-speed, multicolor, volumetric imaging at double the diffraction-limited resolution. We further extend the effective FOV by stitching adjacent images for fast live-cell super-resolution imaging of dozens of cells. Finally, we combine our flat-fielded iSIM with ultrastructure expansion microscopy to collect three-dimensional (3D) images of hundreds of centrioles in human cells, or thousands of purified Chlamydomonas reinhardtii centrioles, per hour at an effective resolution of ~35 nm. Classification and particle averaging of these large datasets enables 3D mapping of posttranslational modifications of centriolar microtubules, revealing differences in their coverage and positioning.

Nitrogen Pollution Impact and Remediation through Low Cost Starch Based Biodegradable polymers

The world does not have too much time to ensure that the fast-growing population has enough land, food, water and energy. The rising food demand has brought a positive surge in fertilizers’ demand and agriculture-based economy. The world is using 170 million tons of fertilizer every year for food, fuel, fiber, and feed. The nitrogenous fertilizers are being used to meet 48% of the total food demand of the world. High fertilizer inputs augment the reactive nitrogen levels in soil, air, and water. The unassimilated reactive nitrogen changes into a pollutant and harms the natural resources. The use of controlled-release fertilizers for slowing down the nutrients’ leaching has recently been practiced by farmers. However, to date, monitoring of the complete discharge time and discharge rate of controlled released fertilizers is not completely understood by the researchers. In this work, corn starch was thermally processed into a week gel-like coating material by reacting with urea and borate. The granular urea was coated with native and processed starch in a fluidized bed reactor having bottom-up fluid delivery system. The processed starch exhibited better thermal and mechanical stability as compared to the native starch. Unlike the pure starch, the storage modulus of the processed starch dominated the loss modulus. The release time of urea, coated with processed starch, remained remarkably larger than the uncoated urea.

Velocimetry and response surface regression analysis of a swirling bed tested with mesh-coupled axial blade distributor

Fluidized bed technology is being used in several industrial processes. The well-controlled fluidization of a bed material is a prerequisite for successful implementation of this technology. Several variants of distributors are being tested for fluidized beds; however, scant information is available on their working regimes. In this study, an annular distributor was constructed by fixing blades between two concentric rings and covering the assembly with a wire mesh. This new distributor design was tested for fluidization of batches of a spherical bed material at different blade angles and superficial air velocities (SAVs). High-speed imaging and MATLAB supported velocimetry techniques were used to generate velocity vector fields of fluidized beds. These fields were analyzed further for bed velocity measurements at different bed zones. A response surface regression model was applied on the data to predict the response of the bed parameters. Statistically, the bed velocity was predicted to be about 0.497 m/s with the confidence interval in the range of 0.4948-0.4999. The experimental bed velocity remained between 0.531 m/s and 0.538 m/s under an optimized blade angle of 60°, SAV of 2.3 m/s, and bed weight of 500 g.

Effect of Urea and Borate Plasticizers on Rheological Response of Corn Starch

Although starch based materials have an array of fascinating industrial applications, the native starches do not show good mechanical strength, thermal stability, and rheological properties for their use in the mainstream processing industry. For example, the use of starches for producing controlled release fertilizers is a new research endeavor with detailed knowledge still to come. The thermal processing of native starches with water as a plasticizer results in poor physical and pasting properties of the final product. Therefore in this study, corn starch was thermally processed with urea and borate in a water medium. The pure starch (PS), starch-urea (SU), starch-borate (SB), and starch-urea-borate (SUB) samples were prepared and characterized for their rheological traits. The PS sample exhibited a peak viscosity of 299 cP after 17 min of thermal processing. Further heating of the suspension caused a decrease in viscosity of 38 points due to thermal cracking of the starch granules. A similar trend was depicted in the viscosity measurements of SU, SB, and SUB adhesives. However, the viscosity of these samples remained slightly higher than that for PS. Also, the reduction in viscosity after the peak value was not as notable as for PS. The modified starch behaved like a gel and its storage modulus was significantly higher than the loss modulus. The lower magnitudes of storage and loss moduli revealed that the modified starch was in the form of a weak gel and not a solid. The PS is more fluid in nature with dominating loss modulus at lower angular frequencies.

Formulation, Evaluation and release rate characteristics of medicated jelly of vitamin C

Medicated jelly formulations are patient friendly dosage form for pediatric, geriatric and dysphagic patients. These formulations offer rapid dissolution and absorption of drugs through oral mucosa therefore show the early onset of action. The objective of the study was to develop and evaluate oral jelly formulations of vitamin C. Slurry method was adopted using glucose 103gm, sugar 67gm, gelatin 10gm and sorbitol 6.56gm. Preformulation studies were performed including the organoleptic profile, pH, and solubility of both drugs. The medicated jelly of Vitamin C was prepared and evaluated for physical characteristics, weight variation, syneresis, pH, taste and palatability, drug content, release rate characteristics and stability studies. All the jellies were found to have patient welcoming taste and were palatable. All formulations showed more than 50% drug release within 15 minutes, while 93% drug was released in 30 minutes. The results of release kinetics showed that the formulation followed the zero order release kinetics. Thus the drug was released at constant rate independent of the drug concentration involved in the process. All the medicated jellies were found to remain stable stored for 60 days at different temperatures. The present study revealed that medicated jellies of vitamin C could be employed orally in an effective form as an alternative solid oral dosage form for special population such as pediatrics, geriatrics and patients with dysphagia.

Preparation of Chito-Oligomers by Hydrolysis of Chitosan in the Presence of Zeolite as Adsorbent

An increasing interest has recently been shown to use chitin/chitosan oligomers (chito-oligomers) in medicine and food fields because they are not only water-soluble, nontoxic, and biocompatible materials, but they also exhibit numerous biological properties, including antibacterial, antifungal, and antitumor activities, as well as immuno-enhancing effects on animals. Conventional depolymerization methods of chitosan to chito-oligomers are either chemical by acid-hydrolysis under harsh conditions or by enzymatic degradation. In this work, hydrolysis of chitosan to chito-oligomers has been achieved by applying adsorption-separation technique using diluted HCl in the presence of different types of zeolite as adsorbents. The chito-oligomers were retrieved from adsorbents and characterized by differential scanning calorimetry (DSC), liquid chromatography/mass spectroscopy (LC/MS), and ninhydrin test.

Nodular fasciitis in the pediatric population: a single center experience

PURPOSE

To describe our experience with nodular fasciitis in the pediatric population, in an attempt to contribute additional information that may be used to develop a more comprehensive characterization of the disease.

METHODS

A twenty-year retrospective chart review of patients 18 years or younger diagnosed with nodular fasciitis at a single, large, academic institution.

RESULTS

Five patients were treated for nodular fasciitis during the study period. The majority (60%) were male and all presented with rapidly enlarging masses that were excised surgically. The median age at presentation was 14 years. Most (60%) lesions were located in the upper extremities and 80% had no related symptomatology or disability. All lesions were less than 3 cm in greatest dimension and 4 patients had no signs of recurrence (one patient was lost to follow-up). Pathologic, immunohistochemical, and long-term follow-up data were lacking in our cohort.

CONCLUSION

The characteristics of nodular fasciitis in children at our institution are slightly different than those which have been reported thus far based on no patients with head and neck disease or antecedent trauma to the affected area. Due to variability in clinical presentation and histologic findings, additional studies are necessary to provide more practical, consistent and effective management strategies.

Date palm (Phoenix dactylifera L.) leaves as biomonitors of atmospheric metal pollution in arid and semi-arid environments

The leaves of date palms were evaluated as a possible biomonitor of heavy metal contamination in Ma'an city, Jordan. Concentrations of (Fe), (Pb), (Zn), (Cu), (Ni), and (Cr) were determined in washed and unwashed leaves and soil samples collected from different sites with different degrees of metal contamination (urban, suburban, industrial, highway and rural sites); separate leaves were taken from outside the city to be used as a control sample. Samples collected from industrial sites were found to have high concentrations of all metals except those of Cu, Ni and Pb, which were found at high levels in the highway site samples which is associated with the road traffic. The difference between unwashed and washed samples showed that metal pollutants exist as contaminants, particularly Pb, Zn and Ni, which varied in concentration, depending on the source of the metal.

The results of arthroscopic versus mini-open repair for rotator cuff tears at mid-term follow-up

Background

To prospectively evaluate patients who underwent a "mini-open" repair versus a completely arthroscopic technique for small to large size rotator cuff tears.

Methods

Fifty-two patients underwent "mini-open" or all arthroscopic repair of a full thickness tear of the rotator cuff. Patients who complained of shoulder pain and/or weakness and who had failed a minimum of 6 weeks of physical therapy and had at least one sub-acromial injection were surgical candidates. Pre and post-operative clinical evaluations included the following: 1) demographics; 2) Simple Shoulder Test (SST); 3) University of California, Los Angeles (UCLA) rating scale; 4) visual analog pain assessment (VAS); and 5) pre-op SF12 assessment. Descriptive analysis was performed for patient demographics and for all variables. Pre and post outcome scores, range of motion and pain scale were compared using paired t-tests. Analysis of variance (ANOVA) was used to evaluate any effect between dependent and independent variables. Significance was set at p is less than or equal to 0.05.

Results

There were 31 females and 21 males. The average follow-up was 50.6 months (27 – 84 months). The average age was similar between the two groups [arthroscopic x = 55 years/mini-open x = 58 years, p = 0.7]. Twenty-seven patients underwent arthroscopic repair and 25 underwent repair with a mini-open incision. The average rotator cuff tear size was 3.1 cm (range: 1–5 centimeters). There was no significant difference in tear size between the two groups (arthroscopic group = 2.9 cm/mini-open group = 3.2 cm, p = 0.3). Overall, there was a significant improvement from pre-operative status in shoulder pain, shoulder function as measured on the Simple Shoulder test and UCLA Shoulder Form. Visual analog pain improved, on average, 4.4 points and the most recent Short Shoulder Form and UCLA scores were 8 and 26 respectively. Both active and passive glenohumeral joint range of motion improved significantly from pre-operatively.

Conclusion

Based upon the number available, we found no statistical difference in outcome between the two groups, indicating that either procedure is efficacious in the treatment of small and medium size rotator cuff tears.

Level of Evidence

Type III

A study of the junction between the straight sinus and the great cerebral vein

In the present study 20 human brains were used to verify the presence of a small body projecting into the floor of the straight sinus at its junction with the great cerebral vein. The elevation could be identified at the anterior end of the floor of the straight sinus with an empty cavity underlying it. Histologically, the elevation was found to consist of interwoven bundles of collagen fibres covered by vascular endothelium continuous with that of the straight sinus. The importance of such an elevation in the regulation of blood flow from the great cerebral vein to the straight sinus is discussed from a hydrodynamic point of view.

Host-Parasite Relationships of Meloidogyne arenaria and M. incognita on Susceptible Soybean

Pathogenicity and reproduction of single and combined populations of Meloidogyne arenaria and M. incognita on a susceptible soybean (Glycine max cv. Davis) were investigated. Significant galling and egg mass production were observed on roots of greenhouse-grown soybean inoculated with M. arenaria and M. incognita, in combination and individually. M. arenaria produced more galls and egg masses than M. incognita, whereas in combined inoculation with both nematode species, gall and egg production was intermediate. In growth chamber tests, inoculations with M. arenaria and M. incognita, singly or in combination, produced more galls and egg masses at 30 C than at 25 C. At 25 C, M. arenaria alone produced significantly more galls and egg masses than the combined M. arenaria plus M. incognita, while M. incognita produced the fewest. At 30 C, numbers of egg masses produced by M. arenaria did not differ significantly from combined M. arenaria and M. incognita. In temperature tank tests, M. incognita produced more galls and egg masses at 28 C than at 24 C soil temperature. In contrast, numbers of galls, egg masses, and eggs of M. arenaria were slightly higher at 24 C than at 28 C. Combined inoculum of both nematode species produced greater numbers of galls at 24 C than at 28 C.

Quantitative and histomorphological studies on the geniculate ganglion of the facial nerve in man

The human geniculate ganglion was studied histologically and quantitatively. It appeared pyramidal in shape. The mean diameter of the side of the triangle constituting its base was 1,050 micrometer and its mean height 1,800 micrometer; the volume of the ganglion was 26 X 10(7) micrometer 3. The ganglionic cells were arranged in clusters with longitudinally extending bundles of nerve fibres in between. At the apex of the ganglion compact neurons were delineated from those in the rest of the ganglion by a bundle of nerve fibres. Moreover, scattered solitary nerve cells were met with between fibres of the greater petrosal and the chorda tympani nerves. The mean neuronal population was 1,070, the mean cell volume 11,913 micrometer 3, the cell territory 242,990 micrometer 3 and the volume of the intercellular space 231,077 micrometer 3. Extraganglionic vessels approximated the ganglion perpendicular to its long axis, while further intraganglionic vessels extended in a direction parallel to the long axis of the ganglion and vertical terminal ramifications formed dense vascular channels around the capsule of the nerve cells. The significance of that pattern of blood supply was discussed.

Rare tumors of the intestines and rectum

Some rare tumors of the intestines and rectum (eight cases) have been presented and discussed. All were successfully managed without operative mortality. I have presented some observations deduced from these cases which might aid in the diagnosis of such rare tumors--the importance of palpating the terminal ileum in any abdominal operation and the necessity for a frozen section biopsy from suspicious schistosomal masses of the sigmoid colon or the rectum before deciding to resect them. I have discussed cases of carcinoma of the rectum where microscopic schistosomal deposits were spotted and stressed that in such cases it is a mere coincidental association.

The surgical gallbladder

A series of 412 personally performed cholecystectomies is analyzed and discussed. Surgical cases were divided into groups based on whether or not the gallbladder was visualized by cholecystography. A third group required immediate surgery without attempting radiologic investigation. We do not accept the diagnosis of dyskinesia which is a radiological finding as an indication for surgery and no such cases are included in the series. Quite a number of cases operated on for "chronic cholecystitis" were found at surgery to have other less common pathological lesions, as proved by later histologic examination of the excised gallbladders. Bilharzial gallbladder disease is discussed and the new terms bilharzial cholecystitis and bilharzioma of the gallbladder are suggested for the lesions described. We stress the need to explore, inspect and aspirate the common bile duct in every case of calculous cholecystitis as the only alternative to operative cholangiography. By so doing biliary fistulas were completely eliminated from the series.