DIRT/µ - Automated extraction of root hair traits using combinatorial optimization.

Similar to any microscopic appendages, such as cilia or antennae, phenotyping of root hairs has been a challenge due to their complex intersecting arrangements in two-dimensional (2D) images and the technical limitations of automated measurements. Digital Imaging of Root Traits at Microscale (DIRT/µ) addresses this issue by computationally resolving intersections and extracting individual root hairs from 2D microscopy images. This solution enables automatic and precise trait measurements of individual root hairs. DIRT/µ rigorously defines a set of rules to resolve intersecting root hairs and minimizes a newly designed cost function to combinatorically identify each root hair in the microscopy image. As a result, DIRT/µ accurately measures traits such as root hair length (RHL) distribution and root hair density (RHD), which are impractical for manual assessment. We tested DIRT/µ on three datasets to validate its performance and showcase potential applications. By measuring root hair traits in a fraction of the time manual methods require, DIRT/µ eliminates subjective biases from manual measurements. Automating individual root hair extraction accelerates phenotyping and quantifies trait variability within and among plants, creating new possibilities to characterize root hair function and their underlying genetics.

Escaping the ESKAPE pathogens: A review on antibiofilm potential of nanoparticles.

ESKAPE pathogens, a notorious consortium comprising Enterococcusfaecium, Staphylococcusaureus, Klebsiellapneumoniae, Acinetobacterbaumannii, Pseudomonasaeruginosa, and Enterobacter species, pose formidable challenges in healthcare settings due to their multidrug-resistant nature. The increasing global cases of antimicrobial-resistant ESKAPE pathogens are closely related to their remarkable ability to form biofilms. Thus, understanding the unique mechanisms of antimicrobial resistance of ESKAPE pathogens and the innate resilience of biofilms against traditional antimicrobial agents is important for developing innovative strategies to establish effective control methods against them. This review offers a thorough analysis of biofilm dynamics, with a focus on the general mechanisms of biofilm formation, the significant contribution of persister cells in the resistance mechanisms, and the recurrence of biofilms in comparison to planktonic cells. Additionally, this review highlights the potential strategies of nanoparticles for managing biofilms in the ESKAPE group of pathogens. Nanoparticles, with their unique physicochemical properties, provide promising opportunities for disrupting biofilm structures and improving antimicrobial effectiveness. The review has explored interactions between nanoparticles and biofilms, covering a range of nanoparticle types such as metal, metal-oxide, surface-modified, and functionalized nanoparticles, along with organic nanoparticles and nanomaterials. The additional focus of this review also encompasses green synthesis techniques of nanoparticles that involve plant extract and supernatants from bacterial and fungal cultures as reducing agents. Furthermore, the use of nanocomposites and nano emulsions in biofilm management of ESKAPE is also discussed. To conclude, the review addresses the current obstacles and future outlooks in nanoparticle-based biofilm management, stressing the necessity for further research and development to fully exploit the potential of nanoparticles in addressing biofilm-related challenges.

Diverse Response to Local Pharmacological Blockade of Sirt1 Cleavage in Age-Induced versus Trauma-Induced Osteoarthritis Female Mice.

Objective: Previous studies have shown that the cleavage of Sirt1 contributes to the development of osteoarthritis (OA). In fact, OA was effectively abrogated by the intra-articular (IA) administration of two compounds, one blocking Sirt1 cleavage (CA074me) and the other activating Sirt1 (SRT1720), using a post-traumatically induced model (PTOA) in young female mice. In this study, we attempted to understand if this local treatment is effective in preventing age-associated OA (AOA) progression and symptoms. Design: A group of 17-month-old female C57BL/6J mice were IA administered with CA074me and/or SRT1720 or their combination. Joint histopathological analysis and bone histomorphometry were carried out, with an assessment of knee mechanical hyperalgesia. A serum analysis for NT/CT Sirt1 was carried out along with immunohistochemistry for articular cartilage to detect p16INK4A or γH2A.X. Similarly, meniscal cartilage was monitored for Lef1 and Col1a1 deposition. The data were compared for young female mice subjected to post-traumatic OA (PTOA). Results: Similar to PTOA, combination-treated AOA exhibited improved knee hyperalgesia, yet structural improvements were undetected, corresponding to unchanged NT/CT Sirt1 serum levels. Both AOA and PTOA exhibited unchanged staining for nuclear p16INK4A or γH2A.X and lacked a correlation with OA severity. Contrarily to PTOA, the combination treatment with AOA did not exhibit a local reduction in the Lef1 and Col1 targets. Conclusions: When targeting Sirt1 cleavage, the PTOA and AOA models exhibited a similar pain response to the combination treatment; however, they displayed diverse structural outcomes for joint-related damage, related to Lef1-dependent signaling. Interestingly, nuclear p16INK4A was unaffected in both models, regardless of the treatment's effectiveness. Finally, these findings highlight the variations in the responses between two highly researched OA preclinical models, reflecting OA pathophysiology heterogeneity and variations in gender-related drug-response mechanisms.

Evaluation of In-Vitro Activity of Ceftaroline Against Methicillin-Resistant Staphylococcus aureus Clinical Isolates.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major causes of hospital and community-acquired infections. Fewer drugs, such as vancomycin, teicoplanin, and daptomycin, are effective against it, but they come with high toxicity. Fifth-generation cephalosporins like ceftaroline and second-generation cefuroxime are effective against MRSA. Limited studies are available on ceftaroline resistance in the literature. This study was undertaken to determine ceftaroline resistance in MRSA in a tertiary care hospital in Eastern India. A cross-sectional, hospital-based study was carried out with MRSA isolates obtained from various clinical samples of patients. Identification of the isolates to the species level was performed by an automated Vitek system, and selected samples were genotypically confirmed by detecting the mecA gene via real-time PCR. Out of a total of 334 Staphylococcus aureus isolates examined in this study, the prevalence of MRSA was seen in 59.3% (198/334), and methicillin-sensitive Staphylococcus aureus was in 40.7% (136/334). Of the total 198 MRSA isolates, ceftaroline intermediate MRSA was seen in 8.6% (17/198), and ceftaroline sensitive MRSA was in 91.4% (181/198), respectively. Among the 17 ceftaroline intermediate MRSA isolates, 88.2% (15/17) showed a minimum inhibitory concentration (MIC) of 2 µg/ml, and 11.8% (2/17) showed an MIC of 3 µg/ml. All the remaining 91.4% (181/198) isolates were sensitive to ceftaroline and showed an MIC ≤1 µg/ml. Real-time PCR confirmed the presence of the mecA gene in MRSA isolates. In this present study, not a single isolate was resistant to ceftaroline, suggesting that it, being a safer drug, can be used in place of glycopeptides such as vancomycin or teicoplanin and linezolid, where resistance has already been detected. The rational use of ceftaroline could be useful in clinical settings, and further studies will confirm the findings.

Comparative Evaluation of Cartridge-Based Abbott ID NOW Test With Probe-Based Real-Time Reverse Transcription Polymerase Chain Reaction Assay for Detection of SARS-CoV-2.

BACKGROUND: The gold standard test for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recommended by WHO is real-time reverse transcription polymerase chain reaction (RT-PCR), which has a turnaround time of five to six hours. Abbott ID NOW (Abbott Diagnostics Scarborough, Inc., Scarborough, ME, USA), the cartridge-based loop-mediated isothermal amplification (LAMP) assay, was approved by FDA for Emergency Use Authorization as rapid point of care testing. The present study was planned to evaluate the performance of the cartridge-based Abbott ID NOW test by comparing it to the currently used standard probe-based real-time RT-PCR method for detection of SARS-CoV-2. METHODOLOGY: A cross-sectional study was conducted in a tertiary care hospital in the eastern part of India after getting institutional ethics committee (IEC) approval. Two hundred fifty-nine cases of various age groups of both sexes who were advised for testing for SARS-CoV-2 were included in the study. Nasopharyngeal swabs were collected according to protocol advisory by the Indian Council of Medical Research (ICMR), India. Dry swabs were sent for Abbott ID NOW testing and swabs in viral transport medium were sent for probe-based RT-PCR assay using the CoviPath kit (Thermo Fisher Scientific, Bangalore, India). The data were collected and statistical analysis was performed using Statistical Package for Social Sciences (SPSS) (IBM Corp., Armonk, NY, USA). Sensitivity, specificity, positive and negative predictive values for ID NOW were calculated taking RT-PCR as the gold standard.  Results: Out of 259 patients enrolled in the study, 49% were symptomatic for coronavirus disease 2019 (COVID-19). The prevalence rate of SARS-CoV-2 was 20.84% among the study population. Sensitivity and specificity, positive and negative predictive values of ID NOW test in comparison to RT-PCR assay was found to be 87%, 98%, 92.1% and 96.8% respectively. ID NOW detected seven out of 54 (12.9%) cases as false negative who were found to be positive with RT-PCR, with mean Ct value of the target genes >34. CONCLUSIONS: In this study the overall sensitivity for ID NOW assay was found to be lower, but specificity, positive and negative predictive values were found to be higher. It had the highest correlation to RT-PCR among symptomatic patients and at higher viral loads. Due to the ease of use and shortest result time for detecting COVID-19, ID NOW test could be used as a point-of-care test. But for all tests, the results should be interpreted according to the clinical and epidemiological context.

Nanoemulsion-based dosage forms for the transdermal drug delivery applications: A review of recent advances.

INTRODUCTION: Nanoemulsion-based drug delivery approaches have witnessed massive acceptance over the years and acquired a significant foothold owing to their tremendous benefits over the others. It has widely been used for transdermal delivery of hydrophobic and hydrophilic drugs with solubility, lipophilicity, and bioavailability issues. AREAS COVERED: The review highlights the recent advancements and applications of transdermal nanoemulsions. Their utilities and characteristics, clinical pertinence showcasing intellectual properties and advancements, potential in treating disorders accompanying liquid, semisolid, and solid dosage forms, the ability to modulate a drug's physicochemical properties, and regulatory status are thoroughly summarized. EXPERT OPINION: Despite tremendous therapeutic utilities and extensive investigations, the transdermal nanoemulsion-based technologies yet tackles several challenges such as optimum use of surfactant mixtures, economic burden due to high energy consumption during production, lack of concrete regulatory requirement, etc. Provided with the concrete guidelines on the safe use of surfactants, stability, use of scalable and economical methods, and the use of NE as a transdermal system would solve the purpose best as nanoemulsion shows remarkable improvement in drug release profiles and bioavailability of many drugs. Nevertheless, a better understanding of nanoemulsion technology holds a promising outlook and would land more opportunities and better delivery outcomes.

Root hairs vs. trichomes: Not everyone is straight!

Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, we show a previously unreported 'hooked' hair structure growing below-ground in common bean. The unique 'hooking' shape distinguishes the 'hooked hair' morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.

Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis.

Pathophysiological defects in water homeostasis can lead to renal failure. Likewise, common genetic disorders associated with abnormal cytoskeletal dynamics in the kidney collecting ducts and perturbed calcium and cAMP signaling in the ciliary compartment contribute to chronic kidney failure. We show that collecting ducts in mice lacking the A-Kinase anchoring protein AKAP220 exhibit enhanced development of primary cilia. Mechanistic studies reveal that AKAP220-associated protein phosphatase 1 (PP1) mediates this phenotype by promoting changes in the stability of histone deacetylase 6 (HDAC6) with concomitant defects in actin dynamics. This proceeds through a previously unrecognized adaptor function for PP1 as all ciliogenesis and cytoskeletal phenotypes are recapitulated in mIMCD3 knock-in cells expressing a phosphatase-targeting defective AKAP220-ΔPP1 mutant. Pharmacological blocking of local HDAC6 activity alters cilia development and reduces cystogenesis in kidney-on-chip and organoid models. These findings identify the AKAP220-PPI-HDAC6 pathway as a key effector in primary cilia development.

Preoperative magnetic resonance imaging use and oncologic outcomes in premenopausal breast cancer patients.

Breast magnetic resonance imaging (MRI) delineates disease extent sensitively in newly diagnosed breast cancer patients, but improved cancer outcomes are uncertain. Young women, for whom mammography is less sensitive, are expected to benefit from MRI-based resection. We identified 512 women aged ≤50 years, undergoing breast-conserving treatment (BCT: tumor-free resection margins and radiotherapy) during 2006-2013 through Northwestern Medicine database queries; 64.5% received preoperative MRI and 35.5% did not. Tumor and treatment parameters were similar between groups. We estimated the adjusted hazard ratios (aHR) for local and distant recurrences (LR and DR), using multivariable regression models, accounting for important therapeutic and prognostic parameters. LR rate with MRI use was 7.9 vs. 8.2% without MRI, aHR = 1.03 (95% CI 0.53-1.99). DR rate was 6.4 vs. 6.6%, aHR = 0.89 (95% CI 0.43-1.84). In 119 women aged ≤40, results were similar to LR aHR = 1.82 (95% CI 0.43-7.76) and DR aHR = 0.93 (95% CI 0.26-3.34). Sensitivity analyses showed similar results. The use of preoperative MRI in women aged ≤50 years should be reconsidered until there is proof of benefit.

InSight Care Pilot Program: Redefining Seeing a Patient.

PURPOSE: Early detection and management of symptoms in patients with cancer improves outcomes. However, the optimal approach to symptom monitoring and management is unknown. InSight Care is a mobile health intervention that captures symptom data and facilitates patient-provider communication to mitigate symptom escalation. PATIENTS AND METHODS: Patients initiating antineoplastic treatment at a Memorial Sloan Kettering regional location were eligible. Technology supporting the program included the following: a predictive model that identified patient risk for a potentially preventable acute care visit; a secure patient portal enabling communication, televisits, and daily delivery of patient symptom assessments; alerts for concerning symptoms; and a symptom-trending application. The main outcomes of the pilot were feasibility and acceptability evaluated through enrollment and response rates and symptom alerts, and perceived value evaluated on the basis of qualitative patient and provider interviews. RESULTS: The pilot program enrolled 100 high-risk patients with solid tumors and lymphoma (29% of new treatment starts v goal of 25%). Over 6 months of follow-up, the daily symptom assessment response rate was 56% (the goal was 50%), and 93% of patients generated a severe symptom alert. Patients and providers perceived value in the program, and archetypes were developed for program improvement. Enrolled patients were less likely to use acute care than were other high-risk patients. CONCLUSION: InSight Care was feasible and holds the potential to improve patient care and decrease facility-based care. Future work should focus on optimizing the cadence of patient assessments, the workforce supporting remote symptom management, and the return of symptom data to patients and clinical teams.

A rhodamine based biocompatible chemosensor for Al3+, Cr3+ and Fe3+ ions: extraordinary fluorescence enhancement and a precursor for future chemosensors.

A rhodamine based chemosensor, 3-(((2-(3',6'-bis(ethylamino)-2',7'-dimethyl-3-oxospiro[isoindoline-1,9'-xanthen]-2-yl)ethyl)imino)methyl)-2-hydroxy-5-methylbenzaldehyde (HL-CHO), has been developed for the detection of Al3+, Cr3+ and Fe3+ ions. The absorbance of HL-CHO at 528 nm increases significantly in HEPES buffer in methanol : water (9 : 1, v/v) (pH 7.4) in the presence of Al3+, Cr3+ and Fe3+ ions with the alteration of solution color from colorless to pink. The fluorescence intensity of the probe at 550 nm enhances by 1465, 588 and 800 fold in the presence of Al3+, Cr3+ and Fe3+ ions, respectively. To the best of our knowledge, this huge increase in fluorescence intensity with Al3+ and Cr3+ has not been observed for other rhodamine based chemosensing systems. The weak fluorescence and no coloration of the probe are due to the existence of a spirolactam ring. The trivalent cations induce the opening of the spirolactam ring and consequently change the color and the fluorescence intensity followed by the 1 : 1 complex formation with HL-CHO which are evident from Job's analysis, ESI mass spectral analysis and elemental analysis. The quantum yield and lifetime of HL-CHO have increased considerably in the presence of the trivalent cations. The high sensitivity of the probe towards all the cations is evident from the nM order of LOD values. This has been used in living cell imaging studies with the human neuroblastoma SH-SY5Y cell line. Having appended -CHO groups for Schiff-base condensation with other amines, HL-CHO could be a potential precursor for future chemosensors.

Identifying Breast Cancer Distant Recurrences from Electronic Health Records Using Machine Learning.

Accurately identifying distant recurrences in breast cancer from the Electronic Health Records (EHR) is important for both clinical care and secondary analysis. Although multiple applications have been developed for computational phenotyping in breast cancer, distant recurrence identification still relies heavily on manual chart review. In this study, we aim to develop a model that identifies distant recurrences in breast cancer using clinical narratives and structured data from EHR. We applied MetaMap to extract features from clinical narratives and also retrieved structured clinical data from EHR. Using these features, we trained a support vector machine model to identify distant recurrences in breast cancer patients. We trained the model using 1,396 double-annotated subjects and validated the model using 599 double-annotated subjects. In addition, we validated the model on a set of 4,904 single-annotated subjects as a generalization test. In the held-out test and generalization test, we obtained F-measure scores of 0.78 and 0.74, area under curve (AUC) scores of 0.95 and 0.93, respectively. To explore the representation learning utility of deep neural networks, we designed multiple convolutional neural networks and multilayer neural networks to identify distant recurrences. Using the same test set and generalizability test set, we obtained F-measure scores of 0.79 ± 0.02 and 0.74 ± 0.004, AUC scores of 0.95 ± 0.002 and 0.95 ± 0.01, respectively. Our model can accurately and efficiently identify distant recurrences in breast cancer by combining features extracted from unstructured clinical narratives and structured clinical data.

Using natural language processing and machine learning to identify breast cancer local recurrence.

BACKGROUND: Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local recurrences in breast cancer patients can reduce the time-consuming work of a manual chart review. METHODS: We design a novel concept-based filter and a prediction model to detect local recurrences using EHRs. In the training dataset, we manually review a development corpus of 50 progress notes and extract partial sentences that indicate breast cancer local recurrence. We process these partial sentences to obtain a set of Unified Medical Language System (UMLS) concepts using MetaMap, and we call it positive concept set. We apply MetaMap on patients' progress notes and retain only the concepts that fall within the positive concept set. These features combined with the number of pathology reports recorded for each patient are used to train a support vector machine to identify local recurrences. RESULTS: We compared our model with three baseline classifiers using either full MetaMap concepts, filtered MetaMap concepts, or bag of words. Our model achieved the best AUC (0.93 in cross-validation, 0.87 in held-out testing). CONCLUSIONS: Compared to a labor-intensive chart review, our model provides an automated way to identify breast cancer local recurrences. We expect that by minimally adapting the positive concept set, this study has the potential to be replicated at other institutions with a moderately sized training dataset.

Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird.

The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra finch. Genes involved in early developmental pathways including TGF-ß, BMP, and Wnt signaling, which have been shown to be involved in feather patterning, bone morphogenesis, and skeletal muscle development, revealed signs of adaptive evolution and provided useful clues on the phenotypes of peacock. Innate and adaptive immune genes involved in complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the predictions of the Hamilton-Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding toward the phenotypic evolution of Indian peacock.

Remarkable difference in Al3+ and Zn2+ sensing properties of quinoline based isomers.

Two positional isomers, 4-methyl-2-((quinolin-6-ylimino)methyl)phenol (6-QMP) and 4-methyl-2-((quinolin-2-ylimino)methyl)phenol (2-QMP), have been synthesized to compare their fluorescence sensing properties. 6-QMP and 2-QMP have been synthesized by Schiff-base condensation between 2-hydroxy-5-methylbenzaldehyde and the respective amine (6-aminoquinoline for 6-QMP and 2-aminoquinoline for 2-QMP) under mild conditions. These compounds have been characterized by standard methods. 6-QMP and 2-QMP have been found to be dual fluorescence chemosensors for Al3+ and Zn2+ ions but the increment of fluorescence intensity varies. 6-QMP can detect Al3+ (emission at 543 nm) and Zn2+ (emission at 525 nm) by the enhancement of emission intensity by 97 and 79 fold, respectively, with the same excitation wavelength at 415 nm. However, 2-QMP shows two different excitation and emission wavelengths for the detection of Al3+ (emission at 376 nm; λex = 330 nm) and Zn2+ (emission at 550 nm; λex = 435 nm). The increase in emission intensity is low (4.5 fold for Al3+ and 35 fold for Zn2+) compared to that with 6-QMP. The enhancement of intensity may be explained by the PET mechanism. Both the probes form a 1 : 1 complex with both the metal ions as indicated by the elemental and different spectral analysis. 6-QMP shows better sensitivity towards both the metal ions than 2-QMP. Both the probes are able to detect Al3+ and Zn2+ ions by producing distinct color changes that can be observed by the naked eye. Some theoretical calculations have been performed to investigate spectral transitions of the probes along with their aluminum and zinc compounds. These compounds have been used for living cell imaging studies. A comparison with the recently published studies has been made.

Potassium-regulated distal tubule WNK bodies are kidney-specific WNK1 dependent.

With-no-lysine (WNK) kinases coordinate volume and potassium homeostasis by regulating renal tubular electrolyte transport. In the distal convoluted tubule (DCT), potassium imbalance causes WNK signaling complexes to concentrate into large discrete foci, which we call "WNK bodies." Although these structures have been reported previously, the mechanisms that drive their assembly remain obscure. Here, we show that kidney-specific WNK1 (KS-WNK1), a truncated kinase-defective WNK1 isoform that is highly expressed in the DCT, is critical for WNK body formation. While morphologically distinct WNK bodies were evident in the distal tubules of mice subjected to dietary potassium loading and restriction, KS-WNK1 knockout mice were deficient in these structures under identical conditions. Combining in vivo observations in kidney with reconstitution studies in cell culture, we found that WNK bodies are dynamic membraneless foci that are distinct from conventional organelles, colocalize with the ribosomal protein L22, and cluster the WNK signaling pathway. The formation of WNK bodies requires an evolutionarily conserved cysteine-rich hydrophobic motif harbored within a unique N-terminal exon of KS-WNK1. We propose that WNK bodies are not pathological aggregates, but rather are KS-WNK1-dependent microdomains of the DCT cytosol that modulate WNK signaling during physiological shifts in potassium balance.

ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches.

The experimental methods for the prediction of molecular toxicity are tedious and time-consuming tasks. Thus, the computational approaches could be used to develop alternative methods for toxicity prediction. We have developed a tool for the prediction of molecular toxicity along with the aqueous solubility and permeability of any molecule/metabolite. Using a comprehensive and curated set of toxin molecules as a training set, the different chemical and structural based features such as descriptors and fingerprints were exploited for feature selection, optimization and development of machine learning based classification and regression models. The compositional differences in the distribution of atoms were apparent between toxins and non-toxins, and hence, the molecular features were used for the classification and regression. On 10-fold cross-validation, the descriptor-based, fingerprint-based and hybrid-based classification models showed similar accuracy (93%) and Matthews's correlation coefficient (0.84). The performances of all the three models were comparable (Matthews's correlation coefficient = 0.84-0.87) on the blind dataset. In addition, the regression-based models using descriptors as input features were also compared and evaluated on the blind dataset. Random forest based regression model for the prediction of solubility performed better (R2 = 0.84) than the multi-linear regression (MLR) and partial least square regression (PLSR) models, whereas, the partial least squares based regression model for the prediction of permeability (caco-2) performed better (R2 = 0.68) in comparison to the random forest and MLR based regression models. The performance of final classification and regression models was evaluated using the two validation datasets including the known toxins and commonly used constituents of health products, which attests to its accuracy. The ToxiM web server would be a highly useful and reliable tool for the prediction of toxicity, solubility, and permeability of small molecules.

Streptococcus pneumoniae TIGR4 Phase-Locked Opacity Variants Differ in Virulence Phenotypes.

Streptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity and which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization, whereas opaque variants are associated with invasive disease. In recent work, colony phase variation was shown to occur by means of recombination events to generate multiple alleles of the hsdS targeting domain of a DNA methylase complex, which mediates epigenetic changes in gene expression. A panel of isogenic strains were created in the well-studied S. pneumoniae TIGR4 background that are "locked" in the transparent (n = 4) or opaque (n = 2) colony phenotype. The strains had significant differences in colony size which were stable over multiple passages in vitro and in vivo. While there were no significant differences in adherence for the phase-locked mutant strains to immortalized epithelial cells, biofilm formation and viability were reduced for the opaque variants in static assays. Nasopharyngeal colonization was stable for all strains, but the mortality rates differed between them. Transcript profiling by transcriptome sequencing (RNA-seq) analyses revealed that the expression levels of certain virulence factors were increased in a phase-specific manner. As epigenetic regulation of phase variation (often referred to as "phasevarion") is emerging as a common theme for mucosal pathogens, these results serve as a model for future studies of host-pathogen interactions. IMPORTANCE A growing number of bacterial species undergo epigenetic phase variation due to variable expression or specificity of DNA-modifying enzymes. For pneumococci, this phase variation has long been appreciated as being revealed by changes in colony opacity, which are reflected in changes in expression or accessibility of factors on the bacterial surface. Recent work showed that recombination-generated variation in alleles of the HsdS DNA methylase specificity subunit mediated pneumococcal phase variation. We generated phase-locked populations of S. pneumoniae TIGR4 expressing a single nonvariant hsdS allele and observed significant differences in gene expression and virulence. These results highlight the importance of focused pathogenesis studies within specific phase types. Moreover, the generation of single-allele hsdS constructs will greatly facilitate such studies.

2-Hydroxy-naphthyl functionalized mesoporous silica for fluorescence sensing and removal of aluminum ions.

Mesoporous silica functionalized with a 2-hydroxy-naphthyl moiety has been synthesized and characterized by standard techniques like powder X-ray diffraction, N2 adsorption/desorption studies, transmission electron microscopy and spectral studies like FT-IR, UV-visible, fluorescence and 13C and 29Si solid state NMR. The functionalized silica material showed significant enhancement in its emission intensity in the presence of Al3+ ions whereas other metal ions could not bring about any increase in its emission intensity. They either quench the emission or do not alter the intensity significantly making the functionalized material a fluorescence chemosensor for Al3+. The sensitivity of the probe towards Al3+ has been determined to be high with a low limit of detection value. As functionalized silica is not soluble in common solvents, it has been effectively used to bind and remove Al3+ from a solution. Theoretical calculations on a model system have been performed to investigate the electronic spectral transitions.

Renal Tubular Ubiquitin-Protein Ligase NEDD4-2 Is Required for Renal Adaptation during Long-Term Potassium Depletion.

Adaptation of the organism to potassium (K+) deficiency requires precise coordination among organs involved in K+ homeostasis, including muscle, liver, and kidney. How the latter performs functional and molecular changes to ensure K+ retention is not well understood. Here, we investigated the role of ubiquitin-protein ligase NEDD4-2, which negatively regulates the epithelial sodium channel (ENaC), Na+/Cl- cotransporter (NCC), and with no-lysine-kinase 1 (WNK1). After dietary K+ restriction for 2 weeks, compared with control littermates, inducible renal tubular NEDD4-2 knockout (Nedd4LPax8/LC1 ) mice exhibited severe hypokalemia and urinary K+ wasting. Notably, expression of the ROMK K+ channel did not change in the distal convoluted tubule and decreased slightly in the cortical/medullary collecting duct, whereas BK channel abundance increased in principal cells of the connecting tubule/collecting ducts. However, K+ restriction also enhanced ENaC expression in Nedd4LPax8/LC1 mice, and treatment with the ENaC inhibitor, benzamil, reversed excessive K+ wasting. Moreover, K+ restriction increased WNK1 and WNK4 expression and enhanced SPAK-mediated NCC phosphorylation in Nedd4LPax8/LC1 mice, with no change in total NCC. We propose a mechanism in which NEDD4-2 deficiency exacerbates hypokalemia during dietary K+ restriction primarily through direct upregulation of ENaC, whereas increased BK channel expression has a less significant role. These changes outweigh the compensatory antikaliuretic effects of diminished ROMK expression, increased NCC phosphorylation, and enhanced WNK pathway activity in the distal convoluted tubule. Thus, NEDD4-2 has a crucial role in K+ conservation through direct and indirect effects on ENaC, distal nephron K+ channels, and WNK signaling.