Extraction of Value-Added Minerals from Various Agricultural,Industrial and Domestic Wastes

Environmental pollution is one of the major concerns throughout the world. The rise of industrialization has increased the generation of waste materials, causing environmental degradation and threat to the health of living beings. To overcome this problem and effectively handle waste materials, proper management skills are required. Waste as a whole is not only waste, but it also holds various valuable materials that can be used again. Such useful materials or elements need to be segregated and recovered using sustainable recovery methods. Agricultural waste, industrial waste, and household waste have the potential to generate different value-added products. More specifically, the industrial waste like fly ash, gypsum waste, and red mud can be used for the recovery of alumina, silica, and zeolites. While agricultural waste like rice husks, sugarcane bagasse, and coconut shells can be used for recovery of silica, calcium, and carbon materials. In addition, domestic waste like incense stick ash and eggshell waste that is rich in calcium can be used for the recovery of calcium-related products. In agricultural, industrial, and domestic sectors, several raw materials are used; therefore, it is of high economic interest to recover valuable minerals and to process them and convert them into merchandisable products. This will not only decrease environmental pollution, it will also provide an environmentally friendly and cost-effective approach for materials synthesis. These value-added materials can be used for medicine, cosmetics, electronics, catalysis, and environmental cleanup.     

Opening of a cryptic pocket in β-lactamase increases penicillinase activity

Understanding the functional role of protein-excited states has important implications in protein design and drug discovery. However, because these states are difficult to find and study, it is still unclear if excited states simply result from thermal fluctuations and generally detract from function or if these states can actually enhance protein function. To investigate this question, we consider excited states in β-lactamases and particularly a subset of states containing a cryptic pocket which forms under the Ω-loop. Given the known importance of the Ω-loop and the presence of this pocket in at least two homologs, we hypothesized that these excited states enhance enzyme activity. Using thiol-labeling assays to probe Ω-loop pocket dynamics and kinetic assays to probe activity, we find that while this pocket is not completely conserved across β-lactamase homologs, those with the Ω-loop pocket have a higher activity against the substrate benzylpenicillin. We also find that this is true for TEM β-lactamase variants with greater open Ω-loop pocket populations. We further investigate the open population using a combination of NMR chemical exchange saturation transfer experiments and molecular dynamics simulations. To test our understanding of the Ω-loop pocket’s functional role, we designed mutations to enhance/suppress pocket opening and observed that benzylpenicillin activity is proportional to the probability of pocket opening in our designed variants. The work described here suggests that excited states containing cryptic pockets can be advantageous for function and may be favored by natural selection, increasing the potential utility of such cryptic pockets as drug targets.

While it is well established that proteins are dynamic molecules (1), it is often unclear what these dynamics mean for function. An experimentally derived structural snapshot of a protein, such as a crystal structure, is frequently assumed to represent the (highest probability, lowest energy) ground state. This snapshot is also frequently assumed to be the functional state of the protein. In fact, rigidifying the active site or increasing the probability of the ground-state conformation is often used as a design strategy for improving catalytic activity (2, 3). In opposition to this common assumption, there are several compelling examples of functionally relevant excited states (4–9). However, it is still unclear if excited states in general play a role in function.Here, we consider an important class of excited states that contain a “cryptic” pocket, or a pocket which is absent in the ligand-free, experimentally determined structure(s). These states are of particular interest because of the potential utility of cryptic pockets as drug targets (10). These pockets provide a means to drug otherwise “undruggable” proteins and a means to enhance a desired protein activity rather than just inhibit an undesired one (11, 12). One concern, however, with the use of cryptic pockets as drug targets is that it is uncertain if there is a selective pressure to maintain the existence of a given pocket or if drug binding to that pocket could be trivially evolved away. This is at least partially because it is unknown if excited states containing cryptic pockets are simply a byproduct of the dynamic nature of proteins or if they play a bigger role in protein function.Despite the many examples of systems which are known to contain cryptic pockets (13–15), their functional relevance remains unclear because these pockets are notoriously difficult to find and study. Identification of a cryptic pocket often requires simultaneous discovery of a ligand that binds to it (16). Fortunately, recent advances in computational and experimental tools allow us to better identify and study these pockets (1, 17). To increase sampling during molecular dynamics simulations, adaptive sampling methods like fluctuation amplification of specific traits (FAST) (18) and replica exchange methods like sampling water interfaces through scaled Hamiltonians (SWISH) (19) have been developed. To analyze these datasets, methods such as Markov state models (MSMs) (20) and exposons (21) have been developed. These computational tools can then be used to inform experimental methods like room temperature crystallography (22), NMR relaxation techniques (23–25), and thiol-labeling assays (26). Previous work using these methods has shown that many different kinds of proteins have cryptic pockets and that these pockets can be targeted with drugs to allosterically affect functional sites (11, 12, 27, 28). However, it is still unclear if cryptic pockets have implications for function in the absence of ligand binding.To explore the functional relevance of excited states containing cryptic pockets, we consider a set of class A β-lactamases. β-lactamases are enzymes that confer bacteria with antibiotic resistance by hydrolyzing β-lactam antibiotics such as benzylpenicillin and cefotaxime. TEM β-lactamase in particular is an established model system for studying cryptic pockets. TEM has two known and well-characterized cryptic pockets. The first, which was found serendipitously during a drug-screening campaign, is between helices 11 and 12 (16). The second, which was more recently identified in our laboratory (21), forms when the Ω-loop undocks from the protein, so we call this pocket the Ω-loop pocket (Fig. 1). The Ω-loop pocket was discovered in molecular dynamics simulations, confirmed using thiol-labeling experiments, and subsequently shown to exert control over catalysis at the adjacent active site (21). We know the Ω-loop structure is important as it is necessary for the deacylation of β-lactam antibiotics (29), and it has been previously shown that changes in Ω-loop conformations are connected to cefotaxime activity (30, 31).Open in a separate windowFig. 1.The Ω-loop pocket seen in TEM may open in other β-lactamase homologs. The structures of four β-lactamase homologs (Left) overlay well. TEM (Protein Data Base [PDB]: 1xpb) is shown in green, CTX-M-9 (PDB: 1ylj) is shown in cyan, MTB (PDB: 2gdn) is shown in orange, and GNCA (PDB: 4b88) is shown in magenta. The open Ω-loop pocket structure in TEM (Right) was identified in molecular dynamics simulations.As we have also found that the Ω-loop pocket is present in CTX-M-9 β-lactamase (21), we hypothesize that this pocket may play a role in the enzyme’s function. To test this hypothesis, we first examine if the Ω-loop pocket is conserved across β-lactamase homologs and if the presence of the pocket is correlated with increased activity against classic β-lactam substrates. Here, we mean conservation of the phenomenon of cryptic pocket opening rather than conservation of the specific amino acid identities in that region of the protein. We then use activity data for TEM variants and combine NMR with molecular dynamics to gain insight into how the open Ω-loop pocket affects the hydrolysis reaction for different substrates. Finally, we design mutations to modulate the population of the open Ω-loop pocket to explicitly test whether pocket dynamics are predictive of enzymatic activity.     

Relation of urinary endothelin-1 to stress-induced pressure natriuresis in healthy adolescents

We hypothesize that delayed natriuresis during mental stress increases the risk of hypertension and other diseases. Our preclinical studies demonstrate an important role for renal endothelin-1 (ET-1) in regulating sodium excretion. Thus, we predict ET-1 may be linked to the delayed stress response in at-risk individuals. We hypothesize that reduced renal ET-1 accounts for derangements in sodium handling under stress, a link never explored in a large human cohort. We determined urinary ET-1 excretion in three observational studies of changes in sodium excretion during mental stress, in which 776 healthy youth (15–19 years) enrolled in a 5-hour protocol (2 hours of rest before and after 1 hour of mental stress). In all studies, 60-minute urine samples were obtained throughout the protocol. Subjects were grouped as retainers (reduced sodium excretion during stress relative to baseline) or excreters (increased sodium excretion during stress relative to baseline). In excreters, ET-1 excretion was significantly increased from baseline to stress (+0.02 pg/min; P < .001). In contrast, ET-1 excretion was significantly higher (P = .028) in retainers than excreters at baseline but significantly reduced in retainers under stress (?0.02 pg/min; P < .001). ET-1 excretion declined further in retainers during recovery but returned to prestress levels in excreters. Albumin excretion and albumin-to-creatinine ratio were significantly higher in retainers (P = .022, P < .001, respectively). Thus, loss of ET-1–dependent natriuresis may account for sodium retention during stress and may predispose retainers to renal diseases such as hypertension and kidney disease.     

Three-Dimensional Anorectal Manometry Enhances Diagnostic Gain by Detecting Sphincter Defects and Puborectalis Pressure

Digestive Diseases and Sciences - Constipation and fecal incontinence (FI) are common and are often evaluated with anorectal manometry. Three-dimensional high-resolution anorectal manometry (HRAM)...     

Targeting the PI3K/Akt signaling pathway in gastric carcinoma: A reality for personalized medicine?

Frequent activation of phosphatidylinositol-3 kinases (PI3K)/Akt/mTOR signaling pathway in gastric cancer (GC) is gaining immense popularity with identification of mutations and/or amplifications of PIK3CA gene or loss of function of PTEN, a tumor suppressor protein, to name a few; both playing a crucial role in regulating this pathway. These aberrations result in dysregulation of this pathway eventually leading to gastric oncogenesis, hence, there is a need for targeted therapy for more effective anticancer treatment. Several inhibitors are currently in either preclinical or clinical stages for treatment of solid tumors like GC. With so many inhibitors under development, further studies on predictive biomarkers are needed to measure the specificity of any therapeutic intervention. Herein, we review the common dysregulation of PI3K/Akt/mTOR pathway in GC and the various types of single or dual pathway inhibitors under development that might have a superior role in GC treatment. We also summarize the recent developments in identification of predictive biomarkers and propose use of predictive biomarkers to facilitate more personalized cancer therapy with effective PI3K/Akt/mTOR pathway inhibition.     

The Window Matters: A Systematic Review of Time Restricted Eating Strategies in Relation to Cortisol and Melatonin Secretion

Time-Restricted Eating is an eating pattern based on the circadian rhythm which limits daily food intake (usually to ≤12 h/day), unique in that no overt restriction is imposed on the quality, nor quantity, of food intake. This paper aimed to examine the effects of two patterns of TRE, traditional TRE, and Ramadan fasting, on two markers of circadian rhythm, cortisol and melatonin. PubMed and Web of Science were searched up to December 2020 for studies examining the effects of time restricted eating on cortisol and melatonin. Fourteen studies met our inclusion criteria. All Ramadan papers found statistically significant decrease in melatonin (p < 0.05) during Ramadan. Two out of the three Ramadan papers noted an abolishing of the circadian rhythm of cortisol (p < 0.05). The non-Ramadan TRE papers did not examine melatonin, and cortisol changes were mixed. In studies comparing TRE to control diets, Stratton et al. found increased cortisol levels in the non-TRE fasting group (p = 0.0018) and McAllister et al. noted no difference. Dinner-skipping resulted in significantly reduced evening cortisol and non-significantly raised morning cortisol. Conversely, breakfast skipping resulted in significantly reduced morning cortisol. This blunting indicates a dysfunctional HPA axis, and may be associated with poor cardio-metabolic outcomes. There is a paucity of research examining the effects of TRE on cortisol and melatonin. The contrasting effect of dinner and breakfast-skipping should be further examined to ascertain whether timing the feeding window indeed has an impact on circadian rhythmicity.     

Interactions between tumor cells and microenvironment in breast cancer: a new opportunity for targeted therapy

Breast cancer remains the leading cause of morbidity and second-leading cause of death in women. Despite efforts to uncover new targeted therapies, a vast number of women die due to refractory or recurrent breast tumors. Most breast cancer studies have focused on the intrinsic characteristics of breast tumor cells, including altered growth, proliferation, and metabolism. However, emerging research suggests that the tumor microenvironment can substantially affect relapse rates and therapeutic responses. In this review, we discuss the interactions between the tumor and microenvironment in breast cancer, with regard to mutational profiles and altered metabolism that could serve as potential therapeutic targets. We also describe current technologies available to study these interactions.     

Elevated level of prostate specific antigen among prostate cancer patients and high prevalence in the Gangetic zone of Bihar, India

Prostate cancer (CaP) is a common reproductive cancer among men. This study was conducted to correlate the cancer incidence with Gangetic zone and to correlate the tumor marker prostate specific antigen (PSA) level in serum with different age groups and stage of malignancy. Patients suffering from CaP in the pathology unit of Mahavir Cancer Sansthan (Hospital and Research Centre), Patna, Bihar, India were studied from June 2009 to May 2010. PSA level in the serum of CaP patients was estimated by ELISA method. CaP incidence was highly recorded in Gangetic zone than the non-Gangetic zone. Maximum patients were in the 56 - 75 years age group with a marked predominance. Results of PSA examination showed that serum PSA level was not correlating with the age of patient and stage of malignancy. Significantly, elevated level of more than 10 ng/ml of PSA was recorded among the studied cancer patients. In this study, it is concluded that Gangetic zone habitat have high risk of CaP and elevated level of PSA was marked in Bihar, India.     

Comparative study of final visual outcome between open- and closed-globe injuries following surgical treatment of traumatic cataract

Objective  

The objective of this work is to compare final visual outcomes in cases of surgically treated traumatic cataract between open-globe and closed-globe groups, as classified by the Birmingham Eye Trauma Terminology system.