Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.     

High Capacity and High‐Rate NASICON‐Na3.75V1.25Mn0.75(PO4)3 Cathode for Na‐Ion Batteries via Modulating Electronic and Crystal Structures

Sodium superionic conductor (NASICON) cathodes are attractive for Na‐ion battery applications as they exhibit both high structural stability and high sodium ion mobility. Herein, a comprehensive study is presented on the structural and electrochemical properties of the NASICON‐Na_3+yV_2?yMn_y(PO₄)₃ (0 ≤ y ≤ 1) series. A phase miscibility gap is observed at y = 0.5, defining two solid solution domains with low and high Mn contents. Although, members of each of these domains Na_3.25V_1.75Mn_0.25(PO₄)₃ and Na_3.75V_1.25Mn_0.75(PO₄)₃ reversibly exchange sodium ions with high structural integrity, the activity of the Mn³⁺/Mn²⁺ redox couple is found to be absent and present in the former and latter candidate, respectively. Galvanostatic cycling and rate studies reveal higher capacity and rate capability for the Na_3.75V_1.25Mn_0.75(PO₄)₃ cathode (100 and 89 mA h g^?1 at 1C and 5C rate, respectively) in the Na_3+yV_2?yMn_y(PO₄)₃ series. Such a remarkable performance is attributed to optimum bottleneck size (≈5 Ų) and modulated V‐ and Mn‐redox centers as deduced from Rietveld analysis and DFT calculations, respectively. This study shows how important it is to manipulate electronic and crystal structures to achieve high‐performance NASICON cathodes.     

Resveratrol and black tea polyphenol combination synergistically suppress mouse skin tumors growth by inhibition of activated MAPKs and p53

Cancer chemoprevention by natural dietary agents has received considerable importance because of their cost-effectiveness and wide safety margin. However, single agent intervention has failed to bring the expected outcome in clinical trials; therefore, combinations of chemopreventive agents are gaining increasing popularity. The present study aims to evaluate the combinatorial chemopreventive effects of resveratrol and black tea polyphenol (BTP) in suppressing two-stage mouse skin carcinogenesis induced by DMBA and TPA. Resveratrol/BTP alone treatment decreased tumor incidence by ～67% and ～75%, while combination of both at low doses synergistically decreased tumor incidence even more significantly by ～89% (p<0.01). This combination also significantly regressed tumor volume and number (p<0.01). Mechanistic studies revealed that this combinatorial inhibition was associated with decreased expression of phosphorylated mitogen-activated protein kinase family proteins: extracellular signal-regulated kinase 1/2, c-Jun N-terminal kinase 1/2, p38 and increased in total p53 and phospho p53 (Ser 15) in skin tissue/tumor. Treatment with combinations of resveratrol and BTP also decreased expression of proliferating cell nuclear antigen in mouse skin tissues/tumors than their solitary treatments as determined by immunohistochemistry. In addition, histological and cell death analysis also confirmed that resveratrol and BTP treatment together inhibits cellular proliferation and markedly induces apoptosis. Taken together, our results for the first time lucidly illustrate that resveratrol and BTP in combination impart better suppressive activity than either of these agents alone and accentuate that development of novel combination therapies/chemoprevention using dietary agents will be more beneficial against cancer. This promising combination should be examined in therapeutic trials of skin and possibly other cancers.     

Expanded roles for multicargo and class 1B effector chaperones in type III secretion

Bacterial type III secretion systems (T3SS) are complex protein assemblies that mediate the secretion of protein substrates outside the cell. Type III secretion chaperones (T3SC) are always found associated with T3SS, and they serve in multiple roles to ensure that protein substrates are efficiently targeted for secretion. Bacterial pathogens with T3SS express T3SC proteins that bind effectors, a process important for effector protein delivery into eukaryotic cells during infection. In this minireview, we focus on multicargo and class 1B T3SC that associate with effectors within significant pathogens of animals and plants. As a primary role, multicargo and class 1B T3SC form homodimers and specifically bind different effectors within the cytoplasm, maintaining the effectors in a secretion-competent state. This role makes T3SC initial and central contributors to effector-mediated pathogenesis. Recent findings have greatly expanded our understanding of cellular events linked to multicargo T3SC function. New binding interactions with T3SS components have been reported in different systems, thereby implicating multicargo T3SC in critical roles beyond effector binding. Three notable interactions with the YscN, YscV, and YscQ family members are well represented in the literature. Similar T3SC interactions are reported in the putative related flagellar T3SS, suggesting that secretion mechanisms may be more similar than previously thought. The evidence implicates multicargo and class 1B T3SC in effector binding and stabilization, in addition to T3SS recruitment and docking events.     

Functional and Complementary Phosphorylation State Attributes of Human Insulin-like Growth Factor-Binding Protein-1 (IGFBP-1) Isoforms Resolved by Free Flow Electrophoresis

Fetal growth restriction (FGR) is a common disorder in which a fetus is unable to achieve its genetically determined potential size. High concentrations of insulin-like growth factor-binding protein-1 (IGFBP-1) have been associated with FGR. Phosphorylation of IGFBP-1 is a mechanism by which insulin-like growth factor-I (IGF-I) bioavailability can be modulated in FGR. In this study a novel strategy was designed to determine a link between IGF-I affinity and the concomitant phosphorylation state characteristics of IGFBP-1 phosphoisoforms. Using free flow electrophoresis (FFE), multiple IGFBP-1 phosphoisoforms in amniotic fluid were resolved within pH 4.43–5.09. The binding of IGFBP-1 for IGF-I in each FFE fraction was determined with BIAcore biosensor analysis. The IGF-I affinity (K) for different IGFBP-1 isoforms ranged between 1.12e−08 and 4.59e−07. LC-MS/MS characterization revealed four phosphorylation sites, Ser(P)⁹⁸, Ser(P)¹⁰¹, Ser(P)¹¹⁹, and Ser(P)¹⁶⁹, of which Ser(P)⁹⁸ was new. Although the IGF-I binding affinity for IGFBP-1 phosphoisoforms across the FFE fractions did not correlate with phosphopeptide intensities for Ser(P)¹⁰¹, Ser(P)⁹⁸, and Ser(P)¹⁶⁹ sites, a clear association was recorded with Ser(P)¹¹⁹. Our data demonstrate that phosphorylation at Ser¹¹⁹ plays a significant role in modulating affinity of IGFBP-1 for IGF-I. In addition, an altered profile of IGFBP-1 phosphoisoforms was revealed between FGR and healthy pregnancies that may result from potential site-specific phosphorylation. This study provides a strong basis for use of this novel approach in establishing the linkage between phosphorylation of IGFBP-1 and FGR. This overall strategy will also be broadly applicable to other phosphoproteins with clinical and functional significance.The insulin-like growth factor (IGF)¹ axis plays an important role in human fetal growth and development. Insulin-like growth factor-binding protein-1 (IGFBP-1) is a major IGF-binding protein in amniotic fluid (AF) (1, 2). The physiological role of IGFBP-1 is considered to be highly dependent on its differential phosphorylation (3–5). Phosphorylation of IGFBP-1 increases its affinity for IGF-I (6), suggesting that IGFBP-1 may modulate the action of IGF-I specifically with respect to fetal and placental growth (4, 7).AF is a dynamic and complex biofluid and reflects the physiological status of the developing fetus (8). Fetal growth restriction (FGR) is a condition in which a fetus is unable to achieve its genetically determined potential size. The concentration of total IGFBP-1 is increased in FGR (9–12). Multiple phosphorylated species of IGFBP-1 have been detected during healthy pregnancy in both maternal circulation and in AF throughout gestation (1, 13, 14). Several studies have considered the clinical implications of IGFBP-1 phosphorylation, focusing on correlating variable ratios of high to low concentrations of IGFBP-1 phosphoisoforms with fetal outcome in FGR pregnancies (15–19). Although phosphorylation of IGFBP-1 has since been suggested to be critical, the predictive or functional value of IGFBP-1 phosphorylation in FGR is still not clear. The inconsistency in measurements of variable degrees of IGFBP-1 phosphorylation by ELISAs has resulted in inconclusive findings (20).IGFBP-1 phosphoisoforms have been characterized previously using conventional methods (1, 13, 14). IGFBP-1, although relatively abundant in AF, still represents less than 0.01% of the total protein content (21). With restricted volumes available from clinical samples, isolation of functional IGFBP-1 phosphoisoforms using traditional approaches (13, 22, 23) is challenging. Our goal is to obtain a comprehensive understanding of the clinical and functional implications of IGFBP-1 phosphorylation in human FGR pregnancies. We developed an efficient, reproducible, and entirely liquid-based native IEF separation technology based on free flow electrophoresis (FFE) (24) to facilitate characterization of both the state of phosphorylation and IGF-I binding kinetics of variably phosphorylated IGFBP-1 isoforms in a clinical sample. As a prerequisite to application of this approach clinically, we also evaluated representative AF samples to determine whether or not differential patterns of IGFBP-1 phosphorylation exist in FGR and whether these changes could be attributed to augmentation of IGF-I affinity in the disease.     

Gender differences in self-reported constipation characteristics,symptoms, and bowel and dietary habits among patients attending a specialty clinic for constipation

Objectives: This study assessed gender differences in the frequency of various characteristics of constipation, constipation-specific symptoms, and bowel and dietary habits, as well as the effects of independent but associated risk factors.Methods: A cross-sectional study of patients aged ≥18 years with a primary diagnosis of constipation (ie, constipation, slow-transit constipation, outlet dysfunction constipation) was conducted at a tertiary referral center; patients were excluded if they had a primary diagnosis of fecal incontinence. Patients completed both a clinical questionnaire to obtain information on demographic characteristics and medical history and an unvalidated self-report questionnaire relating to the characteristics and symptoms of constipation as well as various bowel and dietary habits. Likert scales were used to assess 4 characteristics of constipation (frequency of constipation, duration of constipation symptoms of ≥1 month, bowel movement frequency, stool consistency) and the frequency of occurrence of 6 constipation symptoms (abdominal pain, abdominal bloating, incomplete evacuation, unsuccessful attempts at evacuation, pain with evacuation, straining with evacuation). The bowel habits that were evaluated included time spent at each evacuation; frequency of needing to change position to evacuate; use of anal digitation to evacuate; and the use of laxatives, enemas, stool softeners, foods, drinks, or other aids. The dietary habits that were evaluated included use of dietary fiber, use of fiber supplements, and water intake.Results: Of the 518 patients, the majority were female (79.0%), white (76.3%), and employed (62.0%), with a mean (SD) age of 52.4 (16.5) years (range, 18.6–91.5 years). After controlling for a number of related conditions, women were more likely than men to have infrequent bowel movements (adjusted odds ratio [AOR] = 2.97; 95% CI, 1.67–5.28), abnormal stool consistency (ie, hard or pelletlike stools) (AOR = 3.08; 95% CI, 1.80–5.28), and a longer duration of constipation symptoms (AOR = 2.00; 95% CI, 1.05–3.82). In addition, women were more likely to report an increased frequency of occurrence of abdominal pain (AOR = 2.22; 95% CI, 1.22–4.05), bloating (AOR = 2.65; 95% CI, 1.50–4.70), unsuccessful attempts at evacuation (AOR = 1.74; 95% CI, 1.01–3.00), and the use of anal digitation to evacuate stool (AOR = 3.37; 95% CI, 1.15–9.90).Conclusions: The women in this specialty-based clinic study experienced a number of constipation symptoms and abnormal bowel habits more frequently than did men. These findings warrant replication in both population- and specialty clinic-based samples. In addition, the physiologic mechanisms that underlie these gender differences warrant investigation.     

Poly-β-hydroxybutyrate accumulation in cyanobacteria under photoautotrophy

Poly-β-hydroxybutyrate (PHB) is a biodegradable and biocompatible polymer that has immense potential in the field of environmental, agricultural and biomedical sciences. An alternative host system has been explored in this study for low-cost production. Examination of 25 cyanobacterial species from 19 different genera for photoautrophic production of polyhydroxyalkanoates (PHAs) under batch culture demonstrated that 20 species were poly-β-hydroxybutyrate (PHB) accumulators, while others were found to be negative. Presence of PHB was confirmed by UV-spectroscopy, (1)H-NMR spectroscopy and GC-MS analysis. Accumulation of PHB in cyanobacteria was found to be species specific. The PHB extracted from Nostoc muscorum exhibited comparable material properties with the commercial PHB, thus advocating its potential applications in various fields.     

Differential specificity in water imbibition of indian arid zone seeds

Studies on seeds of 40 arid zone plant species have revealed that seeds exhibit differential specificity in water inhibition percentage. Most of these seeds show very poor imbibition capacity and that takes place within the first three hours, after which this uptake becomes very slow. This low hydrature and quick water uptake wherever it takes place is correlated with the erratic rainfall in the Indian arid zone. Most of the leguminous seeds are impermeable to water because of hard seed coatedness. However, those seeds which imbibed showed a very high percentage of water uptake.