Elucidating photocycle in large Stokes shift red fluorescent proteins: Focus on mKeima.

Large Stokes shift red fluorescent proteins (LSS-RFPs) are genetically encoded and exhibit a significant difference of a few hundreds of nanometers between their excitation and emission peak maxima (i.e., the Stokes shift). These LSS-RFPs (absorbing blue light and emitting red light) feature a unique photocycle responsible for their significant Stokes shift. The photocycle associated with this LSS characteristic in certain RFPs is quite perplexing, hinting at the complex nature of excited-state photophysics. This article provides a brief review on the fundamental mechanisms governing the photocycle of various LSS-RFPs, followed by a discussion on experimental results on mKeima emphasizing its relaxation pathways which garnered attention due to its >200 nm Stokes shift. Corroborating steady-state spectroscopy with computational studies, four different forms of chromophore of mKeima contributing to the cis-trans conformers of the neutral and anionic forms were identified in a recent study. Furthering these findings, in this account a detailed discussion on the photocycle of mKeima, which encompasses sequential excited-state isomerization, proton transfer, and subsequent structural reorganization involving three isomers, leading to an intriguing temperature and pH-dependent dual fluorescence, is explored using broadband femtosecond transient absorption spectroscopy.

Vibrio parahaemolyticus thermostable direct haemolysin induces non-classical programmed cell death despite caspase activation.

Thermostable direct haemolysin (TDH) is the key virulence factor secreted by the human gastroenteric bacterial pathogen Vibrio parahaemolyticus. TDH is a membrane-damaging pore-forming toxin. It evokes potent cytotoxicity, the mechanism of which still remains under-explored. Here, we have elucidated the mechanistic details of cell death response elicited by TDH. Employing Caco-2 intestinal epithelial cells and THP-1 monocytic cells, we show that TDH induces some of the hallmark features of apoptosis-like programmed cell death. TDH triggers caspase-3 and 7 activations in the THP-1 cells, while caspase-7 activation is observed in the Caco-2 cells. Interestingly, TDH appears to induce caspase-independent cell death. Higher XIAP level and lower Smac/Diablo level upon TDH intoxication provide plausible explanation for the functional inability of caspases in the THP-1 cells, in particular. Further exploration reveals that mitochondria play a central role in the TDH-induced cell death. TDH triggers mitochondrial damage, resulting in the release of AIF and endonuclease G, responsible for the execution of caspase-independent cell death. Among the other critical mediators of cell death, ROS is found to play an important role in the THP-1 cells, while PARP-1 appears to play a critical role in the Caco-2 cells. Altogether, our work provides critical new insights into the mechanism of cell death induction by TDH, showing a common central theme of non-classical programmed cell death. Our study also unravels the interplay of crucial molecules in the underlying signalling processes. Our findings add valuable insights into the role of TDH in the context of the host-pathogen interaction processes.

Early and Effective Diagnosis of Sepsis Using Flow Cytometry.

Objective Sepsis is a major global health issue due to its high death and morbidity rates. To avoid the negative effects of sepsis and decrease mortality, it is vital to diagnose and treat it as soon as possible. Blood cultures can take up to 2 days to give result, and they are not always reliable. According to recent studies, neutrophil CD64 expression might be a sensitive and specific option for assessing sepsis. This study aimed to evaluate the diagnostic performance of a flow cytometry analysis for the expression of neutrophil CD64 in sepsis and its comparison with other standard tests in a tertiary care center. Materials and Methods Prospective analysis on 40 blood samples from suspected sepsis patients admitted to intensive care units with criteria for the systemic inflammatory response syndrome on presentation was performed for expression of neutrophil CD64, C-reactive protein, procalcitonin, and complete blood count. Ten healthy volunteers were also enrolled in this prospective study. The laboratory results were compared in different groups. Results The neutrophil CD64 had the highest diagnostic value to differentiate between patients of sepsis and nonsepsis groups with a sensitivity of 100% (95% confidence interval [CI]: 77.19-100%) and 100% (95% CI: 55.32-86.83%); specificity of 90.00% (95% CI: 59.58-99.49%) and 87.24% (95% CI: 66.69-99.61%); and likelihood ratio of 10.00 and 7.84, respectively. Conclusion The neutrophil CD64 expression provides a more sensitive, specific, and novel marker for the early detection of sepsis in critically ill patients.

Unveiling the Role of Hidden Isomers in Large Stokes Shift in mKeima: Harnessing pH-Sensitive Dual-Emission in Bioimaging.

Elucidating the origin of large Stokes shift (LSS) in certain fluorescent proteins absorbing in blue/blue-green and emitting in red/far-red has been quite illusive. Using a combination of spectroscopic measurements, corroborated by theoretical calculations, the presence of four distinct forms of the chromophore of the red fluorescent protein mKeima is confirmed, two of which are found to be emissive: a feeble bluish-green fluorescence (∼520 nm), which is enhanced appreciably in a low pH or deuterated medium but significantly at cryogenic temperatures, and a strong emission in red (∼615 nm). Using femtosecond transient absorption spectroscopy, the trans-protonated form is found to isomerize within hundreds of femtoseconds to the cis-protonated form, which further yields the cis-deprotonated form within picoseconds followed by structural reorganization of the local environment of the chromophore. Thus, the mechanism of LSS is substantiated to proceed via stepwise excited-state isomerization followed by proton transfer involving three isomers, leaving the fourth one (trans-deprotonated) as a bystander. The exquisite pH sensitivity of the dual emission is further exploited in fluorescence microscopy.

Histological Spectrum of Post Covid Debridement Tissues: Salient Histomorphological Features With Respect to Identification Fungal Elements.

Background: Secondary bacterial and fungal infections in COVID patients have been documented during current pandemic. The present study provides detailed account of histomorphology of debridement tissue received for suspected fungal infections. The primary objective was to determine the morphological characteristics that must be recognized for the identification of fungal hyphae. Methods: The detailed histological examination of debridement tissue was performed. Demographic and clinical findings with treatment provided was recorded. Presence or absence of necrosis and lecocytoclasis was noted. Results: A total of 110 cases of debrided tissues were included in the study. Eosinophilic granular necrosis with lecocytoclasis was observed in 103cases; fungal elements were identified in 89.3% (92/103) of these. Eleven cases where necrosis was observed, strong suspicion of fungus was reported, 6 of them displayed fungus on KOH preparation, 3 on repeat biopsy. However, in 2 of these cases, neither KOH nor repeat biopsies identified the fungus. Mucor with aspergillus was observed in 7 cases and actinomyces in 3. In all these 10 cases dense fungal colonies were evident. In 7 cases careful observation revealed fruiting bodies of aspergillus. Cotton ball appearance of actinomyces was evident. Mucor infection in current disease was so rampant that aseptate ribbon like branching mucor hyphae were evident on H&E sections. Diabetes was significantly associated with fungal infection (97.2%; 70/72; P < .005). 90% [19/21] of the patients who were on room air and diagnosed with fungal infection were diabetic. Conclusions: Eosinophilic granular necrosis with the presence of neutrophilic debris in a case of suspected fungal disease suggests the presence of fungal elements. This warrants processing of the entire tissue deposited for examination, careful observation, application of fungal stains, and repeat biopsy if clinical suspicion is strong. Moreover, uncontrolled diabetes is more frequently associated with secondary fungal infection in COVID patients as compared to oxygen therapy.

Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Sesamum indicum L.).

Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development.

Pore formation-independent cell death induced by a ß-barrel pore-forming toxin.

Vibrio cholerae cytolysin (VCC) is a ß-barrel pore-forming toxin (ß-PFT). It exhibits potent hemolytic activity against erythrocytes that appears to be a direct outcome of its pore-forming functionality. However, VCC-mediated cell-killing mechanism is more complicated in the case of nucleated mammalian cells. It induces apoptosis in the target nucleated cells, mechanistic details of which are still unclear. Furthermore, it has never been explored whether the ability of VCC to trigger programmed cell death is stringently dependent on its pore-forming activity. Here, we show that VCC can evoke hallmark features of the caspase-dependent apoptotic cell death even in the absence of the pore-forming ability. Our study demonstrates that VCC mutants with abortive pore-forming hemolytic activity can trigger apoptotic cell death responses and cytotoxicity, similar to those elicited by the wild-type toxin. VCC as well as its pore formation-deficient mutants display prominent propensity to translocate to the target cell mitochondria and cause mitochondrial membrane damage. Therefore, our results for the first time reveal that VCC, despite being an archetypical ß-PFT, can kill target nucleated cells independent of its pore-forming functionality. These findings are intriguing for a ß-PFT, whose destination is generally expected to remain limited on the target cell membranes, and whose mode of action is commonly attributed to the membrane-damaging pore-forming ability. Taken together, our study provides critical new insights regarding distinct implications of the two important virulence functionalities of VCC for the V. cholerae pathogenesis process: hemolytic activity for iron acquisition and cytotoxicity for tissue damage by the bacteria.

Current Perspective on the Membrane-Damaging Action of Thermostable Direct Hemolysin, an Atypical Bacterial Pore-forming Toxin.

Thermostable direct hemolysin (TDH) is the major virulence determinant of the gastroenteric bacterial pathogen Vibrio parahaemolyticus. TDH is a membrane-damaging pore-forming toxin (PFT). TDH shares remarkable structural similarity with the actinoporin family of eukaryotic PFTs produced by the sea anemones. Unlike most of the PFTs, it exists as tetramer in solution, and such assembly state is crucial for its functionality. Although the structure of the tetrameric assembly of TDH in solution is known, membrane pore structure is not available yet. Also, the specific membrane-interaction mechanisms of TDH, and the exact role of any receptor(s) in such process, still remain unclear. In this mini review, we discuss some of the unique structural and physicochemical properties of TDH, and their implications for the membrane-damaging action of the toxin. We also present our current understanding regarding the membrane pore-formation mechanism of this atypical bacterial PFT.

Pore-forming toxins in infection and immunity.

The integrity of the plasma membranes is extremely crucial for the survival and proper functioning of the cells. Organisms from all kingdoms of life employ specialized pore-forming proteins and toxins (PFPs and PFTs) that perforate cell membranes, and cause detrimental effects. PFPs/PFTs exert their damaging actions by forming oligomeric pores in the membrane lipid bilayer. PFPs/PFTs play important roles in diverse biological processes. Many pathogenic bacteria secrete PFTs for executing their virulence mechanisms. The immune system of the higher vertebrates employs PFPs to kill pathogen-infected cells and transformed cancer cells. The most obvious consequence of membrane pore-formation by the PFPs/PFTs is the killing of the target cells due to the disruption of the permeability barrier function of the plasma membranes. PFPs/PFTs can also activate diverse cellular processes that include activation of the stress-response pathways, induction of programmed cell death, and inflammation. Upon attack by the PFTs, host cells may also activate pathways to repair the injured membranes, restore cellular homeostasis, and trigger inflammatory immune responses. In this article, we present an overview of the diverse cellular responses that are triggered by the PFPs/PFTs, and their implications in the process of pathogen infection and immunity.

Sequence Diversity in the Pore-Forming Motifs of the Membrane-Damaging Protein Toxins.

Pore-forming proteins/toxins (PFPs/PFTs) are the distinct class of membrane-damaging proteins. They act by forming oligomeric pores in the plasma membranes. PFTs and PFPs from diverse organisms share a common mechanism of action, in which the designated pore-forming motifs of the membrane-bound protein molecules insert into the membrane lipid bilayer to create the water-filled pores. One common characteristic of these pore-forming motifs is that they are amphipathic in nature. In general, the hydrophobic sidechains of the pore-forming motifs face toward the hydrophobic core of the membranes, while the hydrophilic residues create the lining of the water-filled pore lumen. Interestingly, pore-forming motifs of the distinct subclass of PFPs/PFTs share very little sequence similarity with each other. Therefore, the common guiding principle that governs the sequence-to-structure paradigm in the mechanism of action of these PFPs/PFTs still remains an enigma. In this article, we discuss this notion using the examples of diverse groups of membrane-damaging PFPs/PFTs.

N-Terminal Region of Vibrio parahemolyticus Thermostable Direct Hemolysin Regulates the Membrane-Damaging Action of the Toxin.

Thermostable direct hemolysin (TDH) of Vibrio parahemolyticus is a membrane-damaging pore-forming toxin with potent cytolytic/cytotoxic activity. TDH exists as a tetramer consisting of protomers with a core ß-sandwich domain, flanked by an 11-amino acid long N-terminal region (NTR). This NTR could not be modeled in the previously determined crystal structure of TDH. Moreover, the functional implication of NTR for the membrane-damaging action of TDH remains unknown. In the present study, we have explored the implications of NTR for the structure-function mechanism of TDH. Our data show that the presence of NTR modulates the physicochemical property of TDH in terms of augmenting the amyloidogenic propensity of the protein. Deletion of NTR compromises the binding of TDH toward target cell membranes and drastically affects the membrane-damaging cytolytic/cytotoxic activity of the toxin. Mutations of aromatic/hydrophobic residues within NTR also confer compromised cell-killing activity. Moreover, covalent trapping of NTR, via an engineered disulfide bond, against the core ß-sandwich domain also abrogates the cytolytic/cytotoxic activity of TDH. This observation suggests that an unrestrained configuration of NTR is crucial for the membrane-damaging action of TDH. On the basis of our study, we propose a model explaining the role of NTR in the membrane-damaging function of TDH.

Structural Basis and Functional Implications of the Membrane Pore-Formation Mechanisms of Bacterial Pore-Forming Toxins.

Pore-forming toxins (PFTs) are a distinct class of membrane-damaging protein toxins documented in a wide array of life forms ranging from bacteria to humans. PFTs are known to act as potent virulence factors of the bacterial pathogens. Bacterial PFTs are, in general, secreted as water-soluble molecules, which upon encountering target host cells assemble into transmembrane oligomeric pores, thus leading to membrane permeabilization and cell death. Interaction of the PFTs with the target host cells can also lead to plethora of cellular responses having critical implications for the bacterial pathogenesis processes, host-pathogen interactions, and host immunity. In this review, we present an overview of our current understanding of the structural aspects of the membrane pore-formation processes employed by the bacterial PFTs. We also discuss the functional implications of the PFT mode of actions, in terms of eliciting diverse cellular responses.

Diagnostic accuracy of spot albumin creatinine ratio and its association with fetomaternal outcome in preeclampsia and eclampsia.

INTRODUCTION: Hypertensive disorders in pregnancy are one of the leading causes of maternal and perinatal mortality. Proteinuria is one of the common and important features of preeclampsia. To evaluate the diagnostic accuracy of albumin-creatinine ratio (ACR) in woman with preeclampsia and eclampsia and examine the association between ACR and fetomaternal outcome. MATERIALS AND METHODS: Prospective study carried out over a period of 1 year in the Department of Obstetrics and Gynaecology, after informed consent and ethical clearance total ninety pregnant women from gestational age 20 to 40 weeks were enrolled, including, thirty preeclampsia, thirty antepartum eclampsia, considered as cases and thirty normotensive pregnant women as controls. Preeclampsia was defined as per National High Blood Pressure Education Program 2000 working group. All patients were asked for a spot midstream urine sample, followed by 24 h urine collection. Urinary protein was estimated by the sulfosalicylic acid method and creatinine by the Jaffe's method. The urinary ACR was determined by automated analyzer. RESULTS: Mean value of urinary ACR of controls was significantly lower (0.103 ± 0.037) as compared to both groups. On comparing between groups the difference was significant (<0.001), a strong correlation between urinary ACR levels and 24 h urinary proteins was observed. CONCLUSION: In our study, an association of raised ACR values with severity of disease as well as with adverse fetomaternal outcome was observed.

The rs2070895 (-250G/A) Single Nucleotide Polymorphism in Hepatic Lipase (HL) Gene and the Risk of Coronary Artery Disease in North Indian Population: A Case-Control Study.

INTRODUCTION: Several Single Nucleotide Polymorphisms (SNPs) in lipid transport genes have been shown to be associated with Coronary Artery Disease (CAD). The Hepatic Lipase (HL)glycoprotein is a key component that catalyzes the hydrolysis of triglycerides and phospholipids in all major classes of lipoproteins. AIM: We studied whether the HL gene-250G/A polymorphism affect blood lipid level and the CAD in a North Indian population. MATERIALS AND METHODS: A total number of 477 subjects were enrolled in the study after approval of the Institutional Ethics Committee. Out of 477 subjects, 233 were with coronary artery disease as study group and 244 subjects without coronary artery disease as control group. All subjects recruited with matched ethnicity in age group of 40-70 years. Blood samples were collected in EDTA vials and genomic DNA was extracted from blood using the phenol-chloroform method. Lipid profile was estimated by using a commercially available kit. Polymorphisms in the HL (-250 G/A) gene were analysed by using restriction fragment length polymorphism-polymerase chain reaction (PCR-RFLP) method. The effect of this polymorphism on plasma lipids, lipoproteins and coronary artery disease was determined. RESULTS: In Human Hepatic Lipase (LIPC)-250G/A genotype, the frequencies of GG, GA and AA genotype in CAD group was 80.69%, 15.45% and 3.86%, respectively; in the control group, the corresponding frequencies were 90.16%, 9.02% and 0.82%, respectively. A significant difference was found in the genotype (LIPC-250G/A) distribution between the two groups. Further logistic regression analysis indicated that the GA and AA genotypes in SNP-250G/A were significantly associated with CAD in all genetic models (In codominant model- GA vs. GG, OR=1.91, 95% CI=1. 09-3.37, p=0. 03 and AA vs. GG, OR= 5.26, 95% CI= 1.10-24.60, p=0.04; in dominant model- GA+AA vs. GG, OR=2.19, p=0.004 and in recessive model- AA vs. GG+GA, OR=5.26, p=0.04 whereas, A allele at nucleotide -250G/A in the LIPC gene had an association with increased risk of CAD (OR=2.33, p=<0.008). CONCLUSION: Our findings indicated that the higher frequency of a dominant model (GA+AA) as well as mutant allele A of LIPC-250 G/A polymorphism is significantly associated with risk of CAD and the lipid profile can be used as a predictor of CAD.

Demographic risk factors, affected anatomical sites and clinicopathological profile for oral squamous cell carcinoma in a north Indian population.

BACKGROUND: Oral cancer is a common form of cancer in India, particularly among men. About 95% are squamous cell carcinomas. Tobacco along with alcohol are regarded as the major risk factors. OBJECTIVES: (i) To determine associations of oral squamous cell carcinoma (OSCC) with respect to gender, age group, socioeconomic status and risk habits; (ii) To observe the distribution of affected oral anatomical sites and clinico-pathological profile in OSCC patients. MATERIALS AND METHODS: This is an unmatched case-control study during period January 2012 to December 2013. Total of 471 confirmed OSCC patients and 556 control subjects were enrolled. Data on socio-demography, risk habits with duration and medical history were recorded. RESULTS: There were significant associations between OSCC with middle age (41-50years; unadjusted OR=1.63, 95%CI=1.05-2.52, p=0.02) (51-60 years; unadjusted OR=1.79, 95%CI=1.15-2.79, p=0.009) and male subjects (unadjusted OR=2.49, 95%CI=1.89-3.27, p=0.0001). Cases with both habits of tobacco chewing and smoking were at a higher risk for OSCC than tobacco chewing alone (unadjusted OR=0.52, 95%CI=0.38-0.72, p=0.0001), duration of risk habits also emerged as a responsible factor for the development of carcinoma. The majority of patients were presented in well-differentiated carcinomas (39.9%). Prevalence of advance stages (TNM stage III, IV) was 23.4% and 18.3% respectively. The buccal mucosa was the most common (35.5%) affected oral site. CONCLUSIONS: In most Asian countries, especially India, there is an important need to initiate the national level public awareness programs to control and prevent oral cancer by screening for early diagnosis and support a tobacco free environment.

The correlation of routine tear function tests and conjunctival impression cytology in dry eye syndrome.

PURPOSE: To establish the strength of the association between routine tear function tests and conjunctival impression cytology (CIC) and to determine whether they simulate the morphological and cytological changes that occur on the ocular surface in dry eye. What are the sensitivity, specificity and positive predictive values of these tests when CIC is considered the gold standard? METHODS: The tear film profile included tear film break up time (TBUT), Schirmer's-1, Rose Bengal scores (RBS), and impression cytology. CIC samples were obtained from the inferior bulbar conjunctiva and stained with periodic acid-Schiff and counter stained with hematoxylin and eosin. RESULTS: The mean Schirmer's value was 11.66 ± 5.90 in patients and 17.17 ± 2.97 in controls (p < 0.001). The mean TBUT in participants was 8.88 ± 3.54 and 13.53 ± 2.12 in controls (p < 0.001). Patients had a mean goblet cell density (GCD) of 490 ± 213, while the value for controls was 1,462 ± 661 (p < 0.001). Abnormal CIC was observed in 46.7% cases of dry eye and in 32.8% of controls. The correlation coefficient (L) for Schirmer's was 0.2 and 0.24 for participants and controls, respectively, while TBUT values were 0.26 and 0.38, RBS were 0.5 and 0.5, and GCD was 0.8 and 0.6 in cases and controls, respectively. CONCLUSIONS: GCD, RBS, and TBUT were better predictors of morphological and cytological changes in the conjunctiva than Schirmer's in dry eye syndrome. The sensitivity of tear function tests in diagnosing dry eye was TBUT > Schirmer's > RBS, and the specificity was Schirmer's > TBUT > RBS in decreasing order when CIC was considered the gold standard.

Oral contraceptive pills decrease pulmonary airway resistance in healthy north Indian women.

OBJECTIVES: Oral contraceptive pills (OCPs) are hormonal pills used by females to prevent conception; they are a combination of estrogen and progestin. There is, however, compelling evidence that throughout the reproductive life of a woman, her airways are subject to the influence of the cyclical variations in sex hormones which occur in relation to circadian rhythms. The present study has been designed to investigate the effects of OCPs on airway resistance in terms of spirometric parameters in OCP users and nonusers. MATERIALS AND METHODS: A total of 100 women (age: 20-40 years) ware selected for the present study. The subjects were provided with a one-month supply of OCPs. The constituents per tablet of MALA-N used were levonorgestrel 0.15 mg and ethinylestradiol 0.03 mg. Peak expiratory flow rate (PEFR), forced expiratory flow in expiring 25-75% air (FEF 25-75), forced expiratory volume percentage in one second (FEV1% or FEV1/FVC), forced vital capacity (FVC), and forced expiratory volume in one second (FEV1) were recorded. RESULTS: In our study, the FEF 25-75and PEFR increased significantly in OCP users, showing that these hormone pills decrease the resistance offered by small bronchioles.