Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorometric Determination of Drugs Containing α -Methylene Sulfoxide Functional Groups Using - Methylnicotinamide Chloride as a Fluorogenic Agent

A simple fluorometric method, using 𝑁1-methylnicotinamide chloride (NMNCl) as a fluorogenic reagent, has been developed, adapted, and validated for the quantitative estimation of drugs containing α-methylene sulfoxide functional groups. The proposed method has been applied successfully to the determination of sulindac (1), omeprazole (2), lansoprazole (3), pantoprazole (4), and rabeprazole (5) in the pure form, laboratory-prepared mixtures, pharmaceutical dosage forms, spiked human plasma samples, and in hospitalized patient's or volunteer's blood. For the standard solutions of 1, 2, 3, 4, and 5, the method showed linearity over concentration ranging between 1–50 𝜇g/mL, 50–1200 ng/mL, 100–1500 ng/mL, 10–1500 ng/mL, and 20–2200 ng/mL, respectively. For the spiked human plasma of 1, 2, 3, 4, and 5, the linearity was shown over concentration ranging between 1–50 μg/mL, 75–1200 ng/mL, 100–1400 ng/mL, 10–1500 ng/mL, and 50–2100 ng/mL, respectively. The method showed good accuracy, specificity, and precision in both laboratory-prepared mixtures and spiked human plasma samples. The proposed method is simple, does not need sophisticated instrumentation, suitable for quality control application, bioavailability, and bioequivalency studies. Besides, the sensitivity and detection limits are comparable to sophisticated chromatographic methods.
Multiple histidines in the periplasmic domain of the Salmonella enterica sensor kinase SsrA enhance signaling in response to extracellular acidification

The two‐component regulatory system SsrA‐SsrB in Salmonella enterica controls expression of a virulence gene program required for intracellular survival in host cells. SsrA signaling is induced within the acidic host vacuole in which the bacteria reside; however, the mechanism by which SsrA senses this intracellular environment is unknown. Here, we show that the periplasmic sensor domain of SsrA is enriched in histidine residues that increase SsrA signaling below external pH of 6. While no single histidine accounted for the full acid‐responsiveness of SsrA, we localized the acid‐responsiveness principally to five histidines in the C‐terminal end of the periplasmic sensor domain, with input from additional histidines in the N‐terminal end of the senor. A sensor mutant lacking critical pH‐responsive histidines was defective for acid‐promoted activity, yet retained basal activity similar to wild type at neutral pH, indicating that the role of these histidines is to enhance signaling in response to acidification. In support of this, a pH‐blind mutant was insensitive to the vacuole acidification blocking activity of bafilomycin, and was attenuated for competitive fitness during infection of mice. Our data demonstrate that SsrA contains a histidine‐rich periplasmic sensor that enhances signaling in response to the innate host defense of vacuolar acidification.
Cytochrome c biogenesis in Campylobacter jejuni requires cytochrome c6 (CccA; Cj1153) to maintain apocytochrome cysteine thiols in a reduced state for haem attachment

The microaerophilic food‐borne pathogen Campylobacter jejuni uses complex cytochrome‐rich respiratory chains for growth and host colonisation. Cytochrome c biogenesis requires haem ligation to reduced apocytochrome cysteines, catalysed by the cytochrome c synthase, CcsBA. While ccsBA could not be deleted, we showed that the thiol reductase DsbD and the CcsX homologue Cj1207 are involved in, but not essential for, cytochromes c biogenesis. Mutant phenotypic analyses and biochemical studies with purified proteins revealed that the mono‐haem c‐type cytochromes Cj1153 (CccA) and Cj1020 (CccB) and the di‐haem Cj0037 (CccC) are electron donors to the cb‐oxidase (CcoNOQP), with CccC being more efficient than CccA. Remarkably, cccA deletion or site‐directed mutagenesis resulted in an almost complete loss of all other c‐type cytochromes. Cytochrome c structural and biogenesis genes were still transcribed in the cccA deletion mutant and the quinol oxidase genes (cioAB) were up‐regulated. Cytochrome c production could be rescued in this mutant by growth with exogenous dithiothreitol or L‐cysteine, suggesting that in the absence of CccA, apocytochrome c haem binding motifs become oxidised, preventing haem attachment. Our results identify CccA, the most abundant periplasmic c‐type cytochrome in C. jejuni, as a novel and unexpected protein required for cytochrome c biogenesis in this pathogen.
A Study of the Effects of Physical Activity on Asthmatic Symptoms and Obesity Risk in Elementary School–Aged Children

Background Children with moderate persistent asthma are often reluctant to engage in physical activity and as a result are more prone to obesity and increased incidence of asthma attacks. Purpose This study developed an asthma program that included physical activity and asthma management education for elementary schoolchildren with moderate persistent asthma to evaluate the effectiveness of the program in reducing asthma symptoms while increasing lung functions. Methods This study utilized a quantitative, nonexperimental, nonrandomized longitudinal design that collected participants' asthma and physical exercise histories and forced vital capacity (FVC) volumes before and after the asthma program (n = 10). Results This asthma program significantly improved asthma control among participants by reducing the number of weekly and monthly emergency visits (P < .01), increasing participation in physical activities (P < .01), and increasing the average FVC volume from 1.93 ± 0.30 L to 2.74 ± 0.37 L (P < .01), indicating improved lung conditions. Discussion This study shows that enhanced physical activity and asthma management education for children with moderate persistent asthma can reduce asthmatic symptoms, such as wheezing, coughing, and shortness of breath, while potentially decreasing the risk of obesity later in life. Translation to Health Education Practice Educators and parents should consider taking more active roles in encouraging children with moderate persistent asthma to participate in more supervised physical activities in order to control asthma symptoms and to reduce risk for obesity.
Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways

Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid‐based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best‐studied MCPs highlighting atomic‐level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.
Type‐II NADH:quinone oxidoreductase from Staphylococcus aureus has two distinct binding sites and is rate limited by quinone reduction

A prerequisite for any rational drug design strategy is understanding the mode of protein–ligand interaction. This motivated us to explore protein–substrate interaction in Type‐II NADH:quinone oxidoreductase (NDH‐2) from Staphylococcus aureus, a worldwide problem in clinical medicine due to its multiple drug resistant forms. NDHs‐2 are involved in respiratory chains and recognized as suitable targets for novel antimicrobial therapies, as these are the only enzymes with NADH:quinone oxidoreductase activity expressed in many pathogenic organisms.
[Microarchitecture assessment of human trabecular bone: description of methods].

Trabecular bone microarchitecture changes in relation to mechanical stress, effects of age, osteoporosis and anti-osteoporotic drugs. In vivo, these anomalies can be evaluated using textural parameters on high resolution radiographs and images of DXA. It is possible to extract morphological and topological parameters: apparent on MRI images and 3D with a dedicated device called High resolution peripheral quantitative computed tomography (HR-pQCT) with a resolution close to the size of the trabeculae. In vitro, it is possible to obtain on bone samples a 2D analysis by histomorphometry and a 3D analysis from 10 µm images obtained by synchrotron radiation or conventional micro-CT.
The zinc cluster proteins Upc2 and Ecm22 promote filamentation in Saccharomyces cerevisiae by sterol biosynthesis‐dependent and ‐independent pathways

The transition between a unicellular yeast form to multicellular filaments is crucial for budding yeast foraging and the pathogenesis of many fungal pathogens such as Candida albicans. Here, we examine the role of the related transcription factors Ecm22 and Upc2 in Saccharomyces cerevisiae filamentation. Overexpression of either ECM22 or UPC2 leads to increased filamentation, whereas cells lacking both ECM22 and UPC2 do not exhibit filamentous growth. Ecm22 and Upc2 positively control the expression of FHN1, NPR1, PRR2 and sterol biosynthesis genes. These genes all play a positive role in filamentous growth, and their expression is upregulated during filamentation in an Ecm22/Upc2‐dependent manner. Furthermore, ergosterol content increases during filamentous growth. UPC2 expression also increases during filamentation and is inhibited by the transcription factors Sut1 and Sut2. The expression of SUT1 and SUT2 in turn is under negative control of the transcription factor Ste12. We suggest that during filamentation Ste12 becomes activated and reduces SUT1/SUT2 expression levels. This would result in increased UPC2 levels and as a consequence to transcriptional activation of FHN1, NPR1, PRR2 and sterol biosynthesis genes. Higher ergosterol levels in combination with the proteins Fhn1, Npr1 and Prr2 would then mediate the transition to filamentous growth.
Association of Posttraumatic Stress Disorder With rs2267735 in the ADCYAP1R1 Gene: A Meta-Analysis.

Recent studies point to the potential role of the (pituitary) adenylate cyclase activating polypeptide receptor 1 (ADCYAP1R1) gene, which has been implicated in stress response, in posttraumatic stress disorder (PTSD). Multiple genetic association studies have examined potential PTSD risk related to this gene, with mixed results. We conducted a meta-analysis of rs2267735 in ADCYAP1R1 in PTSD. A literature search was conducted using PubMed and PsycINFO, resulting in nine studies that met criteria for inclusion in analysis. Biostat's Comprehensive Meta-Analysis was used to conduct the main meta-analysis on the combined sex sample, as well as two subanalyses examining effects separately in female and male participants. Results indicated that the C allele of rs2267735 conferred significant risk for PTSD in the combined sex data, OR = 1.210, 95% CI [1.007, 1.454], p = . 042, and in the subsample of women and girls, OR = 1.328, 95% CI [1.026, 1.719], p = . 031; but not in the subsample of men and boys, OR = 0.964, 95% CI [0.733, 1.269], p = . 796. These results provide evidence for an association between ADCYAP1R1 and PTSD and indicate that there may indeed be sex differences. Implications of these findings, including the role of rs2267735 as one modulator of the stress system, are discussed.
Transfer of the methicillin resistance genomic island among staphylococci by conjugation

Methicillin resistance creates a major obstacle for treatment of Staphylococcus aureus infections. The resistance gene, mecA, is carried on a large (20 kb to > 60 kb) genomic island, staphylococcal cassette chromosome mec (SCCmec), that excises from and inserts site‐specifically into the staphylococcal chromosome. However, although SCCmec has been designated a mobile genetic element, a mechanism for its transfer has not been defined. Here we demonstrate the capture and conjugative transfer of excised SCCmec. SCCmec was captured on pGO400, a mupirocin‐resistant derivative of the pGO1/pSK41 staphylococcal conjugative plasmid lineage, and pGO400::SCCmec (pRM27) was transferred by filter‐mating into both homologous and heterologous S. aureus recipients representing a range of clonal complexes as well as S. epidermidis. The DNA sequence of pRM27 showed that SCCmec had been transferred in its entirety and that its capture had occurred by recombination between IS257/431 elements present on all SCCmec types and pGO1/pSK41 conjugative plasmids. The captured SCCmec excised from the plasmid and inserted site‐specifically into the chromosomal att site of both an isogenic S. aureus and a S. epidermidis recipient. These studies describe a means by which methicillin resistance can be environmentally disseminated and a novel mechanism, IS‐mediated recombination, for the capture and conjugative transfer of genomic islands.
The Influence of the Corticus Study on Steroid Use for Septic Shock in Scottish Intensive Care Units

The publication of the CORTICUS study in January 2008 suggested that the use of low-dose steroids in patients with septic shock did not improve survival or reversal of shock. This result contradicted results from the original trial by Annane in 2002. We carried out a telephone survey of all the intensive care units in Scotland eight weeks following the publication of the CORTICUS study, with the aim of assessing any change in practice since its publication. Prior to CORTICUS, 62% of Scottish intensive care units prescribed steroids routinely in all patients with septic shock requiring vasopressors. Eight weeks following the publication of CORTICUS, only six (25%) units had changed or planned to change their practice. Despite this relatively small change, 50% of the medical staff we questioned claimed that the CORTICUS study had affected their own individual practice.
A partial metabolic pathway enables group b streptococcus to overcome quinone deficiency in a host bacterial community

Aerobic respiration metabolism in Group B Streptococcus (GBS) is activated by exogenous heme and menaquinone. This capacity enhances resistance of GBS to acid and oxidative stress and improves its survival. In this work, we discovered that GBS is able to respire in the presence of heme and 1,4‐dihydroxy‐2‐naphthoic acid (DHNA). DHNA is a biosynthetic precursor of demethylmenaquinone (DMK) in many bacterial species. A GBS gene (gbs1789) encodes a homolog of the MenA 1,4‐dihydroxy‐2‐naphthoate prenyltransferase enzyme, involved in the synthesis of demethylmenaquinone. In this study, we showed that gbs1789 is involved in the biosynthesis of long‐chain demethylmenaquinones (DMK‐10). The Δgbs1789 mutant cannot respire in the presence of heme and DHNA, indicating that endogenously synthesized DMKs are cofactors of the GBS respiratory chain. We also found that isoprenoid side chains from GBS DMKs are produced by the protein encoded by the gbs1783 gene, since this gene can complement an Escherichia coli ispB mutant defective for isoprenoids chain synthesis. In the gut or vaginal microbiote, where interspecies metabolite exchanges occur, this partial DMK biosynthetic pathway can be important for GBS respiration and survival in different niches.
Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism

Quinate and shikimate can be degraded by a number of microbes. Dehydroshikimate dehydratases (DSDs) play a central role in this process, catalyzing the conversion of 3‐dehydroshikimate to protocatechuate, a common intermediate of aromatic degradation pathways. DSDs have applications in metabolic engineering for the production of valuable protocatechuate‐derived molecules. Although a number of Gram‐negative bacteria are known to catabolize quinate and shikimate, only limited information exists on the quinate/shikimate catabolic enzymes found in these organisms. Here, we have functionally and structurally characterized a putative DSD designated QuiC1, which is present in some pseudomonads. The QuiC1 protein is not related by sequence with previously identified DSDs from the Gram‐negative genus, Acinetobacter, but instead shows limited sequence identity in its N‐terminal half with fungal DSDs. Analysis of a Pseudomonas aeruginosa quiC1 gene knock‐out demonstrates that it is important for growth on either quinate or shikimate. The structure of a QuiC1 enzyme from P. putida reveals that the protein is a fusion of two distinct modules: an N‐terminal sugar phosphate isomerase‐like domain associated with DSD activity and a novel C‐terminal hydroxyphenylpyruvate dioxygenase‐like domain. The results of this study highlight the considerable diversity of enzymes that participate in quinate/shikimate catabolism in different microbes.
Bordetella adenylate cyclase toxin interacts with filamentous haemagglutinin to inhibit biofilm formation in vitro

Bordetella pertussis, the causative agent of whooping cough, secretes and releases adenylate cyclase toxin (ACT), which is a protein bacterial toxin that targets host cells and disarms immune defenses. ACT binds filamentous haemagglutinin (FHA), a surface‐displayed adhesin, and until now, the consequences of this interaction were unknown. A B. bronchiseptica mutant lacking ACT produced more biofilm than the parental strain; leading Irie et al. to propose the ACT‐FHA interaction could be responsible for biofilm inhibition. Here we characterize the physical interaction of ACT with FHA and provide evidence linking that interaction to inhibition of biofilm in vitro. Exogenous ACT inhibits biofilm formation in a concentration‐dependent manner and the N‐terminal catalytic domain of ACT (AC domain) is necessary and sufficient for this inhibitory effect. AC Domain interacts with the C‐terminal segment of FHA with ∼650 nM affinity. ACT does not inhibit biofilm formation by Bordetella lacking the mature C‐terminal domain (MCD), suggesting the direct interaction between AC domain and the MCD is required for the inhibitory effect. Additionally, AC domain disrupts preformed biofilm on abiotic surfaces. The demonstrated inhibition of biofilm formation by a host‐directed protein bacterial toxin represents a novel regulatory mechanism and identifies an unprecedented role for ACT.
Robust Min‐system oscillation in the presence of internal photosynthetic membranes in cyanobacteria

The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ‐ring formation and represents one of the best‐understood examples of emergent protein self‐organization in nature. The oscillatory patterns of the Min‐system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self‐organization by sterically occluding or sequestering MinCDE from the plasma membrane. Here, it was shown that the Min system in the cyanobacterium Synechococcus elongatus PCC 7942 oscillates from pole‐to‐pole despite the potential spatial constraints imposed by their extensive thylakoid network. Moreover, reaction‐diffusion simulations predict robust oscillations in modeled cyanobacterial cells provided that thylakoid network permeability is maintained to facilitate diffusion, and suggest that Min proteins require preferential affinity for the plasma membrane over thylakoids to correctly position the FtsZ ring. Interestingly, in addition to oscillating, MinC exhibits a midcell localization dependent on MinD and the DivIVA‐like protein Cdv3, indicating that two distinct pools of MinC are coordinated in S. elongatus. Our results provide the first direct evidence for Min oscillation outside of E. coli and have broader implications for Min‐system function in bacteria and organelles with internal membrane systems.
HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin

Antitoxins encoded by type II toxin – antitoxin (TA) modules neutralize cognate toxins by direct protein – protein contact and in addition, regulate TA operon transcription by binding to operators in the promoter regions. On top of the simple negative feed‐back regulation, canonical type II TA operons are regulated by a mechanism called ‘Conditional Cooperativity’(CC). In CC, the cellular toxin:antitoxin (T:A) ratio controls the transcription‐rate such that low T:A ratios favour repression and high T:A ratios favour de‐repression of TA operon transcription. Here a new molecular mechanism that secures selective synthesis of antitoxin in the presence of excess toxin was unravelled. The hicAB locus of E. coli K‐12 encodes HicA mRNase and HicB antitoxin. It was shown that hicAB is transcribed by two promoters, an upstream one that is activated by CRP‐cAMP and competence factor Sxy and a downstream one that is autorepressed solely by HicB. Excess HicA destabilizes the HicB•operator complex in vitro and consistently, activates hicAB transcription in vivo. Remarkably, the hicAB transcript synthesized from the HicB‐controlled promoter produces HicB but not HicA. Thus, the HicA‐mediated derepression of hicAB transcription provides a mechanism that conditionally and selectively stimulates synthesis of HicB antitoxin under conditions of excess HicA toxin.
SurR is a master regulator of the primary electron flow pathways in the order Thermococcales

The sulfur response regulator, SurR, is among a handful of known redox‐active transcriptional regulators. First characterized from the hyperthermophile Pyrococcus furiosus, it is unique to the archaeal order Thermococcales. P. furiosus has two modes of electron disposal. Hydrogen gas is produced when the organism is grown in the absence of elemental sulfur (S0) and H2S is produced when grown in its presence. Switching between these metabolic modes requires a rapid transcriptional response and this is orchestrated by SurR. We show here that deletion of SurR causes severely impaired growth in the absence of S0 since genes essential for H2 metabolism are no longer activated. Conversely, a strain containing a constitutively active SurR variant displays a growth phenotype in the presence of S0 due to constitutive repression of S0‐responsive genes. During a metabolic shift initiated by addition of S0 to the growth medium, both strains demonstrate a de‐regulation of genes involved in the SurR regulon, including hydrogenase and related S0‐responsive genes. These results demonstrate that SurR is a master regulator of electron flow within P. furiosus, likely affecting the pools of ferredoxin, NADPH and NADH, as well as influencing metabolic pathways and thiol/disulfide redox balance.