Ultrafast spectroscopy of the hydrophilic carotenoid crocin at various pH.

This study delves into the pH-dependent effects on the excited-state behavior of crocin, a hydrophilic carotenoid with diverse functions in biological systems. Steady-state spectroscopy demonstrates notable changes in absorption and fluorescence spectra, characterized by a pH-dependent blue shift and altered resolution of vibrational bands. Transient absorption spectra further elucidate these effects, highlighting a significant blue shift in the S1-Sn peak with increasing pH. Detailed kinetic analysis shows the pH-dependent dynamics of crocin's excited states. At pH 11, a shortening of effective conjugation is observed, resulting in a prolonged S1/ICT lifetime. Conversely, at pH 9, our data suggest a more complex scenario, suggesting the presence of two distinct crocin species with different relaxation patterns. This implies structural alterations within the crocin molecule, potentially linked to the deprotonation of hydroxyl groups in crocin and/or saponification at high pH.

Time-Resolved Spectroelectrochemical Dynamics of Carotenoid 8'-apo-ß-Carotenal.

This work examines the influence of applied external voltage in bulk electrolysis on the excited-state properties of 8'-apo-ß-carotenal in acetonitrile by steady-state and ultrafast time-resolved absorption spectroscopy. The data collected under bulk electrolysis were compared with those taken without applied voltage. The steady-state measurements showed that although intensity of the S0 -S2 absorption band varies with the applied voltage, the spectral position remain nearly constant. Comparison of transient absorption spectra shows that the magnitude of the ICT-like band decreases during the experiment under applied voltage condition, and is associated with a prolongation of the S1 /ICT-like lifetime from 8 ps to 13 ps. Furthermore, switching off the applied voltage resulted in returning to no-voltage data within about 30 min. Our results show that the amplitude of the signal associated with the ICT state can be tuned by applying an external voltage.

Evaluation of volumetric asymmetry of the dorsolateral prefrontal cortex and medial temporal lobe in Alzheimer's disease using the atlas-based method.

Brain areas affected during neurodegenerative disease progression are considered anatomically connected to the first affected areas. The dorsolateral prefrontal cortex (DLPFC) has connections with the medial temporal lobe (MTL), which includes regions that become atrophic in Alzheimer's disease. In this study, we aimed to investigate the degree of volumetric asymmetry of DLPFC and MTL structures. This is a cross-sectional volumetric study involving 25 Alzheimer's disease patients and 25 healthy adults who underwent MRI with a 3D turbo spin echo sequence at 1.5 Tesla. The atlas-based method incorporated MRIStudio software to automatically measure the volume of brain structures. We compared the asymmetry index and volumetric changes across study groups and correlated them with Mini-Mental State Examination scores. We observed significant volumetric rightward lateralization in the DLPFC and superior frontal gyrus in Alzheimer's disease patients compared to the healthy controls. There was a significant volume loss in the MTL structures of Alzheimer's disease patients. Atrophy of MTL structures was positively correlated with right DLPFC volume changes in Alzheimer's disease patients. Volumetric asymmetry of the DLPFC may be a characteristic for determining disease progression in Alzheimer's disease patients. Future studies are recommended to evaluate whether these volumetric asymmetrical changes are specific to Alzheimer's disease and whether asymmetry measurements can serve as diagnostic markers.

Halogen-Bonded BODIPY Frameworks with Tunable Optical Features*.

The ability to tune the optical features of BODIPY materials in the solid state is essential for their photorelated application and requires efficient control of the crystal packing. In this study, such control of BODIPY supramolecular assemblies was achieved by deliberate design and synthesis of a BODIPY containing a strong halogen-bond (XB) acceptor (-NO2 ) and donor (I, Br) to mediate XB interactions. The di-halogenated structures formed isostructural mono-coordinate motif B3, B4 (1D tubular structure) and symmetric bifurcated motif B4-II (1D zigzag chains structure) through N-O⋅⋅⋅I, Br XB interactions. These XB interactions promote singlet-to-triplet intersystem crossing and triplet-to-singlet reverse intersystem crossing due to partial delocalization of oxygen electrons onto Br and I, which leads to unexpected fluorescence enhancement of B4-II. Finally, the indirect optical band gaps of B3, B4 and B4-II were amenable to tuning in the range of 1.85-2.50 eV by XB-driven crystal packings.

Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures.

In this study, we have investigated the cheese starter culture as a microbial community through a question: can the metabolic behaviour of a co-culture be explained by the characterized individual organism that constituted the co-culture? To address this question, the dairy-origin lactic acid bacteria Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. lactis, Streptococcus thermophilus and Leuconostoc mesenteroides, commonly used in cheese starter cultures, were grown in pure and four different co-cultures. We used a dynamic metabolic modelling approach based on the integration of the genome-scale metabolic networks of the involved organisms to simulate the co-cultures. The strain-specific kinetic parameters of dynamic models were estimated using the pure culture experiments and they were subsequently applied to co-culture models. Biomass, carbon source, lactic acid and most of the amino acid concentration profiles simulated by the co-culture models fit closely to the experimental results and the co-culture models explained the mechanisms behind the dynamic microbial abundance. We then applied the co-culture models to estimate further information on the co-cultures that could not be obtained by the experimental method used. This includes estimation of the profile of various metabolites in the co-culture medium such as flavour compounds produced and the individual organism level metabolic exchange flux profiles, which revealed the potential metabolic interactions between organisms in the co-cultures.

Single Nucleotide Polymorphism Analysis in HIV and Kaposi's Sarcoma Disease by Microarray Technique.

BACKGROUND: Emergence of Kaposi's Sarcoma in the cases other than HIV, following the use of immunosuppressant drugs, demonstrates that it is related to weak immunity. The fact that this malignancy does not occur in every HIV-positive patient suggests that genetic predisposition may also be effective. Replacement of one of the base pairs of adenine, guanine, cytosine, and thymine that constitute the DNA sequence in the human genome with another base pair can affect susceptibility to disease, response to treatment, and immunity. OBJECTIVE: The purpose of this study is to analyze the Single Nucleotide Polymorphism that could predispose to Kaposi's sarcoma of an HIV-infected patient and to identify which nucleotides such SNPs correspond to, using the microarray technology. MATERIALS AND METHODS: The blood samples of individuals, one of whom was diagnosed with Kaposi's Sarcoma HIV (+) visiting the outpatient clinic of infectious diseases polyclinic of Harran University Research and Practice Hospital and of a healthy individual with no Kaposi's Sarcoma, were used in the study. Following the DNA isolation of the blood samples taken from the respective individuals, a SNP analysis was conducted on the microarray device. 204,000 SNPs obtained were scanned later on in the databases in an attempt to identify the SNPs related to Kaposi's Sarcoma. RESULTS: In the 204,000 SNP screenings, we scrutinized the SNPs that differ in the case of Kaposi's Sarcoma [KS (+) and HIV (+)] on the basis of Control [KS(-) and HIV(-)] and HIV+ [KS(-)], and two SNPs of the ENDRA gene, three SNPs of the ADRA1A gene, six SNPs of the STIM1 gene, four SNPs of the EFNB2 gene, and one SNP of the CD209 gene were found to be different. However, when it comes to all SNPs (all the 204.000 SNPs) screened in terms of allele, it was observed that the AA and BB alleles were lower in the patient with Kaposi's Sarcoma [KS (+) and HIV (+)] compared to other groups and AB alleles were found to be higher than others in the patient with Kaposi's sarcoma [KS] (+) and HIV (+)]. CONCLUSION: In the microarray study we have conducted, 204,000 SNPs were screened for Control (HIV-) HIV (+) and HIV (+) patient with Kaposi's Sarcoma. It was found that 32,362 of those SNPs had different alleles in the Kaposi's Sarcoma [KS + HIV (+)] patient, while they had the same ones in the control [KS (-) and HIV (-)] and HIV + [KS (-)] group. 16 of the 32,362 SNPs took place among the genes related to Kaposi's Sarcoma. In the cases of Kaposi's Sarcoma with suspected diagnosis, it can be used as a beneficial laboratory test.

Volume estimation of brain ventricles using Cavalieri's principle and Atlas-based methods in Alzheimer disease: Consistency between methods.

Automatic estimations of brain ventricles are needed to assess disease progression in neurodegenerative disorders such as Alzheimer Disease (AD). The objectives of this study are to evaluate the diagnostic performances of an automated volumetric assessment tool in estimating lateral ventricle volumes in AD and to compare this with Cavalieri's principle, which is accepted as the gold standard method. This is across-sectional volumetric study including 25 Alzheimer patients and 25 healthy subjects undergoing magnetic resonance images (MRI) with a 3D turbo spin echo sequence at 1.5 Tesla. The Atlas-based method incorporated MRIStudio software to automatically measure he volumes of brain ventricles. To compare the corresponding measurements, we used manual point-counting and semi-automatic planimetry methods based on Cavalieri's principle. Bland-Altman test results indicated an excellent agreement between Cavalieri's principle and the Atlas-based method in all volumetric measurements (p < 0.05). We obtained a 64% sensitivity and 92% specificity for lateral ventricular volumes according to the Atlas-based method. AD subjects had significantly larger left and right lateral ventricle volume (LVV) when compared to control subjects in respect to three volumetric methods (p < 0.01). Lateral ventricle-to-brain ratio (VBR) statistically increased 49.23% in measurements done with the point-counting method, 45.12% with the planimetry method, and 45.49% with the Atlas-based method in AD patients (p < 0.01). As a result, the Atlas-based method may be used instead of manual volumetry to estimate brain volumes. Additionally, this method provides rapid and accurate estimations of brain ventricular volumes in-vivo examination of MRI.

Recent chemo-/biosensor and bioimaging studies based on indole-decorated BODIPYs.

BODIPY is an important fluorophores due to its enhanced photophysical and chemical properties including outstanding thermal/photochemical stability, intense absorption/emission profiles, high photoluminescence quantum yield, and small Stokes' shifts. In addition to BODIPY, indole and its derivatives have recently gained attention because of their structural properties and particularly biological importance, therefore these molecules have been widely used in sensing and biosensing applications. Here, we focus on recent studies that reported the incorporation of indole-based BODIPY molecules as reporter molecules in sensing systems. We highlight the rationale for developing such systems and evaluate detection limits of the developed sensing platforms. Furthermore, we also review the application of indole-based BODIPY molecules in bioimaging studies. This article includes the evaluation of indole-based BODIPYs from synthesis to characterization and a comparison of the advantages and disadvantages of developed reporter systems, making it instructive for researchers in various disciplines for the design and development of similar systems.

The novel anthracene decorated dendrimeric cyclophosphazenes for highly selective sensing of 2,4,6-trinitrotoluene (TNT).

Novel fluorescent anthracene-decorated cyclotri- and cyclotetraphosphazenes (5 and 6) are designed and synthesized, and their chemosensor behaviors against nitroaromatic compounds are examined by UV/Vis and fluorescence spectroscopies for addressing the sensors with cyclophosphazenes for 2,4,6-trinitrotoluene detection. The fluorescence intensities of (5 and 6) are found to be selectively quenched by only 2,4,6-trinitrotoluene through the non-covalent π⋯π stacking interactions between anthracene-substituted cyclophosphazenes and 2,4,6-trinitrotoluene. In addition, cyclic voltammetry and theoretical calculation of novel sensor systems are studied. The proposed fluorescent sensor systems are critical in terms of practical detection of 2,4,6-trinitrotoluene.

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris.

Leuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique feature of the obligate heterolactic fermentation, which leads to the production of lactate, ethanol, and/or acetate, and the final product profile of PKP highly depends on the energetics and redox state of the organism. Another characteristic of the L. mesenteroides subsp. cremoris is the production of aroma compounds in dairy fermentation, such as in cheese production, through the utilization of citrate. Considering its importance in dairy fermentation, a detailed metabolic characterization of the organism is necessary for its more efficient use in the industry. To this aim, a genome-scale metabolic model of dairy-origin L. mesenteroides subsp. cremoris ATCC 19254 (iLM.c559) was reconstructed to explain the energetics and redox state mechanisms of the organism in full detail. The model includes 559 genes governing 1088 reactions between 1129 metabolites, and the reactions cover citrate utilization and citrate-related flavor metabolism. The model was validated by simulating co-metabolism of glucose and citrate and comparing the in silico results to our experimental results. Model simulations further showed that, in co-metabolism of citrate and glucose, no flavor compounds were produced when citrate could stimulate the formation of biomass. Significant amounts of flavor metabolites (e.g., diacetyl and acetoin) were only produced when citrate could not enhance growth, which suggests that flavor formation only occurs under carbon and ATP excess. The effects of aerobic conditions and different carbon sources on product profiles and growth were also investigated using the reconstructed model. The analyses provided further insights for the growth stimulation and flavor formation mechanisms of the organism.

Azaindole-BODIPYs: Synthesis, fluorescent recognition of hydrogen sulfate anion and biological evaluation.

The synthesized and sensing capability of two novel azaindole substituted mono and distyryl BODIPY dyes against bisulfate anion were reported. Structural characterizations of the targeted compounds were conducted by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, 1H and 13C NMR spectroscopies. Photophysical properties of the azaindole substituted BODIPY compounds were investigated employing absorption and fluorescence spectroscopies in acetonitrile solution. It was found that the final compounds 3 and 4 exhibited exclusively selective and sensitive turn-off sensor behavior on HSO4- anion. Additionally, the stoichiometry ratio of the targeted compounds to bisulfate anion was measured 0.5 by Job's method. Also, density function theory was performed to the optical response of the sensor for targeted compounds. Furthermore, the cytotoxicity of Azaindole-BODIPYs was examined against living human leukemia K562 cell lines.

A Solution-Processable meso-Phenyl-BODIPY-Based n-Channel Semiconductor with Enhanced Fluorescence Emission.

The molecular design, synthesis, and characterization of an acceptor-donor-acceptor (A-D-A) semiconductor BDY-Ph-2T-Ph-BDY comprising a central phenyl-bithiophene-phenyl π-donor and BODIPY π-acceptor end-units is reported. The semiconductor shows an optical band gap of 2.32 eV with a highly stabilized HOMO/LUMO (-5.74 eV/-3.42 eV). Single-crystal X-ray diffraction (XRD) reveals D-A dihedral angle of ca. 66° and strong intermolecular "C-H ⋅⋅⋅ π (3.31 Å)" interactions. Reduced π-donor strength, increased D-A dihedral angle, and restricted intramolecular D-A rotations allows for both good fluorescence efficiency (ΦF =0.30) and n-channel OFET transport (µe =0.005 cm2 /V ⋅ s; Ion /Ioff =104 -105 ). This indicates a much improved (6-fold) fluorescence quantum yield compared to the meso-thienyl BODIPY semiconductor BDY-4T-BDY. Photophysical studies reveal important transitions between locally excited (LE) and twisted intramolecular charge-transfer (TICT) states in solution and the solid state, which could be controlled by solvent polarity and nano-aggregation. This is the first report of such high emissive characteristics for a BODIPY-based n-channel semiconductor.

Genome-Scale Brain Metabolic Networks as Scaffolds for the Systems Biology of Neurodegenerative Diseases: Mapping Metabolic Alterations.

Systems-based investigation of diseases requires integrated analysis of cellular networks and high-throughput data of gene products. The use of genome-scale metabolic networks for such integration has led to the elucidation of cellular mechanisms for several cell types from microorganisms to plants. It has become easier and cheaper to generate high-throughput data over years in the form of transcriptome, proteome and metabolome. This has tremendously improved the quality and quantity of information extracted from such data enabling the documentation of active pathways and reactions in cell metabolism. A number of omics-based datasets for several neurodegenerative diseases are now available in public repositories. This increases the potential of using genome-scale brain metabolic networks as a scaffold for this type of data to map metabolic alterations for the purpose of elucidating disease mechanisms and for the diagnosis and treatment of such disorders. This chapter first reviews omics data collected for neurodegenerative diseases to map their effect on metabolism. Later, the potential for genome-scale metabolic modeling of such data is reviewed and discussed in light of recently reconstructed brain metabolic networks at genome-scale.

Comparison of three methods for estimating volume of the uterine layers in healthy women: a stereological study / Comparación de tres métodos para estimar el volumen de las capas uterinas en mujeres sanas: un estudio estereológico

Aim of this study is to measure the volume of the uterine layers in healthy women according to the menstrual cycle phases and to test the agreement between three methods. The study was performed with 28 healthy women. Participants were divided into three groups as follicular (n=7), luteal (n=10) and postmenopausal phase (n=11). We used the point-counting and planimetry method in MR images and the ellipsoid methods in images obtained by transvaginal ultrasonography. Spearman correlation analysis showed significant negative correlations between the volumes of uterine layers and age (p<0.01). The volumes of the total uterus, the total myometrium and the endometrium measured with planimetry and point-counting methods were significantly lower in the postmenopausal women (p<0.01). While volumes of total uterus and the total myometrium significantly lower in the postmenopausal group in measurements done using ellipsoid method, the decrease in the volume of the endometrium was not statistically significant. The Bland-Altman test results indicated an excellent agreement between point-counting and planimetry methods in the volumetric measurements. The ellipsoid method might be inadequate for determining uterine layers volume particularly the endometrium volume. The stereological methods permit unbiased and efficient estimation of volume of uterine layers in vivo examination of MRI.

El objetivo de este estudio fue medir el volumen de las capas uterinas en mujeres sanas de acuerdo con las fases del ciclo menstrual y probar la concordancia de tres métodos. El estudio se realizó en 28 mujeres sanas. Las participantes se dividieron en tres grupos, folicular (n=7), luteal (n=10) y fase posmenopáusica (n=11). Utilizamos el método de conteo puntual y planimetría en imágenes de resonancia magnética y utilizamos los métodos elipsoides en imágenes obtenidas por ultrasonografía transvaginal. El análisis de correlación de Spearman mostró correlaciones negativas significativas entre los volúmenes de las capas uterinas y la edad (p <0,01). Se midieron con planimetría los volúmenes total de útero, el miometrio y endometrio, los métodos de recuento de puntos fueron significativamente más bajos en las mujeres posmenopáusicas (p <0,01). Por otra parte, el volumen total de útero y el total del miometrio fue significativamente menor en el grupo posmenopáusico en las mediciones realizadas con el método elipsoide. La disminución en el volumen del endometrio no fue estadísticamente significativa. Los resultados de las pruebas de Bland-Altman indicaron una excelente concordancia entre los métodos de recuento de puntos y de planimetría en las mediciones volumétricas. El método elipsoide puede ser inadecuado para determinar el volumen de las capas uterinas, particularmente en el volumen del endometrio. Los métodos estereológicos permiten una estimación imparcial y eficiente del volumen de las capas uterinas en el examen in vivo de la resonancia magnética.

Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma.

Developments in genome scale metabolic modeling techniques and omics technologies have enabled the reconstruction of context-specific metabolic models. In this study, glioblastoma multiforme (GBM), one of the most common and aggressive malignant brain tumors, is investigated by mapping GBM gene expression data on the growth-implemented brain specific genome-scale metabolic network, and GBM-specific models are generated. The models are used to calculate metabolic flux distributions in the tumor cells. Metabolic phenotypes predicted by the GBM-specific metabolic models reconstructed in this work reflect the general metabolic reprogramming of GBM, reported both in in-vitro and in-vivo experiments. The computed flux profiles quantitatively predict that major sources of the acetyl-CoA and oxaloacetic acid pool used in TCA cycle are pyruvate dehydrogenase from glycolysis and anaplerotic flux from glutaminolysis, respectively. Also, our results, in accordance with recent studies, predict a contribution of oxidative phosphorylation to ATP pool via a slightly active TCA cycle in addition to the major contributor aerobic glycolysis. We verified our results by using different computational methods that incorporate transcriptome data with genome-scale models and by using different transcriptome datasets. Correct predictions of flux distributions in glycolysis, glutaminolysis, TCA cycle and lipid precursor metabolism validate the reconstructed models for further use in future to simulate more specific metabolic patterns for GBM.

Malformations of cortical development: 3T magnetic resonance imaging features.

Malformation of cortical development (MCD) is a term representing an inhomogeneous group of central nervous system abnormalities, referring particularly to embriyological aspect as a consequence of any of the three developmental stages, i.e., cell proliferation, cell migration and cortical organization. These include cotical dysgenesis, microcephaly, polymicrogyria, schizencephaly, lissencephaly, hemimegalencephaly, heterotopia and focal cortical dysplasia. Since magnetic resonance imaging is the modality of choice that best identifies the structural anomalies of the brain cortex, we aimed to provide a mini review of MCD by using 3T magnetic resonance scanner images.

Measures of ventricles and evans' index: from neonate to adolescent.

Ventricle sizes are important for the early diagnosis of hydrocephalus or for follow-up after ventriculostomy. Diameters of ventricles may change, especially in childhood. This study aims to provide normative data about ventricle diameters. Among 14,854 cranial MRI performed between 2011 and 2013, 2,755 images of Turkish children aged 0-18 years were obtained. After exclusions, 517 images were left. Four radiologists were trained by a pediatric radiologist. Twenty images were assessed by all radiologists for a pilot study to see that there was no interobserver variation. There were 10-22 children in each age group. The maximum width of the third ventricle was 5.54 ± 1.29 mm in males in age group 1 and 4.98 ± 1.08 mm in females in age group 2. The Evans' index was <0.3 and consistent with the literature. The third ventricle/basilar artery width ratio was found to be >1 and <2 in all age groups and both gender groups. Our study showed the ventricle size data of children in various age groups from newborn to adolescent. The ventricle volume/cerebral parenchyma ratio seems to decrease with age. We think that these data can be applied in clinical practice, especially for the early diagnosis of hydrocephalus.

Measures of pituitary gland and stalk: from neonate to adolescence.

OBJECTIVE: The aim of this study is to provide normative data about pituitary diameters in a pediatric population. Pituitary imaging is important for the evaluation of the hypothalamo-pituitary axis defect. However, data about normal pituitary gland diameters and stalk are limited, especially in children. Structure and the measurements of pituitary gland and pituitary stalk may change due to infection, inflammation, or neoplasia. METHODS: Among 14,854 cranial/pituitary gland magnetic resonance imaging scans performed from 2011 to 2013, 2755 images of Turkish children aged between 0 and 18 were acquired. After exclusions, 517 images were left. Four radiologists were educated by an experienced pediatric radiologist for the measurement and assessment of the pituitary gland and pituitary stalk. Twenty cases were measured by all radiologists for a pilot study and there was no interobserver variability. RESULTS: There were 10-22 children in each age group. The maximum median height of the pituitary gland was 8.48±1.08 and 6.19±0.88 mm for girls and boys, respectively. Volumes were also correlated with gender similar to height. Minimum median height was 3.91±0.75 mm for girls and 3.81±0.68 mm for boys. The maximum and minimum pituitary stalk basilar artery ratios for girls were 0.73±0.12 and 0.59±0.10 mm. The ratios for boys were 0.70±0.12 and 0.56±0.11 mm. CONCLUSION: Our study demonstrated the pituitary gland and stalk size data of children in various age groups from newborn to adolescent. It is thought that these data can be applied in clinical practice. Future prospective follow-up studies with larger samples, which correlate the structural findings with the clinical and laboratory results are awaited.

Sonographic measurement of diuretic-induced renal length changes: are they correlated with renal function?

OBJECTIVES: The purposes of this study were to prospectively identify diuretic-induced renal length changes and to determine whether the percentages of the renal length changes allow estimation of the differential renal function. METHODS: Twenty-three children (14 boys and 9 girls; mean age, 7.83 years) who were undergoing technetium Tc 99m diethylenetriamine pentaacetic acid or technetium Tc 99m mercaptoacetyltriglycine diuretic renography were included in this study. Renal lengths were measured by sonography just before and 15 to 20 minutes after diuretic injection. The Spearman test was used to assess the correlation between renal length increases due to diuretic injection and the differential renal function. RESULTS: The mean renal lengths ± SD measured before and after diuretic administration were 91.52 ± 20.87 and 95.38 ± 21.46 mm, respectively. The increase in renal length after diuretic administration was statistically significant (P < .001). There was a positive correlation between the renal length change and functional status (P = .006). CONCLUSIONS: Renal length may change after diuretic injection according to the functional status, and the sonographic measurements of these changes may be used as an alternative to other imaging methods in estimation of renal function.