Serratia ficaria isolated from sputum specimen

Serratia ficaria was first described in 1979 as a Gram-negative facultative anaerobic rod. S. ficaria was found in figs, but also isolated from human specimens in a few cases. We now report an isolate of S. ficaria from sputum specimen.A 46-year-old man was suffering from a chronic renal failure of five years, four months of peritoneal dialysis and one week of fever due to respiratory tract infection, accompanied by cough. Sputum culture yielded a Gram-negative rod. It was identified as S. ficaria and the antibiotic susceptibility test was performed by automated Vitek II (bioMerieux). The tested S. ficaria strain was susceptible to amikacin, gentamicin, cefepime, trimethoprim-sulfamethoxazole, imipenem, meropenem, tigecycline and ciprofloxacin. This strain was resistant to ampicillin, amoxicillin-clavulanic acid, cephalothin, cefoxitine, cefuroxime and ceftriaxone. The patient was treated successfully (80 mg trimethoprim/400 mg sulfamethoxazole twice daily for 7 days)S. ficaria is an opportunistic pathogen responsible for intestinal colonization or serious infections such as septicaemia, gall bladder empyema in immunocompromised patients. The fig tree and fig play an important role in human colonization. It should be remembered that S. ficaria infections may be encountered frequently especially in fig tree culture zones.     

LEDPatNet19: Automated Emotion Recognition Model based on Nonlinear LED Pattern Feature Extraction Function using EEG Signals

Electroencephalography (EEG) signals collected from human brains have generally been used to diagnose diseases. Moreover, EEG signals can be used in several areas such as emotion recognition, driving fatigue detection. This work presents a new emotion recognition model by using EEG signals. The primary aim of this model is to present a highly accurate emotion recognition framework by using both a hand-crafted feature generation and a deep classifier. The presented framework uses a multilevel fused feature generation network. This network has three primary phases, which are tunable Q-factor wavelet transform (TQWT), statistical feature generation, and nonlinear textural feature generation phases. TQWT is applied to the EEG data for decomposing signals into different sub-bands and create a multilevel feature generation network. In the nonlinear feature generation, an S-box of the LED block cipher is utilized to create a pattern, which is named as Led-Pattern. Moreover, statistical feature extraction is processed using the widely used statistical moments. The proposed LED pattern and statistical feature extraction functions are applied to 18 TQWT sub-bands and an original EEG signal. Therefore, the proposed hand-crafted learning model is named LEDPatNet19. To select the most informative features, ReliefF and iterative Chi2 (RFIChi2) feature selector is deployed. The proposed model has been developed on the two EEG emotion datasets, which are GAMEEMO and DREAMER datasets. Our proposed hand-crafted learning network achieved 94.58%, 92.86%, and 94.44% classification accuracies for arousal, dominance, and valance cases of the DREAMER dataset. Furthermore, the best classification accuracy of the proposed model for the GAMEEMO dataset is equal to 99.29%. These results clearly illustrate the success of the proposed LEDPatNet19.     

Application of near‐infrared (NIR) spectroscopy for screening of raw materials used in the cell culture medium for the production of a recombinant therapeutic protein

Control of raw materials based on an understanding of their impact on product attributes has been identified as a key aspect of developing a control strategy in the Quality by Design (QbD) paradigm. This article presents a case study involving use of a combined approach of Near‐infrared (NIR) spectroscopy and Multivariate Data Analysis (MVDA) for screening of lots of basal medium powders based on their impact on process performance and product attributes. These lots had identical composition as per the supplier and were manufactured at different scales using an identical process. The NIR/MVDA analysis, combined with further investigation at the supplier site, concluded that grouping of medium components during the milling and blending process varied with the scale of production and media type. As a result, uniformity of blending, impurity levels, chemical compatibility, and/or heat sensitivity during the milling process for batches of large‐scale media powder were deemed to be the source of variation as detected by NIR spectra. This variability in the raw materials was enough to cause unacceptably large variability in the performance of the cell culture step and impact the attributes of the resulting product. A combined NIR/MVDA approach made it possible to finger print the raw materials and distinguish between good and poor performing media lots. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Effects of Ni(2+), Co(2+), and Mn(2+) on desensitized butyrylcholinesterase prepared from human serum

Human serum butyrylcholinesterase (BChE) has been converted into a stable but less active desensitized form when heated at 45°C for 24 h. The desensitized BChE follows Michaelis-Menten kinetics, whereas native enzyme exhibits slightly negative cooperativity with respect to butyrylthiocholine binding. In this study, we investigated the effects of Ni²⁺, Co²⁺, and Mn²⁺ on the desensitized BChE. It is found that all three ions were noncompetitive inhibitors of the desensitized BChE, and K _i values have been determined as 7.816±1.060 mM, 48.722±4.635 mM, and 84.795±5.249 mM for Ni²⁺, Co²⁺, and Mn²⁺, respectively. In our previous study, these ions were linear mixed-type inhibitors of the native BChE. This finding confirms that desensitized BChE changes to a different conformation than native BChE. From the comparison of K _i values of the trace elements, it can be said that Ni²⁺ is a more effective inhibitor of the desensitized BChE than Co²⁺ and Mn²⁺.     

Interaction prediction and classification of PDZ domains

Background  

PDZ domain is a well-conserved, structural protein domain found in hundreds of signaling proteins that are otherwise unrelated. PDZ domains can bind to the C-terminal peptides of different proteins and act as glue, clustering different protein complexes together, targeting specific proteins and routing these proteins in signaling pathways. These domains are classified into classes I, II and III, depending on their binding partners and the nature of bonds formed. Binding specificities of PDZ domains are very crucial in order to understand the complexity of signaling pathways. It is still an open question how these domains recognize and bind their partners.     

Impaired glucose tolerance: its relevance to early endothelial dysfunction.

We studied the effects of acute glycemia on plasma nitric oxide (NO; nitrite plus nitrate) levels, Cu-Zn Superoxide dismutase (Cu-Zn SOD) activity and thiobarbituric acid-reactive substances (TBARS) levels in age-matched female subjects before and two hours after glucose loading. According to the results of glucose loading, subjects were divided in the three groups as normal (n = 13, NGT), impaired (n = 11, IGT) and diabetic glucose tolerance (n = 10, DGT). Plasma NO levels were significantly higher in subjects with DGT than in subjects with NGT (p< 0.001) and IGT (p< 0.05) at baseline. Two hours after glucose loading, plasma NO levels were significantly decreased in subjects with IGT and DGT (p< 0.001 and p< 0.001). Although plasma TBARS levels in subject with NGT did not change from the baseline levels after glucose loading, TBARS levels were significantly elevated in subjects with DGT and IGT (p< 0.001 and p< 0.001). Plasma Cu-Zn SOD activities were within a similar range in all subjects at baseline. Cu-Zn SOD activities were significantly increased in subjects with NGT, and were significantly decreased in subjects with IGT and DGT (p< 0.001 and p< 0.001) after glucose loading. There was a positive correlation between NO and glucose in subjects with NGT (r = 0.34, p< 0.01) and a negative correlation between NO and TBARS in IGT sum DGT during glucose tolerance (r= -0.38, p< 0.01). We suggest that NO availability was decreased when the blood glucose levels were only moderately elevated above normal levels. This might be related with the enhanced oxidative stress.     

An ECT2-centralspindlin complex regulates the localization and function of RhoA

In anaphase, the spindle dictates the site of contractile ring assembly. Assembly and ingression of the contractile ring involves activation of myosin-II and actin polymerization, which are triggered by the GTPase RhoA. In many cells, the central spindle affects division plane positioning via unknown molecular mechanisms. Here, we dissect furrow formation in human cells and show that the RhoGEF ECT2 is required for cortical localization of RhoA and contractile ring assembly. ECT2 concentrates on the central spindle by binding to centralspindlin. Depletion of the centralspindlin component MKLP1 prevents central spindle localization of ECT2; however, RhoA, F-actin, and myosin still accumulate on the equatorial cell cortex. Depletion of the other centralspindlin component, CYK-4/MgcRacGAP, prevents cortical accumulation of RhoA, F-actin, and myosin. CYK-4 and ECT2 interact, and this interaction is cell cycle regulated via ECT2 phosphorylation. Thus, central spindle localization of ECT2 assists division plane positioning and the CYK-4 subunit of centralspindlin acts upstream of RhoA to promote furrow assembly.     

Levels of cytokines (IL-1beta, IL-2, IL-6, IL-8, TNF-alpha) and trace elements (Zn, Cu) in breast milk from mothers of preterm and term infants

It has been well documented that human milk contains several immunomodulator components which are important during infant period when the newborn's immune system is still under development. In this study, we aim at examining levels of cytokines, zinc (Zn), and copper (Cu) in milk from mothers of premature and mature infants, and comparing changes during lactation periods consequently. Milk was collected from total of 40 mothers (group M: mothers of mature infants, n = 20; group PM: mothers of premature infants, n = 20) from four lactation stages: colostrum (0-7 days), transitional (7-14 days), mature milk (21 days), and mature milk (2nd month). Levels of cytokines (interleukin [IL]-lbeta, IL-2, IL-6, IL-8, tumor necrosis factor-alpha [TNF-alpha]) were determined by chemiluminesence method, whereas atomic absorption spectrophotometer was used for the determination of Zn and Cu levels. Cytokine levels were determined to be high in colostrum and transient milk from mothers of full-term infants, whereas their levels were reduced drastically in the 21st day and the 2nd month milk (P < .01, P < .001). Similar trends were observed in milk from mothers of premature infants, but cytokine levels were significantly lower in colostrum compared to colostrum from mothers of mature infants (P < .01). The differences in cytokine levels were continuous in transient milk (P < .05) and mature milk (21 days) (P < .05), whereas there was no statistically significant differences between milk from both groups of mothers in the 2nd month (P > .05). Zn levels in milk from mothers of premature infants were significantly lower compared to the ones from mothers of mature infants (P < .01) and these differences continued through the 2nd month. Although Cu levels were lower in milk from mothers of premature infants, there was no statistically significant difference except colostrum (P > .05). Our results clearly demonstrate that the level of immunomodulating agents such as cytokines and trace elements in milk from mothers of premature infants is less than the level of the same agents in milk from mothers of full-term infants. Although there are commercially available products for infant feeding, human milk is still the best natural nutrient for newborns. Therefore, when premature infants are breastfed, necessary precautions such as supplemantary diets must be considered for possible infections and risks related with immune system deficiency.     

A Remarkable Age-Related Increase in SIRT1 Protein Expression against Oxidative Stress in Elderly: SIRT1 Gene Variants and Longevity in Human

Aging is defined as the accumulation of progressive organ dysfunction. Controlling the rate of aging by clarifying the complex pathways has a significant clinical importance. Nowadays, sirtuins have become famous molecules for slowing aging and decreasing age-related disorders. In the present study, we analyzed the SIRT1 gene polymorphisms (rs7895833 A>G, rs7069102 C>G and rs2273773 C>T) and its relation with levels of SIRT1, eNOS, PON-1, cholesterol, TAS, TOS, and OSI to demonstrate the association between genetic variation in SIRT1 and phenotype at different ages in humans. We observed a significant increase in the SIRT1 level in older people and found a significant positive correlation between SIRT1 level and age in the overall studied population. The oldest people carrying AG genotypes for rs7895833 have the highest SIRT1 level suggesting an association between rs7895833 SNP and lifespan longevity. Older people have lower PON-1 levels than those of adults and children which may explain the high levels of SIRT1 protein as a compensatory mechanism for oxidative stress in the elderly. The eNOS protein level was significantly decreased in older people as compared to adults. There was no significant difference in the eNOS level between older people and children. The current study is the first to demonstrate age-related changes in SIRT1 levels in humans and it is important for a much better molecular understanding of the role of the longevity gene SIRT1 and its protein product in aging. It is also the first study presenting the association between SIRT1 expression in older people and rs7895833 in SIRT1 gene.