Study of pellet formation of filamentous fungi Rhizopus oryzae using a multiple logistic regression model

Fungal pellet formation is an important topic of fermentation research. It has been reported that many factors such as agitation, medium nutrients, pH, polymer additives, and inoculum size influence the formation of fungal pellets. However, a few studies on the effects of all of these factors on fungal pellet formation have been reported. This paper conducted a comprehensive investigation using a completely randomized design (CRD) on a filamentous fungus, Rhizopus oryzae NRRL 395, in order to discover the effects of the above factors on fungal pellet formation. In addition, other factors, such as addition of biodegradable polymers and spore storage time that have not been reportedly studied were examined and their effects on pellet formation were investigated. A multiple logistic regression model was established to predict the probability of pellet formation using the above factors and their interactions as predictor variables. Model building and diagnostics were obtained using the Statistical Analysis System (SAS 9.0) program. The model developed in this study can be used to predict the pellet formation of other R. oryzae strains as well.     

Chemokine changes during oral wound healing

The oral mucosa is susceptible to tissue injury from many causes, including infection, autoimmune disorders, surgical and accidental trauma, and gingival and periodontal inflammation; however, little is known about the events that influence wound healing in the mouth. Recent studies in non-oral tissues have implicated immune system-derived factors, in particular chemokines, in the wound healing process. Tissues from mice with experimental gingival wounds were studied for expression of genes for four chemokine ligands or receptors (CCL19, CCL20, CCL25, and CCR5) that are important in leukocyte trafficking or inflammation. Notably, during the peak phase of wound healing, chemokine gene expression was up-regulated for CCL19, CCL20, and CCL25, and down-regulation of CCR5, suggesting an orchestrated process of chemokine-mediated recruitment or retention of lymphocytes and macrophages into wound areas, while simultaneously suppressing a potentially adverse inflammatory response. These findings have implications for developing therapeutic strategies aimed at promoting more effective tissue healing at oral surfaces.     

Identifying hypermethylated CpG islands using a quantile regression model

Background  

DNA methylation has been shown to play an important role in the silencing of tumor suppressor genes in various tumor types. In order to have a system-wide understanding of the methylation changes that occur in tumors, we have developed a differential methylation hybridization (DMH) protocol that can simultaneously assay the methylation status of all known CpG islands (CGIs) using microarray technologies. A large percentage of signals obtained from microarrays can be attributed to various measurable and unmeasurable confounding factors unrelated to the biological question at hand. In order to correct the bias due to noise, we first implemented a quantile regression model, with a quantile level equal to 75%, to identify hypermethylated CGIs in an earlier work. As a proof of concept, we applied this model to methylation microarray data generated from breast cancer cell lines. However, we were unsure whether 75% was the best quantile level for identifying hypermethylated CGIs. In this paper, we attempt to determine which quantile level should be used to identify hypermethylated CGIs and their associated genes.     

Plasma membrane changes during corpus luteum regression

Structural and biochemical changes were examined in the plasma membrane of luteal cells during corpus luteum regression. Structural alterations as indicated by an increase in the liquid-crystalline to gel phase transition temperature and a decrease in plasma membrane fluidity were observed during luteolysis in microsomes and in plasma membranes prepared from prostaglandin F2 alpha-treated rats, when samples were examined by wide angle x-ray diffraction and fluorescence polarization. In addition, a significant increase in activity of the lipolytic enzyme phospholipase A2 appeared during incubation of plasma membrane samples and dispersed luteal cells at 40 degrees C in the presence of 1.0 mM CaCl2. Similar incubation conditions also produced a drop in human chorionic gonadotropin (hCG) binding in luteal samples from prostaglandin F2 alpha-treated rats. These results indicate that during luteolysis there are important structural changes in the plasmalemma of regressing luteal cells. These alterations appear related to an increase in phospholipase A2 activity and a decrease in hCG receptors. These modifications may account for the decrease in function during corpus luteum regression.     

Porcine adrenal prolactin receptors: characterization, changes during neonatal development and effects of hypoprolactinemia

1. Adrenal prolactin (PRL) receptors were identified within the adrenal cortex of pigs (Sus domesticus), and found to be located specifically on isolated zona fasciculata/reticularis cells (6437 sites per cell). 2. These PRL receptors were associated with binding to [125I]-oPRL which was characterized as being time and temperature dependent, specific for PRL, saturable, of high affinity (Ka = 10(10)/M) with a single class of binding sites, and irreversible except under extreme conditions. 3. The concentrations (fmol/mg protein) of PRL receptors decreased by 35% (P less than 0.05) between 3 and 10 days of age, and subsequently remained constant until 30 days of age. Total content (fmol/paired adrenals) increased progressively (2-fold, P less than 0.05) between 3 and 30 days of age. 4. Short-term (less than 16 hr) and prolonged (7 weeks) hypoprolactinemia (46-64% of control levels, P less than 0.05) were not associated with changes in numbers of porcine adrenal unoccupied PRL receptors.     

Mechanical property of a TIM-barrel protein

The mechanical response of a TIM-barrel protein to an applied pressure has been studied. We generated structures under an applied pressure by assuming the volume change to be a linear function of normal mode variables. By Delaunay tessellation, the space occupied by protein atoms is divided uniquely into tetrahedra, whose four vertices correspond to atomic positions. Based on the atoms that define them, the resulting Delaunay tetrahedra are classified as belonging to various secondary structures in the protein. The compressibility of various regions identified with respect to secondary structural elements in this protein is obtained from volume changes of respective regions in two structures with and without an applied pressure. We found that the β barrel region located at the core of the protein is quite soft. The interior of the β barrel, occupied by side chains of β strands, is the softest. The helix, strand, and loop segments themselves are extremely rigid, while the regions existing between these secondary structural elements are soft. These results suggest that the regions between secondary structural elements play an important role in protein dynamics. Another aspect of tetrahedra, referred to as bond distance, is introduced to account for rigidities of the tetrahedra. Bond distance is a measure of separation of the atoms of a tetrahedron in terms of number of bonds along the polypeptide chain or side chains. Tetrahedra with longer bond distances are found to be softer on average. From this behavior, we derive a simple empirical equation, which well describes the compressibilities of various regions. © 1997 Wiley-Liss Inc.     

Estimation of human circadian phase via a multi-channel ambulatory monitoring system and a multiple regression model

Reliable detection of circadian phase in humans using noninvasive ambulatory measurements in real-life conditions is challenging and still an unsolved problem. The masking effects of everyday behavior and environmental input such as physical activity and light on the measured variables need to be considered critically. Here, we aimed at developing techniques for estimating circadian phase with the lowest subject burden possible, that is, without the need of constant routine (CR) laboratory conditions or without measuring the standard circadian markers, (rectal) core body temperature (CBT), and melatonin levels. In this validation study, subjects (N = 16) wore multi-channel ambulatory monitoring devices and went about their daily routine for 1 week. The devices measured a large number of physiological, behavioral, and environmental variables, including CBT, skin temperatures, cardiovascular and respiratory function, movement/posture, ambient temperature, and the spectral composition and intensity of light received at eye level. Sleep diaries were logged electronically. After the ambulatory phase, subjects underwent a 32-h CR procedure in the laboratory for measuring unmasked circadian phase based on the "midpoint" of the salivary melatonin profile. To overcome the complex masking effects of confounding variables during ambulatory measurements, multiple regression techniques were applied in combination with the cross-validation approach to subject-independent prediction of circadian phase. The most accurate estimate of circadian phase was achieved using skin temperatures, irradiance for ambient light in the blue spectral band, and motion acceleration as predictors with lags of up to 24 h. Multiple regression showed statistically significant improvement of variance of prediction error over the traditional approaches to determining circadian phase based on single predictors (motion acceleration or sleep log), although CBT was intentionally not included as the predictor. Compared to CBT alone, our method resulted in a 40% smaller range of prediction errors and a nonsignificant reduction of error variance. The proposed noninvasive measurement method could find applications in sleep medicine or in other domains where knowing the exact endogenous circadian phase is important (e.g., for the timing of light therapy).     

Systemic hemodynamic changes during the development of DOCA-salt hypertension. The effect of neonatal sympathectomy

The elevation of the cardiac index was discovered at the initial stage of DOCA-salt hypertension in rats. The blood pressure rise at the stage of stable hypertension was caused by an increase in the total peripheral vascular resistance. Neonatal sympathectomy prevented the development of DOCA-salt hypertension and elevation of the cardiac index revealed in control sympathectomized rats.     

Mechanical unloading impairs keratinocyte migration and angiogenesis during cutaneous wound healing.

Although initially thought to improve an individual's ability to heal, mechanical unloading promoted by extended periods of bed rest has emerged as a contributing factor to delayed or aberrant tissue repair. Using a rat hindlimb unloading (HLU) model of hypogravity, we mimicked some aspects of physical inactivity by removing weight-bearing loads from the hindlimbs and producing a systemic cephalic fluid shift. This model simulates bed rest in that the animal undergoes physiological adaptations, resulting in a reduction in exercise capability, increased frequency of orthostatic intolerance, and a reduction in plasma volume. To investigate whether changes associated with prior prolonged bed rest correlate with impaired cutaneous wound healing, we examined wound closure, angiogenesis, and collagen content in day 2 to day 21 wounds from rats exposed to HLU 2 wk before excisional wounding. Wound closure was delayed in day 2 wounds from HLU rats compared with ambulatory controls. Although the levels of proangiogenic growth factors, fibroblast growth factor-2 (FGF-2), and vascular endothelial growth factor (VEGF) were similar between the two groups, wound vascularity was significantly reduced in day 7 wounds from HLU animals. To further examine this disparity, total collagen content was assessed but found to be similar between the two groups. Taken together, these results suggest that keratinocyte and endothelial cell function may be impaired during the wound healing process under periods of prolonged inactivity or bed rest.     

Identification of relevant properties for epitopes detection using a regression model

A B-cell epitope is a part of an antigen that is recognized by a specific antibody or B-cell receptor. Detecting the immunogenic region of the antigen is useful in numerous immunodetection and immunotherapeutics applications. The aim of this paper is to find relevant properties to discriminate the location of potential epitopes from the rest of the protein surface. The most relevant properties, identified using two evaluation approaches, are the geometric properties, followed by the conservation score and some chemical properties, such as the proportion of glycine. The selected properties are used in a patch-based epitope localization method including a Single-Layer Perceptron for regression. The output of this Single-Layer Perceptron is used to construct a probability map on the antigen surface. The predictive performances of the method are assessed by computing the AUC using cross validation on two benchmark data sets and by computing the AUC and the precision for a third independent test set.     

Assessing the suitable cultivation areas for Scutellaria baicalensis in China using the Maxent model and multiple linear regression

Cultivating medical plants is an efficient way not only to meet the increasingly high demand for plant-based drugs but also to protect wild populations from overexploitation. The environments of cultivation areas should be suitable for both plant growth and accumulation of bioactive constituents. Scutellaria baicalensis Georgi (Huang-qin or Chinese skullcap) is a widely used herb that is suffering rapid population decline in China. To promote better cultivation of this herb, this paper reports a new approach for predicting potentially suitable cultivation areas and for building a mathematical relationship between environmental factors and the active ingredient content in S. baicalensis using the Maxent model and multiple linear regression. The results showed that extreme temperatures and precipitation had considerable impacts on the potential distribution of S. baicalensis. Higher annual mean temperature, precipitation seasonality, and lower isotherms contributed to higher baicalin content. The potential cultivation areas for S. baicalensis were mainly distributed in northeast China. Northeastern Inner Mongolia, part of Hebei and the regions in southwestern Liaoning Province were found to be highly suitable for cultivating S. baicalensis in China. The results of this study can allow growers and pharmaceutical companies to identify suitable areas for planting herbs, which could prevent the blind cultivation of this species in unsuitable habitats while ensuring the quality of S. baicalensis.