The effect of heat stress on performance, fertility, and adipokines involved in regulating systemic immune response during lipolysis of early lactating dairy cows.

The aim of this study was to assess the potential effect of heat stress on dairy cow productivity, fertility, and biochemical blood indices during the early lactation stage in a temperate climate. Additionally, the study aimed to determine the role of leptin and adiponectin in regulating the immune response accompanying lipolysis after calving in dairy cows. The study included 100 clinically healthy Polish Holstein-Friesian dairy cows selected based on parity and 305 d of milk yield from 5 commercial farms with similar herd management and housing systems. Prospective cohort data were recorded from calving day until 150 d in milk, and microclimate loggers installed inside the barns were used to record temperature and relative humidity data to calculate daily temperature-humidity index (THI) on the calving day, through +7, +14, and +21 d during early lactation. Additionally, monthly productive performance parameters such as milk yield, chemical composition, fatty acids composition, and fertility indices were analyzed. Results showed that the THI from calving day through +7, +14, and +21 d during early lactation was negatively associated with fertility parameters such as delayed first estrus postpartum and an elongated calving interval, respectively, by 29, 27, 25, and 16 d. Furthermore, an increase in THI value during early lactation was associated with an elongated artificially inseminated service period, days open, and intercalving period. Increasing THI from calving day (0 d) through +7, +14, and up to +21 d during early lactation was also linked to decreased milk yield by 3.20, 4.10, 5.60, and 5.60 kg, respectively. The study also found that heat stress during early lactation was associated with a lower body condition score in dairy cows and higher concentrations of leptin, nonesterified fatty acids, and ß-hydroxybutyrate, accompanied by a drastic reduction in adipose tissue-secreted adiponectin levels after calving. Additionally, heat stress-induced lipolysis in adipose tissue caused an inflammatory response that increased biochemical blood indices associated with immune responses such as cytokines, acute phase proteins, and heat shock protein. These findings suggest that exposing dairy cows to heat stress during early lactation can negatively affect their productive performance, fertility, and biochemical blood indices in subsequent lactations. Thus, farm management changes should be implemented during early lactation to mitigate the negative consequences of heat stress occurrence.

Short- and long-term effects of initial serum total protein, average starter feed intake during the last week of the preweaning period, and rearing body gain on primiparous dairy heifers' performance.

The aim of this study was to evaluate the short- and long-term effects of initial serum total protein (STP) concentration, average starter feed intake (SI) during the last week of the preweaning period, and average daily gain (ADG) on the growth, fertility, and performance of Holstein heifers during their first lactation. Eighty-four female Holstein dairy calves were weaned at d 56 of age and then the study continued until the end of the first lactation. Growth performance, including body weight, ADG, withers height, and its change were analyzed monthly from 3 to 450 d of life, and reproduction data and performance in the first lactation of primiparous dairy heifers over a 4-yr period (2015 to 2019) were recorded. In the first 24 h of life, calves received 4 L of colostrum (<2 h and <12 h after birth); on d 2 and 3: 2 feedings/d of 2 L of transition milk; from d 4 to 49: 6 L/d of milk replacer (150 g of powder/L as-fed) in 3 feedings; and from d 50 to 56: 2 L/d of milk replacer in 1 feeding. The calves were fed pelleted starter feed from d 4 to 56, and after that from 8 wk until 3 mo of age, a dry total mixed ration with an 85:15 ratio of weaning pelleted starter to straw. From 3 to 7 mo and from 8 mo of age to calving, the total mixed ration contained 16.9% and ~14.0% crude protein, respectively, on a dry matter basis and ~2.40 Mcal of metabolizable energy/kg on a dry matter basis. The results of the current study showed that the initial STP concentration of primiparous dairy heifers was associated with improved growth performance, especially greater body weight and withers height. In addition, with increasing levels of initial STP concentration, age at first estrus, artificial insemination (AI) service, pregnancy, and calving was decreased by 16, 18, 25, and 25 d, respectively. Initial STP concentration was positively correlated with milk production and increased total milk yield and yield of energy-corrected milk by about 1,558 kg and 1,149 kg during first lactation. Calves with higher average starter feed intake during the last week of the preweaning period had better growth performance, which in turn was positively associated with fertility parameters, accelerated first estrus (by 17 d), and reduced age at AI service (by 13 d). Preweaning ADG was favorably associated with fertility performance of heifers, with faster occurrence of first estrus and a reduction in age at AI service, pregnancy, and calving. Also, increasing preweaning ADG increased milk yield, energy-corrected milk, and 4% fat-corrected milk at 305 DIM by about 829, 754, and 763 kg at first lactation of primiparous heifers. These results indicate that in the rearing period, particular attention should be paid to the initial STP concentration, average SI during the last week of this period, and rearing ADG to increase growth, fertility, and performance in the first lactation of primiparous dairy heifers.

Effect of oat hay provision method on growth performance, rumen fermentation and blood metabolites of dairy calves during preweaning and postweaning periods.

The comparison of the effects of all forage offering methods would be particularly useful information in modeling growth performance and rumen fermentation of dairy calves. Therefore, this study attempted to evaluate the effects of methods of oat hay provision on growth performance, rumen fermentation and biochemical blood indices of dairy calves during preweaning and postweaning periods. At birth, 40 female Polish Holstein-Friesian calves (3 days of age; 39.6 ± 0.39 kg BW) were randomly assigned to four treatment groups differing in the access to chopped oat hay: CON (control, starter without oat hay), OH (starter feed containing 10% DM basis oat hay), OH-FC (starter feed containing 10% DM basis oat hay and oat hay fed as free-choice provision in different buckets) and FC (starter feed and oat hay fed as free-choice provision in different buckets). The calves were weaned on day 56, and then the study continued until day 84. Intakes of starter feed and oat hay were recorded daily, whereas BW and hip height (HH) on day 3 and then every 14 days. Samples of blood were collected on the initiation of experiment and then every 14 days, and rumen contents on day 28, 56 and 84. No treatment effects were found for starter, starch, CP, total DM intake, average daily gain, feeding efficiency, change in HH, ruminal fluid pH, concentrations of ruminal propionate and NH3-N, concentrations of urea nitrogen and non-esterified fatty acids in the blood. There were differences between treatments in terms of ruminal total volatile fatty acids and molar concentrations of acetate, butyrate and acetate to propionate ratio; highest in OH and OH-FC groups, especially during the postweaning period. On the other hand, lower concentrations of iso-valerate were found in OH and OH-FC groups on day 56 and 84. The concentrations of IGF-I throughout the experiment and ß-hydroxybutyrate during the postweaning period in the blood were influenced by treatment, with the greatest values observed in OH and OH-FC calves. Results of this study indicate that starter feed containing chopped oat hay improves rumen fermentation parameters, which might allow successful transition from preruminant to mature ruminant state. Also, providing chopped oat hay with pelleted starter feed seems to be a better method than free-choice supplementation.

Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways.

The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 µs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.

Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning.

Carbon monoxide (CO) is a leading cause of poisoning deaths worldwide, without available antidotal therapy. Recently, a potential treatment for CO poisoning was introduced, based on binding of CO by neuroglobin (Ngb) with a mutated distal histidine (H64Q). Here, we present an atomistic mechanism of CO trapping by H64Q Ngb revealed by nonadiabatic molecular dynamics. We focused on CO photodissociation and recombination of CO to wild type (WT) and H64Q Ngb. Our results demonstrate that the distribution of CO within the proteins differs substantially due to rearrangement of amino acids surrounding the distal heme pocket. This leads to the decrease of the distal pocket volume in H64Q Ngb in comparison to WT Ngb, trapping migrating CO molecules in the distal pocket. We show that the mutation implicates the shortening of the time scale of CO geminate recombination, making H64Q Ngb 2.7 times more frequent binder than WT Ngb.

Subacute ruminal acidosis affects fermentation and endotoxin concentration in the rumen and relative expression of the CD14/TLR4/MD2 genes involved in lipopolysaccharide systemic immune response in dairy cows.

The first objective of this study was to investigate the effects of subacute ruminal acidosis (SARA) on fermentation, ruminal free lipopolysaccharides (LPS), and expression of the cluster of differentiation 14 (CD14), toll-like receptor 4 (TLR4), and myeloid differentiation protein 2 (MD2) complex in white blood cells involved in the systemic immune response in dairy cows. The second objective was a study of whether increased expression of the LPS receptor complex led to increases in the concentrations of plasma high-density lipoprotein (HDL) and serum Ca. Three hundred five dairy cows located in 13 Polish high-yielding dairy commercial farms were selected according to their days in milk (40-150 d; average = 75), 305-d milk yield (10,070-12,041 kg; average = 10,940), and number of lactations (primiparous, n = 139 and multiparous, n = 166). Next, the herds were segregated into 3 groups based on the percentages of cows with an assigned value of ruminal fluid pH: SARA-positive, SARA-risk, and SARA-negative herds. Moreover, 305 selected dairy cows were divided according to the classification based on ruminal fluid pH into 3 groups as healthy (pH >5.81), risk (pH 5.8-5.6) and acidotic cows (pH <5.6). Rumen fluid samples were collected via rumenocentesis. In the AC group, we recorded higher concentrations of ruminal free LPS [4.57 Log10 endotoxin units (EU)/mL; 42,206 EU/mL] compared with the healthy group (4.48 Log10 EU/mL; 34,179 EU/mL). Similarly, the concentration of ruminal free LPS was higher in SARA-positive herds (4.60 Log10 EU/mL; 43,000 EU/mL) compared with SARA-negative herds (4.47 Log10 EU/mL; 32,225 EU/mL). The relative mRNA abundance of genes associated with the function of LPS receptors, such as CD14, TLR4, and MD2, in white blood cells differed between all experimental groups on both cow and herd levels. In the acidotic group, we recorded higher concentrations of HDL (78.16 vs. 68.32 mg/dL) and serum amyloid A (10.80 vs. 9.16 µg/mL) and lower concentrations of Ca (8.26 vs. 10.16 mg/dL) and haptoglobin (470.19 vs. 516.85 ng/mL) compared with the healthy group. Similar results were obtained in the SARA herd status analysis, but the concentration of lipopolysaccharide-binding protein differed statistically. Moreover, the pH of ruminal fluid was negatively correlated with relative mRNA abundance of genes such as CD14, TLR4, MD2, and concentrations of serum HDL and serum amyloid A, although positively correlated with serum Ca. The results indicated that decreases in ruminal fluid pH increased the release of free LPS into the rumen and stimulated the expression of the LPS receptor complex and immune response. Moreover, an increase in the expression of the LPS receptor led to higher concentrations of plasma HDL and lower serum Ca, which may be a protective mechanism against endotoxemia. However, the biological significance of these results needs to be investigated further in larger field trials.

Relationship between pH of ruminal fluid during subacute ruminal acidosis and physiological response of the Polish Holstein-Friesian dairy cows.

The aim of the study was to investigate the effect of ruminal fluid pH depression on biochemical indices of blood, urine, feces, and milk, and to determine which of them may be helpful as a marker for the diagnosis of subacute ruminal acidosis (SARA). Ruminal fluid samples were obtained by rumenocentesis from 305 cows representing 13 commercial dairy herds. The herds were selected based on percentages of cows with an assigned value of ruminal fluid pH segregated into three groups as: SARA-positive herd, if at least 25% of the ruminal fluid samples indicated a pH < 5.6; SARA-risk herd, if less than 25% of ruminal fluid samples indicated a pH < 5.6, but at least 33% showed a pH ≤ 5.8; and SARA-negative herd, if less than 25% of the ruminal fluid samples indicated a pH < 5.6, but less than 33% exhibited a pH = 5.8. Moreover, the dairy cows were divided according to the ruminal fluid pH into three groups as follows: healthy cows (HC, pH>5.80, n = 196), risk cows (RC, pH 5.8 - 5.6, n = 51), and acidotic cows (AC, pH < 5.6, n = 58). Almost 19% (58/305) of the cows were classified as acidotic (pH < 5.6) and 46.2% of the herds as SARA-positive. In the AC group, higher concentrations of insulin-like growth factor-I (IGF-I), non-esterified fatty acids (NEFA), rectal temperature and lower blood pH, compared with those of the HC group, were recorded. Moreover, in the SARA-positive herds, higher concentrations of IGF-I and the lowest blood pH, compared with SARA-negative herds, were observed. The lowering of ruminal fluid pH increased the blood IGF-I and NEFA concentrations and the rectal temperature and decreased the blood pH. These measures are indicators of the physiological changes that occur as part of the pathogenesis of the condition and may be helpful for the diagnosis of the SARA syndrome when serial measurements are conducted.

Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations.

Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

Assessment of oxidative/nitrative modifications of plasma proteins, selected ROTEM parameters and kinetics of fibrinogen polymerization in patients with multiple myeloma at diagnosis.

Patients with multiple myeloma (MM) are at increased risk of thrombosis. Growing evidence indicates that oxidative and nitrative modifications of proteins, including fibrinogen, may lead to changes in hemostasis. The study compares samples from patients with MM at diagnosis and healthy volunteers with regard to the oxidative/nitrative modifications of proteins, ROTEM and thrombin-catalyzed fibrin polymerization. The content of carbonyl groups in plasma proteins of patients with MM was significantly higher than in controls (2.981 vs. 1.807 nmol/mg of protein, p = 0.005), while no differences were seen in the concentrations of nitrated proteins. Maximum clot firmness readings were significantly higher in the samples of patients than in controls according to FIBTEM test (23.5 vs. 15 mm, p = 0.006). The lag time of the fibrin polymerization process and the velocity of clot lysis (V Lys) were found to be significantly higher in the group of MM patients than controls. In contrast, no marked differences were identified between studied groups in reference to maximal velocity of fibrin polymerization process (V max), maximal absorbance (A max) and plasmin amidolytic activity values. In conclusion, our study demonstrates that at the time of diagnosis, patients with MM demonstrated greater oxidative stress than healthy volunteers, which is reflected in a higher amount of carbonylated proteins. Some prothrombotic features found in ROTEM tests in MM patients were not confirmed by turbidimetry.

Prevalence and consequence of subacute ruminal acidosis in Polish dairy herds.

The aim of this study was to estimate the prevalence of subacute ruminal acidosis (SARA) in Polish high-yielding dairy herds. Also, the relationships between the chemical composition of the diet and the feed particle size, ruminal pH and the occurrence of this metabolic disease and the fermentation profile were determined. Rumen fluid samples were obtained from a total of 213 cows from nine dairy herds (≥20 cows per herd) via rumenocentesis. Almost 14% (30/213) of cows as acidotic (pH<5.6) were found, which is indicative of SARA. Moreover, 44% of the herds were classified as SARA-positive and 56% as SARA-negative. Results of the current study suggested that the physically effective NDF (NDF>1.18 mm) -to-starch ratio could be better indices than peNDF>1.18 mm to preventing the occurrence of SARA, and their level should not be lower than 1.00. Also, linear negative relationships between rumen fluid pH and concentration of propionate, valerate and total VFA were determined. According to the herd's SARA status and rumen fluid biochemical indices, there were significant differences between the pH of rumen fluid (p ≤ 0.01), concentrations of acetate (p ≤ 0.05), propionate (p ≤ 0.05), n-butyrate (p ≤ 0.01), n-valerate (p ≤ 0.01), the sum of VFA (p ≤ 0.01) and ammonia (p ≤ 0.05) in SARA-positive herds compared to SARA-negative herds. The better understanding the strategy of ruminant nutrition to coordinate energy conversion and the role of the ruminal pH in regulating N-NH3 production, absorption through rumen mucosa, urea secretion, the more successfully we can utilize these processes with due recognition of animal needs and welfare, as well as prevention of SARA occurrence.

Food protein-induced enterocolitis syndrome

Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-, cell-mediated food allergy of unknown prevalence and pathophysiology. Onset is typically during the first year of life; seafood-induced FPIES may start in adulthood. Acute FPIES manifests within 1-4 hours after ingestion with repetitive emesis, pallor, and lethargy progressing to dehydration and hypovolemic shock in 15% of cases. Chronic FPIES manifests with intermittent emesis, watery diarrhea, and poor growth progressing to dehydration and hypovolemic shock over a period of days to weeks. Chronic FPIES has been only reported in infants aged less than 3 months fed with cow milk (CM) or soy formula. The most common triggers are CM, soy, rice, and oat. Diagnosis of FPIES relies on recognition of a pattern of clinical symptoms and may be missed owing to the absence of typical allergic symptoms (eg, urticaria, wheezing) and delayed onset in relation to food ingestion. Physician-supervised food challenge is recommended if diagnosis or the trigger food is not clear and to evaluate for resolution. Testing for food-specific IgE is usually negative, although a subset of patients, usually with CM-induced FPIES may develop sensitization to foods. Such atypical FPIES tends to have a more prolonged course. Despite the potential severity of the reactions, no fatalities have been reported, and FPIES has a favorable prognosis. In most cases, FPIES resolves by age 3-5 years, although persistence of CM-induced FPIES and soy FPIES into adulthood has been reported. The first international consensus guidelines on diagnosis and management of FPIES were published in 2017. Given that the pathophysiology of FPIES is poorly understood, there are no diagnostic biomarkers and no therapies to accelerate resolution. These unmet needs warrant future investigations to improve the care of patients with FPIES (AU)

SEIOA es una alergia alimentaria con patofisiología y prevalencia desconocidas, que típicamente comienza en el primer año de vida, mientras que la producida por pescado suelo tener su comienzo en adultos. La forma aguda se manifiesta entre la hora y 4 horas tras la ingesta del alimento con emesis, palidez, letargia progresiva por deshidratación y shock hipovolémico en el 15% de los casos. La forma crónica se manifiesta con emesis intermitente, diarreas y crecimiento pobre con progresión hacia la deshidratación y shock hipovolémico en un periodo de días o semanas. La forma crónica se ha podido observar únicamente en niños menores de 3 años alimentados con leche de vaca o fórmula de soja. Los desencadenantes más frecuentes son la leche de vaca, la soja, el arroz y avena. El diagnóstico es clínico y puede ser difícil debido a la ausencia de síntomas alérgicos típicos (urticaria, asma…) y a la relación retardada con la ingesta. Es recomendable la provocación controlada si el diagnóstico clínico o el alimento implicado no son claros y también para evaluar la evolución. La IgE específica suele ser negativa, aunque una parte de los pacientes puede desarrollar alergia mediada por IgE. Estos pacientes manifiestan un curso más prolongado. A pesar de la potencial severidad de las reacciones, no se han reportado casos fatales y tiene un pronóstico favorable. La mayoría de los niños consiguen la resolución entre los 3 y 5 años aunque existen casos de persistencia en adultos. Las guías del primer consenso internacional sobre el diagnóstico y tratamiento de esta enfermedad se publicarán en el 2017. Debido a la poco conocida patofisiología, no existen biomarcadores ni terapia que acelere su resolución. Son necesarios estudios que permitan investigar y mejorar la clínica de estos pacientes (AU)

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.

In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The mapping retains the main structural changes occurring during the dissociation. The topological similarity of the reduced paths may be easily studied using the Fréchet distances, and we show that this measure facilitates machine learning classification of the diffusion pathways. Further, low-dimensional configuration space allows for identification of residues active in transport during the ligand diffusion from a protein. The utility of this approach is illustrated by examination of the configuration space of cytochrome P450cam involved in expulsing camphor by means of enhanced all-atom molecular dynamics simulations. The expulsion trajectories are sampled and constructed on-the-fly during molecular dynamics simulations using the recently developed memetic algorithms [ Rydzewski, J.; Nowak, W. J. Chem. Phys. 2015 , 143 ( 12 ), 124101 ]. We show that the memetic algorithms are effective for enforcing the ligand diffusion and cavity exploration in the P450cam-camphor complex. Furthermore, we demonstrate that machine learning techniques are helpful in inspecting ligand diffusion landscapes and provide useful tools to examine structural changes accompanying rare events.

Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations.

This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads to an increase of the main- and side-chain entropies in proteins. We show that such over-minimization may diverge the protein structures from the near-native attraction basin which possesses a minimum of free energy. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein conformation. This measure may help in selection of adequate number of energy minimization steps in protein modelling and, thus, in preservation of the near-native protein conformation.

Memetic algorithms for ligand expulsion from protein cavities.

Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a pheromone concept is introduced to optimize an expulsion force. In IA, hybrid learning protocols are exploited to predict ligand exit paths. They are tested on three protein channels with increasing complexity: M2 muscarinic G-protein-coupled receptor, enzyme nitrile hydratase, and heme-protein cytochrome P450cam. In these cases, the memetic methods outperform simulated annealing and random acceleration molecular dynamics. The proposed algorithms are general and appropriate in all problems where an accelerated transport of an object through a network of channels is studied.

Study on the zona pellucida 4 (ZP4) gene sequence and its expression in the ovaries of patients with polycystic ovary syndrome.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a common endocrine disorder of unknown pathology, involving reproductive and metabolic abnormalities. Oocyte-specific genes are a group of genes expressed exclusively in ovarian tissue; therefore, they can play an important role in ovarian pathologies such as PCOS. The zona pellucida 4 (ZP4) gene encodes glycoprotein which is a part of the extracellular matrix of oocyte. MATERIALS AND METHODS: We analyzed 87 patients with PCOS, which were divided into four groups depending on their phenotype. In each patient, we performed profound clinical and biochemical analysis, including the measurement of serum androgens. The ovarian tissue samples were used to perform a real-time polymerase chain reaction and immunohistochemical staining using anti-ZP4 monoclonal antibodies. The ZP4 gene was sequenced from peripheral lymphocytes. RESULTS: The expression of ZP4 was present in early antral follicles and was stronger in mature follicles. The subgroup of patients with eumenorrhea and without hyperandrogenism presented the highest expression of ZP4 in ovarian tissue. In one case, we found a mutation of the ZP4 gene. No correlations were found between the ZP4 expression level and biochemical or clinical indices. CONCLUSIONS: Data from this and animal studies suggest a possible relationship between androgens and ZP4 expression. ZP4 expression is highest among patients with PCOS and a regular cycle, and this is a consequence of the presence of mature follicles in this group. In some patients with PCOS and infertility, ZP4 mutation can be found.

Nine steps to risk-informed wellhead protection and management: a case study.

Wellhead-protection zones are commonly delineated on the basis of advective travel-time analysis without considering any aspects of model uncertainty. In the past decade, research efforts have produced quantifiable risk-based safety margins for protection zones. These margins are based on well-vulnerability criteria (e.g., travel times, exposure times, peak concentrations) and take model and parameter uncertainty into account. There are three main reasons why practitioners still refrain from applying these new techniques. (1) They fear the additional areal demand of probabilistic safety margins; (2) probabilistic approaches are allegedly complex, not readily available and require huge computing resources, and (3) uncertainty bounds are fuzzy, whereas final decisions are binary. The primary goal of this paper is to show that these reservations are unjustified. We present a straightforward, computationally affordable framework that offers risk-informed decision support for robust and transparent wellhead delineation under uncertainty. We show that reliability levels can be increased by exchanging delineated low-risk areas for previously nondelineated high-risk areas. We also show that further improvements may often be available with only little additional delineated area. As proof of our concept, we illustrate our key points with the example of a pumped karstic well catchment, located in Germany.

Identifying tinnitus-related genes based on a side-effect network analysis.

Tinnitus, phantom sound perception, is a worldwide highly prevalent disorder for which no clear underlying pathology has been established and for which no approved drug is on the market. Thus, there is an urgent need for new approaches to understand this condition. We used a network pharmacology side-effect analysis to search for genes that are involved in tinnitus generation. We analyzed a network of 1,313 drug-target pairs, based on 275 compounds that elicit tinnitus as side effect and their targets reported in databases, and used a quantitative score to identify emergent significant targets that were more common than expected at random. Cyclooxigenase 1 and 2 were significant, which validates our approach, since salicylate is a known tinnitus generator. More importantly, we predict previously unknown tinnitus-related targets. The present results have important implications toward understanding tinnitus pathophysiology and might pave the way toward the design of novel pharmacotherapies.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e97; doi:10.1038/psp.2013.75; published online 29 January 2014.