Halogen–water–hydrogen bridges in biomolecules

The importance of water in biological systems has long been recognized in chemistry and biology communities. In this article we describe a new manner by which water affects biomolecular behaviors, called halogen–water–hydrogen bridge (XWH bridge), that is, one hydrogen bonding (H-bonding) in water-mediated H-bond bridge is replaced by halogen bonding (X-bonding). Although behaving similarly to water-mediated H-bond motif, the XWH bridge usually stands in multifurcated forms and possesses stronger directionality. Quantum mechanical analysis on several model and real systems reveals that the XWH bridges are more thermodynamically stable than other water-involved interactions, and this stability is further enhanced by the cooperation of X-bonding and H-bonding. Crystal structure survey clearly demonstrates the significance of XWH bridges in stabilization of biomolecular conformations and in mediation of protein–protein, protein–nucleic acid, and receptor–ligand recognition and binding. These findings shed light into the potential value of XWH bridges in drug design and biological engineering.     

Mobility unevenness in rock–paper–scissors models

We investigate a tritrophic system whose cyclic dominance is modelled by the rock–paper–scissors game. We consider that organisms of one or two species are affected by movement limitations, which unbalances the cyclic spatial game. Performing stochastic simulations, we show that mobility unevenness controls the population dynamics. In the case of one slow species, the predominant species depends on the level of mobility restriction, with the slow species being preponderant if the mobility limitations are substantial. If two species face mobility limitations, our outcomes show that being higher dispersive does not constitute an advantage in terms of population growth. On the contrary, if organisms move with higher mobility, they expose themselves to enemies more frequently, being more vulnerable to being eliminated. Finally, our findings show that biodiversity benefits in regions where species are slowed. Biodiversity loss for high mobility organisms, common to cyclic systems, may be avoided with coexistence probability being higher for robust mobility limitations. Our results may help biologists understand the dynamics of unbalanced spatial systems where organisms’ dispersal is fundamental to biodiversity conservation.     

Environment–host–parasite interactions in mass-reared insects

The mass production of insects is rapidly expanding globally, supporting multiple industrial needs. However, parasite infections in insect mass-production systems can lower productivity and can lead to devastating losses. High rearing densities and artificial environmental conditions in mass-rearing facilities affect the insect hosts as well as their parasites. Environmental conditions such as temperature, gases, light, vibration, and ionizing radiation can affect productivity in insect mass-production facilities by altering insect development and susceptibility to parasites. This review explores the recent literature on environment–host–parasite interactions with a specific focus on mass-reared insect species. Understanding these complex interactions offers opportunities to optimise environmental conditions for the prevention of infectious diseases in mass-reared insects.     

The DNA–DNA spacing in gemini surfactants–DOPE–DNA complexes

Gemini surfactants from the homologous series of alkane-α,ω-diyl-bis(dodecyldimethylammonium bromide) (CnCS12, number of spacer carbons n = 2 – 12) and dioleoylphosphatidylethanolamine (DOPE) were used for cationic liposome (CL) preparation. CLs condense highly polymerized DNA creating complexes. Small-angle X-ray diffraction identified them as condensed lamellar phase L_α^C in the studied range of molar ratios CnGS12/DOPE in the temperature range 20 – 60 °C. The DNA–DNA distance (d_DNA) is studied in dependence to CnGS12 spacer length and membrane surface charge density. The high membrane surface charge densities (CnGS12/DOPE = 0.35 and 0.4 mol/mol) lead to the linear dependence of d_DNA vs. n correlating with the interfacial area of the CnGS12 molecule.     

Dipole–Dipole Interactions in Microtubules

Dimers in microtubules possess a dipole moment with components along three axes. The interaction energy among all dipole components in a microtubule was calculated for an un-deformed and an elliptically deformed microtubule in a dry condition. The interaction energy was found to increase with deformation. The total interaction energy among all dipoles is positive, which implies that the un-deformed cylindrical shape of a microtubule represents a condition of minimum energy. This suggests that the cylindrical shape of microtubules is a consequence of dipole–dipole interactions. There may be other causes as well but these are not discussed in this paper. From these results, the contributions of the dipole–dipole interaction energy to the microtubule longitudinal and transverse flexural rigidities were calculated. It is shown that the longitudinal contribution to the elastic modulus is approximately 50–60% of the total measured value while the calculated transverse contribution is smaller than the longitudinal contribution by a factor of approximately 3. The ratio of the measured axial to the measured transverse flexural rigidity is approximately 125, in agreement with recent observations. However, these values are uncertain for reasons discussed in the text.     

Parent–Offspring Conflict in Primates

Parent–offspring conflict (POC) theory (Trivers, 1974) has stimulated controversy in evolutionary biology and behavioral ecology. The theory has been criticized by some primate behavioral researchers on both conceptual and empirical grounds. First, it has been argued that it would be more advantageous to mothers and offspring to agree over the allocation of parental investment and to cooperate rather than to disagree and engage in conflict. Second, some studies have provided data suggesting that primate mothers and offspring engage in behavioral conflict over the scheduling of their activities rather than parental investment. In reality, parent–offspring interactions are likely to involve both cooperation and conflict, and the hypothesis that mothers and infants squabble over the scheduling of their activities is not incompatible with POC theory. Furthermore, the predictions of POC theory are supported by a number of empirical studies of primates. POC theory has enhanced our understanding of the dynamics of parent–offspring relationships in many animal species, and it is very likely that future studies of primates will continue to benefit from using POC theory as an explanatory framework.     

Auditory–vocal mirroring in songbirds

Mirror neurons are theorized to serve as a neural substrate for spoken language in humans, but the existence and functions of auditory–vocal mirror neurons in the human brain remain largely matters of speculation. Songbirds resemble humans in their capacity for vocal learning and depend on their learned songs to facilitate courtship and individual recognition. Recent neurophysiological studies have detected putative auditory–vocal mirror neurons in a sensorimotor region of the songbird''s brain that plays an important role in expressive and receptive aspects of vocal communication. This review discusses the auditory and motor-related properties of these cells, considers their potential role on song learning and communication in relation to classical studies of birdsong, and points to the circuit and developmental mechanisms that may give rise to auditory–vocal mirroring in the songbird''s brain.     

Structure–function correlations in tyrosinases

Tyrosinases are metalloenzymes belonging to the type-3 copper protein family which contain two copper ions in the active site. They are found in various prokaryotes as well as in plants, fungi, arthropods, and mammals and are responsible for pigmentation, wound healing, radiation protection, and primary immune response. Tyrosinases perform two sequential enzymatic reactions: hydroxylation of monophenols and oxidation of diphenols to form quinones which polymerize spontaneously to melanin. Two other members of this family are catechol oxidases, which are prevalent mainly in plants and perform only the second oxidation step, and hemocyanins, which lack enzymatic activity and are oxygen carriers. In the last decade, several structures of plant and bacterial tyrosinases were determined, some with substrates or inhibitors, highlighting features and residues which are important for copper uptake and catalysis. This review summarizes the updated information on structure–function correlations in tyrosinases along with comparison to other type-3 copper proteins.     

Trends in schistosomiasis-related mortality in Brazil, 2000–2011

Schistosomiasis is an important public health problem, with high morbidity and mortality in endemic countries. We analysed the epidemiological characteristics and time trends of schistosomiasis-related mortality in Brazil. We performed a nationwide study based on official mortality data obtained from the Brazilian Mortality Information System. We included all deaths in Brazil between 2000 and 2011, in which schistosomiasis was mentioned on the death certificate as an underlying or associated cause of death (multiple causes of death). We calculated crude and age-adjusted mortality rates (per 100,000 inhabitants), and proportional mortality rates. Trends over time were assessed using joinpoint regression models. Over the 12-year study period, 12,491,280 deaths were recorded in Brazil. Schistosomiasis was mentioned in 8,756 deaths, including in 6,319 (72.2%) as an underlying cause and in 2,437 (27.8%) as an associated cause. The average annual age-adjusted mortality rate was 0.49 deaths/100,000 inhabitants (95% confidence interval: 0.46–0.52) and proportional mortality rate was 0.070% (95% confidence interval: 0.069–0.072). Males (0.53 deaths/100,000 inhabitants), those aged ⩾70 years (3.41 deaths/100,000 inhabitants), those of brown race/colour (0.44 deaths/100,000 inhabitants), and residents in the Northeast region of Brazil (1.19 deaths/100,000 inhabitants) had the highest schistosomiasis-related death rates. Age-adjusted mortality rates showed a significant decrease at a national level (Annual Percent Change: −2.8%; 95% confidence interval: −4.2 to −2.4) during the studied period. We observed decreasing mortality rates in the Northeast (Annual Percent Change: −2.5%; 95% confidence interval: −4.2 to −0.8), Southeast (Annual Percent Change: −2.2%; 95% confidence interval: −3.6 to −0.9), and Central-West (Annual Percent Change: −7.9%; 95% confidence interval: −11.3 to −4.3) regions, while the rates remained stable in the North and South regions. Despite the reduced mortality, schistosomiasis is still a neglected cause of death in Brazil, with considerable regional differences. Sustainable control measures should focus on increased coverage, and intensified and tailored control measures, to prevent the occurrence of severe forms of schistosomiasis and associated deaths.     

Nuclear protein in the liver in protein–calorie deficiency

1. The effect of protein–calorie deficiency on nuclear proteins was studied in growing and adult rats by using chemical and electrophoretic methods of fractionation. 2. After 7 days on protein-deficient diets, the amount of neutral-soluble proteins increased, and their electrophoretic pattern changed, with the appearance of a new component. 3. The histone fraction of the liver nuclei in rapidly growing rats was lower than that in either deficient or adult animals. 4. The possible role of nuclear proteins in relation to synthesis of the proteins and nucleic acids of the other parts of the cells is discussed.     

Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions

An original experimental method of direct molecular fishing has been developed for identification of potential partners of protein–protein and protein–peptide interactions. It is based on combination of surface plasmon resonance technology (SPR), size exclusion and affinity chromatography and mass spectrometric identification of proteins (LC-MS/MS). Previously, we demonstrated applicability of this method for protein interactomics using experimental model system, as well as in the pilot study in the frame of the Human Proteome Project (HPP). In the present paper, this method was successfully applied to identify possible molecular partners of 7 target proteins encoded by genes of 18 chromosome (also in the frame of the HPP). Fishing on the affinity sorbents with immobilized target proteins as ligands was carried out using total lysate of human liver tissue as well as pooled sets of fractions (individual for each bait-protein) obtained by means of a combination of size exclusion chromatography and SPR analysis for the presence of potential prey-proteins in each fraction. As a result we obtained lists of possible molecular partners of all 7 proteins and performed a comparative evaluation of direct fishing specificity for these target proteins. Direct molecular fishing was also successfully used for search of potential protein partners interacting with different isoforms of amyloid-beta peptide, playing a key role in the development of Alzheimer’s disease. The synthetic peptides that are analogues of the metal-binding domain isoforms of beta-amyloid were used as molecular baits and the fishing was performed in various fractions of immortalized human neural cells. As a result, 13 potential partner proteins were identified in the cytosol fraction of the cells by fishing on amyloid-beta peptide (1-16).     

Trends in regional cancer mortality in Taiwan 1992–2014

BackgroundAlthough the cancer mortality rate in Taiwan has been declining in recent years, no study has yet reported any regional differences in cancer mortality rates in Taiwan. We hypothesized that regional cancer mortality rates in Taiwan, an ethnically homogeneous society, exhibited no significant variations.MethodsWe investigated the trends in Taiwan regional cancer mortality between 1992 and 2014. We analyzed regional age-standardized cancer mortality rates for lung, liver, colon, stomach, oral, breast, and prostate cancers using the Taiwan Longitudinal Health Insurance Database and Demographic Database. Furthermore, we applied Joinpoint regression analysis to evaluate the trends across different regions.ResultsThere are clear regional variations in mortality rates for liver, stomach, and oral cancers, but not for lung, colon, breast, and prostate cancers. The regional death rates of oral cancer, especially for eastern Taiwan, not only elevate the fastest (APC = 14.78% per year, P < 0.001) but also show the largest disparities between men and women. Regional death rates for stomach cancer, which declined most rapidly, are converging in both general and gender groups. Liver cancer is the only one with regional variations whose trends do not all go in the same direction. We also demonstrated that northern Taiwan has significant regional advantages with respect to cancer mortality.ConclusionsSome but not all cancers in Taiwan show regional disparities. Liver, stomach, and oral cancers in Taiwan exhibit clear regional variations in mortality rates. In particular, the regional variations in oral cancer mortality rates are consistent with those in alcohol consumption.     

Mycotoxins in several Polish food products in 2004–2005

In 2004–2005, samples of several selected Polish foods such as cereal products, nuts, dried fruits, coffee and culinary spices collected from Warsaw market and taken from food producers were analyzed on presence of aflatoxin B₁, B₂, G₁, G₂ (AF), ochratoxin A (OTA), zearalenone (ZEA) and deoxynivalenol (DON). After extraction and clean-up of extracts on immunoaffinity columns (IAC), mycotoxin analyses were carried out by HPLC using fluorescence and UV detectors. The concentrations of aflatoxins and ochratoxin A depending on the kind of sample ranged from 0.02 to 7.8 (one sample, of peanuts) and 0.02–11.9 μg/kg (one coffee sample), respectively. The levels of ZEA and DON were found to be below 50 °g/kg.     

Molecular regulation of hypothalamus–pituitary–gonads axis in males

The hypothalamic–pituitary–gonadal axis (HPG) plays vital roles in reproduction and steroid hormone production in both sexes. The focus of this review is upon gene structures, receptor structures and the signaling pathways of gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH) and follicle-stimulating hormone (FSH). The hormones' functions in reproduction as well as consequences resulting from mutations are also summarized. Specific characteristics of hormones such as the pulsatile secretions of GnRH are also covered. The different regulators of the HPG axis are introduced including kisspeptin, activin, inhibin, follistatin, androgens and estrogen. This review includes not only their basic information, but also their unique function in the HPG axis. Here we view the HPG axis as a whole, so relations between ligands and receptors are well described crossing different levels of the HPG axis. Hormone interactions and transformations are also considered. The major information of this article is depicted in three figures summarizing the current discoveries on the HPG axis. This article systematically introduces the basic knowledge of the HPG axis and provides information of the current advances relating to reproductive hormones.     

Grazer diversity effects in an eelgrass–epiphyte–microphytobenthos system

The dramatic loss of biodiversity and its consequences for ecosystem processes have been of considerable interest in recent ecological studies. However, the complex and interacting processes influencing diversity effects in multitrophic systems are still poorly understood. We used an experimental eelgrass system to study the effects of changing richness of three consumer species on the biomass, diversity and taxonomic composition of both epiphytic and benthic microalgal assemblages. After 1 week, consumer richness enhanced the grazing impact on epiphyte biomass relative to single consumer treatments and a positive effect of consumer richness on prey diversity was found. Moreover, strong effects of consumer species identity on taxonomic composition were found in both microalgal assemblages. However, the effects of consumer richness were not consistent over time. The consequences of high nutrient availability seemed to have masked consumer richness effects.     

Gene–gene and gene–environment interactions in ulcerative colitis

Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene–gene and gene–environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust Case–Control Consortium (WTCCC) IBD GWAS was used as a replication cohort. We applied logic regression (LR), a novel adaptive regression methodology, to search for high-order interactions. Exploratory genotype correlations with UC sub-phenotypes [extent of disease, need of surgery, age of onset, extra-intestinal manifestations and primary sclerosing cholangitis (PSC)] were conducted. The combination of 133 UC loci yielded good UC risk predictability [area under the curve (AUC) of 0.86]. A higher cumulative allele score predicted higher UC risk. Through LR, several lines of evidence for genetic interactions were identified and successfully replicated in the WTCCC cohort. The genetic interactions combined with the gene-smoking interaction significantly improved predictability in the model (AUC, from 0.86 to 0.89, P = 3.26E?05). Explained UC variance increased from 37 to 42 % after adding the interaction terms. A within case analysis found suggested genetic association with PSC. Our study demonstrates that the LR methodology allows the identification and replication of high-order genetic interactions in UC GWAS datasets. UC risk can be predicted by a 133 loci and improved by adding gene–gene and gene–environment interactions.     

Shaping the science–industry–policy interface in synthetic biology

Current advances in the emerging field of synthetic biology and the improvements in key technologies promise great impacts, not only on future scientific development, but also on the economy. In this paper we will adopt the triple helix concept for analyzing the early stages of a new field of science and innovation, namely synthetic biology. Synthetic biology is based on the creation and assembly of parts in order to create new and more complex structures and functions. These features of synthetic biology raise questions related to standardization and intellectual property, but also to security and public perception issues that go beyond the classical biotechnology discussions. These issues concern all involved actors in the synthetic biology field and affect the interrelationship between science, industry and policy. Based on the results of the recently finished EU FP-6 funded project TESSY (http://www.tessy-europe.de), the article analyzes these issues. Additionally, it illustrates the setting of clear framework conditions for synthetic biology research and development and the identification and definition of common goals for the future development of the field which will be needed for efficient science–industry–policy interaction. It was shown that it will be crucial to develop approaches that consider the needs of science and industry, on the one hand, and comply with the expectations of society, on the other hand. As synthetic biology is a global activity, the involvement of national decision-makers in international initiatives will further stimulate the development of the field.     

X–linked Recessive Inheritance in the Ehlers–Danlos Syndrome

Two families are described in which the Ehlers–Danlos syndrome is apparently transmitted as an X-linked recessive character. The results of tests for the Xg blood groups and for colour vision show that the locus for the Ehlers–Danlos syndrome is not close to that for the Xg groups nor very close to the locus for deutan colour-blindness.The clinical features of this variety of the Ehlers–Danlos syndrome include considerable hyperextensibility of the skin and a bruising tendency.     

Fluid–structure interaction in a fully coupled three-dimensional mitral–atrium–pulmonary model

This paper aims to investigate detailed mechanical interactions between the pulmonary haemodynamics and left heart function in pathophysiological situations (e.g. atrial fibrillation and acute mitral regurgitation). This is achieved by developing a complex computational framework for a coupled pulmonary circulation, left atrium and mitral valve model. The left atrium and mitral valve are modelled with physiologically realistic three-dimensional geometries, fibre-reinforced hyperelastic materials and fluid–structure interaction, and the pulmonary vessels are modelled as one-dimensional network ended with structured trees, with specified vessel geometries and wall material properties. This new coupled model reveals some interesting results which could be of diagnostic values. For example, the wave propagation through the pulmonary vasculature can lead to different arrival times for the second systolic flow wave (S2 wave) among the pulmonary veins, forming vortex rings inside the left atrium. In the case of acute mitral regurgitation, the left atrium experiences an increased energy dissipation and pressure elevation. The pulmonary veins can experience increased wave intensities, reversal flow during systole and increased early-diastolic flow wave (D wave), which in turn causes an additional flow wave across the mitral valve (L wave), as well as a reversal flow at the left atrial appendage orifice. In the case of atrial fibrillation, we show that the loss of active contraction is associated with a slower flow inside the left atrial appendage and disappearances of the late-diastole atrial reversal wave (AR wave) and the first systolic wave (S1 wave) in pulmonary veins. The haemodynamic changes along the pulmonary vessel trees on different scales from microscopic vessels to the main pulmonary artery can all be captured in this model. The work promises a potential in quantifying disease progression and medical treatments of various pulmonary diseases such as the pulmonary hypertension due to a left heart dysfunction.