Advances in high-resolution quantitative proteomics: implications for clinical applications

The advances in high-resolution mass spectrometry instrumentation, capable of accurate mass measurement and fast acquisition, have enabled new approaches for targeted quantitative proteomics. More specifically, analyses performed on quadrupole-orbitrap mass spectrometers operated in parallel reaction monitoring (PRM) mode leverage the intrinsic high resolving power and trapping capabilities. The PRM technique offers unmatched degrees of selectivity and analytical sensitivity, typically required to analyze peptides in complex samples, such as those encountered in biomedical research or clinical studies. The features of PRM have provoked a paradigm change in targeted experiments, by decoupling acquisition and data processing. It has resulted in a new analytical workflow comprising distinct methods for each step, thus enabling much larger flexibility. The PRM technique was further enhanced by a new data acquisition scheme, allowing dynamic parameter settings. The potential of the technique may radically impact future quantitative proteomics studies.     

South Amerindian craniofacial morphology: diversity and implications for Amerindian evolution

The most compelling models concerning the peopling of the Americas consider that modern Amerindians share a common biological pattern, showing affinities with populations of the Asian Northeast. The aim of the present study was to assess the degree of variation of craniofacial morphology of South American Amerindians in a worldwide context. Forty-three linear variables were analyzed on crania derived from American, Asian, Australo-Melanesian, European, South-Saharan African, and Polynesian regions. South America was represented by seven Amerindian samples. In order to understand morphologic diversity among Amerindians of South America, variation was estimated using regions and local populations as units of analysis. Variances and F(ST) values were calculated for each unit, respectively. Both analyses indicated that morphologic variation in Southern Amerindians is extremely high: an F(ST) of 0.01531 was obtained for Southern Amerindians, and values from 0.0371-0.1205 for other world regions. Some aspects linked to the time and mode of the peopling of the Americas and various microevolutionary processes undergone by Amerindians are discussed. Some of the alternatives proposed to explain this high variation include: a greater antiquity of the peopling than what is mostly accepted, a peopling by several highly differentiated waves, an important effect of genetic drift, and gene flow with Paleoamericans. A combination of some of these alternatives explains at least some of the variation.     

Exploring the dark genome: implications for precision medicine

Mammalian Genome - The increase in the number of both patients and healthcare practitioners who grew up using the Internet and computers (so-called “digital natives”) is likely to...     

Molecular forensics: applications,implications and limitations.

Genotyping with DNA probes can theoretically identify each person on earth. Naturally occurring variations in the nucleotide sequence of DNA (DNA sequence polymorphisms) result in genetic differences between people. The Southern blot technique can reveal characteristic DNA banding patterns at a specific genetic locus. The polymorphic DNA banding patterns at several genetic loci can be combined to help construct individual DNA "fingerprints". Such fingerprints can resolve identity in criminal and paternity cases. The appropriate technology is being used in North American law enforcement agency laboratories. Although some technical drawbacks still exist, DNA genotyping with the Southern blot technique and even newer methods will likely become the standard for individual identification. An understanding of the principles underlying DNA genotyping is required before informed decisions can be made regarding its potential widespread application.     

Craniofacial anthropometry: Practical measurements of the head and face for clinical,surgical and research use.

By J.C. Kolar and E.M. Salter. Springfield, IL: Charles C. Thomas. 1996. xxiii + 334 pp. ISBN 0-398-06616-7. $69.95 (cloth).     

Patterns of covariation in the hominoid craniofacial skeleton: implications for paleoanthropological models

Living species are often used as analogues for fossil ones. When this is done, the implicit assumption is made that hominids and living hominoids vary in the same way. This paper addresses the validity of this assumption by comparing patterns of facial variation among humans and African apes. In particular, it addresses three major questions that underlie approaches to reconstructing hominid relationships. First, is phenotypic variation similar between closely related species? Second, if it is dissimilar, why? Third, is it feasible to use analogue species for modeling purposes? Measurements are obtained from 542 crania of adult apes and humans. Care is taken to choose homologous data, and account for differences in population size and structure. Variance/covariance and correlation matrices among the species are compared using common principal component (CPC) analysis, random skewers methods and matrix correlations. Morphological distances (D(2)) are calculated between population means, and between randomized pairs of individuals within each population, to evaluate intraspecific variation. Morphological distances are also calculated between randomized pairs of individuals using the variation patterns of analogue populations, in order to evaluate the efficacy of such substitutions. Results show that while the hominoids share a similar pattern of facial variation overall, the patterns do diverge. This difference generally corresponds to the phylogenetic relationships among these species, suggesting that patterns of variation may have diverged through time in the large bodied hominoids. Because interpretation of relationships in the fossil record is confounded by a lack of understanding of how variation changes through time, exploration of such patterns of divergence can provide important clues to understanding human evolution. Additionally, neglecting to account for this divergence when using living analogues as variation "yardsticks" can give rise to interpretations of the fossil record that are more speciose than is warranted.     

Birdsong and anthropogenic noise: implications and applications for conservation

The dramatic increase in human activities all over the world has caused, on an evolutionary time scale, a sudden rise in especially low-pitched noise levels. Ambient noise may be detrimental to birds through direct stress, masking of predator arrival or associated alarm calls, and by interference of acoustic signals in general. Two of the most important functions of avian acoustic signals are territory defence and mate attraction. Both of these functions are hampered when signal efficiency is reduced through rising noise levels, resulting in direct negative fitness consequences. Many bird species are less abundant near highways and studies are becoming available on reduced reproductive success in noisy territories. Urbanization typically leads to homogenization of bird communities over large geographical ranges. We review current evidence for whether and how anthropogenic noise plays a role in these patterns of decline in diversity and density. We also provide details of a case study on great tits (Parus major), a successful urban species. Great tits show features that other species may lack and make them unsuitable for city life. We hypothesize that behavioural plasticity in singing behaviour may allow species more time to adapt to human-altered environments and we address the potential for microevolutionary changes and urban speciation in European blackbirds (Turdus merula). We conclude by providing an overview of mitigating measures available to abate noise levels that are degrading bird breeding areas. Bird conservationists probably gain most by realizing that birds and humans often benefit from the same or only slightly modified measures.     

Improving structure and transparency in reliability evaluations of data under REACH: suggestions for a systematic method

Abstract

The goal of identifying hazardous chemicals registered under the Registration, Evaluation, Authorization and restriction of CHemicals (REACH) Regulation and taking appropriate risk management measures relies on robust data registrations. However, the current procedures for European chemical manufacturers and importers to evaluate data under REACH neither support systematic evaluations of data nor transparently communicate these assessments. The aim of this study was to explore how using a data evaluation method with predefined criteria for reliability and establishing principles for assigning reliability categories could contribute to more structured and transparent evaluations under REACH. In total, 20 peer-reviewed studies for 15 substances registered under REACH were selected for an in-depth evaluation of reliability with the SciRAP tool. The results show that using a method for study evaluation, with clear criteria for assessing reliability and assigning studies to reliability categories, contributes to more structured and transparent reliability evaluations. Consequently, it is recommended to implement a method for evaluating data under REACH with predefined criteria and fields for documenting and justifying the assessments to increase consistency of data evaluations and transparency.     

Albumin and mammalian cell culture: implications for biotechnology applications

Albumin has a long historical involvement in design of media for the successful culture of mammalian cells, in both the research and commercial fields. The potential application of albumins, bovine or human serum albumin, for cell culture is a by-product of the physico-chemical, biochemical and cell-specific properties of the molecule. In this review an analysis of these features of albumin leads to a consideration of the extracellular and intracellular actions of the molecule, and importantly the role of its interactions with numerous ligands or bioactive factors that influence the growth of cells in culture: these include hormones, growth factors, lipids, amino acids, metal ions, reactive oxygen and nitrogen species to name a few. The interaction of albumin with the cell in relation to these co-factors has a potential impact on metabolic and biosynthetic activity, cell proliferation and survival. Application of this knowledge to improve the performance in manufacturing biotechnology and in the emerging uses of cell culture for tissue engineering and stem cell derived therapies is an important prospect.     

Maxillary sinus variation in hybrid macaques: implications for the genetic basis of craniofacial pneumatization

There has been a long‐standing debate regarding the diversification of paranasal sinuses, namely pneumatized spaces in the face. Functional adaptation and structural constraints have generally been suggested to explain sinus diversification in vertebrates. Here we investigated variation in the maxillary sinus and the external facial cranium in hybrid Taiwanese–Japanese macaques to estimate the genetic basis of phenotypic differences. The Taiwanese macaques have a large sinus, whereas the Japanese macaques have a small sinus; they are also significantly different in their external craniofacial morphology. Variations in the hybrids' external craniofacial morphology can be mostly explained by a simple additive model. In contrast, their sinus morphology significantly deviates from the value expected under this additive model, wherein most hybrids have a large sinus, similar to that in Taiwanese macaques, regardless of the degree of hybridization. When the whole structure is considered, a novel phenotype can be seen in the hybrids. Our results suggest that the sinus and face are independent of each other, both genetically and developmentally, and that the small sinus is mainly caused by intrinsic genetic factors, rather than being structurally constrained by the craniofacial architecture. Such genetic factors may have contributed to the enigmatic diversity of craniofacial pneumatization. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 333–347.     

Nestorone: clinical applications for contraception and HRT

The 19-nor derivatives of progesterone are referred to as "pure" progestational molecules as they bind almost exclusively to the progesterone receptor (PR) without interfering with receptors of other steroids. In this category is Nestorone, which has strong progestational activity and antiovulatory potency with no androgenic or estrogenic activity in vivo. These properties make it highly suitable for use in contraception and hormonal therapy (HT). Due to its high potency, very low doses of Nestorone may be delivered via long-term sustained-release delivery systems. Nestorone, 75 or 100 microg per day, released by vaginal ring has suppressed ovulation in women, with inhibition of follicular maturation. A vaginal ring releasing both 150 microg of Nestorone and 15 microg of ethinyl estradiol per day has effectively suppressed ovulation for 13 consecutive cycles. Nestorone has also been used effectively in a single implant for contraception in breastfeeding women and shows promise for use in transdermal systems as a contraceptive or for HT when combined with estrogen.     

Renal nucleoside transporters: physiological and clinical implications.

Renal handling of physiological and pharmacological nucleosides is a major determinant of their plasma levels and tissue availabilities. Additionally, the pharmacokinetics and normal tissue toxicities of nucleoside drugs are influenced by their handling in the kidney. Renal reabsorption or secretion of nucleosides is selective and dependent on integral membrane proteins, termed nucleoside transporters (NTs) present in renal epithelia. The 7 known human NTs (hNTs) exhibit varying permeant selectivities and are divided into 2 protein families: the solute carrier (SLC) 29 (SLC29A1, SLC29A2, SLC29A3, SLC29A4) and SLC28 (SLC28A1, SLC28A2, SLC28A3) proteins, otherwise known, respectively, as the human equilibrative NTs (hENTs, hENT1, hENT2, hENT3, hENT4) and human concentrative NTs (hCNTs, hCNT1, hCNT2, hCNT3). The well characterized hENTs (hENT1 and hENT2) are bidirectional facilitative diffusion transporters in plasma membranes; hENT3 and hENT4 are much less well known, although hENT3, found in lysosomal membranes, transports nucleosides and is pH dependent, whereas hENT4-PMAT is a H+-adenosine cotransporter as well as a monoamine-organic cation transporter. The 3 hCNTs are unidirectional secondary active Na+-nucleoside cotransporters. In renal epithelial cells, hCNT1, hCNT2, and hCNT3 at apical membranes, and hENT1 and hENT2 at basolateral membranes, apparently work in concert to mediate reabsorption of nucleosides from lumen to blood, driven by Na+ gradients. Secretion of some physiological nucleosides, therapeutic nucleoside analog drugs, and nucleotide metabolites of therapeutic nucleoside and nucleobase drugs likely occurs through various xenobiotic transporters in renal epithelia, including organic cation transporters, organic anion transporters, multidrug resistance related proteins, and multidrug resistance proteins. Mounting evidence suggests that hENT1 may have a presence at both apical and basolateral membranes of renal epithelia, and thus may participate in both selective secretory and reabsorptive fluxes of nucleosides. In this review, the renal handling of nucleosides is examined with respect to physiological and clinical implications for the regulation of human kidney NTs and adenosine signaling, intracellular nucleoside transport, and nephrotoxicities associated with some nucleoside drugs.     

Nonbiological factors affecting track censuses: implications for sampling design and reliability

Track census is a widely used method for rapid faunal assessments, which assumes that differences in track count numbers mainly reflect differences in species abundance due to some biological factors. However, some methodological and climatic variables might affect results of track censuses. Here, we tested the effect of climatic variables, such as maximum temperature, humidity, wind speed or days since last rain, and methodological factors such as censusing day period, distance from transect to vegetation edge, substrate condition or observer, on the number of tracks of mammal carnivores and some of their potential prey detected in sandy substrates. We sampled 2?×?2 km² located within the scrubland area of Doñana National Park (southwestern Spain) for carnivore and several potential prey tracks. Our results showed differences in the number of tracks detected between observers and a significant interaction between observers and the day period when censuses were carried out. Moreover, the variables increasing the quality of the substrate (higher environmental humidity, lower wind speed and days since last rain) not only led to a greater detection of carnivore tracks but, depending on the size of the species sampled other variables such as distance from transects to the vegetation border, also affected results. We recommend restricting sampling to certain fixed weather conditions when planning to monitor relative animal abundance from track censuses. When not possible, climatic or methodological variables should be included as covariates in analyses that try to test for the biological factors affecting wildlife abundance, taking into account that these variables, which affect the number of tracks detected could vary between years.     

Branched N-glycans and their implications for cell adhesion, signaling and clinical applications for cancer biomarkers and in therapeutics

Branched N-glycans are produced by a series of glycosyltransferases including N-acetylglucosaminyltransferases and fucosyltransferases and their corresponding genes. Glycans on specific glycoproteins, which are attached via the action of glycosyltransferases, play key roles in cell adhesion and signaling. Examples of this are adhesion molecules or signaling molecules such as integrin and E-cadherin, as well as membrane receptors such as the EGF and TGFβ receptors. These molecules also play pivotal roles in the underlying mechanism of a variety of disease such as cancer metastasis, diabetes, and chronic obstructive pulmonary disease (COPD). Alterations in the structures of branched N-glycans are also hall marks and are useful for cancer biomarkers and therapeutics against cancer. This mini-review describes some of our recent studies on a functional glycomics approach to the study of branched N-glycans produced by N-acetylglucosaminyltransferases III, IV, V and IX (Vb) (GnT-III, GnT-IV, V and IX (Vb)) and fucosyltransferase 8 (Fut8) and their patho-physiological significance, with emphasis on the importance of a systems glycobiology approach as a future perspective for glycobiology.