QTL identification of grain protein concentration and its genetic correlation with starch concentration and grain weight using two populations in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Protein is one of the three main storage chemical components in maize grains, and is negatively correlated with starch concentration (SC). Our objective was to analyse the influence of genetic backgrounds on QTL detection for protein concentration (PC) and to reveal the molecular genetic associations between PC and both SC and grain weight (GWP). Two hundred and eighty-four (Pop1) and 265 (Pop2) F_2:3 families were developed from two crosses between one high-oil maize inbred GY220 and two normal maize inbreds 8984 and 8622 respectively, and were genotyped with 185 and 173 pairs of SSR markers. PC, SC and GWP were evaluated under two environments. Composite interval mapping (CIM) and multiple interval mapping (MIM) methods were used to detect single-trait QTL for PC, and multiple-trait QTL for PC with both SC and GWP. No common QTL were shared between the two populations for their four and one PC QTL. Common QTL with opposite signs of effects for PC and SC/GWP were detected on three marker intervals at bins 6.07–6.08, 8.03 and 8.03–8.04. Multiple-traits QTL mapping showed that tightly-linked QTL, pleiotropic QTL and QTL having effects with opposite directions for PC and SC/GWP were all observed in Pop1, while all QTL reflected opposite effects in Pop2.     

Mediators of ocular angiogenesis

Angiogenesis is the formation of new blood vessels from pre-existing vasculature. Pathologic angiogenesis in the eye can lead to severe visual impairment. In our review, we discuss the roles of both pro-angiogenic and anti-angiogenic molecular players in corneal angiogenesis, proliferative diabetic retinopathy, exudative macular degeneration and retinopathy of prematurity, highlighting novel targets that have emerged over the past decade.     

Facial Skin Coloration Affects Perceived Health of Human Faces

Numerous researchers have examined the effects of skin condition, including texture and color, on the perception of health, age, and attractiveness in human faces. They have focused on facial color distribution, homogeneity of pigmentation, or skin quality. We here investigate the role of overall skin color in determining perceptions of health from faces by allowing participants to manipulate the skin portions of color-calibrated Caucasian face photographs along CIELab color axes. To enhance healthy appearance, participants increased skin redness (a*), providing additional support for previous findings that skin blood color enhances the healthy appearance of faces. Participants also increased skin yellowness (b*) and lightness (L*), suggesting a role for high carotenoid and low melanin coloration in the healthy appearance of faces. The color preferences described here resemble the red and yellow color cues to health displayed by many species of nonhuman animals.     

Cytogenetic effects of nine <Emphasis Type="Italic">Helichrysum</Emphasis> taxa in human lymphocytes culture

Helichrysum Mill. (Asteraceae) species have been used in folk medicine for thousands of years in the world. The in vitro cytogenetic effects in human lymphocytes of nine Helichrysum taxa used in Turkey folk medicine were investigated. Blood samples were obtained from healthy donors, non-smoking volunteers, which were incubated and exposed to increasing concentrations of methanol extracts of Helichrysum taxa (0.01, 0.05, 0.1, 0.5 and 1 mg/mL). The inhibitory effects of H. stoechas (L.) Moench subsp. barrelieri (Ten.) Nyman, H. armenium DC. subsp. armenium, H. armenium DC. subsp. araxinum (Kirp.) Takht., H. plicatum DC. subsp. plicatum, H. compactum Boiss. and H. artvinense P.H.Davis & Kupicha on the mitotic index and replication index indicate that these taxa can have genotoxic and mutagenic effects. They should therefore not be used freely in alternative medicine although their antiproliferative activity may suggest anticarcinogenic properties. Increase effects of H. stoechas subsp. barrelieri, H. armenium subsp. armenium, H. armenium subsp. araxinum, H. chasmolycicum P.H.Davis, H. plicatum subsp. plicatum, H. compactum and H. artvinense on the micronucleus rates showed that these taxa can have genotoxic and carcinogenic effects.     

Xenotransplantation: Biotechnological Aspects and Current Attitudes

Xenotransplantation of organs from the large domestic species will only be successful if the donor animals have been genetically modified, in particular regarding the α-Gal epitope, certain human complements (CD55 and CD59) and/or H-transferase. This requires, among other things, major embryo-technological efforts, and the rate of success is still far from an acceptable level in the domestic species. It is currently poor, but the progress is very good. In this brief review certain embryo-technological problems will be addressed with the focus on the pig as potential organ donor. In addition, certain views of the Danish ad hoc Committee on Gene Technology on xenotransplantation will be presented in this context as they are supposed to mirror the concern and the views of the issues important for the public and each individual.     

A rare hybridization event in two common Caribbean wrasses (genus <Emphasis Type="Italic">Halichoeres</Emphasis>; family Labridae)

Molecular tools were used to evaluate the hybrid status of a specimen with intermediate colour pattern between Halichoeres bivittatus and Halichoeres garnoti from Belize. Phylogenetic analyses of the two species, eight Halichoeres species from new and old world lineages and two outgroups showed that the study species are closely related and that H. garnoti is the maternal contributor to the putative hybrid specimen, based on partial mitochondrial COI data. Direct sequencing of Intron 1 of the nuclear ribosomal protein S7 identified H. bivittatus as sister to H. garnoti with the putative hybrid specimen in an intermediate position, due to heterozygosity at nucleotides alternatively fixed in the two putative parent species. This is consistent with the hybrid status of the specimen, with parental contributions from both H. garnoti and H. bivittatus. These results, combined with no evidence of introgression between the two parent species (based on the mtDNA and the single investigated nuclear marker) and the biogeography and ecology of these species suggests that this is a rare event with minimal evolutionary implications.     

A conservation and rigidity based method for detecting critical protein residues

Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine or Alanine. The other method uses evolutionary conservation to find functional interfaces in proteins.

Results

We applied the two methods to a dataset of proteins, including biomolecules with experimentally known critical residues as determined by the free energy of unfolding. Our results show that the combination of the two methods can detect the vast majority of critical residues in tested proteins.

Conclusions

Our results show that the combination of the two methods has the potential to detect more information than each method separately. Future work will provide a confidence level for the criticalness of a residue to improve the accuracy of our method and eliminate false positives. Once the combined methods are integrated into one scoring function, it can be applied to other domains such as estimating functional interfaces.

     

Predicting beta-turns in proteins using support vector machines with fractional polynomials

Background

β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design.

Results

We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features.

Conclusions

In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods.

     

B-cell depletion in SLE: clinical and trial experience with rituximab and ocrelizumaband implications for study design

B cells are believed to be central to the disease process in systemic lupuserythematosus (SLE), making them a target for new therapeutic intervention. In recentyears there have been many publications regarding the experience in SLE of B-celldepletion utilising rituximab, an anti-CD20 mAb that temporarily depletes B cells,reporting promising results in uncontrolled open studies and in routine clinical use.However, the two large randomised controlled trials in extra-renal lupus (EXPLORERstudy) and lupus nephritis (LUNAR study) failed to achieve their primary endpoints.Based on the clinical experience with rituximab this failure was somewhat unexpectedand raised a number of questions and concerns, not only into the true level ofbenefit of B-cell depletion in a broad population but also how to test the true levelof effectiveness of an investigational agent as we seek to improve the design oftherapeutic trials in SLE. A better understanding of what went wrong in these trialsis essential to elucidate the underlying reasons for the disparate observations notedin open studies and controlled trials. In this review, we focus on various factorsthat may affect the ability to accurately and confidently establish the level oftreatment effect of the investigational agent, in this case rituximab, in the twostudies and explore hurdles faced in the randomised controlled trials investigatingthe efficacy of ocrelizumab, the humanised anti-CD20 mAb, in SLE. Further, based onthe lessons learned from the clinical trials, we make suggestions that could beimplemented in future clinical trial design to overcome the hurdles faced.