Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates

During higher primate evolution, gene conversion seems to have occurred often between the red and green photo-pigment genes, which are tandemly linked on the X chromosome. To understand this phenomenon better, intron 4 sequences of the red and green pigment genes of a male human (an Asian Indian), a male chimpanzee, and a male baboon were amplified by PCR and sequenced. The data show that the intron 4 sequences between the two genes have been strongly or completely homogenized in the three species studied. Apparently recent gene conversion events have occurred in introns 4 of the red and green pigment genes in humans and chimpanzees. Two or more conversion events may have occurred at different times in introns 4 of the two pigment genes in baboons. The divergence between the two genes is significantly lower in intron 4 than in exons 4 and 5 in each species, contrary to the usual situation that introns evolve faster than exons. It is most likely that strong natural selection for maintaining the distinct functions of exons 4 and 5 of the red and green pigment genes has acted against sequence homogenization of these exons.      

Nisin adsorption on hydrophilic and hydrophobic surfaces: evidence of its interactions and antibacterial activity

Study of peptides adsorption on surfaces remains a current challenge in literature. A complementary approach, combining X‐ray photoelectron spectroscopy (XPS) and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) was used to investigate the antimicrobial peptide nisin adsorption on hydrophilic and hydrophobic surfaces. The native low density polyethylene was used as hydrophobic support and it was grafted with acrylic acid to render it hydrophilic. XPS permitted to confirm nisin adsorption and to determine its amount on the surfaces. ToF‐SIMS permitted to identify the adsorbed bacteriocin type and to observe its distribution and orientation behavior on both types of surfaces. Nisin was more oriented by its hydrophobic side to the hydrophobic substrate and by its hydrophilic side to the outer layers of the adsorbed peptide, in contrast to what was observed on the hydrophilic substrate. A correlation was found between XPS and ToF‐SIMS results, the types of interactions on both surfaces and the observed antibacterial activity. Such interfacial studies are crucial for better understanding the peptides interactions and adsorption on surfaces and must be considered when setting up antimicrobial surfaces. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Root and inorganic nitrogen distributions in sesbania fallow,natural fallow and maize fields

One hypothesis for a benefit of integrating trees with crops is that trees with deep root systems can capture and pump up nutrients from below the rooting zone of annual crops. Few studies have compared both root and nutrient distribution for planted trees, crops and grassland vegetation. A field study was conducted on a Kandiudalfic Eutrudox in the highlands of western Kenya to measure rooting characteristics and distribution of inorganic N and water in three land-use systems (LUS): (i) Sesbania sesban (L.) Merr. fallow, (ii) uncultivated natural weed fallow and (iii) unfertilized maize (Zea mays L.) monoculture. The maximum rooting depth was 1.2 m in the maize LUS, 2.25 m in a 13-month-old natural fallow, and > 4 m in a 15-month-old sesbania fallow. Total root length was 1.26 km m^-2 for the maize LUS, 5.98 km m^-2 for the natural fallow, and 4.56 km m^-2 to 4 m for the sesbania fallow. Root length to 1.2 m was greater (p < 0.01) for natural fallow than for maize and sesbania fallow. A considerable portion of the sesbania root length to 4 m was in the subsoil; 47% was at 1.2 to 4 m and 31% was at 2.25 to 4 m. Deep rooting of sesbania coincided with lower soil water below 2 m in the sesbania fallow than the natural fallow. Nitrate-N, but not ammonium-N, to 4 m was affected by LUS. Total nitrate to 4 m was 199 kg N ha^-1 for the maize LUS, 42 kg N ha^-1 for the natural fallow and 51 kg N ha^-1 for the sesbania fallow. Soil nitrate in the maize LUS was highest at 0.3 to 1.5-m depth on this Oxisol with anion sorption capacity. No such accumulation of subsoil nitrate was present under sesbania and natural fallow.     

The role of survivin in angiogenesis during zebrafish embryonic development

Background  

Survivin is the smallest member of the inhibitor of apoptosis (IAP) gene family. Recently, the zebrafish survivin-1 gene has been cloned, showing remarkable sequence identity and similarity over the BIR domain compared with human and mouse survivin gene. Here we investigated the role of survivin in angiogenesis during zebrafish development. Morpholinos (MOs) targeting the 5' untranslated region (UTR) (Sur_UTR) and sequences flanking the initiation codon (Sur_ATG) of zebrafish survivin-1 gene were injected into embryos at 1–4 cell stage. Vasculature was examined by microangiography and GFP expression in Tg(fli1:EGFP) ^y1 embryos. Results: In embryos co-injected with Sur_UTR and Sur_ATG-MOs, vasculogenesis was intact but angiogenesis was markedly perturbed, especially in the inter-segmental vessels (ISV) and dorsal longitudinal anastomotic vessels (DLAV) of the trunk, the inner optic circle and optic veins of developing eyes and the sub-intestinal vessels. Apoptosis was increased, as shown by TUNEL staining and increase in caspase-3 activity. Efficacy of Sur_UTR and Sur_ATG-MOs was demonstrated by translation inhibition of co-injected 5'UTR survivin:GFP plasmids. The phenotypes could be recapitulated by splice-site MO targeting the exon2-intron junction of survivin gene and rescued by survivin mRNA. Injection of human vascular endothelial growth factor (VEGF) protein induced ectopic angiogenesis and increased survivin expression, whereas treatment with a VEGF receptor inhibitor markedly reduced angiogenesis and suppressed survivin expression. Conclusion: Survivin is involved in angiogenesis during zebrafish development and may be under VEGF regulation.     

Bioconductor: open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.     

Asynchronous adaptive time step in quantitative cellular automata modeling

Background  

The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation.     

Generation of Human Alloantigen-specific T Cells from Peripheral Blood

The study of human T lymphocyte biology often involves examination of responses to activating ligands. T cells recognize and respond to processed peptide antigens presented by MHC (human ortholog HLA) molecules through the T cell receptor (TCR) in a highly sensitive and specific manner. While the primary function of T cells is to mediate protective immune responses to foreign antigens presented by self-MHC, T cells respond robustly to antigenic differences in allogeneic tissues. T cell responses to alloantigens can be described as either direct or indirect alloreactivity. In alloreactivity, the T cell responds through highly specific recognition of both the presented peptide and the MHC molecule. The robust oligoclonal response of T cells to allogeneic stimulation reflects the large number of potentially stimulatory alloantigens present in allogeneic tissues. While the breadth of alloreactive T cell responses is an important factor in initiating and mediating the pathology associated with biologically-relevant alloreactive responses such as graft versus host disease and allograft rejection, it can preclude analysis of T cell responses to allogeneic ligands. To this end, this protocol describes a method for generating alloreactive T cells from naive human peripheral blood leukocytes (PBL) that respond to known peptide-MHC (pMHC) alloantigens. The protocol applies pMHC multimer labeling, magnetic bead enrichment and flow cytometry to single cell in vitro culture methods for the generation of alloantigen-specific T cell clones. This enables studies of the biochemistry and function of T cells responding to allogeneic stimulation.     

Time-dependent Autoinactivation of Phospho-Thr286-��Ca2+/Calmodulin-dependent Protein Kinase II

Ca²⁺/calmodulin-dependent protein kinase II (αCaMKII) is thought to exert its role in memory formation by autonomous Ca²⁺-independent persistent activity conferred by Thr²⁸⁶ autophosphorylation, allowing the enzyme to remain active even when intracellular [Ca²⁺] has returned to resting levels. Ca²⁺ sequestration-induced inhibition, caused by a burst of Thr^305/306 autophosphorylation via calmodulin (CaM) dissociation from the Thr^305/306 sites, is in conflict with this view. The processes of CaM binding, autophosphorylation, and inactivation are dissected to resolve this conflict. Upon Ca²⁺ withdrawal, CaM sequential domain dissociation is observed, starting with the rapid release of the first (presumed N-terminal) CaM lobe, thought to be bound at the Thr^305/306 sites. The time courses of Thr^305/306 autophosphorylation and inactivation, however, correlate with the slow dissociation of the second (presumed C-terminal) CaM lobe. Exposure of the Thr^305/306 sites is thus not sufficient for their autophosphorylation. Moreover, Thr^305/306 autophosphorylation and autoinactivation are shown to occur in the continuous presence of Ca²⁺ and bound Ca²⁺/CaM by time courses similar to those seen following Ca²⁺ sequestration. Our investigation of the activity and mechanisms of phospho-Thr₂₈₆-αCaMKII thus shows time-dependent autoinactivation, irrespective of the continued presence of Ca²⁺ and CaM, allowing a very short, if any, time window for Ca²⁺/CaM-free phospho-Thr²⁸⁶-αCaMKII activity. Physiologically, the time-dependent autoinactivation mechanisms of phospho-Thr²⁸⁶-αCaMKII (t½ of ∼50 s at 37 °C) suggest a transient kinase activity of ∼1 min duration in the induction of long term potentiation and thus memory formation.Ca²⁺/calmodulin-dependent protein kinase II (αCaMKII)² is essential in hippocampal learning and N-methyl-d-aspartate receptor-dependent synaptic plasticity, causing long term potentiation (1, 2). The exact mechanisms of αCaMKII in memory functions have not yet been identified.αCaMKII is a broad specificity Ser/Thr protein kinase, which catalyzes the phosphorylation of over 100 protein and peptide substrates in vitro (3). Uniquely, the CaMKII family possesses two distinct kinase mechanisms. The first mechanism is a “canonical” intrasubunit phosphorylation, commonly found in monomeric kinases, in which the phosphorylatable residue of the substrate bound to the helical subdomain of the catalytic domain at the active site is lined up with the terminal phosphate of ATP (4). Although there is a large number of potential “canonical” substrates for αCaMKII at the synapse (5), so far AMPA receptors have been shown to be possible physiological substrates of αCaMKII (6). For the purpose of this study, syntide 2, a commonly used peptide substrate derived from phosphorylation site 2 of glycogen synthase (7), was chosen.The second mechanism, intersubunit autophosphorylation, takes advantage of the oligomeric organization of CaMKII (8). The most important autophosphorylation site in the α isoform is Thr²⁸⁶, which resides in the vicinity of the autoinhibitory domain (9). Peptide substrates with homologous sequences to this region have been reported to be phosphorylated by αCaMKII. This, however, occurs with a low V_max, and these substrates show properties of a non-competitive inhibitor with respect to phosphorylation of “canonical” substrates (10) and of Thr²⁸⁶ autophosphorylation itself (11). Examples of such substrates include autocamtide, a peptide substrate derived from the autoinhibitory region (12) and the NR2B subunit of the N-methyl-d-aspartate receptor, which has been identified as a potential physiological target of phospho-Thr²⁸⁶-αCaMKII at the postsynaptic membrane (13). The possible physiological significance of NR2B phosphorylation is not yet known. There is evidence to suggest that Thr²⁸⁶ autophosphorylation is required to achieve full activity of the enzyme, since the unphosphorylatable T286A mutant enzyme has much diminished activity compared with wild type enzyme (14, 15).Thr²⁸⁶ autophosphorylation causes CaM “trapping,” a >10⁴-fold increase in the affinity of αCaMKII for Ca²⁺/CaM (16–18). At the same time, Thr²⁸⁶ autophosphorylation is also attributed to confer Ca²⁺- and CaM-independent persistent “autonomous” kinase activity to αCaMKII. However, due to the extremely high affinity of phospho-Thr₂₈₆-αCaMKII for Ca²⁺/CaM, [Ca²⁺] of <10 nm is required to achieve full dissociation of Ca²⁺/CaM, since CaM trapping occurs by virtue of Ca²⁺ trapping (19). Partial activity measured upon partial Ca²⁺ withdrawal therefore may not always reflect Ca²⁺/CaM-free enzyme (9). Furthermore, the physiological resting [Ca²⁺] range is 50–100 nm; therefore, phospho-Thr²⁸⁶-αCaMKII is likely always to have residual Ca²⁺/CaM bound. This may be partially Ca²⁺-saturated CaM (19).Persistent autonomous activity conferred by Thr²⁸⁶ autophosphorylation is thought to enable αCaMKII to function as a memory molecule (20, 21). In contrast, however, following the development of chemical long term potentiation, rapid inactivation has also been reported (22). The extent of an autonomous activity is further obscured by the finding that Ca²⁺ sequestration induces a burst of autophosphorylation at residues Thr^305/306, followed by a loss of activity (23). Moreover, when examined across a broad range of [Ca²⁺], the Ca²⁺/CaM dependence of phospho-Thr²⁸⁶-αCaMKII activity is apparent (19). It is thus vital to establish the mechanisms of activation and inactivation of αCaMKII at the molecular level in order to understand how it may function physiologically in learning and memory. To this end, it is necessary to dissect the mechanisms of Ca²⁺/CaM dissociation, Thr^305/306 autophosphorylation, and inactivation of phospho-Thr²⁸⁶-αCaMKII and to establish the time window for autonomous Ca²⁺/CaM-independent activity.