Individual dispersal,landscape connectivity and ecological networks

Connectivity is classically considered an emergent property of landscapes encapsulating individuals' flows across space. However, its operational use requires a precise understanding of why and how organisms disperse. Such movements, and hence landscape connectivity, will obviously vary according to both organism properties and landscape features. We review whether landscape connectivity estimates could gain in both precision and generality by incorporating three fundamental outcomes of dispersal theory. Firstly, dispersal is a multi‐causal process; its restriction to an ‘escape reaction’ to environmental unsuitability is an oversimplification, as dispersing individuals can leave excellent quality habitat patches or stay in poor‐quality habitats according to the relative costs and benefits of dispersal and philopatry. Secondly, species, populations and individuals do not always react similarly to those cues that trigger dispersal, which sometimes results in contrasting dispersal strategies. Finally, dispersal is a major component of fitness and is thus under strong selective pressures, which could generate rapid adaptations of dispersal strategies. Such evolutionary responses will entail spatiotemporal variation in landscape connectivity. We thus strongly recommend the use of genetic tools to: (i) assess gene flow intensity and direction among populations in a given landscape; and (ii) accurately estimate landscape features impacting gene flow, and hence landscape connectivity. Such approaches will provide the basic data for planning corridors or stepping stones aiming at (re)connecting local populations of a given species in a given landscape. This strategy is clearly species‐ and landscape‐specific. But we suggest that the ecological network in a given landscape could be designed by stacking up such linkages designed for several species living in different ecosystems. This procedure relies on the use of umbrella species that are representative of other species living in the same ecosystem.     

Seascape genetics of the stalked kelp Pterygophora californica and comparative population genetics in the Santa Barbara Channel

We conducted a population genetic analysis of the stalked kelp, Pterygophora californica, in the Santa Barbara Channel, California, USA. The results were compared with previous work on the genetic differentiation of giant kelp, Macrocystis pyrifera, in the same region. These two sympatric kelps not only share many life history and dispersal characteristics but also differ in that dislodged P. californica does not produce floating rafts with buoyant fertile sporophytes, commonly observed for M. pyrifera. We used a comparative population genetic approach with these two species to test the hypothesis that the ability to produce floating rafts increases the genetic connectivity among kelp patches in the Santa Barbara Channel. We quantified the association of habitat continuity and oceanographic distance with the genetic differentiation observed in stalked kelp, like previously conducted for giant kelp. We compared both overall (across all patches) and pairwise (between patches) genetic differentiation. We found that oceanographic transit time, habitat continuity, and geographic distance were all associated with genetic connectivity in P. californica, supporting similar previous findings for M. pyrifera. Controlling for differences in heterozygosity between kelp species using Jost's D_EST, we showed that global differentiation and pairwise differentiation were similar among patches between the two kelp species, indicating that they have similar dispersal capabilities despite their differences in rafting ability. These results suggest that rafting sporophytes do not play a significant role in effective dispersal of M. pyrifera at ecologically relevant spatial and temporal scales.     

Connections Between Benthic Populations and Local Strandings of the Southern Bull Kelp Durvillaea Antarctica Along the Continental Coast of Chile1

Floating seaweeds are important dispersal vectors in marine ecosystems. However, the relationship between benthic populations and stranded seaweeds has received little attention. After detachment, a fraction of floating specimens returns to the shore, resulting in strandings that fluctuate in space and time. It has been hypothesized that the availability of stranded seaweeds is related to their benthic abundance on adjacent coasts. Using the large fucoid Durvillaea antarctica, we tested whether stranded biomasses are higher at sites with dense adjacent benthic populations. Benthic abundance of D. antarctica along the continental coast of Chile was estimated using three approximations: (i) availability of potentially suitable habitat (PSH), (ii) categorical visual abundance estimates in the field, and (iii) abundance measurements in the intertidal zone. Higher PSH for D. antarctica was observed between 31° S–32° S and 40° S–42° S than between 33° S and 39° S. Lowest benthic biomasses were estimated for the northern latitudes (31° S–32° S). Regression models showed that the association between stranded biomass and PSH was highest when only the extent of rocky shore 10 km to the south of each beach was included, suggesting relatively short-distance dispersal and asymmetrical transport of floating kelps, which is further supported by low proportions of rafts with Lepas spp. (indicator of rafting). The results indicate that stranded biomasses are mostly subsidized by nearby benthic populations, which can partly explain the low genetic connectivity among populations in the study region. Future studies should also incorporate other local factors (e.g., winds, currents, wave-exposure) that influence stranding dynamics.     

The commercially important shoemaker spinefoot,Siganus sutor,connects coral reefs to neighbouring seagrass meadows

Spatial management of fish populations can potentially be optimized by determining the area of influence of a particular species. We performed an acoustic tagging study implemented on Denis Island in the Seychelles to assess the area of influence of the heavily targeted shoemaker spinefoot, Siganus sutor. We investigated whether this species acts as a mobile link between coral patches and seagrass meadows, and whether their movements differed between day and night. The study incorporated an array of 22 acoustic stations deployed within dense coral patches, seagrass meadows and mixed habitats of both seagrass and coral. Fifteen S. sutor carrying internal acoustic tags were monitored from November 2016 until May 2017. Detection patterns revealed them to be diurnal herbivores, with only rare nocturnal movements. Home-range estimates showed that individuals differed in their spatial range extents and habitats used, covering ~15% of the total shallow subtidal coastline of the island. However, they displayed very small daily movements (<200 m), concentrated mainly around sites within mixed coral and seagrass habitats. An optimal number of detections was recorded when the coral to seagrass area ratio was approximately 1.6:1. This ratio was confirmed through statistical prediction modelling. Identification of such links of commercially important species between networked habitats may help authorities consider incorporating seagrass meadows of the Seychelles into management discussions, which are currently lacking.     

TMEM126A is a mitochondrial located mRNA (MLR) protein of the mitochondrial inner membrane

Background

Hereditary optic neuropathies (HONs) are a heterogeneous group of disorders that affect retinal ganglion cells (RGCs) and axons that form the optic nerve. Leber's Hereditary Optic Neuropathy and the autosomal dominant optic atrophy related to OPA1 mutations are the most common forms. Nonsyndromic autosomal recessive optic neuropathies are rare and their existence has been long debated. We recently identified the first gene responsible for these conditions, TMEM126A. This gene is highly expressed in retinal cellular compartments enriched in mitochondria and supposed to encode a mitochondrial transmembrane protein of unknown function.

Methods

A specific polyclonal antibody targeting the TMEM126A protein has been generated. Quantitative fluorescent in situ hybridization, cellular fractionation, mitochondrial membrane association study, mitochondrial sub compartmentalization analysis by both proteolysis assays and transmission electron microscopy, and expression analysis of truncated TMEM126A constructs by immunofluorescence confocal microscopy were carried out.

Results

TMEM126A mRNAs are strongly enriched in the vicinity of mitochondria and encode an inner mitochondrial membrane associated cristae protein. Moreover, the second transmembrane domain of TMEM126A is required for its mitochondrial localization.

Conclusions

TMEM126A is a mitochondrial located mRNA (MLR) that may be translated in the mitochondrial surface and the protein is subsequently imported to the inner membrane. These data constitute the first step toward a better understanding of the mechanism of action of TMEM126A in RGCs and support the importance of mitochondrial dysfunction in the pathogenesis of HON.

General significance

Local translation of nuclearly encoded mitochondrial mRNAs might be a mechanism for rapid onsite supply of mitochondrial membrane proteins.     

Angelman syndrome and severe infections in a patient with de novo 15q11.2–q13.1 deletion and maternally inherited 2q21.3 microdeletion

Angelman syndrome is a neurodevelopmental disorder characterized by mental retardation, severe speech disorder, facial dysmorphism, secondary microcephaly, ataxia, seizures, and abnormal behaviors such as easily provoked laughter. It is most frequently caused by a de novo maternal deletion of chromosome 15q11–q13 (about 70–90%), but can also be caused by paternal uniparental disomy of chromosome 15q11–q13 (3–7%), an imprinting defect (2–4%) or in mutations in the ubiquitin protein ligase E3A gene UBE3A mostly leading to frame shift mutation. In addition, for patients with overlapping clinical features (Angelman-like syndrome), mutations in methyl-CpG binding protein 2 gene MECP2 and cyclin-dependent kinase-like 5 gene CDKL5 as well as a microdeletion of 2q23.1 including the methyl-CpG binding domain protein 5 gene MBD5 have been described. Here, we describe a patient who carries a de novo 5 Mb-deletion of chromosome 15q11.2–q13.1 known to be associated with Angelman syndrome and a further, maternally inherited deletion 2q21.3 (~ 364 kb) of unknown significance. In addition to classic features of Angelman syndrome, she presented with severe infections in the first year of life, a symptom that has not been described in patients with Angelman syndrome. The 15q11.2–q13.1 deletion contains genes critical for Prader–Willi syndrome, the Angelman syndrome causing genes UBE3A and ATP10A/C, and several non-imprinted genes: GABRB3 and GABRA5 (both encoding subunits of GABA A receptor), GOLGA6L2, HERC2 and OCA2 (associated with oculocutaneous albinism II). The deletion 2q21.3 includes exons of the genes RAB3GAP1 (associated with Warburg Micro syndrome) and ZRANB3 (not disease-associated). Despite the normal phenotype of the mother, the relevance of the 2q21.3 microdeletion for the phenotype of the patient cannot be excluded, and further case reports will need to address this point.     

ELP[Ⅰ]50标签在重组硫氧还蛋白分离纯化中的应用及PEG对其相变温度的影响

[目的]使用自行设计的类弹性蛋白(Elastin-like protein,ELP) ELP[Ⅰ]50作为非色谱纯化标签,分离纯化重组硫氧还蛋白(Thioredoxin,Trx),并研究聚乙二醇(Polyethyleneglycol,PEG)对ELP[Ⅰ]50-Trx相变温度(Inverse temperature transition,Tt)的影响.[方法]人工合成Trx基因,将其亚克隆到自行构建的表达载体pET28编码ELP[Ⅰ]50标签下游,转入大肠杆菌BLR(DE3)进行表达.融合蛋白表达后,采用可逆相变循环(Inverse transition cycling,ITC)分离纯化,并检测不同浓度PEG时的Tt值.[结果]成功表达、分离纯化出融合蛋白ELP[Ⅰ]50-Trx,检测出该蛋白浓度为25 μmol/L时,Tt为28.6℃;而当PEG的浓度为5％、10％、15％、20％时,Tt分别降至22.3℃、15.9℃、6℃、0℃.[结论]ELP[Ⅰ]50标签高效纯化重组蛋白具有操作简便、成本较低、易于扩大的优势,而PEG能降低蛋白的Tt值,进一步增强分离纯化效果,扩大使用范围,可望应用于分离纯化多种重组蛋白.     

Cloning,characterization and expression of a cDNA encoding a granulin-like polypeptide in Ciona savignyi

Previous study in our laboratory confirmed that a novel polypeptide, CS5931 derived from Ciona savignyi possesses potent antitumor activity. In the present study, the full length cDNA of CS5931 precursor, termed Cs-pgrn-1 was cloned. The complete cDNA sequence of this gene consists of 685 bp containing an open reading frame (ORF) of 522 bp (173 amino acid residues). In silico analysis revealed that the polypeptide consists of two identical domains, similar with granulin (GRN) found in other species, and each of the domain encodes a polypeptide identical with CS5931. Phylogenetic analysis confirmed that CS5931 shares high homology with Ciona intestinalis GRN and is conserved during evolution. The polypeptide also shows high similarity with human GRN A, B, and C. Prediction of 3D protein structure revealed the 3D structure of CS5931 is very similar with human GRN A. The CS5931 was expressed using a prokaryotic expression system and the purified polypeptide inhibited the growth of several tumor cell lines in vitro via apoptotic pathway. Our study revealed that CS5931 has the potential to be developed as a novel antitumor agent.     

Stability of ultramer as copy number standards in real-time PCR

Since commercial copy number standards are not always available for real-time PCR, alternative sources of DNA are used. Unfortunately, stored genomic DNA or PCR amplicon has been shown to be unstable, resulting in variable copy number. More recently, the use of ultramer as copy number standard has been reported. However, there is little information on the stability of ultramer under different storage conditions. Thus the aim of this study was to determine the stability of ultramer as copy number standard under different storage conditions using different mixing methods. We found that ultramer copy number was not affected by storage at either 4 °C or − 20 °C over a period of 30 days. Furthermore, the method of mixing the ultramer did not appear to contribute to variability in results. Irrespective of storage temperature or mixing method, there was less than 5% variance in Ct value over a period of 30 days. A duplicate set of standards costs approximately $0.01. Therefore, the use of ultramer as copy number standards in real-time PCR, is cost effective and convenient.     

Salvianolic acid B inhibits the amyloid formation of human islet amyloid polypeptideand protects pancreatic beta‐cells against cytotoxicity

The misfolding of human islet amyloid polypeptide (hIAPP) is regarded as one of the causative factors of type 2 diabetes mellitus (T2DM). Salvia miltiorrhiza (Danshen), one of the most commonly used of traditional Chinese medicines, is often used in Compound Recipes for treating diabetes, however with unclear mechanisms. Since salvianolic acid B (SalB) is the most abundant bioactive ingredient of salvia miltiorrhiza water‐extract. In this study, we tested whether SalB has any effect on the amyloidogenicity of hIAPP. Our results clearly suggest that SalB can significantly inhibit the formation of hIAPP amyloid and disaggregate hIAPP fibrils. Furthermore, photo‐crosslinking based oligomerization studies suggest SalB significantly suppresses the toxic oligomerization of hIAPP monomers. Cytotoxicity protection effects on pancreatic INS‐1 cells by SalB were also observed using MTT‐based assays, potentially due to the inhibition on the membrane disruption effects and attenuated mitochondria impairment induced by hIAPP. These results provide evidence that SalB may further be studied on the possible pharmacological treatment for T2DM. Proteins 2013. © 2012 Wiley Periodicals, Inc.