Molecular phylogenetics of Reig's short-tailed opossum (Monodelphis reigi) and its distributional range extension into Guyana

Reig's short-tailed opossum (Monodelphis reigi) was recently described morphologically, based on a single specimen from southeastern Venezuela. It was considered most similar to M. adusta, which is allopatrically distributed in the Andes and surrounding areas, but there has not been an explicit study of systematic relationships with other species of Monodelphis. We report the first occurrence from Guyana of this rare species that was previously known by only the holotype. In a molecular phylogenetic analysis of mitochondrial cytochrome b sequence variation, it groups within a well-supported monophyletic clade that includes M. adusta, M. handleyi, M. osgoodi, and M. peruviana. M. adusta was found to be the sister taxon to the rest of the adusta-complex. M. reigi is the basal taxon (sister species) of remaining adusta-complex forms. This corroborates earlier morphological studies suggesting close affinity of these taxa. As presently known, M. reigi is endemic to the highland regions (>1,000 m asl) of the Guiana Shield of northern South America, and is the only taxon within the M. adusta species complex that does not occur in the Andes or adjacent lowland regions. Based on previous molecular dating of Didelphidae, this suggests that there was a dispersal event from the Andes to the Guiana Highlands in the Miocene that gave rise to M. reigi.     

Variable Loop Glycan Dependency of the Broad and Potent HIV-1-Neutralizing Antibodies PG9 and PG16

The HIV-1-specific antibodies PG9 and PG16 show marked cross-isolate neutralization breadth and potency. Antibody neutralization has been shown to be dependent on the presence of N-linked glycosylation at position 160 in gp120. We show here that (i) the loss of several key glycosylation sites in the V1, V2, and V3 loops; (ii) the generation of pseudoviruses in the presence of various glycosidase inhibitors; and (iii) the growth of pseudoviruses in a mutant cell line (GnT1^−/−) that alters envelope glycosylation patterns all have significant effects on the sensitivity of virus to neutralization by PG9 and PG16. However, the interaction of antibody is not inhibited by sugar monosaccharides corresponding to those found in glycans on the HIV surface. We show that some of the glycosylation effects described are isolate dependent and others are universal and can be used as diagnostic for the presence of PG9 and PG16-like antibodies in the sera of HIV-1-infected patients. The results suggest that PG9 and PG16 recognize a conformational epitope that is dependent on glycosylation at specific variable loop N-linked sites. This information may be valuable for the design of immunogens to elicit PG9 and PG16-like antibodies, as well as constructs for cocrystallization studies.It is argued that an effective HIV vaccine should include a component that induces a broadly neutralizing antibody response (2, 3, 21, 25, 32, 37, 39, 54). The key target for broadly neutralizing HIV antibodies is the envelope spike, which consists of a compact, metastable heterodimeric trimer of the glycoproteins gp120 and gp41 (43, 62).gp120 is one of the most heavily glycosylated proteins known, with up to 50% of its mass arising from carbohydrates attached to roughly 25 N-linked glycosylation sites (31) determined by the NXT/S consensus sequence (where X can be any amino acid except Pro) (1). Glycosylation significantly impacts the folding and conformation of envelope spikes, thus affecting antigenicity and immunogenicity (30, 35). Carbohydrates are generally poorly immunogenic, and the dense covering of glycans is often referred to as the “silent face” or “glycan shield” (58). The glycans have also been suggested to have an important role in viral transmission through interaction with lectins, in particular the C-type lectin DC-SIGN, which is found on the surfaces of dendritic cells and is thought to aid the transport of virus to anatomical sites rich in CD4⁺ T cells, such as lymph nodes (8, 16).Although the positioning of N-linked protein glycosylation is encoded by the protein sequence (1), the type of glycan displayed (high mannose, hybrid, or complex) is not under direct genetic control but is determined by the three-dimensional structure of a protein and its interaction with the biosynthetic cellular environment, including accessibility to glycan-processing enzymes (50). For example, highly clustered glycans prevent access of the processing enzymes, leading to high-mannose-type glycans being displayed (6, 23). Therefore, the glycosylation of recombinant HIV envelope proteins can vary significantly depending on the protein sequence, structure, and the cell in which they are expressed (50). Although the positions of many glycans are relatively conserved between isolates and clades (60), there can be variation in the occupancy and precise nature of the glycans displayed at these positions on recombinant envelope (7, 17-19, 61). However, we have recently observed major differences between the glycosylation of recombinant envelope proteins and envelope expressed on the virion surface, with the latter being dominated by Man_5-9GlcNAc₂ oligomannose glycans (9). Nevertheless, significant glycan heterogeneity remains on the virion surface.Recently, two new neutralizing antibodies, PG9 and PG16, were isolated from an African clade A-infected donor and shown to be both broad and potent (56). From a panel of 162 viruses, PG9 neutralized 127 and PG16 neutralized 119 viruses at a median potency that exceeded that of the broadly neutralizing antibodies—2G12, b12, 2F5, and 4E10—by about an order of magnitude. In a TZM-bl neutralization assay, PG9 has been shown to neutralize 87% of a panel of 82 viruses (M. Seaman, unpublished data). Both PG9 and PG16 show preferential trimer binding and interact with an epitope formed from conserved regions of the V1/V2 and V3 variable loops. Mutation of N160, an N-linked glycosylation site in the V2 loop, completely abolishes PG9 and PG16 neutralization, suggesting the N160 glycan is important in forming the PG9 and PG16 epitope. Further, PG9 shows significant binding to monomeric gp120 DU422 and treatment of the glycoprotein with Endo H (removing high-mannose glycans) results in significant reduction in antibody binding. Occasionally, neutralization of some pseudoviruses by PG16 in particular has revealed an unusual neutralization profile with a shallow slope and plateaus at <100%. We hypothesized that this unusual neutralization profile may be related to antibody sensitivity to glycosylation and, more specifically, could be due to glycan profile or partial glycosylation at critical sites.We show here that loss of any one of several glycosylation sites in the V1, V2, and V3 loops has significant effects on the sensitivity of pseudovirus to neutralization by PG9 and PG16. Generating pseudovirus in the presence of various glycosidase inhibitors also has notable effects on antibody neutralization. We show that some of these effects are isolate dependent and others are universal and can be used to help identify the presence of PG9 and PG16-like antibodies in the serum of HIV-1-infected patients (57). For some isolates displaying aberrant neutralization profiles as described above, we found that changing the glycan profile on the HIV-1 trimer using glycosidase inhibitors or a mutant cell line resulted in higher neutralization plateaus and neutralization profiles with the more usual sigmoidal shape. Changes in sensitivity to neutralization were also observed for some but not all isolates. The antibody-gp120 interaction was not inhibited by sugar monosaccharides found in glycans on the HIV envelope. The results suggest PG9 and PG16 recognize a conformational epitope that is dependent on the glycosylation at specific variable loop N-linked glycosylation sites. This information may be valuable for the design of immunogens to elicit PG9 and PG16-like antibodies, as well as constructs for cocrystallization studies.     

Autophagy in myocardium of murine hearts subjected to ischemia followed by reperfusion

Autophagy in myocardium has been thought to be cardioprotective, but its extent after transient or prolonged myocardial ischemia remains unclear. Accordingly, we characterized its magnitude in myocardium of murine hearts subjected to ischemia with or without reperfusion. Ten-week-old transgenic GFP-LC3 mice and C57Bl6 mice were subjected to coronary ligation for 1 or 4 h followed by 24 h of reperfusion (1HTL, 4HTL) or to 24 h of persistent ligation (24HPL). Their hearts were analyzed by fluorescence microscopy, electron microscopy, and by Western blotting. Fluorescent GFP-LC3 dots indicative of autophagy were absent in infarct zones and reduced markedly in the peri-infarct zones compared with dots in sham controls (p ≤ 0.05). The LC3-II/LC3-I ratio indicative of autophagy did not increase in LV homogenates from hearts following ischemia. Phosphorylation of ribosomal protein S6 increased in LV homogenates in hearts from mice subjected to 4HTL and 24HPL (p ≤ 0.05). Virtually no autophagic cells recognizable by electron microscopy were evident in infarct or peri-infarct zones. Autophagy is virtually absent within 24 h in the center of zones of infarction and is decreased significantly in the peri-infarct zones compared with that in normal hearts.     

ApoA-I mimetic peptides promote pre-β HDL formation in vivo causing remodeling of HDL and triglyceride accumulation at higher dose

Reverse cholesterol transport promoted by HDL-apoA-I is an important mechanism of protection against atherosclerosis. We have previously identified apoA-I mimetic peptides by synthesizing analogs of the 22 amino acid apoA-I consensus sequence (apoA-I(cons)) containing non-natural aliphatic amino acids. Here we examined the effect of different aliphatic non-natural amino acids on the structure-activity relationship (SAR) of apoA-I mimetic peptides. These novel apoA-I mimetics, with long hydrocarbon chain (C(5-8)) amino acids incorporated in the amphipathic α helix of the apoA-I(cons), have the following properties: (i) they stimulate in vitro cholesterol efflux from macrophages via ABCA1; (ii) they associate with HDL and cause formation of pre-β HDL particles when incubated with human and mouse plasma; (iii) they associate with HDL and induce pre-β HDL formation in vivo, with a corresponding increase in ABCA1-dependent cholesterol efflux capacity ex vivo; (iv) at high dose they associate with VLDL and induce hypertriglyceridemia in mice. These results suggest our peptide design confers activities that are potentially anti-atherogenic. However a dosing regimen which maximizes their therapeutic properties while minimizing adverse effects needs to be established.     

Crystallohydrodynamics for solving the hydration problem for multi-domain proteins: open physiological conformations for human IgG.

Hydrodynamic methods provide a route for studying the low-resolution conformation--in terms of time-averaged spatial orientation of the Fab' and Fc domains relative to each other--of the human IgG subclasses, IgG1, IgG2, IgG3 and IgG4 in the environment in which many exist naturally---a solution. Representative modelling strategies are now available using 'shell-bead' or 'shell' modelling of the surface of the molecules with the size-independent programme SOLPRO [J. Garcia de la Torre, S.E. Harding, B. Carrasco, Eur. Biophys. J. 28 (1999) 119-132]. The shell model fits to the equivalent inertial surface ellipsoids of the published crystal structures for the Fab' and Fc domains of IgG are made and an apparent hydration delta(app) of 0.51g/g for Fab' and 0.70 g/g for the glycoprotein Fc are obtained, which yield an average value of (0.59+/-0.07) g/g for the intact antibody (2 Fab'+1 Fc). The relative orientations of these domains for each of the IgG subclasses is then found (using where appropriate a cylindrical hinge) from SOLPRO by modelling the Perrin function, P (i.e. 'frictional ratio due to shape') using this delta(app) and experimentally measured sedimentation coefficients. All the IgG subclasses appear as open, rather than compact structures with the degree of openness IgG3>IgG1>(IgG2, IgG4), with IgG3 and IgG1 non-coplanar. The hingeless mutant IgGMcg, with s degrees (20,w) approximately 6.8 S yields a coplanar structure rather similar to IgG2 and IgG4 and consistent with its crystallographic structure. The extension of this procedure for representing solution conformations of other antibody classes and other multi-domain proteins is indicated.     

Hierarchical analysis of wild Atlantic salmon (Salmo salar) fecundity in relation to body size and developmental traits

Using data from wild Atlantic salmon Salmo salar returning to spawn in seven Scottish rivers, we developed a model of fecundity based on individual body size and key developmental traits. We used a novel approach to model selection which maximises predictive accuracy for application to target river stocks to select the best from a suite of Bayesian hierarchical models. This approach aims to ensure the optimal model within the candidate set includes covariates that best predict out-of-sample data to estimate fecundity in areas where no direct observations are available. In addition to body size, the final model included the developmental characteristics of age at smolting and years spent at sea. Using two independent long-term monitoring datasets, the consequences of ignoring these characteristics was revealed by comparing predictions from the best model with models that omitted them.     

The flagella of ‘Candidatus Liberibacter asiaticus’ and its movement in planta

Citrus huanglongbing (HLB) is the most devastating citrus disease worldwide. ‘Candidatus Liberibacter asiaticus’ (Las) is the most prevalent HLB causal agent that is yet to be cultured. Here, we analysed the flagellar genes of Las and Rhizobiaceae and observed two characteristics unique to the flagellar proteins of Las: (i) a shorter primary structure of the rod capping protein FlgJ than other Rhizobiaceae bacteria and (ii) Las contains only one flagellin-encoding gene flaA (CLIBASIA_02090), whereas other Rhizobiaceae species carry at least three flagellin-encoding genes. Only flgJ_Atu but not flgJ_Las restored the swimming motility of Agrobacterium tumefaciens flgJ mutant. Pull-down assays demonstrated that FlgJ_Las interacts with FlgB but not with FliE. Ectopic expression of flaA_Las in A. tumefaciens mutants restored the swimming motility of ∆flaA mutant and ∆flaAD mutant, but not that of the null mutant ∆flaABCD. No flagellum was observed for Las in citrus and dodder. The expression of flagellar genes was higher in psyllids than in planta. In addition, western blotting using flagellin-specific antibody indicates that Las expresses flagellin protein in psyllids, but not in planta. The flagellar features of Las in planta suggest that Las movement in the phloem is not mediated by flagella. We also characterized the movement of Las after psyllid transmission into young flush. Our data support a model that Las remains inside young flush after psyllid transmission and before the flush matures. The delayed movement of Las out of young flush after psyllid transmission provides opportunities for targeted treatment of young flush for HLB control.     

Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.     

Low Blood Long Chain Omega-3 Fatty Acids in UK Children Are Associated with Poor Cognitive Performance and Behavior: A Cross-Sectional Analysis from the DOLAB Study

Background

Omega-3 long-chain polyunsaturated fatty acids (LC-PUFA), especially DHA (docosahexaenonic acid) are essential for brain development and physical health. Low blood Omega-3 LC-PUFA have been reported in children with ADHD and related behavior/learning difficulties, as have benefits from dietary supplementation. Little is known, however, about blood fatty acid status in the general child population. We therefore investigated this in relation to age-standardized measures of behavior and cognition in a representative sample of children from mainstream schools.

Participants

493 schoolchildren aged 7–9 years from mainstream Oxfordshire schools, selected for below average reading performance in national assessments at age seven.

Method

Whole blood fatty acids were obtained via fingerstick samples. Reading and working memory were assessed using the British Ability Scales (II). Behaviour (ADHD-type symptoms) was rated using the revised Conners’ rating scales (long parent and teacher versions). Associations were examined and adjusted for relevant demographic variables.

Results

DHA and eicosapentaenoic acid (EPA), accounted for only 1.9% and 0.55% respectively of total blood fatty acids, with DHA showing more individual variation. Controlling for sex and socio-economic status, lower DHA concentrations were associated with poorer reading ability (std. OLS coeff. = 0.09, p = <.042) and working memory performance (0.14, p = <.001). Lower DHA was also associated with higher levels of parent rated oppositional behavior and emotional lability (−0.175, p = <.0001 and −0.178, p = <.0001).

Conclusions

In these healthy UK children with below average reading ability, concentrations of DHA and other Omega-3 LC-PUFA were low relative to adult cardiovascular health recommendations, and directly related to measures of cognition and behavior. These findings require confirmation, but suggest that the benefits from dietary supplementation with Omega-3 LC-PUFA found for ADHD, Dyspraxia, Dyslexia, and related conditions might extend to the general school population.     

Anticancer Activity of Amauroderma rude

More and more medicinal mushrooms have been widely used as a miraculous herb for health promotion, especially by cancer patients. Here we report screening thirteen mushrooms for anti-cancer cell activities in eleven different cell lines. Of the herbal products tested, we found that the extract of Amauroderma rude exerted the highest activity in killing most of these cancer cell lines. Amauroderma rude is a fungus belonging to the Ganodermataceae family. The Amauroderma genus contains approximately 30 species widespread throughout the tropical areas. Since the biological function of Amauroderma rude is unknown, we examined its anti-cancer effect on breast carcinoma cell lines. We compared the anti-cancer activity of Amauroderma rude and Ganoderma lucidum, the most well-known medicinal mushrooms with anti-cancer activity and found that Amauroderma rude had significantly higher activity in killing cancer cells than Ganoderma lucidum. We then examined the effect of Amauroderma rude on breast cancer cells and found that at low concentrations, Amauroderma rude could inhibit cancer cell survival and induce apoptosis. Treated cancer cells also formed fewer and smaller colonies than the untreated cells. When nude mice bearing tumors were injected with Amauroderma rude extract, the tumors grew at a slower rate than the control. Examination of these tumors revealed extensive cell death, decreased proliferation rate as stained by Ki67, and increased apoptosis as stained by TUNEL. Suppression of c-myc expression appeared to be associated with these effects. Taken together, Amauroderma rude represented a powerful medicinal mushroom with anti-cancer activities.