Activity of broadly neutralizing antibodies, including PG9, PG16, and VRC01, against recently transmitted subtype B HIV-1 variants from early and late in the epidemic

For the development of a neutralizing antibody-based human immunodeficiency virus type 1 (HIV-1) vaccine, it is important to characterize which antibody specificities are most effective against currently circulating HIV-1 variants. We recently reported that HIV-1 has become more resistant to antibody neutralization over the course of the epidemic, and we here explore whether this increased neutralization resistance is also observed for the newly identified broadly neutralizing antibodies (BrNAbs) PG9, PG16, and VRC01. Furthermore, we performed a comprehensive analysis of the neutralizing sensitivity of currently circulating recently transmitted subtype B viruses to the currently most known BrNAbs. Virus variants isolated less than 6 months after seroconversion from individuals who seroconverted between 2003 and 2006 (n = 21) were significantly more resistant to neutralization by VRC01 than viruses from individuals who seroconverted between 1985 and 1989 (n = 14). In addition, viruses from contemporary seroconverters tended to be more resistant to neutralization by PG16, which coincided with the presence of more mutations at positions in the viral envelope that may potentially influence neutralization by this antibody. Despite this increased neutralization resistance, all recently transmitted viruses from contemporary seroconverters were sensitive to at least one BrNAb at concentrations of ≤5 μg/ml, with PG9, PG16, and VRC01 showing the greatest breadth of neutralization at lower concentrations. These results suggest that a vaccine capable of eliciting multiple BrNAb specificities will be necessary for protection of the population against HIV-1 infection.     

Longer V1V2 region with increased number of potential N-linked glycosylation sites in the HIV-1 envelope glycoprotein protects against HIV-specific neutralizing antibodies

Human immunodeficiency virus type 1 (HIV-1) has the ability to adapt to the host environment by escaping from host immune responses. We previously observed that escape from humoral immunity, both at the individual and at a population level, coincided with longer variable loops and an increased number of potential N-linked glycosylation sites (PNGS) in the viral envelope glycoprotein (Env) and, in particular, in variable regions 1 and 2 (V1V2). Here, we provide several lines of evidence for the role of V1V2 in the resistance of HIV-1 to neutralizing antibodies. First, we determined that the increasing neutralization resistance of a reference panel of tier-categorized neutralization-sensitive and -resistant HIV-1 variants coincided with a longer V1V2 loop containing more PNGS. Second, an exchange of the different variable regions of Env from a neutralization-sensitive HIV-1 variant into a neutralization-resistant escape variant from the same individual revealed that the V1V2 loop is a strong determinant for sensitivity to autologous-serum neutralization. Third, exchange of the V1V2 loop of neutralization-sensitive HIV-1 variants from historical seroconverters with the V1V2 loop of neutralization-resistant HIV-1 variants from contemporary seroconverters decreased the neutralization sensitivity to CD4-binding site-directed antibodies. Overall, we demonstrate that an increase in the length of the V1V2 loop and/or the number of PNGS in that same region of the HIV-1 envelope glycoprotein is directly involved in the protection of HIV-1 against HIV-specific neutralizing antibodies, possibly by shielding underlying epitopes in the envelope glycoprotein from antibody recognition.     

Microsatellite based typing of Aspergillus fumigatus: strengths, pitfalls and solutions

Microsatellites, or short tandem repeats (STR's), are popular tools to discriminate between microbial isolates. Here, we report on the robustness of a microsatellite panel for discrimination of Aspergillus fumigatus isolates. Two major PCR artefacts (stutter peaks and minus-A peaks) can complicate correct interpretation of STR data. We investigated the effect of alterations to the various components of the PCR amplification mixtures on these PCR artefacts and on the reproducibility of this assay. Some extreme conditions led to a loss of signal, but, under all conditions where a signal was obtained, identical typing results were produced. Furthermore, pitfalls with the exchange of results between labs are discussed. These pitfalls are primarily associated with sizing of the obtained PCR fragments.     

Reciprocal interactions between the cabbage root fly (Delia radicum) and two glucosinolate phenotypes of Barbarea vulgaris

The cabbage root fly, Delia radicum L. (Diptera: Anthomyiidae), has a life cycle with spatially separated components: adults live and oviposit above ground, whereas larvae feed and pupate below ground. Oviposition choice is affected by shoot glucosinolates. However, little is known about below‐ground plant defence against D. radicum. Here, we investigate the effect of glucosinolates on oviposition preference and performance of D. radicum, using two naturally occurring heritable chemotypes of Barbarea vulgaris R. Br. (Brassicaceae) with different glucosinolate profiles: BAR‐type plants (the most common and genetically dominant glucosinolate profile, dominated by glucobarbarin) and NAS‐type plants (the recessive phenotype, dominated by gluconasturtiin). Performance was studied by applying 10 neonate D. radicum larvae per plant and measuring pupal biomass after 18 days. There was no difference in retrieval, but pupae had a higher biomass after development on BAR‐type plants. On average, BAR‐type plants received 1.8 times more eggs than NAS types, but this difference was not statistically significant. In a separate experiment, we compared the physiological response of both chemotypes to D. radicum feeding. Infestation reduced root and shoot biomass, root sugar and amino acid levels, and shoot sugar levels. Except for shoot sugar levels, these responses did not differ between the two chemotypes. Shoot or root glucosinolate profiles did not change on infestation. As glucosinolate profiles were the only consistent difference between the chemotypes, it is likely that this difference caused the reduced biomass of D. radicum pupae on NAS‐type plants. In an experimental garden, plants were heavily infested by root flies, but we found no differences in the percentage of fallen‐over flower stalks between the chemotypes. Overall, we found more pupae in the soil near BAR‐type plants, but this was not statistically significant. The results of the performance experiment suggest that BAR‐type plants may be more suitable hosts than NAS‐type plants.     

A heritable glucosinolate polymorphism within natural populations of Barbarea vulgaris

In natural populations of Barbarea vulgaris we found two distinctly different glucosinolate profiles. The most common glucosinolate profile is dominated (94%) by the hydroxylated form, (S)-2-hydroxy-2-phenylethyl-glucosinolate (glucobarbarin, BAR-type), whereas in the other type 2-phenylethyl-glucosinolate (gluconasturtiin, NAS-type) was most prominent (82%). NAS-type plants have a 108-fold increase of gluconasturtiin concentration in rosette leaves compared to BAR-type plants. The glucosinolate composition of both chemotypes is consistent throughout all plant organs and after induction with jasmonic acid. Although the glucosinolate profile of the roots has a more diverse composition than other plant organs, it still matches the chemotype. In 12 natural populations that we sampled in Germany, Belgium, France and Switzerland solely BAR-type plants were found. However, eight out of the 15 Dutch populations that were sampled contained 2-22% NAS-type plants. Controlled crosses showed that the chemotype was heritable and determined by a single gene with two alleles. The allele coding for the BAR-type was dominant and the allele for the NAS-type was recessive. The different glucosinolate profiles will yield different hydrolysis products upon damage, and therefore we expect them to differentially affect the multitrophic interactions associated with B. vulgaris in their natural environment.     

Resistance QTL confirmed through development of QTL-NILs for barley leaf rust resistance

Near-isogenic lines (NILs) differing with regard to disease QTLs provide valuable material for a more detailed study into the genetic basis of quantitative resistance. Previously obtained information on QTLs that show an effect on leaf rust (Puccinia hordei) in barley was used in a marker-assisted backcross programme. The genome origin in backcross plants was controlled through AFLP marker analysis and graphical genotyping. Plants obtained after the third generation of backcrossing sufficiently resembled the recurrent parent. For one QTL, BC₃S₁ plants were evaluated in a disease test and genotyped. NILs containing the desired QTL in homozygous condition in a recipient background were finally obtained. A disease test and verification of the marker genotype confirmed the identity of the NILs. Simultaneous with the backcross programme a simulation study on efficiency of marker-assisted backcrossing was performed.     

A revision of fossil eagle owls (Aves: Strigiformes: Bubo) from Europe and the description of a new species,Bubo ibericus,from Cal Guardiola (NE Iberian Peninsula)

The European fossil record of eagle owls, genus Bubo Duméril 1806 Duméril AMC. 1806. Zoologie Analytique, ou Méthode Naturelle de Classification des Animaux, rendue plus Facile à l’Aide de Tableaux Synoptiques. Paris: H. L. Perronneau. [Google Scholar], is thought to extend back into the Miocene, but records of Bubo before the Middle Pleistocene are scarce and mainly constituted by non-diagnostic or fragmentary specimens. Apart from a number of fossil species of Bubo of uncertain validity, i.e. Bubo? florianae Kretzoi 1957 Kretzoi M. 1957. Bird remains from the Hipparion-fauna of Csákvár. Aquila. 63:239–248. [Google Scholar], Bubo lignitum Giebel 1860 Giebel CG. 1860. Zur Fauna der Braunkohlen Formation von Rippersroda in Thüringen. Zeitschrift für die Gesammten Naturwissenschaften. 16:147–153. [Google Scholar], and Bubo perpastus (Ballman 1976 Ballmann P. 1976. Fossile Vögel aus dem Neogen der Halbinsel Gargano (Italien). Zweiter Teil Scripta Geol. 38:1–59. [Google Scholar]), most fossil Bubo material is unassigned to species or assigned to the extant Bubo bubo (Linnaeus 1758) on the basis of size, especially for Early Pleistocene records. Given the ambiguity about the validity of the earliest records, here we revise the pre-Middle Pleistocene fossil record of Bubo in Europe. Our results indicate that, in Europe, Bubo is first recorded in the Late Pliocene/Early Pleistocene of Italy. By the Early Pleistocene, three taxa can be distinguished: Bubo ibericus sp. nov. from Cal Guardiola (Spain), Bubo sp. nov. indet. from Soave Cava Sud (Italy) and Bubo sp. from various sites across Europe. By the Middle Pleistocene, Eurasian environments experienced a substantial increase in severity and duration of glacial periods which might have led to the replacement of extinct species of Bubo by the recent B. bubo and Bubo scandiacus.     

Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans

To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.

In response to heat, ectotherms exhibit an adaptive response characterized by changes in membrane fluidity. This study in the nematode Caenorhabditis elegans shows that neuronal HSF-1 is critical for this remodeling, suggesting a neuronal thermostat-based mechanism that can non-cell-autonomously coordinate the animal’s response to heat.