Control of innate immune signaling and membrane targeting by the Hepatitis C virus NS3/4A protease are governed by the NS3 helix α0

Hepatitis C virus (HCV) infection is sensed in the host cell by the cytosolic pathogen recognition receptor RIG-I. RIG-I signaling is propagated through its signaling adaptor protein MAVS to drive activation of innate immunity. However, HCV blocks RIG-I signaling through viral NS3/4A protease cleavage of MAVS on the mitochondrion-associated endoplasmic reticulum (ER) membrane (MAM). The multifunctional HCV NS3/4A serine protease is associated with intracellular membranes, including the MAM, through membrane-targeting domains within NS4A and also at the amphipathic helix α(0) of NS3. The serine protease domain of NS3 is required for both cleavage of MAVS, a tail-anchored membrane protein, and processing the HCV polyprotein. Here, we show that hydrophobic amino acids in the NS3 helix α(0) are required for selective cleavage of membrane-anchored portions of the HCV polyprotein and for cleavage of MAVS for control of RIG-I pathway signaling of innate immunity. Further, we found that the hydrophobic composition of NS3 helix α(0) is essential to establish HCV replication and infection. Alanine substitution of individual hydrophobic amino acids in the NS3 helix α(0) impaired HCV RNA replication in cells with a functional RIG-I pathway, but viral RNA replication was rescued in cells lacking RIG-I signaling. Therefore, the hydrophobic amphipathic helix α(0) of NS3 is required for NS3/4A control of RIG-I signaling and HCV replication by directing the membrane targeting of both viral and cellular substrates.     

Strong influences of a dominant,ground‐nesting ant on recruitment,and establishment of ant colonies and communities

Many factors drive the organization of communities including environmental factors, dispersal abilities, and competition. In particular, ant communities have high levels of interspecific competition and dominance that may affect community assembly processes. We used a combination of surveys and nest supplementation experiments to examine effects of a dominant ground‐nesting ant (Pheidole synanthropica) on (1) arboreal twig‐nesting, (2) ground‐foraging, and (3) coffee‐foraging ant communities in coffee agroecosystems. We surveyed these communities in high‐ and low‐density areas of P. synanthropica over 2 years. To test for effects on twig ant recruitment, we placed artificial nesting resources on coffee plants in areas with and without P. synanthropica. The first sampling period revealed differences in ant species composition on the ground, in coffee plants, and artificial nests between high‐ and low‐density sites of P. synanthropica. High‐density sites also had significantly lower recruitment of twig ants and had species‐specific effects on twig ant species. Prior to the second survey period, abundance of P. synanthropica declined in the high‐density sites, such that P. synanthropica densities no longer differed. Subsequent sampling revealed no difference in total recruitment of twig ants to artificial nests between treatments. Likewise, surveys of ground and coffee ants no longer showed significant differences in community composition. The results from the first experimental period, followed by survey results after the decline in P. synanthropica densities suggest that dominant ants can drive community assembly via both recruitment and establishment of colonies within the community.     

Opposite Roles of NMDA Receptors in Relapsing and Primary Progressive Multiple Sclerosis

Synaptic transmission and plasticity mediated by NMDA receptors (NMDARs) could modulate the severity of multiple sclerosis (MS). Here the role of NMDARs in MS was first explored in 691 subjects carrying specific allelic variants of the NR1 subunit gene or of the NR2B subunit gene of this glutamate receptor. The analysis was replicated for significant SNPs in an independent sample of 1548 MS subjects. The C allele of rs4880213 was found to be associated with reduced NMDAR-mediated cortical excitability, and with increased probability of having more disability than the CT/TT MS subjects. MS severity was higher in the CC group among relapsing-remitting MS (RR-MS) patients, while primary progressive MS (PP-MS) subjects homozygous for the T allele had more pronounced clinical worsening. Mean time to first relapse, but not to an active MRI scan, was lower in the CC group of RR-MS patients, and the number of subjects with two or more clinical relapses in the first two years of the disease was higher in CC compared to CT/TT group. Furthermore, the percentage of relapses associated with residual disability was lower in subjects carrying the T allele. Lesion load at the MRI was conversely unaffected by the C or T allele of this SNP in RR-MS patients. Axonal and neuronal degeneration at the optical coherence tomography was more severe in the TT group of PP-MS patients, while reduced retinal nerve fiber thickness had less consequences on visual acuity in RR-MS patients bearing the T allele. Finally, the T allele was associated with preserved cognitive abilities at the Rao’s brief repeatable neuropsychological battery in RR-MS. Signaling through glutamate NMDARs enhances both compensatory synaptic plasticity and excitotoxic neurodegeneration, impacting in opposite ways on RR-MS and PP-MS pathophysiological mechanisms.     

Intestinal Methanobrevibacter smithii but not total bacteria is related to diet‐induced weight gain in rats

It is increasingly understood that gastrointestinal (GI) methanogens, including Methanobrevibacter smithii, influence host metabolism.

Objective:

Therefore, we compared M. smithii colonization and weight gain in a rat model under different dietary conditions.

Design and Methods:

Sprague‐Dawley rats were inoculated with M. smithii or vehicle (N = 10/group), fed normal chow until day 112 postinoculation, high‐fat chow until day 182, then normal chow until day 253. Thereafter, five rats from each group were fed high‐fat and normal chow until euthanasia.

Results:

Both groups exhibited M. smithii colonization, which increased following inoculation only for the first 9 days. Change to high‐fat chow correlated with significant increases in weight (P < 0.00001) and stool M. smithii (P < 0.01) in all rats, with stool M. smithi decreasing on return to normal chow. Rats switched back to high‐fat on day 253 further increased weight (P < 0.001) and stool M. smithii (P = 0.039). Euthanasia revealed all animals had higher M. smithii, but not total bacteria, in the small intestine than in the colon. Rats switched back to high‐fat chow had higher M. smithii levels in the duodenum, ileum, and cecum than those fed normal chow; total bacteria did not differ in any bowel segment. Rats which gained more weight had more bowel segments colonized, and the lowest weight recorded was in a rat on high‐fat chow which had minimal M. smithii colonization.

Conclusions:

We conclude that M. smithii colonization occurs in the small bowel as well as in the colon, and that the level and extent of M. smithii colonization is predictive of degree of weight gain in this animal model.     

Incorporating Conservation Zone Effectiveness for Protecting Biodiversity in Marine Planning

Establishing different types of conservation zones is becoming commonplace. However, spatial prioritization methods that can accommodate multiple zones are poorly understood in theory and application. It is typically assumed that management regulations across zones have differential levels of effectiveness (“zone effectiveness”) for biodiversity protection, but the influence of zone effectiveness on achieving conservation targets has not yet been explored. Here, we consider the zone effectiveness of three zones: permanent closure, partial protection, and open, for planning for the protection of five different marine habitats in the Vatu-i-Ra Seascape, Fiji. We explore the impact of differential zone effectiveness on the location and costs of conservation priorities. We assume that permanent closure zones are fully effective at protecting all habitats, open zones do not contribute towards the conservation targets and partial protection zones lie between these two extremes. We use four different estimates for zone effectiveness and three different estimates for zone cost of the partial protection zone. To enhance the practical utility of the approach, we also explore how much of each traditional fishing ground can remain open for fishing while still achieving conservation targets. Our results show that all of the high priority areas for permanent closure zones would not be a high priority when the zone effectiveness of the partial protection zone is equal to that of permanent closure zones. When differential zone effectiveness and costs are considered, the resulting marine protected area network consequently increases in size, with more area allocated to permanent closure zones to meet conservation targets. By distributing the loss of fishing opportunity equitably among local communities, we find that 84–88% of each traditional fishing ground can be left open while still meeting conservation targets. Finally, we summarize the steps for developing marine zoning that accounts for zone effectiveness.     

Using RAD‐seq to develop sex‐linked markers in a haplodiplontic alga

For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) to identify sex‐linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD‐seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non‐native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female‐linked and 19 putatively male‐linked sequences. Four female‐ and eight male‐linked markers amplified in all three life cycle stages. Using one female‐ and one male‐linked marker that were sex‐specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non‐native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD‐seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex‐linked markers in other haplodiplontic macroalgae for which genomes are lacking.     

Expression of somite segmentation genes in amphioxus: a clock without a wavefront?

In the basal chordate amphioxus (Branchiostoma), somites extend the full length of the body. The anteriormost somites segment during the gastrula and neurula stages from dorsolateral grooves of the archenteron. The remaining ones pinch off, one at a time, from the tail bud. These posterior somites appear to be homologous to those of vertebrates, even though the latter pinch off from the anterior end of bands of presomitic mesoderm rather than directly from the tail bud. To gain insights into the evolution of mesodermal segmentation in chordates, we determined the expression of ten genes in nascent amphioxus somites. Five (Uncx4.1, NeuroD/atonal-related, IrxA, Pcdhdelta2-17/18, and Hey1) are expressed in stripes in the dorsolateral mesoderm at the gastrula stage and in the tail bud while three (Paraxis, Lcx, and Axin) are expressed in the posterior mesendoderm at the gastrula and neurula stages and in the tail bud at later stages. Expression of two genes (Pbx and OligA) suggests roles in the anterior somites that may be unrelated to initial segmentation. Together with previous data, our results indicate that, with the exception that Engrailed is only segmentally expressed in the anterior somites, the genetic mechanisms controlling formation of both the anterior and posterior somites are probably largely identical. Thus, the fundamental pathways for mesodermal segmentation involving Notch-Delta, Wnt/beta-catenin, and Fgf signaling were already in place in the common ancestor of amphioxus and vertebrates although budding of somites from bands of presomitic mesoderm exhibiting waves of expression of Notch, Wnt, and Fgf target genes was likely a vertebrate novelty. Given the conservation of segmentation gene expression between amphioxus and vertebrate somites, we propose that the clock mechanism may have been established in the basal chordate, while the wavefront evolved later in the vertebrate lineage.     

Boro-norleucine as a P1 residue for the design of selective and potent DPP7 inhibitors

Dipeptide-based inhibitors with C-substituted (alkyl or aminoalkyl) alpha-amino acids in the P2 position and boro-norleucine (boro-Nle) in the P1 position were synthesized. Relative to boro-proline, boro-Nle as a P1 residue was shown able to significantly dial out DPP4, FAP, DPP8, and DPP9 activity. Dab-boro-Nle (4g) proved to be the most selective and potent DPP7 inhibitor with a DPP7 IC50 value of 480 pM.     

Comparative morphometric and chemical analyses of phenotypes of two invasive ambrosia beetles (Euwallacea spp.) in the United States

The polyphagous shot hole borer (PSHB), Euwallacea sp., was first detected in 2003 in Los Angeles County, California, USA. Recently, this invasive species has become a major pest of many hardwood trees in urban and wildland forests throughout southern California. PSHB is nearly identical in morphology and life history to the tea shot hole borer (TSHB), Euwallacea fornicatus, an invasive pest of hardwoods in Florida, USA and many other parts of the world. However, molecular studies have suggested that the taxa are different species. We conducted morphometric and chemical analyses of the phenotypes of Euwallacea sp. collected in southern California (Los Angeles County) and E. fornicatus collected in Florida (Miami‐Dade County). Our analyses indicated that PSHB has 3 larval instars. The third larval instar was separated from the first 2 instars by head capsule width with 0 probability of misclassification. The body length, head width, and pronotal width of PSHB adult males were significantly less than those of females. Head width and pronotal width of female PSHB were significantly less than those of female TSHB. In contrast, body length, and ratio of body length to pronotal width of female PSHB were significantly greater than those of female TSHB. However, females of these 2 species could not be separated completely by these 4 measurements because of the overlapping ranges. Cuticular hydrocarbons detected in both species were exclusively alkanes (i.e., n‐alkanes, monomethylalkanes, dimethylalkanes, and trimethylalkanes). Cuticular hydrocarbon profiles of PSHB males and females were similar, but they both differed from that of TSHB females. Cuticular hydrocarbons of PSHB were predominantly internally branched dimethylalkanes with backbones of 31 and 33 carbons, whereas cuticular hydrocarbons of TSHB females were dominated by internally branched monomethylalkanes and dimethylalkanes with backbones of 28 and 29 carbons. Multiple compounds within these classes appear to be diagnostic for PSHB and TSHB, respectively.