The mycobacterial Mpa–proteasome unfolds and degrades pupylated substrates by engaging Pup's N‐terminus

Mycobacterium tuberculosis, along with other actinobacteria, harbours proteasomes in addition to members of the general bacterial repertoire of degradation complexes. In analogy to ubiquitination in eukaryotes, substrates are tagged for proteasomal degradation with prokaryotic ubiquitin‐like protein (Pup) that is recognized by the N‐terminal coiled‐coil domain of the ATPase Mpa (also called ARC). Here, we reconstitute the entire mycobacterial proteasome degradation system for pupylated substrates and establish its mechanistic features with respect to substrate recruitment, unfolding and degradation. We show that the Mpa–proteasome complex unfolds and degrades Pup‐tagged proteins and that this activity requires physical interaction of the ATPase with the proteasome. Furthermore, we establish the N‐terminal region of Pup as the structural element required for engagement of pupylated substrates into the Mpa pore. In this process, Mpa pulls on Pup to initiate unfolding of substrate proteins and to drag them toward the proteasome chamber. Unlike the eukaryotic ubiquitin, Pup is not recycled but degraded with the substrate. This assigns a dual function to Pup as both the Mpa recognition element as well as the threading determinant.     

Estimating population structure from AFLP amplification intensity

In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific F_IS and F_ST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species.     

The Importance of Amine-degrading Enzymes on the Biogenic Amine Degradation in Fermented Foods: A review

Biogenic amines (BAs) are a class of harmful compounds often be found in high protein foods, especially naturally fermented foods. BAs derive from free amino acid decarboxylation through microbial activities and can cause toxic effects (headache, heart palpitations, vomiting) on humans, depending on individual sensitivity. Indigenous amine-degrading strains or strains producing amine-degrading enzymes (ADEs) have drawn great attention since they play an important role in affecting BA accumulation, and enzymes/genes involved in the biosynthetic mechanisms. They also help maintain the sensory quality of the final products. Besides, due to ADEs’ harmless catalytic products, they can be further utilized in fermented foods and beverages to reduce BAs. This review describes in detail the mechanisms of BAs formation, as well as the diversity of ADEs able to degrade BAs in a model or real food systems. A deeper knowledge of this issue is crucial because ADEs’ activities are often associated with strains rather than species or genera. Moreover, this information can help to improve the selection and characterization of strains for further applications as starters or bioprotective cultures, to obtain high-quality foods with reduced BAs contents.     

Spatially patterned guild structure in larval parasitoids of cyclically outbreaking winter moth populations

1. Wide temporal fluctuations in host abundance are a potential source of instability and stochasticity in the spatiotemporal population dynamics of associated parasitoid species. Within parasitoid guilds (i.e. parasitoids with similar modes of host utilisation), a conceivable outcome is guild organisation according to a lottery model, in which guild members attain local dominance by colonising previously emptied habitats during increasing host density, before other guild members. In the spatial dimension, an expected manifestation of such dynamics is variable guild structure even across homogeneous habitats. 2. We examined the extent of large‐scale spatial patterning of guild characteristics in larval parasitoid wasps associated with cyclically outbreaking populations of the geometrid moth Operophtera brumata in northern Fennoscandia. The study was performed at the onset of the crash‐phase of the geometrid's outbreak cycle, along a 70‐km transect in costal northern Norway, characterised by largely homogeneous environmental conditions, except for a small climatic gradient. 3. There was a distinct large‐scale spatial turnover in dominance among the major parasitoid groups (i.e. guild structure) in O. brumata along the transect, whereas the total prevalence rate of the guild and its diversity showed no consistent variation. Guild structure was unrelated to host density. 4. Although group‐specific responses to a slight spatial climatic gradient cannot be rejected as a causal mechanism, we conclude that our results are consistent with the expectation from large‐scale stochastic extinction‐recolonisation dynamics among functionally equivalent parasitoids relying on a host with strongly cyclic population fluctuations.     

Association of wintering raptors with Conservation Reserve Enhancement Program grasslands in Pennsylvania

ABSTRACT Conservation grasslands can provide valuable habitat resource for breeding songbirds, but their value for wintering raptors has received little attention. We hypothesized that increased availability of grassland habitat through the Conservation Reserve Enhancement Program (CREP) has resulted in an increase or redistribution in numbers of four species of raptors in Pennsylvania since 2001. We tested this by analyzing winter raptor counts from volunteer surveys, conducted from 2001 to 2008, for Red‐tailed Hawks (Buteo jamaicensis), Rough‐legged Hawks (Buteo lagopus), Northern Harriers (Circus cyaneus), and American Kestrels (Falco sparverius). During that period, numbers of wintering Northern Harriers increased by more than 20% per year. Log‐linear Poisson regression models show that all four species increased in the region of Pennsylvania that had the most and longest‐established conservation grasslands. At the county scale (N= 67), Bayesian spatial models showed that spatial and temporal population trends of all four species were positively correlated with the amount of conservation grassland. This relationship was particularly strong for Northern Harriers, with numbers predicted to increase by 35.7% per year for each additional 1% of farmland enrolled in CREP. Our results suggest that conservation grasslands are likely the primary cause of the increase in numbers of wintering Northern Harriers in Pennsylvania since 2001.     

Microsatellite analyses of the trout of northwest Mexico)

The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity=0.35, and a mean F _st=0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.     

Cultural and genetic evolution in mountain white-crowned sparrows: song dialects are associated with population structure

Bird song often varies geographically within a species; when this geographic variation has distinct boundaries, the shared song types are referred to as song dialects. How dialects are produced and their adaptive significance are longstanding problems in biology, with implications for the role of culture in the evolution and ecology of diverse organisms, including humans. Here we test the hypothesis that song dialect, a culturally transmitted trait, is related to the population genetic structure of mountain white-crowned sparrows (Zonotrichia leucophrys oriantha). To address this, we compared microsatellite allele frequencies from 18 sample sites representing eight dialect regions in the Sierra Nevada. Pairwise genetic distances were not significantly correlated with geographic distances either within or between dialects, nor did dialect groups form distinct genetic groups according to neighbor-joining or UPGMA analysis, and most variation in allele frequencies occurred among individuals rather than at higher levels. However, most of the remaining variation was attributable to differences among, rather than within, dialect regions, and this among-dialect component of variance was statistically significant. Moreover, when controlling for the effect of geographic distance, song dissimilarity and genetic distance between site pairs were significantly correlated. Thus, song dialects appear to be associated with reductions in, but not strict barriers to, gene flow among dialect regions.     

The probability that beneficial mutations are lost in populations with periodic bottlenecks

Population bottlenecks affect the dynamics of evolution, increasing the probability that beneficial mutations will be lost. Recent protocols for the experimental study of evolution involve repeated bottlenecks-when fresh media are inoculated during serial transfer or when chemostat tubes are changed. Unlike population reductions caused by stochastic environmental factors, these bottlenecks occur at known, regular intervals and with a fixed dilution ratio. We derive the ultimate probability of extinction for a beneficial mutation in a periodically bottlenecked population, using both discrete and continuous approaches. We show that both approaches yield the same approximation for extinction probability. From this, we derive an approximate expression for an effective population size.     

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.