Cryptic species and colonization processes in Ophryotrocha (Annelida,Dorvilleidae) inhabiting vertebrate remains in the shallow‐water Mediterranean

Over the past several years, there has been growing interest in how bones of decaying mammals are colonized in the marine seabed. One of the most common opportunistic taxa occurring worldwide on bones is dorvilleid polychaetes of the genus Ophryotrocha. In a recent study in the Mediterranean, Ophryotrocha puerilis and Ophryotrocha alborana were two of the most abundant species occurring in experimentally deployed bones. These species have direct development and this makes them a suitable model to study the mechanisms and processes allowing organisms lacking a dispersive larval phase to colonize new substrates. Here, we address the colonization processes at the molecular level for populations of O. puerilis and O. alborana on experimentally deployed mammal bones in the shallow‐water Mediterranean collected over a year at 3‐month intervals. High genetic distances between some of the O. puerilis organisms collected indicated the occurrence of at least two cryptic sibling species (O. puerilis ‘Shallow’ and O. puerilis ‘Deep’) apart from O. puerilis sensu stricto. This was corroborated with phylogenetic analyses using an alignment of three concatenated genes (COI, 16S, H3) and with species delimitation analyses using COI. The haplotype network inferred from COI sequences for O. puerilis ‘Shallow’ showed a few common haplotypes shared between the two trimesters analysed and several other less represented haplotypes only present in one trimester. Thus, colonization of these experimental bones may have been achieved by a few organisms that arrived to the bones and were able to reseed, and by several individuals arriving to the experimental bones and not persisting across time. In contrast, the haplotype network for O. alborana revealed that none of the haplotypes present in three different trimesters were shared, suggesting that the populations arriving at the bones during each trimester were totally replaced by new individuals during the subsequent trimesters. Our study suggests that different species of shallow‐water Ophryotrocha occurring in the Mediterranean may have different patterns of substrate colonization despite sharing similar life histories.     

The Role of Electrostatic Interactions in Binding of Histone H3K4me2/3 to the Sgf29 Tandem Tudor Domain

Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage. Herein, we report thermodynamic analyses for the recognition of histone H3K4me3 and H3K4me2 by the tandem tudor domain of Sgf29 and its recognition site variants. Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29. This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.     

Unbiased and efficient log-likelihood estimation with inverse binomial sampling

The fate of scientific hypotheses often relies on the ability of a computational model to explain the data, quantified in modern statistical approaches by the likelihood function. The log-likelihood is the key element for parameter estimation and model evaluation. However, the log-likelihood of complex models in fields such as computational biology and neuroscience is often intractable to compute analytically or numerically. In those cases, researchers can often only estimate the log-likelihood by comparing observed data with synthetic observations generated by model simulations. Standard techniques to approximate the likelihood via simulation either use summary statistics of the data or are at risk of producing substantial biases in the estimate. Here, we explore another method, inverse binomial sampling (IBS), which can estimate the log-likelihood of an entire data set efficiently and without bias. For each observation, IBS draws samples from the simulator model until one matches the observation. The log-likelihood estimate is then a function of the number of samples drawn. The variance of this estimator is uniformly bounded, achieves the minimum variance for an unbiased estimator, and we can compute calibrated estimates of the variance. We provide theoretical arguments in favor of IBS and an empirical assessment of the method for maximum-likelihood estimation with simulation-based models. As case studies, we take three model-fitting problems of increasing complexity from computational and cognitive neuroscience. In all problems, IBS generally produces lower error in the estimated parameters and maximum log-likelihood values than alternative sampling methods with the same average number of samples. Our results demonstrate the potential of IBS as a practical, robust, and easy to implement method for log-likelihood evaluation when exact techniques are not available.     

Quantitative PCR method to detect a 13-kb deletion in the MURR1 gene associated with copper toxicosis and HIV-1 replication

The recently discovered locus for copper toxicosis (CT) in Bedlington terriers (BT) has a 13-kb deletion enveloping the 187-bp exon-2 of the MURR1 gene. This MURR1 gene is not only involved with biliary copper excretion but also associated with HIV-1 replication. The microsatellite C04107 lying in an intron of the MURR1 gene is highly associated with the disease but shows haplotype diversity. The only solid molecular test for the disease is by showing the deletion in exon-2 in cDNA in liver tissue; this test is not robust on RNA from peripheral leukocytes because of their low MURR1 expression level. Because of these drawbacks, we developed a new quantitative PCR (Q-PCR) protocol. Here we show that the MURR1 exon-2/exon-3 ratio measured by Q-PCR on genomic DNA correlates perfectly with the microsatellite marker and with RT-PCR data from blood samples, buccal swabs, and liver biopsies. In view of the important role of MURR1 in cells of many tissues, this new test has a wide range of applications in comparative biomedical research. Furthermore, Q-PCR on DNA may be a new tool in general to analyze mutations that cannot be approached by standard methods.Robert P. Favier and Bart Spee contributed equally to this work.     

Carbon sequestration potential in European croplands has been overestimated

Yearly, per‐area carbon sequestration rates are used to estimate mitigation potentials by comparing types and areas of land management in 1990 and 2000 and projected to 2010, for the European Union (EU)‐15 and for four country‐level case studies for which data are available: UK, Sweden, Belgium and Finland. Because cropland area is decreasing in these countries (except for Belgium), and in most European countries there are no incentives in place to encourage soil carbon sequestration, carbon sequestration between 1990 and 2000 was small or negative in the EU‐15 and all case study countries. Belgium has a slightly higher estimate for carbon sequestration than the other countries examined. This is at odds with previous reports of decreasing soil organic carbon stocks in Flanders. For all countries except Belgium, carbon sequestration is predicted to be negligible or negative by 2010, based on extrapolated trends, and is small even in Belgium. The only trend in agriculture that may be enhancing carbon stocks on croplands at present is organic farming, and the magnitude of this effect is highly uncertain. Previous studies have focused on the potential for carbon sequestration and have shown quite significant potential. This study, which examines the sequestration likely to occur by 2010, suggests that the potential will not be realized. Without incentives for carbon sequestration in the future, cropland carbon sequestration under Article 3.4 of the Kyoto Protocol will not be an option in EU‐15.     

The impact of climate change on lakes in the Netherlands: a review

Climate change will alter freshwater ecosystems but specific effects will vary among regions and the type of water body. Here, we give an integrative review of the observed and predicted impacts of climate change on shallow lakes in the Netherlands and put these impacts in an international perspective. Most of these lakes are man-made and have preset water levels and poorly developed littoral zones. Relevant climatic factors for these ecosystems are temperature, ice-cover and wind. Secondary factors affected by climate include nutrient loading, residence time and water levels. We reviewed the relevant literature in order to assess the impact of climate change on these lakes. We focussed on six management objectives as bioindicators for the functioning of these ecosystems: target species, nuisance species, invading species, transparency, carrying capacity and biodiversity. We conclude that climate change will likely (i) reduce the numbers of several target species of birds; (ii) favour and stabilize cyanobacterial dominance in phytoplankton communities; (iii) cause more serious incidents of botulism among waterfowl and enhance the spreading of mosquito borne diseases; (iv) benefit invaders originating from the Ponto-Caspian region; (v) stabilize turbid, phytoplankton-dominated systems, thus counteracting restoration measures; (vi) destabilize macrophyte-dominated clear-water lakes; (vii) increase the carrying capacity of primary producers, especially phytoplankton, thus mimicking eutrophication; (viii) affect higher trophic levels as a result of enhanced primary production; (ix) have a negative impact on biodiversity which is linked to the clear water state; (x) affect biodiversity by changing the disturbance regime. Water managers can counteract these developments by reduction of nutrient loading, development of the littoral zone, compartmentalization of lakes and fisheries management.     

Exclusive frugivory and seed dispersal of Rhamnus alaternus in the bird breeding season

We studied avian frugivory and seed dispersal in a dioecious shrub, Rhamnus alaternus, focusing on the quantitative and qualitative components of effectiveness. The study took place at three locations in the northeast of the Iberian Peninsula, and examined bird behaviour, intensity of feeding, and the consequences for seedling emergence. The coincidence between the bird breeding season and fruit ripening of R. alaternus in the absence of other ripe fruit, generates a monospecific interaction. The extant frugivorous species were mainly legitimate seed dispersers and their abundance was low. Sylvia melanocephala and S. undata were the most important at one site whereas S. atricapilla, Erithacus rubecula and Turdus merula predominated at the other two sites. Fruit handling took place directly on the branches. Bird species used microhabitats differently as first post-feeding perch, which usually was a short distance away. The low density of frugivorous birds in all localities, among others factors, resulted in satiation of the disperser community and many mature fruits unconsumed. Both adults and juveniles feed upon the plants and their foraging patterns are similar. Adults of S. melanocephala were observed to feed fruit to nestlings and consequently a second phase of dispersal potentially arises from the transport of fecal sacs. Pulp removal and passage through the digestive tract increased the probability of seedling emergence. This plant-dispersal interaction has important consequences, both positive and negative for the plant. Positively, the fruiting of R. alaternus at a time when other ripe fruits are not available avoids interspecific competition for seed dispersers. In addition, a low density of seed rain may reduce intraspecific competition. Negatively, the low density and small size of the breeding frugivorous bird community limit fruit handling and removal away from the parent plants, while the territorial behaviour of birds at that time of the year reduces the potential distances of seed dispersal.     

Effect of increasing GnRH and PGF2α dose during Double-Ovsynch on ovulatory response,luteal regression,and fertility of lactating dairy cows

Ovsynch-type synchronization of ovulation protocols have suboptimal synchronization rates due to reduced ovulation to the first GnRH treatment and inadequate luteolysis to the prostaglandin F_2α (PGF_2α) treatment before timed artificial insemination (TAI). Our objective was to determine whether increasing the dose of the first GnRH or the PGF_2α treatment during the Breeding-Ovsynch portion of Double-Ovsynch could improve the rates of ovulation and luteolysis and therefore increase pregnancies per artificial insemination (P/AI). In experiment 1, cows were randomly assigned to a two-by-two factorial design to receive either a low (L) or high (H) doses of GnRH (Gonadorelin; 100 vs. 200 μg) and a PGF_2α analogue (cloprostenol; 500 vs. 750 μg) resulting in the following treatments: LL (n = 263), HL (n = 277), LH (n = 270), and HH (n = 274). Transrectal ultrasonography and serum progesterone (P4) were used to assess ovulation to GnRH1, GnRH2, and luteal regression after PGF_2α during Breeding-Ovsynch in a subgroup of cows (n = 651 at each evaluation). Pregnancy status was assessed 29, 39, and 74 days after TAI. In experiment 2, cows were randomly assigned to LL (n = 220) or HH (n = 226) treatment as described for experiment 1. For experiment 1, ovulation to GnRH1 was greater (P = 0.01) for cows receiving H versus L GnRH (66.6% [217/326] vs. 57.5% [187/325]) treatment, but only for cows with elevated P4 at GnRH1. Cows that ovulated to GnRH1 had increased (P < 0.001) fertility compared with cows that did not ovulate (52.2% vs. 38.5%); however, no effect of higher dose of GnRH on fertility was detected. The greater PGF_2α dose increased luteal regression primarily in multiparous cows (P = 0.03) and tended to increase fertility (P = 0.05) only at the pregnancy diagnosis 39 days after TAI. Overall, P/AI was 47.0% at 29 days and 39.7% at 74 days after TAI; P/AI did not differ (P = 0.10) among treatments at 74 days (LL, 34.6%; HL, 40.8%; LH, 42.2%; HH, 40.9%) and was greater (P < 0.001) for primiparous cows than for multiparous cows (46.1% vs. 33.8%). For experiment 2, P/AI did not differ (P = 0.21) between H versus L treatments (44.2% [100/226] vs. 40.5% [89/220]). Thus, despite an increase in ovulatory response to GnRH1 and luteal regression to PGF_2α, there were only marginal effects of increasing dose of GnRH or PGF_2α on fertility to TAI after Double-Ovsynch.