Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers

The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (～31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ～0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.     

Long-term beneficial effect of a 16-week very low calorie diet on pericardial fat in obese type 2 diabetes mellitus patients

Pericardial fat accumulation has been associated with an increased cardiovascular risk. A very low calorie diet (VLCD) improves the cardiovascular risk profile in patients with type 2 diabetes mellitus (T2DM), by improving the metabolic profile, heart function, and triglyceride (TG) stores in (non)adipose tissues. However, long-term effects of a VLCD on pericardial fat volume and tissue-specific TG accumulation have not been documented. The aim of this study was therefore to assess the effects of a 16-week VLCD and of subsequent 14 months follow-up on a regular diet on pericardial fat in relation to other TG stores in obese T2DM patients. We included 14 obese patients with insulin-treated T2DM (mean ± s.e.m.: age 53 ± 2 years; BMI 35 ± 1 kg/m(2)). Pericardial fat and other (non)adipose TG stores were measured using magnetic resonance (MR) imaging and proton spectroscopy before and after a 16-week VLCD and after a 14-month follow-up without dietary interventions. A 16-week VLCD reduced body weight, pericardial fat, hepatic TG content, visceral and subcutaneous abdominal fat volumes to 78, 83, 16, 40, and 53% of baseline values respectively, (all P < 0.05). After an additional 14 months of follow-up on a regular diet, the reduction in pericardial fat volume sustained, despite a substantial regain in body weight, visceral abdominal fat, and hepatic TG content (respectively 90, 83 and 73% of baseline values). In conclusion, VLCD-induced weight loss in obese T2DM patients is accompanied by a substantial decrease in pericardial fat volume, which is sustained even after subsequent weight regain.     

Evolutionary pressures on simple sequence repeats in prokaryotic coding regions

Simple sequence repeats (SSRs) are indel mutational hotspots in genomes. In prokaryotes, SSR loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. By analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of SSRs in coding regions. We demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are most strongly avoided across genomes. We thoroughly characterize SSR density and variability as a function of N→C position along protein sequences. Using codon-shuffling algorithms that preserve amino acid sequence, we assess evolutionary pressures on SSRs. We find that coding sequences suppress repeats in the middle of proteins, and enrich repeats near termini, yielding U-shaped SSR density curves. We show that for many species this characteristic shape can be attributed to purely biophysical constraints of protein structure. In multiple cases, however, particularly in certain pathogenic bacteria, we observe over enrichment of SSRs near protein N-termini significantly beyond expectation based on structural constraints. This increases the probability that frameshifts result in non-functional proteins, revealing that these species may evolutionarily tune SSR positions in coding regions to facilitate phase variation.     

The impact of bottlenecks on microbial survival,adaptation, and phenotypic switching in host–pathogen interactions

Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein different phenotypes have distinct transmission probabilities between hosts. We show that under stringent bottlenecks, such that only one phenotype can initiate new infections, there exists a threshold stochastic switching rate below which all pathogen lineages go extinct, and above which survival is a near certainty. We determine how quickly stochastic switching rates can evolve by computing a fitness landscape for the evolutionary dynamics of switching rates, and analyzing its dependence on both the stringency of bottlenecks and the duration of within‐host growth periods. We show that increasing the stringency of bottlenecks or decreasing the period of growth results in faster adaptation of switching rates. Our model provides strong theoretical evidence that bottlenecks play a critical role in accelerating the evolutionary dynamics of pathogens.     

Malaria parasites release vesicle subpopulations with signatures of different destinations

Malaria is the most serious mosquito‐borne parasitic disease, caused mainly by the intracellular parasite Plasmodium falciparum. The parasite invades human red blood cells and releases extracellular vesicles (EVs) to alter its host responses. It becomes clear that EVs are generally composed of sub‐populations. Seeking to identify EV subpopulations, we subject malaria‐derived EVs to size‐separation analysis, using asymmetric flow field‐flow fractionation. Multi‐technique analysis reveals surprising characteristics: we identify two distinct EV subpopulations differing in size and protein content. Small EVs are enriched in complement‐system proteins and large EVs in proteasome subunits. We then measure the membrane fusion abilities of each subpopulation with three types of host cellular membranes: plasma, late and early endosome. Remarkably, small EVs fuse to early endosome liposomes at significantly greater levels than large EVs. Atomic force microscope imaging combined with machine‐learning methods further emphasizes the difference in biophysical properties between the two subpopulations. These results shed light on the sophisticated mechanism by which malaria parasites utilize EV subpopulations as a communication tool to target different cellular destinations or host systems.     

Life history and reproductive ecology of the endangered Itasenpara bitterling Acheilognathus longipinnis (Cyprinidae) in the Himi region,central Japan

The life history, reproductive ecology and habitat utilization of the Itasenpara (deepbody) bitterling Acheilognathus longipinnis were investigated in a lowland segment of the Moo River in Toyama Prefecture, central Honshu, Japan. Analysis of 1285 individuals revealed that the study population comprised a single size class, an age at maturation of 3 months and a life span of 1 year. On the basis of the growth pattern, the life cycle was divided into two stages: the juvenile stage, characterized by rapid growth, and the adult stage at which growth ceased. Spawning by A. longipinnis was recorded between early September and late October. Female A. longipinnis in the 0+ year age class began to mature when they reached a standard length (L_S) of 56·4 mm. Mature females had a large clutch size (maximum 273 eggs) and deposited highly adhesive and relatively large eggs (2·55 mm³; major axis, 3·12 mm; minor axis, 1·22 mm) via a short ovipositor (mean length, 21·5 mm) into freshwater mussels. The embryos remained in the gill cavities of the freshwater mussels (used as a spawning substratum) and emerged as juveniles (L_S, 9 mm). Habitat utilization during spawning was analysed using a generalized linear model. The best‐fit model showed that three environmental factors (freshwater mussel availability, water depth and vegetation cover) were important variables for habitat utilization by A. longipinnis. Shallow areas (water depth, 250–330 mm) created for rice paddy management and areas with an abundance of cover were particularly effective for predator avoidance. These results suggest that maintenance of water level fluctuations corresponding with rice cultivation and the abundance of vegetation on the river bank (particularly avoidance of concrete revetments) is essential for conservation of this species under current practices for rice cultivation in Japan.     

Effects of lipophilic and water-soluble membrane probes on ethylene synthesis in apple and Penicillium digitatum

Several chemicals were used to probe the in situ ethylene formingenzyme systems in apple tissue and Penicillium digilatum. 2,4-Dinitrofluorobenzene,a membrane permeant probe, inhibited ethylene production effectivelyin apples but far less effectively in P. digitatum. In contrast,salicylaldehyde, another membrane permeant probe, effectivelyinhibited the P. digitatum system but, except at 0.1 mM concentration,little influenced the apple system. l,5-Difluoro-2,4-dinitrobenzene(DFDNB), a membrane permeant probe which cross-links proteinswith proteins and with phospholipids, strongly inhibited ethylenebiosynthesis in both apple and P. digitatum, whereas dimethylsuberimidate, the protein cross-linking reagent, inhibited slightlythe apple system but not P. digitatum system. Picrylsulfonate(TNBS), a non-permeant membrane probe, up to 0.1 mM, did notinhibit any of the two systems studied. However, in the presenceof exogenous methionine in the apple system and glutamate inP. digitatum, TNBS at 0.1 and 1 mM caused inhibition of ethylenesynthesis. These probes did not affect respiration of appleslices under similar incubating conditions, excepting for DFDNBwhich on longer incubation did inhibit respiration, but theeffect on ethylene synthesis was 15 times greater. Divalentcation ionophores, A23187 [GenBank] and X537 A, had no effect on ethylenesynthesis in both the systems. The water soluble iron chelatingagent, o-phenanthroline, was a more potent inhibitor of theapple system but minimally affected P. digitatum. In contrast,the lipophilic chelator, bathophenanthroline, was a more potentinhibitor of the P. digitatum system. Assay of the fatty acidcomposition of polar lipids from crude membrane fractions showedconsiderably greater linoleic to linolenic ratio in P. digitatumthan in apple. We suggest that the ethylene formations in appleand P. digitatum are sensitive to a modification of membranestructure and that specific chelator-sensitive metals (perhapsiron and copper) are involved in ethylene synthesis in boththese systems. ¹ On leave from the M.S. University of Baroda (India); presentaddress: Department of Plant Genetics, The Weizmann Instituteof Science, Rehovot, Israel. ²Present address: Agricultural Research Organization, The VolcaniCenter, Bet-Dagan, Israel. (Received February 23, 1979; )     

Rab27a is required for human cytomegalovirus assembly

Human cytomegalovirus (HCMV) completes its final envelopment on intracellular membranes before it is released from the cell. The mechanisms underlying these processes are not understood. Here we studied the role of Rab27a, a regulator of lysosome-related organelle transport, in HCMV production. HCMV infection increased Rab27a expression, and recruitment of Rab27a to membranous strutures at the assembly site. Immuno-gold labelling demonstrated association of Rab27a with viral envelopes. CMV production was reduced after knock-down of Rab27a, and in Rab27a-deficient ashen melanocytes. This study shows a requirement for Rab27a in the CMV life cycle and suggests that CMV and LRO biogenesis share common molecular mechanisms.     

Factors Influencing the Breeding Activity in Male Masu Salmon, Oncorhynchus masou: The Relationship with Body Size

Synopsis Male body size has been emphasized as an important factor contributing to the breeding success of individuals. However, the operational sex ratio (OSR: ratio of mature females to males) during the breeding season significantly change due to differences in the breeding timing and period within and between males and females and may influence the selective advantage of the male large body size for mates. We examined the reproductive ecology of masu salmon Oncorhynchus masou, inhabiting Lake Toya, Hokkaido, northern Japan. Precipitation triggered the upstream migration, although males migrated into the river earlier than females. As a result, the OSR in the river changed markedly during the breeding season, as did the size structure of males in the river. Large males migrated into the river earlier than the smaller males. Differential male survival resulted in the different population size structure between the early and late periods. Under these conditions, we analyzed which males were more successful in releasing the more sperm throughout the breeding season by estimating the decrease in the sperm content in male carcasses. The body size and sperm-releasing success of the males were not related. With a weak male-biased OSR and synchronous timing of reproduction in females, males that had entered the river succeeded in releasing the sperm regardless of body size. Such a fluctuating advantage for different body sizes likely contributes to the maintenance of the size variation in the male salmon.