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As neuroscience literature suggests, extreme capsule is considered a whiter matter tract. Nevertheless, it is not clear whether extreme capsule itself is an association fiber pathway or only a bottleneck for other association fibers to pass. Via our review, investigating anatomical position, connectivity and cognitive role of the bundles in extreme capsule, and by analyzing data from the dissection, it can be argued that extreme capsule is probably a bottleneck for the passage of uncinated fasciculus (UF) and inferior fronto-occipital fasciculus (IFOF), and these fasciculi are responsible for the respective roles in language processing.

Inheritance of the mitochondrial genome does not follow the rules of conventional Mendelian genetics. The mitochondrial DNA (mtDNA) is present in many copies per cell and is inherited through the maternal germline. In addition, mutations in the mtDNA will give rise to heteroplasmy, the coexistence of different mtDNA variants within a single cell, whose levels can vary considerably between cells, organs or organisms. The inheritance and subsequent accumulation of deleterious variants are the cause of severe progressive mitochondrial disorders and play a role in many other conditions, including aging, cancer and neurodegenerative disorders. Here, we discuss the processes that give rise to cell-to-cell variability in mtDNA composition, focussing on somatic mtDNA segregation and on less conventional sources of heteroplasmy: non-maternal inheritance and mtDNA recombination. Understanding how mtDNA variants and mutations emerge and evolve within an organism is of crucial importance to prevent and cure mitochondrial disease and can potentially impact more common aging-associated conditions.

We study the optimal single-step coarse toll design problem for the bottleneck model where the toll level and tolling duration have maximum acceptable upper bounds and the unconstrained optimal solution exceeds the upper bounds. We consider proportional user heterogeneity where users’ values of time and schedule delay vary in fixed proportions. Three classic coarse tolling models are studied, the ADL, Laih and braking models. In the ADL model, untolled users form a mass arrival at the bottleneck following the last tolled user. In the Laih model, there is a separated waiting facility for untolled users to wait until the toll ends. In the braking model, untolled users can choose to defer their arrival at the bottleneck to avoid paying the toll. We find that, in the ADL and the Laih models, the optimal solution chooses the maximum acceptable toll level and tolling duration. The ADL model further requires the tolling period to be started as late as possible to eliminate the queue at the toll ending moment. In the braking model, if the upper bound of the tolling duration is too small, no toll should be charged. Otherwise the optimal solution chooses the maximum acceptable tolling duration and may choose a toll price less than the maximum acceptable level.

The first-best solution for a transportation bottleneck is to impose a first-best peak-load toll that varies continuously over time, reaching its maximum value at the most desirable crossing time. This eliminates all wasteful queueing. With homogeneous values of time, the private costs of consumers are unchanged, but the large maximum value of the first-best toll may make it politically infeasible. In this paper, I consider continuously time-varying partial peak-load tolls that have a much lower maximum value, but which still achieve a large fraction of the efficiency gain of the first-best toll. With heterogeneous values of time, a partial peak-load toll can leave all consumers with unchanged or decreased private costs even when the first-best toll does not do this.

Cancer stem cells (CSCs) are responsible for cancer initiation, drug resistance, and aggressive tumor phenotypes. Our lab has established a novel method to induce CSCs from induced pluripotent stem (iPS) cells in a microenvironment mimicking chronic inflammation. The converted cells acquired CSC characteristics and developed malignant tumors. Recently, we demonstrated that nonmutagenic chemical inhibitors accelerated the conversion of mouse iPS (miPS) cells into CSCs. Here, we investigated the effects of AZD-6244, a MEK1/2-specific inhibitor, on the conversion of iPS cells into CSCs. The miPS cells were cultured for one week in the presence of the conditioned medium (CM) of Lewis lung carcinoma (LLC) cells and AZD-6244, PD0325901, a pan-MEK inhibitor, or GDC-0879, a B-Raf inhibitor. As a result, AZD-6244 enhanced the conversion of iPS cells into CSCs and upregulated AKT phosphorylation as same as GDC-0879 and PD0325901. The converted cells maintained their self-renewal ability and stemness gene expression. The expression of the CSC markers CD24, CD44 and CD133 was higher in the cells cultured with MAPK inhibitors than in those cultured without MAPK inhibitors. Moreover, converted cells gained migration and invasion abilities assessed by in vitro assays. Therefore, the inhibition of MEK1/2 was found to be critical for the conversion of normal stem cells into CSCs in the tumor-inducing microenvironment.

Developing a mechanistic understanding of plant growth regulation requires studying cell division and cell expansion in addition to molecular studies. A recent time-lapse confocal microscopy study (Fox, S. et al. PLoS Biol. 2018:16;e2005952) quantifying these processes in individual cells in growing organs in combination with multiscale modeling provides profound new insights into the regulatory mechanisms involved.

This study examines the effects of bottleneck congestion and an optimal time-varying congestion toll on the spatial structure of cities. We develop a model in which heterogeneous commuters choose departure times from home and residential locations in a monocentric city with a bottleneck located between a central downtown and an adjacent suburb. We then demonstrate that commuters sort themselves temporally and spatially on the basis of their value of travel time and their flexibility. Furthermore, we reveal that introducing an optimal congestion toll alters the urban spatial structure, which contrasts with the previous literature. We further demonstrate through an example that congestion tolling can cause the city to physically expand outward, which helps rich commuters but hurts poor commuters.

This paper investigates the step tolling problem in an activity-based bottleneck model in which activity scheduling utilities of commuters at home and at work vary by the time of day. The commuters choose their departure times from home to work in the morning to maximize their own scheduling utility. Step tolling models with homogeneous and heterogeneous preferences are presented. The properties of the models and the optimal step toll schemes with constant and linear time-varying marginal activity utilities are analytically explored and compared. It was found that for a given number of toll steps the efficacy of a step toll in terms of queuing removal rate is higher in the activity-based bottleneck model with linear marginal utilities than in the conventional bottleneck model with constant marginal utilities, and ignoring the preference heterogeneity of commuters would underestimate the efficacy of a step toll.

This paper uses the bottleneck model of Vickrey (1969) to empirically measure the social cost of traffic congestion in the US. Using a detailed trip-level data, we estimate extra travel time over and above hypothetical free-flow travel time, which we call “queuing time”, for each average commute trip. The estimated individual queuing time implies that the annual cost of congestion borne by all US commuters is about 29 billion dollars. We find that a higher level of congestion in a city may be attributed to a smaller per capita road stock in the city. This paper also empirically quantifies a toll that depends both on the commuter's arrival time and trip distance.

The traditional bottleneck model for road congestion promotes the implementation of a triangular, and time varying, charge as the optimal solution for the road congestion externality. However, cognitive and technological barriers put a practical limit to the degree of differentiation real world implementations can handle. The traditional approach to accommodate for this concern has been a step toll, with the single step coarse charge as its simplest case. In this paper the authors study how efficiency of the coarse charge can be improved by differentiating its level and timing across groups of travellers. The authors use the traditional bottleneck model to analyse how the coarse charge can be differentiated over two groups of travellers assuming inelastic peak-hour demand. The results of the authors' analysis indicate that differentiating the coarse charge across two groups of travellers considerably improves its efficiency without increasing cognitive effort and decision making costs for the individual traveller. A numeric illustration reveals a welfare gain of 69% of the first-best charge, up from 53% for the generic coarse charge. This increase is similar to what is obtained by moving from the coarse charge to a generic two step toll. Once different groups have been defined, one could in fact achieve the same gains by temporal separation of drivers, for example by use of license plate numbers. The presented charging regime has a considerable degree of flexibility with respect to the share of travellers to attribute to each scheme, which further adds to its merits in practical applicability.

Neurostimulation techniques allow us to manipulate the activity of nervous systems, and even that of single neurons. In this piece, researchers discuss what they see as the current key bottlenecks to controlling neural biology.

Ancient Lake Titicaca (Bolivia, Peru) is home to several endemic species flocks, including representatives of the caenogastropod genus Heleobia. Preliminary analyses indicated that past geological and limnological events had an important effect on intralacustrine speciation events in Heleobia spp. However, the role of allopatric speciation due to vicariance events has not been assessed in detail before, even though several biogeographic barriers are conceivable. This study therefore assesses evolutionary patterns in the Heleobia flock in space and time based on mitochondrial DNA sequencing data of 103 specimens from Lake Titicaca and the surrounding Altiplano. Specifically, the degree of genetic distinctness of populations at various geographical scales and the timing of population expansion events were inferred. A TCS network analysis indicated that many terminal haplotypes belong to Altiplano species, whereas central haplotypes are typically associated with Lake Titicaca taxa. AMOVAs based on geographical groupings resulted in a significant partitioning of variance in Altiplano vs. Titicaca taxa but not in taxa from the northern vs. southern basins of the lake. Mismatch analyses suggested that the Heleobia flock underwent sudden spatial and demographic expansions during the Middle/Late Pleistocene. Based on these findings, the working hypothesis of vicariant speciation has to be rejected. Instead, a Middle Pleistocene lake level lowstand (possibly interglacial MIS9), which resulted in the desiccation of the southern and the salinization of the northern basin, may have caused a severe bottleneck in Heleobia spp. Recovery from these limnological conditions might then have triggered sudden spatial and demographic expansion events.

This note demonstrates how the redistribution of revenue from a Pigouvian policy can distort incentives and handicap the social objectives of the policy by creating a moral hazard problem. Based on the Levinson (2005) game theory model, I develop a three-player bottleneck congestion game that emulates a repeated prisoner’s dilemma and derive efficient tolls. This conceptual game demonstrates the distortionary effects from a revenue-neutral toll policy with lump-sum revenue redistribution and the equity-efficiency tradeoff.

The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity.

Extensive theoretical research has been conducted on the morning commute problem building on the bottleneck model (Vickrey in Am Econ Rev 59(2):251–260, 1969). There have been far fewer studies assessing the bottleneck model and its extensions using real data. This paper presents an analysis of empirical data from the toll plaza of the San Francisco–Oakland Bay Bridge, which is a major regional bottleneck. The Bay Bridge transitioned from a constant toll to a peak step toll on July 1, 2010, so the site is well-suited for assessing many relevant extensions to the classic bottleneck model for the morning commute, including theories for congestion pricing. This paper uses traffic data from the Bay Bridge to address two areas of theoretical work on bottleneck congestion: (1) heterogeneous schedule preferences, and (2) equilibrium response to step tolls. The results suggest that the predicted equilibrium for the morning commute is consistent with observed traffic patterns, especially at the beginning of the rush. The data can be analyzed through the lens of relevant theories to quantify commuters’ value of earliness and lateness relative to queuing delay. The pattern of queuing suggests that the peak step toll has not been implemented in a socially optimal way.

Information on the demographic and genetic consequences of overexploitation of large marine vertebrates is often difficult to demonstrate on ecological time scales. We investigate the genetic impacts of recent commercial activities along Mexico’s Pacific coast on the nesting colonies of a long-lived vertebrate of conservation concern, the olive ridley turtle (Lepidochelys olivacea). This species was severely impacted by a commercial fishery between 1960 and 1990 (e.g. >350,000 individuals were caught in a single year), depleting important nesting areas within few decades. Microsatellite DNA variation of 334 samples representing 18 nesting sites revealed a clear signature of recent bottlenecks associated with changes in allelic diversity. Consistent with theoretical expectations and other empirical studies, we found no evidence for bottlenecks based on measures of heterozygosity. The bottleneck signal was strong across the highly connected metapopulation and also apparent in six nesting sites in a pattern consistent with the history of demographic disequilibria produced by their overexploitation. In addition, we clarify population structure across Mexico and show that Mismaloya, a key colony where human harvest led to a dramatic change in the species’ reproduction mode, has not been supplemented by gene flow after the bottleneck and has diverged genetically from other demes. This is perhaps the first study to detect recent signatures of anthropogenic-driven population declines in sea turtles using genetics. This enables managers to consider information about genetic signatures of contemporary demographic changes during the development of conservation management plans and during population monitoring.

The Mbeya region of Tanzania has a genetically complex HIV epidemic with multiple subtypes and recombinant forms circulating, together with a high frequency of dual infections with more than one subtype. This study aimed to determine whether this impacted the HIV-1 transmission bottleneck. A total of 210 env sequences from 22 participants were generated from recently infected women from Mbeya using the single genome amplification approach. Participants were infected with subtypes C ( n = 9), A ( n = 4), or D ( n = 1), and recombinants AC ( n = 4), CD ( n = 2), AD ( n = 1), or ACD ( n = 1). Sixteen participants (73%) were infected with a single variant; five (23%) with multiple variants; and one (4%) was dually infected. Thus the frequency of single variant infections was similar to cohorts located in genetically restricted subtype B or C epidemics, suggesting that multiple circulating subtypes and unique recombinant forms do not have a significant impact on the transmission bottleneck.

International audience; The paper examines the question of the redistribution of toll revenue as seen in a bottleneck congestion model. Our objective is to analyse the impact of this redistribution on total cost and on modal split between railroad and road. Following Tabuchi's two-mode model (Tabuchi, T., 1993. Bottleneck congestion and modal split. Journal of Urban Economics 34, 414-431.), we integrate a redistribution of toll revenue towards public transport into our study. In this context, we investigate two kinds of road toll regimes: a fine toll and a uniform toll. We will consider two types of railroad fare: when it is set equal to the marginal cost and when it is set equal to average cost. These models allow us to show that toll policy to be more efficient as long as toll revenue is directed towards public transport when the railroad fare is equal to average cost. © 2010 Elsevier Ltd.

Population bottlenecks are ubiquitous in nature, and are an inherent feature of the experimental protocol for many laboratory selection experiments. These bottlenecks can have profound effects on the rate and trajectory of evolution. In particular, there is a trade-off between sampling the population too frequently and imposing infrequent, but more severe, bottlenecks. In this paper we consider the effects of population bottlenecks, assuming a burst-death model for the life history of the organism under study. This model assumes that generation times are exponentially distributed and that at each generation, individuals in the population have a fixed number of offspring. The model also allows for a constant death rate between bottlenecks. We use this model to estimate the optimal bottleneck ratio, that is, the fraction of the population that should be sampled at each bottleneck in order to maximize the probability that beneficial mutations occur and are not lost. We find that the optimal ratio is roughly constant with respect to many of the model parameters, and that sampling about 20% of the population will maximize the rate of adaptation.

A number of recent research studies have focused on theoretical and experimental investigation of a bottleneck in a metabolic reaction network. However, there is no study on how the bottleneck affects the performance of a fermentation process when a product is highly toxic and remarkably influences the growth and death of cells. The present work therefore studies the effect of bottleneck on product concentrations under different product toxicity conditions. A generalized bottleneck model in a fed-batch fermentation is constructed including both the bottleneck and the product influences on cell growth and death. The simulation result reveals that when the toxic product strongly influences the cell growth and death, the final product concentration is hardly changed even if the bottleneck is removed, whereas it is markedly changed by the degree of product toxicity. The performance of an ethanol fermentation process is also discussed as a case example to validate this result. In conclusion, when the product is highly toxic, one cannot expect a significant increase in the final product concentration even if removing the bottleneck; rather, it may be more effective to somehow protect the cells so that they can continuously produce the product.

Dynamic logarithmic gains (normalised time-varying sensitivities) or their products with metabolite concentrations, called an instantaneous bottleneck ranking indicator (instantaneous BR indicator), can express the time courses of bottleneck enzyme ranking. The integrated value of the instantaneous BR indicator, called an overall BR indicator, provides a ranking of bottleneck enzymes over the entire reaction period of time. Owing to the property of the logarithmic gains, these BR indicators are allowed to include both positive and negative values and in turn raise several questions on the identification of a bottleneck enzyme. To eliminate these questions, the present work studies the identification of bottleneck enzymes in four ethanol fermentation systems using suspended and immobilised cells at pH 4.5 and 5.5 as case studies. These systems consist of both intracellular reactions without cell growth (intracellular reaction systems) and those with cell growth (cell growth systems). The analyses of the intracellular reaction systems reveal that both the suspended and immobilised cell systems at pH 5.5 are not robust. In the cell growth systems, therefore, the analyses are conducted only for the suspended and immobilised cell models at pH 4.5. The enzyme glyceraldehyde 3-phosphate dehydrogenase (gapd) initially has the largest logarithmic gains under all conditions, whereas the system becomes insensitive to it over time. Interestingly, the instantaneous BR indicator for gapd is negatively large. Also, other indicators change in positive and/or negative regions. To deal with these values of different signs, all the indicators are integrated to obtain and rank the overall BR indicators in the order of the magnitudes of their absolute values. The result shows that the ranking of enzymes are completely identical to that of the final ethanol concentrations obtained by finitely increasing or decreasing the relevant enzyme activities in accordance with the signs of overall BR indicators. This result indicates that the enzymes must be ranked in the order of the magnitudes of their absolute values to determine a bottleneck enzyme. As a result, the analyses of the intracellular reaction systems reveal that the bottleneck enzyme is switched from a membrane-bound glucose transporter enzyme to phosphofructokinase when the cell-retaining condition is changed from suspension to immobilisation. In the cell growth systems, gapd is identified as the most likely bottleneck enzyme, suggesting that the gapd activity must be decreased to increase the ethanol productivity.

High-throughput mapping of latent heat flux (λET) is critical to efforts to optimize water resources management and to accelerate forest tree breeding for improved drought tolerance. Ideally, investigation of the energy response at the tree level may promote tailored irrigation strategies and, thus, maximize crop biomass productivity. However, data availability is limited and planning experimental campaigns in the field can be highly operationally complex. To this end, a multi-platform multi-sensor observational approach is herein developed to dissect the λET signature of a black poplar (Populus nigra) breeding population (“POP6”) at the canopy level. POP6 comprised more than 4600 trees representing 503 replicated genotypes, whose parents were derived from contrasting environmental conditions. Trees were trialed in two adjacent plots where different irrigation treatments (moderate drought [mDr] and well-watered [WW]) were applied. Data collected from satellite and unmanned aerial vehicles (UAVs) remote sensing as well as from ground-based proximal sensors were integrated at consistent spatial aggregation and combined to compute the surface energy balance of the trees through a modified Priestley-Taylor method. Here, we demonstrated that λET response was significantly different between WW and mDr trees, whereby genotypes in mDr conditions exhibited larger standard deviations. Importantly, genotypes classified as drought tolerant based on the stress susceptibility index (SSI) presented λET values significantly higher than the rest of the population. This study confirmed that water limitation in mDr settings led to reduced soil moisture in the tree root zone and, thus, to lower λET. These results pave the way to breeding poplar and other bioenergy crops with this underexploited trait for higher λET. Most notably, the illustrated work demonstrates a multi-platform multi-sensor data fusion approach to tackle the global challenge of monitoring landscape-scale ecosystem processes at fine resolution.

Background Growth rate management in fast-growing bacteria is currently an active research area. In spite of the huge progress made in our understanding of the molecular mechanisms controlling the growth rate, fundamental questions concerning its intrinsic limitations are still relevant today. In parallel, systems biology claims that mathematical models could shed light on these questions. Methods This review explores some possible reasons for the limitation of the growth rate in fast-growing bacteria, using a systems biology approach based on constraint-based modeling methods. Results Recent experimental results and a new constraint-based modelling method named Resource Balance Analysis (RBA) reveal the existence of constraints on resource allocation between biological processes in bacterial cells. In this context, the distribution of a finite amount of resources between the metabolic network and the ribosomes limits the growth rate, which implies the existence of a bottleneck between these two processes. Any mechanism for saving resources increases the growth rate. General Significance Consequently, the emergence of genetic regulation of metabolic pathways, e.g. catabolite repression, could then arise as a means to minimise the protein cost, i.e. maximising growth performance while minimising the resource allocation. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

A number of cell surface antigens of the infective stages of malaria parasites (genus Plasmodium) have been proposed as vaccine candidates, but high levels of polymorphism at the loci encoding these antigens are problematic for vaccine effectiveness. In order to test for the effects of anti-malarial control measures (including drugs and vector control) on polymorphism at antigen-encoding loci, we analyzed sequences of four antigen-encoding loci from P. vivax and two from P. falciparum collected in 2006-2007 from two areas of Thailand: (1) the NW, where malaria cases have remained high until recently; and (2) the South, where control measures have caused a dramatic decline in numbers of cases since 1990. Polymorphism in non-repeat regions of antigen-encoding loci was dramatically reduced in the South compared to the NW. These results suggest a two-pronged strategy for malaria eradication: (1) strenuous non-vaccine control measures that will cause a severe population bottleneck in the parasite; and (2) a subsequent local vaccine focused on one or a few locally occurring alleles at antigen-encoding loci.

Fishery assessment models meant to determine sustainability of commercial marine Wsh failed to predict recent stock collapses due to overexploitation. One Xaw of assessment models is that they strongly rely on catch and age-composition statistics, but largely ignore the genetic background of the studied populations. We examined population genetic structure of sardine (Sardina pilchardus) in the centraleastern and northeastern Atlantic Ocean and Mediterranean Sea to aid Wshery management of this heavily Wshed small pelagic species. We found that sardine has a striking mitochondrial control region, and sequenced a fragment of 387 bp of its 5 -end in 261 individuals collected oV the coasts of Morocco (Dakhla, Tantan, SaW, Larache, and Nador), Portugal (Quarteira), Spain (Pasajes, Barcelona), and Greece (Kavala). High levels of haplotypic diversity rendered a rather unresolved NJ phylogeny. The recovered tree had no phylogeographic structuring except for the clustering of 13 individuals of SaW. In contrast, individuals grouped together according to the presence or absence of a 13-bp insertion in the sequence. ST pairwise comparisons and molecular variance analyses supported genetic diVerentiation between the population of Pasajes (Bay of Biscay), and those of the Mediterranean Sea and Moroccan coast, with a contact zone around the Strait of Gibraltar. This result conWrms the existence of two subspecies, S. pilchardus pilchardus and S. pilchardus sardina that were previously identiWed based on meristics and morphometry. Mismatch distribution analysis showed that sardine populations are expanding since the Pleistocene. Surprisingly, the population of SaW showed strong and statistically signiWcant levels of genetic diVerentiation that could be related with isolation and genetic drift. Comparative analysis of the SaW population versus the rest including mismatch distributions, and a Bayesian skyline plot suggest that the SaW population likely underwent an early genetic bottleneck. The genetic singularity of the SaW population could have been responsible for the historical collapse of this sardine stock in the 1970s., This work received partial Wnancial support from AECI-MAE (Agencia Española de Cooperación Internacional-Ministerio de Asuntos Exteriores) Project No 168/03/P to T.A. and R.Z. L.R. was supported by a Swiss Science Foundation postdoctoral fellowship (823A-061218) and E.G.G. by a MEC (Ministerio de Educación y Ciencia) predoctoral grant.

Aerobic rice has been considered a promising rice cultivation system as water scarcity is increasing in the world. This article summarizes the advances in aerobic rice management researches in the North China Plain, focusing on yield formation and its bottleneck. High-yielding and good-quality aerobic rice varieties adapted to aerobic soil conditions have been released officially and adopted by farmers in North China. The varieties Handao 502 and Handao 297 have been recognized as the most promising varieties reaching a yield level ranging 3.5-5.0 t ha^(-1) with 450-650 mm water input. Compared with lowland rice, water input in aerobic rice was more than 50% lower, and water productivity was 60% higher. Researches on responses of rice cultivars to nitrate nitrogen (N) and ammonium N supplied at early growth stages provided the first evidence for a preference of aerobic rice HD297 for nitrate N supply, compared with the lowland rice variety. Zinc uptake studies demonstrated that introduction of aerobic rice system on calcareous soils may increase zinc deficiency problems. Sink size was identified as the limitation of aerobic rice yield, because its spikelet number m^(-2) was too low (20000-24000) compared with the lowland rice. For future research, more attention is suggested to be paid to yield formation focusing on effects of water regimes on tiller dynamics. Understanding of nutrient uptake and response to fertilization effects are also urgently required to establish optimized crop management technology. Additionally, alternative cropping systems based on aerobic rice should be established, and key sustainability and environmental impact issues in the systems need to be identified.

The number of variables at play in the expression and purification of a single protein dwarf those involved in sequencing a genome. Although certain trends are apparent, there is no one-size-fits-all approach to the process of purifying proteins. Thus, whereas numerous genome sequencing projects are providing an overwhelming number of interesting open reading frames for structural biologists to study, fully realizing the potential of this resource is still only a distant hope. We will discuss several current approaches to high throughput expression and purification as well as strategies that have served us well to quickly identify lead protein expression constructs in the context of a core service protein expression and purification laboratory. The use of the baculovirus expression vector system and implementation of a purification screening method will be emphasized.

Jacobaea vulgaris (Asteraceae) is a species of Eurasian origin that has become a serious non-indigenous weed in Australia, New Zealand, and North America. We used neutral molecular markers to (1) test for genetic bottlenecks in invasive populations and (2) to investigate the invasion pathways. It is for the first time that molecular markers were used to unravel the process of introduction in this species. The genetic variation of 15 native populations from Europe and 16 invasive populations from Australia, New Zealand and North America were compared using the amplified fragment length polymorphisms (AFLP's). An analysis of molecular variance showed that a significant part (10%) of the total genetic variations between all individuals could be explained by native or invasive origin. Significant among-population differentiation was detected only in the native range, whereas populations from the invasive areas did not significantly differ from each other; nor did the Australian, New Zealand and North American regions differ within the invasive range. The result that native populations differed significantly from each other and that the amount of genetic variation, measured as the number of polymorphic bands, did not differ between the native and invasive area, strongly suggests that introductions from multiple source populations have occurred. The lack of differentiation between invasive regions suggests that either introductions may have occurred from the same native sources in all invasive regions or subsequent introductions took place from one into another invasive region and the same mix of genotypes was subsequently introduced into all invasive regions. An assignment test showed that European populations from Ireland, the Netherlands and the United Kingdom most resembled the invasive populations.

In cases of inherited pathogenic mitochondrial DNA (mtDNA) mutations, a mother and her offspring generally have large and seemingly random differences in the amount of mutated mtDNA that they carry. Comparisons of measured mtDNA mutation level variance values have become an important issue in determining the mechanisms that cause these large random shifts in mutation level. These variance measurements have been made with samples of quite modest size, which should be a source of concern because higher-order statistics, such as variance, are poorly estimated from small sample sizes. We have developed an analysis of the standard error of variance from a sample of size n, and we have defined error bars for variance measurements based on this standard error. We calculate variance error bars for several published sets of measurements of mtDNA mutation level variance and show how the addition of the error bars alters the interpretation of these experimental results. We compare variance measurements from human clinical data and from mouse models and show that the mutation level variance is clearly higher in the human data than it is in the mouse models at both the primary oocyte and offspring stages of inheritance. We discuss how the standard error of variance can be used in the design of experiments measuring mtDNA mutation level variance. Our results show that variance measurements based on fewer than 20 measurements are generally unreliable and ideally more than 50 measurements are required to reliably compare variances with less than a 2-fold difference.

Highly efficient biosynthesis of the commercially valuable carotenoid astaxanthin by microbial cells is an attractive alternative to chemical synthesis and microalgae extraction. With the goal of enhancing heterologous astaxanthin production in Saccharomyces cerevisiae, metabolic engineering and protein engineering were integrated to improve both the expression and activity of rate-limiting enzymes. Firstly, to increase the supply of β-carotene as a key precursor for astaxanthin, a positive mutant of GGPP synthase (CrtE03M) was overexpressed together with three other rate-limiting enzymes tHMG1, CrtI and CrtYB. Subsequently, to accelerate the conversion of β-carotene to astaxanthin, a color screening system was developed and adopted for directed evolution of β-carotene ketolase (OBKT), generating a triple mutant OBKTM (H165R/V264D/F298Y) with 2.4-fold improved activity. After adjusting copy numbers of the above-mentioned rate-limiting enzymes to further balance the metabolic flux, a diploid strain YastD-01 was generated by mating two astaxanthin-producing haploid strains carrying the same carotenogenic pathway. Finally, further overexpression of OCrtZ and OBKTM in YastD-01 resulted in accumulation of 8.10mg/g DCW (47.18mg/l) of (3S, 3'S)-astaxanthin in shake-flask cultures. This combinatorial strategy might be also applicable for alleviation of metabolic bottleneck in biosynthesis of other value-added products, especially colored metabolites.

The present study investigates the genetic diversity of Scarus ghobban, a recently introduced parrotfish in the Mediterranean Sea via the Suez Canal. Two mitochondrial and one nuclear DNA regions were sequenced and phylogenetic relationships investigated, from samples collected from Lebanon and across its natural range. Scarus ghobban clustered in two major clades, Pacific Ocean and Indian Ocean, indicating strong population structure, or cryptic speciation. Expectedly, Mediterranean samples clustered with Indian Ocean-Red Sea individuals. However, unlike other recent Lessepsian invaders, S. ghobban displayed high genetic diversity. These results underscore that genetic diversity is a poor predictor of success of an invasive species.

A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20–100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A ‘primerless’ PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.

It is our contention that functional pharmacology, particularly in vivo, must play a greater role in drug discovery if the promises of reductionist techniques are to be brought to full fruition. Despite the advent of high-throughput screening, combinatorial chemistry and informatics, the number of new chemical entities (NCEs) coming on the market has fallen. While the advent of these methodologies makes it possible to move very quickly from molecular target to lead compound, the problem of demonstrating therapeutic utility remains. Has proof of concept (in vivo) become the bottleneck in drug discovery? This article focuses on this problem, and discusses what can be done about it.

Retinal ganglion cells, the neurons that selectively die in glaucoma and other optic neuropathies, are endowed with an exceedingly active metabolism and display a particular vulnerability to mitochondrial dysfunction. Mitochondria are exquisitely dynamic organelles that are continually responding to endogenous and environmental cues to readily meet the energy demand of neuronal networks. The highly orchestrated regulation of mitochondrial biogenesis, fusion, fission, transport and degradation is paramount for the maintenance of energy-expensive synapses at RGC dendrites and axon terminals geared for optimal neurotransmission. The present review focuses on the progress made to date on understanding the biology of mitochondrial dynamics and quality control and how dysregulation of these processes can profoundly affect retinal ganglion cell viability and function in optic nerve diseases.

Background Platelet lysates (PL) represent a promising replacement for xenogenic growth supplement for adipose-derived stem cell (ASC) expansions. However, fresh platelets from human blood donors are not clinically feasible for large-scale cell expansion based on their limited supply. Therefore, we tested PLs prepared via three methods from outdated buffy coat–derived platelet concentrates (PCs) to establish an efficient and feasible expansion of ASCs for clinical use. Methods PLs were prepared by the freeze-thaw method from freshly drawn platelets or from outdated buffy coat–derived PCs stored in the platelet additive solution, InterSol. Three types of PLs were prepared from outdated PCs with platelets suspended in either (1) InterSol (not manipulated), (2) InterSol + supplemented with plasma or (3) plasma alone (InterSol removed). Using these PLs, we compared ASC population doubling time, cell yield, differentiation potential and cell surface markers. Gene expression profiles were analyzed using microarray assays, and growth factor concentrations in the cell culture medium were measured using enzyme-linked immunosorbent assay (ELISA). Results Of the three PL compositions produced from outdated PCs, removal of Intersol and resuspension in plasma prior to the first freezing process was overall the best. This specific outdated PL induced ASC growth kinetics, surface markers, plastic adherence and differentiation potentials comparable with PL from fresh platelets. ASCs expanded in PL from fresh versus outdated PCs exhibited different expressions of 17 overlapping genes, of which 10 were involved in cellular proliferation, although not significantly reflected by cell growth. Only minor differences in growth factor turnover were observed. Conclusion PLs from outdated platelets may be an efficient and reliable source of human growth supplement allowing for large-scale ASC expansion for clinical use.

Life history and behavioral traits are often difficult to discern from the fossil record, but evolutionary rates of genes and their changes over time can be inferred from extant genomic data. Under the neutral theory, molecular evolutionary rate is a product of mutation rate and the proportion of neutral mutations [1, 2]. Mutation rates may be shared across the genome, whereas proportions of neutral mutations vary among genes because functional constraints vary. By analyzing evolutionary rates of 1,185 genes in a phylogeny of 89 mammals, we extracted historical profiles of functional constraints on these rates in the form of gene-branch interactions. By applying a novel statistical approach to these profiles, we reconstructed the history of ten discrete traits related to activity, diet, and social behaviors. Our results indicate that the ancestor of placental mammals was solitary, seasonally breeding, insectivorous, and likely nocturnal. The results suggest placental diversification began 10-20 million years before the K-Pg boundary (66 million years ago), with some ancestors of extant placental mammals becoming diurnal and adapted to different diets. However, from the Paleocene to the Eocene-Oligocene transition (EOT, 33.9 mya), we detect a post-K-Pg nocturnal bottleneck where all ancestral lineages of extant placentals were nocturnal. Although diurnal placentals may have existed during the elevated global temperatures of the Paleocene-Eocene thermal maximum [3], we hypothesize that diurnal placentals were selectively extirpated during or after the global cooling of the EOT, whereas some nocturnal lineages survived due to preadaptations to cold environments [4].

This paper generalizes the model of bottleneck congestion such that formation and development of traffic jams is explicitly formulated. The model is applied to the peak-load problem for the morning rush hour: every morning, a fixed number of commuters travel across a roadway, and each of them chooses departure time to minimize commuting cost consisting of travel time cost, scheduling cost, and toll. Equilibrium and optimal patterns of departure are solved and optimal peak-load toll is derived. Incorporating traffic jams alters the earlier results in the literature. That is, road users may be better off from paying the optimal peak-load toll. Conditions under which such a result is obtained are identified by simulations.

This paper analyzes the possibilities to relieve congestion using rewards instead of taxes, as well as combinations of rewards and taxes. The model considers a Vickrey-ADL model of bottleneck congestion with endogenous scheduling. With inelastic demand, a fine (time-varying) reward is equivalent to a fine toll, and to a continuum of combinations of time-varying tolls and rewards (including fine feebates). When demand is price sensitive, a reward becomes less attractive from the efficiency viewpoint, because it attracts additional users to the congested bottleneck. As a result, both the second-best optimal rate of participation in the scheme, and the relative efficiency that can be achieved with it, decreases when demand becomes more elastic. Our analytical and simulation results for coarse schemes suggest that a coarse reward is less effective than a coarse feebate, which is itself less effective than a coarse toll. The most efficient coarse system is the step toll, which is also allowed to be positive in the shoulder period.

Since the development of molecular diagnosis of mtDNA disease, there has been increasing pressure on clinical geneticists for genetic counseling of this uniquely difficult group. However, these advances have revolutionized neither prognostication nor prenatal diagnosis of mitochondrial diseases. This inability to predict risk of affected offspring in mtDNA diseases is largely due to the uniparental inheritance of multiple copies of mtDNA. Recently, however, the prospects for prenatal diagnosis of mtDNA diseases have taken a turn for the better.

This paper analyzes e fficient pricing at a congested airport dominated by a single firm. Unlike much of the previous literature, we combine a dynamic (bottleneck) model of congestion and a vertical structure model that explicitly considers the role of airlines and passengers. We show that when a Stackelberg leader interacts with a competitive fringe, charging the congestion toll that is derived for fully atomistic carriers to both leader and fringe yields the first-best outcome. This holds regardless of the leader's internalization of congestion in the unregulated equilibrium, and regardless of the assumed demand substitution pattern between firms. This result implies that the financial deficit under optimal pricing may be less severe than what earlier studies suggest. Finally, we show that there are various alternative toll regimes that also induce the welfare maximizing outcome, and therefore widen the set of choices for regulators.

Enzyme assemblies such as type II polyketide synthases (PKSs) produce a wide array of bioactive secondary metabolites. While the molecules produced by type II PKSs have found remarkable clinical success, the biosynthetic prowess of these enzymes has been stymied by 1) the inability to reconstitute the bioactivity of the minimal PKS enzymes in vitro and 2) limited exploration of type II PKSs from diverse phyla. To begin filling this unmet need, we expressed, purified, and characterized the ketosynthase chain length factor (KS-CLF) and acyl carrier protein (ACP) from Ktedonobacter racemifer (Kr). Using E. coli as a heterologous host, we obtained soluble proteins in titers signifying improvements over previous KS-CLF heterologous expression efforts. Characterization of these enzymes reveals that KrACP has self-malonylating activity. Sedimentation velocity analytical ultracentrifugation (SV-AUC) analysis of holo-KrACP and KrKS-CLF indicates that these enzymes do not interact in vitro, suggesting that the acylated state of these proteins might play an important role in facilitating biosynthetically relevant interactions. These results lay important groundwork for optimizing the interaction between KrKS-CLF and KrACP and exploring the biosynthetic potential of other non-actinomycete type II PKSs.

We consider toll systems designed to alleviate queueing problems that result from a road bottleneck. Optimal road pricing is capable of eliminating queueing time completely, but has practical difficulties because it requires continuously changeable charges. Because of these difficulties, a step-toll scheme has been considered as an alternative to reduce queueing time. However, previous literatures do not contain an analysis of the multi-step toll and the amount of queueing time removal that can be achieved by varying amounts of step tolls. They may be important for policy makers who are considering the introduction of step pricing under some circumstances. This paper is proposed to solve these problems. We show that at most n /( n + 1) of the total queueing time can be eliminated with the optimal n -step toll. Suboptimal n -step tolls are also derived to achieve an under- n /( n + 1) quequeing removal (where n = 1, 2 and 3).

This paper analyzes commuting congestion when there is mass transit parallel to a road with a bottleneck between a residential area and a workplace. We investigate the optimality and efficiency of several railroad fare and road toll regimes and provide practical rules for attaining the social optimum. A welfare comparison is also made between these regimes, and it is shown that the road tolls are effective especially in the case of heavy road congestion.

Drawing on Vickrey (Amer. Econ. Rev. 59, 251–261 (1969)) and subsequent literature, this paper provides a thorough economic analysis of the simplest bottleneck model of road congestion with peak-load demand: In the morning rush hour, a fixed number of identical individuals, one per car, must travel from home to work, between which is a bottleneck of given capacity. The costs of travel include queuing time and schedule delay (time early or late for work). The frequency distribution of departure times adjusts so that in equilibrium all individuals have the same travel costs. The paper extends the previous literature by examining a coarse toll and solving for optimal capacities. The application of congestion tolls can generate efficiency gains by altering the frequency distribution of departure times. Previous estimates of the efficiency gains from congestion tolling are likely to be substantially downward-biased because they have ignored this effect.

A combination of batch fermentations and genome scale flux balance analysis were used to identify and quantify the rate limiting reactions in the xylulose transport and utilization pathway. Xylulose phosphorylation by xylulokinase was identified as limiting in wild type Saccharomyces cerevisiae, but transport became limiting when xylulokinase was upregulated. Further experiments showed xylulose transport through the HXT family of non-specific glucose transporters. A genome scale flux balance model was developed which included an improved variable sugar uptake constraint controlled by HXT expression. Model predictions closely matched experimental xylulose utilization rates suggesting the combination of transport and xylulokinase constraints is sufficient to explain xylulose utilization limitation in S. cerevisiae.

Genetic diversity, genetic relationship and bottleneck were evaluated in 5 native Turkish goat breeds (Angora, Kills, Honamli, Hair and Norduz goat breeds) using 20 microsatellite markers. In order to investigate the genetic characterization of these goat breeds, this study was carried out with 20 different microsatellite markers in 4 different multi-locus polymerase chain reaction (PCR) systems. Twenty microsatellite loci analyses revealed that the average number of alleles per locus (15.65 allele/locus) and levels of heterozygosity (0.5192-0.9400) were fairly high. The calculated overall F-IS value for all populations was 0.03656 +/- 0.033 and it was not significant. All the populations were in the Hardy-Weinberg equilibrium. According to F-ST values, a medium level of genetic diversity was found between the Angora goat breed and other breeds. Among the other breeds, genetic diversity was low and this diversity was statistically significant. All loci were polymorphic in all populations. Results of various analyses, such as allelic variation analysis, heterozygosity analysis, F statistics, STRUCTURE test and factorial correspondence analysis, indicated that the Angora goat breed is different than the other goat breeds. Furthermore, analysis showed that the other native goat breeds could not be distinguished from each other; these breeds were grouped together. Non-significant heterozygote excess on the basis of the TPM model, as revealed from the Wilcoxon signed-rank tests, along with a normal 'L'-shaped distribution of mode-shift test, indicated no bottleneck in Angora, Kilis, Honamli, Hair and Norduz goat populations. The results obtained from the analysis of 20 microsatellite loci indicated that goat breeds other than the Angora goat breed cannot be genetically distinguished from each other. (C) 2011 Elsevier B.V. All rights reserved.

Whole genome sequencing (WGS) can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.

A conventional view holds that population bottlenecks cause massive losses of genetic variability, thus endangering the viability of the derived population. Although some alleles that were infrequent in the parent population may be lost new empirical evidence from Drosophila and housefly populations has demonstrated that genetic variance available to selection may actually increase following a single severe bottleneck. Several theoretical models support this view, and suggest that the increase may result from conversion of balanced epistatic variance to additive variance that becomes immediately available to selection. These effects appear to be greatest on the inheritance of quantitative characters, releasing new variance through the disruption of covariance matrices that underlie and interrelate quantitative traits. Thus, character change in adaptation and speciation may, in some instances, be promoted by founder events.