A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations.

BackgroundEukaryotic cell proliferation involves DNA replication, a tightly regulated process mediated by a multitude of protein factors. In budding yeast, the initiation of replication is facilitated by the heterohexameric origin recognition complex (ORC). ORC binds to specific origins of replication and then serves as a scaffold for the recruitment of other factors such as Cdt1, Cdc6, the Mcm2-7 complex, Cdc45 and the Dbf4-Cdc7 kinase complex. While many of the mechanisms controlling these associations are well documented, mathematical models are needed to explore the network's dynamic behaviour. We have developed an ordinary differential equation-based model of the protein-protein interaction network describing replication initiation.ResultsThe model was validated against quantified levels of protein factors over a range of cell cycle timepoints. Using chromatin extracts from synchronized Saccharomyces cerevisiae cell cultures, we were able to monitor the in vivo fluctuations of several of the aforementioned proteins, with additional data obtained from the literature. The model behaviour conforms to perturbation trials previously reported in the literature, and accurately predicts the results of our own knockdown experiments. Furthermore, we successfully incorporated our replication initiation model into an established model of the entire yeast cell cycle, thus providing a comprehensive description of these processes.ConclusionsThis study establishes a robust model of the processes driving DNA replication initiation. The model was validated against observed cell concentrations of the driving factors, and characterizes the interactions between factors implicated in eukaryotic DNA replication. Finally, this model can serve as a guide in efforts to generate a comprehensive model of the mammalian cell cycle in order to explore cancer-related phenotypes

The economic case for low carbon cities

In this paper, we conduct a comparative analysis of the results of five recently completed studies that examined the economic case for investment in low-carbon development in five cities: Leeds in the UK, Kolkata in India, Lima in Peru, Johor Bahru in Malaysia and Palembang in Indonesia. The results demonstrate that there is a compelling economic case for cities in both developed and developing country contexts to invest, at scale, in cost-effective forms of low-carbon development. The studies show that these cost-effective investments, for example in building energy efficiency, small-scale renewables and more efficient vehicles and transport systems, could lead to significant reductions (in the range of 14-24% relative to business-as-usual trends) in urban energy use and carbon emissions over the next 10 years. The financial savings generated by these investments would be equivalent to between 1.7% and 9.5% of annual city-scale GDP. Securing these savings would require an average investment of $3.2 billion per city, but with an average payback period of approximately two years at commercial interest rates. The results therefore show that large-scale low-carbon investments can appeal to local decision-makers and investors on direct, short-term economic grounds. They also indicate that climate mitigation ought to feature prominently in economic development strategies as well as in the environment and sustainability strategies that are often more peripheral to, and less influential in, city-scale decision making. If these findings were replicated and similar investments were made in cities globally, then we estimate that they could generate reductions equivalent to 10-18% of global energy-related greenhouse gas emissions in 2025. While the studies therefore offer some grounds for optimism, they also highlight the institutional capacities that need to be built and the policy interventions and financing mechanisms that need to be adopted before these opportunities can be exploited. If these were all in place, initiatives to exploit the cost-effective opportunities for low-carbon development in cities could build momentum for change in cities that for a time could be globally significant. However, the studies also demonstrate that, in rapidly growing cities, the carbon savings from cost-effective investments could be quickly overwhelmed – in as little as seven years – by the impacts of sustained population and economic growth. They therefore highlight the pressing need for wider decarbonization (particularly of electricity supply) and deeper decarbonization (through more structural changes in urban form and function) if truly low-carbon cities are to emerge

Sustainable urban infrastructure for all: Lessons on solar-powered street lights from Kampala and Jinja, Uganda

Providing access to affordable, reliable, sustainable and modern energy for all is the seventh Sustainable Development Goal. The New Urban Agenda also commits to the provision of inclusive and safe streets that are free from crime and violence, including gender-based violence. Solar-powered street lights can contribute to these goals by increasing the electricity supply, improving safety in urban areas and protecting the environment. This paper offers lessons from the cities of Kampala and Jinja in Uganda, where solar street lighting has proven cheaper to build and operate than conventional street lights. It has also generated a range of economic and social benefits, including lower crime rates, better road safety, a more vibrant night-time economy and higher property values. Tens of thousands of working hours a day – equivalent to 14,000 full-time jobs nationwide – could be added to the economy by extending trading beyond daylight hours. Based on this case study, installing and maintaining solar-powered LED street lights across sub-Saharan Africa rather than conventional grid-based options could reduce upfront installation costs by at least 25 percent, electricity consumption from street lighting by 40 percent and maintenance costs of new roads by up to 60 percent. Lighting new roads in sub-Saharan Africa with solar would be an opportunity to generate between 96 and 160 GW of distributed renewable energy across the sub-continent, more than doubling sub-Saharan Africa’s current energy generation capacity of 92 GW

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state

Supporting decent livelihoods through sustainable service provision: Lessons on solid waste management from Kampala, Uganda

Better waste management could cut up to a fifth of global greenhouse gas emissions, making it an essential part of delivering the Paris climate agreement. A waste management strategy which supports the 15 to 20 million people who informally work in the waste sector globally can also contribute to achieving the first Sustainable Development Goal (SDG) of ending poverty, and the eighth SDG of decent work for all. Partnerships with community-based organisations and small enterprises involved in waste management can generate multiple economic and social benefits in a sector otherwise notorious for appalling conditions and the vulnerability of workers. This paper offers lessons from Kampala, Uganda, where community-based organisations and small enterprises play an important role in municipal solid waste management, especially in informal settlements. One example from Kampala is the Luchacos cooperative, which uses organic waste to produce biomass briquettes – an energy source for cooking that simultaneously reduces both urban air pollution and deforestation. If the Luchacos model could be scaled up to replace half of all charcoal use in Kampala, almost 12,000 additional people would find employment in the biomass briquette industry. Similarly, the private firm Plastic Recycling Industries (PRI) contracts 120 community-based organisations and small enterprises to collect almost one-fifth of Kampala’s plastic waste. 80 percent of the 1,200 employees contracted by these organisations are women, who earn nearly three times as much as they would working as individual waste pickers. Both Luchacos and PRI work closely with the Kampala Capital City Authority (KCCA). These examples from Kampala highlight how national governments can improve and expand solid waste management services by supporting municipalities to take a more strategic, multi-stakeholder approach to waste management. They can stimulate positive social and economic impacts by designing a framework which requires the systematic inclusion and support of community-based and small-scale enterprises in waste management processes, rather than only seeking partnerships with large private firms. This could involve establishing procurement policies that are more accessible for community-based organisations and small enterprises, providing public land for waste sorting, facilitating links between formal and informal operations, and reforming regulation to favour locally-led initiatives over large-scale technological solutions. The outcome would be an upgraded municipal waste management system that is more economically efficient, socially inclusive and environmentally sustainable

Resolving the complexity of the human genome using single-molecule sequencing

The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome - 78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The birth of a human-specific neural gene by incomplete duplication and gene fusion

Background: Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. Results: 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. Conclusions: Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage