A CRISPR-Cas assisted shotgun mutagenesis method for evolutionary genome engineering

Genome mutagenesis drives the evolution of organisms. Here, we developed a CRISPR-Cas assisted random mutation (CARM) technology for whole genome mutagenesis. The method leverages an entirely random gRNA library and SpCas9-NG to randomly damage genomes in a controllable shotgun-like manner that then triggers diverse and abundant mutations via low-fidelity repair. As a proof-of-principle, CARM was applied to evolve the capacity of Saccharomyces cerevisiae BY4741 to produce β-carotene. After seven rounds of iterative evolution over two months, a β-carotene hyper-producing strain, C7-143, was isolated with a 10.5-fold increase in β-carotene production and 857 diverse genomic mutants that comprised indels, duplications, inversions, and chromosomal rearrangements. Transcriptomic analysis revealed that the expression of 2,541 genes of strain C7-143 were significantly altered, suggesting that the metabolic landscape of the strain was deeply reconstructed. In addition, CARM was applied to evolve the industrially relevant Saccharomyces cerevisiae CEN.PK2-1C, the S-adenosyl-L-methionine production of which was increased to 2.28 times after just one round. Thus, CARM is a user-friendly and practical strategy for genetic remodeling and reverse engineering to investigate complicated organismal metabolism.

Further Strategy Analysis of Cybersecurity Incidents

In current socio-economic processes, info-communication services play a determining role, modifying the activities of certain actors. The growing dependence that has developed over the past two decades has imposed the need to give political will to security, which has led to an iterative evolution of the regulatory environment. Therefore, the regulatory framework requires certain entities to develop safeguards including controls that enhance both prevention and response in a manner commensurate with the business value of the information to be protected. However, due to the nature of cybersecurity, developing such countermeasures is not the task of a standalone organization but all entities in cyberspace in a wide range, from individuals to the public sector. Therefore, each entity involved must design protection capabilities in a manner commensurate with the risk, which requires strategic tools and methods and drives organizations to learn from their security incidents. Following our previous paper “Business strategy analysis of cybersecurity incidents” (Bederna et al.) on the topic, this paper reviews the essential formal security strategy formulation tools applied in the cases of Yahoo! and Estonia. Both are based on publicly available information. The analysis confirms the importance of managements’ or the government’s attitude and support for solving cybersecurity challenges.

Business Strategy analysis of Cybersecurity Incidents

In the current social and economic processes, information and communication services play a decisive role, changing several entities’ operations. The growing dependence that has developed over the last two decades made the security needs introduced political will, which has resulted in an iterative evolution of the regulatory environment. Hence, the legal framework requires that several entities develop protection that includes controls enhancing both preventive and reactive in a risk-proportionate manner under the business value to be protected. Nevertheless, due to the nature of cybersecurity, the development of such capabilities is not the task of a single organisation but all entities involved in cyberspace, including, e.g., individuals, non-profit and for-profit organisations, public sector actors. Therefore, each involved entity should design protection capabilities in a risk-proportionate manner, which requires strategic approaches and tools and requires organisations to learn from security incidents. This paper reviews the essential formal security strategy formulation tools, applying in the Facebook’s case based on publicly available information. The analysis aims to confirm the importance of management’s attitude and support for tackling cybersecurity’s challenges.

Spatial Fuzzy Clustering and Its Application for MRI and CT Image Segmentation

Due to the low segmentation accuracy and sensitivity to initial contour in image segmentation of CV model, an image segmentation algorithm based on CV model combined with spatial fuzzy c-means was proposed for MRI and CT image segmentation with unclear boundary, artifact and high noise. Based on the rough segmentation of the image by using the fuzzy c-means clustering algorithm in the spatial domain, the initial contour is set by using the clustering information to assist the CV model, and the target region is segmented by iterative evolution. The experimental results showed that when the number of iterations was only 50, the Dice coefficient of our algorithm for segmentation of brain MRI images was 89.17%, 38.9% higher than the traditional CV model. It can be seen that the algorithm has higher discrimination and better segmentation effect for medical images.

The largest known cowrie and the iterative evolution of giant cypraeid gastropods

Based on the fossil record, we explore the macroevolutionary relationship between species richness and gigantism in cowries (Cypraeidae), the best-studied family of gastropods, with a global diversity distribution that parallels that of tropical corals, mangroves and seagrasses. We introduce Vicetia bizzottoi sp. nov. based on a Priabonian fossil found in northeastern Italy, the largest documented cowrie found so far and the youngest of a lineage of Eocene Gisortiinae species. The Gisortiinae stratigraphic record in western Europe indicates that species selection favoured large size and armouring of the shell. Palaeoecology and per-stage species richness suggest that gigantism occurred in peripheral habitats with respect to diversity hotspots, where smaller species were favoured. The Eocene–Oligocene boundary was marked by a turnover and the Chattian global warming favoured small-sized species of derived clades. Species selection leading to gigantism is further documented in Miocene lineages of Zoila and Umbilia, in the southern hemisphere, two extant genera distributed at the periphery of modern diversity hotspots, suggesting that the negative relationship between size and diversity is a recurring pattern in the evolutionary history of cowries. This palaeontological evidence is projected onto the existing hypotheses that explain analogous biogeographic patterns in various other taxa. Likewise, body size-species richness negative relationship was possibly driven in cowries by physiological, ecological and life history constraints.

The ammonite septum is not an adaptation to deep water: re-evaluating a centuries-old idea

The shells of ammonoid cephalopods are among the most recognizable fossils, whose fractally folded, internal walls (septa) have inspired many hypotheses on their adaptive value. The enduring explanation for their iterative evolution is that they strengthen the shell against pressure at increasing water depths. The fossil record does not definitively support this idea and much of the theoretical mechanical work behind it has suffered from inaccurate testing geometries and conflicting results. By using a different set of mathematical methods compared with previous studies, I generate a system of finite-element models that explore how different parameters affect the shell's response to water pressure. Increasing the number of initial folds of the septa ultimately has little to no effect on the resulting stress in the shell wall or the septum itself. The introduction of higher-order folds does reduce the tensile stress in the shell wall; however, this is coupled with a higher rate of increase of tensile stress in the septum itself. These results reveal that the increase in complexity should not be expected to have a significant effect on the shell's strength and suggests that the evolution of ammonitic septa does not reflect a persistent trend towards deeper-water habitats.

Iterative evolution of large-bodied hypercarnivory in canids benefits species but not clades

Ecological specialization has costs and benefits at various scales: traits benefitting an individual may disadvantage its population, species or clade. In particular, large body size and hypercarnivory (diet over 70% meat) have evolved repeatedly in mammals; yet large hypercarnivores are thought to be trapped in a macroevolutionary “ratchet”, marching unilaterally toward decline. Here, we weigh the impact of this specialization on extinction risk using the rich fossil record of North American canids (dogs). In two of three canid subfamilies over the past 40 million years, diversification of large-bodied hypercarnivores appears constrained at the clade level, biasing specialized lineages to extinction. However, despite shorter species durations, extinction rates of large hypercarnivores have been mostly similar to those of all other canids. Extinction was size- and carnivory-selective only at the end of the Pleistocene epoch 11,000 years ago, suggesting that large hypercarnivores were not disadvantaged at the species level before anthropogenic influence.

Arceoaster hintei n. gen. n. sp., a late Silurian homeomorphic asteroid (Echinodermata, Hudsonasteridae)

The late Silurian Arceoaster hintei new genus new species (Asteroidea, Echinodermata) is based on a single complete specimen from the lower Hunton Group of southern Oklahoma. Overall ossicular arrangement enables assignment of the new genus to the Paleozoic stem-family Hudsonasteridae; however, Arceoaster n. gen. is homeomorphic with members of the post-Paleozoic crown-group Goniasteridae. Because Arceoaster n. gen. is a hudsonasterid, and because similar morphologic expressions are not known among described taxa from later in the Paleozoic or the early Mesozoic, similarities between Arceoaster n. gen. and later genera are homoplastic, thereby providing an example of iterative evolution within Asteroidea. The Arceoaster n. gen. specimen is associated with a rich and diverse invertebrate fauna typical of its time interval and environmental setting; nothing suggests an unusual habitat. Selective pressures leading to homoplasy are conjectural, although robust construction among extant asteroids has been associated with a defensive life strategy.UUID: http://zoobank.org/b1d8461d-7e54-43cc-8719-97304ca3fd7a