Evolutionary Platform Research Articles

Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system

Canonical prokaryotic type I CRISPR-Cas adaptive immune systems contain a multicomponent effector complex called Cascade, which degrades large stretches of DNA via Cas3 helicase-nuclease activity. Recently, a highly precise subtype I-F1 CRISPR-Cas system (HNH-Cascade) was found that lacks Cas3, the absence of which is compensated for by the insertion of an HNH endonuclease domain in the Cas8 Cascade component. Here, we describe the cryo-EM structure of Selenomonas sp. HNH-Cascade (SsCascade) in complex with target DNA and characterize its mechanism of action. The Cascade scaffold is complemented by the HNH domain, creating a ring-like structure in which the unwound target DNA is precisely cleaved. This structure visualizes a unique hybrid of two extensible biological systems-Cascade, an evolutionary platform for programmable DNA effectors, and an HNH nuclease, an adaptive domain with a spectrum of enzymatic activity.

In-situ encapsulation of angiotensin converting enzyme (ACE) based on mesoporous ZIF-8 coated with polydopamine (PDA): Effect, mechanism and application

Immobilized angiotensin converting enzyme (ACE) utilizes specific interaction between ACE and ACE inhibitors to screen drugs for hypertension therapy, but traditional immobilized ACE is insufficient to achieve satisfactory effect for the poor immobilization efficiency and stability. In this work, mesoporous ZIF-8 (mZIF-8) coated with polydopamine (PDA) was developed as an enzyme-immobilization platform for the first time. Molecular docking was used to study the mechanism of ACE induced mZIF-8 synthesis. The immobilized enzyme ACE@mZIF-8/PDA were shown to possess mesoporous structures with ACE encapsulation efficiency of ∼90%. Compared with the free enzyme, ACE@mZIF-8/PDA exhibited enhanced tolerance to temperature, pH, unfolding and proteolytic agents, with excellent reusability (maintained 82.29% ± 4.11% of initial activity after being reused 10 times) and storage stability (retaining 93.12% ± 3.271% residual activity after 30 days). Molecular docking research conformed ACE induced the triggered nucleation of MOFs via binding with MOFs precursors. Moreover, ACE@mZIF-8/PDA was used as high-performance adsorbent for enrichment of ACE inhibitory peptides. The noncompetitive inhibitory peptide GF-6 and competitive inhibitory peptide VPP could be captured synchronously, which avoided the loss of active substances. These results indicated that the ACE@mZIF-8/PDA provides an evolutionary platform for rapid screening of inhibitory peptides.

Effect of Propeptide Mutations on the Directed Evolution of Rhizomucor miehei Lipase.

A series of mutants of Rhizomucor miehei lipase (RML) screened through four rounds of directed evolution were studied. Mutants' triglyceride hydrolysis activity was assessed, and their genes were sequenced. Results showed that mutations in the propeptide can improve the activity of RML during evolution. Two parts of propeptide (wild-type and mutant) and mature region were connected by molecular simulation technology. The spatial structure of the most positive mutants containing the mutations in the propeptide was mainly characterized by the increase in the opening angle of the lid structure in the mature region of RML, the enhancement of the hydrophobicity of the active center, and the triad of the active center shifted outward. The three indexes above explain the mechanism of propeptide mutations on the activity change of the target protein. In addition, statistical analysis of all the mutants screened in directed evolution showed that: (1) most of the mutants with increased activity contained mutations of the propeptide, (2) in the later stage of directed evolution, the number of active mutants decreased gradually, and the mutations of inactivated protein mainly occurred in the mature region, and (3) in the last round of directed evolution, the mutations distributed in the propeptide improved the mutant activity further. The results showed that the propeptide reduced RML's evolutionary pressure and delayed the emergence of the evolutionary platform. These findings reveal the role of propeptide in the evolution of RML and provide strategies for the molecular transformation of other lipases.

Digital Platforms for SMME Enablement

The challenges facing SMME’s are diverse ranging from skills challenges to value chain optimization, concept management and operations management. The entrepreneur navigates a typical SMME cycle from idea generation to sustainable business single-handed. Each phase of SMME development is a challenge but is not unique to the individual SMME. Financial management, marketing, logistics, people management and general strategy to execution against challenges are endured and overcome by SMME’s. SMME’s form the majority of businesses, in most economies and is a source of GDP growth. SMME failure rates are high across the globe with significant challenges to survive. Innovation centers, incubation models and various other interventions have impacted SMME survival but more should be done. The research presented in this paper revolves around a theoretical digital platform for SMME sustainability. The platform is evolutionary and based on large corporate processes and systems, subdued and modified for SMME support. Core SMME processes are digitalized and provide for a single strategy. The evolutionary platform builds over time and evolves to an intuitive digital SMME support system. An initial literature analysis leading onto a theoretical SMME framework and systems dynamics model is presented.

Ultra-deep long-read sequencing detects IS-mediated gene duplications as a potential trigger to generate arrays of resistance genes and a mechanism to induce novel gene variants such as blaCTX-M-243.

Extended-spectrum β-lactamases (ESBLs) are enzymes that can render their hosts resistant to various β-lactam antibiotics. CTX-M-type enzymes are the most prevalent ESBLs and the main cause of resistance to third-generation cephalosporins in Enterobacteriaceae. The number of described CTX-M types is continuously rising, currently comprising over 240 variants. During routine screening we identified a novel blaCTX-M gene. To characterize a novel blaCTX-M variant harboured by a multidrug-resistant Escherichia coli isolate of sequence type ST354. Antibiotic susceptibilities were determined using broth microdilution. Genome and plasmid sequences were reconstructed using short- and long-read sequencing. The novel blaCTX-M locus was analysed using long-read and Sanger sequencing. Plasmid polymorphisms were determined in silico on a single plasmid molecule level. The novel blaCTX-M-243 allele was discovered alongside a nearly identical blaCTX-M-104-containing gene array on a 219 kbp IncHI2A plasmid. CTX-M-243 differed from CTX-M-104 by only one amino acid substitution (N109S). Ultra-deep (2300-fold coverage) long-read sequencing revealed dynamic scaling of the blaCTX-M genetic contexts from one to five copies. Further antibiotic resistance genes such as blaTEM-1 also exhibited sequence heterogeneity but were stable in copy number. We identified the novel ESBL gene blaCTX-M-243 and illustrate a dynamic system of varying blaCTX-M copy numbers. Our results highlight the constant emergence of new CTX-M family enzymes and demonstrate a potential evolutionary platform to generate novel ESBL variants and possibly other antibiotic resistance genes.

Reprogramming Nonribosomal Peptide Synthesis by Surgical Mutation

Nonribosomal peptide synthetases produce highly modified bioactive peptides, many of which are used therapeutically. As such, they have been the target of intense protein engineering to enable biosynthetic access to peptide variants with improved drug properties or altered bioactivities. In this account, we describe our ongoing efforts to reprogram nonribosomal peptide synthesis by surgical mutation. In contrast to ribosomal biosynthesis, nonribosomal peptide synthesis has proven difficult to engineer, arguably due to a lack of suitable tools. To address this limitation, we have established a high-throughput assay that provides unprecedented control over the gatekeeper adenylation domains responsible for building block selection and incorporation. Expansion of this strategy to other building blocks and domains promises to make it a powerful evolutionary platform for tailoring assembly lines for custom synthesis of peptide therapeutics.1. Nonribosomal Peptides2. Reprogramming A Domains for Clickable Amino Acids3 A High-Throughput A Domain Assay4 Reprogramming A Domains for β-Amino Acids5 Downstream Processing6 Conclusions and Outlook

An evolutionary platform for alternate bearing in fruit trees

Alternate bearing has been and still is a major problem in fruit trees. From the point of view of a horticulturist it is a tree productivity syndrome which must be addressed by agro-technical means in order to eliminate or, at least, mitigate the alternation cycle. ‘Masting’ is a widespread forest tree irregular sexual reproduction pattern that has attracted ecologists who wonder about the survival-advantage of this behavior. From an evolutionary perspective alternate bearing and masting seem to be related and may share a common bio-evolutionary mechanism, responsible for ‘yield alternation’. A recently developed resource budget model, based on nonlinear chaos dynamics, seems to account for a broad spectrum of yield alternation patterns. From an evolutionary standpoint, one may envision a domestication-evolutionary continuum from extreme masting, through intermediate alternate bearing, down to regular yield of fully-managed fruit trees. Domestication records of pecan (Carya illinoiensis) support this hypothesis. The alternate bearing of fruit trees appears to be mediated by a ‘fruit overload’ signal but resource depletion still plays a critical role in the alternate bearing of numerous tree crops.

On-Chain Governance of Decentralized Autonomous Organizations: Blockchain Organization Using Semada

This paper initiates an analysis of the consequences of different options in the choice of regulatory protocols and reward structures when founding distributed autonomous organizations (DAOs) on a blockchain. The Semada Team invites all interested parties to participate in and contribute to this joint vision herein and related research projects. With the proper incentives, independent and selfish actors can be organized to collaborate productively toward a common goal. The objective is to identify the ideal protocols that should be chosen for promoting the values and goals of any particular DAO. On-chain governance gives DAOs the opportunity to achieve complete decentralization, anonymity, and autonomy. The first incentive structure that encourages healthy collaboration is a focus on long-term reputation instead of instantly fungible currency rewards. When the focus is on reputation instead of more fungible rewards, damaging arbitrage is demotivated. The Semada platform is a fully decentralized and autonomous blockchain distributed application (DApp) which vests users with verified reputation. Semada is designed to be secure against all known attacks on digital reputation, including Sybil attacks and tyranny of the majority. The next major concern for creating a healthy DAO is a governance model that rewards value enhancing contributions from DAO members, deters bad actors, and evolves over time as circumstances change. No single, static protocol for running a DAO can be complicated enough to properly reflect the will of its members, while remaining immune to gaming by naturally selfish parties. Yet, DAO governance requires a clear system for reaching consensus on new protocols for DAO member behavior. We propose a clear procedure for achieving on-chain regulatory and legislative governance. Semada is designed as an evolutionary platform which rewards continual development of new governance protocols to anticipate and react to inevitable internal and external attacks. Unlike centralized platforms with reputational elements, the decentralized Semada platform gives users complete power to improve the platform and police any diminishments. Semada incentivices value-enhancing contributions and legitimate policing by sharing the totality of all profits amongst its users.

A Study on Evolutionary Perspectives of ‘Emotions’ and ‘Mood’ on Biological Evolutionary Platform

This study endeavours to define evolutionary perspectives of emotions and mood on biological evolutionary platform. Emotions and Mood are two separate entities of the mental apparatus. 'Mood' is the energy level of the mind at a given particular moment, whereas 'emotion' is a specific sensation or feeling in the mind that provides directional drive to the other faculties of the mind – memory, intelligence, and physical activities – for their actions to be performed to pursue a specific goal. Present study supports that every emotion has been developed individually in the course of biological evolution, and they all have been evolved to maintain the survival needs. According to ‘Emotion Model’ posited by Das, each emotion is distinct and different with a specific survival role and physiologically can be qualitatively and quantitatively determined on different emotion scales. So there is no such existence of as such primary and secondary emotions. Furthermore, each emotion has some certain expressing habits, which both are suited for adapting with the emotion provoking situations and are used for inter-communication purposes. This study also clarifies how evolution of emotions has been an important tool in sociobiology maintaining the bridge between Darwin's evolution theory and Hamilton’s inclusive fitness theory, and has become responsible for entire social evolution.

Securing Paternity by Mutilating Female Genitalia in Spiders

Competition between males and their sperm over access to females and their eggs has resulted in manifold ways by which males try to secure paternity, ranging from physically guarding the female after mating to reducing her receptivity or her attractiveness to subsequent males by transferring manipulative substances or by mechanically sealing the female reproductive tract with a copulatory plug. Copulations may also result in internal damage of the female genitalia; however, this is not considered as a direct adaptation against sperm competition but as a collateral effect. Here, we present a drastic and direct mechanism for securing paternity: the removal of coupling structures on female genitalia by males. In the orb-weaving spider Larinia jeskovi males remove the scapus, a crucial coupling device on the female external genital region. Reconstruction of the coupling mechanism using micro-CT-scanned mating pairs revealed that several sclerites of the male genitalia interact to break off the scapus. Once it is removed, remating cannot occur due to mechanical coupling difficulties. In the field, male-inflicted genital damage is very prevalent since all female L. jeskovi were found to be mutilated at the end of the mating season. External genital mutilation is an overlooked but widely spread phenomenon since 80 additional spider species were found for which male genital manipulation can be suspected. Interlocking genitalia provide an evolutionary platform for the rapid evolution of this highly effective mechanism to secure paternity, and we suspect that other animal groups with interlocking genital structures might reveal similarly drastic male adaptations.

Speech in action: degree of hand preference for grasping predicts speech articulation competence in children.

Highlights: Degree of lateralization for grasping predicts the maturity of the language production system in young, typically-developing children.In this report we provide compelling evidence for the relationship between right hand grasp-to-mouth (i.e., feeding) movements and language development. Specifically, we show that children (4–5 years old) who are more right-hand lateralized in picking up small food items for consumption show enhanced differentiation of the “s” and “sh” sounds. This result suggests that left hemisphere control of hand-to-mouth gestures may have provided an evolutionary platform for the development of language. The current investigation presents the exciting possibility that early right hand-to-mouth training could accelerate the development of articulation skills.

Approaching neuropsychological tasks through adaptive neurorobots

Neuropsychological phenomena have been modelized mainly, by the mainstream approach, by attempting to reproduce their neural substrate whereas sensory-motor contingencies have attracted less attention. In this work, we introduce a simulator based on the evolutionary robotics platform Evorobot* in order to setting up in silico neuropsychological tasks. Moreover, in this study we trained artificial embodied neurorobotic agents equipped with a pan/tilt camera, provided with different neural and motor capabilities, to solve a well-known neuropsychological test: the cancellation task in which an individual is asked to cancel target stimuli surrounded by distractors. Results showed that embodied agents provided with additional motor capabilities (a zooming/attentional actuator) outperformed simple pan/tilt agents, even those equipped with more complex neural controllers and that the zooming ability is exploited to correctly categorising presented stimuli. We conclude that since the sole neural computational power cannot explain the (artificial) cognition which emerged throughout the adaptive process, such kind of modelling approach can be fruitful in neuropsychological modelling where the importance of having a body is often neglected.

Community Care of North Carolina: An Evolutionary Platform for Medicaid Innovation

Community Care of North Carolina: An Evolutionary Platform for Medicaid Innovation

Neocortical development as an evolutionary platform for intragenomic conflict

Embryonic development in mammals has evolved a platform for genomic conflict between mothers and embryos and, by extension, between maternal and paternal genomes. The evolutionary interests of the mother and embryo may be maximized through the promotion of sex-chromosome genes and imprinted alleles, resulting in the rapid evolution of postzygotic phenotypes preferential to either the maternal or paternal genome. In eutherian mammals, extraordinary in utero maternal investment in the brain, and neocortex especially, suggests that convergent evolution of an expanded mammalian neocortex along divergent lineages may be explained, in part, by parent-of-origin-linked gene expression arising from parent-offspring conflict. The influence of this conflict on neocortical development and evolution, however, has not been investigated at the genomic level. In this hypothesis and theory article, we provide preliminary evidence for positive selection in humans in the regions of two platforms of intragenomic conflict—chromosomes 15q11-q13 and X—and explore the potential relevance of cis-regulated imprinted domains to neocortical expansion in mammalian evolution. We present the hypothesis that maternal- and paternal-specific pressures on the developing neocortex compete intragenomically to influence neocortical expansion in mammalian evolution.

Linking business ecosystem lifecycle with platform strategy: a triple view of technology, application and organisation

This paper explores platform strategies along the business ecosystem lifecycle (BELC), based on a multiple-case study. Developing observations on platform strategies from a firm level to a business ecosystem level, the study investigates the issue of platform strategy through three views, respectively technology, application and organisation. As a result, a general evolutional pattern of platform strategy along the BELC is identified, where an open strategy emerges at the birth and expansion phases, then a dominating strategy rises at the authority phase, and finally the opportunistic strategy takes over at the renewal phase. This paper connects the core firms in the business ecosystem with the evolutionary platform strategies.

The Plasticity of the β-Trefoil Fold Constitutes an Evolutionary Platform for Protease Inhibition

Proteases carry out a number of crucial functions inside and outside the cell. To protect the cells against the potentially lethal activities of these enzymes, specific inhibitors are produced to tightly regulate the protease activity. Independent reports suggest that the Kunitz-soybean trypsin inhibitor (STI) family has the potential to inhibit proteases with different specificities. In this study, we use a combination of biophysical methods to define the structural basis of the interaction of papaya protease inhibitor (PPI) with serine proteases. We show that PPI is a multiple-headed inhibitor; a single PPI molecule can bind two trypsin units at the same time. Based on sequence and structural analysis, we hypothesize that the inherent plasticity of the β-trefoil fold is paramount in the functional evolution of this family toward multiple protease inhibition.

Evolutionary Platform for Growth of Pulse-oximetry

パルスオキシメータは現在，世界中の手術室やICUで必須の患者モニターとなっている．しかしながら従来のパルスオキシメータ（2波長）では異常ヘモグロビンの検出ができず，その異常ヘモグロビンの存在下では正しい酸素飽和度も測定できなかった．現時点でパルスオキシメータ改良の方向性は二つある．第一は，低灌流，体動あるいは小児に対しての信号検出における鋭敏性と正確性の追求である．第二に（多波長）パルスオキシメータにより，異常ヘモグロビンや正常ヘモグロビンの測定が可能となった（例えばCOヘモグロビン，メトヘモグロビンや総ヘモグロビンなど）．近い将来，無侵襲の多波長パルスオキシメータを用いて，大量出血や低容量などの迅速な診断が実現可能であろう．一方，無侵襲の多機能（多波長）パルスオキシメータから波形解析により得られる新しいパラメーター（灌流指標PI：Perfusion Indexや脈波変動指標PVI：Pleth Variability Index）は有用である．PIは末梢循環を反映するだろう．PVIは動脈圧波形から得られるパラメーター（1回拍出量変動SVV：Stroke Volume Variation）と同様に輸液反応性の判断指標として有望である．結論として，大量出血や低容量に対しての治療や診断的価値は，無侵襲でリアルタイム測定可能な多波長パルスオキシメータを用いることにより周術期患者管理において適応が拡大する可能性が示唆された．

Investigating technical trading strategy via an multi-objective evolutionary platform

Conventional approach in evolutionary technical trading strategies adopted the raw excess returns as the sole performance measure, without considering the associated risk involved. However, every individual has a different degree of risk averseness and thus different preferences between risk and returns. Acknowledging that these two factors are inherently conflicting in nature, this paper considers the multi-objective evolutionary optimization of technical trading strategies, which involves the development of trading rules that are able to yield high returns at minimal risk. Popular technical indicators used commonly in real-world practices are used as the building blocks for the strategies, which allow the examination of their trading characteristics and behaviors on the multi-objective evolutionary platform. While the evolved Pareto front accurately depicts the inherent tradeoff between risk and returns, the experimental results suggest that the positive correlation between the returns from the training data and test data, which is generally assumed in the single-objective approach of this optimization problem, does not necessarily hold in all cases.

Evolutionary origins of human apoptosis and genome-stability gene networks

Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a ‘molecular node’ in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown. Here, using computational methods, we reconstruct the evolutionary scenario that linked apoptosis with genome stability pathways in a functional human gene/protein association network. We found that the entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2. Also, several critical nodes that entangle apoptosis and genome stability are cancer genes (e.g. ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6 and TP53), although their orthologs have arisen in different points of evolution. Our results demonstrate how genome stability and apoptosis were co-opted during evolution recruiting genes that merge both systems. We also provide several examples to exploit this evolutionary platform, where we have judiciously extended information on gene essentiality inferred from model organisms to human.

Evolutionary agent learning

Evolutionary Platform for Agent Learning (EPAL) is a novel methodology for agent learning, based on an extension to genetic programming that Lockheed Martin Advanced Technology Laboratories (LM ATL) developed. EPAL allows software agents to learn how to better operate under external conditions, so they do not repeat their mistakes. It creates both subtle and drastic changes to agent behavior. Subtle changes arise from learning task parameters; drastic changes emerge from learning improved workflows containing new programming constructs and tasks. Although EPAL was constructed for learning by LM ATL developed extendible mobile agent architecture agents, it is a suitable learning methodology for any software agent whose behavior can be represented as a workflow and further decomposed into building blocks, such as operators, tasks, and parameters. Our agents learned to solve a real-world problem that is similar to problems encountered in Navy Fleet Battle Experiment-Juliet. Results for both parameter learning and workflow learning are very encouraging.