SEGMENT RANDOM INSERTION PERTURBATION SCHEME (SRIPS) GENETIC ALGORITHM FOR MANUFACTURING INDUSTRY

This paper lays down a formal framework for simultaneous scheduling of machines- automated guided vehicles (AGVs) and tools in a multi-machine flexible manufacturing system (FMS) while accounting for transport times of parts to minimise makespan. To minimize tooling costs- a central tool magazine (CTM) is suggested so that the tools are ‘shared’. AGVs and tool transporter (TT) carry jobs and tools between machines. The complexity of including sequencing of job operations on machines- assignment of AGVs and tools to job operations and corresponding trip operations such as the empty trip and loaded trip times of AGVs and a CTM in scheduling is greater. The scope of this paper is to propose a nonlinear Mixed Integer Programming (MIP) model to minimize makespan. Since the problem is known to be NP hard- it is conjectured and then verified that the intelligent behaviour of chromosomes and genes can be effectively used to lay down a metaheuristic algorithm known as a segment random insertion perturbation scheme genetic algorithm (SRIPSGA) suitable for the problem at hand- and the results have been tabulated and analyzed.

In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region

We report a systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD (transposition-based random insertion and deletion mutagenesis) was used to generate large libraries with random in-frame InDels across the entire single-chain variable fragment gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (InScaM). An overall 256-fold affinity improvement of an anti–IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach, and suggests that the results of this InDel mutagenesis and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.

The Design of Compact SM4 Encryption and Decryption Circuits That Are Resistant to Bypass Attack

In order to achieve the purpose of defending against side channel attacks, a compact SM4 circuit was designed based on the mask and random delay technique, and the linear transformation module was designed with random insertion of the pseudo operation method. By analyzing the glitch data generated by the S-box of SM4 with different inputs, the security against glitch attacks was confirmed. Then, the DPA (Differential Power Analysis) was performed on the designed circuit. The key could not be successfully obtained even in the case of 100,000 power curves, so that the safety of SM4 against DPA is verified. Finally, using Synopsys DC (Design Compiler, Mountain View, CA94043DC, USA) to synthesize the designed circuit, the results show that the area of the designed circuit in the SMIC 0.18 process is 82,734 μm2, which is 48% smaller than results reported in other papers.

Dynamics of transposable element invasions with piRNA clusters

In mammals and in invertebrates the proliferation of a newly invading transposable element (TE) is thought to be stopped by a random insertion of one member of the invading TE family into a piRNA cluster. This view is known as the trap model. Here we explore the dynamics of TE invasions under the trap model using large-scale computer simulations. We found that piRNA clusters confer a substantial benefit, effectively preventing extinction of host populations from an uncontrollable proliferation of deleterious TEs. We show that TE invasions under the trap model consists of three distinct phases: first the TE rapidly amplifies within the population, next TE proliferation is stopped by segregating cluster insertions and finally the TE is permanently inactivated by fixation of a cluster insertion. Suppression by segregating cluster insertions is unstable and bursts of TE activity may yet occur. The transpositon rate and the population size mostly influence the length of the phases but not the amount of TEs accumulating during an invasion. Solely the size of piRNA clusters was identified as a major factor influencing TE abundance. Investigating the impact of different cluster architectures we found that a single non-recombining cluster (e.g. the somatic cluster flamenco in Drosophila) is more efficient in stopping invasions than clusters distributed over several chromosomes (e.g germline cluster in Drosophila). With the somatic architecture fewer TEs accumulate during an invasion and fewer cluster insertions are required to stop the TE. The inefficiency of the germline architecture stems from recombination among cluster sites which makes it necessary that each diploid carries, on the average, four cluster insertions, such that most individuals will end up with at least one cluster insertion. Surprisingly we found that negative selection in a model with piRNA clusters can lead to a novel equilibrium state, where TE copy numbers remain stable despite only some individuals in a population carrying a cluster insertion. Finally when applying our approach to real data from Drosophila melanogaster we found that the trap model reasonably well accounts for the abundance of germline TEs but not of somatic TEs. The abundance of somatic TEs, such as gypsy, is much lower than expected.

Site-specific transgenesis of the D. melanogaster Y-chromosome using CRISPR/Cas9

Despite the importance of Y-chromosomes in evolution and sex determination, their heterochromatic, repeat-rich nature makes them difficult to sequence and genetically manipulate, and therefore they generally remain poorly understood. For example, the D. melanogaster Y-chromosome, one of the best understood, is widely heterochromatic and composed mainly of highly repetitive sequences, with only a handful of expressed genes scattered throughout its length. Efforts to insert transgenes on this chromosome have thus far relied on either random insertion of transposons (sometimes harboring ‘landing sites’ for subsequent integrations) with limited success or on chromosomal translocations, thereby limiting the types of Y-chromosome related questions that could be explored. Here we describe a versatile approach to site-specifically insert transgenes on the Y-chromosome in D. melanogaster via CRISPR/Cas9-mediated HDR. We demonstrate the ability to insert, and detect expression from, fluorescently marked transgenic transgenes at two specific locations on the Y-chromosome, and we utilize these marked Y-chromosomes to detect and quantify rare chromosomal nondisjunction effects. Finally, we discuss how this Y-docking technique could be adapted to other insects to aid in the development of genetic control technologies for the management of insect disease vectors and pests.

A role for the Smc3 hinge domain in the maintenance of sister chromatid cohesion

Cohesin is a conserved protein complex required for sister chromatid cohesion, chromosome condensation, DNA damage repair, and regulation of transcription. Although cohesin functions to tether DNA duplexes, the contribution of its individual domains to this activity remains poorly understood. We interrogated the Smc3p subunit of cohesin by random insertion mutagenesis. Analysis of a mutant in the Smc3p hinge revealed an unexpected role for this domain in cohesion maintenance and condensation. Further investigation revealed that the Smc3p hinge functions at a step following cohesin’s stable binding to chromosomes and independently of Smc3p’s regulation by the Eco1p acetyltransferase. Hinge mutant phenotypes resemble loss of Pds5p, which binds opposite the hinge near Smc3p’s head domain. We propose that a specific conformation of the Smc3p hinge and Pds5p cooperate to promote cohesion maintenance and condensation.