TARS: A Novel Mechanism for Truly Autonomous Resource Selection in LTE-V2V Mode 4

Effective communication in vehicular networks depends on the scheduling of wireless channel resources. There are two types of channel resource scheduling in Release 14 of the 3GPP, i.e., (1) controlled by eNodeB and (2) a distributed scheduling carried out by every vehicle, known as Autonomous Resource Selection (ARS). The most suitable resource scheduling for vehicle safety applications is the ARS mechanism. ARS includes (a) counter selection (i.e., specifying the number of subsequent transmissions) and (b) resource reselection (specifying the reuse of the same resource after counter expiry). ARS is a decentralized approach for resource selection. Therefore, resource collisions can occur during the initial selection, where multiple vehicles might select the same resource, hence resulting in packet loss. ARS is not adaptive towards vehicle density and employs a uniform random selection probability approach for counter selection and reselection. As a result, it can prevent some vehicles from transmitting in a congested vehicular network. To this end, the paper presents Truly Autonomous Resource Selection (TARS) for vehicular networks. TARS considers resource allocation as a problem of locally detecting the selected resources at neighbor vehicles to avoid resource collisions. The paper also models the behavior of counter selection and resource block reselection on resource collisions using the Discrete Time Markov Chain (DTMC). Observation of the model is used to propose a fair policy of counter selection and resource reselection in ARS. The simulation of the proposed TARS mechanism showed better performance in terms of resource collision probability and the packet delivery ratio when compared with the LTE Mode 4 standard and with a competing approach proposed by Jianhua He et al.

Knock out of CD123 or CLL-1 By CRISPR-Cas9 Editing from Human Hematopoietic Stem Cell Transplants Provide New Possibilities for Increasing Therapeutic Index and Safety for AML Treatment

Acute myeloid leukemia (AML) is a clonal disorder of hematopoiesis and the most common form of acute leukemia in adults. Most patients with AML relapse despite intensive chemotherapy. Allogeneic hematopoietic cell transplant (HCT) has become the standard of care for patients with intermediate or adverse genetics, with >3,500 transplants performed annually in the US. However, leukemia relapse post-HCT occurs in ~40% of these patients with a 2-year survival rate at <20%, necessitating new approaches to reduce relapse and improve overall outcomes. Antigen-specific immunotherapies require cell surface antigens to be uniquely expressed on cancer cells to minimize "on-target, off-tumor" toxicity. CD123 and CLL-1 are highly expressed on normal myeloid cells, thus impeding the use of therapies targeting these antigens due to myelotoxicity. To circumvent such toxicity, we aim to create CD123 or CLL-1 negative human hematopoietic stem and progenitor cells (hHSPCs) for HCT such that this can be combined with subsequent use of targeted therapy against these antigens to prevent post-HCT relapse. Here, we present the pre-clinical evaluation of engineered hHSPCs, derived from mobilized peripheral blood of healthy donors, where CD123 or CLL-1 proteins were ablated by CRISPR/Cas9 gene editing. We have identified highly efficient guide RNAs that result in >80% on-target editing and can achieve greater than 90% biallelic gene knockout (KO). Deep sequencing followed by hybrid capture of up to 1000 potential off-target sites predicted to contain a maximum of 5 mismatches revealed minimal to no detectable off-target editing events. CD123 or CLL-1 KO hHSPCs showed >85% cell viability post-editing. Loss of CD123 or CLL-1 protein did not impact the differentiation of hHSPCs into granulocytic, monocytic, or erythroid lineages in vitro. Additionally, myeloid cells derived from CD123 or CLL-1 KO hHSPCs also retained their function, demonstrating similar phagocytotic capacity and the production of inflammatory cytokines in response to TLR agonists compared to unedited control cells. Importantly, CD123 or CLL-1 KO hHSPCs xenotransplanted into NSG or NBSGW mice showed no defect in long-term engraftment (human chimerism in NBSGW mice 16 weeks post transplant: 92.3±5.1% for CD123 KO, 91.2±4.1% for CLL-1 KO, and 93.4±3.1% unedited hHSPC engrafted mice, n=15 each). This in vivo model confirmed no observable impact on multilineage differentiation after CD123 or CLL-1 deletion either, supported by equal distribution of 10 hematopoietic lineages between groups. Bone marrow analyses revealed persistence of high gene editing frequency after 16 weeks (71±10% from CD123 KO and 86±6% from CLL-1 KO engrafted mice, n=15 each, compared to original 83% input CD123 KO and 86% input CLL-1 hHSPCs). Sorted subpopulations, including granulocytes, monocytes, dendritic cells, and mast cells, from the bone marrow similarly retained high levels of editing. Together these data suggest that there was no counter-selection against CD123 or CLL-1 KO cells, no outgrowth of any cells with particular edits or hematopoietic lineages to warrant tumorigenic concerns. Most notably, proof-of-concept experiments showed that cells depleted of CD123 or CLL-1 protein are indeed protected from the cytotoxicity of CD123 or CLL-1 targeted CAR-T cells. In conclusion, we demonstrate that CD123 or CLL-1 negative human HSPCs can successfully carry out functional hematopoiesis that is resistant to CD123 or CLL-1 targeted therapies. Our findings provide a next-generation HCT strategy that supports the safe and effective use of antigen-directed immunotherapy treatments for patients with AML. Disclosures Luo: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Angelini: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Krishnamurthy: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Lisle: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Isik: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Ghdossi: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Cummins: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Pettiglio: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Hazelbaker: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Ge: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Tavares: Vor Biopharma: Ended employment in the past 24 months. Nikam: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Paik: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Lydeard: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Lin: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company. Chakraborty: Vor Biopharma: Current Employment, Current equity holder in publicly-traded company.

A system for multiplexed selection of aptamers with exquisite specificity without counter-selection

Aptamers have proven to be valuable tools for the detection of small molecules due to their remarkable ability to specifically discriminate between structurally similar molecules. Most aptamer selection efforts have relied on counter-selection to eliminate aptamers that exhibit unwanted cross-reactivity to interferents or structurally similar relatives to the target of interest. However, because the affinity and specificity characteristics of an aptamer library are fundamentally unknowable a priori, it is not possible to determine the optimal counter-selection parameters. As a result, counter-selection experiments require trial-and-error approaches that are inherently inefficient and may not result in aptamers with the best combination of affinity and specificity. In this work, we describe a high-throughput screening process for generating high-specificity aptamers to multiple targets in parallel, while also eliminating the need for counter-selection. We employ a platform based on a modified benchtop sequencer to conduct a massively-parallel aptamer screening process that enables the selection of highly-specific aptamers against multiple structurally similar molecules in a single experiment, without any counter-selection. As a demonstration, we have selected aptamers with high affinity and exquisite specificity for three structurally similar kynurenine metabolites that differ by a single hydroxyl group in a single selection experiment. This process can easily be adapted to other small-molecule analytes, and should greatly accelerate the development of aptamer reagents that achieve exquisite specificity for their target analytes.

GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

Advances in robotic system-assisted genome editing techniques and computer-aided design tools have significantly facilitated the development of microbial cell factories. Although multiple separate software solutions are available for vector DNA assembly, genome editing, and verification, by far there is still a lack of complete tool which can provide a one-stop service for the entire genome modification process. This makes the design of numerous genetic modifications, especially the construction of mutations that require strictly precise genetic manipulation, a laborious, time-consuming and error-prone process. Here, we developed a free online tool called GEDpm-cg for the design of genomic point mutations in C. glutamicum. The suicide plasmid-mediated counter-selection point mutation editing method and the overlap-based DNA assembly method were selected to ensure the editability of any single nucleotide at any locus in the C. glutamicum chromosome. Primers required for both DNA assembly of the vector for genetic modification and sequencing verification were provided as design results to meet all the experimental needs. An in-silico design task of over 10,000 single point mutations can be completed in 5 min. Finally, three independent point mutations were successfully constructed in C. glutamicum guided by GEDpm-cg, which confirms that the in-silico design results could accurately and seamlessly be bridged with in vivo or in vitro experiments. We believe this platform will provide a user-friendly, powerful and flexible tool for large-scale mutation analysis in the industrial workhorse C. glutamicum via robotic/software-assisted systems.

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas

CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and widely applicable genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for tight and inducible control over CRISPR-Cas counter-selection. This control delays CRISPR-Cas counter-selection, granting more time for the editing event (e.g. by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three wild-type bacteria species (Escherichia coli MG1655, Pseudomonas putida KT2440 and Flavobacterium IR1) with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a simple gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.

Development and optimization of Lysis gene E as a counter-selection marker with high selection stringency

Seamless modification of bacteria chromosome is widely performed both in theoretical and in practical research, for this purpose, excellent counter-selection marker genes with high selection stringency are needed. Lysis gene E from bacteriophage PhiX174 was developed and optimized as a counter-selection marker in this paper. Lysis gene E was firstly constructed under the control of pL promoter. At 42 °C, Lysis gene E could effectively kill Escherichia coli. Seamless modification using E as a counter-selection marker also successfully conducted. It also works in another Gram-negative strain Serratia marcescens under the control of Arac/PBAD regulatory system. Through combining lysis gene E and kil, the selection stringency frequency of pL-kil-sd-E cassette in E. coli arrived at 4.9×10−8 and 3.2×10−8 at two test loci, which is very close to the best counter-selection system, inducible toxins system. Under the control of Arac/PBAD, selection stringency of PBAD-kil-sd-E in S. marcescens arrived at the level of 10−7 at four test loci. By introducing araC gene harboring plasmid pKDsg-ack, 5- to 18- fold improvement of selection stringency was observed at these loci, and a surprising low selection stringency frequency 4.9×10−9 was obtained at marR-1 locus, the lowest selection stringency frequency for counter-selection reported so far. Similarly, at araB locus of E. coli selection stringency frequency of PBAD-kil-sd-E was improved to 3×10−9 after introducing plasmid pKDsg-ack. In conclusion, we have developed and optimized a newly universal counter-selection marker based on lysis gene E. The best selection stringency of this new marker exceeds the inducible toxins system several fold.

Targeting chromosome trisomy for chromosome editing

A trisomy is a type of aneuploidy characterised by an additional chromosome. The additional chromosome theoretically accepts any kind of changes since it is not necessary for cellular proliferation. This advantage led us to apply two chromosome manipulation methods to autosomal trisomy in chicken DT40 cells. We first corrected chromosome 2 trisomy to disomy by employing counter-selection markers. Upon construction of cells carrying markers targeted in one of the trisomic chromosome 2s, cells that have lost markers integrated in chromosome 2 were subsequently selected. The loss of one of the chromosome 2s had little impacts on the proliferative capacity, indicating unsubstantial role of the additional chromosome 2 in DT40 cells. We next tested large-scale truncations of chromosome 2 to make a mini-chromosome for the assessment of chromosome stability by introducing telomere repeat sequences to delete most of p-arm or q-arm of chromosome 2. The obtained cell lines had 0.7 Mb mini-chromosome, and approximately 0.2% of mini-chromosome was lost per cell division in wild-type background while the rate of chromosome loss was significantly increased by the depletion of DDX11, a cohesin regulatory protein. Collectively, our findings propose that trisomic chromosomes are good targets to make unique artificial chromosomes.

Horizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria

The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.

How does feedback from phage infections influence the evolution of phase variation in Campylobacter?

Campylobacter jejuni (C. jejuni) causes gastroenteritis following the consumption of contaminated poultry meat, resulting in a large health and economic burden worldwide. Phage therapy is a promising technique for eradicating C. jejuni from poultry flocks and chicken carcasses. However, C. jejuni can resist infections by some phages through stochastic, phase-variable ON/OFF switching of the phage receptors mediated by simple sequence repeats (SSR). While selection strength and exposure time influence the evolution of SSR-mediated phase variation (PV), phages offer a more complex evolutionary environment as phage replication depends on having a permissive host organism. Here, we build and explore several continuous culture bacteria-phage computational models, each analysing different phase-variable scenarios calibrated to the experimental SSR rates of C. jejuni loci and replication parameters for the F336 phage. We simulate the evolution of PV rates via the adaptive dynamics framework for varying levels of selective pressures that act on the phage-resistant state. Our results indicate that growth reducing counter-selection on a single PV locus results in the stable maintenance of the phage, while compensatory selection between bacterial states affects the evolutionary stable mutation rates (i.e. very high and very low mutation rates are evolutionarily disadvantageous), whereas, in the absence of either selective pressure the evolution of PV rates results in mutation rates below the basal values. Contrastingly, a biologically-relevant model with two phase-variable loci resulted in phage extinction and locking of the bacteria into a phage-resistant state suggesting that another counter-selective pressure is required, for instance the use of a distinct phage whose receptor is an F336-phage-resistant state. We conclude that a delicate balance between counter-selection and phage-attack can result in both the evolution of phase-variable phage receptors and persistence of PV-receptor-specific phage.