Profiling Cancer Cells by Cell-SELEX: Use of Aptamers for Discovery of Actionable Biomarkers and Therapeutic Applications Thereof

The identification of tumor cell-specific surface markers is a key step towards personalized cancer medicine, allowing early assessment and accurate diagnosis, and development of efficacious targeted therapies. Despite significant efforts, currently the spectrum of cell membrane targets associated with approved treatments is still limited, causing an inability to treat a large number of cancers. What mainly limits the number of ideal clinical biomarkers is the high complexity and heterogeneity of several human cancers and still-limited methods for molecular profiling of specific cancer types. Thanks to the simplicity, versatility and effectiveness of its application, cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology is a valid complement to the present strategies for biomarkers’ discovery. We and other researchers worldwide are attempting to apply cell-SELEX to the generation of oligonucleotide aptamers as tools for both identifying new cancer biomarkers and targeting them by innovative therapeutic strategies. In this review, we discuss the potential of cell-SELEX for increasing the currently limited repertoire of actionable cancer cell-surface biomarkers and focus on the use of the selected aptamers as components of innovative conjugates and nano-formulations for cancer therapy.

Smart SRUs Pre-Investment Utilizing Oxygen Enrichment Technology

This paper presents an unparalleled engineering assessment conducted to evaluate the feasibility of pre-investing in O2 enrichment technology, with the purpose of increasing the processing capacities of conventional air-based sulfur recovery units (SRUs). Ultimately, the goal is to minimize the overall number of required SRUs for a greenfield gas plant and, consequently, capture a significant cost-avoidance opportunity. The technology review revealed that a high-level O2 enrichment can double the processing capacity of air-based SRU, depending on the H2S content in acid gas. As H2S mole fraction in feed increases, the debottlenecking capability increases. For the project under assessment, the processing capacity of air-based SRUs showed a maximum increase of 80%. On the contrary, operating with high O2 levels, will elevate SRU reaction furnace temperature, and mandates installing high-intensity burners, along with special control and ESD functions, to manage potential risk and ensure safe operation. Additionally, the liquid handling section of SRUs (condensers, collection vessels, degassing vessels, sulfur storage tanks) should be enlarged to accommodate more sulfur production. Typically, the enriched oxygen can be supplied from air separation units (ASUs), which entails significant capital cost. Apart from these special design considerations, there are several advantages for adopting this technology. Oxygen enrichment removes significant nitrogen volumes, which reduces loads on Claus, tail gas treatment, and thermal oxidizer units. Hence, lower capital cost for new plants is acquired due to equipment size reduction. In addition, higher HP steam production and less fuel gas consumption are achieved. Conventionally, O2 enrichment technology is employed in the initial design stage or used to retrofit operating SRUs facilities. However, it is unique to consider O2 enrichment-design requirements as part of new air-based SRUs design for phased program development. The objective is to enable smooth transition to fully O2 enrichment operated SRUs at a later phase of the project without the need for any design modification. This exceptional pre-investment strategy has resulted into reducing the required number of SRUs at phase II from eight to five units; and accordingly, a significant cost avoidance was captured.

Study of the multiple incorporation of modified nucleotides into the growing DNA strand

Objectives. This study investigated the substrate properties of the modified derivatives of triphosphates of purine and pyrimidine deoxynucleosides (5-propynyl-2’-deoxyuridine-5’-triphosphate, 5-propynyl2’-deoxycytidine-5’-triphosphate, 5-methyl-2’-deoxycytidine-5’-triphosphate, and N6-methyl-2’-deoxyadenosine-5’-triphosphate) during their simultaneous incorporation in enzymatic reactions (polymerase chain and primer extension reactions).Methods. The real-time polymerase chain and primer extension reactions were used to study the substrate efficiency of modified deoxynucleotide triphosphates. Various pairwise combinations of modified derivatives were used; specially designed synthetic DNA fragments and libraries for the Systematic Evolution of Ligands by Exponential Enrichment technology were used as templates. Reactions were conducted using DNA polymerases: Taq, Vent (exo-), DeepVent (exo-), and KOD XL.Results. In each case, a pair of compounds (modified dUTP + dCTP, dUTP + dATP, and dCTP + dATP) was selected to study the simultaneous incorporation into the growing DNA strand. The most effective combinations of nucleotides for simultaneous insertion were dU and dC, having 5-propynyl substitution. The Vent (exo-) DNA polymerase was found as the most effective for the modified substrates.Conclusions. The selected compounds can be used for the enzymatic preparation of modified DNA, including aptamers with extended physicochemical properties.

Combustion Enhancement of Pulverized Coal with Targeted Oxygen-Enrichment in an Ironmaking Blast Furnace

In this study, a targeted oxygen-enrichment technology was proposed to enhance coal combustion in an ironmaking blast furnace. The coal flow and combustion characteristics under targeted oxygen-enrichment were investigated using the computational fluid dynamics (CFD) method. The results showed that oxygen utilization and coal burnout were significantly increased under targeted oxygen-enrichment. The coal burnout at 24% O2 concentration was 86.29%, which was the maximum and indicated an increase of 13.13%. However, the cooling effect of room-temperature oxygen had some adverse effects on coal combustion. Given this, the effect of coal particle temperature on coal combustion was investigated based on targeted oxygen-enrichment. The coal combustion process was further enhanced. The coal burnout at a 600 K particle temperature and 25% oxygen concentration was 91.12% and had an increase of 17.96%, which was the maximum.

PENGAYAAN PAKAN BENIH RAJUNGAN (Portunus Pelagicus) STADIA MEGALOPA MELALUI PEMBERIAN BETA KAROTEN

Penelitian ini bertujuan untuk meningkatkan nilai nutrisi pakan alami rotifer dan artemia melalui penambahan beta karoten yang bersumber dari wortel. Penelitian ini dilaksanakan pada bulan Mei 2020 di unit pembenihan kepiting dan rajungan Balai Pe-rikanan Budidaya Air Payau (BPBAP) Takalar. Rancangan penelitian yang digunakan adalah rancangan acak lengkap (RAL) sebanyak 4 perlakuan dan 3 ulangan. Hewan uji yang digunakan adalah larva rajungan (Portunus Pelagicus) stadia megalopa yang ditebar dengan kepadatan 5 ekor/l dan dipelihara sampai memasuki stadia crab. Luaran penelitian yang ditargetkan adalah teknologi pengayaan pakan alami rotifer dan artemia menggunakan beta karoten yang berasal dari wortel. Hasil penelitian menunjukkan bahwa Pemberian frekwensi pakan yang tepat setelah dikayakan dengan beta caroten akan meningkatkan sintasan dan pertumbuhan pada larva rajungan. Frekwensi pakan yang tepat diberikan pada larva rajungan yang terbaik untuk kelang-sungan hidup larva rajungan adalah pemberian pakan 3 kali/hari. This study aims to increase the nutritional value of natural rotifer and artemia feed by adding beta carotene from carrots. This research was conducted in May 2020 at the hatchery unit of the Brackish Water Cultivation Fishery Center (BPBAP) Takalar. The research design used was a completely randomized design (CRD) with 4 treatments and 3 replications. The experimental animals used were small crab larvae (Portunus pelagicus) in the megalopa stage which were stocked with a density of 5 individuals/l and they were kept until entering the crab stage. The target output of this research is natural feed enrichment technology for rotifer and artemia using beta carotene derived from carrots. The results showed that giving the right frequency of feed after being enriched with beta carotene would increase survival and growth in small crab larvae. The best frequency of feed given to small crab larvae for the survival of small crab larvae is feeding 3 times/day.

Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations

The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.

A Deep Learning-Based System (Microscan) for the Identification of Pollen Development Stages and Its Application to Obtaining Doubled Haploid Lines in Eggplant

The development of double haploids (DHs) is a straightforward path for obtaining pure lines but has multiple bottlenecks. Among them is the determination of the optimal stage of pollen induction for androgenesis. In this work, we developed Microscan, a deep learning-based system for the detection and recognition of the stages of pollen development. In a first experiment, the algorithm was developed adapting the RetinaNet predictive model using microspores of different eggplant accessions as samples. A mean average precision of 86.30% was obtained. In a second experiment, the anther range to be cultivated in vitro was determined in three eggplant genotypes by applying the Microscan system. Subsequently, they were cultivated following two different androgenesis protocols (Cb and E6). The response was only observed in the anther size range predicted by Microscan, obtaining the best results with the E6 protocol. The plants obtained were characterized by flow cytometry and with the Single Primer Enrichment Technology high-throughput genotyping platform, obtaining a high rate of confirmed haploid and double haploid plants. Microscan has been revealed as a tool for the high-throughput efficient analysis of microspore samples, as it has been exemplified in eggplant by providing an increase in the yield of DHs production.