Bockenheimer Disease is Associated With a TEK Variant

Bockenheimer disease is a venous malformation involving all tissues of an extremity. Patients have significant morbidity and treatment is palliative. The purpose of this study was to identify the cause of Bockenheimer disease to develop pharmacotherapy for the condition. Paraffin-embedded tissue from 9 individuals with Bockenheimer disease obtained during a clinically-indicated operation underwent DNA extraction. Droplet digital PCR (ddPCR) was used to screen for variants most commonly associated with sporadic venous malformations [TEK (NM_000459.5:c.2740C>T; p.Leu914Phe), PIK3CA (NM_006218.4:c.1624G>A; p.Glu542Lys and NM_006218.4:c.3140A>G; p.His1047Arg)]. ddPCR detected a TEK L914F variant in all 9 patients (variant allele fraction 2%-13%). PIK3CA E542K and H1047R variants were not identified in the specimens. Sanger sequencing and restriction enzyme digestion confirmed variants identified by ddPCR. A pathogenic variant in the endothelial cell tyrosine kinase receptor TEK is associated with Bockenheimer disease. Pharmacotherapy targeting the TEK signaling pathway might benefit patients with the condition.

OriCiro® Cell-Free Cloning System/PASS V4.1.2 v1

OriCiro® Cell-Free Cloning System is a rapid and powerful tool replacing cumbersome DNA cloning (plasmid construction) process relying on E. coli. The system consists of two kits. OriCiro Assembly Kit allows seamless assembly of multiple overlapping DNA fragments. The assembly product can be added directly to OriCiro Amp Kit to get selective amplification of your target circular DNA (Figure 1). The amplified product is supercoiled DNA topologically identical to plasmid DNA isolated from E. coli. 1. OriCiro Assembly Kit: Multiple DNA fragments are assembled seamlessly at 42 ̊C for 30 minutes via ~40 bp overlapping ends (Figure 2). DNA fragments generated by PCR or restriction enzyme digestion are available. Our unique enzyme-based annealing mechanism allows powerful assembly up to 50 fragments simultaneously. 2. OriCiro Amp Kit: The reaction consists of 26 purified enzymes involved in chromosome replication of E. coli. The chromosome replication cycle repeats autonomously at around 30 ̊C, enabling exponential amplification of circular DNA having oriC with extremely high fidelity (10-8 error/base/cycle) (Figure 3). The kit yields up to 1 μg circular DNA per 10 μL reaction at 33 ̊C for 6 hr. The maximum amplification size is 50 kb in the current version of the kit. n.b. OriCiro Amp NEEDS oriC Cassette (0.4 kb) which can be inserted into circular DNA using OriCiro assembly kit. References: 1. T. Mukai, T. Yoneji, K. Yamada, H. Fujita, S. Nara, M. Su'etsugu, Overcoming the Challenges of Megabase-Sized Plasmid Construction in Escherichia coli, ACS Synthetic Biology, 2020, 9 (6), 1315- 1327 2. T. Hasebe, K. Narita, S. Hidaka, M. Su'etsugu, Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction. Life, 2018, 8 (43) 3. M. Su’etsugu, H. Takada, T. Katayama, H. Tsujimoto, Exponential propagation of large circular DNA by reconstitution of a chromosome-replication cycle, Nucleic Acids Research, 2017, 45 (20), 11525– 11534

Coyote and fox: microbiomes tell the tale

Because of their range expansion across North America, coyotes (Canis latrans) now occur sympatrically with numerous other predator species, including red foxes (Vulpes vulpes). This raises several interesting ecological questions, including if and how sympatry affects the diet and gut microbiomes of coyotes and red foxes. We examined the gut microbiomes of sympatric populations of coyotes and red foxes within two different National Parks in Virginia, USA, that differ in land use, vegetation, and anthropogenic disturbance: Prince William Forest Park (PRWI) and Manassas National Battlefield Park (MANA). From 2012 to 2017, scat samples from PRWI and MANA were collected and analyzed. Polymerase Chain Reaction (PCR) amplification of a region of the mitochondrial cytochrome-b gene followed by restriction enzyme digestion of the PCR product was used to determine the origin of each scat sample. Next-Generation DNA sequencing of a hypervariable 16S rRNA gene region was used to determine gut microbiome information about the scat samples. There was no evidence for a difference between the gut microbiomes of red foxes in either location, or for a difference between the gut microbiomes of red foxes at either location and coyotes at the location with lower human disturbance, PRWI. However, the gut microbiomes of coyotes at the location with higher anthropogenic disturbances, MANA, revealed a marked change from those found in red foxes at either location and from those in coyotes at the location with lower disturbances. The gut microbiomes of coyotes subjected to greater human impact revealed clear evidence of dysbiosis, indicative of increased physiological stress and reduced health. We discuss our observations in the context of understanding anthropogenic impacts on coyote and red fox interactions. Our results suggest that physiological stress in the form of human disturbance may play an important role in the composition of the gut microbiome of coyotes, which can affect their overall health.

Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure

A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence. All these methods are based on the long sequence of basic steps of treating cells, nuclei, chromatin, and finally DNA, thus representing a significant technical challenge. Here, we present an in-depth study of the basic steps in the chromatin conformation capture procedure (3С), which was performed using Drosophila Schneider 2 cells as a model. We investigated the steps of cell lysis, nuclei washing, nucleoplasm extraction, chromatin treatment with SDS/Triton X-100, restriction enzyme digestion, chromatin ligation, reversion of cross-links, DNA extraction, treatment of a 3C library with RNases, and purification of the 3C library. Several options were studied, and optimal conditions were found. Our work contributes to the understanding of the 3C basic steps and provides a useful guide to the 3C procedure.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Molecular techniques for the assessment of Cr (VI) reduction by Bacillus thuringiensis

Effluent pollution with Cr (VI) is a worldwide environmental problem. In the Pasto River (southeastern, Colombia), previous studies reported contamination with this metal at points near tanneries. To establish the role of Bacillus thuringiensis in Cr (VI) reduction in water from Pasto River, experiments were carried out with untreated Pasto River water (treatment 1), sterile Pasto River water inoculated with B. thuringiensis (treatment 2), and unsterilized Pasto River water inoculated with B. thuringiensis (treatment 3). All experiments were conducted in bioreactors with a controlled temperature of 20 °C and constant agitation for 156 h. Samples of 20 mL were taken every 12 h from each treatment to track Cr (VI) reduction levels and to confirm microorganism identity via molecular methods involving denaturing gradient gel electrophoresis (DGGE), restriction enzyme digestion profiles (RFLP), and bioinformatic analysis. Cr (VI) reduction was higher in treatment 3 (99:42 %) as opposed to treatment 2 (76:12 %) and treatment 1 (74:46 %). The molecular identity of B. thuringiensis was determined via sequencing of the 16SrRNA gene, and RFLP assessments in all three treatments revealed B. thuringiensis profiles. Since B. thuringiensis was present in all three treatments trough time, Cr (VI) reduction can be attributed to this bacterium.

Directed Recovery and Molecular Characterization of Antibiotic Resistance Plasmids from Cheese Bacteria

Resistance to antimicrobials is a growing problem of worldwide concern. Plasmids are thought to be major drivers of antibiotic resistance spread. The present work reports a simple way to recover replicative plasmids conferring antibiotic resistance from the bacteria in cheese. Purified plasmid DNA from colonies grown in the presence of tetracycline and erythromycin was introduced into plasmid-free strains of Lactococcus lactis, Lactiplantibacillus plantarum and Lacticaseibacillus casei. Following antibiotic selection, the plasmids from resistant transformants were isolated, analyzed by restriction enzyme digestion, and sequenced. Seven patterns were obtained for the tetracycline-resistant colonies, five from L. lactis, and one each from the lactobacilli strains, as well as a single digestion profile for the erythromycin-resistant transformants obtained in L. lactis. Sequence analysis respectively identified tet(S) and ermB in the tetracycline- and erythromycin-resistance plasmids from L. lactis. No dedicated resistance genes were detected in plasmids conferring tetracycline resistance to L. casei and L. plantarum. The present results highlight the usefulness of the proposed methodology for isolating functional plasmids that confer antibiotic resistance to LAB species, widen our knowledge of antibiotic resistance in the bacteria that inhabit cheese, and emphasize the leading role of plasmids in the spread of resistance genes via the food chain.

Molecular Cloning of Selected Regions of Catalytic Domain of CtsK Gene in Escherichia coli – A Feasibility Study

Cathepsin K (CatK), encoded by CtsK gene in human, is involved in bone remodeling through ossification. The objective of the work conducted here was to express catalytic domains of CtsK gene in bacterial expression system as an initial step, facilitating recombinant production of human CatK for downstream applications in pharmacology. Four healthy human blood samples were collected. Genomic DNA was extracted using FlexiGene® whole blood DNA extraction kit. Upon quantification of DNA through NanodropTM spectrophotometer, sufficient quantity and quality was observed. CtsK gene was amplified by Polymerase Chain Reaction (PCR) using two pairs of primers tagged with restriction endonuclease sites of Sal1 and HindIII facilitating molecular cloning and visualized by Agarose Gel Electrophoresis (AGE). Two different bands of size 545bp and 265bp were observed. The bands were dissected and gel purified using GenaxxonTM gel purification kit and sequentially double digested by restriction enzymes; SalI and HindIII. Vector PBS was also subjected to sequential double digestion using same enzymes and visualized via AGE. Double digested insert of size 265bp and vector were ligated using T4 DNA Ligase (all enzymes from PromegaTM). On another trail, ligation of the PCR product with band size 265bp to pGEM-TTM easy vector system (from PromegaTM) was also done and transformed to Top10 Escherichia coli competent cells for expression separately. Cells were grown in LB media in presence of XGAL, IPTG and Ampicillin and transformed cells were screened. In the restriction enzyme digestion and ligation setup, since the insert and vector were both double digested, it is confirmed that white colonies obtained were Escherichia coli cells were transformed with the desired recombinant vector and is therefore confirmatory. In the case of pGEM-TTM ligation, a colony PCR was done using the white colonies obtained and product size was confirmed via AGE. In conclusion, the objective of study was successfully achieved, by expressing a catalytic domain of CtsK. Developments and improvements could be made for expression of entire CatK gene and downstream production of the Cathepsin K protein for effective therapeutic purpose.

DArTseq-Based High-Throughput SilicoDArT and SNP Markers Applied for Association Mapping of Genes Related to Maize Morphology

Today, agricultural productivity is essential to meet the needs of a growing population, and is also a key tool in coping with climate change. Innovative plant breeding technologies such as molecular markers, phenotyping, genotyping, the CRISPR/Cas method and next-generation sequencing can help agriculture meet the challenges of the 21st century more effectively. Therefore, the aim of the research was to identify single-nucleotide polymorphisms (SNPs) and SilicoDArT markers related to select morphological features determining the yield in maize. The plant material consisted of ninety-four inbred lines of maize of various origins. These lines were phenotyped under field conditions. A total of 14 morphological features was analyzed. The DArTseq method was chosen for genotyping because this technique reduces the complexity of the genome by restriction enzyme digestion. Subsequently, short fragment sequencing was used. The choice of a combination of restrictases allowed the isolation of highly informative low copy fragments of the genome. Thanks to this method, 90% of the obtained DArTseq markers are complementary to the unique sequences of the genome. All the observed features were normally distributed. Analysis of variance indicated that the main effect of lines was statistically significant (p < 0.001) for all 14 traits of study. Thanks to the DArTseq analysis with the use of next-generation sequencing (NGS) in the studied plant material, it was possible to identify 49,911 polymorphisms, of which 33,452 are SilicoDArT markers and the remaining 16,459 are SNP markers. Among those mentioned, two markers associated with four analyzed traits deserved special attention: SNP (4578734) and SilicoDArT (4778900). SNP marker 4578734 was associated with the following features: anthocyanin coloration of cob glumes, number of days from sowing to anthesis, number of days from sowing to silk emergence and anthocyanin coloration of internodes. SilicoDArT marker 4778900 was associated with the following features: number of days from sowing to anthesis, number of days from sowing to silk emergence, tassel: angle between the axis and lateral branches and plant height. Sequences with a length of 71 bp were used for physical mapping. The BLAST and EnsemblPlants databases were searched against the maize genome to identify the positions of both markers. Marker 4578734 was localized on chromosome 7, the closest gene was Zm00001d022467, approximately 55 Kb apart, encoding anthocyanidin 3-O-glucosyltransferase. Marker 4778900 was located on chromosome 7, at a distance of 45 Kb from the gene Zm00001d045261 encoding starch synthase I. The latter observation indicated that these flanking SilicoDArT and SNP markers were not in a state of linkage disequilibrium.

Characterization of the Luteinizing Hormone Beta (LH-β) Subunit Gene in the Goat

Background: Luteinizing hormone (LH) plays a critical role in ovulation and maintenance of pregnancy in female and gamete production in male during fertile phase of life. Physiological disturbance of this hormone leads to conditions like delayed ovulation, anovulation, cystic ovarian disease and lack of sexual desire in male. Since, there had been no report of molecular characterization of β-subunit of luteinizing hormone (LH) of Indian goat, the present study aimed to clone and characterize genomic DNA encoding LHβ subunit.Methods: Genomic DNA was extracted from goat blood and amplified using specific LHβ gene primers. After cloning and transformation, plasmids were isolated from randomly selected white colonies. Presence of insert was confirmed by restriction enzyme digestion of plasmids. After confirmation by PCR, plasmids were sent for DNA sequencing. Result: Analysis of sequence revealed an insert of 1006 bp size as expected. Comparison of nucleotide sequence revealed the cloned gene to be is LHβ encoding 141 amino acids. It showed 97.3 and 91.7% similarity with sheep and cattle respectively. Inferred amino acid sequence showed absolute similarity (100%) with sheep and buffalo. The common and essential features such as twelve cysteine molecules, a single potential N-glycosylation site, the CAGY region and another tetrapeptide CGPC are all found in the goat sequence too.