Phthalic acid isomers are the monomers of phthalate molecules, also known as phthalic acid esters, widely employed in the plastics industry. This study aims to investigate the biodegradation of phthalic acid (PA) and terephthalic acid (TPA) by five industry-borne Comamonas testosteroni strains: 3APTOL, 3ABBK, 2B, 3A1, and C8. To assess the ability of C. testosteroni strains to biodegrade phthalic acid isomers in fermentation media, an analytical method was employed, consisting of high-performance liquid chromatography (HPLC) analyses. Subsequently, molecular screening of the genomic and plasmid DNA was conducted to identify the degradative genes responsible for the breakdown of these chemicals. The genes of interest, including ophA2, tphA2, tphA3, pmdA, and pmdB, were screened by real-time PCR. The five C. testosteroni strains effectively degraded 100% of 100 mg/L PA (p = 0.033) and TPA (p = 0.0114). Molecular analyses indicated that all C. testosteroni strains contained the pertinent genes at different levels within their genomes and plasmids, as reflected in the threshold cycle (Ct) values. Additionally, DNA temperature of melting (Tm) analyses uncovered minor differences between groups of genes in genomic and plasmid DNA. C. testosteroni strains could be excellent candidates for the removal of phthalic acid isomers from environmental systems.

BACKGROUND: Eukaryotes\' whole-genome sequencing is crucial for species identification, gene detection, and protein annotation. Oxford Nanopore Technology (ONT) is an affordable and rapid platform for sequencing eukaryotes; however, the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryote genome completeness, gene detection and protein annotation.
METHODS: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively.
RESULTS: Genome completeness was dependent on the assembly method rather than on the read correction tool; however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation.
CONCLUSIONS: We show that three rounds of read correction significantly affect gene detection and protein annotation, which are dependent on assembly quality in preference to assembly completeness.

Incontinentia pigmenti (IP), an X-chromosome dominant genodermatosis caused by mutations in the IKBKG/NEMO gene, is a rare disease affecting the skin, teeth, eyes, and central nervous system. Here, we report two pedigrees of IP and detection of two novel mutations in the IKBKG gene associated with IP via genetic analysis. In addition, different gene mutation types can present with different clinical phenotypes, and the same gene mutation type can show different clinical phenotypes. This study provides clinical cases for further study of the genotype and phenotype of IP and enriches the mutation spectrum of IKBKG gene, which provides a basis for genetic counseling and genetic diagnosis of IP in the future.

Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. This work presents a method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A novel gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. Validation experiments using a sewage sample spiked with two known viruses demonstrate the method\'s efficacy. We achieve 100% recovery of the spiked-in SV40 (Simian virus 40, 5243bp) genome sequence with uniform coverage distribution, and approximately 99.4% for the larger HAd5 genome (Human Adenovirus 5, 35938bp). Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables targeted characterizations of rare viral species and whole-genome amplification of single genomes for accessing the mutational profile in single virus genomes, contributing to an improved understanding of viral ecology.

A surface-enhanced Raman scattering (SERS) strategy combined with a CRISPR/Cas12a system is designed for the amplification-free gene detection of African swine fever virus (ASFV). A SERS sensing probe was fabricated by conjugating plasmonic SERS tags on the magnetic bead (MB) surface with an single-stranded DNA (ssDNA) as a linker. The target ASFV gene-activated Cas12a protein starts the trans-cleavage function on the linker ssDNA, which causes the release of SERS tags, leading to a decrease of the SERS signal detected above the collective MBs. Two signal enhancement strategies were adopted to improve the liquid-phase detection sensitivity arriving at the fM level. One is the unlimited trans-cleavage function of the Cas12a protein, and the other is the magnetic-induced collection of probes that can significantly gather the analytes from the solution to the laser spot and provide SERS hotspots during SERS measurement. Detection range is from 100 nM to 10 fM without the gene amplification steps. This sensing method achieved the SERS detection of ASFV gene in the serum system and the extracted nucleic acids in viral samples with high sensitivity and selectivity at a relative standard deviation of <8%. This sensing platform is mainly in use for site inspection and quick testing of gene samples.

Craniofacial dysmorphism, cardiac abnormalities, ectodermal abnormalities, psychomotor delay, intellectual disability, and short stature are all hallmarks of the extremely rare disorder known as cardiofaciocutaneous syndrome (CFCS). Although CFCS is considered rare, approximately 300 cases have been documented in the literature. In this report, we discuss a patient diagnosed with CFCS without the typical heart malformations but with craniofacial features, skin abnormalities, intellectual disability, and short stature. Genetic testing revealed the presence of three potentially harmful variants: one in the MAP2K1 gene and two in the ATP2B3 and CDC42BPB genes, the significance of which is currently not yet found. Our findings in this case report suggest that the clinical symptoms of CFCS may be atypical, thereby expanding our understanding of the symptom spectrum of the disease. Simultaneously, the link between the clinical symptoms of the patient and the two unknown pathogenic variants has not been established. This case report supplements existing clinical reference material by providing valuable insights into the specific scenario.

UNASSIGNED: The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins.
UNASSIGNED: This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance.
UNASSIGNED: Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed.
UNASSIGNED: The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA.
UNASSIGNED: The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.

Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.

UNASSIGNED: Hyperbilirubinemia is a common disorder in neonates, with premature infants at higher risk of developing the disorder.
UNASSIGNED: Glucose-6-phosphate dehydrogenase (G6PD) gene detection was used to determine the incidence of G6PD deficiency and analyze the etiologies of G6PD deficiency in neonates with hyperbilirubinemia in the Zunyi region with the aim of providing scientific evidence for the clinical diagnosis and treatment.
UNASSIGNED: For the gene detection, 64 neonates with hyperbilirubinemia were selected as the observation group and 30 normal neonates were selected as the control group, and the risk factors for hyperbilirubinemia were investigated by using multivariate logistic regression analysis.
UNASSIGNED: Among the neonates in the observation group, 59 cases had the G1388A mutation (92.19%) and 5 cases had the G1376T mutation (7.81%). No mutation was detected in the control group. In the observation group, the proportion of neonates who were born prematurely, with artificial feeding, with the age of starting feeding of more than 24 h, the time of first bowel movement of more than 24 h, premature rupture of membranes, infection, scalp hematoma, and perinatal asphyxia was higher than that in the control group, and the difference was statistically significant (p< 0.05). Multivariate logistic regression analysis showed that prematurity, infection, scalp hematoma, perinatal asphyxia, the age of starting feeding of more than 24 h, and the time of first bowel movement over 24 h were risk factors for the development of neonatal hyperbilirubinemia (p< 0.05).
UNASSIGNED: The G1338A and G1376T mutations were important features of the genetics of neonatal hyperbilirubinemia, and genetic detection together with the prevention of prematurity, infection, scalp hematoma, perinatal asphyxia, the age of starting feeding, and the time of first bowel movement would help reduce the incidence of this disease.

Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease caused by abnormal lipoprotein metabolism. Patients with FH have a significantly increased risk of coronary artery disease (CAD) due to long-term exposure to high levels of low-density lipoprotein (LDL). The diagnosis of FH relies heavily on gene detection, and examination of LDL receptor (LDLR) function is of great significance in its treatment. This review summarizes the current advances in the screening, diagnosis, and treatment of FH and functional analysis of LDLR gene mutations.