Search Results (153)

Hemp hurds (HHs), an underutilised lignocellulosic biomass (LB) from agricultural waste, offer potential for bioconversion into high-value bioproducts within a circular bioeconomy. Building on prior work involving magnetic nanoparticle-immobilised cellulase hydrolysis of pretreated HH, this study computationally designed candidate phaCAB expression constructs for cellulolytic hosts toward future polyhdroxybutyrate (PHB) production. The objective was to evaluate, in silico, the feasibility of introducing the phaC1, phaA and phaB1 genes from Cupriavidus necator H16 (C. necator) (assembly GCA_000009285.2; loci H16_A1437–H16_A1439) into the cellulolytic hosts Clostridium thermocellum DSM 1313 (C. thermocellum) and Trichoderma reesei RUT C-30 (T. reesei). Coding sequences were retrieved and translated individually and host-specific expression compatibility was assessed via codon adaptation index, effective number of codons, GC content and rare-codon frequency/clustering. Host-specific architectures were designed: three independent tef1-promoter cassettes with fungal Kozak contexts and cbh1 terminators for T. reesei (TrePHB3 integration construct), and a single groEL-promoter operon with graded ribosome-binding sites for the pIKM1-based C. thermocellum construct (pCtPHB1); Escherichia coli BL21 (DE3) (E. coli)/pET-24a(+) served only as an intermediate assembly platform. Clustal Omega alignment, virtual plasmid assembly and simulated restriction digestion (SnapGene) confirmed preservation of the open reading frames and expected fragment sizes. ProtParam analysis indicated instability indices below 40 and negative GRAVY values for PhaC, PhaA and PhaB, indicating overall hydrophilic character. This computational framework links HH valorisation, cellulolytic Consolidated Bioprocessing (CBP) hosts and PHB pathway design within a conceptual biorefinery, supporting future integrated biomass-valorisation platforms; it is computational only and does not demonstrate transformation, expression, PHB accumulation or biomass conversion, which require experimental validation. Full article

Background: DNA Ligase 4 (LIG4) catalyzes the final ligation step during V(D)J recombination. Biallelic pathogenic variants in LIG4 cause severe combined immunodeficiency (SCID), a life-threatening immunodeficiency characterized by the lack of mature T and B cells. Case Presentation: An 18-year-old male exhibited widespread verrucous and keratotic cutaneous lesions across the face, neck, and extremities. The proband manifested early-onset short stature, chronic malnutrition, recurrent pulmonary infections with bronchiectasis, chronic diarrhea, and bilateral tenosynovitis. Immunophenotyping revealed persistent panhypogammaglobulinemia, absent B cells, reduced T and natural killer (NK) cells, and nearly undetectable naïve T cells. Both α-HPV and β-HPV were detected in the cutaneous lesions. Compound heterozygous LIG4 variants (hg19, NM206937.2, c.833G > T; p.Arg278Leu inherited from the mother; c.833G > A; p.Arg278 His inherited from the father) were identified. Conclusions: This study reports a proband with LIG4 syndrome presenting with rare phenotypes of multiple viral warts and combined lymphopenia of T, B, and NK cells. This proband harbors compound heterozygous variants at the same codon (c.833G), which not only confirm the clinical diagnosis but also enrich the known phenotypic spectrum of LIG4 syndrome. Full article

Background: Laterality defects are rare congenital malformations that encompass congenital heart defects (CHDs) together with abnormalities of visceral organ arrangement (situs inversus or situs ambiguous). These defects may be isolated or part of a syndromic presentation with multisystem involvement. While over 50 genes have been implicated in laterality disorders, across multiple modes of inheritance, many cases remain molecularly undiagnosed. We sought to elucidate the molecular basis of dextrocardia, CHDs and visceral heterotaxy in two unrelated individuals of Arab-Muslim descent. Methods: Detailed clinical phenotyping and exome sequencing (ES) were performed for each of the probands, followed by familial segregation analysis. Results: ES revealed a shared homozygous variant in the Dan Domain Family Member 5 (DAND5) gene (NM_152654.3): c.396_397dup, p.(Tyr133SerfsTer11). DAND5 encodes a member of the Cerberus-related DAN protein family, which is involved in the establishment of left body asymmetry. This frameshift variant introduces a premature stop codon within the final exon, which is predicted to escape nonsense-mediated decay (NMD), resulting in a truncated protein lacking the functional DAN domain. Conclusions: DAND5 has recently been suggested as a candidate gene in heterotaxy and CHDs. Our findings further support biallelic loss of function variants in DAND5 autosomal recessive laterality defects. Full article

Brunner syndrome is a rare X-linked neurodevelopmental disorder caused by loss-of-function (LOF) variants in the monoamine oxidase A gene (MAOA), which encodes monoamine oxidase A, a key enzyme involved in the degradation of monoamine neurotransmitters such as serotonin, norepinephrine, and epinephrine. Impaired MAOA activity leads to abnormal monoamine accumulation and disruption of monoaminergic signalling, resulting in intellectual disability and behavioural dysregulation. Here, we systematically summarize the molecular landscape and report a genotype-driven diagnosis of MAOA deficiency in a patient presenting with intellectual disability and no reported family history. Clinical exome sequencing (cES) identified a novel splice-site variant in the MAOA gene that had not been detected by first-line diagnostic approaches. Functional analysis of patient-derived mRNA demonstrated intron 8 retention leading to a premature stop codon, consistent with a LOF mechanism. Based on the molecular diagnosis, the patient received treatment with serotonin antagonist and reuptake inhibitor (SARI) class medication, which was associated with improvement in social behaviour and sleep disturbances. Notably, to the best of our knowledge, this represents the first reported use of SARI therapy in MAOA deficiency. Although SARI therapy in this condition remains off-label, this observation provides preliminary evidence suggesting a potential therapeutic benefit. Our findings expand the mutational spectrum of the MAOA gene and highlight the importance of molecular diagnosis driving personalized management in rare neurogenetic disorders. Full article

The importation of hepatitis B virus (HBV) variants through migration challenges elimination efforts in low-endemicity countries. This study evaluated the seroprevalence, occult hepatitis B infection (OBI), and molecular signatures of HBV among 537 international migrants from 46 countries who arrived in St. Petersburg, Russia. HBsAg, anti-HBs, and anti-HBc were measured by ELISA. This was followed by nested real-time PCR targeting viral genes (S, X) and a human housekeeping gene (HPRT, internal control), amplification of overlapping fragments covering the complete HBV genome, and Sanger sequencing. HBsAg prevalence was 2.61% (95% CI: 1.43–4.34), while anti-HBc was detected in 16.39% (95% CI: 13.36–19.79). HBV DNA was found in 8.19% (44/537; 95% CI: 6.02–10.04) of migrants. Notably, OBI (HBsAg-negative/HBV DNA-positive) was identified in 33 individuals, yielding a prevalence of 6.15% (33/537; 95% CI: 4.27–8.52) in the entire cohort and 6.31% among HBsAg-negative subjects. The findings among OBI cases were as follows: the majority (54.5%) had no detectable anti-HBc or anti-HBs; 30.3% were positive for anti-HBs only; 6.06% were positive for anti-HBc IgG only; 9.09% of cases featured both anti-HBc and anti-HBs. Viral loads in OBI cases were uniformly low (14–53 IU/mL). Genotype D predominated (86.36%, 38/44). The distribution of subgenotypes among all sequenced isolates was as follows: D1 in 36.36% (16/44), D2 in 36.36% (16/44), D3 in 13.64% (6/44), while genotypes A2 (6.82%, 3/44), B4 (4.55%, 2/44), and C2 (2.27%, 1/44) were rare. In the major hydrophilic region (MHR), the most frequent amino acid substitutions were at positions T127P/I (61.4%) and T118R/M/V/A (45.5%). Immune escape mutations were significantly associated with OBI (81.82% of OBI cases versus 18.18% of HBsAg-positive cases; p = 0.003). Drug resistance mutations (L180M + M204V ± T184A) were detected in 11.4% of isolates (all genotype D2). In the precore region, stop codon mutation W28* was found in 31.82% of samples, and the A1762T/G1764A double substitution in the basal core promoter occurred in 25.0%. The high prevalence of OBI, coupled with the accumulation of escape and drug resistance mutations in imported HBV variants, highlights the urgent need to include molecular HBV screening in mandatory medical examinations for arriving migrants to prevent undetected transmission and inform clinical management in receiving countries. Full article

Adenoviral vectors are widely used for gene therapy and vaccine development. To circumvent pre-existing immunity against commonly used human adenovirus type 5, vectors based on rare human serotype or animal adenoviruses have attracted increasing interest. Previously, we constructed vectors based on fowl adenovirus 4 (FAdV-4) and replaced the knob of FAdV-4 fiber2 with that of FAdV-1 fiber1 to generate FAdV4-CF1K vectors with enhanced transduction efficiency in human cells. In this study, we aimed to modify the packaging system to efficiently produce FAdV-4 vectors carrying transgenes toxic to viral replication. Chicken LMH cells failed to form colonies at low seeding densities. We collected used medium from LMH cell cultures and used it as a supplement to adapt LMH cells, generating the colony-competent subclone LMH-C3532. A lentiviral vector encoding a codon-optimized tetracycline repressor (tetR) was transduced into LMH-C3532 to establish a tetR-integrated cell line, LMH-tetR24. An adenoviral plasmid, pKFAV4-CF1K-CtG, was constructed in which a tetracycline operator (tetO)-bearing CMV promoter controlled GFP expression. The SwaI-flanked GFP in this plasmid was replaced with the HA gene from an H5N1 influenza virus to generate pKFAV4-CF1K-CtHA. Linearized adenoviral plasmids were transfected into LMH-tetR24 cells, and recombinant FAdV4-CF1K-CtG and FAdV4-CF1K-CtHA viruses were successfully rescued, amplified, and purified. When infected with FAdV4-CF1K-CtG at various multiplicities of infection (MOI), the progeny virus yield from LMH-tetR24 cells was 4–10 times higher than that from LMH-C3532 cells. For FAdV4-CF1K-CtHA, the yield difference between the two cell lines was even more pronounced, reaching 3–4 orders of magnitude. Overexpression of HA in LMH-C3532 cells negatively affected FAdV4-CF1K-CtHA replication, resulting in smaller and fewer plaques. In conclusion, by separately integrating tetR into packaging cells and TetO into the adenoviral plasmid, we established a system that can be routinely used to package FAdV-4 vectors. Notably, this system facilitates the propagation of FAdV-4 vectors carrying toxic transgenes. Full article

Background/Objectives: Autophagy is a highly conserved eukaryotic cellular process whose dysfunction results in human pathologies including cancer and neurodegenerative disease. First identified in yeast, ATG genes are central players in autophagy. Mutations in core autophagy genes ATG5 and ATG7 have been previously reported to cause rare genetic disorders with autosomal recessive inheritance. Methods: Here we report, for the first time, variants in human ATG9B gene as causative factors for a rare neurodevelopmental disease with autosomal recessive inheritance. Three distinct mutations were detected in three independent families with consanguinity, five patients affected in total. Results: The first variant is an 11-nucleotide deletion resulting in a frameshift. A premature stop codon is added and the C-terminal cytosolic domain of ATG9B protein is truncated. The second one is a point mutation that changes a critical amino acid in the transmembrane domain. The third variant is a 2-nucleotide deletion causing a different truncation product. Patients presented with diverse neurodevelopmental anomalies including intellectual disability, behavioral abnormalities, congenital cerebellar ataxia, mild cerebellar atrophy, and microcephaly. Since human ATG9B is expressed specifically in the placenta, we hypothesized that the disease pathology originates during placental development. To characterize the effects of the first frameshift mutation and gain insight into the specific functions of ATG9B in a physiological setting, we used mammalian cells and a knock-in mouse model. Truncated ATG9B was not stable when expressed in cells. It was localized to perinuclear vesicles like the WT protein, but not to peripheral vesicles. Homozygous knock-in mice were viable, fertile, and displayed no gross phenotypical abnormalities. Histomorphometry analysis of the placenta layers did not reveal a significant difference between mutant and control embryos. The assessments of neurobehavioral tests were similar in wild-type and homozygous knock-in mice. However, knock-in mice had a reduced fear memory trend, which is an amygdala-involved response. Conclusions: In this study, we describe a new rare disease linked to ATG9, including cerebellar ataxia and atrophy, as described for ATG5 and ATG7. Full article

Background: The litchi fruit borer, Conopomorpha sinensis (Lepidoptera: Gracillariidae), is a devastating pest affecting litchi and longan production across Asia. Although a reference mitochondrial genome (mitogenome) has been published, its utility is limited by the lack of precise geographical data and raw sequencing data. Methods: In this study, we sequenced and characterized the complete mitogenome of C. sinensis collected from Taiwan using a hybrid assembly of Illumina and Oxford Nanopore technologies. Results: The assembled mitogenome is 17,301 bp in length with a mean sequencing depth of 19,155-fold, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an AT-rich control region. Notably, we identified a rare tRNA gene rearrangement (trnR-trnA-trnN-trnS1-trnE-trnF) that deviates from the ancestral lepidopteran ditrysian pattern. Comparative analysis revealed a 94.65% overall sequence identity with the reference mitogenome, though the PCGs remained highly conserved at 99.35%. Variant analysis demonstrated that this divergence is predominantly driven by structural variations (228 indels) rather than nucleotide substitutions (2 SNPs) across the entire mitogenome; furthermore, 94.7% of the indels were identified in the control region and intergenic spacers. Subtle differences in codon usage were also observed in the ND6 start codon (ATT vs. ATA) and COX1 stop codon (TAA vs. T). Phylogenetic and molecular clock analyses robustly clustered the Taiwan specimen within the C. sinensis clade. Molecular dating estimates that the Conopomorpha lineage originated during the Late Cretaceous (~77.23 Ma). Notably, the divergence between the Taiwan specimen and the reference lineage was estimated to be negligible (<0.01 Ma) within the protein-coding regions, demonstrating a high degree of purifying selection that maintains coding-sequence stability across geographically distinct specimens, even as substantial variation accumulates in non-coding genomic regions. Conclusions: These findings provide high-resolution genomic resources and a temporal framework for the evolutionary study of Gracillariidae, offering foundational tools for targeted pest management. Full article

The genus Desmidorchis Ehrenb. (Apocynaceae) is a characteristic component of the succulent flora of the Arabian Peninsula, where high levels of endemism and increasing environmental pressures highlight the need for integrated genomic and conservation research. This study assessed the conservation status of three ethnomedicinally important endemics—D. adenensis, D. arabica, and D. awdeliana—and characterizes their complete plastomes to resolve their evolutionary and temporal history. Conservation assessments were conducted following IUCN Red List criteria, and complete plastomes were sequenced and compared within a dataset of 15 subtribe Stapeliinae taxa. Comparative analyses examined the genome structure, divergence hotspots, repetitive sequences, codon usage bias, and selection pressure, while divergence times were estimated using fossil-calibrated molecular clock analyses. All three species were classified as Near Threatened (NT), primarily due to anthropogenic and environmental pressures. Plastome analyses revealed a highly conserved genome structure; however, hypervariable regions, particularly ycf1 and clpP1, exhibited elevated sequence divergence and phylogenetic informativeness. Simple sequence repeats (SSRs) were also identified as potentially informative features at the genus level. Codon usage and Ka/Ks analyses further indicated that most plastid protein-coding genes are under strong purifying selection, whereas only a few loci, particularly clpP1, showed comparatively elevated evolutionary rates. Phylogenomic analyses supported the monophyly of Desmidorchis, with molecular dating indicating recent Pleistocene diversification (~0.34–1.51 Ma), potentially associated with Quaternary climatic oscillations. Overall, this study provides an important genomic foundation for future taxonomic, evolutionary, and conservation studies of rare Arabian taxa. Full article

Cutaneous lichen amyloidosis (CLA) is a rare dermatological condition characterized by amyloid deposition in the skin, presenting as pruritic, hyperkeratotic papules. Although most cases are sporadic, CLA has been associated with multiple endocrine neoplasia type 2A (MEN2A), a hereditary syndrome caused by germline alterations in the RET proto-oncogene. In MEN2A, CLA is typically localized to the interscapular region and linked to RET codon 634 variants, whereas generalized forms are rare. We report a male patient with MEN2A and a generalized form of CLA that preceded the diagnosis of primary hyperparathyroidism (PHPT) and medullary thyroid carcinoma (MTC). Genetic testing using Sanger sequencing identified an ultra-rare heterozygous RET variant, p.Y806C, in exon 14, currently classified as a variant of uncertain significance (VUS). This variant has not been previously described in association with MEN2A. This case may contribute to understanding genotype–phenotype correlations in MEN2A and suggests that atypical or generalized CLA may be an early clinical clue warranting consideration of RET genetic testing. Full article

Gephyrocharax atracaudatus is a rare freshwater fish in Panama. This study provides a comprehensive analysis of the mitochondrial genome of G. atracaudatus, highlighting its gene composition, codon usage, evolutionary pressures, and phylogenetic relationships. The findings reveal unique evolutionary patterns and divergence times of G. atracaudatus that enhance the understanding of the genetic diversity within Characiformes. The increasing availability of genomic data has prompted taxonomic revisions for numerous Characiformes species, encompassing corrections to species names, subfamily, and family classifications. This study reconfirmed the classification of G. atracaudatus as “Gephyrocharax, Stevardiinae, Stevardiidae, Characiformes”. A cross-analysis model for species differentiation and tracking was established using divergence time comparison and phylogenetic analysis. The results show that G. atracaudatus, Hyphessobrycon roseus and Pristella maxillaris converge on one branch, indicating that the genetic relationship may be the most similar, and it occurred approximately 90.45 Mya in the Cretaceous. This study establishes a robust model framework for understanding the evolution of G. atracaudatus, and correctly determines the biological classification status of G. atracaudatus, providing basic data support for clarifying the evolution mode of Characiformes. Full article

EBV genomic variation has been shown to contribute to the development of certain EBV-associated cancers. While EBV genomic variation has been extensively studied at the nucleotide level, it remains unclear how synonymous codon usage contributes to viral adaptation across epithelial cancer contexts. Here, we analyzed 1148 EBV genomes with annotated tumor origins to investigate genome-wide genetic differentiation and codon usage patterns of 13 core genes across NPC- and GC-associated viruses and EBV types. SNP-based analyses revealed partial genetic separation between NPC-EBV and GC-EBV, characterized by both rare GC-associated risk variants and common protective haplotypes. Codon usage patterns, however, showed strong gene-specific structure: EBNA2 and EBNA3 clustered primarily by EBV type, whereas EBNA1 and LMP2A were more sensitive to tumor background. Codon bias analyses suggested heterogeneous contributions of mutational pressure and natural selection across genes and lineages, whereas lytic BALF genes displayed highly conserved codon usage despite cancer-associated variants. Collectively, this study demonstrates that codon usage patterns of specific EBV genes are associated with tumor background and are jointly shaped by gene function and viral lineage structure. Full article

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus–host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An “intact” ASP ORF (defined as >150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an “intact” ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential. Full article

Carotenoid-based coloration significantly influences the ornamental appeal and market value of aquatic species. This study identifies the genetic basis of yellow body coloration in the large yellow croaker (Larimichthys crocea), a commercially important aquaculture species in China. Through a genome-wide association study (GWAS), we identified a 10 bp deletion (bco1l-Δ10) in the bco1l gene, a critical enzyme in carotenoid metabolism. This deletion, located in exon 10, causes a frameshift mutation and premature stop codon, resulting in loss of the enzymatic function essential for carotenoid cleavage. Sanger sequencing confirmed that all yellow juveniles were homozygous for the deletion, while none of the wild-type juveniles harbored this mutation. Functional assays demonstrated that the recombinant Bco1l-Δ10 protein failed to catalyze β-carotene cleavage, validating the genetic association with the yellow phenotype. The bco1l-Δ10 mutation was detected only in a limited number of juvenile individuals, indicating it is a rare occurrence in the population. Our findings provide a valuable genetic marker for marker-assisted selection (MAS) to enhance yellow pigmentation in aquaculture breeding programs, offering a potential strategy to improve the market value of L. crocea. Full article

Hepatitis B virus (HBV) genotype F is one of the most genetically divergent and evolutionarily ancient HBV lineages and predominantly circulates in indigenous and admixed populations of the Americas. Here, we performed a comprehensive evolutionary and inferred functional characterization of the HBV genotype F via the largest curated dataset of complete genomes. Phylogenomic reconstruction, recombination screening, and phylogenetic network analyses were integrated with codon-based selective pressure inference, surface protein posttranslational modification profiling, mutational analysis of antigenic regions, and reverse transcriptase (RT) drug resistance assessment. The HBV-F subgenotype exhibited a well-resolved phylogenetic structure and limited intragenotypic recombination, while intergenotypic recombination contributed substantially to reticulate evolutionary signals. Selective pressure analyses revealed strong purifying selection in replication-associated domains of the polymerase, in contrast to episodic adaptive evolution in surface-exposed and regulatory proteins, particularly the X protein. N-glycosylation sites in large surface proteins are highly conserved. Some mutations in the major hydrophilic region (MHR) were significantly detected, whereas RT drug resistance mutations were rare and followed canonical lamivudine-associated pathways. Collectively, these findings highlight the balance between deep evolutionary conservation and localized adaptive flexibility in shaping the HBV genotype F and provide a genotype-specific framework for interpreting viral fitness, immune interactions, and antiviral resistance. Full article