Search Results (1,653)

Transposable elements (TEs) are inserted into the genome and may change its properties; those occurring in or near regulatory regions may also alter gene expression. Given the challenges of detecting insertions in short-read sequencing, we analyzed structural variants in polar and brown bear genomes by a reciprocal alignment of one species’ sample genomes to a reference sequence of the other species, thus inferring TE insertion as the other genome’s “deletions”. With this approach, we detected short interspersed elements (SINEs) belonging to the CAN SINE family as dominant fixed TEs. We observed a non-random distribution of CAN SINE insertion positions near both protein- and RNA-coding genes, where TEs often overlap UTRs or occur in their vicinity. In contrast, SINEs avoid coding sequences, suggesting TE insertions that would disrupt such sequences are under purifying selection. We used black bear as an outgroup and determined that most of the CAN SINE insertions in the polar bear genome were derived, since they are not present in black or brown bear, while there is no dominant trend for CAN SINE insertions in brown bear relative to the outgroup. Many of the genes with UTRs affected by CAN SINEs are potentially relevant to the differences between the species (body shape, size, etc.) or to Arctic-adaptation phenotypes such as fur color, metabolism, and the immune system. This supports a model that CAN SINEs have contributed to regulatory evolution in bears and provides further evidence of such events across carnivore genomes in the animal kingdom. Full article

Gaussian networks are degree-four symmetric interconnection networks defined over residue classes of Gaussian integers. Earlier work showed that, when the generator $\alpha =a+bi$ satisfies $gcd(a,b)=1$, the real and imaginary dimensions directly form two edge-disjoint Hamiltonian cycles. A later construction extended the result to the non-coprime case $gcd(a,b)=d>1$, but its proof relied on long node-sequence tables and separate odd/even cases for d. This paper presents a unified closed-form construction that covers both $d=1$ and $d>1$, and both odd and even d, without separate case tables. In the rectangular representation with d rows and $r=(a^2+b^2)/d$ columns, the construction uses a constant-time local switch rule, meaning constant time per individual switch, for each $q=1,2,\dots ,d-1$ at column $a_q=q-1$. Each switch removes two horizontal edges and inserts two vertical edges. The switched horizontal structure forms the first Hamiltonian cycle, while its edge-complement in the Gaussian network forms the second Hamiltonian cycle. Thus, the full edge set is partitioned into two edge-disjoint Hamiltonian cycles. The construction requires $O\left(d\right)$ switch-generation time and $O\left(N\right)$ time to list the two cycles, where $N=a^2+b^2$. Exhaustive validation for all $1\le a\le b\le 100$, excluding only the degenerate $N=2$ network, and large-scale validation up to $N=3,250,000$ confirm implementation correctness and demonstrate practical scalability. Full article

In this paper, we consider the so-called Choulet sequence $a_n$, $n=0,1,2,3,\dots$ For any complex numbers $a_0,a_1,k,l$, it is defined by the formula $a_{n+1}={\sum }_{j=0}^n{a}_j{a}_{n-j}+k(n+1)+l$ for $n=1,2,3,\dots$ We derive the recurrence formula of the form $(n+1)a_n+{\sum }_{j=1}^5(u_j+n{v}_j)a_{n-j}=0$ for $n\ge 5$, where $u_j,v_j$, $j=1,\dots ,5$, are some constants that depend on $a_0,a_1,k,l$, but not on n. In the case when $k=0$, we obtain a shorter recurrence formula $(n+1)a_n+{\sum }_{j=1}^4(u_j+n{v}_j)a_{n-j}=0$ for $n\ge 4$. Both these formulas correspond to the recurrence formulas presented in the OEIS (The On-Line Encyclopedia of Integer Sequences) for many initial vectors $(a_0,a_1,k,l)\in {\mathbb{Z}}^4$. Most of them are listed as conjectures. So here we verify all of them using the same procedure by just inserting the values of $a_0,a_1,k,l$ into the derived formulas. We also show that the Choulet sequence is a linear recurrence sequence if and only if $(k,l)=(-a_1^2,2a_1^2+a_1-2a_0{a}_1)$. Full article

Background/Objectives: Breast cancer (BC) is the most frequently diagnosed malignancy among women worldwide, yet tumor genomic data from Latin American and admixed populations remain limited. This gap affects the interpretation of cancer-associated variants and may limit the representation of these populations in genomic research. This study aimed to characterize the genomic landscape of breast tumors from Ecuadorian women and contextualize variant interpretation through genetic ancestry analysis. Methods: Breast tissue samples from 23 Ecuadorian mestizo women with suspected malignancy were analyzed. After histopathological confirmation, 21 breast tumors were included in the final cohort. Targeted next-generation sequencing was performed using a 94-gene cancer panel. Variants were annotated and classified according to clinical significance. Because matched normal DNA was unavailable, variant allele frequency was used as an exploratory approach to infer putative somatic, putative germline, indeterminate, or putative homozygous germline profiles. Putative germline and indeterminate variants were interpreted using ACMG/AMP criteria, whereas putative somatic variants were evaluated using the AMP/ASCO/CAP framework. Genetic ancestry was inferred using ancestry-informative insertion/deletion markers. Results: Seventy-two unique variants across 40 genes were identified, including 14 pathogenic, 10 likely pathogenic, and 48 variants of uncertain significance. Pathogenic and likely pathogenic alterations were detected in clinically relevant genes, including TP53, BRCA2, PTEN, CDH1, RAD51C, MSH6, NF1, CYLD, and SDHB. Variants of uncertain significance represented 66.7% of all detected variants and affected several cancer-associated and DNA repair genes. The cohort showed a trihybrid ancestry profile, with predominant Native American ancestry, followed by European and African contributions. Conclusions: This study expands BC genomic data from an underrepresented Ecuadorian cohort and highlights the coexistence of clinically relevant alterations with a high burden of variants of uncertain significance. The findings underscore the limitations of tumor-only sequencing and current variant interpretation frameworks in admixed populations. Larger studies integrating matched normal DNA, ancestry-informed analyses, functional validation, and broader sequencing strategies could help improve variant interpretation in Latin American populations. Full article

Background/Objectives: Melophagus ovinus is an economically important ectoparasite of small ruminants with a broad global distribution. Although mitochondrial genomes are widely used in population genetic studies, the D-loop region of M. ovinus remains poorly characterized because its high AT content and repetitive structure complicate amplification, assembly, and sequencing. Methods: We sequenced the mitochondrial genome of M. ovinus collected from Qinghai using an integrative approach combining Illumina paired-end sequencing, targeted PCR amplification, and Nanopore long-read sequencing. Comparative genomic analysis was performed against published mitogenomes from Gansu (MH024396) and Xinjiang (NC_037368). Results: The Qinghai mitochondrial genome contained the typical 37 mitochondrial genes within a 14,728 bp conserved region. Comparative analysis revealed exceptionally high conservation (>99.6% sequence identity) among Qinghai, Gansu, and Xinjiang isolates outside the D-loop region. Notably, the D-loop exhibited length polymorphism, with different assembly strategies or samples yielding lengths ranging from 317 bp to 2385 bp. Targeted long-read sequencing of ten individuals identified a predominant D-loop variant of approximately 844 bp in nine samples and a markedly shorter variant of approximately 164 bp in one sample. The short variant was characterized by extensive deletions and a novel 45 bp insertion. Support for this variant was obtained from independent Illumina DNA-seq, RNA-seq, Nanopore sequencing, and de novo assembly analyses. Conclusions: This study provides preliminary evidence for D-loop structural heterogeneity in M. ovinus, suggesting remarkable length polymorphism and complex indel patterns that require further validation. These findings significantly expand the genomic resources available for this important veterinary parasite and establish a foundation for future population genetic and evolutionary studies. Full article

Hepatocyte nuclear factor 4α (HNF4A) is a critical transcription factor that regulates the differentiation and metabolism of intestinal epithelial cells. However, its role in piglet growth remains unclear. In this study, the tissue expression of HNF4A was examined using RT-qPCR, and the putative functional SNPs were analyzed by integrating bioinformatics and DNA sequencing. Association analysis was performed in 156 Min pigs and 160 Landraces, and the biological function of the identified genetic variant was explored using a dual-luciferase reporter assay. The results showed that HNF4A was widely expressed in liver, kidney and gastrointestinal tissues, with significantly higher expression in the liver of adult pigs than in newborn piglets (p < 0.05). A 20 bp InDel was identified in the first intron of porcine HNF4A. Allele frequency analysis showed that the Del allele (20 bp deletion) was dominant in Landrace and Duroc pigs, while the In allele (20 bp insertion) was dominant in Min and Jinhua pigs. Association analysis revealed that Min pigs with the In/Del genotype had significantly higher body weights at 14, 21, 28 and 35 days and higher average daily gain (ADG) than those of the In/In animals (p < 0.05). Landrace piglets with the Del/Del genotype exhibited significantly higher body weight at 21 and 28 days than those of the In/Del genotype (p < 0.05). The dual-luciferase reporter assay suggested that the plasmid carrying the In allele exhibited higher transcriptional activity than the Del allele (p < 0.05). Notably, the genotype associated with superior growth performance differed between the two breeds. Collectively, a 20 bp InDel within HNF4A was identified, which might affect piglet growth partially by modulating its transcription, and further study in other populations with different genetic backgrounds is needed before its application in pig breeding. Full article

Adaptive reuse of post-industrial heritage is often studied through technical performance, formal intervention strategies, or decision-support models. While these approaches clarify important aspects of reuse, they give limited attention to how projects evolve through the combined effects of architectural decisions, governance arrangements, financing mechanisms, policy instruments, social programs, and inherited fabric. This paper examines adaptive reuse as a time-structured project trajectory. It applies a hybrid methodology combining within-case reconstruction and comparative cross-case analysis to seven European projects in Brussels, Essen, Rotterdam, San Sebastián, Florence, Vienna, and Barcelona. The cases are analyzed across six dimensions: Asset & Context, Governance & Finance, Circularity, Social & Cultural, Policy & Design, and Outcomes & Transfer. The comparison shows that adaptive capacity depends on the alignment of governance, project time, and intervention strategy. Governance determines who can revise decisions and under what conditions; adaptation time is produced through funding horizons, approval procedures, institutional continuity, and civic or public stewardship; and strategies of retention, replacement, reversible insertion, and incremental occupation distribute future risk differently across project phases. From this synthesis, the paper extracts ten conditional lessons that frame adaptive reuse as configuration knowledge: transferable insights whose relevance depends on the interaction among governance capacity, temporal sequencing, inherited fabric, financing, policy support, and social objectives. The paper argues that knowledge transfer in adaptive reuse should be understood as disciplined translation across comparable constraints, not as the replication of models, rankings, or best-practice templates. Full article

Background: Autosomal recessive intellectual developmental disorder-13 (MRT13; OMIM #613192) is a rare neurodevelopmental disorder caused by pathogenic variants in TRAPPC9. Most reported variants are single-nucleotide variants (SNVs), small insertions/deletions, or copy number variants (CNVs), whereas complex structural variants (SVs) remain poorly characterized. Objectives: This study sought to review the clinical and molecular spectrum of TRAPPC9-related disorder, harmonize reported variants, explore genotype–phenotype correlations, and expand the mutational spectrum by reporting a novel patient with a cryptic SV. Methods: We report a novel patient whose diagnostic workup included array-CGH, whole-exome sequencing, karyotyping, and optical genome mapping. Additionally, a systematic literature search was primarily conducted in PubMed/MEDLINE from 2009 to January 2026, with Embase, Web of Science, Google Scholar, Orphanet, OMIM, and ClinVar used as supplementary sources. Patients carrying pathogenic/likely pathogenic TRAPPC9 variants were included. Clinical and molecular data were extracted and descriptively summarized. Genotype–phenotype correlations were explored. Reported variants were re-annotated using MANE Select reference transcripts. Results: The reported patient showed biallelic TRAPPC9 disruption due to two independently inherited structural variants: a maternal ~35 kb intragenic deletion involving exons 10–12, identified by 400K array-CGH, and a paternal balanced translocation t(4;8) disrupting TRAPPC9 within intron 8, characterized by trio-OGM and paired-end whole-genome sequencing (PE-WGS). Thirty-one studies reporting 75 previously published patients were included in the literature review; together with the novel patient described here, the final cohort comprised 76 patients. Intellectual disability was present in 100% of cases, followed by brain MRI abnormalities (95.9%), microcephaly (82.3%), motor delay (71.4%), dysmorphic features (69.8%), obesity (52.8%), behavioral abnormalities/autism spectrum disorder (49.2%/43.8%), and epilepsy (15.9%). Most patients (84.2%) harbored homozygous variants. Thirty-two distinct sequence variants were identified, predominantly loss-of-function. CNVs were identified in 13.2% of patients. No genotype–phenotype correlations were identified. Conclusions: The systematic review provides an updated and harmonized overview of the clinical and molecular spectrum of TRAPPC9-related disorder, supporting the presence of a recognizable phenotype and confirming the predominance of loss-of-function variants. Our case further highlights the contribution of cryptic structural variants to the mutational spectrum of TRAPPC9 and the diagnostic value of advanced genomic approaches. Full article

Due to overfishing, eutrophication of rivers and lakes, and irrational stocking practices, the diversity of wild native carp populations has declined, leading to germplasm degradation and a decrease in fish quality, thereby affecting the sustainable development of fisheries. In this study, a novel hybrid crucian carp lineage (designated LWR) was successfully established via distant hybridization using Dongting Lake crucian carp (LC, ♀) and Hefang crucian carp (WR, ♂) as parental stocks. Systematic analyses were conducted on the morphology, ploidy, fertility, growth performance, survival rate, and molecular genetics of LWR. The results reveal that LWR is an allodiploid (2n = 100), with a chromosome number identical to that of its parents. Gonadal development in the hybrid progeny (LWR) was normal, with both sexes being fertile and reaching sexual maturity at one year of age. Morphologically, LWR exhibited intermediate traits with a paternal bias, characterized by a deep-bodied and elongated shape. In terms of growth performance, LWR displayed significant heterosis (approximately 145% and 271% higher than the body weight of the maternal parent at 6 months and 1 year). Molecular genetic analysis indicated that the 5S rDNA sequences of LWR were predominantly inherited from the paternal parent WR, with insertions, deletions, recombination, and mutations detected. The mtDNA sequences exhibited 99.78% similarity to those of the maternal parent LC, following maternal inheritance with sporadic nucleotide variations. These findings offer a new paradigm for hybridization and a theoretical foundation for the improvement and sustainable utilization of indigenous crucian carp germplasm resources, the selective breeding of improved aquaculture strains, and the sustainable development of fisheries. Full article

Background/Objectives: Genomic testing has transformed rare-disease diagnostics, yet a substantial proportion of individuals remain without a molecular diagnosis even after short-read exome sequencing (SR-ES) or short-read genome sequencing (SR-GS) and repeated conventional analysis. Methods: To address this persistent gap, we evaluated a coordinated multimodal reanalysis framework for deeply investigated families with suspected monogenic disease. Six families (20 individuals; 8 affected individuals) that had remained unsolved after prior comprehensive testing were reviewed prospectively in weekly interdisciplinary case conferences over one year. Available data included SR-ES, SR-GS, long-read genome sequencing (LR-GS), RNA-seq, optical genome mapping, mobile-element analysis, and mitochondrial genome analysis. The goal was not to test a single modality in isolation, but to assess whether systematic escalation across complementary assays plus continued reinterpretation could improve case resolution. Results: Three families (50%) achieved a reportable molecular diagnosis, two (33%) yielded strong candidate findings requiring additional evidence, and one (17%) remained without a definitive new molecular diagnosis, although reinterpretation of a previously identified NOTCH3 variant provided a possible partial explanation. Resolved cases included compound-heterozygous variants in KLHL40, a 119 kb multi-exon deletion in TTN, and a recurrent insertion in RNU4-2. Candidate findings included biallelic NARS2 variants and a 1.3 kb intragenic deletion involving ZEB2. Functional transcriptomic analyses supported the KLHL40 and TTN diagnoses but did not demonstrate a splicing consequence for the candidate NARS2 intronic variant in cardiac tissue. Conclusions: This small pilot cohort is not intended to estimate general diagnostic yield, but it demonstrates that a coordinated multimodal framework can reveal different sources of added value, including structural variant discovery, orthogonal functional support, and reinterpretation of existing short-read data as knowledge evolves. These findings underscore that archived short-read exome and genome data can retain substantial diagnostic value years after initial testing, particularly when reanalyzed with updated pipelines, expanded disease gene knowledge, and orthogonal multimodal evidence. Adoption of iterative, team-based multimodal strategies may help resolve the most complex unsolved rare-disease cases. Full article

Background/Objectives: Respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and parainfluenza virus type 3 (PIV3) are leading causes of acute respiratory infections in children and the elderly, yet no licensed T-cell vaccines are available. This study aimed to develop multivalent T-cell vaccine candidates against these pathogens using a live attenuated influenza virus (LAIV) vector platform. Methods: Conserved F, N, and M proteins of RSV, hMPV, and PIV3 were identified through multiple sequence alignments. Fragments enriched with experimentally confirmed and predicted T-cell epitopes were selected using the IEDB and NetMHCpan servers. These fragments were assembled into polyepitope immunogenic cassettes, and their selected order was determined by thermodynamic analysis of mRNA secondary structures using the RNAfold Web Server. The selected cassettes were cloned into the neuraminidase (NA) gene of a cold-adapted LAIV vector. Recombinant viruses were rescued by reverse genetics and assessed for replicative fitness in embryonated chicken eggs and MDCK cells, NA enzymatic activity and genetic stability upon serial passaging. Results: Four cassettes were designed for RSV, three for hMPV, and one for PIV3, all containing fragments with multiple T-cell epitopes. Three recombinant viruses of LAIV/RSV type and three of LAIV/hMPV type were successfully rescued, while attempts to recover the remaining recombinant viruses, i.e., LAIV/RSV and LAIV/PIV3, were not successful. All rescued recombinant viruses replicated to titers comparable to the parental LAIV strain and retained the full-length insert for at least eight passages in eggs. Importantly, NA enzymatic activity of the LAIV vector was not compromised by the insertion of the polyepitope T-cell cassettes. Conclusions: We developed a panel of recombinant T cell-based vaccine candidates against RSV and hMPV using the LAIV vector platform. These recombinant viruses encode conserved T-cell epitopes of the target viruses while retaining the biological properties of LAIV strains. Taken together, these characteristics warrant further evaluation of these recombinant viruses in appropriate relevant in vitro models to directly assess their immunogenicity in terms of stimulating a T-cell response against target pathogens. Full article

Background: Upland cotton (Gossypium hirsutum) is a major natural fiber crop and an important model for studying genome evolution and gene function in polyploid plants. However, its large and highly redundant genome presents substantial challenges for efficient and coordinated multiplex genome editing. Methods: Here, we developed a high-efficiency CRISPR/Cas12a-based multiplex genome editing system in cotton by integrating a tRNA–crRNA polycistronic expression strategy with a Bean yellow dwarf virus (BeYDV)-derived replicon. Results: This platform enabled coordinated expression of multiple crRNAs and simultaneous targeting of 16 loci within a centromere-proximal region of chromosome D03 (18.65–24.47 Mb). In individual transgenic lines, up to 10 target sites were edited concurrently, with nine targets exhibiting editing efficiencies above 56% and the highest efficiency reaching 96.46%. High-density multiplex editing predominantly induced small insertions and deletions at target loci. Notably, edited plants exhibited reduced growth and pronounced cytological abnormalities, including chromosome bridges, lagging chromosomes, and abnormal meiotic products. Transcriptome analysis revealed widespread dysregulation of genes involved in chromosome segregation and cell cycle regulation. Despite these functional perturbations, HiFi long-read sequencing detected no large-scale chromosomal rearrangements, indicating that genome instability arises from cumulative local perturbations rather than global structural alterations. Conclusions: Together, our results establish an efficient multiplex genome editing platform in cotton and highlight potential constraints of high-density editing on genome stability in complex plant genomes. Full article

This review discusses the role of human epidermal growth factor receptor 2 (HER2/ERBB2) as a key oncogenic driver in non-small cell lung cancer (NSCLC), including exon 20 activating mutations, gene amplification, and protein overexpression. These forms differ in their biological effects and predictive value, but HER2 mutations, especially exon 20 insertions, are the primary oncogenic mechanism. Regarding diagnosis, Next-Generation Sequencing (NGS) is used to identify mutations, whereas Immunohistochemistry (IHC) and in situ hybridization are used to assess HER2 expression. Concerning treatment, in advanced HER2-positive, Non-Squamous NSCLC tumors, the first-line treatment is Platinum-based + Pemetrexed chemotherapy, with or without immunotherapy, because no HER2-targeted antibody therapy has yet been approved for initial treatment. After progression, HER2-targeted antibody-drug conjugates like Trastuzumab-Deruxtecan and Ado Trastuzumab-Emtansine may offer patients clinical benefits. New HER2-selective tyrosine kinase inhibitors, such as zongertinib and sevabertinib, have shown promising results, including patients previously treated with antibody–drug conjugates (ADCs). Recent advances, including next-generation ADCs such as SHR-A1811 and A166, and bispecific antibodies, such as zenocutuzumab for NRG1 fusion–positive disease, which are also expanding treatment options. Overall, advances in diagnostics and new targeted therapies are changing how HER2-altered NSCLC is treated and are helping to make care more personalized. Full article

Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6′)-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome–mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings. Full article

Background/Objectives: Somatic CALR gene insertions/deletions in exon 9, causing frameshift, are a diagnostic sign of myeloproliferative neoplasms (MPNs). Besides the most common somatic mutations of type I (52 bp deletion) and type II (5 bp insertion), there are rare ones whose significance is not always clear. This study evaluates the frequency of rare mutations and demonstrates a germline rather than somatic nature for some of them. Methods: A retrospective analysis of 8417 blood samples subjected to molecular diagnosis of myeloproliferative neoplasm (MPN) was performed. Cases suspected as germline variants were sequenced, and paired samples (when available) of buccal epithelium were analyzed. Results: We have identified 632 CALR gene mutation-positive cases. Most of the cases were typical insertions/deletions (5 bp/52 bp). Non-type I/II frameshift or nonframeshift mutations were observed in 68 cases (11%). The buccal swab samples obtained from 4 patients confirmed the germline nature of these variants. It is worth noting that the MPN diagnosis for three of these patients was made considering the presence of the JAK2 V617F mutation (two cases) or BCR::ABL1 translocation (one case). In one case, the diagnosis of MPN was reclassified to CML. Conclusions: Non-type I/II CALR mutations, according to our data, could be found in 0.8% of MPN-suspected cases, and may not be associated with the diagnosis. The detection of a non-standard CALR mutation with an allelic frequency close to 50% should raise suspicion of the possibility of a germline CALR variant, and such cases should be investigated further. Full article