Search Results (63)

Deposition of intramuscular fat (IM), also known as marbling, is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms underlying the differential deposition of adipose tissue in distinct anatomical areas in beef cattle is key to the development of strategies for marbling enhancement while limiting the accumulation of excessive subcutaneous adipose tissue (SAT). The objective of this exploratory study was to define the IM and SAT transcriptional heterogeneity at the whole tissue and single-nuclei levels in beef steers. Longissimus dorsi muscle samples (9–11th rib) were collected from two finished beef steers at harvest to dissect matched IM and adjacent SAT (backfat). Total RNA from IM and SAT was isolated and sequenced in an Illumina NovaSeq 6000. Nuclei from the same samples were isolated by dounce homogenization, libraries generated with 10× Genomics, and sequenced in an Illumina NovaSeq 6000, followed by analysis via Cell Ranger pipeline and Seurat in RStudio (v4.3.2) By the expression of signature marker genes, single-nuclei RNA sequencing (snRNAseq) analysis identified mature adipocytes (AD; ADIPOQ, LEP), adipose stromal and progenitor cells (ASPC; PDGFRA), endothelial cells (EC; VWF, PECAM1), smooth muscle cells (SMC; NOTCH3, MYL9) and immune cells (IMC; CD163, MRC1). We detected six cell clusters in SAT and nine in IM. Across IM and SAT, AD was the most abundant cell type, followed by ASPC, SMC, and IMC. In SAT, AD made up 50% of the cellular population, followed by ASPC (31%), EC (14%), IMC (1%), and SMC (4%). In IM depot, AD made up 23% of the cellular population, followed by ASPC at 19% of the population, EC at 28%, IMC at 7% and SMC at 12%. The abundance of ASPC and AD was lower in IM vs. SAT, while IMC was increased, suggesting a potential involvement of immune cells on IM deposition. Accordingly, both bulk RNAseq and snRNAseq analyses identified activated pathways of inflammation and metabolic function in IM. These results demonstrate distinct transcriptional cellular heterogeneity between SAT and IM depots in beef steers, which may underly the mechanisms by which fat deposits in each depot. The identification of depot-specific cell populations in IM and SAT via snRNAseq analysis has the potential to reveal target genes for the modulation of fat deposition in beef cattle. Full article

Background: Ligusticum L. plants exhibit significant morphological variation in leaves, flowers, bracteoles and mericarps, thus the classifications of members for the genus have always been controversial. Among them, the taxonomic problem of Ligusticum multivittatum Franch. is the most prominent, which has not been sufficiently resolved so far. Methods: to clarify the taxonomic position of Ligusticum multivittatum, we performed phylogenetic analyses based on plastome data and ITS sequences. Meanwhile, we conducted comprehensively comparative plastome analyses between Ligusticum multivittatum and fifteen Ligusticopsis species. Results: Both analyses robustly supported that Ligusticum multivittatum nested in genus Ligusticopsis Leute and formed a clade with fifteen Ligusticopsis species, belonged to the Selineae tribe, which was distant from the type species of Ligusticum (Ligusticum scoticum), located in the Acronema clade.The comparative results showed that sixteen plastomes were highly similar and conservative in genome structure, size, gene content and arrangement, codon bias, SSRs and SC/IR. These findings imply that Ligusticum multivittatum is a member of Ligusticopsis, which was further verified by their shared morphological characters: stem base clothed in fibrous remnant sheaths, white petals, pinnate bracteoles, dorsally compressed mericarps with slightly prominent dorsal ribs, winged lateral ribs and numerous vittae in the commissure and in each furrow. Therefore, combining with the evidences of phylogenetic analyses, plastome comparison and morphological features, we affirmed that Ligusticum multivittatum indeed belonged to Ligusticopsis and transformed it into Ligusticopsis conducted by Pimenov was reasonable. Conclusions: Our study not only confirms the classification of Ligusticum multivittatum by integrating evidences, but also provides a reference for resolving taxonomy of contentious taxa. Full article

Spondylocostal dysostosis (SCDO) is a group of rare genetic disorders characterized by segmental vertebral defects and rib deformities due to congenital misalignment, fusion, or reduction in the number of ribs. The causes of the disease have been found in seven genes, including DLL3 (SCDO1, OMIM 602768), MESP2 (SCDO2, OMIM 608681), LFNG (SCDO3, OMIM 609813), HES7 (SCDO4, OMIM 608059), TBX6 (SCDO5, OMIM 602427), RIPPLY2 (SCDO6, OMIM 616566), and DLL1 (SCDO7). Among these, SCDO4, characterized by a short trunk, short neck, and mild nonprogressive scoliosis, is a rare form of reported cases. SCDO4 is identified as caused by homozygous or compound heterozygous variants in the HES7 gene (NM_001165967.2; NP_001159439.1). This study reports a novel homozygous HES7 splice variant (c.43-9T>A) detected in an SCDO4 patient by whole-exome sequencing and confirmed by Sanger sequencing. This variant was evaluated as an acceptor loss variant in intron 1 in the HES7 transcript by in silico analysis and was inherited from the patient’s parent. This study also reviews previous reports to provide a comprehensive overview of SCDO and help us to understand the pathogenesis to develop future treatment strategies. Full article

Gorlin-Goltz syndrome (GGS) is also known as Nevoid basal cell carcinoma syndrome (NBCCS). In the most common manifestation, GGS is diagnosed based on multiple cysts in the jaw bones, namely OKCs (odontogenic keratocysts). Other features might include major and minor clinical and radiological criteria to confirm this syndrome. Quite commonly, BCCs (basal cell carcinomas), bifid ribs, palmar and plantar pits, and ectopic calcification of the falx cerebri can be found in the majority of patients. Currently, the mutation of the PTCH1 gene seems to be responsible for GGS occurrence, while the male-to-female ratio is 1:1. The following radiological study based on OPGs and CBCT confirmed multiple cystic lesions in jaw bones, confirmed to be OKCs in the histopathological evaluation with an occurrence of numerous skin BCC lesions. In cases of most oral OKC cystic lesions, either surgical removal, curettage, or enucleation with or without any bone grafting can be used with a good amount of success. Rarely, some stable bone osteosynthesis procedures have to be carried out to avoid pathological bone fractures after cyst removal. A special consideration should include the temporomandibular joint. TMJ surgery and the replacement of the joint with an alloplastic material can be performed to improve biting, chewing, proper mouth opening, and maintain good patient occlusion. The authors want to present how effective and simple a standard dental panoramic radiograph combined with CBCT is and how it is suitable for GGS detection. They also want to underline how a standard TMJ prosthesis can be used as an alternative to a custom-made prosthesis. Full article

Background and Clinical Significance: Basal cell nevoid carcinoma syndrome, or Gorlin–Goltz Syndrome (GGS), is a genetic disease caused by germline mutations in genes involved in the Sonic HedgeHog (SHH) signaling pathway, mainly in the PTCH1 gene. PTCH1 is a receptor for SHH, and the activation of SHH signaling exerts a direct effect on the proliferation and maintenance of stem cells; alteration of its signaling could promote a favorable microenvironment for the maintenance of tumor viability. The main clinical manifestations of patients with GGS include multiple basal cell carcinomas, odontogenic keratocysts, calcification of the falx cerebri, palmoplantar fossae, hypertelorism, prognathism, fused or bifid ribs, and macrocephaly, which occur at different stages of life. Case Presentation: Here, the case of a 48-year-old woman is described, for whom a clinical and histopathological diagnosis of GGS was made due to the presence of two major criteria (multiple odontogenic keratocysts and calcification of the falx cerebri) and one minor criterion (congenital anomalies), according to Kimonis. Additionally, an end-point RT-PCR assay showed a decrease in PTCH1 gene expression. A conservative therapy was established, and satisfactory results were obtained in a follow-up period of 18 months. Conclusions: Kimonis' clinical criteria are important for establishing the diagnosis of Gorlin syndrome. Full article

The FBLN1 gene encodes the fibulin-1 protein, the first member of the ECM glycoprotein family, and is crucial for embryonic development and organ tissue formation in mammals. Our previous transcriptome analysis identified the FBLN1 gene and suggested its potential role in influencing slaughter traits by regulating ECM function. This study aims to uncover key genetic variants (InDel and CNV) within the FBLN1 gene and examine its relationship with slaughter traits in beef cattle. In this study, the beef cattle genetic resources population Gaoqing black cattle were selected (n = 641), leading to the identification of three polymorphic InDel loci (13 bp insertion, 28 bp insertion, and 24 bp insertion) and two CNVs. Association analysis revealed that InDel polymorphisms in Gaoqing black cattle were significantly correlated with certain slaughter traits (p < 0.05), such as left limb weight and right limb weight. In addition, the CNV loci were significantly correlated with traits such as skirt steak and round small intestine (p < 0.05), and reached extremely significant levels (p < 0.01) in certain traits such as chunky II and high rib. In summary, the identified InDel and CNV polymorphisms in the FBLN1 gene represent potential molecular markers associated with slaughter traits in Gaoqing black cattle. These findings provide valuable insights for marker-assisted selection to enhance genetic improvement in beef cattle breeding. Full article

Helicobacter pylori infects at least half the population worldwide, and its highly diverse genomic content correlates with its geographic distribution because of its prolonged relationship with humans. The extremely low infection prevalence alongside low inflammation severity observed in some countries might be caused by strains with low virulence potential. Therefore, this study aimed to investigate whole-genome analysis datasets of Sri Lankan H. pylori strains. H. pylori strains were isolated from biopsy specimens and underwent whole-genome sequencing to investigate their antibiotic resistance and virulence potential. The prevalence of H. pylori infection in Sri Lanka is extremely low (1.7% in a previous study), and only six H. pylori strains were successfully isolated from bacterial culture. Antibiotic resistance analysis showed a high prevalence of metronidazole resistance (83.3%, five out of six strains), and investigation of the related genes showed truncation of the rdxA and frxA genes and single-nucleotide polymorphisms in the rdxA, frxA, ribF, omp11, and fur genes. Most virulence genes of the 144 assessed were present, except for the cag pathogenicity island (cagPAI) (absent in four out of six strains), babA/B/C, and tlpB genes. An incomplete type 4 secretion system (tfs) was found in three strains. A pan-genome analysis with non-Sri Lankan H. pylori strains showed that the htpX gene was found only in Sri Lankan strains (p-corrected = 0.0008). A phylogenetic analysis showed that the Sri Lankan strains clustered with strains from hpAsia2 and hpEurope. This comparative genomic study shows that H. pylori strains with low virulence potential are present in countries with a low prevalence of infection and disease severity, indicating a strain-type geographical pattern. The tailored guidelines for screening and treatment strategy for each region are necessary to obtain effective and efficient eradication. Full article

Fungi play an increasingly important role in the biological control of insect pests. Aspergillus oryzae XJ1 is highly virulent to locust adults and nymphs, which are a destructive economic pest worldwide. Because of its host association with locusts, which is unique in Aspergillus, in this study, we examined the genetic relationships of A. oryzae XJ1 within Aspergillus. We sequenced the genome of A. oryzae XJ1 and compared it with the genomes of other Aspergillus species. The complete genome of A. oryzae XJ1 is 37.9 Mb, comprising 11,720 putative genes, assembled into eight chromosomes. The genome size is similar to that of other A. oryzae strains. Phylogenomic analysis indicated that A. oryzae XJ1 was most closely related to A. flavus NRRL3357, not A. oryzae RIB40. Core/pan-genome analysis of A. oryzae XJ1 and other Aspergillus species revealed that A. oryzae XJ1 had 704 strain-specific genes, whereas A. flavus NRRL3357, A. oryzae KDG 21, and A. parasiticus NRRL 2999 had 646, 955, and 779 unique genes, respectively. The A. oryzae XJ1 genome showed structural differences compared with the genomes of A. oryzae RIB40 and A. flavus NRRL3357 in genomic synteny analysis. These results indicate that A. oryzae XJ1 is genetically distinct at the genome level from other Aspergillus species, including A. oryzae and A. flavus, and may be as a distinct species. This will provide new insight into the classification of Aspergillus based on genomics. Full article

Ciliopathies are rare congenital disorders caused by defects in the structure or function of cilia, which can lead to a wide range of clinical manifestations. Among them, a subset known as skeletal ciliopathies exhibits significant phenotypic overlap and primarily affects skeletal development. This group includes several syndromes with overlapping but distinct clinical features, such as short-rib polydactyly syndrome (SRPS), Jeune asphyxiating thoracic dystrophy (JATD), Mainzer–Saldino syndrome (MZSDS), and cranioectodermal dysplasia (CED), also called Sensenbrenner syndrome. The most characterized features of skeletal ciliopathies are short stature, rhizomelic limb shortening, and thoracic narrowing to varying extents, with JATD presenting the most severe form. Here, we report a fetus with an extension of skeletal ciliopathy phenotype and compound heterozygous variants in the IFT140 gene. The affected fetus had multiple malformations, including increased nuchal transparency (NT), shortened and thick long bones, hypoplastic tibia and fibula, absence of bladder, flat nose, and frontal bossing. Our findings expand the mutation spectrum of IFT140, and the clinical spectrum associated with skeletal ciliopathies, highly relevant in diagnosis prenatal settings. Full article

Pediococcus pentosaceus, which often occurs in fermented foods, is characterized by numerous positive effects on the human health, such as the presence of possible probiotic abilities, the reduction of cholesterol levels, satisfactory antimicrobial activity, and certain therapeutic functions. This study was conducted with the goal of describing the genomic content of Pediococcus pentosaceus ENM104, a strain known for its inhibitory effects against pathogenic bacteria and its remarkable probiotic potential, including the induction of significant reductions in cholesterol levels and the production of γ-aminobutyric acid (GABA). The P. pentosaceus ENM104 chromosome is circular. The chromosome is 1,734,928 bp with a GC content of 37.2%. P. pentosaceus also harbors a circular plasmid, pENM104, that is 71,811 bp with a GC content of 38.1%. Functional annotations identified numerous genes associated with probiotic traits, including those involved in stress adaptation (e.g., heat stress: htpX, dnaK, and dnaJ), bile tolerance (e.g., ppaC), vitamin biosynthesis (e.g., ribU, ribZ, ribF, and btuD), immunomodulation (e.g., dltA, dltC, and dltD), and bacteriocin production (e.g., pedA). Notably, genes responsible for lowering cholesterol levels (bile salt hydrolase, bsh) and GABA synthesis (glutamate/GABA antiporter, gadC) were also identified. The in vitro assay results using cell-free supernatants of P. pentosaceus ENM104 revealed antibacterial activity against carbapenem-resistant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii, and the inhibition zone diameter increased progressively over time. This comprehensive study provides valuable insights into the molecular characteristics of P. pentosaceus ENM104, emphasizing its potential as a probiotic. Its notable cholesterol-lowering, GABA-producing, and antimicrobial capabilities suggest promising applications in the pharmaceutical and food industries. Future research should focus on further exploring these functional properties and assessing the strain’s efficacy in clinical settings. Full article

KIAA0586 variants have been associated with a wide range of ciliopathies, mainly Joubert syndrome (JS, OMIM #616490) and short-rib thoracic dysplasia syndrome (SRTD, OMIM #616546). However, the hypothesis that this gene is involved with hydrolethalus syndrome (HSL, OMIM #614120) and orofaciodigital syndrome IV (OMIM #258860) has already been raised. Ciliopathies’ clinical features are often overlapped despite differing in phenotype severity. Besides KIAA0586, HYLS1 and KIF7 are also known for being causative of ciliopathies, indicating that all three genes may have similar or converging genomic pathways. Overall, the genotypic and phenotypic spectrum of ciliopathies becomes wider and conflicting while more and more new variants are added to this group of disorders’ molecular pot. In this case report we discuss the first Brazilian individual clinically diagnosed with hydrolethalus syndrome and molecular findings that demonstrate the role of KIAA0586 as a causative gene of a group of genetic disorders. Also, recent reports on individuals with intronic and exonic variants combined leading to ciliopathies support our patient’s molecular diagnosis. At the same time, we discuss variable expressivity and overlapping features in ciliopathies. Full article

Aspergillus flavus produces aflatoxin, a carcinogenic fungal toxin that poses a threat to the agricultural and food industries. There is a concern that the distribution of aflatoxin-producing A. flavus is expanding in Japan due to climate change, and it is necessary to understand what types of strains inhabit. In this study, we sequenced the genomes of four Aspergillus strains isolated from agricultural fields in the Ibaraki prefecture of Japan and identified their genetic variants. Phylogenetic analysis based on single-nucleotide variants revealed that the two aflatoxin-producing strains were closely related to A. flavus NRRL3357, whereas the two non-producing strains were closely related to the RIB40 strain of Aspergillus oryzae, a fungus widely used in the Japanese fermentation industry. A detailed analysis of the variants in the aflatoxin biosynthetic gene cluster showed that the two aflatoxin-producing strains belonged to different morphotype lineages. RT-qPCR results indicated that the expression of aflatoxin biosynthetic genes was consistent with aflatoxin production in the two aflatoxin-producing strains, whereas the two non-producing strains expressed most of the aflatoxin biosynthetic genes, unlike common knowledge in A. oryzae, suggesting that the lack of aflatoxin production was attributed to genes outside of the aflatoxin biosynthetic gene cluster in these strains. Full article

Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future. Full article

Myogenic transcription factors with a basic helix–loop–helix (bHLH) such as MYOD, myogenin, MRF4, and MYF5 contribute to muscle differentiation and regulation. The MYF5 gene located on chromosome 12 encodes for myogenic factor 5 (MYF5), which has a role in skeletal and extraocular muscle development and rib formation. Variants in MYF5 were found to cause external ophthalmoplegia with rib and vertebral anomalies (EORVA), a rare recessive condition. To date, three homozygous variants in MYF5 have been reported to cause EORVA in six members of four unrelated families. Here, we present a novel homozygous MYF5 frameshift variant, c.596dupA p. (Asn199Lysfs*49), causing premature protein termination and presenting with external ophthalmoplegia, ptosis, and scoliosis in three siblings from a consanguineous family of Pakistani origin. With four MYF5 variants now discovered, genetic testing and paediatric assessment for extra-ocular features should be considered in all cases of congenital ophthalmoplegia. Full article

Bone morphogenetic protein 6 (BMP-6) is a constituent of the TGF-β superfamily, known for its ability to stimulate bone and cartilage formation. The investigation of bmp6’s involvement in the formation of intermuscular bones in fish has garnered significant attention in recent years. The rib cage is an important skeletal structure that plays a protective function for internal organs in fish. However, there has been limited research conducted on the effects of the bmp6 gene on rib development. Silver carp is one of four major fish in China, favoured for its affordability and tender muscle. Nevertheless, the presence of numerous intermuscular bones in silver carp significantly hinders the advancement of its palatability and suitability for processing. This study showcases the effective utilisation of CRISPR/Cas9 technology for the purpose of disrupting the bmp6 gene in silver carp, leading to the creation of chimeras in the P₀ generation, marking the first instance of such an achievement. The chimeras exhibited complete viability, normal appearance, and partial intermuscular bones loss, with approximately 30% of them displaying rib bifurcation or bending. Subsequently, a transcriptome analysis on ribs of P₀ chimeras and wild-type silver carp was conducted, leading to the identification of 934 genes exhibiting differential expression, of which 483 were found to be up-regulated and 451 were found to be down-regulated. The results of the KEGG analysis revealed that the “NF-kappa B signalling pathway”, “Hippo signalling pathway”, “osteoclast differentiation”, and “haematopoietic cell lineage” exhibited enrichment and displayed a significant correlation with bone development. The up-regulated genes such as tnfα, fos, and ctgf in pathways may facilitate the proliferation and differentiation of osteoclasts, whereas the down-regulation of genes such as tgfb2 and tgfbr1 in pathways may hinder the formation and specialisation of osteoblasts, ultimately resulting in rib abnormalities. This study presents novel findings on the impact of bmp6 gene deletion on the rib development of silver carp, while simultaneously investigating the previously unexplored molecular mechanisms underlying rib defects in fish. Full article