Sequence Analysis Of Region Research Articles

First Isolation, Molecular Identification, and Phylogenetic Characterization of A3B5 Very Virulent Infectious Bursal Disease Virus in Pullets in Chile

Infectious bursal disease virus (IBDV) is an important pathogen affecting the poultry industry worldwide. IBDV serotype 1, including classical virulent strains (cvIBDV), variant strains (varIBDV), and very virulent strains (vvIBDV), is pathogenic for chickens. IBDV mainly infects immature B-lymphocytes in the bursa of Fabricius, weakening the humoral immune response and leading to secondary infections and increased morbidity and mortality. The Laboratory of Avian Pathology received ten live 8-week-old pullets from a laying hen operation experiencing increased mortality, prostration, diarrhea, and sudden death. Upon necropsy, the affected birds presented swollen, hemorrhagic, and edematous bursa of Fabricius, as well as hemorrhage in the breast and thigh muscles. RT-PCR confirmed that the samples from the bursa of Fabricius were positive for IBDV. Phylogenetic analysis of the VP1 and VP2 gene nucleotide sequences classified the strain, isolated in embryonated chicken eggs, as the A3B5 genotype. Amino acid sequence analysis of the VP2 hypervariable region revealed the presence of amino acid residues commonly found in vvIBDV. Additional studies are required to investigate the epidemiological situation of this genotype in Chile and to evaluate current vaccination plans and their effectiveness against new variants.

Investigation and Identification of Fungal Diseases of Aloe barbadensis in China.

The Aloe barbadensis industry plays an important role in the economic development of Yuanjiang county of Yuxi city in Yunnan province, China. In order to reduce the harm of diseases and ensure the quality of products, the occurrence of A. barbadensis was investigated. The pathogenic fungi of wild and cultivated species of A. barbadensis were isolated by a tissue separation method, and DNA sequencing was carried out by using the sequence analysis of the ribosomal rDNA-ITS region, and the pathogenic fungi were classified and identified by finally combining morphological observations. The results showed that the main fungal diseases were root rot and leaf rot disease caused by Fusarium oxysporum, leaf spot disease caused by Curvularia lunata, anthracnose caused by Colletotrichum boninense, and brown spot disease caused by Alternaria alternata on A. barbadensis.

Molecular and biochemical methods for species identification among the genus Cuscuta

Genus Cuscuta (Convolvulaceae) comprises of stem holoparasitic plants that are scientifically highly valuable, as they cause extensive crop damage. They exhibit high morphological similarity, which complicates their species identification. Determining the taxonomical status of obtained specimens from Bulgaria, is crucial for exploring the genetic diversity of the genus and establishing the phylogenetic relationships within the taxon. Thereby different correlations with geographic region and particular environmental conditions can be established. This study employs molecular and biochemical methods, including ITS region sequence analysis of rDNA, RAPD analysis, and HPLC/MS analysis of flavonoids, to identify Cuscuta species and conduct phylogenetic analysis. Overall, a successful identification has been made - while ITS PCR products provide more accurate species identification and phylogenic information, RAPD profiles are convenient for quick identification. Detailed investigation of the RAPD profiles is required due to differences correlating with the habitats of the species. Nevertheless, flavonoid profiles prove themselves as a valuable biochemical marker for species identification. All of the aforementioned methods are suitable and useful for species identification among the genus Cuscuta, depending on the needs and aims of the conducted analysis.

Genetic Characteristics of the Env Regions in HIV-1-Infected Subjects in Baoding City, Hebei Province, China.

The envelope glycoprotein (Env) on the surface of the human immunodeficiency virus (HIV-1) is a crucial protein that mediates binding to host cell receptors and subsequent membrane fusion. Env, as the sole target for neutralizing antibodies, holds unique importance in vaccine design. Therefore, analyzing the genetic characteristics of the Env region offers reference data for vaccine and drug design. From December 2021 to December 2022, 145 newly diagnosed, HIV-1-infected individuals in Baoding City were recruited into this study. The HIV-1 env gene sequence was successfully obtained from 142 of the 145 blood specimens, and the sequences were submitted to the Quality Control Tool (http//:HIV-DB Sequence Quality Control Tool (lanl.gov)) to analyze the viral subtype. The coreceptor tropism was predicted using the Geno2pheno web tool with falsepositive rate (FPR) values of 5%-15%, and the net charges of the third variable (V3) loop were calculated by Variable Region Characteristics (lanl.gov). The results showed that half of the patients were infected with the CCR5-tropic virus (50.0%, 71/142). In HIV-1 subtype CRF01_AE infection, the use of CXCR4 is expected to predominate, while in HIV-1 subtype CRF07_BC infection, CCR5 coreceptors are expected to be used predominantly. Sequence analysis of the V3 loop region revealed that subtypes CRF01_AE and CRF07_BC have similar median net charges (~3.0). Furthermore, GPGQ was found to be the major terminal tetrapeptide of the CRF07_ BC and CRF01_AE strains in this study. These findings enhance our understanding of the characteristics of the HIV-1 epidemic and provide important implications for HIV-1 vaccine design and clinical treatment.

Molecular characterization of circulating infectious bursal disease viruses in chickens from different Egyptian governorates during 2023

Infectious bursal disease virus (IBDV) induces severe immunosuppression in chickens, leading to significant economic losses in the global poultry industry. This study investigated 52 chicken flocks, including commercial broilers, layers, and baladi, from various Egyptian governorates in 2023. These flocks exhibited symptoms of depression, along with kidney and bursa lesions, indicative of IBDV infection. Pooled Bursal homogenates were tested using RT-PCR with VP2-specific primers, revealing that 20 flocks tested positive for IBDV. Six representative samples were selected from 20 positive flocks for isolation in embryonated chicken eggs. The embryonic lesions observed included haemorrhage, skull swelling, and liver necrosis with a pale-yellow appearance, in addition to congestion and thickening in the chorioallantoic membrane (CAM). Partial amplification of the VP2 gene from the harvested embryo suspensions of the six IBDV isolates was performed for sequencing. Phylogenetic analysis of the sequences revealed that five IBDV isolates (VV4, VV5, VV6, VV10, and VV16) belonged to the very virulent strain group A3 cluster, whereas one isolate (VV2) clustered with Chinese Variant strains in the A2d group. Sequence analysis of the hypervariable region (HVR) of VP2 compared to that of Egypt-USC-IBD-1-2019 and vvIBDV/Beh21/Egypt/18 highly virulent IBDV strains revealed several amino acid mutations. The VP2 HVR of all isolates maintained the serine-rich heptapeptide sequence SWSASGS, which is adjacent to the major hydrophilic peak B and serves as a virulence marker. Histopathological examination revealed that bursae from chickens infected with vvIBDV exhibited marked interlobular oedema and lymphoid depletion. In contrast, bursae from chickens infected with Variant IBDV showed massive lymphoid depletion, with hyperplasia of the bursal capsule. These findings highlight the circulation of both virulent and Variant IBDV strains in Egyptian chicken flocks, complicating disease control. Consequently, there is a need to update vaccination programs and vaccine strains for IBDV in Egypt.

Distribution patterns of Calonectria (Ascomycota, Sordariomycetes, Hypocreales, Nectriaceae) species complexes related to diseased leaves and soil habitats during leaf blight outbreak season in Eucalyptus plantations in southern China.

Calonectria leaf blight caused by Calonectria species is one of the most important diseases associated with Eucalyptus plantations in Asia and South America. This study aimed to clarify the distribution patterns of Calonectria species residing in different species complexes associated with diseased trees and soils during leaf blight outbreak season in Eucalyptus plantations in southern China. In this study, 482 Calonectria isolates obtained from diseased Eucalyptus trees and soils under these trees in eight sampling sites in three provinces were identified by DNA sequence analyses of tef1, tub2, cmdA, and his3 gene regions. Six species residing in three species complexes were identified: Calonectriapseudoreteaudii and C.acaciicola in the Calonectriareteaudii species complex; C.hongkongensis, C.aconidialis, and C.chinensis in C.kyotensis species complex; and C.auriculiformis in C.cylindrospora species complex. The habitats of Calonectria in different species complexes differed, C.reteaudii species complex inhabits in both diseased trees and soils, C.kyotensis species complex only in soils. The Calonectria leaf blight in the sampled regions was caused by species in the C.reteaudii species complex but not by the species in the C.kyotensis species complex. These findings suggest that the species in the C.reteaudii species complex should receive more attention in disease management, as they are the primary cause of the disease in the sampled regions.

Molecular Identification of Mycoplasma agassizii in Confiscated Tortoises in Madagascar.

Mycoplasmosis is of concern for chelonian conservation. We detected a Mycoplasma sp. in confiscated radiated tortoises (Astrochelys radiata) and spider tortoises (Pyxis arachnoides). Sequence analysis of the 16S-23S ribosomal RNA intergenic spacer region was consistent with Mycoplasma agassizii. Mycoplasma spp. have not been previously reported in native tortoises in Madagascar.

Microscopy and molecular survey of Hepatozoon spp. in domestic cats and their ticks: First report of H. silvestris from Türkiye

Hepatozoonosis is a tick-borne infection caused by protozoan species of the Hepatozoon genus in the family Hepatozoidae. This study aimed to determine the presence and prevalence of Hepatozoon spp. in domestic cats and their ticks, to characterize the genotypes, to reveal phylogenetic relationships, and to assess the risk factors associated with infection. Blood samples were collected in EDTA tubes from 311 cats that were brought to the Veterinary Faculty, Animal Hospital for treatment or routine control purposes. Smears were prepared from the buffy coat and examined microscopically for the presence of Hepatozoon spp. gamonts. Ticks were collected during the clinical examination of the cats and the species were identified. Genomic DNA obtained from buffy coats and ticks were analyzed using PCR analyses targeting the 18S rRNA gene region of Hepatozoon spp. The results showed that Hepatozoon spp. gamonts in neutrophils were determined in five samples as 1.6 % (5/311). A total of 58 (18.64 %, 58/311) were positive for the PCR analyses. Twelve ticks were collected from the cats, and all were identified as Rhipicephalus turanicus. Hepatozoon spp. were found in seven (58.3 %) ticks by molecular analyses. Sequence analysis of the 18S rRNA gene region of 58 positive isolates revealed the presence of H. felis (n = 25, 43.1 %) and H. silvestris (n = 33, 56.9 %) species in cats and H. felis in Rh. turanicus (n = 7). This study also presents the first report of H. silvestris in domestic cats from Türkiye. Phylogenetic analyses showed that our H. felis isolates clustered in H. felis genotype I and our H. silvestris were stated in the same cluster with Italian isolates.

Osteoporosis in postmenopausal women is associated with disturbances in gut microbiota and migration of peripheral immune cells

BackgroundPostmenopausal osteoporosis (PMO) results from a reduction in bone mass and microarchitectural deterioration in bone tissue due to estrogen deficiency, which may increase the incidence of fragility fractures. In recent years, the “gut-immune response-bone” axis has been proposed as a novel potential approach in the prevention and treatment of PMO. Studies on ovariectomized murine model indicated the reciprocal role of Th17 cells and Treg cells in the aetiology of osteoporosis. However, the relationship among gut microbiota, immune cells and bone metabolic indexes remains unknown in PMO.MethodsA total of 77 postmenopausal women were recruited for the study and divided into control (n = 30), osteopenia (n = 19), and osteoporosis (n = 28) groups based on their T score. The frequency of Treg and Th17 cells in lymphocytes were analyzed by flow cytometry. The serum levels of interleukin (IL)-10, 17 A, 1β, 6, tumor necrosis factor (TNF)-α, and lipopolysaccharide (LPS) were determined via enzyme-linked immunosorbent assay. Additionally, 16S rRNA gene V3-V4 region sequencing analysis was performed to investigate the gut microbiota of the participants.ResultsThe results demonstrated decreased bacterial richness and diversed intestinal composition in PMO. In addition, significant differences of relative abundance of the gut microbial community in phylum and genus levels were found, mainly including increased Bacteroidota, Proteobacteria, and Campylobacterota, as well as reduced Firmicutes, Butyricicoccus, and Faecalibacterium. Intriugingly, in the osteoporosis group, the concentration of Treg cells and associated IL-10 in peripheral circulation was negatively regulated, while other chronic systemic proinflammatory cytokines and Th17 cells showed opposite trends. Moreover, significantly elevated plasma lipopolysaccharide (LPS) in patients with osteoporosis indicated that disrupted intestinal integrity and permeability. A correlation analysis showed close relationships between gut bacteria and inflammation.ConclusionsCollectively, these observations will lead to a better understanding of the relationship among bone homeostasis, the microbiota, and circulating immune cells in PMO. The elevated LPS levels of osteoporosis patients which not only indicate a breach in intestinal integrity but also suggest a novel biomarker for assessing osteoporosis risk linked to gut health.

First Report of Rhizoctonia solaniAG‐4 HGI Causing Corky Cracks on Potato Tubers in Mauritius

ABSTRACTPotato (Solanum tuberosum L.) is of great economic importance for Mauritius. During a disease survey carried out in a field in one of the major potato‐growing regions of Mauritius, corky cracked lesions with halo and mycelial growth were observed on the skin surfaces of around 45% of tubers. The suspected fungus from the affected areas was isolated on amended potato dextrose agar and after 7 days, several fast‐growing, pale brown Rhizoctonia‐like colonies with a few sclerotia were observed. Additionally, microscopic analysis revealed some cells being multinucleate, forming hyphal branching at right angles with slight constriction together with septum near the branch base. Pathogenicity tests confirmed development of the same symptoms on potato tubers and the causal agent was reisolated successfully. Sequence analysis of the ITS region of representative isolate P114 amplified using ITS1F/ITS4 primers showed that it was identical to several isolates of multinucleate Rhizoctonia solani AG‐4 HGI, and neighbour‐joining phylogenetic analyses confirmed the identification. To our knowledge, this is the first report of R. solani AG‐4 HGI‐infecting potato tubers and causing corky cracks in Mauritius.

Genetic Diversity of Bluefish Population in Türkiye Coastal

Bluefish (Pomatomus saltatrix) is a commercially important, highly migratory predatory fish species distributed along the coasts of Türkiye. Conservation and sustainability of bluefish populations requires knowledge of the genetic structure of the population, but There are no genetic studies on bluefish in Türkiye. In this study, the population structure of Bluefish in the coastal regions of Türkiye was investigated by sequence analysis of mitochondrial DNA gene regions (Cytochrome b and Displacement-loop) and nuclear gene region (Rhodopsin). We tried to identify bluefish samples collected from 14 regions in the coastal region of Türkiye by analyzing two mtDNA gene sequences (Cyt b and D-loop) and nuclear gene region (Rhodopsin). While a total of 35 haplotypes were found in the Cytb gene region, a total of 132 haplotypes were found in the D-loop (control region) gene region. A single haplotype was detected in all stations for Rhodopsin. Also, the maximum likelihood trees based on Cyt b and D-loop sequences suggested relationship of Bluefish populations from Türkiye and the world. Results showed a low level of genetic differentiation between Bluefish populations in the study area, but Aegean and Mediterranean populations are more diverse than other populations due to migratory trait of this species.

Fungal endophytes Fusarium solani SGGF14 and Alternaria tenuissima SGGF21 enhance the glycyrrhizin production by modulating its key biosynthetic genes in licorice (Glycyrrhiza glabra L.).

To identify promising fungal endophytes that are able to produce glycyrrhizin and enhance it in licorice and the mechanisms involved. Fifteen fungal endophytes were isolated from Glycyrrhiza glabra L. rhizomes among which SGGF14 and SGGF21 isolates were found to produce glycyrrhizin by 4.29 and 2.58µg g-1 dry weight in the first generation of their culture. These isolates were identified as Fusarium solani and Alternaria tenuissima, respectively, based on morphological characteristics and sequence analysis of internal transcribed spacer, TEF1, ATPase, and CAL regions. Subsequently, G. glabra plants were inoculated with these fungal isolates to examine their effect on glycyrrhizin production, plant growth parameters and the expression of key genes involved in glycyrrhizin pathway: SQS1, SQS2, bAS, CAS, LUS, CYP88D6, and CYP72A154. Endophytes were able to enhance glycyrrhizin content by 133%-171% in the plants. Natural control (NC) plants, harboring all natural endophytes, had better growth compared to SGGF14- and SGGF21-inoculated and endophyte-free (EF) plants. Expression of SQS1, SQS2, CYP88D6, and CYP72A154 was upregulated by inoculation with endophytes. LUS and CAS were downregulated after endophyte inoculation. Expression of bAS was higher in SGGF21-inoculated plants when compared with NC, EF, and SGGF14-inoculated plants. Two selected fungal endophytes of G. glabra can produce glycyrrhizin and enhance glycyrrhizin content in planta by modulating the expression of key genes in glycyrrhizin biosynthetic pathway.

An Emerging Disease of Chickpea, Basal Stem Rot Caused by Diaporthe aspalathi in China.

Chickpea (Cicer arietinum L.) is an important legume crop worldwide. An emerging disease, basal stem rot with obvious wilt symptoms, was observed in the upper part of chickpea plants during the disease survey in Qiubei County of Yunnan Province. Three fungal isolates (ZD36-1, ZD36-2, and ZD36-3) were obtained from the diseased tissue of chickpea plants collected from the field. Those isolates were morphologically found to be similar to Diaporthe aspalathi. Molecular sequence analyses of multiple gene regions (ITS, tef1, tub2, cal, and his3) indicated that the three isolates showed a high identity with D. aspalathi. Pathogenicity and host range tests of the isolates were performed on the original host chickpea and eight other legume crops. The isolates were strongly pathogenic to chickpea and appeared highly pathogenic to soybean, cowpea, and mung bean; moderated or mild pathogenic to adzuki bean and common bean; however, the isolates did not cause symptoms on grass pea (Lathyrus sativus). Diaporthe aspalathi was previously reported as a main pathogen causing the southern stem canker in soybean. To our knowledge, this is the first report of D. aspalathi inducing basal stem rot on chickpea worldwide.

Molecular Identification of Encephalitazoon intestinalis and the Prevalence of Renal Microsporidiosis in Renal Transplant Recipients in Türkiye.

In patients with end-stage kidney disease, kidney transplantation is the kidney replacement therapy option that provides the most successful survival. However, immunosuppression agents administered after kidney transplantation can increase the risk of opportunistic infections. Microsporidia are obligate intracellular pathogens that can be fatal in immunosuppressed patients. The present study aimed to determine the prevalence of microsporidia in kidney transplantation recipients and the molecular characterization of the detected species. To evaluate the prevalence of renal microsporidiosis in kidney transplant recipients, the urine samples from a total of 325 patients were analyzed by real-time and nested polymerase chain reaction for Encephalitozoon spp. and Enterocytozoon bieneusi. Only one (0.4%) sample from the adult patient was positive for the Encephalitozoon species, while no positivity was found in pediatric patients. It was determined as Encephalitozoon intestinalis by ITS rRNA gene region sequence analysis. A microsporidia species obtained from humans in Türkiye has been characterized for the first time and registered in GenBank. Our epidemiological results show that the prevalence of renal microsporidiosis in kidney transplant recipients is very low. In addition, as a result of the phylogenetic analysis of the detected isolate, it was observed that it was 100% identical to the isolates reported from dogs in Kayseri, Türkiye. This situation provided essential data regarding the zoonotic transmission dynamics of microsporidia.

Complete coding region sequence analyses and antigenic characterization of emerging lineage G-IX of foot- and-mouth disease virus serotype Asia1

Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.

Phytophthora polonica and Phytophthora hydropathica from Clade 9 Associated with Alder Decline in Bulgaria.

A number of Phytophthora species have been identified as destructive plant pathogens and invasive species. They have the potential to affect a wide range of host plants and cause diseases in agricultural and forest ecosystems. Two Phytophthora species from rhizosphere soil samples collected from declining Alnus glutinosa in Bulgaria were isolated in the autumn of 2022. They were identified as Phytophthora polonica and Phytophthora hydropathica according to the DNA sequence analysis of the ITS region, as well as their morphological and physiological characteristics. The pathogenicity of both species to common and gray alder was evaluated by the inoculation of detached leaves and cuttings. Experimental data proved that P. polonica and P. hydropathica are able to cause leaf necrosis not only on A. glutinosa from which they were derived, but also on A. incana. No significant deference in the aggressiveness of the studied isolates from both Phytophthora species against the two tested plants was observed. Therefore, P. polonica and P. hydropathica were determined as potential threats for alder ecosystems in the country. This is the first report for the isolation of P. polonica in Bulgaria and represents the most southeastern point of the species distribution in Europe.

Diversity of unique, nonmycorrhizal endophytic fungi in cultivated Phalaenopsis orchids: A pilot study.

Orchids comprise one of the largest, most diverse, and most broadly distributed families of flowering plants and contribute significantly to habitat biodiversity. One key aspect of orchid growth and development is the formation of mycorrhizal symbioses with compatible endophytic fungi, which are maintained throughout the life of the plant. Substantial efforts to identify the fungi that form mycorrhizal symbioses across a range of orchid species have often also uncovered numerous nonmycorrhizal, endophytic fungi. These fungi could also have significant effects on orchid growth and development and are beginning to be analyzed more closely, particularly in wild species. The role of endophytic fungi in the production, distribution, and continued growth by the hobbyist of orchids is not known. As an initial step toward characterizing nonmycorrhizal endophytic fungi associated with cultivated orchids, we undertook a survey of fungi residing within roots of Phalaenopsis plants growing in home environments. Sequence analysis of ITS regions amplified from total DNA isolated from roots allowed rapid identification of endophytic fungi to the class level and may offer a useful initial screening method for beneficial species, for example, in horticultural settings. ITS-PCR sequences subsequently obtained from individual fungi cultured from surface-sterilized orchid roots corroborated the findings of the initial screen, while also providing a more complete characterization of the array of fungal taxa that were present. Although lower in diversity than has been reported for orchids growing in the wild, these endophytes have the potential to substantially enhance the growth and disease resistance of horticultural orchids.

Genetic and pathogenic characterization of Rhizoctonia solani AG-4 isolates obtained from common bean

Common bean (Phaseolus vulgaris L.) is the most important grain legume. Crop production of common bean is affected by a number of diseases, such as Rhizoctonia root rot, being detected worldwide. Herein, we aimed to genetically and pathologically characterize Rhizoctonia solani isolates obtained from different provinces in Turkey. Anastomosis groups (AG) and subgroups of isolates were identified based on the sequence analysis of the rDNA-ITS region. The most prevalent subgroup was AG-4 HGIII, according to BLAST analysis and the phylogeny of resultant sequences, followed by AG-4 HGI and AG-4 HGII, respectively. iPBS retrotransposons highly supported the phylogenetic tree and provided a high level of genetic variability among isolates to discriminate AG subgroups. The results indicated that the iPBS DNA marker system based on retrotransposons could be used to discriminate Rhizoctonia isolates relying on AG grouping. The virulence of the pathogen isolates changed from 3.67 to 5 based on the agar-plate assay on the susceptible cv. Gina. The reactions of thirty common bean cultivars were also evaluated against the most aggressive isolate in each subgroup. The reaction assay showed significant differences among both isolates and cultivars; the highest disease severity among cultivars was observed to AG-4 HGI, followed by AG-4 HGIII and AG-4 HGII, respectively. None of the cultivars showed resistance to all AG subgroups. Screening of AGs among the isolates and selecting cultivars are critical to managing Rhizoctonia disease due to the range of host suitability according to AG subgroups.

Clinicopathological characteristics and gene mutations in 11 patients with lipoprotein glomerulopathy

Objective Lipoprotein glomerulopathy (LPG) is a rare disorder characterized by the development of glomerular lipoprotein thrombosis. LPG exhibits familial aggregation, with mutations in the apolipoprotein E (APOE) gene identified as the leading cause of this disease. This study aimed to investigate APOE gene mutations and the clinicopathological features in eleven LPG patients. Methods Clinicopathological and follow-up data were obtained by extracting DNA, followed by APOE coding region sequencing analysis. This study analyzed clinical and pathological manifestations, gene mutations, treatment and prognosis. Results The mean age of the eleven patients was 33.82 years. Among them, five had a positive family history for LPG, ten presented with proteinuria, four exhibited nephrotic syndrome, and six presented with microscopic hematuria. Dyslipidemia was identified in ten patients. In all renal specimens, there was evident dilation of glomerular capillary lumens containing lipoprotein thrombi, and positive oil red O staining was observed in frozen sections of all samples. APOE gene testing revealed that one patient had no mutations, while the remaining ten patients exhibited mutations in the APOE gene, with three patients presenting with multiple mutations simultaneously. Following the confirmation of LPG diagnosis, treatment with angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB) was initiated, and the disease progressed slowly. Conclusion LPG is histologically characterized by lamellated lipoprotein thrombi in glomeruli, and kidney biopsy is essential for diagnosis. Mutations in the APOE gene are the leading cause of LPG. This study revealed clinicopathological characteristics and APOE gene mutations in patients with LPG, which helps us better understand the disease.

Evolution of the enhancer-rich regulatory region of the gene for the cell-type specific transcription factor POU1F1

Precise spatio-temporal expression of genes in organogenesis is regulated by the coordinated interplay of DNA elements such as promoter and enhancers present in the regulatory region of a given locus. POU1F1 transcription factor plays a crucial role in the development of somatotrophs, lactotrophs and thyrotrophs in the anterior pituitary gland, and in maintaining high expression of growth hormone, prolactin and TSH. In mouse, expression of POU1F1 is controlled by a region fenced by two CTCF sites, containing 5 upstream enhancer elements, designated E-A (5′ to 3′). Elements C, B and A correspond to elements shown previously to play a role in pituitary development and hormonal expression; functional roles for elements E and D have not been reported. We performed comparative sequence analysis of this regulatory region and discovered that three elements, B, C and E, are present in all vertebrate groups except Agnatha. One very long (>2 kb) element (A) is unique to mammals suggesting a specific change in regulation of the gene in this group. Using DNA accessibility assay (ATAC-seq) we showed that conserved elements in anterior pituitary of four non-mammals are open, suggesting functionality as regulatory elements. We showed that, in many non-mammalian vertebrates, an additional upstream exon closely follows element E, leading to alternatively spliced transcripts. Here, element E functions as an alternative promoter, but in mammals this feature is lost, suggesting conversion of alternative promoter to enhancer. Our work shows that regulation of POU1F1 changed markedly during the course of vertebrate evolution, use of a low number of enhancer elements combined with alternative promoters in non-mammalian vertebrates being replaced by use of a unique combination of regulatory units in mammals. Most importantly, our work suggests that evolutionary conversion of alternate promoter to enhancer could be one of the evolutionary mechanisms of enhancer birth.