Single-strand Conformation Polymorphism Research Articles

Effect of genetic polymorphisms in LALBA and Prolactin genes on milk traits in Barki ewes

This study investigated the genetic polymorphisms in Alpha-lactalbumin (LALBA) and Prolactin (PRL) genes in the Egyptian Barki sheep. The investigated genes were previously identified to be associated with milk and reproductive traits in several livestock species. Nevertheless, little is known about their contribution to milk traits in Egyptian sheep. Milk traits of daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP) were available for 256 and 233 Barki ewes for LALBA and PRL, respectively. The association analysis between the phenotypes of milk traits was carried out using the general linear model implemented in SAS software. The single strand conformation polymorphism identified 3 (A, B and C) and 2 (G and C) distinctive alleles in LALBA and PRL, respectively. Allele frequencies for LALBA variants were 0.73 (A), 0.16 (B) and 0.11 (C), and 0.63 (G), and 0.37 (C) for PRL variants. Results showed that age and parity of the ewe significantly (P < 0.05) influenced the studied milk traits. Additionally, a significant (P < 0.05) effect of LALBA variants was reported on milk composition but not DMY. Likewise, a significant (P < 0.05) effect of PRL variants was observed on DMY and TSP. Interestingly, Animals with BB genotypes of LALBA gene produced milk with high FP (5.65 ± 1.25 %), PP (5.77 ± 1.17 %), LP (7.4 ± 1.22 %) and lower TSP (13.06 ± 5.1 %) compared with animals that carry other genotypes. Regarding the PRL polymorphisms, the heterozygote ewes (GC) tended to significantly produce more milk (368.57 ± 20.39 g/day) with higher TSP (19.81 ± 1.57) compared with the homozygotes. This study reported the LALBA and PRL as candidate genes with significant effects on milk yield and composition, which may be appropriate for a wide range of selection programs with breeding objectives that focus on milk yield and composition in sheep. However, further investigations with larger sample size are recommended to confirm these findings with higher accuracy.

Association of ovine follistatin gene polymorphisms with body measurements, fat-tail traits and morphometric of head in Iranian Mehraban sheep

The mature body size of sheep is a polygenic trait that is used as a main selection criterion for increasing meat production through genetic selection. The purpose of this study was to characterize polymorphisms of the follistatin gene (FST locus), which is known to regulate muscle hypertrophy by inhibiting both myostatin and activin. Using single-strand conformation polymorphism analysis (SSCP) and Sanger sequencing, we examined polymorphisms of the ovine FST gene (OAR_v.3.1; Chr 16, NC_019473.1) in Iranian Mehraban sheep (n = 100, seven-month-old male lambs) with records of body measurements, fat-tails, and head morphometry. Among the nine SSCP patterns A to I, we identified five single nucleotide polymorphisms (SNPs), including g.25632659 G>C, g.25632701 G>A, g.25633069 A>G, g.25633069 A>T, and g.25634085 G>C. The only amino acid-altering variant was g.25632659 G>C in exon 3 (p.216Thr > Ser). According to a subsequent statistical analysis, SSCP patterns A (g.25632659 G/C, g.25632701 G/G), B (g.25632659 C/C, g.25632701 G/A), C (g.25632659 C/C, g.25632701 A/A), D (homozygous reference; g.25633069 A/A), E (heterozygous; g.25633069 A/G) and F (homozygous variant; g.25633069 T/T) were significantly (P < 0.05) connected with body measurements. Furthermore, patterns A and B had significantly (P ≤ 0.05) longer forehead lengths than the lambs with the pattern C. Pattern I (homozygous variant; g.25634085 C/C) was significantly associated with an increased mouth width, and decreased eye length compared to patterns H (heterozygous; g.25634085 G/C) and G (homozygous reference; g.25634085 G/G). The findings of this study provide primary evidence of linking between the polymorphisms of the FST gene and body size in a small panel of Iranian Mehraban sheep population.

Clinical significance of SPOP and APC gene alterations in colorectal cancer in Indian population.

Speckle-Type Poz Protein (SPOP) involved in the regulation of proteasome-mediated degradation of several oncoproteins, resulting in cancer initiation and progression. Mutations in Adenomatous Polyposis Coli (APC) gene is reported in most sporadic and hereditary colorectal cancer (CRC). Identifying the cellular changes involved in carcinogenesis when APC is mutated is an important issue that needs attention. The tumor suppressive function of SPOP and APC has long been a major focus in the research field of colorectal cancer. However, the clinical significance of SPOP and APC gene alteration in CRC has not been established to date. Mutational analysis was performed by single-strand conformational polymorphism followed by Sanger sequencing, methylation status by methylation-specific PCR, and protein expression by immunohistochemistry on 142 tumor tissues along with their adjacent non-cancerous specimens. The overall survival (OS) and recurrence free survival (RFS) were estimated by Kaplan-Meier Curve. Mutation rates of APC and SPOP gene were 2.8% and 11.9% while that of promoter hypermethylation were 37% and 47%, respectively. The grade of differentiation and Lymph node metastasis were significantly correlated with APC methylation pattern (p ≤ 0.05). The down regulation of APC was more often seen in colonic cancer compared to rectal cancer (p = 0.07) and more commonly in T3-4 depth of invasion (p = 0.07) and in patients without lymphovascular and perineural invasion (p = 0.007, p = 0.08 respectively). The median overall survival and recurrence free survival (RFS) was 67 & 36months while 3-yr and 5-yr OS and RFS were 61.1% & 56.4% and 49.2% & 44.8%, respectively. APC promoter methylation had a better overall survival (p = 0.035) while loss of SPOP expression had a worse survival (p = 0.09). Our findings reveal high percentage of SPOP gene mutations in CRC. A significant link is found between promoter hyper methylationand protein expression in all mutant cases of APC and SPOP, suggesting that both genes may be associated in the development of colorectal cancer in people of Indian decent. Hypermethylation of APC gene and loss of SPOP expression have shown an association with disease prognosis and could be further studied looking at its potential role in planning adjuvant treatment in CRC patients.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

One intron variant in the oocyte expressed protein (OOEP) gene is associated with twinning rate, prolificacy, and several body measurement traits in Awassi ewes

Awassi breed is an important sheep in the Middle East, but its lower twinning potential is a limitation against improvement. Due to the dynamic role of oocyte-expressed protein (OOEP) gene in controlling folliculogenesis, this study was conducted to evaluate the possible association between OOEP and twinning rate, as well as body measurement traits, in Awassi ewes. A total of 232 Awassi ewes (123 ewes-producing singletons and 109 ewes-producing twins) were included in this study. Three PCR fragments (OOEP-1 to OOEP-3) were designed to cover the majority of OOEP sequences and genotyped by single-strand conformation polymorphism (SSCP) method. One nucleic acid variant was identified in the intron-2 of OOEP-3, or rs430263839:A>G. Ewes with rs430263839:AG genotype showed variable significant values of larger head length, chest and abdominal circumferences, and higher prolificacy and twinning rates than ewes with the rs430263839:AA genotype. The conducted computations predicted that the detected SNP had caused altered splicing mechanisms in ewes with rs430263839:AG genotype. The increased abdominal and chest diameters in ewes with the rs430263839:AG genotype were thought to help the uterus accommodate more lambs. The predicted splicing alteration caused by this SNP is the putative mechanism by which these ewes may improve reproductive and productive traits. This is the first study that demonstrated the importance of OOEP as a potential biomarker for the twinning rate, prolificacy, and some body measurement traits in Awassi ewes with an opportunity to be introgressed to other breeds using large-scale association analysis.

Genetic variants and altered expression of SERPINF1 confer disease susceptibility in patients with otosclerosis.

Otosclerosis (OTSC) is a focal and diffuse bone disorder of the human middle ear characterized by abnormal bone growth and deposition at the stapes' footplate. This hinders the transmission of acoustic waves to the inner ear leading to subsequent conductive hearing loss. The plausible convections for the disease are genetic and environmental factors with yet an unraveled root cause. Recently, exome sequencing of European individuals with OTSCrevealed rare pathogenic variants in the Serpin Peptidase Inhibitor, Clade F (SERPINF1)gene. Here, we sought to investigate the causal variants of SERPINF1 in the Indian population. The gene and protein expression was also evaluated in otosclerotic stapes to ameliorate our understanding of the potential effect of this gene in OTSC. A total of 230 OTSC patients and 230 healthy controls were genotyped by single-strand conformational polymorphism and Sanger sequencing methods. Bycomparing the case controls, we identified five rare variants (c.72 C > T, c.151 G > A, c.242 C > G, c.823 A > T, and c.826 T > A) only in patients. Four variants c.390 T > C (p = 0.048), c.440-39 C > T (p = 0.007), c.643 + 9 G > A (p = 0.035), and c.643 + 82 T > C (p = 0.005) were found to be significantly associated with the disease. Down-regulation of SERPINF1 transcript level in otosclerotic stapes was quantified by qRT-PCR, ddPCR and further validated by in situ hybridization. Similarly, reduced protein expression was observed by immunohistochemistry and immunofluorescence in otosclerotic stapes that corroborate with immunoblotting of patients' plasma samples. Our findings identified that SERPINF1 variants are associated with the disease. Furthermore, reduced expression of SERPINF1 in otosclerotic stapes might contribute to OTSC pathophysiology.

Dahuang Zhechong pill attenuates hepatic sinusoidal capillarization in liver cirrhosis and hepatocellular carcinoma rat model via the MK/integrin signaling pathway.

Dahuang Zhechong pill (DHZCP), a traditional Chinese medicine, was derived from the famous book Unk "Synopsis of Prescriptions of the Golden Chamber" during the Han dynasty. Owing to its ability to invigorate the circulation of blood in Chinese medicine, DHZCP is usually used for treating liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Clinical application have shown that DHZCP exhibits satisfactory therapeutic effects in HCC adjuvant therapy; however, little is known about its underlying mechanisms. We aimed to clarify the mechanism of DHZCP against hepatic sinusoidal capillarization in rats with LC and HCC by inhibiting the MK/integrin signaling pathway of liver sinusoidal endothelial cells (LSECs). The contents of 29 characteristic components in DHZCP were determined by ultraperformance liquid chromatography-tandem mass spectrometry. DEN (Diethylnitrosamine)-induced LC and HCC rat models were constructed, and DHZCP was administered when the disease entered the LC stage. After 4 or 12 weeks of administration, hematoxylin and eosin staining, Masson staining, Metavir score, and SSCP (Single strand conformation polymorphism) gene mutation detection were used to confirm tissue fibrosis and cancer. The levels of NO, ET-1 and TXA2, which can regulate vasomotor functions and activate the MK/Itgα6/Src signaling pathway were evaluated by using immunohistochemistry, chemiluminescence, immunofluorescence, Western blot analysis, and enzyme-linked immunosorbent assay (ELISA). Similar methods were also used to evaluate the levels of VEGF, VEGFR, Ang-2 and Tie, which can promote pathological angiogenesis and activate the MK/Itgα4/NF-κB signaling pathway. In vitro cell experiments were performedusing potential pharmacodynamic molecules targeting integrins in DHZCP were selected by molecular docking, and the effects of these molecules on the function of LSECs were studied by Itgα4+ and Itgα6+ cell models. At the stage of LC, the animal experiments demonstrated that DHZCP mainly inhibited the MK/Itgα6 signaling pathway to increase the number and size of hepatic sinus fenestration, reversed the ET-1/NO and TXA2/NO ratios, regulated hepatic sinus relaxation and contraction balance, reduced the portal vein pressure, and inhibited cirrhotic carcinogenesis. At the HCC stage, DHZCP could also significantly inhibit the MK/Itgα4 signaling pathway, reduce pathological angiogenesis, and alleviate disease progression. The results of the cell experiments showed that Rhein, Naringenin, Liquiritin and Emodin-8-O-β-D-glucoside (PMEG) were involved in vascular regulation by affecting the MK/integrin signaling pathway. Liquiritin and PMEG mainly blocked the MK/α6 signal, which is important in regulating the vasomotor function of the liver sinus. Naringenin and Rhein mainly acted by blocked the signaling of MK/α4 action signal, which are potent molecules that inhibit pathological angiogenesis. DHZCP could improve the hepatic sinusoidal capillarization of LC and HCC by inhibiting the MK/Itgα signaling pathway and inhibited disease progression. Rhein, Naringenin, Liquiritin and PMEG were the main active molecules that affected the MK/Itgα signaling pathway.

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

Dva ko-nasleđena SNPs gena telomeraza reverzne transkriptaze (TERT) koja se dovode u vezu sa pacijentima od raka pluća u Iraku

Background: The telomerase reverse transcriptase (TERT) gene is essential polymorphic loci linked to most malignant tumors. This study assessed the association between the TERT gene and non-small cell lung carcinoma (NSCLC) in Iraq. Methods: Genomic DNA samples were extracted from a total of 200 samples of blood. Four specific PCR fragments were designed to amplify four high-frequency rs2735940, rs2736098, rs2736100, and rs10069690 SNPs within the TERT gene. Single-strand conformation polymorphism (SSCP) followed by sequencing reactions were used for genotyping and validating the amplified fragments. Results: Individuals with the genotype rs2735940: A/G were at a significantly greater risk of developing NSCLC (P=0.0299; OD 2.3158; Cl95% 1.0853 to 4.9414). Individuals with the genotype rs2736098: C/T were also significantly associated with the increased likelihood of developing NSCLC (P=0.0363; OD 2.1583; Cl95% 1.0503 to 4.4351). Linkage disequilibrium analysis showed that both SNPs showed a very high level of patient coinheritance. The LD plot showed that allele T of rs2736098 had collaborated with allele G of rs2735940 to generate TG haplotype in patients. According to our findings, both TERTrs2735940: A/G and TERT-rs2736098: C/T SNPs were found to be significant associations with the elevated risk of NSCLC. Both SNPs showed the highest values of co-inheritance in patients. This co-inheritance is mainly represented by alleles rs2735940: A and rs2736098: C. Both pathogenic T and G alleles have generated TG haplotype that is only available in patients' samples. Conclusion: This study suggests employing the haplotype TG as a promising biomarker for the early diagnosis of NSCLC. These findings need further validation by largescale investigation with a larger size of samples in the study population.

Polimorfismo dos genes DGAT e LEP e sua associação com características de carcaça e perfil lipídico da carne de bovinos nelore

ABSTRACT The objective of this study was to evaluate the association of polymorphisms in the diacylglycerol acyltransferase ( DGAT ) and leptin ( LEP ) genes with the performance, carcass characteristics, meat quality, and lipid profile of Nellore cattle. A total of 100 intact male Nelore cattle were used to analyze the performance, carcass, physicochemical and centesimal composition, and fatty acid profile of beef. To identify the polymorphisms, the PCR–single-strand conformation polymorphism (SSCP) technique was applied to genomic DNA extracted from muscle tissue. The SSCP technique revealed the presence of four band patterns for the DGAT gene (AC, AD, AE and BB) with five alleles (A, B, C, D and E). For the LEP gene, five band patterns (AA, AB, AC, BB and BC) with three alleles (A, B and C) were observed. For the LEP gene, the AB genotype was associated with higher backfat thickness and ribs weight, while the BB genotype was associated with lower ribs yield; higher hindquarter yield was associated with AC and BB genotypes. Higher contents of C17:0, C18:0 and lower contents of C18:2ω6C, total polyunsaturated fatty acids, total ω6 and ratio of polyunsaturated and saturated fatty acids (PUFA/SFA) were verified for the AC genotype of the LEP gene. The AC and AA genotypes of the LEP gene were associated with higher means of C15:0 and C18:1ω9t. For the DGAT gene, the highest C24:0 content was associated with the AE genotype and the lowest with the AD and BB genotypes. Polymorphisms in the DGAT and LEP genes influence carcass parameters and the lipid profile of the meat of Nellore cattle.

Microbiomes of soil and roots of two palm species infected with ‘Candidatus Phytoplasma palmae’ in two different ecosystems: Single strand conformation polymorphism analysis

Microbiomes of soil and roots of two palm species infected with ‘Candidatus Phytoplasma palmae’ in two different ecosystems: Single strand conformation polymorphism analysis

SEQUENCE VARIATIONS AND HAPLOTYPIC DIVERSITY IN THE MYOSTATIN GENE OF NIGERIAN CATTLE BREEDS

The myostatin gene (MSTN) encodes myostatin protein (MSTN), whose function involves regulating muscle growth and development. Using Polymerase Chain Reaction coupled with Single Strand Conformational Polymorphism analysis with nucleotide sequencing, a total of 161 animals from four different breeds and cross breeds of Nigerian cattle were genotyped at the introns 1 and 2 region, as well as exons 1, 2 and 3. Sixteen SNPs were identified, two (c.374- 796C&gt;T and c.374-762C&gt;T) of which are novel and are reported here. The identification of new as well as previously reported genetic variations in MSTN within this species provides more insight into the polymorphic nature of this gene. Thus, providing an important resource forfurther studies around genomic selection and breeding.

​Identification of Lactic Acid Bactria in Dairy Products using Culture-independent Methods: A Review

The microbiota of dairy products is composed of starter and non-starter lactic acid bacteria, as well as other bacteria, yeasts and filamentous fungi that form secondary microbiota and play an important role in cheese ripening. The use of combined LAB strains based on compatibility and/or coexistence tests plays an important role in food production and preservation, while combinations of strains that exhibit mutually inhibitory properties must be avoided. For centuries, researchers have focused on the exploration of autochthonous LAB biodiversity from various ecological dairy niches in order to address its role in texture and flavour formation and to select strains for use as starter cultures. Recent advanced technological tools like next-generation sequencing machines have played a significant role in the fast and accurate characterization and isolation of microbial communities from dairy products. However, the characterization and isolation of LAB using culture-independent methods is also a reliable and cost-effective method for studying a bacterial community without prior cultivation. These methods include single-strand conformation polymorphism (SSCP-PCR), denaturing gradient gel electrophoresis (DGGE), thermal gradient gel electrophoresis (TGGE), real-time PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), automated ribosomal intergenic spacer analysis (ARISA), and fluorescence in situ hybridization (FISH). Therefore the goal of this review is to compare and describe the most recent culture-independent molecular-based methods for the characterization and isolation of LAB in dairy products.

Single and combined effects of Pythium oligandrum Po37 and a consortium of three rhizobacterial strains on Sclerotinia stem rot severity and tomato growth promotion

Individual plant growth-promoting rhizobacterial (PGPR) strains (Bacillus thuringiensis B2, Bacillus subtilis B10 and Enterobacter cloacae B16) and their combination were used, with or without Pythium oligandrum, against Sclerotinia sclerotiorum. In vitro, all biological control agents (BCAs) reduced successfully hyphal growth of the targeted pathogenic fungus. They displayed antifungal activity by more than 50% compared to controls. In planta trials were conducted two years in the row and led to a significant decrease in stem rot severity two months after the antagonist’s application onto infected tomato plants. The reduction reached 75% using rhizobacterial mixtures and 72% using P. oligandrum alone, compared to controls. The plant growth-promoting potential of the three-strain consortium and P. oligandrum was also assessed. Increased height in disease-free plants was obtained with rhizobacterial mixtures (60%) compared to P. oligandrum (47%). The BCA’s mixture increased the height of treated plants inoculated with S. sclerotiorum (up to 80%) compared to inoculated and untreated plants. The fresh weight of the aerial parts and roots of disease-free plants was increased by 42 and 30% over control following their treatment with mixtures of rhizobacteria and P. oligandrum alone, respectively. On plants inoculated with S. sclerotiorum in both trials, the highest growth-enhancing effect was achieved using the combined treatment based on P. oligandrum and the three-strain rhizobacterial consortium (Po37 + B2 + B10 + B16). The rhizospheric microbial communities were assessed using Single Strand Conformational Polymorphism (SSCP). Differences in the genetic structure of the fungal and bacterial communities were observed following treatments applied in both trials.

A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes

This study aimed to assess the possible association of oxytocin (OXT) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR—single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C > A → p.Arg55Leu). A significant (p < 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all in silico tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.

Helicobacter pylori virulent genes and host interleukin 1 are associated with demographic factors for an increased risk of gastritis

AimHelicobacter pylori is a predominant pathogen for the human race and causes gastrointestinal diseases as well as can be an increased risk for cancer. This study examined the bacterial and host genes involved in gastritis and the environmental influences to understand the disease outcome. MethodsPolymerase chain reaction assay was used to analyze the variations in virulence-associated genes of H. pylori in gastritis patients. Human interleukin 1 beta gene polymorphisms and IL-1 receptor antagonist gene (IL-1RN intron 2) variable number tandem repeats were evaluated by PCR and single-strand conformation polymorphism analysis, respectively. Various demographic factors were analyzed and all the statistical tests were two-sided. ResultsInfection with cagA, cagA – Asian lineage positive strains of H. pylori was associated with an increased risk for gastritis. IL-1B-511*T carriers homozygous for the short allele of IL-1RN (IL-1RN*2/*2) had an increased risk for gastritis for the cagA carrier. The odd ratio (OR – 0.17; 95% CI – 0.03 to 0.08; P = 0.04) was significant in certain bacterial (cagA) and host (IL-1RN*2) high-risk genotypes in the gastritis patients. ConclusionThe pathogen and the host genetics in relation to lifestyle habits provide a tool for defining the high-risk individuals and strategize H. pylori eradication programs.

Genotyping and Identification of Antigen B Gene Polymorphism of Echinococcus granulosus in Edirne, Thrace, and the First Report of Genotype G2 (Tasmanian Sheep Strain) in Turkey

Echinococcus granulosus is the causative agent of cystic echinococcosis in humans and livestock. It is common worldwide. Cystic echinococcosis is still an important public health problem in Turkey, which is an endemic region. To genotype Echinococcus granulosus isolates and investigate antigen B gene polymorphism in Thrace, Turkey. A cross-sectional study. Seventy-five hydatid cyst materials obtained between June 2020 and May 2021 were included in the study. Hydatid cyst materials were collected from 12 humans from various hospitals in Edirne and 63 from slaughterhouse animals during the same period. Cyst materials were localized in 8 livers and 4 lungs in humans, 23 livers and 17 lungs in cattle, and 13 livers and 10 lungs in sheep. In the first step, the 12S ribosomal RNA gene was amplified by polymerase chain reaction for all samples and run on an agarose gel. Band patterns were used for strain typing. Then, the selected samples that represented each of the band patterns obtained by single-strand conformation polymorphism analysis were sequenced for AgB1, AgB2, mt-CO1, and mt-ND1 genes. Three different genotypes in Edirne, Thrace, Turkey, were observed for Echinococcus granulosus: G1 (domestic sheep strain), G2 (Tasmanian sheep strain), and G3 (buffalo strain). G1 was the dominant genotype in Edirne, and G3 was the second most common. Additionally, polymorphism in AgB1 and AgB2 gene regions was found. This study is the first to report on Echinococcus granulosus G2 (Tasmania sheep strain) in Turkey and G3 (buffalo strain) and antigen B polymorphism in Thrace. The study results will contribute to the prevention and control programs for cystic echinococcosis in Turkey and worldwide.

CRISPR/LbCas12a-mediated targeted mutation of Gracilariopsis lemaneiformis (Rhodophyta).

CRISPR/LbCas12a-mediated targeted mutation of Gracilariopsis lemaneiformis (Rhodophyta).

Detection of Theileria orientalis Genotypes from Cattle in Kyrgyzstan.

The ikeda and chitose genotypes of Theileria orientalis, which for many years were thought to be benign, cause a disease that results in significant economic losses in the cattle industry. This study was carried out in order to determine the genotypes of T. orientalis in cattle in Kyrgyzstan, and 149 archived DNA samples known to be T. orientalis were analyzed by the PCR amplification of the major piroplasm surface protein (MPSP) gene region. Single-Strand Conformation Polymorphism (SSCP) analysis was performed to uncover the nucleotide changes in the archived DNA samples, and 15 samples showing different band profiles were subjected to sequence analysis. As a result of the sequence analysis, it was seen that the samples belonged to the buffeli and chitose A genotypes. In order to identify mixed genotypes, PCR was performed using primers specific for these genotypes, and buffeli (type 3), chitose (type 1) and buffeli+chitose were found to be positive in 26.2%, 2% and 71.8% of samples, respectively. As a result of this study, we showed the presence of buffeli (type 3) and chitose (type 1) genotypes of T. orientalis in cattle in Kyrgyzstan. Comprehensive epidemiological studies are needed to understand the clinical infections caused by the pathogenic chitose A and to determine the geographical distribution and different genotypes of T. orientalis.

Map-based cloning and transcriptome analysis of the more-tiller and small-grain mutant in rice.

A G to T nucleotide substitution of OsTSG2 led to more tillers and smaller grains in rice by participating in phytohormone signal transduction and starch and sucrose metabolism. Rice is one of the most important food crops worldwide. Grain size and tiller number are the most important factors determining rice yield. The more-tiller and small-grain 2 (tsg2) mutant in rice, developed by ethyl methanesulfonate (EMS) mutagenesis, has smaller grains, more tillers, and a higher yield per plant relative to the wild-type (WT). Based on the genetic analysis, the tsg2 traits were conferred by a single recessive nuclear gene located on the long arm of chromosome 2. After fine-mapping the OsTSG2 locus, a G to T nucleotide substitution was identified, which resulted in an A to S mutation in a highly conserved domain of the growth-regulation factor protein. The single-strand conformation polymorphism (SSCP) marker was developed based on the SNP associated with the phenotypic segregation of traits. The functional complementation of OsTSG2 from the tsg2 mutant to the WT led to an increase in grain size and weight. The differentially expressed genes (DEGs) identified by RNA sequencing were involved in phytohormone signal transduction and starch and sucrose metabolism. Enzyme-linked immunosorbent assay (ELISA) analysis detected variation in the indole acetic acid (IAA) and jasmonic acid (JA) content in the tsg2 inflorescence, while the cellular organization, degree of chalkiness, gel consistency, amylose content, and alkaline spreading value were affected in the tsg2 grains. The findings elucidated the regulatory mechanisms of the tsg2 traits. This mutant could be used in marker-assisted breeding for high-yield and good-quality rice.