CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.

MOTIVATION: Taxonomic classification of short reads and taxonomic profiling of metagenomic samples are well-studied yet challenging problems. The presence of species belonging to groups without close representation in a reference dataset is particularly challenging. While k-mer-based methods have performed well in terms of running time and accuracy, they tend to have reduced accuracy for such novel species. Thus, there is a growing need for methods that combine the scalability of k-mers with increased sensitivity. RESULTS: Here, we show that using locality-sensitive hashing (LSH) can increase the sensitivity of the k-mer-based search. Our method, which combines LSH with several heuristics techniques including soft lowest common ancestor labeling and voting, is more accurate than alternatives in both taxonomic classification of individual reads and abundance profiling. AVAILABILITY AND IMPLEMENTATION: CONSULT-II is implemented in C++, and the software, together with reference libraries, is publicly available on GitHub https://github.com/bo1929/CONSULT-II.

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.

MOTIVATION: With the wide availability of single-cell RNA-seq (scRNA-seq) technology, population-scale scRNA-seq datasets across multiple individuals and time points are emerging. While the initial investigations of these datasets tend to focus on standard analysis of clustering and differential expression, leveraging the power of scRNA-seq data at the personalized dynamic gene co-expression network level has the potential to unlock subject and/or time-specific network-level variation, which is critical for understanding phenotypic differences. Community detection from co-expression networks of multiple time points or conditions has been well-studied; however, none of the existing settings included networks from multiple subjects and multiple time points simultaneously. To address this, we develop Multi-subject Dynamic Community Detection (MuDCoD) for multi-subject community detection in personalized dynamic gene networks from scRNA-seq. MuDCoD builds on the spectral clustering framework and promotes information sharing among the networks of the subjects as well as networks at different time points. It clusters genes in the personalized dynamic gene networks and reveals gene communities that are variable or shared not only across time but also among subjects. RESULTS: Evaluation and benchmarking of MuDCoD against existing approaches reveal that MuDCoD effectively leverages apparent shared signals among networks of the subjects at individual time points, and performs robustly when there is no or little information sharing among the networks. Applications to population-scale scRNA-seq datasets of human-induced pluripotent stem cells during dopaminergic neuron differentiation and CD4+ T cell activation indicate that MuDCoD enables robust inference for identifying time-varying personalized gene modules. Our results illustrate how personalized dynamic community detection can aid in the exploration of subject-specific biological processes that vary across time. AVAILABILITY AND IMPLEMENTATION: MuDCoD is publicly available at https://github.com/bo1929/MuDCoD as a Python package. Implementation includes simulation and real-data experiments together with extensive documentation.

Endoscopic outcomes using a novel through-the-scope tack and suture system for gastrointestinal defect closure: a systematic review and meta-analysis.

BACKGROUND: Closure of gastrointestinal defects can reduce postprocedural adverse events. Over-the-scope clips and an over-the-scope suturing system are widely available, yet their use may be limited by defect size, location, operator skill level, and need to reinsert the endoscope with the device attached. The introduction of a through-the-scope helix tack suture system (TTSS) allows for closure of large irregular defects using a gastroscope or colonoscope, without the need for endoscope withdrawal. Since its approval 3 years ago, only a handful of studies have explored outcomes using this novel device. METHODS: Multiple databases were searched for studies looking at TTSS closure from inception until August 2023. The primary outcomes were the success of TTSS alone and TTSS with clips for complete defect closure. Secondary outcomes included complete closure based on procedure type (endoscopic mucosal resection [EMR], endoscopic submucosal dissection [ESD]) and adverse events. RESULTS: Eight studies met the inclusion criteria (449 patients, mean defect size 34.3 mm). Complete defect closure rates for TTSS alone and TTSS with adjunctive clips were 77.2% (95%CI 66.4-85.3; I2=79%) and 95.2% (95%CI 90.3-97.7; I2=42.5%), respectively. Complete defect closure rates for EMR and ESD were 99.2% (95%CI 94.3-99.9; I2 = 0%) and 92.1% (95%CI 85-96; I2=0%), respectively. The adverse event rate was 5.4% (95%CI 2.7-10.3; I2=55%). CONCLUSION: TTSS is a novel device for closure of postprocedural defects, with relatively high technical and clinical success rates. Comparative studies of closure devices are needed.

Gold(I)-catalyzed synthesis of N-alkenyl 2-pyridonyl sec-amines.

N-Alkenyl 2-pyridonyl amines are afforded in high yields via a gold-catalyzed rearrangement of 2-propargyloxypyridine and 2-(but-3-yn-1-yloxy)pyridine under acidic conditions. This approach exhibits significant utility due to its outstanding efficiency of conversion in the synthesis of secondary amines as a one-pot reaction. The initial step of the method involves a cyclization reaction for the production of pyridinium salts, followed by the next stage, where rearrangement is accomplished through the nucleophilic addition phenomenon. This approach provides the conversion of primary amines into secondary amines, resulting in a single product. Furthermore, the methodology presents a high degree of tolerance towards several pyridine and aniline derivatives, resulting in the formation of products with excellent yields.

Expression of placental growth factor, neuropilin-1, and neuropilin-2 in primary pterygium tissue.

PURPOSE: The aim of this study was to evaluate the expression of placental growth factor (PLGF), neuropilin-1 (NP-1), and neuropilin-2 (NP-2) molecules in primary pterygium tissue compared with normal conjunctival tissue. METHODS: The records of 42 patients who underwent excision surgery with autografts for primary pterygium (pterygium group) and 20 patients who underwent conjunctival nevus excision surgery (control group) in the same period were reviewed retrospectively. The samples obtained from the pterygium tissues in the pterygium group and the clean conjunctival tissues adjacent to the nevus in the control group were collected from the archive. Immunohistochemical stains of the primary antibodies-1/100 diluted PLGF, NP-1, and NP-2 (Abcam Cambridge Science Park, UK)-were applied to all groups. Staining intensities and the percentage of positive cells in epithelial, endothelial, stromal, and inflammatory cells were analyzed by an experienced pathologist. RESULTS: The positivity rates of PLGF and NP-2 expression in epithelial, endothelial, stromal, and inflammatory cells were found to be higher in the pterygium group than in the control group (PLGF: p < 0.001, p < 0.001, p = 0.001, and p < 0.001, respectively; NP-2: p < 0.001 for all). Staining intensities for PLGF and NP-2 were higher in the pterygium group than in the control group (PLGF: p < 0.001, p < 0.001, p = 0.005, and p < 0.001, respectively; NP-2: p < 0.001, p < 0.001, p = 0.001, and p < 0.001, respectively). However, no significant differences were found in any cell type in terms of NP-1 expression positivity rates (p = 0.730, p = 0.121, p = 0.524, and p = 0.624, respectively) or staining intensity (p = 0.716, p = 0.147, p = 0.147, and p = 0.780, respectively). CONCLUSION: PLGF and NP-2 levels were found to be higher in pterygium tissue, while there was no difference in NP-1. These results indicate the possible roles of NP-2 and PLGF in primary pterygium.

Genome-Based Reclassification of Anoxybacillus geothermalis Filippidou et al. 2016 as a Later Heterotypic Synonym of Anoxybacillus rupiensis Derekova et al. 2007.

In this study, our aim was to elucidate the relationship between Anoxybacillus rupiensis DSM 17127T and Anoxybacillus geothermalis GSsed3T through whole-genome phylogenetic analysis. The obtained 16S rRNA gene sequence from the genome of A. rupiensis DSM 17127T exhibited a 99.8% similarity with A. geothermalis GSsed3T. In the phylogenetic trees constructed using whole-genome sequences and 16S rRNA gene sequences, A. rupiensis DSM 17127T and A. geothermalis GSsed3T were observed to form a clade, indicating a close relationship between them. Moreover, the average amino acid identity, average nucleotide identity, and digital DNA-DNA hybridization values calculated between A. rupiensis DSM 17127T and A. geothermalis GSsed3T exceeded the threshold values typically used for species demarcation. Furthermore, the phylogenomic analysis based on the core genome of the strains in question provided additional support for the formation of a monophyletic clade by A. rupiensis DSM 17127T and A. geothermalis GSsed3T. Most phenotypic and chemotaxonomic features between both strains were almost identical except for a few exceptions. These findings suggest that both strains should be classified as belonging to the same species, and we propose that A. geothermalis GSsed3T is a later heterotypic synonym of A. rupiensis DSM 17127T.

Genetic Investigation of the Trail Mechanism in Diabetic and Non-diabetic Obese Patients.

Obesity is an important healthcare issue caused by abnormally increased adipose tissue because of energy-intake overcoming energy expenditure. Disturbances in the physiological function of adipose tissue mediate the development of diabetes. It is a metabolic disease that results from decreased insulin-levels and/or changes in the insulin action mechanism. Tumor Necrosis Factor-Associated Apoptosis-Inducing Ligand(TRAIL), which is a member of the Tumor Necrosis Factor(TNF)-family with an important role in adipose tissue biology, is included in many studies with its ability to induce apoptosis in cancer cells, but the number of human-studies conducted on the gene related to its protective-role against diabetes and obesity at this level is insufficient. Our study was carried out as a case and control and included three groups (80 diabetic obese, 80 non-diabetic obese, and 80 healthy individuals as the control group). The Real-Time-PZR(RT-qPZR), and DNA Sanger-Sequencing Methods were used for gene expression and gene squences. As a result of the analyses, TRAIL gene expression level was found to be higher in the controls than in the diabetic-obese and non-diabetic-obese group. This change in TRAIL gene expression suggests that TRAIL maybe a protective factor against diabetes. The presence of rs781673405, rs143353036, rs1244378045, rs767450259, rs759369504, rs750556128, and rs369143448 mutations, which was determined with the Sequencing-Method, was shown for the first time in the present study. In addition, it is the first study in which human TRAIL gene-expression and sequencing were performed together. We believe that these data will make an important contribution to the literature.

Comparison of blood ΒHBA measurement devices for diagnosis of subclinical pregnancy toxaemia in sheep: A field study.

Pregnancy toxaemia is a serious disease that occurs during the last trimester of pregnancy in sheep. Yet, in most cases, the disease may have a subclinical course. This study was aimed at comparing blood ßHBA measurement devices for diagnosis of subclinical pregnancy toxaemia in late pregnant sheep. In the study, a total of 50 blood samples were collected from Romanov (n = 30) and cross-bred Hamdani (n = 20) sheep. Blood ßHBA levels were measured using TaiDoc TD-4235 and CentriVet ßHBA hand-held meter. Randox ßHBA (Ranbut) assay was used as a reference laboratory method to compare hand-held meters. ßHBA value of 0.8 mmol/L was set as the cut-off value for diagnosis of subclinical pregnancy toxaemia. Statistical analyses were carried out using Minitab 21 and Jamovi software. In the study, the correlation of Randox-TaiDoc TD-4235 and Randox-CentriVet was .822 (p < .001) and .728 (p < .001), respectively. Based on the Ranbut assay, nine ewes out of 50 were diagnosed with subclinical pregnancy toxaemia. Specificity (detection of healthy ewes) and sensitivity (detection of ewes with subclinical pregnancy toxaemia) for TaiDoc TD-4235 and CentriVet hand-held meters were 100%, 77.8%, and 100%, 66.7%, respectively. In the receiver operating characteristic (ROC) analysis, areas under the ROC curve (AUC) were 0.976 and 0.920 for TaiDoc and CentriVet, respectively. Bland-Altman analysis revealed a bias of 0.092 mmol/L for TaiDoc and a bias of 0.132 mmol/L for CentriVet. TaiDoc hand-held meter shows a better correlation with the Randox Ranbut assay and greater sensitivity compared to the CentriVet hand-held meter. In conclusion, both TaiDoc and CentriVet hand-held meters can be securely used in the diagnosis of subclinical pregnancy toxaemia in sheep. For these reasons, subclinical pregnancy toxaemia and these devices will be evaluated within the scope of herd management programme in the sheep industry. It should also be taken into account that these conditions will affect the future fertility of the mother and offspring.

Anti-Müllerian hormone: A novel biomarker for detecting bovine freemartinism.

The anti-Müllerian hormone (AMH) indicates ovarian reserve in cattle, maintaining a consistent trajectory post-puberty. In heterosexual pregnancies, the development of the Müllerian duct in female foetuses is inhibited, resulting in an anticipated minimal or absent ovarian reserve capacity. This investigation aimed to compare AMH levels in healthy Holstein heifers that had reached puberty with those of freemartin animals of the same breed and age. The study incorporated Holstein heifers reaching puberty between 11 and 15 months of age in Group 1 (G1, n = 20) and freemartin animals in Group 2 (G2, n = 19, 16). AMH measurements (AMH-1/AMH-2) were recorded at 12-day intervals for the study participants. Notably, AMH levels in three freemartin animals could not be detected, prompting statistical analysis based on measurements from the remaining 16 freemartin animals in G2. A statistically significant correlation was observed between two separate measurements in G1 and G2 (p < .001). Furthermore, AMH-1 and AMH-2 levels were statistically higher in G1 than in G2 (p < .001). In G1, AMH-1 levels ranged from 227 to 677 pg/mL, with an average of 367.3 ± 25.5 pg/mL, and AMH-2 levels ranged from 234 to 645 pg/mL, with an average of 380.8 ± 24.4 pg/mL. Conversely, in G2, AMH-1 levels ranged from 10 to 72 pg/mL, with an average of 26.8 ± 4.44 pg/mL, and AMH-2 levels ranged from 12 to 68 pg/mL, with an average of 28.75 ± 4.18 pg/mL. The mean AMH levels in G1 were approximately 14 times higher than in G2 (p < .001). Consequently, ROC analysis utilizing AMH-1 and AMH-2 data established cut-off values of ≤72 and ≤ 68 pg/mL respectively for distinguishing freemartin animals. In conclusion, AMH could be used as a reliable biomarker for identifying Holstein freemartin animals.

Real-world evaluation of nivolumab in patients with non-nasopharyngeal recurrent or metastatic head and neck cancer: a retrospective multi-center study by the Turkish Oncology Group (TOG).

OBJECTIVES: Head and neck cancers (HNCs) represent a significant global health concern due to high morbidity and mortality rates. Despite therapeutic advances, the prognosis for advanced or recurrent cases remains challenging. Nivolumab obtained approval for recurrent or metastatic HNC based on the Phase III CheckMate 141 trial. This study aimed to evaluate the real-world outcomes of nivolumab in patients with non-nasopharyngeal HNC. DESIGN: In this multicenter retrospective study, we analyzed 124 patients with recurrent or metastatic non-nasopharyngeal HNC who received nivolumab in the second-line setting and beyond. Data were collected from 20 different cancer centers across Turkey. The effectiveness and safety of the treatment and survival outcomes were evaluated. RESULTS: Nivolumab exhibited favorable clinical responses, yielding an objective response rate of 29.9% and a disease control rate of 55.7%. Safety assessments revealed a generally well-tolerated profile, with no instances of treatment discontinuation or mortality due to side effects. Survival analysis disclosed a median overall survival (OS) of 11.8 (95% CI 8.4-15.2) months. Multivariate analysis revealed that ECOG-PS ≥ 1 (HR: 1.64, p = 0.045), laryngeal location (HR: 0.531, p = 0.024), and neutrophil-to-lymphocyte ratio > 3.5 (HR: 1.97, p = 0.007) were independent predictors of OS. CONCLUSIONS: Nivolumab is an effective and safe treatment option for patients with recurrent or metastatic non-nasopharyngeal HNC in real-world settings. Further studies are needed on factors affecting response to treatment and survival outcomes.

Triglyceride Glucose Index: A Potential Indicator in the Evaluation of Graves Ophthalmopathy.

PURPOSE: To determine the relationship between Graves ophthalmopathy (GO) and triglyceride glucose index (TGI) and to evaluate the predictive importance of this index in terms of GO activity. METHODS: This retrospective study included 20 inactive GO patients, 20 active GO patients, and 20 healthy controls. TGI was calculated using fasting plasma triglyceride and fasting plasma glucose levels and values were compared between the groups. The receiver operating characteristics curve was used to calculate the optimal TGI cutoff value and the sensitivity and specificity of this value between active and inactive GO groups. RESULTS: No significant difference was detected between the groups in terms of age and gender (p = 0.561 and p = 0.762, respectively). TGI value was 8.49 (8.41, 8.67) in the control group, 8.76 (8.74, 8.87) in the inactive GO group, and 9.06 (8.87, 9.08) in the active GO group (p < 0.001 for control group vs. inactive GO group; p < 0.001 for control group vs. active GO group; p = 0.001 for inactive GO group vs. active GO group). The optimal receiver operating characteristics cutoff value of TGI between active and inactive GO groups was 8.86 with 85% sensitivity and 75% specificity (area under curve: 0.837, p < 0.001, 95% confidence interval: 0.711-0.964). CONCLUSION: TGI was higher in both inactive and active GO patients compared with controls. It also appears that TGI may be used as a predictive marker indicating GO activity. This cheap and easily accessible parameter may be beneficial in detecting the disease and monitoring its activity in clinical practice.

Ultrasound and ultrasound shear-wave elastography evaluation of ulceroglandular type of tularemia.

INTRODUCTION: Ultrasound (US) has an important place in imaging ulceroglandular type patients with tularemia. This study is a case series addressing the imaging findings of US and US shear-wave elastography in ulceroglandular type tularemia. DESCRIPTION: Three patients, two women, and one man, were included in our case series. The patients were admitted to our hospital with neck swelling, pain, and a palpable mass. After the diagnosis of tularemia was made as a result of the examinations performed on the patients, they were evaluated again with US and US shear-wave elastography. DISCUSSION: Since there are many diagnoses including ulceroglandular tularemia in the differential diagnosis of swelling, pain, and palpable mass in the neck, the patient must undergo a thorough evaluation process. US shear-wave elastography can provide significant benefits in identification and treatment follow-up in order to understand the ulceroglandular mass formation observed in the neck in tularemia and the stiffness and morphology of the tissues in the lymph nodes where involvement is observed and to distinguish them from the surrounding tissue.

Corneal innervation changes in Alzheimer's: implications for sensory dysfunction.

PURPOSE: To compare, between Alzheimer's disease (AD) patients and healthy individuals, corneal subbasal nerve plexus (CSNP) parameters and corneal sensitivities. METHODS: Twenty-two patients who were followed up with Alzheimer's disease (Alzheimer's group) and 18 age- and gender-matched healthy individuals (control group) were included in this cross-sectional study. CSNP parameters, including nerve fiber length (NFL), nerve fiber density (NFD), and nerve branch density (NBD), were evaluated using in vivo confocal microscopy. Corneal sensitivity was evaluated using a Cochet-Bonnet esthesiometer. The results were compared between the two groups. RESULTS: In the Alzheimer's group, NFL was 12.2 (2.4) mm/mm2, NFD was 12.5 [3.1] fibers/mm2, and NBD was 29.7 [9.37] branches/mm2. In the control group, NFL was 16.5 (2.0) mm/mm2, NFD was 25.0 [3.13] fibers/mm2, and NBD was 37.5 [10.9] branches/mm2. All three parameters were significantly lower in the Alzheimer's group compared to the control group (p < 0.001, p < 0.001, and p = 0.001, respectively). Similarly, corneal sensitivity was significantly lower in the Alzheimer's group (55.0 [5.0] mm) compared to the control group (60.0 [5.0] mm) (p < 0.001). CONCLUSION: We determined that, in AD, corneal sensitivity decreases significantly, in parallel with the decrease in corneal nerves. Changes in the corneal nerve plexus and a decrease in corneal sensitivity may be used in the early diagnosis and follow-up of AD. In addition, ocular surface problems secondary to these changes should also be kept in mind.

Optical Coherence Tomography Angiographic Follow-Up in a Case of Subacute Sclerosing Panencephalitis and Unilateral Necrotising Retinitis.

We present a 20-year-old woman who was diagnosed with subacute sclerosing panencephalitis (SSPE) 20 months after presenting with unilateral retinitis. At presentation, the patient had two inferotemporal macular lesions in her left eye. Corresponding to these areas, optical coherence tomography (OCT) showed hyporeflective spaces with loss of nearly all of the retinal layers. OCT-angiography (OCTA) demonstrated some flow deficit areas with a reduction in the vessel density. Her serum measles antibody titre was high (IgG >5000.0 mIU/ml). Twenty months later the macular lesions had diminished in size, and there was some focal retinal thinning with interruption of the ellipsoid zone. OCTA showed that the flow deficit areas were diminished in size together with the relatively improved perfusion density. Neurological examination disclosed myoclonic jerks. Neuropsychological assessment demonstrated impaired executive function, attention, and narrowed lexical fluency. Measles IgG antibody was high in the cerebrospinal fluid (>230.0 U/ml). Brain magnetic resonance imaging demonstrated bilateral, non-specific, small foci of T2 hyperintensity in the frontoparietal subcortical white matter and centrum semiovale. The present case is the first where OCTA findings of SSPE-related retinal lesions have been described.

Heterologous expression, purification, and characterization of thermo- and alkali-tolerant laccase-like multicopper oxidase from Bacillus mojavensis TH309 and determination of its antibiotic removal potential.

Laccases or laccase-like multicopper oxidases have great potential in bioremediation to oxidase phenolic or non-phenolic substrates. However, their inability to maintain stability in harsh environmental conditions and against non-substrate compounds is one of the main reasons for their limited use. The gene (mco) encoding multicopper oxidase from Bacillus mojavensis TH309 were cloned into pET14b( +), expressed in Escherichia coli, and purified as histidine tagged enzyme (BmLMCO). The molecular weight of the enzyme was about 60 kDa. The enzyme exhibited laccase-like activity toward 2,6-dimethoxyphenol (2,6-DMP), syringaldazine (SGZ), and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). The highest enzyme activity was recorded at 80 °C and pH 8. BmLMCO showed a half-life of ~ 305, 99, 50, 46, 36, and 20 min at 40, 50, 60, 70, 80, and 90 °C, respectively. It retained more than 60% of its activity after pre-incubation in the range of pH 5-12 for 60 min. The enzyme activity significantly increased in the presence of 1 mM of Cu2+. Moreover, BmLMCO tolerated various chemicals and showed excellent compatibility with organic solvents. The Michaelis constant (Km) and the maximum velocity (Vmax) values of BmLMCO were 0.98 mM and 93.45 µmol/min, respectively, with 2,6-DMP as the substrate. BmLMCO reduced the antibacterial activity of cefprozil, gentamycin, and erythromycin by 72.3 ± 1.5%, 79.6 ± 6.4%, and 19.7 ± 4.1%, respectively. This is the first revealing shows the recombinant production of laccase-like multicopper oxidase from any B. mojavensis strains, its biochemical properties, and potential for use in bioremediation.

Genome-based reclassification of Anoxybacillus salavatliensis Cihan et al. 2011 as a later heterotypic synonym of Anoxybacillus gonensis Belduz et al. 2003.

In the present study, we aim to clarify the taxonomic positions of Anoxybacillus salavatliensis DSM 22626T and Anoxybacillus gonensis G2T by using whole genome phylogenetic analysis, biochemical and chemotaxonomic characteristics. The genome sequences of A. salavatliensis DSM 22626T was not available in any database, so it was sequenced in this study. In phylogenetic trees drawn using whole genome sequences and 16S rRNA gene sequences, A. salavatliensis DSM 22626T and A. gonensis G2T clade together and showed high sequence similarity (99.3%) based on 16S rRNA gene. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between A. salavatliensis DSM 22626T and A. gonensis G2T were found to be greater than the threshold values for species demarcation. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. salavatliensis DSM 22626T and A. gonensis G2T formed a monophyletic clade. Most phenotypic and chemotaxonomic features between both strains were almost identical except for a few exceptions. The present results show that A. salavatliensis DSM 22626T is a later heterotypic synonym of A. gonensis G2T.

Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis.

During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2 Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.

Differential expression of angiogenesis-related genes in goat uterus and corpus luteum during pregnancy.

Vascularization and the control of luteal and endometrial development are regulated by hypoxia-inducible factors (HIFs) and vascular endothelial growth factor (VEGF) during pregnancy. In this study, the mRNA and protein expression levels of HIFs (HIF1A, HIF2A and HIF3A) and VEGF in goat uterine and ovarian tissues during various stages of pregnancy were evaluated. A total of 42 Hair goats were used and were allocated into six groups, namely embryo-positive (G1), early pregnancy (G2), mid-term pregnancy (G3), late pregnancy (G4), oocyte-positive group (G5) and diestrus group (G6). The mRNA expression of the examined genes was evaluated by RT-qPCR, and protein expression was evaluated by immunohistochemistry (IHC). In caruncles, HIF1A mRNA expression was greater in G1, G2 and G4 than in G3 (p < .05). HIF1A and HIF2A expression was greater in G1 than in G5 (p < .05). In cotyledons, HIF1A, HIF2A and HIF3A mRNA expression was greater in G2 and G3 compared to G4 (p < .05). In luteal tissue, HIF1A mRNA expression was greater in G1 and G2 than in G3 and G4 (p < .05). In the immunohistochemical examination, HIF1A, HIF2A, HIF3A and VEGF immunoreactions were detected in uterine and luteal tissues. Findings suggest that HIFs and VEGF are involved in the regulation of ovarian functions as well as the processes of implantation and placentation.

Antimicrobial, antibiofilm, and anticancer potential of silver nanoparticles synthesized using pigment-producing Micromonospora sp. SH121.

Silver nanoparticles (AgNPs) have gained interest as an alternative pharmaceutical agent because of antimicrobial resistance and drug toxicity. Considering the increasing request, eco-friendly, sustainable, and cost-effective synthesis of versatile AgNPs has become necessary. In this study, green-made AgNPs were successfully synthesized using Micromonospora sp. SH121 (Mm-AgNPs). Synthesis was verified by surface plasmon resonance (SPR) peak at 402 nm wavelength in the UV-Visible (UV-Vis) absorption spectrum. Scanning electron microscopy (SEM) analysis depicted that Mm-AgNPs were in the size range of 10-30 nm and spherical. Fourier transform infrared spectroscopy (FTIR) confirmed the existence of bioactive molecules on the surface of nanoparticles. The X-ray diffraction (XRD) analysis revealed the face-centered cubic (fcc) structure of the Mm-AgNPs. Their polydispersity index (PDI) and zeta potential were 0. 284 and -35.3 mV, respectively. Mm-AgNPs (4-32 µg/mL) exhibited strong antimicrobial activity against Bacillus cereus, Enterococcus faecalis, Enterococcus hirae, Escherichia coli, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas putida, Staphylococcus epidermidis, Streptococcus pneumoniae, and Aspergillus flavus. Mm-AgNPs partially inhibited the biofilm formation in Acinetobacter baumannii, E. coli, K. pneumoniae, and Pseudomonas aeruginosa. Furthermore, results showed that low concentrations of Mm-AgNPs (1 and 10 µg/mL) caused higher cytotoxicity and apoptosis in DU 145 cells than human fibroblast cells. Based on the results, Mm-AgNPs have an excellent potential for treating infectious diseases and prostate cancer.

The comparative effect of creep and conventional feeding methods on growth performance and oxidative stress markers in Akkaraman lambs.

This study aimed to determine the effect of conventional and creep-feeding methods on growth performance and oxidative stress in Akkaraman (AKK) lambs. For this purpose, the AKK lambs (n = 60) used in this study were divided into four groups (15 n × 2 sex × 2 feeding methods), and all of them were fed the same ration. In the conventional feeding method, the lambs were taken to their dams for suckling twice a day and then kept in a separate compartment for further feeding. In contrast, in the creep-feeding method, the lambs always stayed with their mothers and had free access to supplementary feed by passing through the creep-feeding area. The data for body weights, body measurements, and saliva samples were collected five times, 14 days apart, to evaluate lambs' growth performance and oxidative stress markers. The results showed a higher (P < 0.05) body weight gain in the creep-fed group than in the conventional-fed group. The difference between creep and conventional feeding was significant (P = 0.033), but the difference between the groups in terms of gender was nonsignificant (P = 0.438). The males fed with the creep-feeding (CR-M) group had the largest body length (BL), pectoral chest width (PCW), chest depth (CD), chest circumference (CC), head length (HL), and head width (HW) measurements. The males fed with the conventional feeding (CO-M) group had the largest wither height (WH) measurement, and females fed with the conventional feeding (CO-F) group had the largest back length (BAL) body size. When the overall improvement in body measurements was considered, it was determined that the body sizes of many males in creep-feeding increased more than those of other feeding groups. The oxidative stress marker malondialdehyde (MDA) was higher (P < 0.001) in the conventional feeding group. Other oxidative stress markers, superoxide dismutase (SOD), catalase (CAT), and glutathione s-transferase (GSH-ST), were higher in the creep-feeding group (P < 0.001). Considering these findings, it is possible to conclude that creep-feeding is superior to conventional feeding to get a higher growth rate and reduce oxidative stress in AKK lambs.