High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population.

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.

Small Warriors of Nature: Novel Red Emissive Chlorophyllin Carbon Dots Harnessing Fenton-Fueled Ferroptosis for In Vitro and In Vivo Cancer Treatment.

The appeal of carbon dots (CDs) has grown recently, due to their established biocompatibility, adjustable photoluminescence properties, and excellent water solubility. For the first time in the literature, copper chlorophyllin-based carbon dots (Chl-D CDs) are successfully synthesized. Chl-D CDs exhibit unique spectroscopic traits and are found to induce a Fenton-like reaction, augmenting photodynamic therapy (PDT) efficacies via ferroptotic and apoptotic pathways. To bolster the therapeutic impact of Chl-D CDs, a widely used cancer drug, temozolomide, is linked to their surface, yielding a synergistic effect with PDT and chemotherapy. Chl-D CDs' biocompatibility in immune cells and in vivo models showed great clinical potential.Proteomic analysis was conducted to understand Chl-D CDs' underlying cancer treatment mechanism. The study underscores the role of reactive oxygen species formation and pointed toward various oxidative stress modulators like aldolase A (ALDOA), aldolase C (ALDOC), aldehyde dehydrogenase 1B1 (ALDH1B1), transaldolase 1 (TALDO1), and transketolase (TKT), offering a deeper understanding of the Chl-D CDs' anticancer activity. Notably, the Chl-D CDs' capacity to trigger a Fenton-like reaction leads to enhanced PDT efficiencies through ferroptotic and apoptotic pathways. Hence, it is firmly believed that the inherent attributes of Chl-CDs can lead to a secure and efficient combined cancer therapy.

Evaluation of the Patients with the Diagnosis of Pontocerebellar Hypoplasia: A Multicenter National Study.

Pontocerebellar hypoplasia (PCH) is a heterogeneous group of neurodegenerative disorders characterized by hypoplasia and degeneration of the cerebellum and pons. We aimed to identify the clinical, laboratory, and imaging findings of the patients with diagnosed PCH with confirmed genetic analysis. We collected available clinical data, laboratory, and imaging findings in our retrospective multicenter national study of 64 patients with PCH in Turkey. The genetic analysis included the whole-exome sequencing (WES), targeted next-generation sequencing (NGS), or single gene analysis. Sixty-four patients with PCH were 28 female (43.8%) and 36 (56.3%) male. The patients revealed homozygous mutation in 89.1%, consanguinity in 79.7%, pregnancy at term in 85.2%, microcephaly in 91.3%, psychomotor retardation in 98.4%, abnormal neurological findings in 100%, seizure in 63.8%, normal biochemistry and metabolic investigations in 92.2%, and dysmorphic findings in 51.2%. The missense mutation was found to be the most common variant type in all patients with PCH. It was detected as CLP1 (n = 17) was the most common PCH related gene. The homozygous missense variant c.419G > A (p.Arg140His) was identified in all patients with CLP1. Moreover, all patients showed the same homozygous missense variant c.919G > T (p.A307S) in TSEN54 group (n = 6). In Turkey, CLP1 was identified as the most common causative gene with the identical variant c.419G > A; p.Arg140His. The current study supports that genotype data on PCH leads to phenotypic variability over a wide phenotypic spectrum.

Neuromuscular disease genetics in under-represented populations: increasing data diversity.

Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.

Evaluation of clinical, laboratory, and molecular genetic features of patients with biotinidase deficiency.

Biotinidase deficiency (BD) is an autosomal recessive inherited metabolic disorder which results from the inability of biotin-dependent carboxylase enzymes to function due to the release and absorption of biotin, leading to neurological and cutaneous findings. In the present study, evaluation of demographic characteristics, clinical findings, laboratory results, molecular genetic characteristics, and genotype-phenotype correlations of cases with BD. Two hundred forty-seven cases were included in the study who were admitted to the Department of Pediatric Metabolism of Ankara Bilkent City Hospital after being identified with potential BD through the Newborn Screening Program (NBS), during family screening or based on suspicious clinical findings, or following the detection of a pathogenic variant in a BTD genetic analysis during the period of October 2020 and February 2022. The medical files of the cases were reviewed retrospectively. An analysis of the admission routes of all cases to our clinic revealed 89.5% NBS, 5.7% family screening, and 4.9% suspicious clinical findings suggestive of BD. Complete enzyme deficiency was identified in 19.8%, partial enzyme deficiency in 55.1%, and heterogenous enzyme deficiency in 9.7%. The most common pathogenic variants were c.1270G > C (p.Asp424His), c.410G > A (p.Arg137His), and c.38_44delGCGCTGinsTCC (p.Cys13Phefs*36) in BTD gene. The c.1270G > C variant was most common in patients with cutaneous symptoms. The c.410G > A and c.38_44delGCGCTGinsTCC variants were more common in the patients with neurological symptoms. The mean activity level in patients with the c.1270G > C homozygous variant was statistically significantly higher than the mean activity level in the c.1270G > C compound heterozygous patients and the activity level of patients without the c.1270G > C variant. The mean activity level in c.410G > A homozygous patients was statistically significantly lower than the mean activity level of the c.410G > A compound heterozygous patients and the activity level of patients without the c.410G > A variant. In the course of our study, four new pathogenic variants were detected, namely: c.190G > A (p.Glu64Lys), c.249 + 5G > T, c.228delA (p.Val77*), and c.682A > G (p.Ile228Val).     Conclusions: The present study has determined the clinical and genetic spectrum of a large group of patients with BD in a single center. The frequent mutations in our study were similar to those reported in literature, and four novel variants were also described. What is Known: • Biotinidase deficiency is an autosomal recessive, treatable inborn error of metabolism. Two hundred ninety-four pathogenic variants in the BTD gene have been identified and the c.1270G > C variant is the most frequent BTD gene mutation in both Turkey and around the world. What is New: • Four new pathogenic variants (c.190G > A, p.Glu64Lys; c.249 + 5G > T; c.228delA, p.Val77*; and c.682A > G, p.Ile228Val) have been identified. It is believed that the c.38_44delGCGGCTGinsTCC variant is more commonly seen in individuals with ocular issues; however, further genotype-phenotype correlations are needed.

High diagnostic yield of targeted next-generation sequencing panel as a first-tier molecular test for the patients with myopathy or muscular dystrophy.

Muscular dystrophies are a heterogeneous group of neuromuscular disorders with a wide range of the clinical and genetic spectrum. Whole-exome sequencing (WES) has been on the rise to become the usual method of choice for molecular diagnosis in patients presenting with muscular dystrophy or congenital or metabolic myopathy phenotype. Here, we used a panel with 47 genes including not only muscular dystrophy but also myopathy-associated genes that had been used as a first-tier approach. A total of 146 patients who were referred to our clinic with the prediagnosis of muscular dystrophy and/or myopathy were included in the study. Dystrophin gene deletion/duplication was ruled out on the patients with a preliminary diagnosis of Duchenne muscular dystrophy. In this study, the molecular etiology of 67 patients was proved with the gene panel with a diagnostic yield of 46%. Causal variants were identified in 23 genes including CAPN3(11), DYSF(9), DMD(8), SGCA(5), TTN(4), LAMA2(3), LMNA(3), SGCB(3), COL6A1(3), DES (2), CAV3(2), FKRP(2), FKTN(2), ANO5, COL6A2, CLCN1, GNE, POMGNT1, POMGNT2, POMT2, SYNE1, TCAP, and FLNC with 16 novel variants. There were 27 patients with uncertain molecular results including the ones who had a variant of uncertain significance, who had only one heterozygous variant for an autosomal recessive disease, and the ones who had two variants in different genes. Molecular diagnosis in muscular dystrophy is essential to plan clinical management and choosing treatment options. Also, the results will affect the reproduction options. Targeted next-generation sequencing is a cost-effective method that reduces the WES requirements with a significant diagnostic rate.

Prevalence of DDC genotypes in patients with aromatic L-amino acid decarboxylase (AADC) deficiency and in silico prediction of structural protein changes.

Aromatic L-amino acid decarboxylase (AADC) deficiency is a rare autosomal recessive genetic disorder affecting the biosynthesis of dopamine, a precursor of both norepinephrine and epinephrine, and serotonin. Diagnosis is based on the analysis of CSF or plasma metabolites, AADC activity in plasma and genetic testing for variants in the DDC gene. The exact prevalence of AADC deficiency, the number of patients, and the variant and genotype prevalence are not known. Here, we present the DDC variant (n = 143) and genotype (n = 151) prevalence of 348 patients with AADC deficiency, 121 of whom were previously not reported. In addition, we report 26 new DDC variants, classify them according to the ACMG/AMP/ACGS recommendations for pathogenicity and score them based on the predicted structural effect. The splice variant c.714+4A>T, with a founder effect in Taiwan and China, was the most common variant (allele frequency = 32.4%), and c.[714+4A>T];[714+4A>T] was the most common genotype (genotype frequency = 21.3%). Approximately 90% of genotypes had variants classified as pathogenic or likely pathogenic, while 7% had one VUS allele and 3% had two VUS alleles. Only one benign variant was reported. Homozygous and compound heterozygous genotypes were interpreted in terms of AADC protein and categorized as: i) devoid of full-length AADC, ii) bearing one type of AADC homodimeric variant or iii) producing an AADC protein population composed of two homodimeric and one heterodimeric variant. Based on structural features, a score was attributed for all homodimers, and a tentative prediction was advanced for the heterodimer. Almost all AADC protein variants were pathogenic or likely pathogenic.

Impact of Inflammation-Related Genes on COVID-19: Prospective Study at Turkish Cohort.

The pandemic coronavirus disease 2019 (COVID-19) has caused a high mortality rate and poses a significant threat to the population. The disease may progress with mild symptoms or may cause the need for intensive care, depending on many factors. In this study, it was aimed to determine if there is a tendency due to genetic factors in COVID-19 patients. Ninety-four of 188 patients with mild clinical and 94 with severe clinical symptoms were included in the study. The targeted panel including coagulopathy (F2, F5), viral invasion (ACE2), and inflammation (CXCL8, IFNAR2, IFNL4, IL10, IL2, IL6, IRF7, TLR3, TLR7, TNF) related genes was performed sequenced by the next generation sequencing (NGS). The variants found were classified and univariate analyses were performed to select candidate variables for logistic model. Risk factors and variants were compared. It was revealed that the presence of 2 or more risk factors caused the disease to progress severely (p < 0.001). Heterozygous IRF7:c.1357-23dup variant had a 2.5 times higher risk for mild disease compared to severe disease. Other variants were found to be more significant in mild disease. Since polymorphic variants were not evaluated in the literature, the findings of our study could not be compared with the literature. However, as variants that may be effective in the severity of infections may differ according to ethnicity. This study has the feature of being a guide for subsequent studies to be carried out especially in Turkish population. Clinical course of the COVID-19 is likely to depend on a variety of risk factors, including age, sex, clinical status, immunology and genetic factors.

Analyzing the Impact of Ramalina digitellata, R. fastigiata, R. fraxinea, and R. polymorpha's Usnic Acid Concentration on Antioxidant, DNA-Protective, Antimicrobial, and Cytotoxic Properties.

The present study is focused on the antimicrobial, antioxidant, cytotoxic, and DNA protective effects of methanol extract obtained from R. digitellata, R. fastigiata, R. fraxinea, and R. polymorpha species that are distributed in Turkey. The highest total phenol content was determined in R. digitellata (144.6 mgGAE/gextract ), and the highest total amount of flavonoids was found in R. fastigiata (20.40 mgGAE/gextract ). The content of usnic acid was determined by High-Performance Liquid Chromatography (HPLC) and the highest amount was found in R. digitellata. DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS [2,2'-azinobis(3-ethylbenzathiazoline-6-sulfonic acid)] radical scavenging methods were used for antioxidant activity. R. fraxinea showed the highest DPPH⋅ and ABTS+ ⋅ scavenging activity. In addition, the DNA protective effect was investigated using pBR322 plasmid DNA, and; all studied species were found to have DNA protective effects. The antibacterial activity was investigated using the disc diffusion method, and the R. digitellata methanol extract showed the best results with a 12.35 mm zone on Proteus mirabilis. On the human lung cancer (A549) and breast cancer (MDA-MB-231) cell lines, cytotoxic activity was assessed using an MTT assay. All lichen extracts were found to have a significant cytotoxic effect on both cancer cell lines at 1000 µg/mL concentration. These results suggest that Ramalina species may be potential candidates for developing new phytopharmaceuticals and functional components.

Clinico-radiological features, molecular spectrum, and identification of prognostic factors in developmental and epileptic encephalopathy due to inosine triphosphate pyrophosphatase (ITPase) deficiency.

Developmental and epileptic encephalopathy 35 (DEE 35) is a severe neurological condition caused by biallelic variants in ITPA, encoding inosine triphosphate pyrophosphatase, an essential enzyme in purine metabolism. We delineate the genotypic and phenotypic spectrum of DEE 35, analyzing possible predictors for adverse clinical outcomes. We investigated a cohort of 28 new patients and reviewed previously described cases, providing a comprehensive characterization of 40 subjects. Exome sequencing was performed to identify underlying ITPA pathogenic variants. Brain MRI (magnetic resonance imaging) scans were systematically analyzed to delineate the neuroradiological spectrum. Survival curves according to the Kaplan-Meier method and log-rank test were used to investigate outcome predictors in different subgroups of patients. We identified 18 distinct ITPA pathogenic variants, including 14 novel variants, and two deletions. All subjects showed profound developmental delay, microcephaly, and refractory epilepsy followed by neurodevelopmental regression. Brain MRI revision revealed a recurrent pattern of delayed myelination and restricted diffusion of early myelinating structures. Congenital microcephaly and cardiac involvement were statistically significant novel clinical predictors of adverse outcomes. We refined the molecular, clinical, and neuroradiological characterization of ITPase deficiency, and identified new clinical predictors which may have a potentially important impact on diagnosis, counseling, and follow-up of affected individuals.

Investigation of sub-chromosomal changes in males with idiopathic azoospermia by chromosomal microarray analysis.

Azoospermia consists of a significant proportion of infertility aetiology in males. Although known genetic abnormalities may explain roughly the third of infertility cases, the exact aetiology is still unclear. Chromosomal microarrays are widely used to detect sub chromosomal abnormalities (e.g., microdeletions and microduplications). This study aimed to investigate aetiology in patients with idiopathic azoospermia by using the chromosomal microarray method to detect possible sub chromosomal changes. Twenty-eight patients (with a mean age of 30.4 ± 9 years) that had been diagnosed with idiopathic azoospermia between January 2019 and December 2020 were included in the study. Genomic DNA isolated from the blood of patients were amplified using polymerase chain reaction and was subjected to chromosomal microarray analysis. A total of six microdeletions were identified as clinically significant: one pathogenic copy number variation (CNV), four likely pathogenic CNVs, and one CNV of unknown clinical significance. However, clinical findings indicated that these microdeletions, with variable expression levels, may affect the spermatogenesis process and induce azoospermia. Future investigations regarding the functional effect of these deletions may contribute to our understanding of azoospermia aetiology.

Age and sex related changes in fattening performance, dermatitis, intestinal histomorphology, and serum IgG level of slow- and fast-growing broilers under the intensive system.

Due to consumers' concerns about broiler welfare, slow-growing broilers (SGB) have also been used in production. Fast-growing broilers (FGB) reach slaughter weight earlier the slow growing. This study was aimed to determine the sex-related changes in fattening performance, dermatitis, intestinal histomorphology, and serum IgG level of SGB and FGB under the intensive system during the 10 weeks. A total of 336 one-day-old broilers were distributed into four equal groups (FGB-female, FGB-male, SGB-female, and SGB-male) consisting of a 2 × 2 factorial design. The main factors were genotype (FGB and SGB) and sex (female and male). Each treatment had 6 duplicates consisting of 14 broilers. They were placed on the litter pens. The experiment lasted 10 weeks. The body weight, body weight gain, feed consumption, and feed-to-gain ratio were determined weekly during the experiment. One broiler close to the average body weight from each pen (6 broilers in the group) has been slaughtered each week and intestinal histomorphology was determined. Additionally, IgG levels in the blood and dermatitis were determined. While the period in which the body weight gain was the highest in the FGB was up to 6 week of age, this period lasted until the 7 week of age in the SGB (P < 0.001). It has been determined that FGB have the best feed efficiency ability during both 6 weeks of fattening period and 10 weeks of fattening period (P < 0.001). The difference between the sex in terms of the feed efficiency appeared after the age of 4 weeks and this difference continued until the age of 9 weeks (P < 0.01). It was determined that villus height, crypt depth, and the ratio of villus height to crypt depth in the jejunum region were higher in FGB from the age of 1 week than in SGB (P < 0.05). It was observed that the incidence of dermatitis increased in the FGB (P < 0.001). It has been determined that the genotype (P < 0.01) and period (P < 0.001) were effective according to the IgG level. These results indicate that 7 and 8 weeks can be considered important periods in terms of economic efficiency in SGB and FGB reared for 10 weeks under the same management systems and it was observed that both genotypes would be more susceptible to diseases at the age of 6 weeks.

A novel missense mutation in the UBE2A gene causes intellectual disability in the large X-linked family.

BACKGROUND: X-linked intellectual disability type Nascimento (XIDTN) is a disorder of the ubiquitin-proteasome pathway of protein degradation controlled by the UBE2A gene. The disease is characterized by intellectual disability, speech impairment, dysmorphic facial features, skin and nail anomalies, and, frequently, seizures. Eight affected males from a four-generation family who have intellectual disability and speech disorders were examined within an extended family of 57 individuals. Methods A number of methods were used for the molecular diagnosis. Conventional karyotype analyses, array-based comparative genomic hybridization (aCGH), whole exome swquencing (WES), sanger sequencing were performed. Results First, the conventional karyotype analyses were normal, and the results of the aCGH analyses were normal. Then, WES revealed a novel missense mutation of the UBE2A gene at exon 4 NM_003336.3: c.182A>G (p.Glu61Gly). Seven affected individuals and nine carriers in the multigenerational, large family were diagnosed through Sanger sequencing. CONCLUSIONS: We identified the mutation causing intellectual disability in the large family and demonstrated its phenotypic effects. Our cases showed that dysmorphic features could be considered mild, whereas intellectual disability and speech disorders are common features in XIDTN. The structure and function of the gene will be better understood in the novel UBE2A mutation. The genotype-phenotype correlation and phenotypic variations in XIDTN were identified through a literature review. Accordingly, XIDTN should be considered in individuals who exhibit an X-linked pedigree pattern and have intellectual disability and speech disorders.

Effect of different carboxylated poly l-lysine and dimethyl sulfoxide combinations on post thaw rabbit sperm functionality and fertility.

Antifreeze proteins are biologically active substances which protect living organisms against freezing injuries. The effect of a synthetic antifreeze protein carboxylated poly l-lysine (CPLL) in the extender was evaluated in the presence of a conventional cryoprotective agent, dimethyl sulfoxide (Me2SO), for freezing rabbit sperm cells. The experiment was conducted according to 2 × 3 factorial design including two Me2SO (5 or 8%) and three CPLL (0, 0.5 or 1%) concentrations. CPLL supplementation improved post-thaw live and live-acrosome intact sperm rates (P<0.01) without a prominent influence on the motility (P>0.05) and live-membrane intact (P>0.05) sperm rates. The most striking effect of CPLL supplementation was seen on the DNA integrity where it reduced DNA fragmentation of sperm cells significantly by interacting Me2SO (P < 0.01) during freezing and thawing. However, it could not replace Me2SO in the extender and did not improve pregnancy rate. In conclusion, CPLL supplementation to the extender in the presence of Me2SO improved sperm quality parameters and post-thaw DNA integrity.

Malonyl coenzyme A decarboxylase deficiency with a novel mutation.

Malonyl-CoA, a product of acetyl-CoA carboxylase is a metabolic intermediate in lipogenic tissues that include liver and adipose tissue, where it is involved in the de novo fatty acid synthesis and elongation. Malonyl-CoA decarboxylase (MLYCD, E.C.4.1.1.9), a 55-kDa enzyme catalyses the conversion of malonyl-CoA to acetyl-CoA and carbon dioxide, thus providing a route for disposal of malonyl-CoA from mitochondria and peroxisomes, whereas in the cytosol, the malonyl-CoA pool is regulated by the balance of MLYCD and acetyl-CoA carboxylase activities. So far, 34 cases with different MLYCD gene defects comprising point mutations, stop codons, and frameshift mutations have been reported in the literature. Here, we describe the follow-up of a patient affected by malonic aciduria upon neonatal onset. Molecular analysis showed novel homozygous mutations in the MLYCD gene. Our findings expand the number of reported cases and add a novel variant to the repertoire of MLYCD mutations.

Photocatalytically Active Graphitic Carbon Nitride as an Effective and Safe 2D Material for In Vitro and In Vivo Photodynamic Therapy.

Thanks to its photocatalytic property, graphitic carbon nitride (g-C3 N4 ) is a promising candidate in various applications including nanomedicine. However, studies focusing on the suitability of g-C3 N4 for cancer therapy are very limited and possible underlying molecular mechanisms are unknown. Here, it is demonstrated that photoexcitation of g-C3 N4 can be used effectively in photodynamic therapy, without using any other carrier or additional photosensitizer. Upon light exposure, g-C3 N4 treatment kills cancer cells, without the need of any other nanosystem or chemotherapeutic drug. The material is efficiently taken up by tumor cells in vitro. The transcriptome and proteome of g-C3 N4 and light treated cells show activation in pathways related to both oxidative stress, cell death, and apoptosis which strongly suggests that only when combined with light exposure, g-C3 N4 is able to kill cancer cells. Systemic administration of the mesoporous form results in elimination from urinary bladder without any systemic toxicity. Administration of the material significantly decreases tumor volume when combined with local light treatment. This study paves the way for the future use of not only g-C3 N4 but also other 2D nanomaterials in cancer therapy.

SMN1 gene copy number analysis for spinal muscular atrophy (SMA) in a Turkish cohort by CODE-SEQ technology, an integrated solution for detection of SMN1 and SMN2 copy numbers and the "2+0" genotype.

INTRODUCTION: Spinal muscular atrophy (SMA) is one of the common autosomal recessive disorders with global heterozygous carrier frequency of 1:50. Due to high carrier frequency, significant morbidity associated with the infantile onset disease and prohibitive cost of recently approved therapy, American College of Medical Genetics and Genomics (ACMG) recommends population based screening for SMA carrier status in eligible individuals in the reproductive age group. CODE-SEQ is a novel proprietary next generation sequencing (NGS) based assay, which is capable of detecting homozygous as well as heterozygous SMN1 exon 7 deletions. Along with the copy number estimation, this assay is capable of detecting single nucleotide polymorphisms (SNPs) associated with silent SMA carrier status or "2+0" genotype. METHODS: We have validated a proprietary CODE-SEQ technology in a blinded cohort of 80 clinically well characterized samples from Turkish population for the detection of SMA carriers as well as affected cases. The results were correlated with gold standard MLPA assay. RESULTS: The copy numbers in exon 7 of SMN1 gene matched with MLPA results in all 80 samples giving 100% correlation. The assay accurately detected the presence/ absence of SNPs associated with "2+0" genotype in the reference samples. None of the tested clinical samples had these SNPs. CONCLUSION: The results of this study support the notion that CODE-SEQ will be extremely useful in detecting SMA genotypes in large-scale population-based screening studies.

Synthesis of Ag and TiO2 modified polycaprolactone electrospun nanofibers (PCL/TiO2-Ag NFs) as a multifunctional material for SERS, photocatalysis and antibacterial applications.

In this study, we reported the design and the fabrication of Ag and TiO2 modified polycaprolactone (PCL) electrospun nanofiber (NF) mats. The as-prepared NF mats were fabricated by one-step electrospinning and it was exploited for three different purposes (i) reusable SERS substrate for quantitative analysis to trace organic pollutants, (ii) photocatalyst for degradation of organic pollutants and (iii) antibacterial agent for killing of bacteria. Three different nanofiber mats, PCL, PCL-TiO2, PCL/TiO2-Ag NFs. were fabricated and further investigated. The morphologies and structures of the as-prepared nanofiber mats were carried out using X-ray diffraction spectroscopy (XRD), field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX) and fourier transform infrared spectroscopy (FT-IR) techniques. PCL/TiO2-Ag NFs served as a highly effective SERS platform with a detection limit of 10 nM for the detection of methylene blue dye (MB). A remarkable feature of the presented platform is the ability to reuse the PCL/TiO2-Ag NFs for SERS analysis of MB; availing from its capability for self-cleaning under UV light. By employing PCL/TiO2-Ag NFs nanocatalyst, complete photocatalytic degradation of the probe analytes MB and ibuprofen (Ibu) under UV irradiation was accomplished not more than 180 min. Moreover, PCL/TiO2-Ag NF mats showed a highly promising bactericidal feature against gram-negative Escherichia coli and gram-positive Staphylococcus aureus bacteria, which immensely emerged due to the presence of Ag NPs. This new trending nanofiber is assumed to lead a bunch of changes in the field of photocatalytic, SERS and antibacterial studies.

Intracellular biosynthesis of PbS quantum dots using Pseudomonas aeruginosa ATCC 27853: evaluation of antibacterial effects and DNA cleavage activities.

Bacterial biosynthesis of quantum dots (QDs) offers a green alternative for the production of nanomaterials with superior properties, such as tunable size dependent emission spectra and a long fluorescence lifetime. In this study, we have achieved intracellular production of PbS QDs using Pseudomonas aeruginosa ATCC 27853. The characterization of these PbS QDS was performed by different techniques, such as Ultraviolet-visible (UV-Vis) spectroscopy, photoluminescence (PL), X-ray diffraction (XRD), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDX) and particle size analysis (DLS). The obtained results confirmed the synthesis of PbS QDs. The PbS QDs showed absorption peaks at 1088 nm (ultraviolet-visible spectrometry) and a luminescence peak at 1572 nm. In addition, the intracellular biosynthesized PbS QDs showed a particle size in the range 3.47-11.45 nm, which is consistent with DLS and sphere-shaped nanocrystals with good crystallinity and a cubic cristalline structure including pure Pb and S elements. Biosynthesized PbS QDs showed antibacterial activity against Proteus mirabilis ATCC 25933 and Escherichia coli ATCC 25922 from Gram (-) bacteria and Bacillus cereus NRLL B-3008 and Micrococcus luteus ATCC 10240 from Gram (+) bacteria. Besides, these current results obtained from the cleavage studies revealed that PbS QDs do not show DNA cleavage activity. Consequently, the microorganism-based intracellular method allows an economic and environmentally friendly way to obtain PbS QDs with superior optical properties and they have a potential to be used in healthcare applications.

Silk protein sericin pretreatment enhances osmotic tolerance and post-thaw sperm quality but reduces the ability of sperm cells to undergo in vitro induced acrosome reaction in rabbit.

Effect of sericin pretreatment of sperm cells on the osmotic tolerance, ability to undergo acrosome reaction induced by calcium ionophore (CI), heparin (H) or lysophosphatidylcholine (LPC), post-thaw sperm quality and in vivo fertility was evaluated in four successive experiments in rabbit. In experiment 1, fresh semen was pretreated with sericin (0, 0.1% or 0.5% w/v) before exposing to fructose solutions adjusted to either 50, 100, 290, 500 or 1000 mOsm/L. Sericin pretreatment increased sperm livability in addition to live-membrane intact and total membrane intact sperm rates (P < 0.05) in 50 and 290 mOsm/L groups. In experiment 2, sperm samples were pretreated by either 0.1 or 0.5% sericin after removal of the semen plasma. CI, H or LPC were used to induce acrosome reaction in pretreated sperm samples. Sericin pretreatment, reduced the ability of sperm cells to undergo acrosome reaction (P < 0.05) in vitro. In experiment 3, ejaculates were frozen with or without sericin pretreatment in DMSO-sucrose extender. In post-thaw samples sericin pretreatment improved total and progressive motility, livability, membrane and acrosome integrity in a dose dependent manner (P < 0.05). In vivo fertility trials by artificial inseminations revealed contradictory results in experiment 4. Although 0.5% sericin pretreatment totally inhibited fertility, 0.1% sericin provided high pregnancy rates. In conclusion; sericin pretreatment enhances osmotic tolerance and post-thaw sperm quality, but reduces the ability of rabbit sperm cells to undergo in vitro induced acrosome reaction, but this effect is restored in vivo by dose dependent manner.