Identification of a mutation in TNRC18 in a patient with clinical features of Fazio-Londe disease

Fazio-Londe disease and Brown-Vialetto-Van Laere syndrome are rare related neurological disorders. Although SLC52A3 and SLC52A2 that encode riboflavin transporters are their only known causative genes, many patients without mutations in these genes have been reported. Clinical and genetic data of a patient with features suggestive of Fazio-Londe disease are presented. Neurological examination revealed significant involvement of cranial nerves and weakness in the lower extremities. Pontobulbar presentations were prominent. EDX study suggested motor neuronopathy. Hearing was normal. She was diagnosed with FL disease. Response to riboflavin supplementation was not favorable. The patient's pedigree suggested recessive inheritance. SLC52A3 and SLC52A2 were screened and mutations were not observed. Results of exome sequencing and segregation analysis suggested that a mutation in TNRC18 is a candidate cause of disease in the patient. The three dimensional structure of the TNRC18 protein was predicted and it was noted that its two conserved domains (BAH and Tudor) interact and that the valine residue affected by the mutation is positioned close to both domains. A mutation in TNRC18 is cautiously reported as the possible cause of FL disease in the patient. The finding warrants further inquiries on TNRC18 about which little is presently known.

Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing

OBJECTIVE

Wound healing is a complex process involving the coordinated interaction of various genes and molecular
pathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug development
to improve successful wound repair interventions.
Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtained
from the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)
were described using the Limma package and shared genes were used as input for weighted gene co-expression
network analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of a
protein-protein interaction (PPI) network was achieved by the STRING and Cytoscape.
Results: A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genes
between nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20
genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,
ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,
HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutic
targets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wnt
signaling pathway".
Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modules
using WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslational
modifications. We found nine down-regulated genes and ten up-regulated genes, which could serve as
potential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and cell
adhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm the
effectiveness and safety of targeted interventions.

The construction of a testis transcriptional cell atlas from embryo to adult reveals various somatic cells and their molecular roles

BACKGROUND

The testis is a complex organ that undergoes extensive developmental changes from the embryonic stage to adulthood. The development of germ cells, which give rise to spermatozoa, is tightly regulated by the surrounding somatic cells.

METHODS

To better understand the dynamics of these changes, we constructed a transcriptional cell atlas of the testis, integrating single-cell RNA sequencing data from over 26,000 cells across five developmental stages: fetal germ cells, infants, childhood, peri-puberty, and adults. We employed various analytical techniques, including clustering, cell type assignments, identification of differentially expressed genes, pseudotime analysis, weighted gene co-expression network analysis, and evaluation of paracrine cell-cell communication, to comprehensively analyze this transcriptional cell atlas of the testis.

RESULTS

Our analysis revealed remarkable heterogeneity in both somatic and germ cell populations, with the highest diversity observed in Sertoli and Myoid somatic cells, as well as in spermatogonia, spermatocyte, and spermatid germ cells. We also identified key somatic cell genes, including RPL39, RPL10, RPL13A, FTH1, RPS2, and RPL18A, which were highly influential in the weighted gene co-expression network of the testis transcriptional cell atlas and have been previously implicated in male infertility. Additionally, our analysis of paracrine cell-cell communication supported specific ligand-receptor interactions involved in neuroactive, cAMP, and estrogen signaling pathways, which support the crucial role of somatic cells in regulating germ cell development.

CONCLUSIONS

Overall, our transcriptional atlas provides a comprehensive view of the cell-to-cell heterogeneity in the testis and identifies key somatic cell genes and pathways that play a central role in male fertility across developmental stages.

A novel missense variant in CDK5RAP2 associated with non-obstructive azoospermia

OBJECTIVE

The most severe type of male infertility is non-obstructive azoospermia (NOA), where there is no sperm in the ejaculate due to failure of spermatogenesis, affecting 10%-20% of infertile men with azoospermia. Genetic studies have identified dozens of NOA genes. The main aim of the present study is to identify a novel monogenic mutation that may cause NOA.

MATERIALS AND METHODS

We studied the pedigree of a consanguineous family with three NOA and one fertile brother by a family-based exome-sequencing, segregation analysis, insilico protein modeling and single-cell RNA sequencing data analysis.

RESULTS

Bioinformatics analysis followed by sanger sequencing revealed that three NOA brothers were homozygous for a rare missense variant in Cyclin Dependent Kinase Regulatory Subunit Associated Protein 2 (Centrosomin) CDK5RAP2 (NM_018249:exon26:c.A4003T:p.R1335W, rs761196443). Protein modeling demonstrated that CDK5RAP2, Arg1335Trp resided nearby the Microtubule Associated Protein RP/EB Family Member 1 (EB1/MAPRE1) interaction site. As a consequence of the R1335W mutation, the positively charged Arginine was replaced by to the hydrophobic tryptophan residue, possibly leading to local instability in the structure and perturbation in the CDK5RAP2-MAPRE1 interaction.

CONCLUSION

Our study reports a novel missense variant of CDK5RAP2 that segregates in homozygosity with male infertility and NOA in a consanguineous family. In silico structural predictions and gene expression data indicate a potential role of the CDK5RAP2 variant in causing defective centrosomic maturation during spermatogenesis.

DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing

BACKGROUND

Drug repurposing is an approach that holds promise for identifying new therapeutic uses for existing drugs. Recently, knowledge graphs have emerged as significant tools for addressing the challenges of drug repurposing. However, there are still major issues with constructing and embedding knowledge graphs.

RESULTS

This study proposes a two-step method called DrugRep-HeSiaGraph to address these challenges. The method integrates the drug-disease knowledge graph with the application of a heterogeneous siamese neural network. In the first step, a drug-disease knowledge graph named DDKG-V1 is constructed by defining new relationship types, and then numerical vector representations for the nodes are created using the distributional learning method. In the second step, a heterogeneous siamese neural network called HeSiaNet is applied to enrich the embedding of drugs and diseases by bringing them closer in a new unified latent space. Then, it predicts potential drug candidates for diseases. DrugRep-HeSiaGraph achieves impressive performance metrics, including an AUC-ROC of 91.16%, an AUC-PR of 90.32%, an accuracy of 84.63%, a BS of 0.119, and an MCC of 69.31%.

CONCLUSION

We demonstrate the effectiveness of the proposed method in identifying potential drugs for COVID-19 as a case study. In addition, this study shows the role of dipeptidyl peptidase 4 (DPP-4) as a potential receptor for SARS-CoV-2 and the effectiveness of DPP-4 inhibitors in facing COVID-19. This highlights the practical application of the model in addressing real-world challenges in the field of drug repurposing. The code and data for DrugRep-HeSiaGraph are publicly available at https://github.com/CBRC-lab/DrugRep-HeSiaGraph .

Fluorescence labeling of anchor-modified Mart-1 peptide for increasing its affinity for HLA-A*0201: Hit two targets with one arrow

One of the most successful strategies in designing peptide-based cancer vaccines is modifying natural epitope peptides to increase their binding strength to human leukocyte antigens (HLAs). Anchor-modified Mart-1 peptide (ELAGIGILTV) is among the artificial epitope peptides with the highest binding affinity for HLA-A*0201. In this study, by fluorescence labeling of its either C- or N-terminus with Nε -(5-carboxyfluorescein)-l-lysine, we not only made it traceable but also drastically increased its binding strength to HLA-A*0201. HLA streptamer, for the first time, is introduced for measuring the binding constants (Ka ) of the labeled peptides. The affinity of the labeled peptides for the HLA-A*201 of the MCF-7 cells was extraordinarily high and co-incubating them with the highest possible amount of the unlabeled peptide, as a competitor, did not significantly prohibit them from binding to the HLA. The reproducibility of the obtained results was confirmed by using the T2 cell line. The HLA-deficient K562 cell line was used as the negative control. With in silico simulations, we found two hydrophobic pockets on both sides of HLA-A*0201 for anchoring the C- or N-terminal 5-carboxyfluorescein probe, which can explain the extraordinary affinity of the labeled peptides for the HLA-A*0201.

Preventing the amyloid-beta peptides accumulation on the cell membrane by applying GHz electric fields: A molecular dynamic simulation

Alzheimer's disease is associated with accumulating different amyloid peptides on the nerve cell membranes. The non-thermal effects of the GHz electric fields in this topic have yet to be well recognized. Hence, in this study, the impacts of 1 and 5 GHz electric fields on the amyloid peptide proteins accumulation on the cell membrane have been investigated, utilizing molecular dynamics (MD) simulation. The obtained results indicated that this range of electric fields did not significantly affect the peptide structure. Moreover, it was found that the peptide penetration into the membrane was increased as the field frequency was increased when the system was exposed to a 20 mv/nm oscillating electric field. In addition, it was observed that the protein-membrane interaction is reduced significantly in the presence of the 70 mv/nm electric field. The molecular level results reported in this study could be helpful in better understanding Alzheimer's disease.

DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs

Drug repurposing or repositioning (DR) refers to finding new therapeutic applications for existing drugs. Current computational DR methods face data representation and negative data sampling challenges. Although retrospective studies attempt to operate various representations, it is a crucial step for an accurate prediction to aggregate these features and bring the associations between drugs and diseases into a unified latent space. In addition, the number of unknown associations between drugs and diseases, which is considered negative data, is much higher than the number of known associations, or positive data, leading to an imbalanced dataset. In this regard, we propose the DrugRep-KG method, which applies a knowledge graph embedding approach for representing drugs and diseases, to address these challenges. Despite the typical DR methods that consider all unknown drug-disease associations as negative data, we select a subset of unknown associations, provided the disease occurs because of an adverse reaction to a drug. DrugRep-KG has been evaluated based on different settings and achieves an AUC-ROC (area under the receiver operating characteristic curve) of 90.83% and an AUC-PR (area under the precision-recall curve) of 90.10%, which are higher than in previous works. Besides, we checked the performance of our framework in finding potential drugs for coronavirus infection and skin-related diseases: contact dermatitis and atopic eczema. DrugRep-KG predicted beclomethasone for contact dermatitis, and fluorometholone, clocortolone, fluocinonide, and beclomethasone for atopic eczema, all of which have previously been proven to be effective in other studies. Fluorometholone for contact dermatitis is a novel suggestion by DrugRep-KG that should be validated experimentally. DrugRep-KG also predicted the associations between COVID-19 and potential treatments suggested by DrugBank, in addition to new drug candidates provided with experimental evidence. The data and code underlying this article are available at https://github.com/CBRC-lab/DrugRep-KG.

Intermediate-aided allostery mechanism for α-glucosidase by Xanthene-11v as an inhibitor using residue interaction network analysis

Exploring allosteric inhibition and the discovery of new inhibitor binding sites are important studies in protein regulation mechanisms and drug discovery. Structural and network-based analyses of trajectories resulting from molecular dynamics (MD) simulations have been developed to discover protein dynamics, landscape, functions, and allosteric regions. Here, an experimentally suggested non-competitive inhibitor, xanthene-11v, was considered to explore its allosteric inhibition mechanism in α-glucosidase MAL12. Comparative structural and network analyses were applied to eight 250 ns independent MD simulations, four of which were performed in the free state and four of which were performed in ligand-bound forms. Projected two-dimensional free energy landscapes (FEL) were constructed from the probabilistic distribution of conformations along the first two principal components. The post-simulation analyses of the coordinates, side-chain torsion angles, non-covalent interaction networks, network communities, and their centralities were performed on α-glucosidase conformations and the intermediate sub-states. Important communities of residues have been found that connect the allosteric site to the active site. Some of these residues like Thr307, Arg312, TYR344, ILE345, Phe357, Asp406, Val407, Asp408, and Leu436 are the key messengers in the transition pathway between allosteric and active sites. Evaluating the probability distribution of distances between gate residues including Val407 in one community and Phe158, and Pro65 in another community depicted the closure of this gate due to the inhibitor binding. Six macro states of protein were deduced from the topology of FEL and analysis of conformational preference of free and ligand-bound systems to these macro states shows a combination of lock-and-key, conformational selection, and induced fit mechanisms are effective in ligand binding. All these results reveal structural states, allosteric mechanisms, and key players in the inhibition pathway of α-glucosidase by xanthene-11v.

Biomarker prediction in autism spectrum disorder using a network-based approach

BACKGROUND

Autism is a neurodevelopmental disorder that is usually diagnosed in early childhood. Timely diagnosis and early initiation of treatments such as behavioral therapy are important in autistic people. Discovering critical genes and regulators in this disorder can lead to early diagnosis. Since the contribution of miRNAs along their targets can lead us to a better understanding of autism, we propose a framework containing two steps for gene and miRNA discovery.

METHODS

The first step, called the FA_gene algorithm, finds a small set of genes involved in autism. This algorithm uses the WGCNA package to construct a co-expression network for control samples and seek modules of genes that are not reproducible in the corresponding co-expression network for autistic samples. Then, the protein-protein interaction network is constructed for genes in the non-reproducible modules and a small set of genes that may have potential roles in autism is selected based on this network. The second step, named the DMN_miRNA algorithm, detects the minimum number of miRNAs related to autism. To do this, DMN_miRNA defines an extended Set Cover algorithm over the mRNA-miRNA network, consisting of the selected genes and corresponding miRNA regulators.

RESULTS

In the first step of the framework, the FA_gene algorithm finds a set of important genes; TP53, TNF, MAPK3, ACTB, TLR7, LCK, RAC2, EEF2, CAT, ZAP70, CD19, RPLP0, CDKN1A, CCL2, CDK4, CCL5, CTSD, CD4, RACK1, CD74; using co-expression and protein-protein interaction networks. In the second step, the DMN_miRNA algorithm extracts critical miRNAs, hsa-mir-155-5p, hsa-mir-17-5p, hsa-mir-181a-5p, hsa-mir-18a-5p, and hsa-mir-92a-1-5p, as signature regulators for autism using important genes and mRNA-miRNA network. The importance of these key genes and miRNAs is confirmed by previous studies and enrichment analysis.

CONCLUSION

This study suggests FA_gene and DMN_miRNA algorithms for biomarker discovery, which lead us to a list of important players in ASD with potential roles in the nervous system or neurological disorders that can be experimentally investigated as candidates for ASD diagnostic tests.

Identification of UBA1 as the causative gene of an X-linked non-Kennedy SBMA

BACKGROUND

Spinal-bulbar muscular atrophy (SBMA; Kennedy's Disease) is a motor neuron disease (MND). Kennedy's Disease is nearly exclusively caused by mutations in the androgen receptor encoding gene (AR). We report results of studies aimed at identification of the genetic cause of a disease that best approximates SBMA in a pedigree (four patients) without mutations in AR.

METHODS

Clinical investigations included thorough neurologic and non-neurologic examinations and testings. Genetic analysis was performed by exome sequencing using standard protocols. UBA1 mutations were modeled on the crystal structure of UBA1.

RESULTS

The clinical features of the patients are described in detail. A missense mutation in UBA1 (c.T1499C; p.Ile500Thr) was identified as the probable cause of the non-Kennedy SBMA in the pedigree. Like AR, UBA1 is positioned on Chromosome X. UBA1 is a highly conserved gene. It encodes ubiquitin like modifier activating enzyme 1 (UBA1) which is the major E1 enzyme of the ubiquitin-proteasome system. Interestingly, UBA1 mutations can also cause infantile-onset X-linked spinal muscular atrophy (XL-SMA). The mutation identified here and the XL-SMA causative mutations were shown to affect amino acids positioned in the vicinity of UBA1's ATP binding site and to cause structural changes.

CONCLUSION

UBA1 was identified as a novel SBMA causative gene. The gene affects protein homeostasis which is one of most important components of the pathology of neurodegeneration. The contribution of this same gene to the etiology of XL-SMA is discussed.

A Novel Missense Variant in Actin Binding Domain of MYH7 Is Associated With Left Ventricular Noncompaction

Cardiomyopathies are a group of common heart disorders that affect numerous people worldwide. Left ventricular non-compaction (LVNC) is a structural disorder of the ventricular wall, categorized as a type of cardiomyopathy that mostly caused by genetic disorders. Genetic variations are underlying causes of developmental deformation of the heart wall and the resultant contractile insufficiency. Here, we investigated a family with several affected members exhibiting LVNC phenotype. By whole-exome sequencing (WES) of three affected members, we identified a novel heterozygous missense variant (c.1963C>A:p.Leu655Met) in the gene encoding myosin heavy chain 7 (MYH7). This gene is evolutionary conserved among different organisms. We identified MYH7 as a highly enriched myosin, compared to other types of myosin heavy chains, in skeletal and cardiac muscles. Furthermore, MYH7 was among a few classes of MYH in mouse heart that highly expresses from early embryonic to adult stages. In silico predictions showed an altered actin-myosin binding, resulting in weaker binding energy that can cause LVNC. Moreover, CRISPR/Cas9 mediated MYH7 knockout in zebrafish caused impaired cardiovascular development. Altogether, these findings provide the first evidence for involvement of p.Leu655Met missense variant in the incidence of LVNC, most probably through actin-myosin binding defects during ventricular wall morphogenesis.

A rare frameshift mutation in SYCP1 is associated with human male infertility

Proper assembly of the synaptonemal complex is essential for successful meiosis, and impairments in the process lead to infertility. Meiotic transverse filament proteins encoded by the SYCP1 (synaptonemal complex protein 1) gene are one of the main components of the synaptonemal complex and play an important role in correct synapsis and recombination. Family-based whole exome sequencing revealed a rare homozygous SYCP1 frameshift mutation (c.2892delA: p.K967Nfs*1) in two men with severe oligozoospermia, followed by validation and segregation through Sanger sequencing. This single nucleotide deletion not only changes lysine 967 (K) into asparagine (N) but also causes a premature stop codon, which leads to deletion of 968-976 residues from the end of the C-tail region of the SYCP1 protein. Although, sycp1 knockout male mice are reported to be sterile with a complete lack of spermatids and spermatozoa, to date no SYCP1 variant has been associated with human oligozoospermia. HADDOCK analysis indicated that this mutation decreases the ability of the truncated SYCP1 protein to bind DNA. Immunodetection of ϒH2AX signal, in SYCP1 mutant semen cells and a 40% DNA fragmentation index might indicate that a small number of DNA double-strand breaks, which require SYCP1 and/or synapsis to be repaired, are not efficiently repaired, resulting in defects in differentiation of germline cells and appearance of the oligozoospermia phenotype. To our knowledge, this is the first report of homozygous SYCP1 mutation that decreases sperm count. Further studies are required to determine the function of the SYCP1 mutation, which is potentially associated with human oligozoospermia.

A comparative life cycle assessment of stretchable and rigid electronics: a case study of cardiac monitoring devices

Stretchable electronics is a new innovation and becoming popular in various fields, especially in the healthcare sector. Since stretchable electronics use less printed circuit boards (PCBs), it is expected that the environmental performance of a stretchable electronics-based device is better than a rigid electronics-based device that provides the same functionalities. Yet, such a study is rarely available. Thus, the main purpose of this research is to perform a comparative life cycle analysis of stretchable and rigid electronics-based devices. This research combines both the case study approach and the research review approach. For the case study, a cardiac monitoring device with both stretchable and rigid electronics is used. The ISO 14044:2006 standard's prescribed LCA approach and ReCiPe 2016 Midpoint (Hierarchist) are followed for the impact assessment using the SimaPro 9.1 software. The LCA results show that the stretchable cardiac monitoring device has better environmental performance in all eighteen impact categories. This research also shows that the manufacturing process of stretchable electronics has lower environmental impacts than those for rigid electronics. The main reasons for the improved environmental performance of stretchable electronics are lower consumption of raw material as well as decreased energy consumption during manufacturing. Based on the LCA results of a cardiac monitoring device, the study concludes that stretchable electronics and their manufacturing process have better environmental performance in comparison with the rigid electronics and their manufacturing process.

Rare missense variant in MSH4 associated with primary gonadal failure in both 46, XX and 46, XY individuals

STUDY QUESTION

Can whole-exome sequencing (WES) reveal a shared pathogenic variant responsible for primary gonadal failure in both male and female patients from a consanguineous family?

SUMMARY ANSWER

Patients with primary ovarian insufficiency (POI) and non-obstructive azoospermia (NOA) were homozygous for the rare missense variant p. S754L located in the highly conserved MSH4 MutS signature motif of the ATPase domain. An oligozoospermic patient was heterozygous for the variant.

WHAT IS KNOWN ALREADY

MSH4 is a meiosis-specific protein expressed at a certain level in the testes and ovaries. Along with its heterodimer partner MSH5, it is responsible for double-strand Holliday junction recognition and stabilization, to ensure accurate chromosome segregation during meiosis. Knockout male and female mice for Msh4 and Msh5 are reportedly infertile due to meiotic arrest. In humans, MSH4 is associated with male and female gonadal failure, with distinct variations in the MutS domain V.

STUDY DESIGN, SIZE, DURATION

This was a retrospective genetics study of a consanguineous family with multiple cases of gonadal failure in both genders. The subject family was recruited in Iran, in 2018.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The proband who is affected by POI, an NOA brother, a fertile sister and their parents were subjected to WES. The discovered variant was validated in these individuals, and the rest of the family was also genotyped by Sanger sequencing. The variant was not detected in 800 healthy Iranian individuals from the Iranome database nor in 30 sporadic NOA and 30 sporadic POI patients. Suggested effect in aberrant splicing was studied by RT-PCR. Moreover, protein homology modeling was used to further investigate the amino acid substitution in silico.

MAIN RESULTS AND THE ROLE OF CHANCE

The discovered variant is very rare and has never been reported in the homozygous state. It occurs in the ATPase domain at Serine 754, the first residue within the highly conserved MutS signature motif, substituting it with a Leucine. All variant effect prediction tools indicated this variant as deleterious. Since the substitution occurs immediately before the Walker B motif at position 755, further investigations based on protein homology were conducted. Considering the modeling results, the nature of the substituted amino acid residue and the distances between p. S754L variation and the residues of the Walker B motif suggested the possibility of conformational changes affecting the ATPase activity of the protein.

LARGE SCALE DATA

We have submitted dbSNP entry rs377712900 to ClinVar under SCV001169709, SCV001169708 and SCV001142647 for oligozoospermia, NOA and POI, respectively.

LIMITATIONS, REASONS FOR CAUTION

Studies in model organisms can shed more light on the role of this variant as our results were obtained by variant effect prediction tools and protein homology modeling.

WIDER IMPLICATIONS OF THE FINDINGS

Identification of variants in meiotic genes should improve genetic counseling for both male and female infertility. Also, as two of our NOA patients underwent testicular sperm extraction (TESE) with no success, ruling out the existence of pathogenic variants in meiotic genes in such patients prior to TESE could prove useful.

STUDY FUNDING/COMPETING INTEREST(S)

This study was financially supported by Royan Institute in Tehran, Iran, and Institut Pasteur in Paris, France. The authors declare no competing interests.

TRIAL REGISTRATION NUMBER

N/A.

The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains

OBJECTIVES

Disruption of protein synthesis, by drug-mediated restriction of the ribosomal nascent peptide exit tunnel (NPET), may inhibit bacterial growth. Here, we have studied the secondary and tertiary structures of domain V of the 23S rRNA in the wild-type and mutant (resistant) H. pylori strains and their mechanisms of interaction with clarithromycin (CLA).

METHODS

H pylori strains, isolated from cultured gastric biopsies, underwent CLA susceptibility testing by E test, followed by PCR amplification and sequencing of domain V of 23S rRNA. The homology model of this domain in H pylori, in complex with L4 and L22 accessory proteins, was determined based on the E. coli ribosome 3D structure. The interactions between CLA and 23S rRNA complex were determined by molecular docking studies.

RESULTS

Of the 70 H pylori strains, isolated from 200 dyspeptic patients, 11 (16%) were CLA-resistant. DNA sequencing identified categories with no (A), A2142G (B), and A2143G (C) mutations. Docking studies of our homology model of 23S rRNA complex with CLA showed deviated positions for categories B and C, in reference to category A, with 12.19 Å and 7.92 Å RMSD values, respectively. In both mutant categories, CLA lost its interactions at positions 2142 and 2587 and gained two new bonds with the L4 accessory protein.

CONCLUSION

Our data suggest that, in mutant H pylori strains, once the nucleotides at positions 2142 and 2587 are detached from the drug, CLA interacts with and is peeled back by the L4 accessory protein, removing the drug-imposed spatial restriction of the NPET.

Biallelic variant in cyclin B3 is associated with failure of maternal meiosis II and recurrent digynic triploidy

Background

Triploidy is one of the most common chromosome abnormalities affecting human gestation and accounts for an important fraction of first-trimester miscarriages. Triploidy has been demonstrated in a few cases of recurrent pregnancy loss (RPL) but its molecular mechanisms are unknown. This study aims to identify the genetic cause of RPL associated with fetus triploidy.

Methods

We investigated genomic imprinting, genotyped sequence-tagged site (STS) markers and performed exome sequencing in a family including two sisters with RPL. Moreover, we evaluated oocyte maturation in vivo and in vitro and effect of the candidate protein variant in silico.

Results

While features of hydatidiform mole were excluded, the presence of triploidy of maternal origin was demonstrated in the fetuses. Oocyte maturation was deficient and all the maternally inherited pericentromeric STS alleles were homozygous in the fetuses. A deleterious missense variant (p.V1251D) of the cyclin B3 gene (CCNB3) affecting a residue conserved in placental mammals and located in a region that can interact with the cyclin-dependent kinase 1 or cyclin-dependent kinase 2 cosegregated in homozygosity with RPL.

Conclusion

Here, we report a family in which a damaging variant in cyclin B3 is associated with the failure of oocyte meiosis II and recurrent fetus triploidy, implicating a rationale for CCNB3 testing in RPL.

Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients

The etiologic agent SARS-CoV-2 has caused the outbreak of COVID-19 which is spread widely around the world. It is vital to uncover and investigate the full genome sequence of SARS-CoV-2 throughout the world to track changes in this virus. To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). R207C, V378I, M2796I, L3606F, and A6407V in ORF1ab were common mutations in these sequences. Also, some of the detected mutations only were found in Iranian data in comparison with all the available sequences of SARS-CoV-2. The position of S protein mutations showed they were far from the binding site of this protein with angiotensin-converting enzyme-2 (ACE2) as the host cell receptor. These results can be helpful to design specific diagnostic tests, trace the SARS-CoV-2 sequence changes in Iran, and explore therapeutic drugs and vaccines.

New insights into resistance of Helicobacter pylori against third- and fourth-generation fluoroquinolones: A molecular docking study of prevalent GyrA mutations

BACKGROUND

Fluoroquinolones hinder bacterial DNA replication by inhibiting DNA gyrase. However, mutations, in the QRDR segment of its A subunit (GyrA), cause antibiotic resistance. Here, the interactions of levofloxacin (LVX), gemifloxacin (GXN), and moxifloxacin (MXN) with Helicobacter pylori GyrA, in LVX-resistant vs -sensitive strains, were studied.

METHODS

Levoflixacin-sensitive (n = 4) and -resistant (n = 9) H pylori strains, randomly selected from another antibiotic susceptibility study, underwent PCR amplification of gyrA gene, spanning the QRDR segment. The amplified gene fragments were sequenced and aligned. The homology model of H pylori GyrA was built based on that of Escherichia coli, and energy minimization was done. The interaction patterns of LVX, GXN, and MXN with GyrA were analyzed via molecular docking studies.

RESULTS

Sequence alignment of the 13 studied strains, created 5 categories of strains: (A) wild type-like (H pylori ATCC26695), (B) N87K-only, (C) D91N-only, (D) N87K + V94L, and (E) D91N + A97V mutations. The minimum inhibitory concentrations (MIC) for LVX-sensitive (category A) and -resistant (categories B-E) strains were <1 mg/L and ≥32 mg/L, respectively. The binding mode of GyrA in category A with LVX identified G35/N87/Y90/D91/V94/G114/S115/I116/D117/G118/D119, as key residues, some residing outside the QRDR segment. Category B strains lost only one interaction (G35), which led to elevated binding free energy (∆G) and full LVX resistance. Categories C-E lost more contacts, with higher ∆G and again full LVX resistance. GXN bound to GyrA of categories A and B via a different set of key residues, while MXN retained the lost contact (G35) in LVX-resistant, category B strains.

CONCLUSION

Using molecular docking tools, we identified the key residues responsible for interaction of GyrA with LVX, GXN, and MXN. In the presence of N87K-only mutation, the loss of one of these contacts (ie, G35) led to full LVX resistance. Yet, GXN and MXN overcame this mutation, by retaining all key contacts with GyrA.

Mechanistic analysis and experimental verification of bicarbonate-controlled enteric coat dissolution: Potential in vivo implications

Enteric coatings have shown in vivo dissolution rates that are poorly predicted by traditional in vitro tests, with the in vivo dissolution being considerably slower than in vitro. To provide a more mechanistic understanding of this, the dependence of the release properties of various enteric-coated (EC) products on bulk pH and bicarbonate molarity was investigated. It was found that, at presumably in vivo-relevant values, the bicarbonate molarity is a more significant determinant of the dissolution profile than the bulk pH. The findings also indicate that this steep relationship between the dissolution of enteric coatings and bicarbonate molarity limits those coatings' performance in vivo. This is attributed to the relatively low bicarbonate molarities in human intestinal fluids. Further, the hydration and dehydrations kinetics of carbonic acid and carbon dioxide are not sufficiently rapid to reach equilibrium in the diffusion layer surrounding a dissolving ionizable solid. This results in the effective pKa of bicarbonate in the diffusion layer being lower than that determined potentiometrically at equilibrium in the bulk surrounding fluid. These results demonstrate the importance of thoroughly investigating the intestinal bicarbonate concentrations and using bicarbonate buffers or properly designed surrogates (if possible) when evaluating enteric drug products during product development and quality control.

Histidine substitution in the most flexible fragments of firefly luciferase modifies its thermal stability

Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C. In line with the common feature of psychrophilic enzymes, the MD data showed that the overall flexibility of H461D was relatively high at low temperature, probably due to a decrease in the number of salt bridges around the mutation site. On the other hand, substitution of His489 by aspartate (H489D) introduced a new salt bridge between the C-terminal and N-terminal domains and increased protein rigidity but only slightly improved its thermal stability. Similar changes were observed for H489K and, to a lesser degree, H489M mutations. Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity.

Genetic diversity of bovine Neospora caninum determined by microsatellite markers

Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed.

Application of merged spectroscopic data combined with chemometric analysis for resolution of hemoglobin intermediates during chemical unfolding

Using tetradecyltrimethylammonium bromide (TTAB) as a surfactant denaturant, and augmentation of different spectroscopic data, helped to detect the intermediates of hemoglobin (Hb) during unfolding process. UV-vis, fluorescence, and circular dichroism spectroscopy were used simultaneously to monitor different aspects of hemoglobin species from the tertiary or secondary structure points of view. Application of the multivariate curve resolution-alternating least square (MCR-ALS), using the initial estimates of spectral profiles and appropriate constraints on different parts of augmented spectroscopic data, showed good efficiency for characterization of intermediates during Hb unfolding. These results indicated the existence of five protein species, including three intermediate-like compounds in this process. The unfolding pathway in the presence of TTAB included conversion of oxyhemoglobin into deoxyhemoglobin, and then ferrylhemoglobin, ferrihemoglobin or aquamethemoglobin, which finally transformed into hemichrome. This is the first application of chemometric analysis on the merged spectroscopic data related to chemical denaturation of a protein. These types of analysis in multisubunit proteins not only increase the domain of information, but also can reduce the ambiguities of the obtained results.

Endocarditis associated with Erysipelothrix rhusiopathiae in a fat-tailed ram

Endocarditis is rarely reported in sheep and information presented for ovine endocarditis is based mostly on comparative findings in the cattle. Infective vegetative endocarditis of the right heart was diagnosed in a 3-year-old fat-tailed ram. Clinical findings included tachycardia, marked brisket edema, jugular veins distention and pulsation and pale mucous membranes. Hematologic abnormality included neutrophilic leukocytosis. Necropsy confirmed severe right atrioventricular and pulmonary valves vegetative endocarditis with evidence of right heart failure. Erysipelothrix rhusiopathiae was isolated from those vegetative lisions.

Carbon supported Fe–Co nanoparticles with enhanced activity and BH4− tolerance used as a cathode in a passive air breathing anion exchange membrane direct borohydride fuel cell

A highly active nanocatalyst, Fe₅₀–Co₅₀/C, for the ORR was introduced, which exhibits excellent tolerance toward NaBH₄ electrooxidation in DBFC.

Evaluation of modified Ziehl-Neelsen, direct fluorescent-antibody and PCR assay for detection of Cryptosporidium spp. in children faecal specimens

To determine the sensitivity and specificity of routine screening methods for cryptosporidiosis, three methods including conventional modified Ziehl-Neelsen (MZN), direct fluorescent-antibody (DFA) and Nested-PCR assay compared together. To this end, their ability to identify the low concentrations of Cryptosporidium spp. oocysts in children fecal samples was evaluated. The sample population of this study was children under 12 years old who had diarrhea and referred to pediatric hospitals in Tehran, Iran. 2,510 stool specimens from patients with diarrhea were screened for Cryptosporidium oocysts by concentration method and MZN. To determine sensitivity and specificity, Nested-PCR and DFA were performed on 30 positive and 114 negative samples which previously had been proved by MZN. By using the microscopic method, DFA assay and PCR analysis, a total of 30 (1.2 %), 28 (1.1 %) and 32 (1.27 %) positive samples were detected respectively. According to the results, the sensitivity, specificity, and positive and negative predictive values of the Nested-PCR assay were 100 %, compared to 94, 100, 100, and 98 %, respectively, for MZN and 87.5, 100, 100, and 96 %, respectively, for DFA. Results of the present study showed that the Nested-PCR assay was more sensitive than the other two methods and laboratories can use the Nested-PCR method for precise diagnosis of Cryptosporidium spp. However, regarding the costs of Nested-PCR and its unavailability in all laboratories and hospitals, MZN staining on smears has also enough accuracy for Cryptosporidium diagnosis.

Heme degradation upon production of endogenous hydrogen peroxide via interaction of hemoglobin with sodium dodecyl sulfate

In this study the hemoglobin heme degradation upon interaction with sodium dodecyl sulfate (SDS) was investigated using UV-vis and fluorescence spectroscopy, multivariate curve resolution analysis, and chemiluminescence method. Our results showed that heme degradation occurred during interaction of hemoglobin with SDS producing three fluorescent components. We showed that the hydrogen peroxide, produced during this interaction, caused heme degradation. In addition, the endogenous hydrogen peroxide was more effective in hemoglobin heme degradation compared to exogenously added hydrogen peroxide. The endogenous form of hydrogen peroxide altered oxyHb to aquamethemoglobin and hemichrome at low concentration. In contrast, the exogenous hydrogen peroxide lacked this ability under same conditions.

Detection of Neospora caninum in ovine abortion in Iran

The present study was designed to assess the importance of ovine neosporosis in abortion of Iraninan sheep. Seventy aborted foetuses and dams from ovine dairy farms in northwest of Iran were analyzed to investigate the role of Neospora caninum (N. caninum) in ovine abortion. Diagnosis of the infection was determined by serology and polymerase chain reaction (PCR). A total of 70 aborted dairy ovine were blood sampled and used to evaluate serological status for N. caninum infection by enzyme-linked immunosorbent assay (ELISA) and extracted DNA from the same aborted foetuses were subjected to PCR. Data were compared using Kruscal-Wallis test. From A total of the 70 sheeps, four (5.7 %) of the dams were seropositive. DNA from aborted foetuses was extracted primarily from placenta and CNS tissues. Extracted DNA from foetuses were analyzed using PCR with primers Np21(+) and Np6(+). Out of the 70 ovine fetuses 8.5 % were considered to be infected by PCR. This study confirms the importance of N. caninum as an important cause of ovine abortion in northwest of Iran.

Incidence and Genetic Characterization of Gongylonema pulchrum in Cattle Slaughtered in Mazandaran Province, Northern Iran

BACKGROUND

The gullet worm, Gongylonema pulchrum Molin, 1857, is a thread-like spirurid nematode found in a variety of mammals worldwide. Its incidences in Iranian cattle of different breed or age have not been reported. The aims of the present study are to disclose the infection status of G. pulchrum in cattle slaughtered in northern region of Iran.

METHODS

Full-length esophagi of cattle of 97 native dairy breed and 41 Holstein-Friesian breed were collected at four local abattoirs in Mazandaran Province, northern Iran, from March 2006 to August 2007, and were examined parasitologically. Eight overlapping segments of the small- and large-subunits of rDNA were amplified by PCR, and the obtained nucleotide sequences were characterized.

RESULTS

The incidences of G. pulchrum in female and male native dairy breed were 38.9% and 24.0%, respectively, whereas those in female and male Holstein-Friesian breed were 4.2% and 0%, respectively. The first internal transcribed spacer (ITS1) region of G. pulchrum rDNA showed an intra-individual variation in the sequence and length, and the variation was ascribed to some unstable repeats of "A" or "CA".

CONCLUSION

Distinct incidences of G. pulchrum infection in native dairy breed and Holstein-Friesian breed might be ascribed to different animal husbandry manners for each breed in Iran; the former breed grazes freely in the pasture, but the latter breed is usually held in a pen. The rDNA sequence of Iranian G. pulchrum, obtained for the first time by us, might facilitate a reliable species identification of the parasite with a wide spectrum of morphological variations.

The first successful pregnancy following injection of testicular round spermatid in Iran

The authors report the healthy delivery of the first successful round spermatid injection in Iran. The male was a 40-year-old with nonobstructive azoospermia whose previous testicular biopsy revealed only round spermatids. The wife was a 29-year-old healthy woman.

Effects of calcitriol or calcium on bone mineral density, bone turnover, and fractures in men with primary osteoporosis: a two-year randomized, double blind, double placebo study

Osteoporosis in men is an emerging public health problem. As calcitriol reduces the rate of vertebral fractures in osteoporotic postmenopausal women, we conducted a prospective study of this treatment in men with primary osteoporosis. Our study was a 2-yr, randomized, double masked, double placebo-controlled trial of calcitriol (0.25 microg twice daily) or calcium (500 mg twice daily) in 41 men with primary osteoporosis and at least 1 baseline fragility fracture. Thirty-three men (85%) completed the study. There were no differences in baseline characteristics. Spinal and femoral neck bone mineral densities at 2 yr were unchanged in both groups. Serum osteocalcin decreased in both groups by 30% (P < 0.05), whereas urine N-telopeptide cross-links decreased only in the calcium group by 30% (P < 0.05). After 2 yr, fractional calcium absorption increased by 34% (P < 0.01) in the calcitriol group. Nineteen incident fragility fractures occurred (14 vertebral and 5 nonvertebral) in 7 men. Over 2 yr, the number of men with vertebral fractures (6 vs. 1; P = 0.097) was similar in both groups. In conclusion, the efficacy of calcitriol remains unproven as a single agent for the treatment of osteoporosis in men.

99Tcm-labelled IgG scanning does not predict the distribution of intestinal inflammation in patients with inflammatory bowel disease

In order to assess the value of 99Tcm-labelled-immunoglobulin G(99Tcm-IgG) in the assessment of the activity and distribution of intestinal inflammation in patients with inflammatory bowel disease (IBD), 99Tcm-IgG scans were performed in 18 patients. Patients were divided clinically into two groups, those with (ten patients) and those without (eight patients), intestinal inflammation. Disease activity and distribution were assessed by 111In-oxine granulocyte scanning and/or histological extent of inflammation at endoscopy or surgery in all patients with IBD and most of those without intestinal inflammation. In the assessment of the presence or absence of inflammation, a sensitivity of 80% and specificity of 87% were achieved. However, when the localization of intestinal inflammation was evaluated, only five of eight true positive scans were concordant with the distribution of intestinal inflammation as determined by other methods. Thus, significant areas of inflammation were missed in five of ten patients with IBD (two false negative, three incorrect localization of inflammation). Although 99Tcm-IgG scanning appears to have moderate sensitivity and acceptable specificity in the detection of intestinal inflammation, it performs poorly in assessing the distribution of inflammation and is, therefore, of little value in the assessment of patients with suspected or proven IBD.

Value of positive technetium-99m leucocyte scans in predicting intestinal inflammation

The value of positive scans of autologous 99mTc-labelled leucocytes in the detection of intestinal inflammation was assessed in 29 patients with known inflammatory bowel disease and a high probability of intestinal inflammation and 58 with a low probability of intestinal inflammation comprising 37 with intestinal symptoms and 21 with suspected abscess. Autologous leucocytes were labelled with 99mTc using either of the established methods. In patients with inflammatory bowel disease, 3/13 with ileocaecal and 1/11 with colonic accumulation of 99mTc were incorrectly diagnosed in that there was no histological evidence of inflammation in those regions. In the low probability patients, all 26 positive images were false positives: there were 19 in the ileocaecal and 7 in colonic regions and no differences between the two subgroups. False positives were more common in low probability than high probability patients (p = 0.011). The results were independent of the 99mTc cell labelling technique used. Three false positive patients also had normal scans for 111In-labelled granulocytes. The time of first detection of 99mTc in the bowel was earlier in true than in false positive patients (92% v 33% within 1 h, p = 0.008), the false positive rates in the first hour of imaging being 5% in high and 15% in low probability patients. In 99mTc scintigraphy, the appearance of the isotope in the intestine occurs commonly in the absence of inflammation irrespective of the cell labelling technique used. In high probability patients, imaging at 1 h can more reliably discriminate true from false positives and retain clinical usefulness. In low probability patients specificity remains unacceptable and 99mTc-labelled leucocyte scanning in these patients is of little value as a positive predictor of intestinal inflammation.

Conversion of an old gamma camera to a bone mineral densitometer

A 1974-vintage 25 cm field of view gamma camera was converted to a bone mineral densitometer using a purpose-built converging collimator with attached C-arm holding a 250 mCi gadolinium (Gd) 153 source. After addition of a second pulse-height analyser, increasing the high voltage gain and connecting to a digital computer, spinal and hip bone mineral density measurements were made. Accuracy of 2% and long-term reproducibility of 2.7% were obtained using an anthropomorphic bone phantom. For lumbar spine measurements in normal volunteers, long-term reproducibility was 3.2% and for osteoporotic (spinal fracture) patients (mean density 831 mg cm-2) reproducibility was 3.7%.

A single-photon emission computed tomography study of hypoperfusion after subarachnoid hemorrhage

We used single-photon emission computed tomography with technetium-99m hexamethylpropylene amine oxime in 18 studies on 13 patients with subarachnoid hemorrhage to determine whether any changes in cerebral blood flow could be correlated with clinical or computed tomographic evidence of delayed ischemia. Among the seven patients without focal neurologic deficits, regional cerebral hypoperfusion was demonstrated in only one who died. Among the 10 patients with aneurysmal subarachnoid hemorrhage, one died before surgery, and six developed postoperative delayed ischemic deficits, of whom two died. Among the patients with angiographically documented aneurysms, regional hypoperfusion correlated with the presence and severity of delayed neurologic deficits, whereas correlative computed tomographic scans showed either early infarction or no relevant abnormality. This technique facilitates early diagnosis of cerebral tissue hypoperfusion due to vasospasm after subarachnoid hemorrhage.

Technetium-99m radiopharmaceutical preparation by surface adsorbed stannous ions

A method of producing technetium-99m (99mTc) radiopharmaceuticals is described, where reduction of pertechnetate occurs through stannous ions adsorbed on the surface of an infusion catheter. This leads to radiopharmaceuticals containing microgram quantities of stannous ions and that, therefore, results in minimal blood-pool labeling and essentially the elimination of tin colloids. Other advantages of the method include a reduction in quantities of ligand required and the possibility to mass produce the "tinned" catheters as technetium "reduction" kits. A wide variety of 99mTc radiopharmaceuticals have been prepared in high yield. Excellent biodistribution in several of these is demonstrated.

Immunoscintigraphy for detection of lymph node metastases from breast cancer

A radiolabelled monoclonal antibody that reacts with human breast cancer was injected into the web space of each hand in eight women with breast cancer, and the axillae were scanned 16-24 h later. Scans were positive in seven axillae with palpable lymph nodes and in two axillae with impalpable lymph nodes (metastases later confirmed by needle aspiration). The scan was negative in one axilla with a palpable mass, and here no tumour cells were obtained on needle aspiration. In a man with axillary lymphoma, no specific binding of antibody was observed. This technique could lead to earlier and more precise diagnosis of lymph node metastasis in patients with breast cancer.

Validity of the Gaussian assumption in the analysis of ROC data obtained from scintigraphic-like images

The Gaussian assumption (GA) has been found experimentally to provide an acceptable fit to ROC data elicited from visual experiments. When the GA is satisfied the two-parameter index D(delta m, s) determines the ROC completely. It is however not known whether the GA is an intrinsic property of the eye-brain system, or whether it is a consequence of the type of visual stimuli selected for the experiments. Using scintigraphic-like images to test the validity of the GA, it is found that (i) series of visual stimuli with as few variables as possible produce ROC data compatible with the GA, but (ii) it is possible to find stimuli for which the GA provides a very poor account of experimental data. These results lead us to doubt that the GA is an intrinsic property of the human visual system.