In vitro proliferation and differentiation of mouse spermatogonial stem cells in decellularized human placenta matrix.

Utilizing natural scaffold production derived from extracellular matrix components presents a promising strategy for advancing in vitro spermatogenesis. In this study, we employed decellularized human placental tissue as a scaffold, upon which neonatal mouse spermatogonial cells (SCs) were cultured three-dimensional (3D) configuration. To assess cellular proliferation, we examined the expression of key markers (Id4 and Gfrα1) at both 1 and 14 days into the culture. Our quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed a notable increase in Gfrα1 gene expression, with the 3D culture group exhibiting the highest levels. Furthermore, the relative frequency of Gfrα1-positive cells significantly rose from 38.1% in isolated SCs to 46.13% and 76.93% in the two-dimensional (2D) and 3D culture systems, respectively. Moving forward to days 14 and 35 of the culture period, we evaluated the expression of differentiating markers (Sycp3, acrosin, and Protamine 1). Sycp3 and Prm1 gene expression levels were upregulated in both 2D and 3D cultures, with the 3D group displaying the highest expression. Additionally, acrosin gene expression increased notably within the 3D culture. Notably, at the 35-day mark, the percentage of Prm1-positive cells in the 3D group (36.4%) significantly surpassed that in the 2D group (10.96%). This study suggests that the utilization of placental scaffolds holds significant promise as a bio-scaffold for enhancing mouse in vitro spermatogenesis.

Therapeutic potential of exosomes in spermatogenesis regulation and male infertility.

BACKGROUND: Spermatogenesis is a fundamental process crucial for male reproductive health and fertility. Exosomes, small membranous vesicles released by various cell types, have recently garnered attention for their role in intercellular communication. OBJECTIVE: This review aims to comprehensively explore the role of exosomes in regulating spermatogenesis, focusing on their involvement in testicular development and cell-to-cell communication. METHODS: A systematic examination of literature was conducted to gather relevant studies elucidating the biogenesis, composition, and functions of exosomes in the context of spermatogenesis. RESULTS: Exosomes play a pivotal role in orchestrating the complex signaling networks required for proper spermatogenesis. They facilitate the transfer of key regulatory molecules between different cell populations within the testes, including Sertoli cells, Leydig cells, and germ cells. CONCLUSION: The emerging understanding of exosome-mediated communication sheds light on novel mechanisms underlying spermatogenesis regulation. Further research in this area holds promise for insights into male reproductive health and potential therapeutic interventions.

Testicular niche repair after gonadotoxic treatments: Current knowledge and future directions.

The testicular niche, which includes the germ cells, somatic cells, and extracellular matrix, plays a crucial role in maintaining the proper functions of the testis. Gonadotoxic treatments, such as chemotherapy and radiation therapy, have significantly improved the survival rates of cancer patients but have also been shown to have adverse effects on the testicular microenvironment. Therefore, repairing the testicular niche after gonadotoxic treatments is essential to restore its function. In recent years, several approaches, such as stem cell transplantation, gene therapy, growth factor therapy, and pharmacological interventions have been proposed as potential therapeutic strategies to repair the testicular niche. This comprehensive review aims to provide an overview of the current understanding of testis damage and repair mechanisms. We will cover a range of topics, including the mechanism of gonadotoxic action, repair mechanisms, and treatment approaches. Overall, this review highlights the importance of repairing the testicular niche after gonadotoxic treatments and identifies potential avenues for future research to improve the outcomes for cancer survivors.

Polycaprolactone/Testicular Extracellular Matrix/Graphene Oxide-Based Electrospun Tubular Scaffolds for Reproductive Medicine: Biomimetic Architecture of Seminiferous Tubules.

Numerous scaffolds are developed in the field of testicular bioengineering. However, effectively replicating the spatial characteristics of native tissue, poses a challenge in maintaining the requisite cellular arrangement essential for spermatogenesis. In order to mimic the structural properties of seminiferous tubules, the objective is to fabricate a biocompatible tubular scaffold. Following the decellularization process of the testicular tissue, validation of cellular remnants' elimination from the specimens is conducted using 4',6-diamidino-2-phenylindole staining, hematoxylin and eosin staining, and DNA content analysis. The presence of extracellular matrix (ECM) components is confirmed through Alcian blue, Orcein, and Masson's trichrome staining techniques. The electrospinning technique is employed to synthesize the scaffolds using polycaprolactone (PCL), extracted ECM, and varying concentrations of graphene oxide (GO) (0.5%, 1%, and 2%). Subsequently, comprehensive evaluations are performed to assess the properties of the synthetic scaffolds. These evaluations encompass Fourier-transform infrared spectroscopy, scanning electron microscopy imaging, scaffold degradation testing, mechanical behavior analysis, methylthiazolyldiphenyl-tetrazolium bromide assay, and in vivo biocompatibility assessment. The PCL/decellularized extracellular matrix with 0.5% GO formulation exhibits superior fiber morphology and enhanced mechanical properties, and outperforms other groups in terms of in vitro biocompatibility. Consequently, these scaffolds present a viable option for implementation in "in vitro spermatogenesis" procedures, holding promise for future sperm production from spermatogonial cells.

A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes.

BACKGROUND: The prevalence of the COVID-19 disease in recent years and its widespread impact on mortality, as well as various aspects of life around the world, has made it important to study this disease and its viral cause. However, very long sequences of this virus increase the processing time, complexity of calculation, and memory consumption required by the available tools to compare and analyze the sequences. RESULTS: We present a new encoding method, named PC-mer, based on the k-mer and physic-chemical properties of nucleotides. This method minimizes the size of encoded data by around 2 k times compared to the classical k-mer based profiling method. Moreover, using PC-mer, we designed two tools: 1) a machine-learning-based classification tool for coronavirus family members with the ability to recive input sequences from the NCBI database, and 2) an alignment-free computational comparison tool for calculating dissimilarity scores between coronaviruses at the genus and species levels. CONCLUSIONS: PC-mer achieves 100% accuracy despite the use of very simple classification algorithms based on Machine Learning. Assuming dynamic programming-based pairwise alignment as the ground truth approach, we achieved a degree of convergence of more than 98% for coronavirus genus-level sequences and 93% for SARS-CoV-2 sequences using PC-mer in the alignment-free classification method. This outperformance of PC-mer suggests that it can serve as a replacement for alignment-based approaches in certain sequence analysis applications that rely on similarity/dissimilarity scores, such as searching sequences, comparing sequences, and certain types of phylogenetic analysis methods that are based on sequence comparison.

An automated ultra-fast, memory-efficient, and accurate method for viral genome classification.

The classification of different organisms into subtypes is one of the most important tools of organism studies, and among them, the classification of viruses itself has been the focus of many studies due to their use in virology and epidemiology. Many methods have been proposed to classify viruses, some of which are designed for a specific family of organisms and some of which are more general. But still, especially for certain categories such as Influenza and HIV, classification is facing performance challenges as well as processing and memory bottlenecks. In this way, we designed an automated classifier, called PC-mer, that is based on k-mer and physicochemical characteristics of nucleotides, which reduces the number of features about 2 k times compared to the alternative methods based on k-mer, and compared to integer and one-hot encoding methods, it is possible to keep the number of features constant despite the growth of the sequence length. In this way, it also increases the training speed by an average of 17.93 times. This improvement in processing complexity is provided while PC-mer can also improve the classifying performance for a variety of virus families.

Bone marrow mesenchymal stem cells' osteogenic potential: superiority or non-superiority to other sources of mesenchymal stem cells?

Skeletal problems are an increasing issue due to the increase in the global aging population. Different statistics reports show that today, the global population is aging that results in skeletal problems, increased health system costs, and even higher mortality associated with skeletal problems. Common treatments such as surgery and bone grafts are not always effective and in some cases, they can even cause secondary problems such as infections or improper repair. Cell therapy is a method that can be utilized along with common treatments independently. Mesenchymal stem cells (MSCs) are a very important and efficient source in terms of different diseases, especially bone problems. These cells are present in different tissues such as bone marrow, adipose tissue, umbilical cord, placenta, dental pulp, peripheral blood, amniotic fluid and others. Among the types of MSCs, bone marrow mesenchymal stem cells (BMMSCs) are the most widely used source of these cells, which have appeared to be very effective and promising in terms of skeletal diseases, especially compared to the other sources of MSCs. This study focuses on the specific potential and content of BMMSCs from which the specific capacity of these cells originates, and compares their osteogenic potential with other types of MSCs, and also the future directions in the application of BMMSCs as a source for cell therapy.

Bone marrow mesenchymal stem cell's exosomes as key nanoparticles in osteogenesis and bone regeneration: specific capacity based on cell type.

Today, communities and their health systems are facing with several challenges associated with the population ageing. Growing number of bone disorders is one of the most serious consequences of aging. According to the reports bone disorders won't just affect the elderly population. Mesenchymal stem cells (MSCs) are multipotent cells that could be derived from a variety of tissues including bone marrow, Wharton's Jelly, adipose tissue, and others. MSCs have been utilized in different researches in the field of regenerative medicine because of their immunosuppression and anti-inflammatory mechanisms (like: inhibiting the activity of antigen presenting cells, and suppressing the activity of T lymphocyte cells, macrophages, and so on.), migration to injured areas, and participation in healing processes. Bone marrow mesenchymal stem cells (BMMSCs) are a type of these cells which can be commonly used in bone research with the promising results. These cells function by releasing a large number of extracellular vesicles (EVs). Exosomes are the most major EVs products produced by BMMSCs. They have the same contents and properties as their parent cells; however, these structures don't have the defects of cell therapy. Proteins (annexins, tetraspannins, etc.), lipids (cholesterol, phosphoglycerides, etc.), nucleic acids (micro-RNAs, and etc.) and other substances are found in exosomes. Exosomes affect target cells, causing them to change their function. The features of BMMSC exosomes' mechanism in osteogenesis and bone regeneration (like: effects on other MSCs, osteoblasts, osteoclasts, and angiogenesis) and also the effects of their micro-RNAs on osteogenesis are the subject of the present review.

WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.

The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing customized network structures. However, a few works focus on more effective factors, such as input encoding method or implementation technology, to address accuracy and efficiency issues in this area. Therefore, in this work, we propose an image-based encoding method, called as WalkIm, whose adoption, even in a simple neural network, provides competitive accuracy and superior efficiency, compared to the existing classification methods (e.g. VGDC, CASTOR, and DLM-CNN) for a variety of biological sequences. Using WalkIm for classifying various data sets (i.e. viruses whole-genome data, metagenomics read data, and metabarcoding data), it achieves the same performance as the existing methods, with no enforcement of parameter initialization or network architecture adjustment for each data set. It is worth noting that even in the case of classifying high-mutant data sets, such as Coronaviruses, it achieves almost 100% accuracy for classifying its various types. In addition, WalkIm achieves high-speed convergence during network training, as well as reduction of network complexity. Therefore WalkIm method enables us to execute the classifying neural networks on a normal desktop system in a short time interval. Moreover, we addressed the compatibility of WalkIm encoding method with free-space optical processing technology. Taking advantages of optical implementation of convolutional layers, we illustrated that the training time can be reduced by up to 500 time. In addition to all aforementioned advantages, this encoding method preserves the structure of generated images in various modes of sequence transformation, such as reverse complement, complement, and reverse modes.

In vitro elimination of EL4 cancer cells from spermatogonia stem cells by miRNA-143- and 206-loaded folic acid-conjugated PLGA nanoparticles.

Aim: MiRNA's-143 and -206 are powerful apoptotic regulators in cancer cells. This study aimed to use miRNA-143- and 206-loaded poly(lactic-co-glycolic) acid (PLGA) nanoparticles conjugated with folic acid to induce apoptosis in the EL4 cancer cells. Materials & methods: The therapy was conducted in six groups: treatment with both miRNAs simultaneously (mixed miRNAs), miRNA-206 treatment, miRNA-143 treatment, blank PLGA, blank polyethylenimine (PEI) and complex PEI-miRNAs. Results: In terms of viability, in mixed miRNAs no synergistic effect was observed on EL4 cell elimination. However, in the single miRNA-206 group, a stronger apoptotic effect was observed than the mixed miRNAs group and single miRNA-143 group alone. Conclusion: MiRNAs' apoptotic induction effects in cancer cells were found to be remarkable.

A comparison between constitutive models for the municipal solid waste.

This paper compares the behavioural models of municipal solid waste (MSW) using the corresponding experimental data. To do so, the proposed models are first reviewed and, then, the algorithms and codes of different models are written. After obtaining each model's algorithm, the same experimental data are considered as input, and the strain-stress curve is plotted for each model. In the first method, the total strain in the waste is obtained based on the summation of the elastic, plastic, biological, and creep strains. Afterward, the equivalent stress is obtained. In this method, using biological changes over time, the age of the waste is calculated as an effective parameter in MSW behaviour. Moreover, the effect of creep on the waste is considered independently. In the second algorithm, MSW is considered as fibre and paste material, and the strain-stress curve is obtained. In this method, the waste is considered as a soil model, and the effect of different parameters are calculated. Due to the complexity of the MSW behaviour and considering various parameters, such as the age of the waste, E changes over time, creep, and biological changes, the Krase model has less error than the other models. Using the soil behaviour model for the waste has a significant error, indicating the difference between the results for the behaviours of the two substances.

Differentiation of human olfactory system-derived stem cells into dopaminergic neuron-like cells: A comparison between olfactory bulb and mucosa as two sources of stem cells.

Cell transplantation has become a possible therapeutic approach in the treatment of neurodegenerative diseases of the nervous system by replacing lost cells. The current study aimed to make a comparison between the differentiation capacity of the olfactory bulb neural stem cells (OB-NSCs) and olfactory ectomesenchymal stem cells (OE-MSCs) into dopaminergic-like neurons under the inductive effect of transforming growth factor ß (TGF-ß). After culturing and treating with TGF-ß, the differentiation capacities of both types of stem cells into dopaminergic neuron-like cells were evaluated. Quantitative real-time polymerase chain reaction analysis 3 weeks after induction demonstrated that the mRNA expression of the dopaminergic activity markers tyrosine hydroxylase (TH), dopamine transporter (DAT), paired box gene 2 (PAX2), and PAX5 in the neuron-like cells derived from OB-NSCs was significantly higher than those derived from OE-MSCs. These findings were further supported by the immunocytochemistry staining showing that the expression of the tyrosine hydroxylase, DAT, PAX2, and paired like homeodomain 3 seemed to be slightly higher in OB-NSCs compared with OE-MSCs. Despite the lower differentiation capacity of OE-MSCs, other considerations such as a noninvasive and easier harvesting process, faster proliferation attributes, longer life span, autologous transplantability, and also the easier and inexpensive cultural process of the OE-MSCs, cumulatively make these cells the more appropriate alternative in the case of autologous transplantation during the treatment process of neurodegenerative disorders like Parkinson's disease.

The effect of the ovarian varicose vein on the DNA methylation in the rat's oocyte.

OBJECTIVES: We intended to determine whether the ovarian varicose which is one of the common etiologies of the pelvic congestion syndrome, has the ability to interfere with the DNA methylation reprogramming in the oocyte and thereby affect the oocyte quality or not. MATERIALS AND METHODS: Varicose model was induced according to the Turner's method in the rats. Briefly, a 20-gauge needle was placed on the left renal vein and a thread was tied over both the needle and the renal vein medial to the insertion of the ovarian vein, and then the needle was removed. Evaluation of prooxidant-antioxidant balance (PAB) was assessed using specific kits and the expression level of the DNA methyltransferase genes Dnmt1, Dnmt3a and Dnmt3L was assessed by Real-time PCR. Immunofluorescent staining for 5-methylcytosine in the oocytes evaluated the global DNA methylation. RESULTS: A significant PAB increase in the ovaries from varicose group was seen. Real-time PCR demonstrated a remarkable decrease in the expression of the Dnmt3a and Dnmt3L which are responsible for de novo DNA methylation in the oocytes. Immunofluorescent staining for 5-mC showed a reduction in the fluorescence intensity in the oocytes collected from the varicose group. CONCLUSION: Our findings from Real-time PCR and immunocytochemistry suggest that the epigenetic parameters in the oocyte could be affected by varicose induction and these epigenetic alteration has the potential to affect the oocyte quality. We suggest that the epigenetic changes could happen in the oocytes after the induction of ovarian varicose and lead to the oocyte quality reduction or even infertility.