In silico analysis of candidate proteins sharing homology with Streptococcus agalactiae proteins and their role in male infertility
Parida, R. and Samanta, L.
Syst Biol Reprod Med 2017;63(1):15-28.
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Leukocytospermia is a condition in which the normal leukocyte count in the semen is significantly augmented. Its association with bacterial infection has caused a major problem in the infertile patients. It has also been proposed that a higher number of leukocytes can control pathogenic infection. The presence of a bacterial infection in the leukocytospermia condition suggests that there are additional factors. This led Rajeshwari Parida and Luna Samanta to use in silico analysis as a springboard to understand the immunological basis of infertility so that a vaccine may be designed. Today’s vaccine cocktail includes antigenic candidates which are recognized by our own immune system as both self as well as non-self. In this particular physiologic condition, it is crucial to design an immunocontraceptive which can target only antigenic candidates i.e., bacterial proteins, without affecting the normal metabolic activities of the body directly. The aim of Parida and Samanta in “In silico analysis of candidate proteins sharing homology with Streptococcus agalactiae proteins and their role in male infertility” in Systems Biology in Reproductive Medicine 63(1) was to delineate the importance of immunocontraception towards the sperm function like motility and not to affect spermatogenesis. Streptococcus agalactiae was selected as a model to determine putative vaccine candidates that can be applied for any pathogen associated with such physiologic infertile condition.
Initiative for standardization of reporting genetics of male infertility
Traven, E., Ogrinc, A., and Kunej, T.
Syst Biol Reprod Med 2017;63(1):58-66.
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The number of publications on the field of genetics of male infertility is increasing, as well as various types of complex information generated by diverse technologies. The data are heterogeneous and dispersed in different publications and databases. Standardized reporting of causative and risk factors of male infertility presents an important issue in order to move the field forward. In the study entitled “Initiative for standardization of reporting genetics of male infertility” in Systems Biology in Reproductive Medicine 63(1) Eva Traven, Ana Ogrinc, and Tanja Kunej proposed an initiative for reporting standardization of genetics of male infertility and collected a set of representative loci associated with male infertility risk. The proposed initiative promotes and provides capabilities to combine complex data, joining male infertility-associated information regardless of the study approach into an organized and comprehensive database. The proposed initiative will facilitate development of biomarkers, design of targeted resequencing panels, prioritization of genomic loci for further functional studies, facilitate development of systems approaches, and development of more effective diagnostic tools.
New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos
Vendrell, X., Fernández-Pedrosa, V., Triviño, J.C., Bautista-Llácer, R., Collado, C., Rodríguez, O., García-Mengual, E., Ferrer, E., Calatayud, C., and Ruiz-Jorro, M.
Syst Biol Reprod Med 2017;63(3):162-178.
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Preimplantation Genetic Screening (PGS) is a well-established method in order to implement the elective single embryo transfer, reducing drastically multiple pregnancies and miscarriage rates, and shortening the time to achieve pregnancy. The microarray-based technologies have been considered the gold standard to determine the chromosomal dose of embryos. However, the global implementation of PGS demands a higher resolution and cost-effective approach. In this scenario, the Next-Generation Sequencing (NGS) represents a paradigm shift. The NGS is an exponential technology that has burst globally into the genomic field, and reproductive genetics is not an exception. This paper, “New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos,” by Venrell et al. shows preclinical validation of a new low-resolution whole-genome sequencing protocol for euploidy analysis of preimplantation embryos. The main novelty of this work is the development of an original workflow, bioinformatic algorithm, and data viewer to detect copy number variations throughout each chromosome in a simultaneous analysis of several embryonic samples. This new comprehensive NGS-based 24-chromosome protocol increases the chromosomal resolution, offering new insights on segmental intrachromosomal imbalances and mosaicism.
RNA-based ovarian cancer research from ‘a gene to systems biomedicine’ perspective
Gov, E., Kori, M., and Yalcin Arga, K.
Syst Biol Reprod Med 2017;63(4):219-238.
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With the leading cause of death from ovarian cancer the need to understand the molecular mechanisms underlying ovarian malignancies has been highlighted. Systems biomedicine approaches serve to generate new information that can help to understand the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets, and to discover new drugs. The evaluation of disease progression mechanisms with a systematic approach and mapping the interactions of biological components have had a meagre impact on understanding the tumorigenesis mechanism. The current trend for efficient diagnosis, prognosis, and treatment is towards ‘systems biomedicine approaches’ and is a hallmark of the emerging network medicine concept. This Review Article entitled “RNA-based ovarian cancer research from ‘a gene to systems biomedicine’ perspective” by Esra Gov, Medi Kori, and Kazim Yalcin Arga provides a comprehensive RNA-based literature review suggesting what could be considered as potential therapeutic targets together with the medical prognostic biomarkers in further studies. Through the development of innovative strategies in the light of the current findings, significant contributions to public health await.
Analysis of embryo intactness and developmental potential following slow freezing and vitrification
Yu, L., Jia, C., Lan, Y., Song, R., Zhou, L., Li, Y., Liang, Y., and Wang, S.
Syst Biol Reprod Med 2017;63(5):285–293.
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The Research Article “Analysis of embryo intactness and developmental potential following slow freezing and vitrification” by Lan Yu, Chanwei Jia, Yonglian Lan, Rui Song, Liying Zhou, Ying Li, Yu Liang, and Shuyu Wang aimed to identify the parameters that are related to day 3 embryo intactness and developmental potential after warming to improve the selection criteria used to cryopreserve and transfer embryos. They also sought to compare the slow freezing and vitrification methods of cryopreservation and to evaluate the viability of non-intact embryos. Cleavage-stage embryos with <50% blastomere survival were analyzed using next-generation sequencing (NGS). The results of this study suggest that vitrification is a better choice than slow freezing for embryo cryopreservation. Embryos showing poor quality (fragmentation >30% with/without a non-stage-specific cell size) and lower cell numbers (4-6 cells) on day 3 should be cultured to the blastocyst stage and then be transfered or vitrified if they develop into good-quality blastocysts. The developmental potential of non-intact embryos is lower than that of intact embryos; however, after they are cultured to the fully expanded blastocyst stage, embryos with <50% blastomere survival can be transferred. However, additional studies are needed to evaluate the possibility of using embryos with less than 50% blastomere survival in a clinical setting.
Aging deteriorates quality of sperm produced by male mice with partial Yq deletion
Kotarska, K., Doniec, A., Bednarska, M., Polański, Z., and Styrna, J.
Syst Biol Reprod Med 2017;63(6):360–363.
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Deletions within the Y-chromosome long arm (Yq) belong to the most frequent genetic causes of reduced male fertility. The current study “Aging deteriorates quality of sperm produced by male mice with partial Yq deletion” by Katarzyna Kotarska, Andrzej Doniec, Magdalena Bednarska, Zbigniew Polański, and Józefa Styrna demonstrated, using a unique mouse model, that aging may intensify problems with fertility caused by Yq deletions. Quality and fertilizing potential of gametes produced by young and older male mice with the intact Y chromosome (B10.BR) persist on the same level but worsen significantly with aging of genetically identical males having deleted Y chromosome (B10.BR-Ydel). This finding is consistent with many recent works describing health disadvantages of late fatherhood.
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