Progress in Biophysics and Molecular Biology 113 (2013) 356e357
Contents lists available at ScienceDirect
Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio
Editorial
Introduction: Systems biology and reproduction The present volume presents ten discrete essays on Systems Biology and Reproduction in one cover with certain premises in context. An ordered system has few different kinds of parts arranged in a pattern. In this definitional scheme, biological systems are not especially well-ordered. It is rather heterogenous, irregular, nonlinear and patternless. Nevertheless, organization does develop in the heap of apparent order-poor arrangements of principles in biological systems without any pre-determined goal. There are complexities in biological systems. It is therefore becoming increasing imperative that biologists start with the art of dealing with the issues of biological complexities. Someway, systems biology gives promises to tackle biological complexities. However, complexity is something that most biologists try to avoid. In the present volume, Biplab Bose makes an account of a biologist in the given conflicts. While there is no concrete theory to master the genesis of complexity in biological systems, it is generally believed that increase in complexities tend to furnish an edge to the evolution and evolvability. Sumeet Agarwal presents a paper to address how systems approach may be employed to effectively delineate this issue in evolution. In particular, he examines the link between the evolvability of a system in terms of how agile it is in responding to novel environments, and the evolvability of certain kinds of gene-network functionality at the computational level. Reproduction is a real physiological challenge for the survivability of an organism, while organismal reproductive success to establish diversity is associated with Waddington’s niche partitioning which can be a source of potential stress (Waddington, 1969). In their essay, David Lovejoy and Dalia Barsyte-Lovejoy highlight how systems approach based on comparative genomics, large scale genomic and epigenetic studies has opened up greater understanding of the integration of stress and reproduction at various levels of the organism. Majumdar continues with this thread of thoughts in his paper to tell us how application of systems approach based on large scale transcriptomic and proteomic information from various testicular somatic and germ cell studies may bring newer and meaningful knowledge. To ensure reproductive success, various aspects of physiology and behaviour need to be tightly orchestrated within and outside. David Kennaway and his associates reflect on the endogenous circadian timing system at the molecular levels that are intimately interwoven with both the timing and functions of various reproductive processes ranging from ovulatory cycle to fertilization, embryo growth, implantation, placentation and parturition. The reproductive success of an organism is largely determined by the history and physiology of ovarian follicle selection that take place on different scales and different levels of endocrine loops, the dynamics of follicle populations within the ovary and the dynamics of cell populations within ovarian follicles. Frederique Clement and Danielle Monniaux give a brilliant account of multi-scale 0079-6107/$ e see front matter Ó 2013 Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.pbiomolbio.2013.11.005
model formulating ovarian follicle selection. We believe such attempt of modelling can become useful complement to experimental studies. Indeed, Maria Street makes the conviction fructified by proposing a network-based analysis to assess the importance of the biochemical variables like IL-6, IGF-II and IGFBP-2 protein concentrations in placental lysates to offer a new insight into placental markers of fetal growth within the IGF and cytokine systems. Epigenetic modifications are widely accepted as playing a critical role in the regulation of gene expression and that of phenotype in multicellular organisms. Epigenetic landscapes during oocyte maturation and pre-implantation embryo development in mammals is important in the process of reproductive success and diversity. Rocio Rivera and Jason Ross, in their paper, shed light into the importance of this aspect of reproduction based on recent studies. In general, these epigenetic markings are cleared and are reestablished in each generation. In a number of model organisms, however, it seems that this clearing is incomplete at some loci in the genome, and environment may influence the establishment of the epigenome. These findings suggest that an environmental event in one generation could affect the phenotype in subsequent generations. Transgenerational epigenetic inheritance thus deals with the inheritance of expression states and thus traits that are not determined by the DNA sequences. The possibility that environmental exposure may cause epigenetic modifications through primarily affecting the soma appears particularly intriguing because it contradicts the established dogma that hereditary information flows only from germline to soma. This somewhat Lamarckian idea is indeed stimulating for a broad spectrum of biologists, and it has already invaded the philosophy of biology (Noble, 2013). In the given scenario, Abhay Sharma gives us a guided tour through direct, indirect and circumstantial evidence and putative mechanisms in various species to show us that much remains to be understood before the issue is settled. As it becomes evident from the journey through different essays, there is a dynamical system with interacting parts in time and space, which however integrate together to finally give rise to behaviour which is selected and stabilized. Per Jensen in the final essay examines whether there exists sufficient evidence to suggest epigenetic modifications can affect the behaviour of animals, and then acquired behavioural alterations can transfer across generation borders. The main purpose of this anthology was to gather at one place different slices of views and thoughts on application of systems biology in understanding different aspects of reproductive physiology. It is our hope that this Special Issue shall stimulate a broad spectrum of biologists to think anew and differently. We, as the invited editors for the Special Issue, wish to thank Professor Denis Noble who encouraged us to take up the challenge of editing this issue. Ultimately, this issue could find the light of day
Editorial / Progress in Biophysics and Molecular Biology 113 (2013) 356e357
because the authors contributed their time and efforts to write and re-write the essays and kindly sent to us. No wonder that a large number of authors indeed did not reply or comply. We wish to thank all the authors for holding our hands throughout the journey and endure the completion of the task, despite their busy schedules and other commitments. The reviewers are truly the unsung heroes, their commitment to the cause is not easy to acknowledge in words. We indeed appreciate their affection and support in preparing the volume. The project would not be complete without the full support from the PBMB teams in Editoral and Production offices, particularly Mr. Manikandan Radhakrishnan, Ms. Wong Sophia and Ms. Arthi Prianka. We do not know how to give them our thanks.
357
References Noble, D., 2013. Physiology is rocking the foundations of evolutionary biology. Exp. Physiol. 98, 1235e1243. Waddington, C.H., 1969. Paradigm for an evolutionary process. In: Waddington, C.H. (Ed.), Towards a Theoretical Biology. Aldine Publishing Co., Chicago, pp. 106e 128.
Debabrata Ghosh* Department of Physiology, All India Institute of Medical Sciences, New Delhi, India Jayasree Sengupta Department of Physiology, North DMC Medical College, Hindu Rao Hospital, Delhi, India * Corresponding author. E-mail address: [email protected] (D. Ghosh).
Contents lists available at ScienceDirect
Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio
Editorial
Introduction: Systems biology and reproduction The present volume presents ten discrete essays on Systems Biology and Reproduction in one cover with certain premises in context. An ordered system has few different kinds of parts arranged in a pattern. In this definitional scheme, biological systems are not especially well-ordered. It is rather heterogenous, irregular, nonlinear and patternless. Nevertheless, organization does develop in the heap of apparent order-poor arrangements of principles in biological systems without any pre-determined goal. There are complexities in biological systems. It is therefore becoming increasing imperative that biologists start with the art of dealing with the issues of biological complexities. Someway, systems biology gives promises to tackle biological complexities. However, complexity is something that most biologists try to avoid. In the present volume, Biplab Bose makes an account of a biologist in the given conflicts. While there is no concrete theory to master the genesis of complexity in biological systems, it is generally believed that increase in complexities tend to furnish an edge to the evolution and evolvability. Sumeet Agarwal presents a paper to address how systems approach may be employed to effectively delineate this issue in evolution. In particular, he examines the link between the evolvability of a system in terms of how agile it is in responding to novel environments, and the evolvability of certain kinds of gene-network functionality at the computational level. Reproduction is a real physiological challenge for the survivability of an organism, while organismal reproductive success to establish diversity is associated with Waddington’s niche partitioning which can be a source of potential stress (Waddington, 1969). In their essay, David Lovejoy and Dalia Barsyte-Lovejoy highlight how systems approach based on comparative genomics, large scale genomic and epigenetic studies has opened up greater understanding of the integration of stress and reproduction at various levels of the organism. Majumdar continues with this thread of thoughts in his paper to tell us how application of systems approach based on large scale transcriptomic and proteomic information from various testicular somatic and germ cell studies may bring newer and meaningful knowledge. To ensure reproductive success, various aspects of physiology and behaviour need to be tightly orchestrated within and outside. David Kennaway and his associates reflect on the endogenous circadian timing system at the molecular levels that are intimately interwoven with both the timing and functions of various reproductive processes ranging from ovulatory cycle to fertilization, embryo growth, implantation, placentation and parturition. The reproductive success of an organism is largely determined by the history and physiology of ovarian follicle selection that take place on different scales and different levels of endocrine loops, the dynamics of follicle populations within the ovary and the dynamics of cell populations within ovarian follicles. Frederique Clement and Danielle Monniaux give a brilliant account of multi-scale 0079-6107/$ e see front matter Ó 2013 Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.pbiomolbio.2013.11.005
model formulating ovarian follicle selection. We believe such attempt of modelling can become useful complement to experimental studies. Indeed, Maria Street makes the conviction fructified by proposing a network-based analysis to assess the importance of the biochemical variables like IL-6, IGF-II and IGFBP-2 protein concentrations in placental lysates to offer a new insight into placental markers of fetal growth within the IGF and cytokine systems. Epigenetic modifications are widely accepted as playing a critical role in the regulation of gene expression and that of phenotype in multicellular organisms. Epigenetic landscapes during oocyte maturation and pre-implantation embryo development in mammals is important in the process of reproductive success and diversity. Rocio Rivera and Jason Ross, in their paper, shed light into the importance of this aspect of reproduction based on recent studies. In general, these epigenetic markings are cleared and are reestablished in each generation. In a number of model organisms, however, it seems that this clearing is incomplete at some loci in the genome, and environment may influence the establishment of the epigenome. These findings suggest that an environmental event in one generation could affect the phenotype in subsequent generations. Transgenerational epigenetic inheritance thus deals with the inheritance of expression states and thus traits that are not determined by the DNA sequences. The possibility that environmental exposure may cause epigenetic modifications through primarily affecting the soma appears particularly intriguing because it contradicts the established dogma that hereditary information flows only from germline to soma. This somewhat Lamarckian idea is indeed stimulating for a broad spectrum of biologists, and it has already invaded the philosophy of biology (Noble, 2013). In the given scenario, Abhay Sharma gives us a guided tour through direct, indirect and circumstantial evidence and putative mechanisms in various species to show us that much remains to be understood before the issue is settled. As it becomes evident from the journey through different essays, there is a dynamical system with interacting parts in time and space, which however integrate together to finally give rise to behaviour which is selected and stabilized. Per Jensen in the final essay examines whether there exists sufficient evidence to suggest epigenetic modifications can affect the behaviour of animals, and then acquired behavioural alterations can transfer across generation borders. The main purpose of this anthology was to gather at one place different slices of views and thoughts on application of systems biology in understanding different aspects of reproductive physiology. It is our hope that this Special Issue shall stimulate a broad spectrum of biologists to think anew and differently. We, as the invited editors for the Special Issue, wish to thank Professor Denis Noble who encouraged us to take up the challenge of editing this issue. Ultimately, this issue could find the light of day
Editorial / Progress in Biophysics and Molecular Biology 113 (2013) 356e357
because the authors contributed their time and efforts to write and re-write the essays and kindly sent to us. No wonder that a large number of authors indeed did not reply or comply. We wish to thank all the authors for holding our hands throughout the journey and endure the completion of the task, despite their busy schedules and other commitments. The reviewers are truly the unsung heroes, their commitment to the cause is not easy to acknowledge in words. We indeed appreciate their affection and support in preparing the volume. The project would not be complete without the full support from the PBMB teams in Editoral and Production offices, particularly Mr. Manikandan Radhakrishnan, Ms. Wong Sophia and Ms. Arthi Prianka. We do not know how to give them our thanks.
357
References Noble, D., 2013. Physiology is rocking the foundations of evolutionary biology. Exp. Physiol. 98, 1235e1243. Waddington, C.H., 1969. Paradigm for an evolutionary process. In: Waddington, C.H. (Ed.), Towards a Theoretical Biology. Aldine Publishing Co., Chicago, pp. 106e 128.
Debabrata Ghosh* Department of Physiology, All India Institute of Medical Sciences, New Delhi, India Jayasree Sengupta Department of Physiology, North DMC Medical College, Hindu Rao Hospital, Delhi, India * Corresponding author. E-mail address: [email protected] (D. Ghosh).
