Male fertility, chromosome abnormalities, and nuclear organization

Numerous studies have implicated the role of gross genomic rearrangements in male infertility, e.g., constitutional aneuploidy, translocations, inversions, Y chromosome deletions, elevated sperm disomy, and DNA damage. The primary purpose of this paper is to review male fertility studies associated with such abnormalities. In addition, we speculate whether altered nuclear organization, another chromosomal/whole genome-associated phenomenon, is also concomitant with male factor infertility. Nuclear organization has been studied in a range of systems and implicated in several diseases. For many applications the measurement of the relative position of chromosome territories is sufficient to determine patterns of nuclear organization. Initial evidence has suggested that, unlike in the more usual 'size-related' or 'gene density-related' models, mammalian (including human) sperm heads display a highly organized pattern including a chromocenter with the centromeres located to the center of the nucleus and the telomeres near the periphery. More recent evidence, however, suggests there may be size- and gene density-related components to nuclear organization in sperm. It seems reasonable to hypothesize therefore that alterations in this pattern may be associated with male factor infertility. A small handful of studies have addressed this issue; however, to date it remains an exciting avenue for future research with possible implications for diagnosis and therapy.     

Hierarchical spatial organization and prioritization of wetlands: a conceptual model for wetland rehabilitation in South Africa

Wetland rehabilitation planning needs to take into account many different aspects of the wetland and its context. In South Africa, much emphasis is placed on the delivery of ecosystem services, poverty relief and skills development for those involved in labour-intensive rehabilitation measures. A framework is presented that facilitates decision-making with regards to wetland rehabilitation planning. This starts with prioritizing which wetlands need attention within a catchment. This is followed by decisions regarding which rehabilitation measures would be effective in improving certain ecosystem services based upon the aims of rehabilitation and the social context of the surrounding catchment. The functional unit that is most suitable to work with for rehabilitation is the Hydrogeomorphic (HGM) Unit, defined as a section of a wetland with more or less uniform hydrological and geomorphological characteristics. An individual wetland may comprise several HGM units, and a HGM Unit itself can be sub-divided into several smaller habitat or vegetation units. Different rehabilitation measures have been identified which are appropriate for the different scales in this spatial framework. Two case studies are presented as examples of how this spatial framework impacts upon the decisions made by the rehabilitation practitioner.     

A conceptual model for the origin of worker behaviour and adaptation of eusociality

In a model based on the wasp family Vespidae, the origin of worker behaviour, which constitutes the eusociality threshold, is not based on relatedness, therefore the origin of eusociality does not depend on inclusive fitness, and workers at the eusociality threshold are not altruistic. Instead, incipient workers and queens behave selfishly and are subject to direct natural selection. Beyond the eusociality threshold, relatedness enables 'soft inheritance' as the framework for initial adaptations of eusociality. At the threshold of irreversibility, queen and worker castes become fixed in advanced eusociality. Transitions from solitary to facultative, facultative to primitive, and primitive to advanced eusociality occur via exaptation, phenotypic accommodation and genetic assimilation. Multilevel selection characterizes the solitary to highly eusocial transition, but components of multilevel selection vary across levels of eusociality. Roles of behavioural flexibility and developmental plasticity in the evolutionary process equal or exceed those of genotype.     

A baboon model for endometriosis: implications for fertility

Endometriosis is one of the most common causes of chronic pelvic pain and infertility in women in the reproductive age group. Although the existence of this disease has been known for over 100 years our current knowledge of its pathogenesis and the pathophysiology of its related infertility remains unclear. Several reasons contribute to our lack of knowledge, the most critical being the difficulty in carrying out objective long-term studies in women. Thus, we and others have developed a model of this disease in the non-human primate, the baboon (Papio anubis). Intraperitoneal inoculation of autologous menstrual endometrium results in the development of endometriotic lesions with gross morphological characteristics similar to those seen in the human. Multiple factors have been implicated in endometriosis-associated infertility. We have described aberrant levels of factors involved in multiple pathways important in the establishment of pregnancy, in the endometrium of baboons induced with endometriosis. Specifically, we have observed dysregulation of proteins involved in invasion, angiogenesis, methylation, cell growth, immunomodulation, and steroid hormone action. These data suggest that, in an induced model of endometriosis in the baboon, an increased angiogenic capacity, decreased apoptotic potential, progesterone resistance, estrogen hyper-responsiveness, and an inability to respond appropriately to embryonic signals contribute to the reduced fecundity associated with this disease.     

A conceptual model for the development of Phytophthora disease in Quercus robur

Here, a conceptual model is presented for the development of Phytophthora disease in pedunculate oak. The model is presented using the causal loop diagram tool and gives an overview of how various abiotic and biotic factors, such as soil moisture, nutrient availability and mycorrhizal colonization, may affect the reproduction and the infective capacity of soil-borne Phytophthora species, the susceptibility of the host and subsequent disease development. It is suggested that the link between the root damage caused by Phytophthora species and overall tree vitality is in the assimilation and allocation of carbon within the plants. The potential impact of environmental factors on these processes is discussed. The model is presented with reference to scenarios related to variation in soil moisture and nutrient availability. The need for species-specific validation of the model and the implications of the model are discussed.     

Self organization of the microtubule network. A diffusion based model

Microtubules form organized polymer networks in cells. Experimental evidence indicates that their mechanical properties do not play a significant role in the generation of such regular patterns. This spatial organization seems closely related to their dynamic behavior. Here we use mathematical modeling to define conditions under which microtubular dynamics result in self organization. We demonstrate that random diffusional processes can generate regular microtubule organizations under specified kinetic conditions which are found to be compatible with the known properties of tubulin polymers. The organizing forces are the tubulin concentration gradients which are generated by the polymer growth. The present analysis has been restricted to the phase of establishment of the microtubule network. The same conceptual framework, applied to steady state pattern maintenance suggests that the kinetic requirements for self organization might ultimately be responsible for such extraordinary in vivo microtubule dynamics, as the rapid turnover and “dynamic instability” of the interphase network.     

盐沼湿地大规模恢复的概念生态模型——以盐城为例

大规模湿地生态恢复是一项耗资巨大、复杂的系统工程,需要以整个区域湿地结构和功能恢复作为基本目标,将时间和空间上分散的研究成果进行系统梳理,形成对区域湿地生态变化及其驱动因素的规律性认识。本研究以盐城盐沼湿地为案例,以1987年作为未干扰或干扰较少的状态,从结构-过程-功能耦合作用角度,确定区域湿地恢复的关键生态特征,包括:健康与动态潮间带湿地系统、碱蓬生态系统生产力与弹性、复杂景观镶嵌与相互作用、潮间带底栖动物丰富与鸟类觅食基地,以及濒危与关键水鸟种群保护。在此基础上,将围垦与土地利用、水管理、全球变化与海平面上升作为驱动区域湿地生态变化的三大外部因素;海岸侵蚀与沉积、区域水格局变化、地形地貌变化、湿地空间变化与连通性丧失,以及互花米草入侵等是影响湿地生态系统变化的内在压力因子;基于这些压力因子与湿地生态系统变化之间复杂作用关系分析,形成了外部驱动力-内在压力源-生态影响-生态特征之间联合作用下的区域湿地恢复概念生态模型。此模型以复杂因果关系研究为基础,直观展示了湿地恢复需要去除或减缓各种压力因子的一般路径,有利于指导大规模盐沼湿地恢复规划与实践。     

A model for economic comparison of swine insemination programs

Optimal artificial insemination schedules are those that result in a high farrowing rate and litter size, while minimizing costs of semen and labor by avoiding unnecessary inseminations. A simulation model programmed in a commercial spreadsheet was developed to permit comparison of alternative schedules. Farrowing rate and litter size for a particular schedule were dependent on the timing of insemination relative to the time of ovulation. Economic return was calculated by multiplying the number of pigs born per bred sow by $33.00 and subtracting the cost of producing a litter of pigs and raising them to weaning ($222.88 per sow plus $2.44 per pig born) and the cost of detection of estrus and breeding. Seven insemination schedules combined with once versus twice per day detection of estrus were simulated in 500 herds of 100 sows each. Inseminations were simulated to occur on schedules of: 1) 0, 12, 24 and 36 h; 2) 12, 24 and 36 h; 3) 0 and 24 h; 4) 12 and 36 h; 5) 12 h; 6) 24 h; and 7) 36 h after first detection of estrus. Schedule 1 was predicted to yield the highest farrowing rate and litter size. Economic return was highest for Schedule 2 with twice per day detection of estrus followed closely by Schedule 1 with once per day detection of estrus at $14.90 and $13.75 per bred sow, respectively. High performance was dependent on insuring that inseminations occurred at an optimum time in as great a proportion of sows as possible.     

A geometrical model for DNA organization in bacteria

Recent experimental studies have revealed that bacteria, such as C. crescentus, show a remarkable spatial ordering of their chromosome. A strong linear correlation has been found between the position of genes on the chromosomal map and their spatial position in the cellular volume. We show that this correlation can be explained by a purely geometrical model. Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus) together with the action of DNA compaction proteins (that organize the chromosome into topological domains) are sufficient to get a linear arrangement of the chromosome along the cell axis. We develop a Monte-Carlo method that allows us to test our model numerically and to analyze the dependence of the spatial ordering on various physiologically relevant parameters. We show that the proposed geometrical ordering mechanism is robust and universal (i.e. does not depend on specific bacterial details). The geometrical mechanism should work in all bacteria that have compacted chromosomes with spatially fixed regions. We use our model to make specific and experimentally testable predictions about the spatial arrangement of the chromosome in mutants of C. crescentus and the growth-stage dependent ordering in E. coli.     

生态系统管理学的概念框架及其生态学基础

系统地要领了生态系统管理学产生的历史背景和发展进程,讨论了生态系统管理的一些基本概念,生态学基础,管理目标及管理体制与实施方式,详细地论述了生态系统的生态学完整性与边界和时空尺度,生态系统的结构,功能与生态系统整体性,生态系统演替与系统动力学特性,生态系统的干扰与系统稳定性,生态系统的复杂性与不确定性,生态系统多样性与可持续生态系统,生态模型与数据收集和监测,人类活动对环境影响的双重性等生态学基础问题,阐述了在维持生态系统产品和服务功能的可持续性总体目标下,各类生态系统管理的具体目标。     

A computational model for the identification of biochemical pathways in the krebs cycle.

We have applied an algorithmic methodology which provably decomposes any complex network into a complete family of principal subcircuits to study the minimal circuits that describe the Krebs cycle. Every operational behavior that the network is capable of exhibiting can be represented by some combination of these principal subcircuits and this computational decomposition is linearly efficient. We have developed a computational model that can be applied to biochemical reaction systems which accurately renders pathways of such reactions via directed hypergraphs (Petri nets). We have applied the model to the citric acid cycle (Krebs cycle). The Krebs cycle, which oxidizes the acetyl group of acetyl CoA to CO(2) and reduces NAD and FAD to NADH and FADH(2), is a complex interacting set of nine subreaction networks. The Krebs cycle was selected because of its familiarity to the biological community and because it exhibits enough complexity to be interesting in order to introduce this novel analytic approach. This study validates the algorithmic methodology for the identification of significant biochemical signaling subcircuits, based solely upon the mathematical model and not upon prior biological knowledge. The utility of the algebraic-combinatorial model for identifying the complete set of biochemical subcircuits as a data set is demonstrated for this important metabolic process.     

A unifying conceptual model for the environmental responses of isoprene emissions from plants

Background and Aims

Isoprene is the most important volatile organic compound emitted by land plants in terms of abundance and environmental effects. Controls on isoprene emission rates include light, temperature, water supply and CO₂ concentration. A need to quantify these controls has long been recognized. There are already models that give realistic results, but they are complex, highly empirical and require separate responses to different drivers. This study sets out to find a simpler, unifying principle.

Methods

A simple model is presented based on the idea of balancing demands for reducing power (derived from photosynthetic electron transport) in primary metabolism versus the secondary pathway that leads to the synthesis of isoprene. This model''s ability to account for key features in a variety of experimental data sets is assessed.

Key results

The model simultaneously predicts the fundamental responses observed in short-term experiments, namely: (1) the decoupling between carbon assimilation and isoprene emission; (2) a continued increase in isoprene emission with photosynthetically active radiation (PAR) at high PAR, after carbon assimilation has saturated; (3) a maximum of isoprene emission at low internal CO₂ concentration (c_i) and an asymptotic decline thereafter with increasing c_i; (4) maintenance of high isoprene emissions when carbon assimilation is restricted by drought; and (5) a temperature optimum higher than that of photosynthesis, but lower than that of isoprene synthase activity.

Conclusions

A simple model was used to test the hypothesis that reducing power available to the synthesis pathway for isoprene varies according to the extent to which the needs of carbon assimilation are satisfied. Despite its simplicity the model explains much in terms of the observed response of isoprene to external drivers as well as the observed decoupling between carbon assimilation and isoprene emission. The concept has the potential to improve global-scale modelling of vegetation isoprene emission.     

A satiation model for the temporal organization of grazing in limpets

1. A compartmental model of the limpet alimentary system was designed to simulate the effects of functional constraints and substrate characteristics on the temporal patterning of grazing in these gastropods. Limitations are imposed by gut capacity and processing time. A maximum operating frequency is set for the radula activity, and a negative feedback on the grazing frequency is related to gut replenishment.
2. When holding constant the 'morphofunctional' parameters of the model, variations in the 'richness' of the substrate (i.e. in the amount of matter extracted per single rasp) generated different patterns of grazing activity, from constant grazing at different frequencies, to the appearance of distinct grazing–non-grazing subphases with a periodicity corresponding to the processing time. Moreover, when varying the digestibility of the matter (i.e. its processing time), temporary saturations were produced.
3. Automatic recording of radula activity in specimens of Patella caerulea L. collected from a Mediterranean boulder beach and transferred to tidal tanks showed that each activity phase (performed during the high-tide period) may be differently structured: from almost continuous grazing, with more or less pronounced and sometimes periodic oscillations, to alternation of grazing and non-grazing subphases. Continuous and non-continuous grazing patterns are shown also by the same specimen during subsequent activity phases.
4. The results of the model are consistent with empirical observations and suggest that satiation events related to the characteristics of the substrate encountered by the limpets when foraging, can produce highly variable grazing patterns with implications for the energetics of foraging in this group of grazers.     

A conceptual model of the dynamics of the Syamozero lake community

We have developed a conceptual mathematical model of the dynamics of a spatially heterogeneous population system, the prototype of which is the Syamozero lake fish community. Based on the analysis of solutions of the model, we show that interrelations between prey and predator populations in two neighboring habitats (pelagic and offshore zones) can lead to both undamped oscillations and stationary values of the population size. The population density was found to be close to the values oblained in the course of long-term observations of the biota of the Syamozero lake. Besides, we showed that the transition to the stationary states can be accompanied by long-term (dozens and hundreds of years) damped oscillations of the prey and predator population size. In natural waters, long-term transition periods can prevent the attainment of stationary regimes of fish community functioning.     

Zones of influence for soil organic matter dynamics: A conceptual framework for data and models

Soil organic matter (SOM) is an indicator of sustainable land management as stated in the global indicator framework of the United Nations Sustainable Development Goals (SDG Indicator 15.3.1). Improved forecasting of future changes in SOM is needed to support the development of more sustainable land management under a changing climate. Current models fail to reproduce historical trends in SOM both within and during transition between ecosystems. More realistic spatio‐temporal SOM dynamics require inclusion of the recent paradigm shift from SOM recalcitrance as an ‘intrinsic property’ to SOM persistence as an ‘ecosystem interaction’. We present a soil profile, or pedon‐explicit, ecosystem‐scale framework for data and models of SOM distribution and dynamics which can better represent land use transitions. Ecosystem‐scale drivers are integrated with pedon‐scale processes in two zones of influence. In the upper vegetation zone, SOM is affected primarily by plant inputs (above‐ and belowground), climate, microbial activity and physical aggregation and is prone to destabilization. In the lower mineral matrix zone, SOM inputs from the vegetation zone are controlled primarily by mineral phase and chemical interactions, resulting in more favourable conditions for SOM persistence. Vegetation zone boundary conditions vary spatially at landscape scales (vegetation cover) and temporally at decadal scales (climate). Mineral matrix zone boundary conditions vary spatially at landscape scales (geology, topography) but change only slowly. The thicknesses of the two zones and their transport connectivity are dynamic and affected by plant cover, land use practices, climate and feedbacks from current SOM stock in each layer. Using this framework, we identify several areas where greater knowledge is needed to advance the emerging paradigm of SOM dynamics—improved representation of plant‐derived carbon inputs, contributions of soil biota to SOM storage and effect of dynamic soil structure on SOM storage—and how this can be combined with robust and efficient soil monitoring.