A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles

Topological change of soil microbiota networks for forest resilience under global warming

Forest management by thinning can mitigate the detrimental impact of increasing drought caused by global warming. Growing evidence shows that the soil microbiota can coordinate the dynamic relationship between forest functions and drought intensity, but how they function as a cohesive whole remains elusive. We outline a statistical topology model to chart the roadmap of how each microbe acts and interacts with every other microbe to shape the dynamic changes of microbial communities under forest management. To demonstrate its utility, we analyze a soil microbiota data collected from a two-way longitudinal factorial experiment involving three stand densities and three levels of rainfall over a growing season in artificial plantations of a forest tree - larix (Larix kaempferi). We reconstruct the most sophisticated soil microbiota networks that code maximally informative microbial interactions and trace their dynamic trajectories across time, space, and environmental signals. By integrating GLMY homology theory, we dissect the topological architecture of these so-called omnidirectional networks and identify key microbial interaction pathways that play a pivotal role in mediating the structure and function of soil microbial communities. The statistical topological model described provides a systems tool for studying how microbial community assembly alters its structure, function and evolution under climate change.

A pleiotropic-epistatic entangelement model of drug response

Because drug response is multifactorial, graph models are uniquely powerful for comprehending its genetic architecture. We deconstruct drug response into many different and interdependent sub-traits, with each sub-trait controlled by multiple genes that act and interact in a complicated manner. The outcome of drug response is the consequence of multileveled intertwined interactions between pleiotropic effects and epistatic effects. Here, we propose a general statistical physics framework to chart the 3D geometric network that codes how epistasis pleiotropically influences a complete set of sub-traits to shape body-drug interactions. This model can dissect the topological architecture of epistatically induced pleiotropic networks (EiPN) and pleiotropically influenced epistatic networks (PiEN). We analyze and interpret the practical implications of the pleiotropic-epistatic entanglement model for pharmacogenomic studies.

Vaginal microbiota networks as a mechanistic predictor of aerobic vaginitis

Aerobic vaginitis (AV) is a complex vaginal dysbiosis that is thought to be caused by the micro-ecological change of the vaginal microbiota. While most studies have focused on how changes in the abundance of individual microbes are associated with the emergence of AV, we still do not have a complete mechanistic atlas of the microbe-AV link. Network modeling is central to understanding the structure and function of any microbial community assembly. By encapsulating the abundance of microbes as nodes and ecological interactions among microbes as edges, microbial networks can reveal how each microbe functions and how one microbe cooperate or compete with other microbes to mediate the dynamics of microbial communities. However, existing approaches can only estimate either the strength of microbe-microbe link or the direction of this link, failing to capture full topological characteristics of a network, especially from high-dimensional microbial data. We combine allometry scaling law and evolutionary game theory to derive a functional graph theory that can characterize bidirectional, signed, and weighted interaction networks from any data domain. We apply our theory to characterize the causal interdependence between microbial interactions and AV. From functional networks arising from different functional modules, we find that, as the only favorable genus from Firmicutes among all identified genera, the role of Lactobacillus in maintaining vaginal microbial symbiosis is enabled by upregulation from other microbes, rather than through any intrinsic capacity. Among Lactobacillus species, the proportion of L. crispatus to L. iners is positively associated with more healthy acid vaginal ecosystems. In a less healthy alkaline ecosystem, L. crispatus establishes a contradictory relationship with other microbes, leading to population decrease relative to L. iners. We identify topological changes of vaginal microbiota networks when the menstrual cycle of women changes from the follicular to luteal phases. Our network tool provides a mechanistic approach to disentangle the internal workings of the microbiota assembly and predict its causal relationships with human diseases including AV.

A New Understanding, Guided by Single-Cell Sequencing, of the Establishment and Maintenance of the Ovarian Reserve in Mammals

BACKGROUND

Oocytes are a finite and non-renewable resource that are maintained in primordial follicle structures. The ovarian reserve is the totality of primordial follicles, present from birth, within the ovary and its establishment, size, and maintenance dictates the duration of the female reproductive lifespan. Understanding the cellular and molecular dynamics relevant to the establishment and maintenance of the reserve provides the first steps necessary for modulating both individual human and animal reproductive health as well as population dynamics.

SUMMARY

This review details the key stages of establishment and maintenance of the ovarian reserve, encompassing germ cell nest formation, germ cell nest breakdown, and primordial follicle formation and activation. Furthermore, we spotlight several formative single-cell sequencing studies that have significantly advanced our knowledge of novel molecular regulators of the ovarian reserve, which may improve our ability to modulate female reproductive lifespans.

KEY MESSAGES

The application of single-cell sequencing to studies of ovarian development in mammals, especially when leveraging genetic and environmental models, offers significant insights into fertility and its regulation. Moreover, comparative studies looking at key stages in the development of the ovarian reserve across species has the potential to impact not just human fertility, but also conservation biology, invasive species management, and agriculture.

The Genetic Architecture of Juvenile Growth Traits in the Conifer Torreya grandis as Revealed by Joint Linkage and Linkage Disequilibrium Mapping

Despite its high economical and ornamental values, Torreya grandis, a dioecious non-timber coniferous species, has long been an underrepresented species. However, the advent and application of advanced genotyping technologies have stimulated its genetic research, making it possible to gain new insight into the genetic architecture of complex traits that may not be detected for model species. We apply an open-pollination (OP) mapping strategy to conduct a QTL mapping experiment of T. grandis, in which nearly 100 unrelated trees randomly chosen from the species' natural distribution and their half-sib progeny are simultaneously genotyped. This strategy allows us to simultaneously estimate the recombination fractions and linkage disequilibrium (LD) coefficients between each pair of markers. We reconstruct a high-density linkage map of 4,203 SNPs covering a total distance of 8,393.95 cM and plot pairwise normalized LD values against genetic distances to build up a linkage-LD map. We identify 13 QTLs for stem basal diameter growth and 4 QTLs for stem height growth in juvenile seedlings. From the linkage-LD map, we infer the evolutionary history of T. grandis and each of its QTLs. The slow decay of QTL-related LDs indicates that these QTLs and their harboring genomic regions are evolutionarily relatively young, suggesting that they can better utilized by clonal propagation rather than through seed propagation. Genetic results from the OP sampling strategy could provide useful guidance for genetic studies of other dioecious species.