Zhu B et al. (2016) PLoS One "Link Prediction in Weighted Networks: A Weighted Mutual Information Model."

Xia Y, Zhu B

[PLoS One, 2016]

The link-prediction problem is an open issue in data mining and knowledge discovery, which attracts researchers from disparate scientific communities. A wealth of methods have been proposed to deal with this problem. Among these approaches, most are applied in unweighted networks, with only a few taking the weights of links into consideration. In this paper, we present a weighted model for undirected and weighted networks based on the mutual information of local network structures, where link weights are applied to further enhance the distinguishable extent of candidate links. Empirical experiments are conducted on four weighted networks, and results show that the proposed method can provide more accurate predictions than not only traditional unweighted indices but also typical weighted indices. Furthermore, some in-depth discussions on the effects of weak ties in link prediction as well as the potential to predict link weights are also given. This work may shed light on the design of algorithms for link prediction in weighted networks.

Gianakas CA et al. (2023) J Cell Biol "Hemicentin-mediated type IV collagen assembly strengthens juxtaposed basement membrane linkage."

Sherwood DR, Chi Q, Gianakas CA, Ramos-Lewis W, Jayadev R, Keeley DP, Kenny IW, Park K

[J Cell Biol, 2023]

Basement membrane (BM) matrices surround and separate most tissues. However, through poorly understood mechanisms, BMs of adjacent tissue can also stably link to support organ structure and function. Using endogenous knock-in fluorescent proteins, conditional RNAi, optogenetics, and quantitative live imaging, we identified extracellular matrix proteins mediating a BM linkage (B-LINK) between the uterine utse and epidermal seam cell BMs in Caenorhabditis elegans that supports the uterus during egg-laying. We found that hemicentin is secreted by the utse and promotes fibulin-1 assembly to jointly initiate the B-LINK. During egg-laying, however, both proteins' levels decline and are not required for B-LINK maintenance. Instead, we discovered that hemicentin recruits ADAMTS9/20, which facilitates the assembly of high levels of type IV collagen that sustains the B-LINK during the mechanically active egg-laying period. This work reveals mechanisms underlying BM-BM linkage maturation and identifies a crucial function for hemicentin and fibulin-1 in initiating attachment and type IV collagen in strengthening this specialized form of tissue linkage.

Banerjee A et al. (2023) Proc Natl Acad Sci U S A "Network inference from short, noisy, low time-resolution, partial measurements: Application to C. elegans neuronal calcium dynamics."

Ott E, Chandra S, Banerjee A

[Proc Natl Acad Sci U S A, 2023]

Network link inference from measured time series data of the behavior of dynamically interacting network nodes is an important problem with wide-ranging applications, e.g., estimating synaptic connectivity among neurons from measurements of their calcium fluorescence. Network inference methods typically begin by using the measured time series to assign to any given ordered pair of nodes a numerical score reflecting the likelihood of a directed link between those two nodes. In typical cases, the measured time series data may be subject to limitations, including limited duration, low sampling rate, observational noise, and partial nodal state measurement. However, it is unknown how the performance of link inference techniques on such datasets depends on these experimental limitations of data acquisition. Here, we utilize both synthetic data generated from coupled chaotic systems as well as experimental data obtained from Caenorhabditis elegans neural activity to systematically assess the influence of data limitations on the character of scores reflecting the likelihood of a directed link between a given node pair. We do this for three network inference techniques: Granger causality, transfer entropy, and, a machine learning-based method. Furthermore, we assess the ability of appropriate surrogate data to determine statistical confidence levels associated with the results of link-inference techniques.

Reilly DK et al. (2019) Curr Biol "Chemical Communication: Linking Behavior and Physiology."

Reilly DK, Srinivasan J

[Curr Biol, 2019]

How does physiological state affect the reproductive behavior of an organism? Two new studies in Caenorhabditis elegans implicate an ancient serotonergic neuronal circuit in the link between these two outputs- reproductive behavior and physiology.

Lopez-Aviles S et al. (2010) Curr Biol "Cell cycle: the art of multi-tasking."

Uhlmann F, Lopez-Aviles S

[Curr Biol, 2010]

Separase is the protease that cleaves the cohesive link between sister chromatids to trigger chromosome segregation in mitosis and meiosis. This enzyme is known to orchestrate additional mitotic events and we now gain new insight into how it promotes cytokinesis in the nematode Caenorhabditis elegans.

Maduro MF (2018) FEBS J "Genetic interaction between DNA replication and the Notch signaling pathway."

Maduro MF

[FEBS J, 2018]

The Notch pathway is a widely conserved cell signaling system found in most metazoans. In Caenorhabditis elegans, GLP-1/Notch signaling is required for developmental cell fate decisions in multiple contexts. A recent report provides a potential link between DNA replication and Notch-dependent proliferation in the C. elegans germline.

Kunert J et al. (2014) Phys Rev E Stat Nonlin Soft Matter Phys "Low-dimensional functionality of complex network dynamics: neurosensory integration in the Caenorhabditis Elegans connectome."

Shlizerman E, Kutz JN, Kunert J

[Phys Rev E Stat Nonlin Soft Matter Phys, 2014]

We develop a biophysical model of neurosensory integration in the model organism Caenorhabditis elegans. Building on experimental findings on the neuron conductances and their resolved connectome, we posit the first full dynamic model of the neural voltage excitations that allows for a characterization of network structures which link input stimuli to neural proxies of behavioral responses. Full connectome simulations of neural responses to prescribed inputs show that robust, low-dimensional bifurcation structures drive neural voltage activity modes. Comparison of these modes with experimental studies allows us to link these network structures to behavioral responses. Thus the underlying bifurcation structures discovered, i.e., induced Hopf bifurcations, are critical in explaining behavioral responses such as swimming and crawling.

Golden A et al. (2003) Dev Cell "Getting (chromosomes) loaded--a new role for timeless."

Golden A, Cohen-Fix O

[Dev Cell, 2003]

A recent study in C. elegans reveals an unanticipated link between sister chromatid cohesion and the TIM-1 protein, a homolog of the Drosophila circadian rhythm protein TIMELESS. The phenotypes of tim-1 mutants suggest that cohesin subunits load onto chromosomes in a stepwise manner. Whether TIM-1 is also involved in circadian rhythms is discussed.

Vellai T et al. (2003) Nature "Genetics: influence of TOR kinase on lifespan in C. elegans."

Orosz L, Takacs-Vellai K, Kovacs AL, Zhang Y, Muller F, Vellai T

[Nature, 2003]

The group of enzymes known as TOR (for 'target of rapamycin') kinases regulates cell growth and proliferation in response to nutrients and hormone-dependent mitogenic signals. Here we show that TOR deficiency in the nematode Caenorhabditis elegans more than doubles its natural lifespan. This new function for TOR signalling in ageing control may represent a link between nutrition, metabolism and longevity.

Mansfeld J et al. (2006) Mol Cell "The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells."

Hawryluk-Gara LA, Wozniak RW, Galy V, Mall M, Pante N, Mattaj IW, Antonin W, Muhlhausser P, Guttinger S, Kutay U, Haselmann U, Mansfeld J

[Mol Cell, 2006]

Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in the nuclear envelope (NE), through which exchange of molecules between the nucleus and cytosol occurs. Biogenesis of NPCs is complex and poorly understood. In particular, almost nothing is known about how NPCs are anchored in the NE. Here, we characterize vertebrate NDC1-a transmembrane nucleoporin conserved between yeast and metazoans. We show by RNA interference (RNAi) and biochemical depletion that NDC1 plays an important role in NPC and NE assembly in vivo and in vitro. RNAi experiments suggest a functional link between NDC1 and the soluble nucleoporins Nup93, Nup53, and Nup205. Importantly, NDC1 interacts with Nup53 in vitro. This suggests that NDC1 function involves forming a link between the NE membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane.