Connecting the dots between septins and the DNA damage checkpoint

In budding yeast, septins are involved in the morphogenesis checkpoint and the DNA damage checkpoint, both of which regulate cell-cycle progression. In this issue of Cell, Kremer et al. (2007) link septins to DNA damage in mammalian cells by identifying a new signaling pathway that includes the adaptors SOCS7 and NCK. As NCK controls actin dynamics, this pathway may connect DNA damage responses and cellular morphology in metazoans.     

Finding the evidence for protein-protein interactions from PubMed abstracts

MOTIVATION: Protein-protein interactions play critical roles in biological processes, and many biologists try to find or to predict crucial information concerning these interactions. Before verifying interactions in biological laboratory work, validating them from previous research is necessary. Although many efforts have been made to create databases that store verified information in a structured form, much interaction information still remains as unstructured text. As the amount of new publications has increased rapidly, a large amount of research has sought to extract interactions from the text automatically. However, there remain various difficulties associated with the process of applying automatically generated results into manually annotated databases. For interactions that are not found in manually stored databases, researchers attempt to search for abstracts or full papers. RESULTS: As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts. A query is generated from two given proteins automatically and abstracts are then collected from PubMed. Following this, target proteins and their synonyms are recognized and their interaction information is extracted from the collection. It was found that 67.37% of the interactions from DIP-PPI corpus were found from the PubMed abstracts and 87.37% of interactions were found from the given full texts. AVAILABILITY: Contact authors.     

Clustering of PubMed abstracts using nearer terms of the domain

Literature search is a process in which external developers provide alternative representations for efficient data mining of biomedical literature such as ranking search results, displaying summarized knowledge of semantics and clustering results into topics. In clustering search results, prominent vocabularies, such as GO (Gene Ontology), MeSH(Medical Subject Headings) and frequent terms extracted from retrieved PubMed abstracts have been used as topics for grouping. In this study, we have proposed FNeTD (Frequent Nearer Terms of the Domain) method for PubMed abstracts clustering. This is achieved through a two-step process viz; i) identifying frequent words or phrases in the abstracts through the frequent multi-word extraction algorithm and ii) identifying nearer terms of the domain from the extracted frequent phrases using the nearest neighbors search. The efficiency of the clustering of PubMed abstracts using nearer terms of the domain was measured using F-score. The present study suggests that nearer terms of the domain can be used for clustering the search results.     

Mammalian milk glycomes: Connecting the dots between evolutionary conservation and biosynthetic pathways

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Hallmarks of aging and immunosenescence: Connecting the dots

Aging is a natural physiological process that features various and variable challenges, associated with loss of homeostasis within the organism, often leading to negative consequences for health. Cellular senescence occurs when cells exhaust the capacity to renew themselves and their tissue environment as the cell cycle comes to a halt. This process is influenced by genetics, metabolism and extrinsic factors. Immunosenescence, the aging of the immune system, is a result of the aging process, but can also in turn act as a secondary inducer of senescence within other tissues. This review aims to summarize the current state of knowledge regarding hallmarks of aging in relation to immunosenescence, with a focus on aging-related imbalances in the medullary environment, as well as the components of the innate and adaptive immune responses. Aging within the immune system alters its functionality, and has consequences for the person's ability to fight infections, as well as for susceptibility to chronic diseases such as cancer and cardiovascular disease. The senescence-associated secretory phenotype is described, as well as the involvement of this phenomenon in the paracrine induction of senescence in otherwise healthy cells. Inflammaging is discussed in detail, along with the comorbidities associated with this process. A knowledge of these processes is required in order to consider possible targets for the application of senotherapeutic agents - interventions with the potential to modulate the senescence process, thus prolonging the healthy lifespan of the immune system and minimizing the secondary effects of immunosenescence.     

Connecting the dots in Huntington's disease with protein interaction networks

Analysis of protein-protein interaction networks is becoming important for inferring the function of uncharacterized proteins. A recent study using this approach has identified new proteins and interactions that might be involved in the pathogenesis of the neurodegenerative disorder Huntington's disease, including a GTPase-activating protein that co-localizes with protein aggregates in Huntington's disease patients.     

Connecting the dots: from actin polymerization to synapse formation

Protrusive behavior of dendritic spines on developing neurons has been previously suggested to mediate the formation of new axodendritic synaptic contacts. A study by Zito et al. in this issue of Neuron links actin polymerization in dendritic spines with the motility that the spines exhibit and the synapses that they form.     

Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstracts

High-throughput genomic technologies enable researchers to identify genes that are co-regulated with respect to specific experimental conditions. Numerous statistical approaches have been developed to identify differentially expressed genes. Because each approach can produce distinct gene sets, it is difficult for biologists to determine which statistical approach yields biologically relevant gene sets and is appropriate for their study. To address this issue, we implemented Latent Semantic Indexing (LSI) to determine the functional coherence of gene sets. An LSI model was built using over 1 million Medline abstracts for over 20,000 mouse and human genes annotated in Entrez Gene. The gene-to-gene LSI-derived similarities were used to calculate a literature cohesion p-value (LPv) for a given gene set using a Fisher's exact test. We tested this method against genes in more than 6,000 functional pathways annotated in Gene Ontology (GO) and found that approximately 75% of gene sets in GO biological process category and 90% of the gene sets in GO molecular function and cellular component categories were functionally cohesive (LPv<0.05). These results indicate that the LPv methodology is both robust and accurate. Application of this method to previously published microarray datasets demonstrated that LPv can be helpful in selecting the appropriate feature extraction methods. To enable real-time calculation of LPv for mouse or human gene sets, we developed a web tool called Gene-set Cohesion Analysis Tool (GCAT). GCAT can complement other gene set enrichment approaches by determining the overall functional cohesion of data sets, taking into account both explicit and implicit gene interactions reported in the biomedical literature. Availability: GCAT is freely available at http://binf1.memphis.edu/gcat.     

Connecting the dots: from nanodomains to physiological functions of REMORINs

REMORINs (REMs) are a plant-specific protein family, proposed regulators of membrane-associated molecular assemblies and well-established markers of plasma membrane nanodomains. REMs play a diverse set of functions in plant interactions with pathogens and symbionts, responses to abiotic stresses, hormone signaling and cell-to-cell communication. In this review, we highlight the established and more putative roles of REMs throughout the literature. We discuss the physiological functions of REMs, the mechanisms underlying their nanodomain-organization and their putative role as regulators of nanodomain-associated molecular assemblies. Furthermore, we discuss how REM phosphorylation may regulate their functional versatility. Overall, through data-mining and comparative analysis of the literature, we suggest how to further study the molecular mechanisms underpinning the functions of REMs.     

Connecting the dots: an invariant migration corridor links the Holocene to the present

Numerous species undergo impressive movements, but due to massive changes in land use, long distance migration in terrestrial vertebrates has become a highly fragile ecological phenomenon. Uncertainty about the locations of past migrations and the importance of current corridors hampers conservation planning. Using archeological data from historic kill sites and modern methods to track migration, we document an invariant, 150 km (one-way) migration corridor used for at least 6000 years by North America's sole extant endemic ungulate. Pronghorn (Antilocapra americana) from the Greater Yellowstone Ecosystem, like other long distant migrants including Serengeti wildebeest (Connochaetes taurinus) and Arctic caribou (Rangifer tarandus), move nearly 50 km d-1, but in contrast to these other species, rely on an invariant corridor averaging only 2 km wide. Because an entire population accesses a national park (Grand Teton) by passage through bottlenecks as narrow as 121 m, any blockage to movement will result in extirpation. Based on animation of real data coupled with the loss of six historic routes, alternative pathways throughout the 60,000 km2 Yellowstone ecosystem are no longer available. Our findings have implications for developing strategies to protect long distance land migrations in Africa, Asia and North America and to prevent the disappearance of ecological phenomena that have operated for millennia.     

Connecting the dots in ethology: applying network theory to understand neural and animal collectives

A major goal shared by neuroscience and collective behavior is to understand how dynamic interactions between individual elements give rise to behaviors in populations of neurons and animals, respectively. This goal has recently become within reach, thanks to techniques providing access to the connectivity and activity of neuronal ensembles as well as to behaviors among animal collectives. The next challenge using these datasets is to unravel network mechanisms generating population behaviors. This is aided by network theory, a field that studies structure–function relationships in interconnected systems. Here we review studies that have taken a network view on modern datasets to provide unique insights into individual and collective animal behaviors. Specifically, we focus on how analyzing signal propagation, controllability, symmetry, and geometry of networks can tame the complexity of collective system dynamics. These studies illustrate the potential of network theory to accelerate our understanding of behavior across ethological scales.     

Connecting the dots: Stopover strategies of an intercontinental migratory songbird in the context of the annual cycle

The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black‐and‐white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time‐schedule, which has previously been linked to habitat conditions experienced in the preceding phase of the annual cycle. Birds in close proximity to their breeding destination accumulate additional energy reserves prior to arrival on the breeding grounds, as reflected by higher migratory condition upon arrival, higher refueling rates measured via blood plasma metabolites, and longer stopover durations compared to birds migrating to breeding destinations farther from the stopover site. However, late birds near their breeding destination were more likely to depart on the day of arrival (i.e., transients), and among birds that stopped over at the site, the average duration of stopover was almost half the time of early conspecifics, suggesting late birds are trying to catch‐up with the overall time‐schedule of migration for optimal arrival time on the breeding grounds. In contrast, birds with long distances remaining to breeding destinations were more likely to depart on the day of arrival and primarily used stopover to rest before quickly resuming migration, adopting similar strategies regardless of a bird's time‐schedule. Our study demonstrates that migrants adjust their en route strategies in relation to their time‐schedule and distance remaining to their breeding destination, highlighting that strategies of migration should be examined in the context of other phases of the annual cycle.