What makes a gene name? Named entity recognition in the biomedical literature

The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources. Precise NER tools are a prerequisite for many applications working on text, such as information retrieval, information extraction or document classification. Over the past years, the problem has achieved considerable attention in the bioinformatics community and experience has shown that NER in the life sciences is a rather difficult problem. Several systems and algorithms have been devised and implemented. In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed.     

What makes the cell differentiate?

In the present paper, I propose a hypothesis whereby the necessity to maintain the permanent energy-dissipating metabolic flux represents the primary force that determines the eukaryotic cell's choice to grow, divide and/or differentiate. This view is based on the universal structure and the strict redox neutrality of the core metabolic network. I propose that the direct substrate level coupling between metabolism and gene expression through epigenetic mechanisms provides a mechanistic explanation of how this control is implemented.     

What makes a species central in a cleaning mutualism network?

Mutualisms often form networks of interacting species, characterized by the existence of a central core of species that potentially drive the ecology and the evolution of the whole community. Centrality measures allow quantification of how central or peripheral a species is within a network, thus informing about the role of each species in network organization, dynamics, and stability. In the present study we addressed the question whether the structural position of species in the network (i.e. their topological importance) relates to their ecological traits. We studied interactions between cleaner and client reef fishes to identify central and peripheral species within a mutualistic network, and investigated five ecological correlates. We used three measures to estimate the level of centrality of a species for distinct structural patterns, such as the number of interactions and the structural proximity to other species. Through the use of a principal component analysis (PCA) we observed that the centrality measures were highly correlated (92.5%) in the studied network, which indicates that the same species plays a similar role for the different structural patterns. Three cleaner and ten client species had positive values of centrality, which suggests that these species are modulating ecological and evolutionary dynamics within the network. Higher centralities were related to higher abundances and feeding habits for client fishes, but not for cleaners. The high correlation between centrality measures in the present study is likely related to the nested structure of the cleaning network. The cleaner species’ set, by having central species that are not necessarily the most abundant ones, bears potentially more vulnerable points for network cohesiveness. Additionally, the present study generalizes previous findings for plant–animal mutualisms, as it shows that the structure of marine mutualisms is also related to a complex interplay between abundance and niche‐related features.     

What makes the prefrontal cortex so appealing in the era of brain imaging? a network analytical perspective

It is thought that the prefrontal cortex (PFC) subserves cognitive control processes by coordinating the flow of information in the cerebral cortex. In the network of cortical areas the central position of the PFC makes difficult to dissociate processing and the cognitive function mapped to this region, especially when using whole brain imaging techniques, which can detect frequently activated regions. Accordingly, the present study showed particularly high rate of increase of published studies citing the PFC and imaging as compared to other fields of the neurosciences on the PubMed. Network measures used to characterize the role of the areas in signal flow indicated specialization of the different regions of the PFC in cortical processing. Notably, areas of the dorsolateral PFC and the anterior cingulate cortex, which received the highest number of citations, were identified as global convergence points in the network. These prefrontal regions also had central position in the dominant cluster consisted exclusively by the associational areas of the cortex. We also present findings relevant to models suggesting that control processes of the PFC are depended on serial processing, which results in bottleneck effects. The findings suggest that PFC is best understood via its role in cortical information processing.     

What makes transposable elements move in the Drosophila genome?

Transposable elements (TEs), by their capacity of moving and inducing mutations in the genome, are considered important drivers of species evolution. The successful invasions of TEs in genomes, despite their mutational properties, are an apparent paradox. TEs' transposition is usually strongly regulated to low value, but in some cases these elements can also show high transposition rates, which has been associated sometimes to changes in environmental conditions. It is evident that factors susceptible to induce transpositions in natural populations contribute to TE perpetuation. Different factors were proposed as causative agents of TE mobilization in a wide range of organisms: biotic and abiotic stresses, inter- and intraspecific crosses and populational factors. However, there is no clear evidence of the factors capable of inducing TE mobilization in Drosophila, and data on laboratory stocks show contradictory results. The aim of this review is to have an update critical revision about mechanisms promoting transposition of TEs in Drosophila, and to provide to the readers a global vision of the dynamics of these genomic elements in the Drosophila genome.     

What makes a fly enter diapause?

Diapause is a dormant state that insects may undergo as a response to changing environmental conditions. In flies, like many insects inhabiting temperate zones, diapause occurs generally during the winter months when ambient temperatures are cool and food sources scarce. Whilst the environmental factors involved in determining diapause have been known for a long time, the genes and molecular events controling its initiation are poorly understood. Here I outline the factors that initiate diapause and highlight recent studies that implicate insulin signaling in its control.     

What makes a specialized endophyte special?

Fungal plant symbionts can be highly specialized on a limited range of host genotypes and species. Understanding the genetic basis of this specialization, the mechanisms governing its establishment and the relationship between specialization and speciation is a major challenge for evolutionary biologists (Timms & Read, 1999 ). A deeper knowledge of evolutionary plant–microbe interactions could be exploited to improve agricultural management, by bringing fungal biodiversity and fungal biomass under greater and more durable human control. Previous studies on pathogens have shown that effectors, that is, small secreted proteins that modulate plant physiology to favour host colonization, play a key role in infection of novel hosts (e.g., Inoue et al., 2017 ) or in host specialization (e.g., Liao et al. ( 2016 )). Like pathogens, endophytes also manipulate the physiology of their hosts and colonize novel hosts to which they specialize (Hardoim et al., 2015 ). These biological characteristics of endophytes raise the question of similarities in the protein arsenal contributing to the specialization of pathogens and endophytes. In this issue of Molecular Ecology, Schirrmann et al. ( 2018 ) used a combination of divergence genome scans and tests for positive selection to investigate the genetic basis of specialization of two subspecies of the symbiont Epichloë typhina occurring on two different grass hosts. Their analyses suggest a key role of effectors as determinants of host specialization. This study paves the way towards the comparative analysis of the genomics of speciation among plant symbionts.     

Age at marriage in Sri Lanka: stabilizing or declining?

Over the last four decades in Sri Lanka, age at first marriage for males increased marginally, and for females it rose considerably, but there has been no recent increase in female age at marriage. Among the younger cohorts, estimated ages at which some married indeed show a declining mean age at marriage. Coale-McNeil estimates indicate that there is no real decline in female age at marriage in Sri Lanka. Marriages were delayed as a result of economic hardship or increased mortality to the mid-1970s, but once the overall economy improved after 1977, more marriages took place. Female age at marriage in Sri Lanka remained slightly below 24 years, the age which is anticipated by younger cohorts, and this level is likely to persist for some time.     

The β-helical domain of bacteriophage T4 controls the folding of the fragment of long tail fibers in a chimeric protein

The key stage of the infection of the Escherichia coli cell with bacteriophage T4, the binding to the surface of the host cell, is determined by the specificity of the long tail fiber proteins of the phage, in particular, gp37. The assembly and oligomerization of this protein under natural conditions requires the participation of at least two additional protein factors, gp57A and gp38, which strongly hinders the production of the recombinant form of gp37. To overcome this problem, a modern protein engineering strategy was used, which involves the construction of a chimeric protein containing a carrier protein that drives the correct folding of the target protein. For this purpose, the trimeric β-helical domain of another protein of phage T4, gp5, was used. It was shown that this domain, represented as a rigid trimeric polypeptide prism, has properties favorable for use as a protein carrier. A fragment of protein gp37 containing five pentapeptide repeats, Gly-X-His-X-His, which determine the binding to the receptors on the bacterial cell surface, was fused in a continuous reading frame to the C-terminus of the domain of gp5. The resulting chimeric protein forms a trimer that has the native conformation of gp37 and exhibits biological activity.