Paralog dispensability shapes homozygous deletion patterns in tumor genomes.

Genomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer cell lines, paralogs have been shown to contribute substantially to genetic robustness-they are generally more dispensable for growth than singletons.

Comparative anatomy and functional implications of variation in the buccal mass in coleoid cephalopods.

In contrast to the well-studied articulated vertebrate jaws, the structure and function of cephalopod jaws remains poorly known. Cephalopod jaws are unique as the two jaw elements do not contact one another, are embedded in a muscular mass and connected through a muscle joint. Previous studies have described the anatomy of the buccal mass muscles in cephalopods and have proposed variation in muscle volume depending on beak shape.

The anatomy of the head muscles in caecilians (Amphibia: Gymnophiona): Variation in relation to phylogeny and ecology?

In limbless fossorial vertebrates such as caecilians (Gymnophiona), head-first burrowing imposes severe constraints on the morphology and overall size of the head. As such, caecilians developed a unique jaw-closing system involving the large and well-developed m. interhyoideus posterior, which is positioned in such a way that it does not significantly increase head diameter.

Is vertebral shape variability in caecilians (Amphibia: Gymnophiona) constrained by forces experienced during burrowing?

Caecilians are predominantly burrowing, elongate, limbless amphibians that have been relatively poorly studied. Although it has been suggested that the sturdy and compact skulls of caecilians are an adaptation to their head-first burrowing habits, no clear relationship between skull shape and burrowing performance appears to exist. However, the external forces encountered during burrowing are transmitted by the skull to the vertebral column, and, as such, may impact vertebral shape.

Regional differences in vertebral shape along the axial skeleton in caecilians (Amphibia: Gymnophiona).

Caecilians are elongate, limbless and annulated amphibians that, as far as is known, all have an at least partly fossorial lifestyle. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, relatively few studies have explored the axial skeleton in limbless tetrapods.

The evolutionary relationship between arm vertebrae shape and ecological lifestyle in brittle stars (Echinodermata: Ophiuroidea).

Ophiuroidea are one of the most diverse classes among extant echinoderms, characterized by their flexible arms composed of a series of ossicles called vertebrae, articulating with each other proximally and distally. Their arms show a wide range of motion, important for feeding and locomotion, associated with their epizoic and non-epizoic lifestyles. It remains to be explored to what degree the phenotypic variation in these ossicles also reflects adaptations to these lifestyles, rather than only their phylogenetic affinity.

The relationship between head shape, head musculature and bite force in caecilians (Amphibia: Gymnophiona).

Caecilians are enigmatic limbless amphibians that, with a few exceptions, all have an at least partly burrowing lifestyle. Although it has been suggested that caecilian evolution resulted in sturdy and compact skulls as an adaptation to their head-first burrowing habits, no relationship between skull shape and burrowing performance has been demonstrated to date. However, the unique dual jaw-closing mechanism and the osteological variability of their temporal region suggest a potential relationship between skull shape and feeding mechanics.

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines.

Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have an identifiable paralog, exploiting synthetic lethality between paralogs may be a broadly applicable approach for targeting gene loss in cancer. However, only a biased subset of human paralog pairs has been tested for synthetic lethality to date.

KBoost: a new method to infer gene regulatory networks from gene expression data.

Reconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions.

From yellow to silver: Transforming cranial morphology in European eel (Anguilla anguilla).

The European eel (Anguilla anguilla) has been extensively studied, especially because of its highly specialized migratory behaviour associated with substantial phenotypic transformations. During this migration, one of those transformations the eel undergoes is from yellow to silver eel, a process known as silvering. Although the cranial morphology during the earlier glass, elver and yellow eel stages are well studied, little is known about actual morphological changes during the transformation process from the yellow to the silver eel stage.

Is variation in tail vertebral morphology linked to habitat use in chameleons?

Chameleons (Chamaeleonidae) are known for their arboreal lifestyle, in which they make use of their prehensile tail. Yet, some species have a more terrestrial lifestyle, such as Brookesia and Rieppeleon species, as well as some chameleons of the genera Chamaeleo and Bradypodion. The main goal of this study was to identify the key anatomical features of the tail vertebral morphology associated with prehensile capacity.

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines.

What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other's loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background.

Morphological and histological characterization of an ectopically mineralized structure in a gilthead sea bream Sparus aurata with opercular deformation.

In this study, we describe an abnormal ectopically mineralized structure (EMS) that was found inside the skull of a juvenile Sparus aurata that also showed a bilateral opercular deformation. The overall phenotype and tissue composition were studied using micro-CT scanning and histological analyses. The ectopic structure occupies a large volume of the brain cavity, partially extruding into the gill cavity.

Head shape disparity impacts pollutant accumulation in European eel.

Several aspects of the life cycle of the critically endangered European eel (Anguilla anguilla) remain poorly understood. One such aspect is the broad-versus narrow-head dimorphism, and how this impacts their overall performance at different stages of their life cycle. At the yellow eel stage, the phenotypes show a trophic divergence.

Musculoskeletal anatomy and feeding performance of pre-feeding engyodontic larvae of the European eel (Anguilla anguilla).

Being part of the elopomorph group of fishes, Anguillidae species show a leptocephalus larval stage. However, due to largely unknown spawning locations and habitats of their earliest life stages, as well as their transparency, these Anguilla larvae are rarely encountered in nature. Therefore, information regarding the early life history of these larvae, including their exogenous feeding strategy and feeding performance, is rather scarce.

Functional and evolutionary anatomy of the African suckermouth catfishes (Siluriformes: Mochokidae): convergent evolution in Afrotropical and Neotropical faunas.

Of those fishes scraping food off substrates and using head parts in substrate attachment for station-holding, the catfish families Loricariidae, Astroblepidae and Mochokidae display the most dramatically adapted morphologies. Loricariidae and Astroblepidae, living in the Neotropical freshwaters, exclusively contain suckermouth catfish species, and their anatomy and head kinematics have already been studied into detail. Among Mochokidae, living in the tropical freshwaters of Africa, only the chiloglanidine subfamily has a sucker mouth, and occupies similar niches in Africa as both Neotropical families do in South America.

Structural tissue organization in the beak of Java and Darwin's finches.

Birds are well known for occupying diverse feeding niches, and for having evolved diverse beak morphologies associated with dietary specialization. Birds that feed on hard seeds typically possess beaks that are both deep and wide, presumably because of selection for fracture avoidance, as suggested by prior studies. It follows then that birds that eat seeds of different size and hardness should vary in one or more aspects of beak morphology, including the histological organization of the rhamphotheca, the cellular interface that binds the rhamphotheca to the bone, and the organization of trabeculae in the beak.

Soft dentin results in unique flexible teeth in scraping catfishes.

Teeth are generally used for actions in which they experience mainly compressive forces acting toward the base. The ordered tooth enamel(oid) and dentin structures contribute to the high compressive strength but also to the minor shear and tensile strengths. Some vertebrates, however, use their teeth for scraping, with teeth experiencing forces directed mostly normal to their long axis.

Dealing with food and eggs in mouthbrooding cichlids: structural and functional trade-offs in fitness related traits.

Background: As in any vertebrate, heads of fishes are densely packed with functions. These functions often impose conflicting mechanical demands resulting in trade-offs in the species-specific phenotype. When phenotypical traits are linked to gender-specific parental behavior, we expect sexual differences in these trade-offs.

Pisodonophis boro (ophichthidae: anguilliformes): specialization for head-first and tail-first burrowing?

The rice paddy eel, Pisodonophis boro (P. boro), is of special interest because of its peculiar burrowing habits. P.