Recognition Of Subfamilies Research Articles

Human ATP Binding Cassette Superfamily and Profiling Subfamily-Specific Motif for Classification

The ATP binding cassette (ABC) transporter superfamily is ubiquitous in all three domains of life. The cellular and molecular functions of ABC transporters are diverse and essential to all living organisms. In human, mutations associated with ABC transporters are known to cause many genetic diseases. Although the members of ABC transporter superfamily share common sequential feature, the subfamily recognition is not a trivial task because of its domain complexity. The functional annotation begins with subfamily recognition. Here, we showed that a motif profiling provides simple and intuitive approach to recognize the subfamily level. Along with relation to the structural feature, the motif profiling approach will be a guide to annotate and understand molecular functions of subfamilies with a big superfamily

Let's be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda).

In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.

The Subfamily-Specific Assembly of Eag and Erg K+ Channels is Determined by Both the Amino and the Carboxyl Recognition Domains

The ether-a-go-go family of Kv channels encompasses three subfamilies: Eag, Erg, and Elk. Members of different ether-a-go-go subfamilies fail to form hetero-tetramers. Although a short stretch of amino acid sequences in the distal C-terminal section has been implicated in subfamily-specific subunit assembly, it remains unclear whether this region serves as the sole and/or principal subfamily recognition domain for Eag and Erg. Here we generated various chimeric constructs between rat Eag1 (rEag1) and human Erg1 (hErg1) subunits. Biochemical and electrophysiological characterizations of the subunit interaction properties of a series of different chimeric and truncation constructs over the C-terminus suggested that the putative C-terminal recognition domain is dispensable for subfamily-specific assembly. Further chimeric analyses over the N- terminus revealed that the N-terminal region may also contain a subfamily recognition domain. Importantly, exchanging either the N-terminal or the C-terminal domain alone led to a virtual loss of the inter-subfamily assembly boundary. By contrast, simultaneously swapping both recognition domains resulted in a reversal of subfamily specificity. Interestingly, introduction of the homologous hErg1 eag domain led to both a fast phase and a slow phase of channel inactivation in the rEag1 N-terminal chimeras. By contrast, the inactivation features were retained in the reverse hErg1 N-chimeras. Furthermore, an eag domain-lacking rEag1 deletion mutant also showed the fast phase of inactivation that was notably attenuated upon co-expression with the rEag1 eag domain fragment, but not with the hErg1 eag domain fragment. Overall, our findings are consistent with the notion that both the N-terminal and the C-terminal recognition domains are required to sustain the subfamily-specific assembly of rEag1 and hErg1, and that the eag domain plays a critical role in regulating the inactivation gating of rEag1.

The Subfamily-specific Assembly of Eag and Erg K+ Channels Is Determined by Both the Amino and the Carboxyl Recognition Domains

A functional voltage-gated K(+) (Kv) channel comprises four pore-forming α-subunits, and only members of the same Kv channel subfamily may co-assemble to form heterotetramers. The ether-à-go-go family of Kv channels (KCNH) encompasses three distinct subfamilies: Eag (Kv10), Erg (Kv11), and Elk (Kv12). Members of different ether-à-go-go subfamilies, such as Eag and Erg, fail to form heterotetramers. Although a short stretch of amino acid sequences in the distal C-terminal section has been implicated in subfamily-specific subunit assembly, it remains unclear whether this region serves as the sole and/or principal subfamily recognition domain for Eag and Erg. Here we aim to ascertain the structural basis underlying the subfamily specificity of ether-à-go-go channels by generating various chimeric constructs between rat Eag1 and human Erg subunits. Biochemical and electrophysiological characterizations of the subunit interaction properties of a series of different chimeric and truncation constructs over the C terminus suggested that the putative C-terminal recognition domain is dispensable for subfamily-specific assembly. Further chimeric analyses over the N terminus revealed that the N-terminal region may also harbor a subfamily recognition domain. Importantly, exchanging either the N-terminal or the C-terminal domain alone led to a virtual loss of the intersubfamily assembly boundary. By contrast, simultaneously swapping both recognition domains resulted in a reversal of subfamily specificity. Our observations are consistent with the notion that both the N-terminal and the C-terminal recognition domains are required to sustain the subfamily-specific assembly of rat Eag1 and human Erg.

Structural and Pharmacological Characterization of Novel Potent and Selective Monoclonal Antibody Antagonists of Glucose-dependent Insulinotropic Polypeptide Receptor

Glucose-dependent insulinotropic polypeptide (GIP) is an endogenous hormonal factor (incretin) that, upon binding to its receptor (GIPr; a class B G-protein-coupled receptor), stimulates insulin secretion by beta cells in the pancreas. There has been a lack of potent inhibitors of the GIPr with prolonged in vivo exposure to support studies on GIP biology. Here we describe the generation of an antagonizing antibody to the GIPr, using phage and ribosome display libraries. Gipg013 is a specific competitive antagonist with equally high potencies to mouse, rat, dog, and human GIP receptors with a Ki of 7 nm for the human GIPr. Gipg013 antagonizes the GIP receptor and inhibits GIP-induced insulin secretion in vitro and in vivo. A crystal structure of Gipg013 Fab in complex with the human GIPr extracellular domain (ECD) shows that the antibody binds through a series of hydrogen bonds from the complementarity-determining regions of Gipg013 Fab to the N-terminal α-helix of GIPr ECD as well as to residues around its highly conserved glucagon receptor subfamily recognition fold. The antibody epitope overlaps with the GIP binding site on the GIPr ECD, ensuring competitive antagonism of the receptor. This well characterized antagonizing antibody to the GIPr will be useful as a tool to further understand the biological roles of GIP.

Influence of Social Environment on Genetically Based Subfamily Signature in the Honeybee

In honeybees, the cuticular hydrocarbon profiles are partly genetically based and differ between subfamilies, which suggests that they might be used by the workers as labels for subfamily recognition. This ability could potentially form the basis for nepotistic conflicts between subfamilies that would be detrimental to the inclusive fitness of the colony. Here we have compared the subfamily hydrocarbon profiles of 5-day-old workers maintained in isolation with those kept in their parental colony. We demonstrate that the cuticular hydrocarbon profiles tend to be less distant between most subfamilies within the hive compared with those held in isolation. The main consequence of this partial homogenization of the majority of subfamily signatures may result in a reduction of the number of recognizable subfamilies in the colony. Nevertheless, a few subfamilies retain very distinct cuticular hydrocarbon profiles.

Phylogeny and classification of the Culicidae (Diptera)

The generic relationships and higher classification of the family Culicidae are examined on the basis of a phylogenetic analysis. New and traditional morphological characters studied and compared throughout the Culicidae resulted in the acquisition of character data relative to the majority of species within each genus. Polymorphisms and morphological observations are discussed and additional information and illustrations are provided for the majority of characters and their character states. The analysis of seventy‐three adult, pupal and fourth‐instar larval characters coded for the thirty‐eight currently recognized genera of mosquitoes resulted in relationships and groupings which differ significantly from traditional hypotheses. The analysis supports the monophyly of the subfamily Anophelinae and the tribes Culicini and Sabethini. The Anophelinae form the most basal clade of the family. The results indicate that Aedini is a paraphyletic assemblage with respect to the Mansoniini, each of which is monophyletic in itself. The Aedini + Mansoniini form a sister group to the Culicini + Sabethini, with the Aedini and the Culicini placed in ancestral relationships to the Mansoniini and the Sabethini, respectively. Based on the topography of generic relationships among more ‘generalized’ mosquitoes, the boundaries and relationships of the tribes Aedeomyiini, Uranotaeniini, Ficalbiini, Hodgesiini, Orthopodomyiini and Culisetini appear to be problematic. Relationships between genera of the tribe Aedini are generally poorly resolved due to a significant amount of polymorphism, especially within the genus Aedes as currently defined. There is no support for separate subfamily recognition for the genus Toxorhynchites, which is downgraded to tribal status as a result of the analysis. The results are discussed in relation to previous hypotheses based on subjective inference and cladistic analyses.

Proteaceae: Diverse approaches toward new syntheses

The 1996 Commemorative Proteaceae Conference drew attention to the large body of work proceeding on all southern continents, the extensive and informative fossil record, and the wide range of studies in ecology and reproductive biology. DNA sequence data and organogeny are producing major insights at the upper taxonomic levels, new phylogenetic hypotheses and classifications are emerging in respect of the recognition of subfamilies and the relationships and composition of tribes, and there is also evidence from morphology and DNA sequence data that several genera are paraphyletic.

Kin discrimination within honey bee ( Apis mellifera) colonies: An analysis of the evidence

Compelling evolutionary arguments lead to the prediction that honey bee workers should discriminate between supersisters and half-sisters within colonies. We review the theoretical support for discrimination during swarming, queen rearing, feeding, and grooming. A survey of the data that tests whether such discrimination takes place shows that, despite substantial effort in a number of laboratories, there is no conclusive evidence for intracolony discrimination in any of the postulated contexts. The strongest suggestive data is in the critical context of queen rearing, but flaws in experimental design or analysis make the best available tests inconclusive. We present new data that shows that cues exist on which discriminations can be made among adult workers in nestmate recognition interactions and in feeding interactions, but our data does not differentiate between subfamily recognition and recognition associated with color phenotypes. We conclude that while selection may favor discrimination between supersisters and half-sisters, as a practical matter such discriminations play no role, or only a minor role, in the biology of the honey bee.

Subfamily recognition and task specialisation in honey bees (Apis mellifera L.) (Hymenoptera : Apidae)

A honey bee (Apis mellifera) queen mates with about ten haploid drones, thus producing colonies composed of about ten subfamilies of super-sisters. An increasing but controversial body of literature supports the views that: (1) Members of each subfamily within a colony can recognise each other, and distinguish supersisters from half-sisters. (2) Members of each subfamily use this recognition information and increase the reproductive fitness of their own subfamily at the expense of half-sisters through behaviour termed nepotism. A mathematical model is developed that shows that task specialisation by subfamilies, and bees that repeatedly undertake the behaviour within subfamilies, can influence the numbers of interactions among super-sisters, relative to the numbers of interactions between half-sisters. The model is then evaluated using a data set pertaining to trophallaxis behaviour in a two-subfamily colony. It is concluded that with this data set, task specialisation and subfamily recognition were indeed confounded, suggesting that the apparent subfamily recognition could easily have been an artefact of task specialisation.

Super and half-sister discrimination by honey bee workers (Apis mellifera L.) in a trophallactic bioassay

Kin recognition and nepotism between honeybee workers (Apis mellifera L.) was analysed in a trophallactic bio-assay. Donor workers were fed dyed sugar syrup and introduced into a recipient group consisting of 12 to 15 workers of the same colony. After allowing for 1 hour of trophallaxis, the distribution of the dyed food was analysed with spectrophotometry. The subfamily composition in the recipient group was varied such that the donor bees had to discriminate between workers of 2 to 7 different patrilines. Donor bees preferentially fed super sisters if few patrilines were present in the recipient group. However, preferential feeding was not observed if the recipient group consisted of workers of more than three subfamilies. Since the natural degree of polyandry causes intracolonial genetic variance to exceed the genetic variability in the experiments, nepotistic behaviour among workers may not reveal intranidal subfamily recognition in honeybees.

Pollen morphology and taxonomy in North American Labiatae

Pollen morphology is described and illustrated based on SEM studies of 118 species of Labiatae (Lamiaceae) native to North America. These include representatives of all the 36 native genera. Pollen in this family is subspheroidal and either tricolpate (subfamily Lamioideae) or hexacolpate (subfamily Nepetoideae). In most of the genera and species, the tectum is conspicuously perforated with or without a supratectal reticulum. A key to facilitate identification of the pollen of the North American Labiatae is provided. The value of pollen as a taxonomic character in this family is discussed. Pollen provides the primary basis for recognition of subfamilies in the Labiatae, but at the tribal level only the Ajugeae has distinctive pollen. Several genera, notably Collinsonia, Salvia, Teucrium, and Trichostema, have pollen that is very different from other genera in this study. At the infrageneric level pollen provides valuable taxonomic characters in several genera, notably Hyptis, Monardella, Salvia, Stachys, Teucrium, and Trichostema. Key words: Labiatae, Lamiaceae, pollen, SEM, North America.

Honey bees dance with their super-sister

Four colonies of honey bees, Apis mellifera, each composed of two subfamilies were separately placed in a screen cage. Bees of each subfamily were found at different frequencies on a pollen feeder, a sucrose feeder and on the roof of the cage, indicating subfamilial genetic variance for foraging preferences. The colonies were then placed in observation hives, and communication dances were observed. The type (pollen or no pollen) and subfamily of dancers and the subfamily of recruits were recorded. Subfamilial variance for nectar or pollen preference and propensity to dance were observed in every case. There was a strong tendency for recruits to follow dances performed by a member of their own subfamily, indicating subfamily recognition. However, at least some of this positive assortment was due to a complex interaction of genotypic differences among subfamilies in their foraging preferences and tendencies to dance.

TAXONOMIC COMMENTS ON THE EURYLAIMIDAE

SUMMARYOn the basis of supposed differences in the shape of the spina externa of the sternum, the number of cervical vertebrae, the deep plantar tendons, the quadrato‐jugal articulation, and the size of the hallux, the Eurylaimidae were put in a separate suborder, the Eurylaimi. All of these characters are now shown to be variable within the family or shared with other suboscine families. It is recommended that the subordinal designation “Eurylaimi” be abandoned and that the family be included in the suborder Tyranni. A number of characters point to the Cotingidae as the nearest possible extant relatives of the Eurylaimidae. The Eurylaimidae consist of a number of unrelated genera with several relict species, and probably represent the remains of an ancient, once more widespread group that became isolated and gave rise to the suboscine fauna in South America while being largely replaced by oscines in the Old World. Recognition of subfamilies within the Eurylaimidae is discouraged. Smitkornis should be considered the most advanced of the eurylaimids. The sequence of suboscine families is discussed and a rearrangement is suggested.