Nutritional benefits from domatia inhabitants in an ant-plant interaction: interlopers do pay the rent

1. How a symbiosis originates and is maintained are important evolutionary questions. Symbioses in myrmecophytes (plants providing nesting for ants) are believed to be maintained by protection and nutrients provided by specialist plant-ants in exchange for nesting spaces (called domatia) and nourishment offered by ant-plants. However, besides the benefits accrued from housing protective ants, the mechanisms contributing to the fitness advantages of bearing domatia have rarely been examined, especially because the domatia trait is usually constitutively expressed, and many myrmecophytes have obligate mutualisms with single ant species resulting in invariant conditions. 2. In the unspecialized ant-plant Humboldtia brunonis (Fabaceae) that offers extrafloral nectar to ants, only some plants produce domatia in the form of hollow internodes. These domatia have a self-opening slit making them more prone to interlopers and are occupied mostly by non-protective ants and other invertebrates, especially arboreal earthworms. The protection mutualism with ants is restricted in geographical extent, occurring only at a few sites in the southernmost part of this plant's range in the Western Ghats of India. 3. We examined nutrient flux from domatia residents to the plant using stable isotopes. We found that between 9% (earthworms) and 17% (protective or non-protective ants) of nitrogen of plant tissues nearest the domatium came from domatia inhabitants. Therefore, interlopers such as earthworms and non-protective ants contributed positively to the nitrogen budget of localized plant modules of this understorey tree. N-15-enriched feeding experiments with protective ants demonstrated that nutrients flowed from domatia inhabitants to nearby plant modules. Fruit set did not differ between paired hand-pollinated inflorescences on domatia and non-domatia bearing branches. This was possibly due to the nutrient flux from domatia to adjacent branches without domatia within localized modules. 4. This study has demonstrated the nutritive role of non-protective ants and non-ant invertebrates, hitherto referred to as interlopers, in an unspecialized myrmecophyte. Our study suggests that even before the establishment of a specialized ant-plant protection mutualism, nutritional benefits conferred by domatia inhabitants can explain the fitness benefits of bearing domatia, and thus the maintenance of a trait that facilitates the establishment of a specialized ant-plant symbiosis.

Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

NrichD no-hyphen'' xlink:type=''simple''>( ext-link-type=''uri'' xlink:href=''http://proline.biochem.iisc.ernet.in/NRICHD/'' xlink:type=''simple''>http://proline.biochem.iisc.ernet.in/NRICHD/)< /named-content> is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural `intermediately related sequences' is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been `enriched' with these artificial intermediary sequences. NrichD database currently contains 3 611 010 artificial sequences that have been generated between 27 882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

An approximation to the QoS aware throughput region of a tree network under IEEE 802.15.4 CSMA/CA with application to wireless sensor network design

In the context of wireless sensor networks, we are motivated by the design of a tree network spanning a set of source nodes that generate packets, a set of additional relay nodes that only forward packets from the sources, and a data sink. We assume that the paths from the sources to the sink have bounded hop count, that the nodes use the IEEE 802.15.4 CSMA/CA for medium access control, and that there are no hidden terminals. In this setting, starting with a set of simple fixed point equations, we derive explicit conditions on the packet generation rates at the sources, so that the tree network approximately provides certain quality of service (QoS) such as end-to-end delivery probability and mean delay. The structures of our conditions provide insight on the dependence of the network performance on the arrival rate vector, and the topological properties of the tree network. Our numerical experiments suggest that our approximations are able to capture a significant part of the QoS aware throughput region (of a tree network), that is adequate for many sensor network applications. Furthermore, for the special case of equal arrival rates, default backoff parameters, and for a range of values of target QoS, we show that among all path-length-bounded trees (spanning a given set of sources and the data sink) that meet the conditions derived in the paper, a shortest path tree achieves the maximum throughput. (C) 2015 Elsevier B.V. All rights reserved.

A fast and accurate performance analysis of beaconless IEEE 802.15.4 multi-hop networks

We develop an approximate analytical technique for evaluating the performance of multi-hop networks based on beaconless IEEE 802.15.4 ( the ``ZigBee'' PHY and MAC), a popular standard for wireless sensor networks. The network comprises sensor nodes, which generate measurement packets, relay nodes which only forward packets, and a data sink (base station). We consider a detailed stochastic process at each node, and analyse this process taking into account the interaction with neighbouring nodes via certain time averaged unknown variables (e.g., channel sensing rates, collision probabilities, etc.). By coupling the analyses at various nodes, we obtain fixed point equations that can be solved numerically to obtain the unknown variables, thereby yielding approximations of time average performance measures, such as packet discard probabilities and average queueing delays. The model incorporates packet generation at the sensor nodes and queues at the sensor nodes and relay nodes. We demonstrate the accuracy of our model by an extensive comparison with simulations. As an additional assessment of the accuracy of the model, we utilize it in an algorithm for sensor network design with quality-of-service (QoS) objectives, and show that designs obtained using our model actually satisfy the QoS constraints (as validated by simulating the networks), and the predictions are accurate to well within 10% as compared to the simulation results in a regime where the packet discard probability is low. (C) 2015 Elsevier B.V. All rights reserved.