Information capacity of specific interactions

Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce “capacity,” the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems and to compute how specificity changes with physical parameters. Using this framework, we find that “shape” coding of interactions has higher capacity than chemical (“color”) coding because the strength of off-target binding is strongly sublinear in binding-site size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.Specific interactions between many species of components are the bedrock of biochemical function, allowing signal transduction along complex parallel pathways and self-assembly of multicomponent molecular machines. Inspired by their role in biology, engineered specific interactions have opened up tremendous opportunities in materials synthesis, achieving new morphologies of self-assembled structures with varied and designed functionality. The two major design approaches for programming specific interactions use either chemical specificity or shape complementarity.Chemical specificity is achieved by dividing binding sites into smaller regions, each of which can be given one of A “colors” or unique chemical identities. Sites bind to each other based on the sum of the interactions between corresponding regions. For example, a recent two-color system paints the flat surfaces of three-dimensional polyhedra with hydrophobic and hydrophilic patterns (1) or with a pattern of solder dots (2), allowing polyhedra to stick to each other based on the registry between their surface patterns. Another popular approach uses DNA hybridization, where specific matching of complementary sequences has been used to self-assemble structures purely from DNA strands (3, 4) and from nanoparticles coated with carefully chosen DNA strands (5–9).Shape complementarity uses the shapes of the component surfaces to achieve specific binding, even though the adhesion is via a nonspecific, typically short-range potential. In the synthetic context, shape-based modulation of attractive forces over a large dynamic range was first proposed and experimentally demonstrated for colloidal particles (10, 11), using tunable depletion forces (12, 13). Recent experiments have explored the range of possibilities opened up by such ideas, from lithographically designed planar particles (14) with undulating profile patterns to “Pacman” particles with cavities that exactly match smaller complementary particles (15). The number of possible shapes that can be made using these types of methods depends on fabrication constraints but the possibilities can be quite rich (16, 17). Using only nonspecific surface attraction, experiments have achieved numerous and complex morphologies such as clusters, crystals, glasses, and superlattices (10, 18–21).A further class of programmable specific interactions combines both chemical specificity and shape complementarity. The canonical example is protein-binding interactions (22); the binding interactions between two cognate proteins are specified by their amino acid sequence, which programs binding pockets with complex shape and chemical specificity. Recent efforts (23, 24) aim to rationally design these protein interactions for self-assembly. Because both the shape of the binding pocket and its chemical specificity are determined by the same amino acid sequence, these two features cannot be controlled independently. Other synthetic systems offer the promise of independent control of chemical and shape binding specificity, giving a larger set of possible interactions.These diverse systems achieve specific interactions through disparate physical mechanisms, with different control parameters for tuning binding specificity. However, they must all solve a common problem (25, 26): create a family of N “lock” and “key” pairs that bind well within pairs but avoid off-target binding across pairs (“crosstalk”). Any crosstalk limits the efficacy of the locks and keys. For example, in the context of DNA-based affinities, although there are 4^L unique sequences of length L, the strong off-target binding severely restricts the number that can be productively used. Analogously, for colloidal systems driven by depletion interactions, there can be significant off-target binding due to partial contact. The performance of a system of specific interactions depends acutely on how the system constraints (e.g., number of available bases, fabrication length scale, etc.) limit its ability to avoid crosstalk.In this paper, we develop a general information theory-based framework for quantitatively analyzing specificity in both natural and synthetic systems. We use a metric based on mutual information to derive a bound on the number of different interacting particles that a system can support before crosstalk overwhelms interaction specificity. Increasing the number of nominally distinct pairs beyond this limit cannot increase the effective number of distinguishable species. We compute this information-theoretic “capacity” for different experimental systems of recent interest, including DNA-based affinities and colloidal experiments in shape complementarity. We show that shape-based coding fundamentally results in lower crosstalk and higher capacity than color-based coding. We also find that shape- and color-based coding can be combined synergistically, giving a superadditive capacity that is greater than the sum of the color and shape parts.     

Anemia, allogenic blood transfusion, and immunomodulation in the critically ill

Anemia and allogenic RBC transfusions are exceedingly common among critically ill patients. Multiple pathologic mechanisms contribute to the genesis of anemia in these patients. Emerging risks associated with allogenic RBC transfusions including the transmission of newer infectious agents and immune modulation predisposing the patient to infections requires reevaluation of current transfusion strategies. Recent data have suggested that a restrictive transfusion practice is associated with reduced morbidity and mortality during critical illness, with the possible exception of acute coronary syndromes. In this article, we review the immune-modulatory role of allogenic RBC transfusions in critically ill patients.     

Hierarchical recruitment of Plk4 and regulation of centriole biogenesis by two centrosomal scaffolds,Cep192 and Cep152

Centrosomes play an important role in various cellular processes, including spindle formation and chromosome segregation. They are composed of two orthogonally arranged centrioles, whose duplication occurs only once per cell cycle. Accurate control of centriole numbers is essential for the maintenance of genomic integrity. Although it is well appreciated that polo-like kinase 4 (Plk4) plays a central role in centriole biogenesis, how it is recruited to centrosomes and whether this step is necessary for centriole biogenesis remain largely elusive. Here we showed that Plk4 localizes to distinct subcentrosomal regions in a temporally and spatially regulated manner, and that Cep192 and Cep152 serve as two distinct scaffolds that recruit Plk4 to centrosomes in a hierarchical order. Interestingly, Cep192 and Cep152 competitively interacted with the cryptic polo box of Plk4 through their homologous N-terminal sequences containing acidic-α-helix and N/Q-rich motifs. Consistent with these observations, the expression of either one of these N-terminal fragments was sufficient to delocalize Plk4 from centrosomes. Furthermore, loss of the Cep192- or Cep152-dependent interaction with Plk4 resulted in impaired centriole duplication that led to delayed cell proliferation. Thus, the spatiotemporal regulation of Plk4 localization by two hierarchical scaffolds, Cep192 and Cep152, is critical for centriole biogenesis.The centrosome is the main microtubule-organizing center in mammalian cells that plays a central role in spindle formation and chromosome segregation during mitosis. Centrosomes are composed of two orthogonally arranged centrioles surrounded by an amorphous mass of electron-dense pericentriolar material (PCM). Centrioles duplicate precisely once per cell cycle and serve as platforms for the assembly of centrosomes, primary cilia, and flagella (1–4).Centriole duplication is initiated by the assembly of a procentriole in early S phase. In Caenorhabditis elegans, a centrosomal scaffold protein, called Spd-2, is required for proper recruitment of a Ser/Thr kinase, Zyg-1 (5), to centrosomes, and this step in turn allows the recruitment of Sas-6, Sas-5, and Sas-4 to the site of procentriole assembly (6, 7). Sas6 plays a pivotal role in self-assembling a cartwheel-like structure at this site of the procentriole with Sas5 and Sas4 (8–12). In Drosophila, the overexpression of polo-like kinase 4 (Plk4; also called Sak), the Zyg-1 ortholog, is sufficient to induce centriole amplification, whereas the depletion of Plk4 disrupts centriole duplication (12, 13). Interestingly, however, Drosophila Spd-2 is dispensable for Plk4-mediated centriole duplication (14). Instead, another scaffold, Asterless, has been suggested to play a critical role in targeting Plk4 to centrosomes (15), hinting that the mechanism underlying Plk4 recruitment is distinct in different organisms.Accumulated evidence in humans suggests that Plk4 is a functional ortholog of C. elegans Zyg-1 and Drosophila Plk4, and that it plays a key role in centriole duplication (16, 17). When overexpressed, Plk4 can induce multiple centriole precursors surrounding a single parental centriole, and centrosomally localized Plk4 appears to be required for this event (16). The cryptic polo box (CPB) present at the upstream of the C-terminal polo box (PB) (18) is necessary and sufficient for targeting Plk4 to centrosomes (16, 19). Interestingly, the CPB comprises two structurally related motifs and forms a homodimer (19) to interact with its binding targets. However, the molecular basis of how Plk4 binds to its targets and localizes to centrosomes remains largely elusive.Studies have shown that Cep152, a human ortholog of Drosophila Asterless, interacts with Plk4 through the CPB (20, 21). However, the depletion of Cep152 does not significantly decrease the level of Plk4 at centrosomes. Recently, Sonnen et al. have shown that a C. elegans Spd-2 ortholog, Cep192, interacts with Plk4 and promotes the recruitment of Plk4 to centrosomes (22). Moreover, Cep192 binds to Cep152, and the depletion of both enhances the Plk4 localization defect (22). Based on these observations, Sonnen et al. proposed that Cep192 cooperates with Cep152 to properly recruit Plk4 to centrosomes and to promote centriole duplication (22).In this study, we demonstrated that disrupting either the Cep192–Plk4 interaction or the Cep152–Plk4 interaction was sufficient to impair centriole duplication. We further showed that Plk4 dynamically localizes to different subcentrosomal regions in a cell cycle-specific manner, and that Cep192 functions at a point upstream of Cep152 to regulate Plk4 localization. Thus, we propose that the spatiotemporal regulation of Plk4 localization by two hierarchical scaffolds, Cep192 and Cep152, is critical for Plk4-dependent centriole biogenesis.     

Mosquito larvicidal and pupicidal activity of Euphorbia hirta Linn. (Family: Euphorbiaceae) and Bacillus sphaericus against Anopheles stephensi Liston. (Diptera: Culicidae)

ObjectiveTo explore the larvicidal and pupicidal activity of Euphorbia hirta (E. hirta) leaf extract and Bacillus sphaericus (B. sphaericus) against the malarial vector, Anopheles stephensi (An. stephensi).MethodsThe larvicidal and pupicidal activity was assayed against An. stephensi at various concentrations ranging from (75-375 ppm) under the laboratory as well as field conditions. The LC₅₀ and LC₉₀ value of the E. hirta leaf extract was determined by probit analysis.ResultsThe plant extract showed larvicidal effects after 24 h of exposure; however, the highest larval mortality was found in the methanol extract of E. hirta against the first to fourth instars larvae and pupae of values LC₅₀= 137.40, 172.65, 217.81, 269.37 and 332.39 ppm; B. sphaericus against the first to fourth instars larvae and pupae of values LC₅₀= 44.29, 55.83, 68.51, 82.19 and 95.55 ppm, respectively. Moreover, combined treatment of values of LC₅₀= 79.13, 80.42, 86.01, 93.00 and 98.12 ppm, respectively. No mortality was observed in the control.ConclusionsThese results suggest methanol leaf extracts of E. hirta and B. sphaericus have potential to be used as an ideal eco-friendly approach for the control of the malarial vector, An. stephensi as target species of vector control programs. This study provides the first report on the combined mosquito larvicidal and pupicidal activity of this plant crude extract and bacterial toxin against An. stephensi mosquitoes.     

Toxicity effect of Delonix elata (Yellow Gulmohr) and predatory efficiency of Copepod,Mesocyclops aspericornis for the control of dengue vector,Aedes aegypti

Objective

To evaluate the toxicity, predatory efficiency of Delonix elata (D. elata) and Mesocyclops aspericornis (M. aspericornis) against dengue vector, Aedes aegypti (Ae. aegypti).

Methods

A mosquitocidal bioassay was conducted at different concentration of plant extract followed by WHO standard method. The probit analysis of each tested concentration and control were observed by using software SPSS 11 version package. The each tested concentration variable was assessed by DMRT method. The predatory efficiency of copepod was followed by Deo et al., 1988. The predator, M. aspericornis was observed for mortality, abnormalities, survival and swimming activity after 24 h treatment of plant and also predation on the mosquito larvae were observed.

Results

D. elata were tested for biological activity against the larvae, and pupae of Ae. aegypti. Significant mortality effects were observed in each life stage. The percentage of mortality was 100% in first and second instars whereas 96%, 92% in third and fourth instars. Fitted probit-mortality curves for larvae indicated the median and 90% lethal concentrations of D. elata for instars 1-4 to be 4.91 (8.13), 5.16 (8.44), 5.95 (7.76) and 6.87 (11.23), respectively. The results indicate that leaf extract exhibits significant biological activity against life stages. The present study revealed that D. elata is potentially important in the control of Ae. aegypti. Similar studies were conducted for predatory efficiency of Copepod, M. aspericornis against mosquito vector Ae. Aegypti. This study reported that the predatory copepod fed on 39% and 25% in I and III instar larvae of mosquito and in combined treatment of D. elata and copepod maximum control of mosquito larval states and at 83%, 80%, 75% and 53% in I, II, III and IV instars, respectively.

Conclusions

The combined action of plant extract and predatory copepod to effectively control mosquito population and reduce the dengue transmitting diseases.     

Studies on defluoridation of water by tamarind seed, an unconventional biosorbent

Tamarind seed, a household waste from the kitchen is used for the sorptive removal of fluoride from synthetic aqueous solution as well as from field water samples. Batch sorptive defluoridation was conducted under variable experimental conditions such as pH, agitation time, initial fluoride concentration, particle size and sorbent dose. Maximum defluoridation was achieved at pH 7.0. Defluoridation capacity decreases with increase in temperature and particle size. Further, defluoridation follows first order kinetics and Langmuir adsorption isotherm. Desorption was carried out with 0.1 N HCl and is 90 per cent. The surface and sorption characteristics were analysed using FTIR and SEM techniques. All these results indicate the involvement of energetic forces such as coulombic interaction in sorption. For domestic and industrial applications, defluoridation with 100% achievement and subsequent regeneration of adsorbent was performed with a household water filter and fixed bed column respectively.     

Tetrahydrocurcumin: effect on chloroquine-mediated oxidative damage in rat kidney

Tetrahydrocurcumin is an antioxidative substance, which is derived from curcumin, the component of turmeric. In the present investigation, the effect of tetrahydrocurcumin and curcumin against chloroquine-induced nephrotoxicity were studied in female wistar rats. Oral administration of tetrahydrocurcumin significantly prevented the occurrence of chloroquine (970 mg/kg body weight)-induced renal damage. Upon administration of tetrahydrocurcumin to chloroquine-treated rats, the level of lipid peroxidation was significantly decreased while the levels of non-enzymic and enzymic antioxidants were significantly increased in kidney. Oral administration (80 mg/kg body weight) attenuated the chloroquine-induced nephrotoxicity by significantly decreased levels of serum urea and creatinine with significant normalization of creatinine clearance. On administration of tetrahydrocurcumin, the depleted renal antioxidant defense system (enzymatic and non-enzymatic antioxidants) was significantly increased in rats treated with chloroquine. These biochemical observations were supplemented by histopathological examination of kidney section. These results suggest that administration of chloroquine imposes an oxidative stress to renal tissue and that tetrahydrocurcumin protects the oxidative damage associated with chloroquine.