Black or white? Physiological implications of roost colour and choice in a microbat

Although roost choice in bats has been studied previously, little is known about how opposing roost colours affect the expression of torpor quantitatively. We quantified roost selection and thermoregulation in a captive Australian insectivorous bat, Nyctophilus gouldi (n=12) in winter when roosting in black and white coloured boxes using temperature-telemetry. We quantified how roost choice influences torpor expression when food was provided ad libitum or restricted in bats housed together in an outdoor aviary exposed to natural fluctuations of ambient temperature. Black box temperatures averaged 5.1 °C (maximum 7.5 °C) warmer than white boxes at their maximum daytime temperature. Bats fed ad libitum chose black boxes on most nights (92.9%) and on 100% of nights when food-restricted. All bats used torpor on all study days. However, bats fed ad libitum and roosting in black boxes used shorter torpor and spent more time normothermic/active at night than food-restricted bats and bats roosting in white boxes. Bats roosting in black boxes also rewarmed passively more often and to a higher skin temperature than those in white boxes. Our study suggests that N. gouldi fed ad libitum select warmer roosts in order to passively rewarm to a higher skin temperature and thus save energy required for active midday rewarming as well as to maintain a normothermic body temperature for longer periods at night. This study shows that colour should be considered when deploying bat boxes; black boxes are preferable for those bats that use passive rewarming, even in winter when food availability is reduced.     

Catalog of mRNA expression patterns for DNA methylating and demethylating genes in developing mouse lower urinary tract

The mouse prostate develops from a component of the lower urinary tract (LUT) known as the urogenital sinus (UGS). This process requires androgens and signaling between mesenchyme and epithelium. Little is known about DNA methylation during prostate development, including which factors are expressed, whether their expression changes over time, and if DNA methylation contributes to androgen signaling or influences signaling between mesenchyme and epithelium. We used in situ hybridization to evaluate the spatial and temporal expression pattern of mRNAs which encode proteins responsible for establishing, maintaining or remodeling DNA methylation. These include DNA methyltrasferases, DNA deaminases, DNA glycosylases, base excision repair and mismatch repair pathway members. The mRNA expression patterns were compared between male and female LUT prior to prostatic bud formation (14.5 days post coitus (dpc)), during prostatic bud formation (17.5 dpc) and during prostatic branching morphogenesis (postnatal day (P) 5). We found dramatic changes in the patterns of these mRNAs over the course of prostate development and identified examples of sexually dimorphic mRNA expression. Future investigation into how DNA methylation patterns are established, maintained and remodeled during the course of embryonic prostatic bud formation may provide insight into prostate morphogenesis and disease.     

Catalog of mRNA expression patterns for DNA methylating and demethylating genes in developing mouse lower urinary tract

The mouse prostate develops from a component of the lower urinary tract (LUT) known as the urogenital sinus (UGS). This process requires androgens and signaling between mesenchyme and epithelium. Little is known about DNA methylation during prostate development, including which factors are expressed, whether their expression changes over time, and if DNA methylation contributes to androgen signaling or influences signaling between mesenchyme and epithelium. We used in situ hybridization to evaluate the spatial and temporal expression pattern of mRNAs which encode proteins responsible for establishing, maintaining or remodeling DNA methylation. These include DNA methyltrasferases, DNA deaminases, DNA glycosylases, base excision repair and mismatch repair pathway members. The mRNA expression patterns were compared between male and female LUT prior to prostatic bud formation (14.5 days post coitus (dpc)), during prostatic bud formation (17.5 dpc) and during prostatic branching morphogenesis (postnatal day (P) 5). We found dramatic changes in the patterns of these mRNAs over the course of prostate development and identified examples of sexually dimorphic mRNA expression. Future investigation into how DNA methylation patterns are established, maintained and remodeled during the course of embryonic prostatic bud formation may provide insight into prostate morphogenesis and disease.     

Insights into the structure of plant-insect communities: Specialism and generalism in a regional set of non-pollinating fig wasp communities

Insects show a multitude of symbiotic interactions that may vary in degree of specialization and structure. Gall-inducing insects and their parasitoids are thought to be relatively specialized organisms, but despite their ecological importance, the organization and structure of the interactions they establish with their hosts has seldom been investigated in tropical communities. Non-pollinating fig wasps (NPFW) are particularly interesting organisms for the study of ecological networks because most species strictly develop their offspring within fig inflorescences, and show a multitude of life history strategies. They can be gall-makers, cleptoparasites or parasitoids of pollinating or of other non-pollinating fig wasps. Here we analysed a set of non-pollinating fig wasp communities associated with six species of Ficus section Americanae over a wide area. This allowed us to investigate patterns of specialization in a diverse community composed of monophagous and polyphagous species. We observed that most NPFW species were cleptoparasites and parasitoids, colonizing figs several days after oviposition by pollinators. Most species that occurred in more than one host were much more abundant in a single preferential host, suggesting specialization. The food web established between wasps and figs shows structural properties that are typical of specific antagonistic relationships, especially of endophagous insect networks. Two species that occurred in all available hosts were highly abundant in the network, suggesting that in some cases generalized species can be more competitive than strict specialists. The Neotropical and, to a lesser extent, Afrotropical NPFW communities seem to be more generalized than other NPFW communities. However, evidence of host sharing in the Old World is quite limited, since most studies have focused on particular taxonomic groups (genera) of wasps instead of sampling the whole NPFW community. Moreover, the lack of quantitative information in previous studies prevents us from detecting patterns of host preferences in polyphagous species.     

Fractionation and electrophoretic patterns of seed protein of Opuntia genus. A preliminary survey as a tool for accession differentiation and taxonomy

At present, little is known about Opuntia seed proteins and their contribution to the characterization and taxonomy of genotypes belong to this genus. The variation among 102 accessions of Mexican Opuntia was studied using electrophoretic patterns by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) of their seed total proteins (STPs) and seed storage proteins (SSPs). Albumins and globulins were the most abundant protein fractions, with contents varied from 2.6 to 11.9 mg/mL and 2.6–9.5 mg/mL, respectively. These were followed by glutelins (2.3–8.5 mg/mL) and prolamins as the lowest (1.1–7.9 mg/mL) of the four protein factions. On the other hand, STPs content varied between 1.13 and 7.12 mg/mL. Regardless of variations in protein content estimated in seeds, the electrophoretic patterns of STPs and SSPs, as outcome of their SDS–PAGE, were not so variable. Furthermore, the individual analysis of each STPs or the SSPs analyses, separately, were not enough to discriminate all accessions, since it was necessary to combine the data resulting from all protein profiles together to differentiate all Opuntia genotypes. The UPGMA analysis indicated that there is no separation between accessions of species of the prickly pear (sweet fruits) and “xoconostle” (acidic fruits), even though the latter were grouped together. Based on biochemical markers analyzed herein, the need for revision of taxonomic assignment of genotypes belonging to the genus Opuntia is suggested.     

Structures composing protein domains

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships.     

Computational prediction for the protein interactions of tyrosinase: Protein experimental interactome MAP

Tyrosinase (EC 1.14.18.1) is a diversely distributed enzyme in various organisms with physiological roles related to pigment production. Tyrosinase has gained the attention of researchers due to its biological functions and potential applications. In this regard, studies on the partner proteins of tyrosinase are important. In this study, we predicted the 3D structure of human tyrosinase and simulated the protein–protein interactions between tyrosinase and binding partners by using the PEIMAP algorithm. As a result, we found that tyrosinase is predicted to bind with G protein-related proteins, potassium voltage-gated channel-related proteins, and vesicle/sorting-related proteins. In particular, GIPC1, GIPC2, GIPC3, TYRP1, and DCT were predicted to primarily bind with tyrosinase. Interacting proteins (103) were secondarily bound to these 5 interacting proteins in the PEIMAP network of tyrosinase. An involvement in melanogenesis was also newly predicted by associating the predicted binding proteins. We simulated the protein–protein bindings by probing the residues of each complex facing toward the predicted site of interaction with tyrosinase. Among the interacting residues, some were predicted to dock to the active site of tyrosinase, which could affect its activity directly. Our computational predictions will be useful for elucidating the protein–protein interactions of tyrosinase and for studying its binding mechanisms and the melanin biosynthesis pathway.     

Allosteric Inhibition as a New Mode of Action for BAY 1213790, a Neutralizing Antibody Targeting the Activated Form of Coagulation Factor XI

Factor XI (FXI), the zymogen of activated FXI (FXIa), is an attractive target for novel anticoagulants because FXI inhibition offers the potential to reduce thrombosis risk while minimizing the risk of bleeding. BAY 1213790, a novel anti-FXIa antibody, was generated using phage display technology. Crystal structure analysis of the FXIa–BAY 1213790 complex demonstrated that the tyrosine-rich complementarity-determining region 3 loop of the heavy chain of BAY 1213790 penetrated deepest into the FXIa binding epitope, forming a network of favorable interactions including a direct hydrogen bond from Tyr102 to the Gln451 sidechain (2.9 Å). The newly discovered binding epitope caused a structural rearrangement of the FXIa active site, revealing a novel allosteric mechanism of FXIa inhibition by BAY 1213790. BAY 1213790 specifically inhibited FXIa with a binding affinity of 2.4 nM, and in human plasma, prolonged activated partial thromboplastin time and inhibited thrombin generation in a concentration-dependent manner.     

Molecular interaction of manganese based carbon monoxide releasing molecule (MnCORM) with human serum albumin (HSA)

In the present study, the interaction between the HSA and MnCORM in vitro under physiological conditions, was investigated through ultraviolet-visible (UV-vis) absorption, fluorescence, time-resolved fluorescence, circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopic techniques and in silico molecular docking methods. Binding parameters such as the binding constant, number of binding sites and binding force were obtained from the fluorescence data. Thermodynamic interaction revealed that the reaction was spontaneous (ΔG < 0) and hydrogen bond and van der Waals interaction were primarily involved in the binding. The changes induced in the secondary structure conformation due to the MnCORM interaction were monitored using CD and FT-IR spectroscopic techniques. The results showed reduction in α-helix conformation and corresponding increase in β-sheet and unordered structures due to slight unfolding. The time-resolved fluorescence decay confirmed the static quenching mechanism of the MnCORM. The molecular docking studies revealed that the MnCORM interacted at Sudlow’s site II of domain IIIA through hydrogen bond and van der Waals interactions. In order to understand the drug distribution and elimination, studies on the drug molecule interaction with HSA are vital. Therefore, it is evident that MnCORM interacts with HSA through ground state complex formation and thus suitable for in vivo delivery.     

Shifts in thermoregulatory strategy during ontogeny in harp seals (Pagophilus groenlandicus)

Heat balance can be difficult for young and/or small animals in polar regions because environmental conditions in combination with small body size or physiological immaturity can increase heat loss. We investigated how thermoregulatory patterns change with ontogeny in 5 age classes of harp seal (Pagophilus groenlandicus) from birth to post-molt to further understand the timing of thermoregulatory development in relation to their potential vulnerability to ongoing fluctuations in the extent and stability of Arctic pack ice. We measured changes in the amount, conductivity, and resistance of the seal pups׳ insulative layers (blubber and fur), the potential for endogenous heat-generation by shivering (muscle enzyme activity), and nonshivering thermogenesis (NST; brown adipose tissue (BAT) uncoupling protein 1 (UCP1) expression and mitochondrial density). There was no significant difference in blubber conductivity among age classes, though the amount of blubber insulation significantly increased from birth to weaning. Pelage conductivity was low (0.12±0.01 W m⁻¹ °C⁻¹) except in 9-day old pups (0.40±0.08 W m⁻¹ °C⁻¹); the significantly higher conductivity may signal the beginning of the molt, and this age group may be the most vulnerable to early water entry. Citrate synthase activity significantly increased (49.68±3.26 to 75.08±3.52 μmol min⁻¹ g wet weight⁻¹) in the muscle; however it is unlikely that increasing a single enzyme greatly impacts heat generation. BAT of younger pups contained UCP1, though expression and mitochondrial density quickly declined, and the ability of pups to produce heat via NST was lost by weaning. While total thermal resistance did not differ, neonatal and early nursing animals gained the majority of their thermal resistance from lanugo (82.5±0.03%); however, lanugo is not insulative when wet, and NST may be important to maintain euthermia and dry the coat if early immersion in water occurs. By late nursing, blubber seems sufficient as insulation (75.87±0.01% of resistance after 4 weeks), but high conductivity of fur may be responsible for retention of UCP1 expression. Weaned animals rely on blubber insulation, and no longer need NST, as wetted fur is no longer a threat to euthermia.     

MRI-based modeling of spleno-mesenteric confluence flow

Characterization of hepatic blood flow magnitude and distribution can lead to a better understanding of the pathophysiology of liver disease. However, the underlying patterns and dynamics of hepatic flow, such as the helical flow structure that often develops following the spleno-mesenteric confluence (SMC) of the hepatic portal vein, have not yet been comprehensively studied. In this study, we used magnetic resonance image (MRI)-based computational models to study the effects of the helical flow structure and SMC geometry on portal blood flow distribution. Additionally, we examined these flow dynamics with four-dimensional (4D) flow MRI in a group of 12 cirrhotic patients and healthy subjects. A validation model was also created to compare computational data to particle image velocimetry (PIV) data. We found significant correlations between flow structure development, vessel geometry, and blood flow distribution in both virtually modified models and in healthy and cirrhotic subjects. However, the direction of these correlations varied among vessel configuration types. Nonetheless, validation model results displayed good qualitative agreement with computational model data.     

Relation of fig fruit characteristics to fruit-eating bats in the New and Old World tropics

Abstract. Long-term studies of a Panamanian fig community have revealed that the figs separate into two major groups based on distinct patterns in fruit characteristics including fruit size, colour, scent and synchrony of ripening. Furthermore, these differences can be linked to sensory, morphological and behavioural capabilities of the figs' primary dispersers. One group of figs attracts primarily bats; the other group is visited mainly by birds. Whereas fruits of 'bat' figs span a wide range of size classes, ripen synchronously and remain green(ish) when ripe, all fruits of 'bird' figs have small fruit which ripen asynchronously and turn red when ripe. Among 'bat' figs, fruit size is correlated with body size of the bats that prefer them. Based on the consistent differences between 'bat' and 'bird' fig fruits in Panama we expect similar patterns in Old World figs. Furthermore, since fig-eating bats of the Old World differ in morphology, behaviour and sensory capabilities from fig-eating bats of the New World we speculate that these differences should be reflected in differences in fruit characteristics of Old and New World 'bat' figs. Personal observations and literature reports of Old World bats and figs are consistent with our predictions.     

Delta-Notch signalling in segmentation

Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.     

Ecological Responses of Frugivorous Bats to Seasonal Fluctuation in Fruit Availability in Amazonian Forests

Lowland Amazon is climatically one of the least seasonal regions on the planet, but little is known about how this is reflected in ecological seasonality. The central objective of this study was to determine whether seasonal fluctuations in the availability of fruit resources in Neotropical forests are sufficiently marked to affect the ecology and physiology of frugivorous bats. Seasonal variations in the overall bat abundance and in the captures, body condition, and reproductive activity of the two most abundant species, Carollia perspicillata and Artibeus planirostris, were studied within a region of central Brazilian Amazonia dominated by a mosaic of nonflooded (terra firme) and seasonally flooded forests (várzea and igapó). Concurrent seasonal changes in fruit availability were measured. The abundance of fruits was markedly seasonal, with far fewer resources available during the low-water season. There was a positive correlation between fruit and bat abundance. Overall, bats did not increase the consumption of arthropods during the period of fruit shortage. In A. planirostris, the body condition declined when fruits were scarcer. In both C. perspicillata and A. planirostris, foraging and reproductive activity were positively correlated with fruit availability. Consequently, the results suggest that resource seasonality is sufficiently marked to affect frugivorous bats and force them to make important eco-physiological adjustments.     

Testing bespoke management of foraging habitat for European turtle doves Streptopelia turtur

Agri-environment schemes (AES) are increasingly being employed to mitigate biodiversity loss in agricultural environments. The European Turtle Dove Streptopelia turtur is an obligate granivorous bird in rapid decline within both the UK (−96% since 1970) and across continental Europe (−77% since 1980), despite widespread uptake of AES. Here, we assess the efficacy of a potentially new, sown agri-environment option designed to provide abundant, accessible seed for S. turtur during the breeding season. During summer 2011 we compared vegetation structure and seed provision on trial plots to control habitat types (existing agri-environment options thought to potentially provide S. turtur foraging habitat) to assess whether trial plots performed better for foraging S. turtur than control habitats. In September 2011 all trial plots were topped (cut) and half of a subset of trial plots were then scarified (60% of soil surface disturbed). Vegetation structure on topped, and topped and scarified trial plots was measured during summer 2012 to determine which management regime was most effective in maintaining suitable sward structure and seed provision into the second year. No control habitat type produced as much seed important in S. turtur diet as trial plots at any point during year one. Trial plots provided accessible vegetation structure early in the season with no difference in vegetation metrics between trial plots and previously published data on S. turtur foraging locations. However, to allow later access, management is required during mid-June to open up the sward through localized topping or scarification. Vegetation structure during year two was generally too dense to attract foraging S. turtur. However, scarifying trial plots during the September following sowing encouraged self-seeding of Fumaria. officinalis (a plant species historically forming a significant proportion of S. turtur diet during the breeding season) into the second year, with this species present in 16% of scarified trial plots compared to only 4% of topped trial plots during year two. Thus, autumn scarification, possibly followed by topping or scarification of part of the trial plots in June, is necessary for trial plots to provide more seed and access for S. turtur than existing agri-environment options during year two. We recommend modifications to our original seed mix in order to reduce vegetation density and improve vegetation structure. The study provides an example of the need to strike the right balance between food abundance and accessibility, through vegetation structure, when designing agri-environment scheme management options that provide food for birds.     

Characterization of two coleopteran α-amylases and molecular insights into their differential inhibition by synthetic α-amylase inhibitor,acarbose

Post-harvest insect infestation of stored grains makes them unfit for human consumption and leads to severe economic loss. Here, we report functional and structural characterization of two coleopteran α-amylases viz. Callosobruchus chinensis α-amylase (CcAmy) and Tribolium castaneum α-amylase (TcAmy) along with their interactions with proteinaceous and non-proteinaceous α-amylase inhibitors. Secondary structural alignment of CcAmy and TcAmy with other coleopteran α-amylases revealed conserved motifs, active sites, di-sulfide bonds and two point mutations at spatially conserved substrate or inhibitor-binding sites. Homology modeling and molecular docking showed structural differences between these two enzymes. Both the enzymes had similar optimum pH values but differed in their optimum temperature. Overall, pattern of enzyme stabilities were similar under various temperature and pH conditions. Further, CcAmy and TcAmy differed in their substrate affinity and catalytic efficiency towards starch and amylopectin. HPLC analysis detected common amylolytic products like maltose and malto-triose while glucose and malto-tetrose were unique in CcAmy and TcAmy catalyzed reactions respectively. At very low concentrations, wheat α-amylase inhibitor was found to be superior over the acarbose as far as complete inhibition of amylolytic activities of CcAmy and TcAmy was concerned. Mechanism underlying differential amylolytic reaction inhibition by acarbose was discussed.