Deriving how far structural information is transmitted through parallel homodimeric coiled‐coils: A correlation analysis of helical staggers

How local conformation is affected by local sequence is fairly well understood for alpha‐helical coiled‐coils, but less is known about how local conformation is influenced by distant features. Here, I describe an approach to detect such an effect, based on computing correlation coefficients of local out‐of‐register alignments, or so‐called “staggers” between the helices, as a function of the axial distance between the staggers. This approach requires parallel homodimers, in which each stagger can occur with two “signs,” where either one helix or the other is shifted towards the N terminus. The signs of such staggers separated by up to 12 residues are strongly correlated, indicating that the conformations of the ends of coiled‐coils are commonly influenced by attached structures. Thus, the structures of coiled‐coil residues aberrantly attached to alternative proteins, such as those resulting from leukemogenic chromosomal rearrangements, may be distinguishable from those in normal tissues, and in turn serve as targets of selective drug design. The signs of helical staggers separated by between 13 and 30 residues are moderately yet significantly correlated, indicating that some of the coiled‐coils transmit this conformational feature axially for at least 45 Å. A positive, albeit noisy, correlation also exists among tropomyosin coiled‐coils for signed staggers separated by the 40‐residue actin repeat distance, consistent with the semi‐flexible tropomyosin filament binding F‐actin and regulating skeletal muscle contraction in a partially cooperative manner. Communication of the signs of axial staggers is explained in part by minimization of main‐chain hydrogen bond deformations. © Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Galactomannanases Man2 and Man5 from Thermotoga species: growth physiology on galactomannans, gene sequence analysis, and biochemical properties of recombinant enzymes

The enzymatic hydrolysis of mannan-based hemicelluloses is technologically important for applications ranging from pulp and paper processing to food processing to gas and oil well stimulation. In many cases, thermostability and activity at elevated temperatures can be advantageous. To this end, the genes encoding beta-mannosidase (man2) and beta-mannanase (man5) from the hyperthermophilic bacteria Thermotoga neapolitana 5068 and Thermotoga maritima were isolated, cloned, and expressed in Escherichia coli. The amino acid sequences for the mannosidases from these organisms were 77% identical and corresponded to proteins with an M(r) of approximately 92 kDa. The translated nucleotide sequences for the beta-mannanase genes (man5) encoded polypeptides with an M(r) of 76 kDa that exhibited 84% amino acid sequence identity. The recombinant versions of Man2 and Man5 had similar respective biochemical and biophysical properties, which were also comparable to those determined for the native versions of these enzymes in T. neapolitana. The optimal temperature and pH for the recombinant Man2 and Man5 from both organisms were approximately 90 degrees C and 7.0, respectively. The presence of Man2 and Man5 in these two Thermotoga species indicates that galactomannan is a potential growth substrate. This was supported by the fact that beta-mannanase and beta-mannosidase activities were significantly stimulated when T. neapolitana was grown on guar or carob galactomannan. Maximum cell densities increased by at least tenfold when either guar or carob galactomannan was added to the growth medium. For T. neapolitana grown on guar at 83 degrees C, Man5 was secreted into the culture media, whereas Man2 was intracellular. These localizations were consistent with the presence and lack of signal peptides for Man5 and Man2, respectively. The identification of the galactomannan-degrading enzymes in these Thermotoga species adds to the list of biotechnologically important hemicellulases produced by members of this hyperthermophilic genera.     

Multivariate multiple test procedures based on nonparametric copula estimation

Multivariate multiple test procedures have received growing attention recently. This is due to the fact that data generated by modern applications typically are high‐dimensional, but possess pronounced dependencies due to the technical mechanisms involved in the experiments. Hence, it is possible and often necessary to exploit these dependencies in order to achieve reasonable power. In the present paper, we express dependency structures in the most general manner, namely, by means of copula functions. One class of nonparametric copula estimators is constituted by Bernstein copulae. We extend previous statistical results regarding bivariate Bernstein copulae to the multivariate case and study their impact on multiple tests. In particular, we utilize them to derive asymptotic confidence regions for the family‐wise error rate (FWER) of multiple test procedures that are empirically calibrated by making use of Bernstein copulae approximations of the dependency structure among the test statistics. This extends a similar approach by Stange et al. (2015) in the parametric case. A simulation study quantifies the gain in FWER level exhaustion and, consequently, power that can be achieved by exploiting the dependencies, in comparison with common threshold calibrations like the Bonferroni or ?idák corrections. Finally, we demonstrate an application of the proposed methodology to real‐life data from insurance.     

Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers

Cloning of highly-secreting recombinant cells is critical for biopharmaceutical manufacturing, but faces numerous challenges including the fact that secreted protein does not remain associated with the producing cell. A fundamentally new approach was developed combining in situ capture and measurement of individual cell protein secretion followed by laser-mediated elimination of all non- and poorly-secreting cells, leaving only the highest-secreting cell in a well. Recombinant cells producing humanized antibody were cultured serum-free on a capture matrix, followed by staining with fluorescently-labeled anti-human antibody fragment. A novel, automated, high-throughput instrument (called LEAP) was used to image and locate every cell, quantify the cell-associated and secreted antibody (surrounding each cell), eliminate all undesired cells from a well via targeted laser irradiation, and then track clone outgrowth and stability. Temporarily sparing an island of helper cells around the clone of interest improved cloning efficiency (particularly when using serum-free medium), and helper cells were easily eliminated with the laser after several days. The in situ nature of this process allowed several serial sub-cloning steps to be performed within days of one another, resulting in rapid generation of clonal populations with significantly increased and more stable, homogeneous antibody secretion. Cell lines with specific antibody secretion rates of > 50 pg/cell per day (in static batch culture) were routinely obtained as a result of this cloning approach, often times representing up to 20% of the clones screened.     

Relationship of stigma behaviors and breeding system in three Mazus (Phrymaceae) species with bilobed stigma

Sensitive stigma has been recognized to facilitate outcrossing. We hypothesized that species with different levels of sensitivity might have corresponding differences in components of their breeding system. In this study, three Mazus species with bilobed stigmas were used to test the hypothesis. We explored stigma behaviors of the species in reaction time, recovery time, permanent closing time, and the minimum pollen load causing permanent closure. We investigated floral traits, pollinator type and behavior, pollination intensity, and natural schedule of pollen deposition on stigma. Moreover, we evaluated the mating system of the species by checking seed set after controlled pollination treatments, namely, natural flowers with open pollination, enclosed flowers without pollination, and enclosed flowers with self and outcross hand pollination. Results indicated that stigma of M. pumilus (N. L. Burman) Steenis was not sensitive, whereas stigmas of M. miquelii Makino and M. stachydifolius (Turcz.) Maxim. closed and reopened quickly in response to pollination. Accordingly, hand pollination treatments revealed that seed set of self-spontaneous pollination in M. pumilus was similar to the other treatments. For M. miquelii, outcross pollen resulted in significantly higher seed set than self-pollen.Mazus stachydifolius was self-incompatible. Additionally, the corresponding characteristics in other components of the breeding system for each species were found. Our study indicated that the sensitivity of bilobed stigma might be linked with floral traits and the mating system in a given species. Sensitive stigma should be regarded as an evolutionary mechanism for enhancement of outcrossing.     

An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: an X-ray crystallography and docking study

In the present study, we report on the X-ray crystallographic structure of a GH32 invertase mutant, (i.e., the Arabidopsis thaliana cell-wall invertase 1-E203Q, AtcwINV1-mutant) in complex with sucrose. This structure was solved to reveal the features of sugar binding in the catalytic pocket. However, as demonstrated by the X-ray structure the sugar binding and the catalytic pocket arrangement is significantly altered as compared with what was expected based on previous X-ray structures on GH-J clan enzymes. We performed a series of docking and molecular dynamics simulations on various derivatives of AtcwINV1 to reveal the reasons behind this modified sugar binding. Our results demonstrate that the E203Q mutation introduced into the catalytic pocket triggers conformational changes that alter the wild type substrate binding. In addition, this study also reveals the putative productive sucrose binding modus in the wild type enzyme.     

Roving females and patient males: a new perspective on the mating strategies of chimpanzees

Mating strategies are sets of decisions aimed at maximizing reproductive success. For male animals, the fundamental problem that these strategies address is attaining mating access to females in a manner that maximizes their chances of achieving paternity. For chimpanzees (Pan troglodytes), despite substantial interest in mating strategies, very little attention has been paid to the most fundamental problem that mating strategies need to solve: finding mates. Only a single model, Dunbar's general model of male mating strategies, exists to explain mate‐searching behaviour in chimpanzees. Under this model, males in most populations are regarded as pursuing a ‘roving’ strategy: searching for and sequestering fertile females who are essentially passive with respect to mate searching. The roving mating strategy is an assumption deeply embedded in the way chimpanzee behaviour is considered; it is implicit in the conventional model for chimpanzee social structure, which posits that male ranging functions both to monitor female reproductive state and to ward these females from other groups of males through collective territoriality: essentially, ranging as mating effort. This perspective is, however, increasingly at odds with observations of chimpanzee behaviour. Herein, I review the logic and evidence for the roving‐male mating strategy and propose a novel alternative, a theoretical framework in which roving is a strategy pursued by female chimpanzees in order to engage successfully in promiscuous mating. Males, unable to thwart this female strategy, instead maximise the number of reproductive opportunities encountered by focusing their behaviour on countering threats to health, fertility and reproductive career. Their prolonged grooming bouts are seen, in consequence, as functioning to mitigate the negative impacts of socially induced physiological stress. In this new framework, the roving‐male strategy becomes, at best, a ‘best of a bad job’ alternative for low‐ranking males when faced with high levels of competition for mating access. Male chimpanzees do not search for mates, but for one another, for food, and, at times, for rivals in other communities. To the extent that female promiscuity functions to counter infanticide risk, mate searching by female chimpanzees—and any associated costs—can be seen as an unavoidable consequence of male sexual coercion. This novel framework is a better fit to the available data than is the conventional account. This review highlights the desperate need for additional work in an area of chimpanzee biology that has been somewhat neglected, perhaps in part because assumptions of roving males have remained unquestioned for too long. It also highlights the need, across taxa, to revisit and revise theory, and to test old assumptions, when faced with contrary data.     

Field and climate‐based model for predicting the density of host‐seeking nymphal Ixodes scapularis,an important vector of tick‐borne disease agents in the eastern United States

Aim Ixodes scapularis is the most important vector of human tick‐borne pathogens in the United States, which include the agents of Lyme disease, human babesiosis and human anaplasmosis, among others. The density of host‐seeking I. scapularis nymphs is an important component of human risk for acquiring Borrelia burgdorferi, the aetiological agent of Lyme disease. In this study we used climate and field sampling data to generate a predictive map of the density of host‐seeking I. scapularis nymphs that can be used by the public, physicians and public health agencies to assist with the diagnosis and reporting of disease, and to better target disease prevention and control efforts. Location Eastern United States of America. Methods We sampled host‐seeking I. scapularis nymphs in 304 locations uniformly distributed east of the 100th meridian between 2004 and 2006. Between May and September, 1000 m² were drag sampled three to six times per site. We developed a zero‐inflated negative binomial model to predict the density of host‐seeking I. scapularis nymphs based on altitude, interpolated weather station and remotely sensed data. Results Variables that had the strongest relationship with nymphal density were altitude, monthly mean vapour pressure deficit and spatial autocorrelation. Forest fragmentation and soil texture were not predictive. The best‐fit model identified two main foci – the north‐east and upper Midwest – and predicted the presence and absence of I. scapularis nymphs with 82% accuracy, with 89% sensitivity and 82% specificity. Areas of concordance and discordance with previous studies were discussed. Areas with high predicted but low observed densities of host‐seeking nymphs were identified as potential expansion fronts. Main conclusions This model is unique in its extensive and unbiased field sampling effort, allowing for an accurate delineation of the density of host‐seeking I. scapularis nymphs, an important component of human risk of infection for B. burgdorferi and other I. scapularis‐borne pathogens.     

Importance of cooperation and affiliation in the evolution of primate sociality

The idea that competition and aggression are central to an understanding of the origins of group‐living and sociality among human and nonhuman primates is the dominant theory in primatology today. Using this paradigm, researchers have focused their attention on competitive and aggressive behaviors, and have tended to overlook the importance of cooperative and affiliative behaviors. However, cooperative and affiliative behaviors are considerably more common than agonistic behaviors in all primate species. The current paradigm often fails to explain the context, function, and social tactics underlying affiliative and agonistic behavior. Here, we present data on a basic question of primate sociality: how much time do diurnal, group‐living primates spend in social behavior, and how much of this time is affiliative and agonistic? These data are derived from a survey of 81 studies, including 28 genera and 60 species. We find that group‐living prosimians, New World monkeys, Old World monkeys, and apes usually devote less than 10% of their activity budget to active social interactions. Further, rates of agonistic behaviors are extremely low, normally less than 1% of the activity budget. If the cost to the actors of affiliative behavior is low even if the rewards are low or extremely variable, we should expect affiliation and cooperation to be frequent. This is especially true under conditions in which individuals benefit from the collective environment of living in stable social groups. Am J Phys Anthropol 128:84–97, 2005. © 2005 Wiley‐Liss, Inc.     

Single‐Ion Conducting Electrolyte Based on Electrospun Nanofibers for High‐Performance Lithium Batteries

Herein, a novel electrospun single‐ion conducting polymer electrolyte (SIPE) composed of nanoscale mixed poly(vinylidene fluoride‐co‐hexafluoropropylene) (PVDF‐HFP) and lithium poly(4,4′‐diaminodiphenylsulfone, bis(4‐carbonyl benzene sulfonyl)imide) (LiPSI) is reported, which simultaneously overcomes the drawbacks of the polyolefin‐based separator (low porosity and poor electrolyte wettability and thermal dimensional stability) and the LiPF₆ salt (poor thermal stability and moisture sensitivity). The electrospun nanofiber membrane (es‐PVPSI) has high porosity and appropriate mechanical strength. The fully aromatic polyamide backbone enables high thermal dimensional stability of es‐PVPSI membrane even at 300 °C, while the high polarity and high porosity ensures fast electrolyte wetting. Impregnation of the membrane with the ethylene carbonate (EC)/dimethyl carbonate (DMC) (v:v = 1:1) solvent mixture yields a SIPE offering wide electrochemical stability, good ionic conductivity, and high lithium‐ion transference number. Based on the above‐mentioned merits, Li/LiFePO₄ cells using such a SIPE exhibit excellent rate capacity and outstanding electrochemical stability for 1000 cycles at least, indicating that such an electrolyte can replace the conventional liquid electrolyte–polyolefin combination in lithium ion batteries (LIBs). In addition, the long‐term stripping–plating cycling test coupled with scanning electron microscope (SEM) images of lithium foil clearly confirms that the es‐PVPSI membrane is capable of suppressing lithium dendrite growth, which is fundamental for its use in high‐energy Li metal batteries.