Antiparallel Conformation of Knob and Hole Aglycosylated Half-Antibody Homodimers Is Mediated by a CH2–CH3 Hydrophobic Interaction

Bispecific antibody and antibody-like molecules are of wide interest as potential therapeutics that can recognize two distinct targets. Among the variety of ways such molecules have been engineered is by creating “knob” and “hole” heterodimerization sites in the CH3 domains of two antibody heavy chains. The molecules produced in this manner maintain their biological activities while differing very little from the native human IgG sequence. To better understand the knob-into-hole interface, the molecular mechanism of heterodimerization, and to engineer Fc domains that could improve the assembly and purity of heterodimeric reaction products, we sought crystal structures of aglycosylated heterodimeric and homodimeric “knob” and “hole” Fc fragments derived from bacterial expression. The structure of the knob-into-hole Fc was determined at 2.64 Å. Except for the sites of mutation, the structure is very similar to that of the native human IgG1 Fc, consistent with a heterodimer interaction kinetic K_D of < 1 nM. Homodimers of the “knob” and “hole” mutants were also obtained, and their X-ray structures were determined at resolutions 2.5 Å and 2.1 Å, respectively. Both kinds of homodimers adopt a head-to-tail quaternary structure and thus do not contain direct knob/knob or hole/hole CH3 interactions. The head-to-tail arrangement was disfavored by adding site-directed mutations at F241 and F243 in the CH2 domains, leading to increases in both rate and efficiency of bispecific (heterodimer) assembly.     

La symbolique des gravures rupestres du Mont Bego

The analysis of imaginary anthropological structures elaborated by Gilbert Durand enables us to identify a symbolic language of ideograms from Mont Bego (circa 2500-1800 BC). There are three main types of figures: figures associated with the Bull- God and with the God of Storms, which come under the first function “heroic”; figures depicting harnessing and reticulates which evoke ploughed fields ands make reference to the feminine and maternal function known as “mystic nocturne”; figures linked to initiation, to the relationship between the first and the second function, which come under the function known as “synthetic nocturne”. These figures are located particularlyon the slab known as the “witch”. A comparative study of the later symbolic figures, presented in worship practises in archaic and then classic Greece and in the Greek-Roman imaginary, helps us to understand that Mediterranean mankind portrays a coherent image of the cosmos. This image is stable from the proto-Ligurian figures of Mont Bego until the forms elaborated by the Greek-Roman religious imaginary, in particular through mysterious rituals.     

小鼠对不同拓扑性质图形的识别

视觉感知的一系列研究都支持大范围拓扑感知的理论．拓扑性质作为整体性质,是视觉感知的基础．视觉对图形拓扑特征差异的感知要优先于对局部特征差异的感知．采用Y迷宫研究了小鼠对不同拓扑性质图形的识别．训练小鼠学习识别圆环和实心矩形这一对拓扑性质不同的图形,之后用拓扑特征相同或不同的其他图形测试小鼠,这些图形包括空心矩形、实心圆、缺口的圆环、缺口的空心矩形．实验结果表明,学会识别圆环(奖励)和实心矩形(无奖励)的小鼠无法区分实心圆和实心矩形以及圆环和空心矩形,但是能够分别从缺口圆环、缺口的空心矩形、实心圆与空心矩形组成的图形对中识别出空心矩形．因此证实了小鼠的视觉系统能够感知拓扑特征的差异并且具有对拓扑性质的概括能力．结果为拓扑知觉对视觉系统来说是基本的这一假设提供了证据．     

Cerebral perfusion pressure in giraffe: modelling the effects of head-raising and -lowering

Loss of consciousness caused by positional changes of the head results from reduced cerebral blood flow (CBF). CBF is related to cerebral perfusion pressure (CPP). CPP is the difference between mean arterial pressure (MAP) at the head and intracranial pressure (ICP). The positional change of the giraffe head between ground level and standing upright is the largest of all animals yet loss of consciousness does not occur. We have investigated the possibility that an increase in CPP protects giraffe from fainting, using a mechanical model that functioned as an anatomical U-tube. It consisted of a rigid ascending “carotid” limb, a collapsible “brain” tube drained by a rigid, “vertebral venous plexus” (VVP) tube, and a collapsible “head” tube drained by a collapsible tube representing the “jugular vein”. The descending tubes could be rotated relative to the “carotid” tube to be horizontal, or at 30°, 45°, and 60° to the vertical to simulate changes in head position. Pressure at the top of the “carotid” tube was intracranial MAP, at the top of the “VVP” tube was ICP, and the difference CPP. In the simulated “head-up” position and a fluid flow rate of 4 L min⁻¹, CPP was ∼170 mmHg. With the VVP tube horizontal, CPP fell from ∼170 to 45 mmHg, but increased to ∼67 mmHg at 30° “down”, to ∼70 mmHg at 45° “down” and to ∼75 at 60° “down”. The fall in CPP in the head-down positions resulted from a decrease in viscous resistance in, and dissipation of pressure to, the “head” and “jugular” tubes. These data provide an estimate of cranial pressure changes in giraffe during positional changes of the head, and suggest that an increase in CPP plays a significant role in maintaining CBF during head-raising and that it may be an important mechanism for preventing fainting in giraffe.     

A model for non-resolvable ambiguities

The dynamical behavior of the perception of ambiguous figures arising from the essentially nonresolvable ambiguity built in the figures themselves is analysed. Two main features of it are explored, the initial transient and the rhythmic alternation of inversions of perspective following it. The initial transient is envisaged in terms of a symmetry breaking disorder-order transformation induced by the attention of the observer. The rhythmic inversions of the ordered structures are classified by a model based on an ideally non linear decision equation for binary systems originally proposed to schematize the observed behavior of neurons. Finally it is suggested that the phenomena relative to the perception of ambiguous figures could represent the simplest ones among more complex situations arising in perception, in concept formation, in the sensing of emotion and in communication in general.     

Neurodegenerative disease-specific induced pluripotent stem cell research

Neurodegenerative disease-specific induced pluripotent stem cell (iPSC) research contributes to the following 3 areas; “Disease modeling”, “Disease material” and “Disease therapy”.“Disease modeling”, by recapitulating the disease phenotype in vitro, will reveal the pathomechanisms. Neurodegenerative disease-specific iPSC-derived non-neuronal cells harboring disease-causative protein(s), which play critical roles in neurodegeneration including motor neuron degeneration in amyotrophic lateral sclerosis, could be “Disease material”, the target cell(s) for drug screening. These differentiated cells also could be used for “Disease therapy”, an autologous cellular replacement/neuroprotection strategy, for patients with neurodegenerative disease.Further progress in these areas of research can be made for currently incurable neurodegenerative diseases.     

Conformational control of spin state in iron(II) tripodal imidazole complexes

Three new iron(II) N₆ tripodal complexes provide information on the role of ligand conformation on spin crossover behavior. The ligands (generated in situ) are the Schiff base condensate of tris(2-aminoethyl)amine (tren) with three equivalents of 4-methyl-5-imidazolecarboxaldehyde, H₃(1), and the condensates of tris(2-aminoethyl)methylammonium ion (N(Me)tren⁺) with three equivalents of 4-methyl-5-imidazolecarboxaldehyde, N(Me)H₃(1)⁺, or with 2-imidazole carboxaldehyde, N(Me)H₃(3)⁺. The structures of [FeH₃(1)](ClO₄)₂, [FeN(Me)H₃(1)](ClO₄)₃ and [FeN(Me)H₃(1)](ClO₄)₃ are reported. The central tren nitrogen atom in these complexes exhibits three different geometries, pyramidal with the nitrogen pointed toward the iron (“N in”, Fe-N distance of 3.050 Å), planar (Fe-N distance of 3.527 Å), and pyramidal with the nitrogen pointed away from the iron atom (“N out”, Fe-N distance of 3.921 Å). With iron(II) the “N in” geometry is high spin while the planar and “N out” geometries are low spin. [FeH₃(1)](ClO₄)₂ exhibits spin crossover behavior between room temperature and 77 K as determined by Mössbauer spectroscopy and also exhibits a conformational change from “N in” to planar over this same temperature range. The structures of [FeN(Me)H₃(1)](ClO₄)₃ and [FeN(Me)H₃ (3)](ClO₄)₃ are locked into the “N out” geometry due to the quaternary nitrogen atom and are low spin even at room temperature. The LS planar and “N out” conformations place a strain on the bond angles of the aliphatic arms of the ligand, which are more pronounced in the “N out” case. The HS “N in” geometry lacks this strain.     

干旱胁迫对鸭茅幼苗根系生长及光合特性的影响

以不同耐旱型鸭茅品种(系)“01998”(敏感型)和“宝兴”(耐旱型)为试材,采用盆栽控水试验方法,研究土壤干旱胁迫对鸭茅幼苗根系生长、生理特性及叶片光合作用的影响,探讨不同品种耐旱机制的差异.结果表明：干旱胁迫下,不同耐旱型鸭茅幼苗的根系活力和根系数量均呈先上升后下降的趋势,当土壤相对含水量降到30%时,根系活力和根数显著增加并达到最大值;干旱胁迫降低了两个品种鸭茅叶片的相对含水量、叶绿素含量、净光合速率、叶片蒸腾速率、气孔导度,提高了电导率和胞间CO₂浓度.干旱胁迫降低了两个品种鸭茅的单株叶面积,品种“01998”的地下及地上生物量下降,而“宝兴”无显著变化.     

A novel fluorescent timer based on bicistronic expression strategy in Caenorhabditis elegans

Fluorescent timers are useful tools for studying the spatial and temporal cellular or molecular events. Based on the trans-splicing mechanism in Caenorhabditis elegans, we constructed a “fluorescent timer” through bicistronic expression of two fluorescent proteins with different maturation times. When used in vivo, this “timer” changes its color over time and therefore can be used to monitor the activity of the targeted promoters in C. elegans. Using this “timer”, we have successfully traced the time-dependent activity of myo-3 promoter which drives expression in body wall muscle and vulval muscle. We found that the myo-3 promoter started to be active about 7 h after egg-laying and sustained its activity in the following hatching process. We have also determined the myo-3 promoter activity during larval development by this “timer”. We anticipate that more new “fluorescent timers” with variable time-resolution could be designed by bicistronic expression of different fluorescent protein pairs.     

Figurations de l’amas stellaire des Pléiades sur deux roches gravées de la région du Mont Bego Z IX. GII. R 4 et Z IX. GIII. R 6

Two engraved rocks are situated 140 m from each other at an altitude of about 2250 m. One of them is called “female dancer”, and the other, “the Pleiads”, and both show a group of seven small pitted areas, of which one is smaller than the others and ‘ identified as the “Pleiads stellar cluster”, often depicted or mentioned during Antiquity and also throughout various historical periods.On each of these rocks, a large halberd, whose handle is oriented east-west, was traced along a natural fissure in the rock and engraved in the center of the composition. The “Pleiads stellar cluster” is represented on each of the two rocks beside the halberd : although situated to the west above the halberd blade on the “female dancer” rock, it is placed to the south and to the left of the halberd handle on “the Pleiads” rock. This difference may mark two distinct calendar data.The position of the different figures in the compositions illustrated on these two rocks, in particular inversions in the representation of some of them may indicate two distinct periods of the agricultural yearly cycle: on the rock called “female dancer”, the “heliacal raise” at summer's end, marking the beginning of the harvest and, on the rock called “the Pleiads”, the “heliacal setting”, just before winter, after the end of the harvest, when the rains soaks the ground and it is time to plow.     

Adapting lacunarity techniques for gradient-based analyses of landscape surfaces

Typically, landscapes are modeled in the form of categorical map patterns, i.e. as mosaics made up of basic elements which are presumed to possess sharp and well-defined boundary lines. Many landscape ecological concepts are based upon this perception. In reality, however, the spatial value progressions of environmental parameters tend to be “gradual” rather than “abrupt”. Therefore, gradient approaches have shifted to the forefront of scientific interest recently. Appropriate methods are needed for the implementation of such approaches. Lacunarity analysis may provide a suitable starting point in this context. We propose adapted versions of standard lacunarity techniques for analyzing ecological gradients in general and the heterogeneity of physical landscape surfaces in particular. A simple way of customizing lacunarity analysis for quantifying the heterogeneity of digital elevation models is to use the value range for defining the box mass used in the calculation process. Furthermore, we demonstrate how lacunarity analysis can be combined with metrics derived from surface metrology, such as the “Average Surface Roughness”. Finally, the “classical” lacunarity approach is used in combination with simple landform indices. The methods are tested using different data sets, including high-resolution digital elevation models. In summary, lacunarity analysis is adopted in order to establish a gradient-based approach for terrain analysis and proves to be a valuable concept for comparing three-dimensional surface patterns in terms of their degree of “heterogeneity”. The proposed developments are meant to serve as a stimulus for making increased use of this simple but effective technique in landscape ecology. They offer a large potential for expanding the methodical spectrum of landscape structure analysis towards gradient-based approaches. Methods like lacunarity analysis are promising, since they do not rely on predefined landscape units or patches and thus enable ecologists to effectively deal with the complexity of natural systems.     

Characterisation of physiological and immunological differences between Pacific oysters (Crassostrea gigas) genetically selected for high or low survival to summer mortalities and fed different rations under controlled conditions

Within the framework of a national scientific program named “MORtalités ESTivales de l'huître creuse Crassostrea gigas” (MOREST), a family-based experiment was developed to study the genetic basis of resistance to summer mortality in the Pacific oyster, Crassostrea gigas. As part of the MOREST project, the second generation of three resistant families and two susceptible families were chosen and pooled into two respective groups: “R” and “S”. These two groups of oysters were conditioned for 6 months on two food levels (4% and 12% of oyster soft-tissue dry weight in algal dry weight per day) with a temperature gradient that mimicked the Marennes-Oléron natural cycle during the oyster reproductive period. Oyster mortality remained low for the first two months, but then rapidly increased in July when seawater temperature reached 19 °C and above. Mortality was higher in “S” oysters than in “R” oysters, and also higher in oysters fed the 12% diet than those fed 4%, resulting in a decreasing, relative order in cumulative mortality as follows; 12% “S” > 12% “R” > 4% “S” > 4% “R”. Although the observed mortality rates were lower than those previously observed in the field, the mortality differential between “R” and “S” oysters was similar. Gonadal development, estimated by tissue lipid content, followed a relative order yielding a direct, positive relationship between reproductive effort and mortality as we reported precedently by quantitative histology. Regarding hemocyte parameters, one of the most striking observations was that reactive oxygen species (ROS) production was significantly higher in “S” oysters than in “R” oysters in May and June, regardless of food level. The absence of known environmental stress under these experimental conditions suggests that the ROS increase in “S” oyster could be related to their higher reproductive activity. Finally, a higher increase in hyalinocyte counts was observed for”S” oysters, compared to “R” oysters, in July, just before mortality. Taken together, our results suggest an association of genetically based resistance to summer mortality, reproductive strategy and hemocyte parameters.     

Genome wide sequence analysis grants unbiased definition of species boundaries in “Candidatus Phytoplasma”

The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species “Ca. P. asteris”, “Ca. P. mali”, “Ca. P. pyri”, “Ca. P. pruni”, and “Ca. P. australiense” were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. “Ca. P. mali” and “Ca. P. pyri” were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution.     

From Fertilization to Adult Sexual Behavior

Research has established the broad mammalian developmental plan that genes on the sex chromosomes influence gonad development which determines gonadal hormone production (or its absence) leading to modification of the genitalia and simultaneously biasing the nervous system to organize adult sexual behavior. This might be considered the “gonad to hormones to behavior” model. It is clear, however, that although this model generally works well it is incomplete. The model does not account for behavioral influences attributed to the environment or to genetic but nongonadal or hormonal factors. In this essay we probe those areas of sexual development that are neither differentiated by hormones nor activated by them. The concept of the environment used for our discussion is very broad; it incorporates considerations of both the molar and the molecular levels. The general sense of the word “environment” as something exterior to the person is retained, even if that something influences intraperson processes. In addition, we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature–nurture discussion.     

Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers?

Recent attempts to examine the biological processes responsible for the general characteristics of mutualistic networks focus on two types of explanations: nonmatching biological attributes of species that prevent the occurrence of certain interactions (“forbidden links”), arising from trait complementarity in mutualist networks (as compared to barriers to exploitation in antagonistic ones), and random interactions among individuals that are proportional to their abundances in the observed community (“neutrality hypothesis”). We explored the consequences that simple linkage rules based on the first two hypotheses (complementarity of traits versus barriers to exploitation) had on the topology of plant–pollination networks. Independent of the linkage rules used, the inclusion of a small set of traits (two to four) sufficed to account for the complex topological patterns observed in real-world networks. Optimal performance was achieved by a “mixed model” that combined rules that link plants and pollinators whose trait ranges overlap (“complementarity models”) and rules that link pollinators to flowers whose traits are below a pollinator-specific barrier value (“barrier models”). Deterrence of floral parasites (barrier model) is therefore at least as important as increasing pollination efficiency (complementarity model) in the evolutionary shaping of plant–pollinator networks.     

The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow

This paper is concerned with a model of “isolation with an initial period of migration”, where a panmictic ancestral population split into n descendant populations which exchanged migrants symmetrically at a constant rate for a period of time and subsequently became completely isolated. In the limit as the population split occurred an infinitely long time ago, the model becomes an “isolation after migration” model, describing completely isolated descendant populations which arose from a subdivided ancestral population. The probability density function of the coalescence time of a pair of genes and the probability distribution of the number of pairwise nucleotide differences are derived for both models. Whilst these are theoretical results of interest in their own right, they also give an exact analytical expression for the likelihood, for data consisting of the numbers of nucleotide differences between pairs of DNA sequences where each pair is at a different, independent locus. The behaviour of the distribution of the number of pairwise nucleotide differences under these models is illustrated and compared to the corresponding distributions under the “isolation with migration” and “complete isolation” models. It is shown that the distribution of the number of nucleotide differences between a pair of DNA sequences from different descendant populations in the model of “isolation with an initial period of migration” can be quite different from that under the “isolation with migration model”, even if the average migration rate over time (and hence the total number of migrants) is the same in both scenarios. It is also illustrated how the results can be extended to other demographic scenarios that can be described by a combination of isolated panmictic populations and “symmetric island” models.     

A Report of Two cases of Al-Awadi Raas-Rothschild Syndrome (AARRS) supporting that “Apparent” Phocomelia differentiates AARRS from Schinzel Phocomelia Syndrome (SPS)

Although there is a long list of syndromes with phocomelia, there are only two syndromes in which there is concurrent pelvic dysplasia and phocomelia: Al-Awadi–Raas-Rothschild syndrome (AARRS) and Schinzel phocomelia syndrome (SPS). Currently, there is a diagnostic confusion between the two syndromes and both have the same MIM entry (MIM 276820). We believe that the two syndromes are different entities and we also believe that the limb defect in SPS is a “true” phocomelia while the limb defect in AARRS is an “apparent” phocomelia. “Apparent” phocomelia describes the most severe form of ulnar ray deficiency in which there is absent ulna with radio-humeral synostosis. “Apparent” phocomelia is diagnosed radiologically by three radiological features: the apparently single bone occupying the arm/forearm appears relatively long, the area of radio-humeral synostosis will have thicker cortex with or without slight angulation, and the lower end of the bone resembles the lower end of a radius and not a humerus. In this paper, we present two new cases of AARRS from two different Saudi Arabian tribes: one case with R292C mutation of WNT7A with bilateral “apparent” phocomelia and a second case with a novel c.814G>T mutation of the WNT7A gene (resulting in wnt7a protein truncation at position 272) with unilateral “apparent” phocomelia. We reviewed previously reported cases of AARRS and SPS to further delineate the differences between these two syndromes. We make the argument that these two syndromes are two different entities and hence require two different MIM entries.     

The state transition mechanism—simply depending on light-on and -off in Spirulina platensis

The state transition in cyanobacteria is a long-discussed topic of how the photosynthetic machine regulates the excitation energy distribution in balance between the two photosystems. In the current work, whether the state transition is realized by “mobile phycobilisome (PBS)” or “energy spillover” has been clearly answered by monitoring the spectral responses of the intact cells of the cyanobacterium Spirulina platensis. Firstly, light-induced state transition depends completely on a movement of PBSs toward PSI or PSII while the redox-induced one on not only the “mobile PBS” but also an “energy spillover”. Secondly, the “energy spillover” is triggered by dissociation of PSI trimers into the monomers which specially occurs under a case from light to dark, while the PSI monomers will re-aggregate into the trimers under a case from dark to light, i.e., the PSI oligomerization is reversibly regulated by light switch on and off. Thirdly, PSI oligomerization is regulated by the local H⁺ concentration on the cytosol side of the thylakoid membranes, which in turn is regulated by light switch on and off. Fourthly, PSI oligomerization change is the only mechanism for the “energy spillover”. Thus, it can be concluded that the “mobile PBS” is a common rule for light-induced state transition while the “energy spillover” is only a special case when dark condition is involved.