New insights on the external features of egg capsules and embryo development in the squid Loligo vulgaris

The embryonic development of the squid Loligo vulgaris was observed from 183 egg masses collected from special devices deployed throughout Cabrera National Park (Baleares Islands, western Mediterranean Sea). Sequence alignment analysis of the cytochrome oxidase I gene revealed that all embryos belonged to L. vulgaris. In total, 549 egg capsules were examined. Viable egg capsules (n = 420) were classified into one of five maturation stages according to the primary external features. The length of the viable egg capsules varied between 40 and 170 mm, and increased with embryonic development. The non-viable capsules (n = 129) were categorized into four groups: I (Ginger root), non-viable II and III, and empty egg capsule (IV). The percentage of non-viable capsules (i.e. grades I, II and III) was 92.25%. Empty capsules accounted for 7.75% of the total non-viable egg capsules. Embryonic development was classified into a second scale of eight stages. Egg capsule stage and embryonic stage were significantly related (n = 420; p < 0.001), facilitating the determination of the embryo developmental phase based on the outward appearance of the egg capsules. The embryo development stage based on the external features of the egg capsules might constitute an innovative tool for in situ embryological data collection. This new method is neither time consuming nor invasive, and could be helpful in fishing cruises, for scuba diving visual census in natural habitats and for laboratory culture. Slight variability in the developmental embryonic stages within egg capsules from the same egg mass was identified. The origin of this asynchrony is discussed. Chronological appearance of organs was similar to that of the six loliginid species previously examined. However, some developmental changes in the timing or rate of events (heterochronies) were observed: Hoyle’s organ was formed earlier in L. vulgaris and the appearance of ventral chromatophores was slightly delayed (2 days) compared with the other species considered.     

Dealing with Distances and Transformations for Fuzzy C-Means Clustering of Compositional Data

Clustering techniques are based upon a dissimilarity or distance measure between objects and clusters. This paper focuses on the simplex space, whose elements??compositions??are subject to non-negativity and constant-sum constraints. Any data analysis involving compositions should fulfill two main principles: scale invariance and subcompositional coherence. Among fuzzy clustering methods, the FCM algorithm is broadly applied in a variety of fields, but it is not well-behaved when dealing with compositions. Here, the adequacy of different dissimilarities in the simplex, together with the behavior of the common log-ratio transformations, is discussed in the basis of compositional principles. As a result, a well-founded strategy for FCM clustering of compositions is suggested. Theoretical findings are accompanied by numerical evidence, and a detailed account of our proposal is provided. Finally, a case study is illustrated using a nutritional data set known in the clustering literature.     

Empirical factors and structure transference: Returning to the London account

We offer a framework to represent the roles of empirical and theoretical factors in theory construction, and examine a case study to illustrate how the framework can be used to illuminate central features of scientific reasoning. The case study provides an extension of French and Ladyman's (1997) analysis of Fritz and Heinz London's model of superconductivity to accommodate the role of the analogy between superconductivity and diamagnetic phenomena in the development of the model between 1935 and 1937. We focus on this case since it allows us to separate the roles of empirical and theoretical factors, and so provides an example of the utility of the approach that we have adopted. We conclude the paper by drawing on the particular framework here developed to address a range of concerns.     

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.     

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels. Two-dimensional Fourier transform electronic spectroscopy has mapped these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted and indirectly observed. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.     

The significance of nitrification for oceanic new production

The flux of organic material sinking to depth is a major control on the inventory of carbon in the ocean. To first order, the oceanic system is at equilibrium such that what goes down must come up. Because the export flux is difficult to measure directly, it is routinely estimated indirectly by quantifying the amount of phytoplankton growth, or primary production, fuelled by the upward flux of nitrate. To do so it is necessary to take into account other sources of biologically available nitrogen. However, the generation of nitrate by nitrification in surface waters has only recently received attention. Here we perform the first synthesis of open-ocean measurements of the specific rate of surface nitrification and use these to configure a global biogeochemical model to quantify the global role of nitrification. We show that for much of the world ocean a substantial fraction of the nitrate taken up is generated through recent nitrification near the surface. At the global scale, nitrification accounts for about half of the nitrate consumed by growing phytoplankton. A consequence is that many previous attempts to quantify marine carbon export, particularly those based on inappropriate use of the f-ratio (a measure of the efficiency of the 'biological pump'), are significant overestimates.     

软弱夹层力学参数取值规范分析

软弱夹层的工程地质性质既与地应力、地下水等环境条件有关,也与其成因性质、粒度成分和矿物成分等有关。试验研究了成因性质、颗粒组成及物质组成相同条件下,软弱夹层抗剪强度参数随含水量、性状指标(W/Wp)和干密度变化的关系,并建立了相关方程。结果表明：夹层强度随含水量和性状指标减小而增大,随干密度增大而增大。因此,在对具体工程的软弱夹层进行强度参数取值时要综合考虑夹层在原位条件下的含水量、颗粒组成、粘土矿物成分及所处的地应力环境等因素。并探讨了重力坝规范中仅用粒度成分定量指标选取软弱结构面抗剪强度参数存在的不足之处。     

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

Many cellular functions involve multi-domain proteins, which are composed of structurally independent modules connected by flexible linkers. Although it is often well understood how a given domain recognizes a cognate oligonucleotide or peptide motif, the dynamic interaction of multiple domains in the recognition of these ligands remains to be characterized. Here we have studied the molecular mechanisms of the recognition of the 3'-splice-site-associated polypyrimidine tract RNA by the large subunit of the human U2 snRNP auxiliary factor (U2AF65) as a key early step in pre-mRNA splicing. We show that the tandem RNA recognition motif domains of U2AF65 adopt two remarkably distinct domain arrangements in the absence or presence of a strong (that is, high affinity) polypyrimidine tract. Recognition of sequence variations in the polypyrimidine tract RNA involves a population shift between these closed and open conformations. The equilibrium between the two conformations functions as a molecular rheostat that quantitatively correlates the natural variations in polypyrimidine tract nucleotide composition, length and functional strength to the efficiency to recruit U2 snRNP to the intron during spliceosome assembly. Mutations that shift the conformational equilibrium without directly affecting RNA binding modulate splicing activity accordingly. Similar mechanisms of cooperative multi-domain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multi-domain proteins.     

Genome sequence and analysis of the tuber crop potato

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.