An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.     

Testing the optimal defense hypothesis in Stryphnodendron adstringens (Fabaceae,Mimosoideae) leaves: the role of structure,number, position and nectar composition of extrafloral nectaries

Stryphnodendron adstringens is a common Cerrado tree that possesses extrafloral nectaries (EFNs) on its leaves, which are located at the base and apex of the rachis and along the secondary veins. The position of EFNs and their nectar production can be affected by defense strategies because plant organs possess different values and herbivory vulnerability. Here we aimed to elucidate anatomy, histochemistry, nectar composition and EFN number on leaves of S. adstringens in the light of the optimal defense hypothesis. We found a convergence on anatomy and histochemical characterization because the three studied types of EFNs have epidermis, secretory parenchyma and vascular tissue, showing phenolic compounds and polysaccharides in the secretory parenchyma cells. The nectar contained glucose, fructose and sucrose, which attract ants of the Camponotus and Cephalotes genus. We found differences in the number of EFNs along the secondary veins and in the nectar composition between EFNs located at the base and apex of the rachis of the leaf. The number of EFNs on the secondary veins increases from the base to the apex, suggesting a strategy to induce ant patrolling over the entire leaf region. EFNs at the base secreted more nectar, which should be related to the protection of the leaf base, which is the part most vulnerable to herbivore attack and the most valued organ. We concluded that EFNs of S. adstringens are anti‐herbivore defenses whose pattern matches the predictions of the optimal defense hypothesis.     

Decomposition and nitrogen dynamics of turtle grass (<Emphasis Type="Italic">Thalassia testudinum</Emphasis>) in a subtropical estuarine system

Seagrass beds are pivotal in the functioning of coastal ecosystems in terms of productivity, organic matter turnover and nutrient cycling. Aiming to document decay and nitrogen (N) dynamics of turtle grass (Thalassia testudinum) in a subtropical estuarine system, decomposition patterns of leaves and rhizomes were characterized and compared. Nitrogen usage during decomposition of tissues, and of live tissues and epiphytes growing on live leaves, was also quantified and compared. Stable isotope ratios allowed tracing N within the seagrass bed, following N incorporation into seagrass tissues from the surrounding media (water, sediment). Leaves had a higher N content and decomposed at a faster rate (~6.4 times) compared to rhizomes. Leaching of soluble materials explain the rapid (0–3 days) initial mass loss of leaves (20%) and rhizomes (18%); with a loss of 85 and 56%, respectively, by the end of the study (77 days). Overall, leaves released N while rhizomes immobilized it. Nitrogen concentration was significantly different among live tissues. The main source of N for both seagrass tissues was the sediment, and water column for epiphytes. Differences in decomposition rates among seagrass tissues can be explained by the quality of the substrate and its susceptibility to microbial use. Seagrass leaves and rhizomes are equally important in taking up nutrients from either the water column or the sediments. This study provides a platform to study energy and matter transfers through detrital foodwebs linked to seagrass meadows.     

Environmental trade-offs across cascading lithium-ion battery life cycles

Purpose

The purpose of this study was to analyze the environmental trade-offs of cascading reuse of electric vehicle (EV) lithium-ion batteries (LIBs) in stationary energy storage at automotive end-of-life.

Methods

Two systems were jointly analyzed to address the consideration of stakeholder groups corresponding to both first (EV) and second life (stationary energy storage) battery applications. The environmental feasibility criterion was defined by an equivalent-functionality lead-acid (PbA) battery. A critical methodological challenge addressed was the allocation of environmental impacts associated with producing LIBs across the EV and stationary use systems. The model also tested sensitivity to parameters such as the fraction of battery cells viable for reuse, service life of refurbished cells, and PbA battery efficiency.

Results and discussion

From the perspective of EV applications, cascading reuse of an LIB in stationary energy storage can reduce net cumulative energy demand and global warming potential by 15 % under conservative estimates and by as much as 70 % in ideal refurbishment and reuse conditions. When post-EV LIB cells were compared directly to a new PbA system for stationary energy storage, the reused cells generally had lower environmental impacts, except in scenarios where very few of the initial battery cells and modules could be reused and where reliability was low (e.g., life span of 1 year or less) in the secondary application.

Conclusions

These findings demonstrate that EV LIB reuse in stationary application has the potential for dual benefit—both from the perspective of offsetting initial manufacturing impacts by extending battery life span as well as avoiding production and use of a less-efficient PbA system. It is concluded that reuse decisions and diversion of EV LIBs toward suitable stationary applications can be based on life cycle centric studies. However, technical feasibility of these systems must still be evaluated, particularly with respect to the ability to rapidly analyze the reliability of EV LIB cells, modules, or packs for refurbishment and reuse in secondary applications.

     

Length–weight relationships of 20 fish species from Bahía de Matanchen,in the southeast Gulf of California,Mexico

Length–weight relationship (LWR) parameters were determined for 20 fish species belonging to 14 genera and seven families. The fishes were collected monthly (May 2013 to February 2014) by soft‐bottom trawls in Bahía de Matanchén, southeast of the Gulf of California. Sizes ranged between 5.5 and 36.0 cm total length (TL) and weighed between 1 and 901 g. The allometric coefficient (b) of the LWR varied from 2.638 for Chloroscombrus orqueta to 3.668 for Neopisthopterus tropicus. This is the first report of LWR estimations for 15 of the species.     

Past,present, and future research in bipolar lichen‐forming fungi and their photobionts

Compared to other organisms, such as vascular plants or mosses, lichen‐forming fungi have a high number of species occurring in both northern and southern hemispheres but are largely absent from intermediate, tropical latitudes. For instance, ca. 160 Antarctic species also occur in polar areas or mountainous temperate regions of the northern hemisphere. Early interpretations of this particular distribution pattern were made in terms of vicariance or long‐distance dispersal. However, it was not until the emergence of phylogenetics and the possibility of dating past diversification and colonization events that these initial hypotheses started to be evaluated. The premise of a relatively recent colonization of the southern hemisphere by boreal lichens through long‐distance dispersal has gained support in recent studies based on either the comparison of genetic affinities (i.e., tree topology) or more robust, statistical migratory models. Still, the scarcity of such studies and a concern that taxonomic concepts for bipolar lichens are often too broad preclude the generation of sound explanations on the mechanisms and origin of such fascinating disjunct distributions. This review provides an up‐to‐date overview of bipolar distributions in lichen‐forming fungi and their photobionts. Evidence provided by recent, molecular‐based studies as well as data on the type of lichen reproduction, dispersal ability, photobiont identity and availability, and habitat preferences are brought together to discuss how and when these distributions originated and their genetic footprints. Ideas for future prospects and research are also discussed.     

Traditional fermented beverages from Mexico as a potential probiotic source

Fermentation is one of the oldest ways of processing food. Some fermented food is produced industrially, but can also be produced in an artisanal way by certain ethnic groups, called traditional fermented foods. In Mexico, there are a variety of traditional fermented beverages which are produced in an artisanal way. They include those made with maize (atole agrio, pozol, and tesgüino), fruit (tepache and colonche), and obtained by plant fermentation (pulque, tuba, and taberna). These beverages have been used since ancient times for religious and medicinal purposes. The medicinal effect may be due to fermented microorganisms. The presence of beneficial microorganisms known as probiotics provides beneficial effects to consumer health, improving the balance of intestinal host, and reducing the risk of gastrointestinal diseases, mainly. Most probiotics belong to the genus Lactobacillus, but Bifidobacterium, Bacillus, and yeast are also found. Therefore, it is important that the microbiological diversity of the beverages is studied and documented. This review includes information on the microbial diversity and probiotic potential of the most important traditional fermented beverages from Mexico.