Shifts in the demographics and behavior of bearded pigs (Sus barbatus) across a land‐use gradient

Beyond broad‐scale investigations of species diversity and abundance, there is little information on how land conversion in the tropics is affecting the behavior and demographics of surviving species. To fill these knowledge gaps, we explored the effects of land‐use change on the ecologically important and threatened bearded pig (Sus barbatus) over seven years in Borneo. Random placement of camera traps across a land‐use gradient of primary forest, logged forest, and oil palm plantations (32,542 trap nights) resulted in 2,303 independent capture events. Land‐use was associated with changes in the age structure and activity patterns of photographed individuals, alongside large changes in abundance shown previously. The proportion of adults recorded declined from 92% in primary forests to 76% in logged forests, and 67% in plantations, likely indicating increased fecundity in secondary forests. Activity level (capture rate) did not vary, but activity patterns changed markedly, from diurnal in primary forests, crepuscular in logged forests, to nocturnal in plantations. These changes corresponded with avoidance of diurnal human activity and may also protect bearded pigs from increased thermal stress in warmer degraded forests. The percentage of adult captures that were groups rather than individuals increased five‐fold from primary forests (4%) to logged forests (20%), possibly due to increased mating or in response to perceived threats from indirect human disturbance. We recommend further investigation of the demographic and behavioral effects of land‐use change on keystone species as altered population structure, activity patterns, and social behavior may have knock‐on effects for entire ecosystems.     

Relationships between chronotype,social jetlag,sleep, obesity and blood pressure in healthy young adults

Sleep disturbances, chronotype and social jetlag (SJL) have been associated with increased risks for major chronic diseases that take decades to develop, such as obesity, metabolic syndrome and cardiovascular disease. Potential relationships between poor sleep, chronotype and SJL as they relate to metabolic risk factors for chronic disease have not been extensively investigated. This prospective study examined chronotype, SJL and poor sleep in relation to both obesity and elevated blood pressure among healthy young adults.

SJL and objective sleep measures (total sleep time, sleep onset latency, wake after sleep onset and sleep efficiency) were derived from personal rest/activity monitoring (armband actigraphy) among 390 healthy adults 21–35 years old. Participants wore the device for 6–10 days at 6-month intervals over a 2-year period (n = 1431 repeated observations). Chronotypes were categorized into morning, intermediate and evening groups using repeated measures latent class analysis. Means of SJL and sleep measures among latent chronotype groups were compared using partial F-tests in generalized linear mixed models. Generalized linear mixed models also were used to generate odds ratios (ORs) with 95% confidence intervals (CIs) examining the relationship between repeated measures of chronotype, SJL, sleep and concurrent anthropometric outcome measures (body mass index, percentage of body fat, waist-to-hip ratio, waist-to-height ratio), systolic blood pressure and diastolic blood pressure.

Sleep latency ≥12 min was associated with increased odds of a high waist-to-height ratio (OR = 1.37; CI: 1.03–1.84). Neither chronotype nor SJL was independently associated with anthropometric outcomes or with blood pressure. Relationships between poor sleep and anthropometric outcomes or blood pressure varied by chronotype. Morning types with total sleep time <6 h, sleep efficiency <85% or wake after sleep onset ≥60 min were more likely to have an increased percentage of body fat, waist-to-hip ratio and waist-to-height ratio relative to those with an intermediate chronotype. Similarly, sleep latency ≥12 min was associated with increased odds of elevated systolic blood pressure (OR = 1.90; CI: 1.15–3.16, p_interaction = 0.02) among morning versus intermediate chronotypes. No relationships between poor sleep and obesity or elevated blood pressure were observed among evening chronotypes.

The results from this study among healthy young adults suggest that poor sleep among morning types may be more strongly associated with obesity and elevated blood pressure relative to those with an intermediate (neutral) chronotype. Sleep-related metabolic alterations among different chronotypes warrant further investigation.     

Understanding the Effects of Molecular Dopant on n‐Type Organic Thermoelectric Properties

Molecular doping is a powerful method to fine‐tune the thermoelectric properties of organic semiconductors, in particular to impart the requisite electrical conductivity. The incorporation of molecular dopants can, however, perturb the microstructure of semicrystalline organic semiconductors, which complicates the development of a detailed understanding of structure–property relationships. To better understand how the doping pathway and the resulting dopant counterion influence the thermoelectric performance and transport properties, a new dimer dopant, (N‐DMBI)₂, is developed. Subsequently, FBDPPV is then n‐doped with dimer dopants (N‐DMBI)₂, (RuCp*mes)₂, and the hydride‐donor dopant N‐DMBI‐H. By comparing the UV–vis–NIR absorption spectra and morphological characteristics of the doped polymers, it is found that not only the doping mechanism, but also the shape of the counterion strongly influence the thermoelectric properties and transport characteristics. (N‐DMBI)₂, which is a direct electron‐donating dopant with a comparatively small, relatively planar counterion, gives the best power factor among the three systems studied here. Additionally, temperature‐dependent conductivity and Seebeck coefficient measurements differ between the three dopants with (N‐DMBI)₂ yielding the best thermoelectric properties. The results of this study of dopant effects on thermoelectric properties provide insight into guidelines for future organic thermoelectrics.     

A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics

The Australian freshwater fish fauna is very unique, but poorly understood. In the Australian Monsoonal Tropics (AMT) biome of northern Australia, the number of described and candidate species has nearly doubled since the last attempt to analyse freshwater fish species composition patterns and determine a bioregionalisation scheme. Here, we utilise the most complete database of catchment‐scale freshwater fish distributions from the AMT to date to: (a) reanalyze spatial patterns of species richness, endemism and turnover of freshwater fishes; (b) propose a biogeographic regionalisation based on species turnover; (c) assess the relationship between species turnover and patterns of environmental change and historic drainage connectivity; and (d) identify sampling gaps. Biogeographic provinces were identified using an agglomerative cluster analysis of a Simpson's beta (β_sim) dissimilarity matrix. A generalised dissimilarity model incorporating eighteen environmental variables was used to investigate the environmental correlates of species turnover. Observed and estimated species richness and endemism were calculated and inventory completeness was estimated based on the ratio of observed to estimated species richness. Three major freshwater fish biogeographic provinces and 14 subprovinces are proposed. These differ substantially from the current bioregionalisation scheme. Species turnover was most strongly influenced by environmental variables that are interpreted to reflect changes in terrain (catchment relief and confinement), geology and climate (runoff perenniality, stream density), and biotic responses to climate (net primary productivity). Past connectivity between rivers during low sea‐level events is also influential highlighting the importance of historical processes in explaining contemporary patterns of biodiversity in the AMT. The inclusion of 49 newly discovered species and candidate species only reinforced known focal points of species richness and endemism in the AMT. However, a number of key sampling gaps remain that need to be filled to fully characterise the proposed bioregionalisation.     

Porphyrin Binding to Gun4 Protein,Facilitated by a Flexible Loop,Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway

In oxygenic phototrophs, chlorophylls, hemes, and bilins are synthesized by a common branched pathway. Given the phototoxic nature of tetrapyrroles, this pathway must be tightly regulated, and an important regulatory role is attributed to magnesium chelatase enzyme at the branching between the heme and chlorophyll pathway. Gun4 is a porphyrin-binding protein known to stimulate in vitro the magnesium chelatase activity, but how the Gun4-porphyrin complex acts in the cell was unknown. To address this issue, we first performed simulations to determine the porphyrin-docking mechanism to the cyanobacterial Gun4 structure. After correcting crystallographic loop contacts, we determined the binding site for magnesium protoporphyrin IX. Molecular modeling revealed that the orientation of α6/α7 loop is critical for the binding, and the magnesium ion held within the porphyrin is coordinated by Asn-211 residue. We also identified the basis for stronger binding in the Gun4-1 variant and for weaker binding in the W192A mutant. The W192A-Gun4 was further characterized in magnesium chelatase assay showing that tight porphyrin binding in Gun4 facilitates its interaction with the magnesium chelatase ChlH subunit. Finally, we introduced the W192A mutation into cells and show that the Gun4-porphyrin complex is important for the accumulation of ChlH and for channeling metabolites into the chlorophyll biosynthetic pathway.     

LLY-507, a Cell-active,Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys³⁷⁰ at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.     

Revival of the genus Tropicoperdix Blyth 1859 (Phasianidae,Aves) using multilocus sequence data

Although Tropicoperdix has been considered to be either a full genus or a species complex within the Phasianid genus Arborophila (hill partridges), there is long‐standing uncertainty regarding the degree of difference that warrants generic separation, including reported anatomical cranial differences. In addition, the intra‐generic taxonomy remains under dispute. Most studies hypothesize that Tropicoperdix comprises three species, while others postulate from one to four species. However, no molecular study has been performed to clarify the systematic and taxonomic uncertainties surrounding Tropicoperdix. In the present study, we performed a series of molecular phylogenetic analyses of Tropicoperdix and Arborophila taxa based on two mitochondrial genes and five nuclear introns. All the results are consistent with the finding that Tropicoperdix and Arborophila are phylogenetically distinct and distant genera, although the precise phylogenetic position of Tropicoperdix remains undetermined. Retrospective examination of external characteristics also supports the generic separation, as well as providing evidence of remarkable multiple character convergence. We propose that Tropicoperdix comprises at least two full species based on mitochondrial data obtained from museum specimens by using a next‐generation sequencing method. © 2015 The Linnean Society of London     

Contributions of juvenile and adult diet to the lifetime reproductive success and lifespan of a spider

Food availability can vary widely for animals in nature and can have large effects on growth, reproduction and survival. While the consequences of food limitation for animals have been extensively studied, significant questions still remain including how ontogenetic variation in food availability contributes to lifetime reproductive success. We tested the effects of juvenile and adult food limitation on the lifetime reproductive success and lifespan of bridge spiders, Larinioides sclopetarius. Food availability was manipulated (low or high) over the entire juvenile and adult stage in a full‐factorial design and reproductive output and lifespan were measured. Juvenile and adult food limitation both reduced lifetime egg and hatchling production with effect sizes that were not significantly different from each other. Unlike some other arthropods, where juvenile food limitation reduces fecundity by reducing adult body size, body size was not affected by juvenile diet in bridge spiders. Clutch size was also significantly reduced by both juvenile and adult food limitation. The effect of adult diet on clutch size was stronger than that of juvenile diet. Juvenile and adult food limitation both extended total lifespan, and adult food limitation extended adult longevity (i.e. time from maturation to death). However, juvenile food limitation decreased adult longevity, in contrast to what would be predicted by dietary or caloric restriction. Compensatory feeding and growth are widely recognized mechanisms through which animals can ameliorate some of the negative effects of periods of food limitation. Yet our results combined with studies of a range of other species suggest that there may be lasting consequences of juvenile food limitation on lifetime reproductive success that cannot be compensated for by adult feeding in some species.     

Engineering Monolignol p-Coumarate Conjugates into Poplar and Arabidopsis Lignins

Lignin acylation, the decoration of hydroxyls on lignin structural units with acyl groups, is common in many plant species. Monocot lignins are decorated with p-coumarates by the polymerization of monolignol p-coumarate conjugates. The acyltransferase involved in the formation of these conjugates has been identified in a number of model monocot species, but the effect of monolignol p-coumarate conjugates on lignification and plant growth and development has not yet been examined in plants that do not inherently possess p-coumarates on their lignins. The rice (Oryza sativa) p-COUMAROYL-Coenzyme A MONOLIGNOL TRANSFERASE gene was introduced into two eudicots, Arabidopsis (Arabidopsis thaliana) and poplar (Populus alba × grandidentata), and a series of analytical methods was used to show the incorporation of the ensuing monolignol p-coumarate conjugates into the lignin of these plants. In poplar, specifically, the addition of these conjugates did not occur at the expense of the naturally incorporated monolignol p-hydroxybenzoates. Plants expressing the p-COUMAROYL-Coenzyme A MONOLIGNOL TRANSFERASE transgene can therefore produce monolignol p-coumarate conjugates essentially without competing with the formation of other acylated monolignols and without drastically impacting normal monolignol production.Lignification of plant cell walls prototypically involves the polymerization of the monolignols (MLs), p-coumaryl alcohol, coniferyl alcohol (CA), and sinapyl alcohol (SA), predominantly by stepwise radical coupling of each monomer to the phenolic end of the growing polymer (Sarkanen and Ludwig, 1971; Boerjan et al., 2003; Ralph et al., 2004). The contribution of various MLs to the lignins depends on plant species, cell type, plant tissue, and tissue age. Although the majority of the lignin polymer is derived from these three MLs, the lignification process has a high degree of metabolic plasticity (Boerjan et al., 2003; Ralph et al., 2004; Ralph, 2007; Vanholme et al., 2012). Of particular interest are ML conjugates in which the ester group can be acetate (Ac; Sarkanen et al., 1967; Ralph, 1996; Ralph and Lu, 1998; Del Río et al., 2007; del Río et al., 2008; Martínez et al., 2008), p-hydroxybenzoate (pBz; Venverloo, 1971; Monties and Lapierre, 1981; Landucci et al., 1992; Tomimura, 1992a, 1992b; Hibino et al., 1994; Sun et al., 1999; Kuroda et al., 2001; Lu et al., 2004, 2015; Morreel et al., 2004; Rencoret et al., 2013), p-coumarate (pCA; Monties and Lapierre, 1981; Ralph et al., 1994; Crestini and Argyropoulos, 1997; del Río et al., 2008, 2012a, 2012b; Withers et al., 2012; Rencoret et al., 2013; Petrik et al., 2014), or ferulate (FA; Grabber et al., 2008; Ralph, 2010; Wilkerson et al., 2014). In all cases, the MLs are acylated before polymerization as proven by the presence in the lignins of unique β-β coupling products that only arise when one or both of the MLs are acylated, preventing the formation of the typical resinols from internal trapping of the quinone methide intermediates by the γ-OH (Lu and Ralph, 2002, 2008; Del Río et al., 2007; Lu et al., 2015).The BAHD acyltransferase, FERULOYL-CoA MONOLIGNOL TRANSFERASE (FMT), was recently identified in Angelica sinensis and transformed into poplar (Populus alba × grandidentata), which naturally incorporates other acylated MLs, namely ML-pBz conjugates, into its lignin (Wilkerson et al., 2014). Plants that incorporate ML-FAs into their lignins have the potential to be particularly important economically, because their lignin backbones are permeated with readily cleavable ester bonds, facilitating lignin breakdown and removal under alkaline pretreatment conditions. Determining the extent to which ML-FAs are incorporated into the lignin polymer is, however, extremely difficult because of the diversity of products generated during the polymerization events, which is described in the supplemental information in Wilkerson et al., 2014.There is currently only one technique, derivatization followed by reductive cleavage (DFRC), that can release diagnostic chemical marker compounds from lignins containing ML-FAs (Lu and Ralph, 2014; Wilkerson et al., 2014). The DFRC method selectively cleaves β-ethers while leaving ester linkages intact. This technique was recently used to show that ML-FA conjugates are fully incorporated into the lignin of the FMT poplar (Wilkerson et al., 2014), but the extent of incorporation, the spatial distribution, the exact mechanism of delivery to the developing cell wall, and the efficiency of incorporation remain largely unknown.The biological role of pCA in lignin has been highly speculative. It is hypothesized that the pCA moieties may function as a radical sensitizer (Takahama and Oniki, 1996, 1997; Takahama et al., 1996; Ralph et al., 2004; Hatfield et al., 2008; Ralph, 2010). Peroxidases and/or laccases readily oxidize pCA to a radical but are poor oxidizers for SA. Free radicals of pCA readily undergo radical transfer to SA, which in turn, forms a homodimer or couples to the end of a growing polymer chain. Conjugating pCA to an ML, like SA, to form SA-pCA, the most prevalent ML-pCA conjugate in grasses, creates a compound with a built-in radical sensitizer that can participate in the polymerization event. The prevalence of these conjugates in potential biofuel crops and the impact that these ester-linked conjugates have on the lignin polymer during pretreatment and downstream fermentation processes have driven the search to find the genes and their enzymes responsible for acylating MLs in monocots (Withers et al., 2012; Marita et al., 2014; Petrik et al., 2014; Wilkerson et al., 2014).In rice (Oryza sativa), enzymes have been characterized that function specifically in the addition of pCA onto hemicelluloses (Bartley et al., 2013) or lignin (Withers et al., 2012; Petrik et al., 2014). The p-COUMAROYL-CoA MONOLIGNOL TRANSFERASE (PMT) was identified as one of many grass-specific BAHD acyltransferases produced by rice and found to coexpress with many ML biosynthetic enzymes (Withers et al., 2012). The enzyme preferentially forms a γ-ester through its specificity toward p-coumaroyl-CoA and an ML, and has kinetic efficiency with p-coumaryl alcohol > SA > CA. In most grasses, the PMT enzyme predominantly produces SA-pCA conjugates that are then incorporated into the lignin polymer (Petrik et al., 2014).To test the role of PMT during cell wall lignification, genetic manipulation of PMT genes has been performed in Brachypodium distachyon and maize (Zea mays), two model monocots. The suppression and overexpression of a BdPMT revealed the PMT to be involved only in the acylation of MLs before polymerization and not in the acylation of hemicelluloses (Petrik et al., 2014). RNA interference-mediated suppression of BdPMT resulted in decreased incorporation of ML-pCA conjugates into the cell wall without adversely affecting growth, height, or digestibility of the mature plants. Even deleterious mutations in the BdPMT gene, which resulted in a complete absence of pCA-acylating B. distachyon lignins, did not affect plant growth or development (Petrik et al., 2014). The arabinose-bound FA and pCA levels remained virtually unchanged in the PMT-misregulated plants, illustrating the specificity of the PMT enzyme for the p-coumaroyl-CoA substrate and its ML acylation. The PMT enzyme identified in maize (pCAT = ZmPMT) also displayed the highest catalytic efficiency with p-coumaroyl-CoA and SA as substrates (Marita et al., 2014). RNAi-mediated suppression of ZmPMT also resulted in decreased production of the ML conjugates. The effect on the lignin polymer when introducing PMT into plants that do not normally express a homologous enzyme is, however, unknown.pCAs, because they favor radical transfer over radical coupling, are overwhelmingly seen as free-phenolic pendant entities on the lignin polymer (Ralph et al., 1994; Ralph, 2010). As a result, the pCA itself can be completely quantified by simple saponification. The units to which the pCA is attached are, like their normal ML-derived counterparts, not fully releasable from lignin as identifiable monomers (during degradative reactions), but the pCA’s terminal location makes p-coumaroylated units more readily releasable and detectable than if they participated in lignification (as FAs do). Examining the effect of PMT and its resulting conjugates on lignification in plants that do not naturally produce such conjugates will contribute to our understanding of the role of PMT in lignification in general.In this study, we aimed to assess the ability of the model eudicot plants Arabidopsis (Arabidopsis thaliana) and poplar, neither of which naturally produces ML-pCA conjugates, to express a PMT gene and incorporate these novel conjugates into their cell wall lignins. We also investigated the effect that the introduction of PMT has on the native levels of ML-pBz conjugates in poplar lignin. Various analytical techniques were optimized and used to examine the cell walls of the transgenic plants for pCA conjugates and determine whether they were specifically incorporated into the lignin polymer in the cell wall.