Analysis of the extreme diversity of salivary alpha-amylase isoforms generated by physiological proteolysis using liquid chromatography-tandem mass spectrometry

Saliva is a crucial biofluid for oral health and is also of increasing importance as a non-invasive source of disease biomarkers. Salivary alpha-amylase is an abundant protein in saliva, and changes in amylase expression have been previously associated with a variety of diseases and conditions. Salivary alpha-amylase is subject to a high diversity of post-translational modifications, including physiological proteolysis in the oral cavity. Here we developed methodology for rapid sample preparation and non-targeted LC-ESI-MS/MS analysis of saliva from healthy subjects and observed an extreme diversity of alpha-amylase proteolytic isoforms. Our results emphasize the importance of consideration of post-translational events such as proteolysis in proteomic studies, biomarker discovery and validation, particularly in saliva. (C) 2012 Elsevier B.V. All rights reserved.

Wood density : a tool to find complementary species for the design of mixed species plantations

The successful establishment and growth of mixed-species forest plantations requires that complementary or facilitatory species be identified. This can be difficult in many tropical areas because the growth characteristics of endemic species are often unknown, particularly when grown at potentially higher densities in plantations than in natural forests. Here, we investigate whether wood density is a useful and readily accessible trait for choosing complementary species for mixed species plantations. Wood density represents the carbon investment per unit volume of stem with a trade-off generally found between fast (low wood density) and slow (high wood density) growing species. To do this, we use data collected from 18 highly diverse mixed species plantations (4–23 mostly native species) aged from 6 to 11 years at the time of data collection located on Leyte Island, Philippines. We found significant negative correlations between wood densities and the height of the most abundant species, as well as with measures of overall stand growth and tree diameter size distribution. Not only do species with denser woods have slower growth rates, but also mixed-species plantations with higher average wood density and higher stem density were also less productive, at least in these young plantations. Similarly, stands with a high diversity in wood densities were less productive. There is growing interest in making greater use of native multi-species mixtures in smallholder and community planting programs in the tropics, and our results show databases of wood density values may help improve their design. In the early development stages of plantations, canopy closure and rapid height growth are usually key silvicultural targets, and wood density values can predict the rapid height development of species. If plantations are being grown for the livelihood of small landholders then the best target is to choose some species with different wood densities. This allows an early harvest of low-wood density species for early income, and will also reduce competition for slower growing trees with higher wood densities for later income generation.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Not drowning, (hand)waving? Molecular phylogenetics, biogeography and evolutionary tempo of the ‘Gondwanan’ midge Stictocladius Edwards (Diptera: Chironomidae)

Many insect clades, especially within the Diptera (true flies), have been considered classically ‘Gondwanan’, with an inference that distributions derive from vicariance of the southern continents. Assessing the role that vicariance has played in the evolution of austral taxa requires testing the location and tempo of diversification and speciation against the well-established predictions of fragmentation of the ancient super-continent. Several early (anecdotal) hypotheses that current austral distributions originate from the breakup of Gondwana derive from studies of taxa within the family Chironomidae (non-biting midges). With the advent of molecular phylogenetics and biogeographic analytical software, these studies have been revisited and expanded to test such conclusions better. Here we studied the midge genus Stictocladius Edwards, from the subfamily Orthocladiinae, which contains austral-distributed clades that match vicariance-based expectations. We resolve several issues of systematic relationships among morphological species and reveal cryptic diversity within many taxa. Time-calibrated phylogenetic relationships among taxa accorded partially with the predicted tempo from geology. For these apparently vagile insects, vicariance-dated patterns persist for South America and Australia. However, as often found, divergence time estimates for New Zealand at c. 50 mya post-date separation of Zealandia from Antarctica and the remainder of Gondwana, but predate the proposed Oligocene ‘drowning’ of these islands. We detail other such ‘anomalous’ dates and suggest a single common explanation rather than stochastic processes. This could involve synchronous establishment following recovery from ‘drowning’ and/or deleteriously warming associated with the mid-Eocene climatic optimum (hence ‘waving’, which refers to cycles of drowning events) plus new availability of topography providing of cool running waters, or all these factors in combination. Alternatively a vicariance explanation remains available, given the uncertain duration of connectivity of Zealandia to Australia–Antarctic–South America via the Lord Howe and Norfolk ridges into the Eocene.

A continent-wide study reveals clear relationships between regional abiotic conditions and post-dispersal seed predation

Aim Large-scale patterns linking energy availability, biological productivity and diversity form a central focus of ecology. Despite evidence that the activity and abundance of animals may be limited by climatic variables associated with regional biological productivity (e.g. mean annual precipitation and annual actual evapotranspiration), it is unclear whether plant–granivore interactions are themselves influenced by these climatic factors across broad spatial extents. We evaluated whether climatic conditions that are known to alter the abundance and activity of granivorous animals also affect rates of seed removal. Location Eleven sites across temperate North America. Methods We used a common protocol to assess the removal of the same seed species (Avena sativa) over a 2-day period. Model selection via the Akaike information criterion was used to determine a set of candidate binomial generalized linear mixed models that evaluated the relationship between local climatic data and post-dispersal seed predation. Results Annual actual evapotranspiration was the single best predictor of the proportion of seeds removed. Annual actual evapotranspiration and mean annual precipitation were both positively related to mean seed removal and were included in four and three of the top five models, respectively. Annual temperature range was also positively related to seed removal and was an explanatory variable in three of the top four models. Main conclusions Our work provides the first evidence that energy and precipitation, which are known to affect consumer abundance and activity, also translate to strong, predictable patterns of seed predation across a continent. More generally, these findings suggest that future changes in temperature and precipitation could have widespread consequences for plant species composition in grasslands, through impacts on plant recruitment.

Impact of gender-focused human resource management on performance : the mediating effects of gender diversity

Gender-focused human resource policies and practices signal an organization’s perspective on gender diversity. The signal produces perceptions that the organization values gender diversity leading to a gender-diverse workforce. In turn, a gender-diverse workforce provides a firm with a competitive advantage which should result in higher performance. This paper tests the mediating effects of gender diversity (at non-management and management levels) in the relationship between gender-focused policies and practices and performance. The findings indicate that non-management gender diversity partially mediates the relationship between gender-focused policies and practices and productivity, and management gender diversity partially mediates the relationship between gender-focused policies and practices and perceived market performance. The results have several theoretical, research and practical implications.

Development and application of Palygorskite porous ceramsite in a biological aerated filter (BAF)

Novel filter Palygorskite porous ceramsite (PC) was prepared using Palygorskite clay, poreforming material sawdust, and sodium silicate with a mass ratio of 10:2:1 after sintering at 700°C for 180 min. PC was characterized with X-ray diffraction, X-ray fluorescence, scanning electron microscopy, elemental, and porosimetry. PC had a total porosity of 67% and specific surface area of 61 m2/g. In order to assess the usefulness of PC as a medium for biological aerated filters (BAF), PC and (commercially available ceramsite) CAC were used to treat wastewater city in two laboratory-scale upflow BAFs. The results showed that the reactor containing PC was more efficient than the reactor containing CAC in terms of total organic carbon (TOC), ammonia nitrogen (NH3-N), and the removal of total nitrogen (TN) and phosphorus (P). This system was found to be more efficient at water temperatures ranging from 20 to 26°C, an air–water (A/W) ratio of 3:1, dissolved oxygen concentration >4.00 mg/L, and hydraulic retention time (HRT) ranging from 0.5 to 7 h. The interconnected porous structure produced for PC was suitable for microbial growth, and primarily protozoan and metazoan organisms were found in the biofilm. Microorganism growth also showed that, under the same submerged culture conditions, the biological mass in PC was significantly higher than in CAC (34.1 and 2.2 mg TN/g, respectively). In this way, PC media can be considered suitable for the use as a medium in novel biological aerated filters for the simultaneous removal of nitrogen and phosphorus.

Recent surveys of bats (Mammalia: Chiroptera) from China. I. Rhinolophidae and Hipposideridae

We conducted surveys of bats in China between 1999 and 2007, resulting in the identification of at least 62 species. In this paper we present data on 19 species, comprising 12 species from the family Rhinolophidae and seven from the Hipposideridae. Rhinolophids captured were Rhinolophus affinis, R. ferrumequinum, R. lepidus, R. luctus, R. macrotis, R. siamensis, R. marshalli, R. rex, R. pearsonii, R. pusillus, R. sinicus and R. stheno. Because of extensive morphological similarities we question the species distinctiveness of R. osgoodi (may be conspecific with R. lepidus), R. paradoxolophus (which may best be treated as a subspecies of R. rex), R. huananus (probably synonymous with R. siamensis), and we are skeptical as to whether R. sinicus is distinct from R. thomasi. Hipposiderids captured were Hipposideros armiger, H. cineraceus, H. larvatus, H. pomona, H. pratti, Aselliscus stoliczkanus and Coelops frithii. Of these species, two rhinolophids (Rhinolophus marshalli and R. stheno) and one hipposiderid (Hipposideros cineraceus) represent new species records for China. We present data on species' ranges, morphology and echolocation call frequencies, as well as some notes on ecology and conservation status. China hosts a considerable diversity of rhinolophid and hipposiderid bats, yet threats to their habitats and populations are substantial.

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity - past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control. © 2014 Nguyen et al.

Conservation genetics of the water mouse, Xeromys myoides Thomas, 1889

The water mouse, Xeromys myoides, is currently recognised as a vulnerable species in Australia, inhabiting a small number of distinct and isolated coastal regions of Queensland and the Northern Territory. An examination of the evolutionary history and contemporary influences shaping the genetic structure of this species is required to make informed conservation management decisions. Here, we report the first analysis undertaken on the phylogeography and population genetics of the water mouse across its mainland Australian distribution. Genetic diversity was assessed at two mitochondrial DNA (Cytochrome b, 1000 bp; D-loop, 400 bp) and eight microsatellite DNA loci. Very low genetic diversity was found, indicating that water mice underwent a recent expansion throughout their Australian range and constitute a single evolutionarily significant unit. Microsatellite analyses revealed that the highest genetic diversity was found in the Mackay region of central Queensland; population substructure was also identified, suggesting that local populations may be isolated in this region. Conversely, genetic diversity in the Coomera region of south-east Queensland was very low and the population in this region has experienced a significant genetic bottleneck. These results have significant implications for future management, particularly in terms of augmenting populations through translocations or reintroducing water mice in areas where they have gone extinct.