Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.     

Neuroprotective and therapeutic effect of Cordyceps militaris on ischemia-induced neuronal death and cognitive impairments

Cordyceps militaris is a type of fungus consumed by people all over the world and renowned for their nutritional benefits and herbal formulas to promote health and longevity. In the present study investigation was carried out to explore the therapeutic properties and neuroprotective effect of the C. militaris on ischemic brain neuronal injury, impairment of memory and learning in experimental rats induced by a global cerebral ischemia-reperfusion injury in WISTAR rats. Vascular Dementia with transient global brain injuries induced by a four-vessel occlusion (4-VO) in WISTAR rats. Further, donepezil (5 mg/kg) and C. militaris was (100 and 300 mg/kg, p.o.) were orally administered for 7 days in 4-VO WISTAR rats. C. militaris has the ability to improve memory impairments due to global cerebral ischemia and scopolamine-induced memory deterioration. Our present findings suggest that C. militaris may be a potential candidate for the neuroprotection of hippocampus and the recovery of various vascular dementia or neuroinflammatory disorders.     

Antidiabetic potential of Caralluma europaea against alloxan-induced diabetes in mice

Medicinal plants play an important role in the management of diabetes mellitus especially in developing countries where resources are lacking. Herbal of natural origin, unlike the synthetic compounds, are more effective, safer and have less side effects. For continuing research on biological properties of Moroccan medicinal plants, the present work was undertaken to evaluate the potential and mechanism of the antidiabetic activity of the Caralluma europaea methanolic extract in alloxan-induced diabetic mice. A high-performance liquid chromatography technique (HPLC) was used to identify and quantify the major phenolic compounds in the methanolic extract. The in vitro antioxidant property was evaluated using 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) scavenging method, reducing power and ß-carotene-linoleic acid assays. The acute toxicity of the extract was evaluated by giving it orally to mice at single doses of 200, 500, 1000, 2000 mg/kg body weight. The antidiabetic effect was conducted on Swiss albino mice. Diabetes was induced with single intraperitonial injection of alloxan monohydrate (200 mg/kg body weight) and animals were treated with methanol extract at a dose of 250 mg/kg and 500 mg/kg body weight. The blood glucose levels were measured and histopathological analysis of pancreas was performed to evaluate alloxan-induced tissue injuries. The main phenols identified and quantified in the extract were ferulic acid, quercetine, 3,4 dihydroxybenzoic acid, rutin, epigallocatechin, and catechin. Ferulic acid was found to be the main phenolic compound ant its proportion was up to 52% of total phenolic compounds, followed by quercetin (36%). The result showed that methanol extract exhibited an antioxidant effect. Acute toxicity studies revealed that C. europaea extract was safe up 2000 mg/kg body weight and approximate LD₅₀ is more than 2000 mg/kg. Moreover, the methanol extract prevented the diabetogenic effect of alloxan and decreased significantly the blood glucose level (P < 0.001) in treated mice. Morphometric study of pancreas revealed that C. europaea extract protected significantly the islets of Langerhans against alloxan-induced tissue alterations.     

Joint effects of climate,tree size,and year on annual tree growth derived from tree-ring records of ten globally distributed forests

Tree rings provide an invaluable long-term record for understanding how climate and other drivers shape tree growth and forest productivity. However, conventional tree-ring analysis methods were not designed to simultaneously test effects of climate, tree size, and other drivers on individual growth. This has limited the potential to test ecologically relevant hypotheses on tree growth sensitivity to environmental drivers and their interactions with tree size. Here, we develop and apply a new method to simultaneously model nonlinear effects of primary climate drivers, reconstructed tree diameter at breast height (DBH), and calendar year in generalized least squares models that account for the temporal autocorrelation inherent to each individual tree's growth. We analyze data from 3811 trees representing 40 species at 10 globally distributed sites, showing that precipitation, temperature, DBH, and calendar year have additively, and often interactively, influenced annual growth over the past 120 years. Growth responses were predominantly positive to precipitation (usually over ≥3-month seasonal windows) and negative to temperature (usually maximum temperature, over ≤3-month seasonal windows), with concave-down responses in 63% of relationships. Climate sensitivity commonly varied with DBH (45% of cases tested), with larger trees usually more sensitive. Trends in ring width at small DBH were linked to the light environment under which trees established, but basal area or biomass increments consistently reached maxima at intermediate DBH. Accounting for climate and DBH, growth rate declined over time for 92% of species in secondary or disturbed stands, whereas growth trends were mixed in older forests. These trends were largely attributable to stand dynamics as cohorts and stands age, which remain challenging to disentangle from global change drivers. By providing a parsimonious approach for characterizing multiple interacting drivers of tree growth, our method reveals a more complete picture of the factors influencing growth than has previously been possible.     

Implementing an appropriate metric for the assessment of greenhouse gas emissions from livestock production: A national case study

Livestock farming is of major economic relevance but also severely contributes to environmental impacts, especially greenhouse gas (GHG) emissions such as methane (CH₄; particularly from ruminant production) and nitrous oxide (N₂O; mainly from manure management and soil cultivated for feed production). In this study, we analyse the impact of GHG emissions from Austrian livestock production, using two metrics: a) the commonly used global warming potential (GWP) over 100 years (GWP₁₀₀ in CO₂-equivalents, CO₂-e), and b) the recently introduced metric GWP*, which describes additional warming as a function of the timeline of short-lived GHG emissions (unit CO₂ warming equivalents, CO₂-we). We first compiled the sectoral (i.e. only direct emissions without upstream processes) GWP₁₀₀ for different livestock categories with a focus on dairy cattle, beef cattle and pigs in Austria between 1990 and 2019. We also estimated product-related (i.e. per kg carcass weight or per litre of milk) GWP₁₀₀ values, including upstream processes. We then calculated the corresponding GWP* metrics, both sectoral and product-related, and compared them with the GWP₁₀₀ values. Decreasing livestock numbers and improved production efficiency were found to result in strong sectoral emission reductions from dairy production (–32 % of GWP₁₀₀ from 1990 to 2019) and from pigs (–32 % CO₂-e). This contrasts with low reductions from other livestock categories and even increases for cattle other than dairy cows (+3 % CO₂-e), mainly due to rising suckler cow numbers. Allocated results per kg milk and kg body mass show quite similar results. Using the GWP* metric, the climate impacts of Austrian livestock production are less severe. When assuming constant management and emission intensity over a period of at least 20 years, the CO₂-we (GWP*) is almost 50 % less than CO₂-e (GWP₁₀₀) per kg Austrian raw milk due to the different impacts of the short-lived CH₄. A similar trend applies to an average cattle carcass (-40 % warming impact). The emission reductions of the shrinking Austrian livestock population represent an important contribution to a climate-neutral agriculture: The CH₄ reductions of livestock production during the past 20 years reduce the current total Austrian CO₂-we by 16 %. Continuous CH₄ reduction, as we show it here for Austrian livestock, is an effective option to tackle the climate crisis in the short term. It shall be stressed that a relatively low GWP* should not be interpreted as a concession for further CH₄ emissions but as an actual reduction of (additional) warming.     

Animal board invited review: Genomic-based improvement of cattle in response to climate change

Climate change brings challenges to cattle production, such as the need to adapt to new climates and pressure to reduce greenhouse emissions (GHG). In general, the improvement of traits in current breeding goals is favourably correlated with the reduction of GHG. Current breeding goals and tools for increasing cattle production efficiency have reduced GHG. The same amount of production can be achieved by a much smaller number of animals. Genomic selection (GS) may offer a cost-effective way of using an efficient breeding approach, even in low- and middle-income countries. As climate change increases the intensity of heatwaves, adaptation to heat stress leads to lower efficiency of production and, thus, is unfavourable to the goal of reducing GHG. Furthermore, there is evidence that heat stress during cow pregnancy can have many generation-long lowering effects on milk production. Both adaptation and reduction of GHG are among the difficult-to-measure traits for which GS is more efficient and suitable than the traditional non-genomic breeding evaluation approach. Nevertheless, the commonly used within-breed selection may be insufficient to meet the new challenges; thus, cross-breeding based on selecting highly efficient and highly adaptive breeds may be needed. Genomic introgression offers an efficient approach for cross-breeding that is expected to provide high genetic progress with a low rate of inbreeding. However, well-adapted breeds may have a small number of animals, which is a source of concern from a genetic biodiversity point of view. Furthermore, low animal numbers also limit the efficiency of genomic introgression. Sustainable cattle production in countries that have already intensified production is likely to emphasise better health, reproduction, feed efficiency, heat stress and other adaptation traits instead of higher production. This may require the application of innovative technologies for phenotyping and further use of new big data techniques to extract information for breeding.     

Preparation and physicochemical properties of a novel hydroxyapatite/chitosan–silk fibroin composite

A novel hydroxyapatite/chitosan–silk fibroin (HA/CTS–SF) composite was prepared for bone repair and replacement by a coprecipitation method. It was revealed that the inorganic phase in the composite was carbonate-substituted HA with low crystallinity. The HA crystallites were found to be needle-like in shape with a typical size of 20–50 nm in length and around 10 nm in width. The composite exhibited a higher compressive strength than the precipitated HA without any organic source involved, which was closely related to the perfect incorporation of chitosan and SF macromolecules into the composite. The chemical interactions occurring between the mineral phase and the organic matrix were thought to improve the interfacial bonding and thus resulted in the enhanced mechanical property of the composite.     

Signal-3L: A 3-layer approach for predicting signal peptides

Functioning as an "address tag" that directs nascent proteins to their proper cellular and extracellular locations, signal peptides have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. To effectively and timely use such a tool, however, the first important thing is to develop an automated method for rapidly and accurately identifying the signal peptide for a given nascent protein. With the avalanche of new protein sequences generated in the post-genomic era, the challenge has become even more urgent and critical. In this paper, we have developed a novel method for predicting signal peptide sequences and their cleavage sites in human, plant, animal, eukaryotic, Gram-positive, and Gram-negative protein sequences, respectively. The new predictor is called Signal-3L that consists of three prediction engines working, respectively, for the following three progressively deepening layers: (1) identifying a query protein as secretory or non-secretory by an ensemble classifier formed by fusing many individual OET-KNN (optimized evidence-theoretic K nearest neighbor) classifiers operated in various dimensions of PseAA (pseudo amino acid) composition spaces; (2) selecting a set of candidates for the possible signal peptide cleavage sites of a query secretory protein by a subsite-coupled discrimination algorithm; (3) determining the final cleavage site by fusing the global sequence alignment outcome for each of the aforementioned candidates through a voting system. Signal-3L is featured by high success prediction rates with short computational time, and hence is particularly useful for the analysis of large-scale datasets. Signal-3L is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-3L/ or http://202.120.37.186/bioinf/Signal-3L, where, to further support the demand of the related areas, the signal peptides identified by Signal-3L for all the protein entries in Swiss-Prot databank that do not have signal peptide annotations or are annotated with uncertain terms but are classified by Signal-3L as secretory proteins are provided in a downloadable file. The large-scale file is prepared with Microsoft Excel and named "Tab-Signal-3L.xls", and will be updated once a year to include new protein entries and reflect the continuous development of Signal-3L.     

A versatile equation to describe reversible enzyme inhibition and activation kinetics: Modeling β-galactosidase and butyrylcholinesterase

Current treatments for Alzheimer's disease involve inhibiting cholinesterases. Conversely, cholinesterase stimulation may be deleterious. Homocysteine is a known risk factor for Alzheimer's and vascular diseases and its active metabolite, homocysteine thiolactone, stimulates butyrylcholinesterase. Considering the opposing effects on butyrylcholinesterase of homocysteine thiolactone and cholinesterase inhibitors, understanding how these molecules alter this enzyme may provide new insights in the management of dementia. Butyrylcholinesterase does not strictly adhere to Michaelis–Menten parameters since, at higher substrate concentrations, enzyme activation occurs. The substrate activation equation for butyrylcholinesterase does not describe the effects of inhibitors or non-substrate activators. To address this, global data fitting was used to generate a flexible equation based on Michaelis–Menten principles. This methodology was first tested to model complexities encountered in inhibition by imidazole of β-galactosidase, an enzyme that obeys Michaelis–Menten kinetics. The resulting equation was sufficiently flexible to permit expansion for modeling activation or inhibition of butyrylcholinesterase, while accounting for substrate activation of this enzyme. This versatile equation suggests that both the inhibitor and non-substrate activator examined here have little effect on the substrate-activated form of butyrylcholinesterase. Given that butyrylcholinesterase inhibition can antagonize stimulation of this enzyme by homocysteine thiolactone, cholinesterase inhibition may have a role in treating Alzheimer and vascular diseases related to hyperhomocysteinemia.     

Joint composite-rotation adiabatic-sweep isotope filtration

Joint composite-rotation adiabatic-sweep isotope filters are derived by combining the composite-rotation [Stuart AC et al. (1999) J Am Chem Soc 121: 5346–5347] and adiabatic-sweep [Zwahlen C et al. (1997) J Am Chem Soc 119:6711–6721; Kupče E, Freeman R (1997) J Magn Reson 127:36–48] approaches. The joint isotope filters have improved broadband filtration performance, even for extreme values of the one-bond ¹H–¹³C scalar coupling constants in proteins and RNA molecules. An average Hamiltonian analysis is used to describe evolution of the heteronuclear scalar coupling interaction during the adiabatic sweeps within the isotope filter sequences. The new isotope filter elements permit improved selective detection of NMR resonance signals originating from ¹H spins attached to an unlabeled natural abundance component of a complex in which the other components are labeled with ¹³C and ¹⁵N isotopes.