Propagating uncertainty to estimates of above-ground biomass for Kenyan mangroves: a scaling procedure from tree to landscape level

Mangroves are globally important carbon stores and as such have potential for inclusion in future forest-based climate change mitigation strategies such as Reduced Emissions from Deforestation and Degradation (REDD+). Participation in REDD+ will require developing countries to produce robust estimates of forest above-ground biomass (AGB) accompanied by an appropriate measure of uncertainty. Final estimates of AGB should account for known sources of uncertainty (measurement and predictive) particularly when estimating AGB at large spatial scales. In this study, mixed-effects models were used to account for variability in the allometric relationship of Kenyan mangroves due to species and site effects. A generic biomass equation for Kenyan mangroves was produced in addition to a set of species-site specific equations. The generic equation has potential for broad application as it can be used to predict the AGB of new trees where there is no pre-existing knowledge of the specific species-site allometric relationship: the most commonly encountered scenario in practical biomass studies. Predictions of AGB using the mixed-effects model showed good correspondence with the original observed values of AGB although displayed a poorer fit at higher AGB values, suggesting caution in extrapolation. A strong relationship was found between the observed and predicted values of AGB using an independent validation dataset from the Zambezi Delta, Mozambique (R2 = 0.96, p = < 0.001). The simulation based approach to uncertainty propagation employed in the current study produced estimates of AGB at different spatial scales (tree – landscape level) accompanied by a realistic measure of the total uncertainty. Estimates of mangrove AGB in Kenya are presented at the plot, regional and landscape level accompanied by 95% prediction intervals. The 95% prediction intervals for landscape level estimates of total AGB stocks suggest that between 5.4 and 7.2 megatonnes of AGB is currently held in Kenyan mangrove forests

Mangroves in peril: unprecedented degradation rates of peri-urban mangroves in Kenya

Marine ecosystems are experiencing unprecedented degradation rates higher than any other ecosystem on the planet, which in some instances are up to 4 times those of rainforests. Mangrove ecosystems have especially been impacted by compounded anthropogenic pressures leading to significant cover reductions of between 35 and 50% (equivalent to 1–2% loss pa) for the last half century. The main objective of this study was to test the hypothesis that peri-urban mangroves suffering from compounded and intense pressures may be experiencing higher degradation rates than the global mean (and/or national mean for Kenya) using Mombasa mangroves (comprising Tudor and Mwache creeks) as a case study. Stratified sampling was used to sample along 22 and 10 belt transects in Mwache and Tudor respectively, set to capture stand heterogeneity in terms of species composition and structure in addition to perceived human pressure gradients using proximity to human habitations as a proxy. We acquired SPOT (HRV/ HRVIR/ HRS) images of April 1994, May 2000 and January 2009 and a vector mangrove map of 1992 at a scale of 1:50 000 for cover change and species composition analysis. Results from image classification of the 2009 image had 80.23% overall accuracy and Cohen's kappa of 0.77, thus proving satisfactory for use in this context. Structural data indicate that complexity index (CI) which captures stand structural development was higher in Mwache at 1.80 compared to Tudor at 1.71. From cover change data, Tudor lost 86.9% of the forest between 1992 and 2009, compared to Mwache at 45.4%, representing very high hitherto undocumented degradation rates of 5.1 and 2.7% pa, respectively. These unprecedentedly high degradation rates, which far exceed not only the national mean (for Kenya of 0.7% pa) but the global mean as well, strongly suggest that these mangroves are highly threatened due to compounded pressures. Strengthening of governance regimes through enforcement and compliance to halt illegal wood extraction, improvement of land-use practices upstream to reduce soil erosion, restoration in areas where natural regeneration has been impaired, provision of alternative energy sources/building materials and a complete moratorium on wood extraction especially in Tudor Creek to allow recovery are some of the suggested management interventions

Novel frontier in wildlife monitoring : Identification of small rodent species from fecal pellets using near-infrared reflectance spectroscopy (NIRS)

Small rodents are prevalent and functionally important across the world's biomes, making their monitoring salient for ecosystem management, conservation, forestry, and agriculture. There is a growing need for cost-effective and noninvasive methods for large-scale, intensive sampling. Fecal pellet counts readily provide relative abundance indices, and given suitable analytical methods, feces could also allow for the determination of multiple ecological and physiological variables, including community composition. In this context, we developed calibration models for rodent taxonomic determination using fecal near-infrared reflectance spectroscopy (fNIRS). Our results demonstrate fNIRS as an accurate and robust method for predicting genus and species identity of five coexisting subarctic microtine rodent species. We show that sample exposure to weathering increases the method's accuracy, indicating its suitability for samples collected from the field. Diet was not a major determinant of species prediction accuracy in our samples, as diet exhibited large variation and overlap between species. fNIRS could also be applied across regions, as calibration models including samples from two regions provided a good prediction accuracy for both regions. We show fNIRS as a fast and cost-efficient high-throughput method for rodent taxonomic determination, with the potential for cross-regional calibrations and the use on field-collected samples. Importantly, appeal lies in the versatility of fNIRS. In addition to rodent population censuses, fNIRS can provide information on demography, fecal nutrients, stress hormones, and even disease. Given the development of such calibration models, fNIRS analytics could complement novel genetic methods and greatly support ecosystem- and interaction-based approaches to monitoring.Peer reviewe

Novel frontier in wildlife monitoring: Identification of small rodent species from fecal pellets using near-infrared reflectance spectroscopy (NIRS)

Small rodents are prevalent and functionally important across the world's biomes, making their monitoring salient for ecosystem management, conservation, forestry, and agriculture. There is a growing need for cost-effective and noninvasive methods for large-scale, intensive sampling. Fecal pellet counts readily provide relative abundance indices, and given suitable analytical methods, feces could also allow for the determination of multiple ecological and physiological variables, including community composition. In this context, we developed calibration models for rodent taxonomic determination using fecal near-infrared reflectance spectroscopy (fNIRS). Our results demonstrate fNIRS as an accurate and robust method for predicting genus and species identity of five coexisting subarctic microtine rodent species. We show that sample exposure to weathering increases the method's accuracy, indicating its suitability for samples collected from the field. Diet was not a major determinant of species prediction accuracy in our samples, as diet exhibited large variation and overlap between species. fNIRS could also be applied across regions, as calibration models including samples from two regions provided a good prediction accuracy for both regions. We show fNIRS as a fast and cost-efficient high-throughput method for rodent taxonomic determination, with the potential for cross-regional calibrations and the use on field-collected samples. Importantly, appeal lies in the versatility of fNIRS. In addition to rodent population censuses, fNIRS can provide information on demography, fecal nutrients, stress hormones, and even disease. Given the development of such calibration models, fNIRS analytics could complement novel genetic methods and greatly support ecosystem- and interaction-based approaches to monitoring

Diquat Derivatives: Highly Active, Two-Dimensional Nonlinear Optical Chromophores with Potential Redox Switchability

In this article, we present a detailed study of structure−activity relationships in diquaternized 2,2′-bipyridyl (diquat) derivatives. Sixteen new chromophores have been synthesized, with variations in the amino electron donor substituents, π-conjugated bridge, and alkyl diquaternizing unit. Our aim is to combine very large, two-dimensional (2D) quadratic nonlinear optical (NLO) responses with reversible redox chemistry. The chromophores have been characterized as their PF_6^− salts by using various techniques including electronic absorption spectroscopy and cyclic voltammetry. Their visible absorption spectra are dominated by intense π → π^* intramolecular charge-transfer (ICT) bands, and all show two reversible diquat-based reductions. First hyperpolarizabilities β have been measured by using hyper-Rayleigh scattering with an 800 nm laser, and Stark spectroscopy of the ICT bands affords estimated static first hyperpolarizabilities β_0. The directly and indirectly derived β values are large and increase with the extent of π-conjugation and electron donor strength. Extending the quaternizing alkyl linkage always increases the ICT energy and decreases the E_(1/2) values for diquat reduction, but a compensating increase in the ICT intensity prevents significant decreases in Stark-based β_0 responses. Nine single-crystal X-ray structures have also been obtained. Time-dependent density functional theory clarifies the molecular electronic/optical properties, and finite field calculations agree with polarized HRS data in that the NLO responses of the disubstituted species are dominated by ‘off-diagonal’ β_(zyy) components. The most significant findings of these studies are: (i) β_0 values as much as 6 times that of the chromophore in the technologically important material (E)-4′-(dimethylamino)-N-methyl-4-stilbazolium tosylate; (ii) reversible electrochemistry that offers potential for redox-switching of optical properties over multiple states; (iii) strongly 2D NLO responses that may be exploited for novel practical applications; (iv) a new polar material, suitable for bulk NLO behavior

Selection of Saccharomyces cerevisiae strains for efficient very high gravity bio-ethanol fermentation processes

An optimized very high gravity (VHG) glucose medium supplemented with low cost nutrient sources was used to evaluate bio-ethanol production by 11 Saccharomyces cerevisiae strains. The industrial strains PE-2 and CA1185 exhibited the best overall fermentation performance, producing an ethanol titre of 19.2% (v/v) corresponding to a batch productivity of 2.5 g l-1 h-1, while the best laboratory strain (CEN.PK 113-7D) produced 17.5% (v/v) ethanol with a productivity of 1.7 g l-1 h-1. The results presented here emphasize the biodiversity found within S. cerevisiae species and that naturally adapted strains, such as PE-2 and CA1185, are likely to play a key role in facilitating the transition from laboratory technological breakthroughs to industrialscale bio-ethanol fermentations.Fundação para a Ciência e a Tecnologia (FCT) - PTDC/BIO/66151/2006, SFRH/ BD/64776/2009, SFRH/BPD/44328/ 200

TYPLEX® Chelate, a novel feed additive, inhibits Campylobacter jejuni biofilm formation and cecal colonization in broiler chickens

Reducing Campylobacter spp. carriage in poultry is challenging, but essential to control this major cause of human bacterial gastroenteritis worldwide. Although much is known about the mechanisms and route of Campylobacter spp. colonization in poultry the literature is scarce on antibiotic-free solutions to combat Campylobacter spp. colonization in poultry. In vitro and in vivo studies were conducted to investigate the role of TYPLEX® Chelate, a novel feed additive, in inhibiting Campylobacter jejuni (C. jejuni) biofilm formation and reducing C. jejuni and Escherichia coli (E. coli) colonization in broiler chickens at market age. In an in vitro study, the inhibitory effect on C. jejuni biofilm formation using a plastic bead assay was investigated. The results demonstrated that TYPLEX® Chelate significantly reduces biofilm formation. For in vivo study, 800 broilers (one-day old) were randomly allocated to 4 dietary treatments in a randomised block design, each having 10 replicate pens with 20 birds per pen. At day 21, all birds were challenged with C. jejuni via seeded litter. At day 42, caecal samples were collected and tested for volatile fatty acid (VFA) concentrations, C. jejuni and E. coli counts. The results showed that TYPLEX® Chelate reduced the carriage of C. jejuni and E. coli in poultry by 2 and 1 log₁₀ per gram caecal sample, respectively, and increased caecal VFA concentrations. These findings support TYPLEX® Chelate as a novel non-antibiotic feed additive that may help produce poultry with a lower public health risk of Campylobacteriosis

A Novel Strategy to Construct Yeast Saccharomyces cerevisiae Strains for Very High Gravity Fermentation

Very high gravity (VHG) fermentation is aimed to considerably increase both the fermentation rate and the ethanol concentration, thereby reducing capital costs and the risk of bacterial contamination. This process results in critical issues, such as adverse stress factors (ie., osmotic pressure and ethanol inhibition) and high concentrations of metabolic byproducts which are difficult to overcome by a single breeding method. In the present paper, a novel strategy that combines metabolic engineering and genome shuffling to circumvent these limitations and improve the bioethanol production performance of Saccharomyces cerevisiae strains under VHG conditions was developed. First, in strain Z5, which performed better than other widely used industrial strains, the gene GPD2 encoding glycerol 3-phosphate dehydrogenase was deleted, resulting in a mutant (Z5ΔGPD2) with a lower glycerol yield and poor ethanol productivity. Second, strain Z5ΔGPD2 was subjected to three rounds of genome shuffling to improve its VHG fermentation performance, and the best performing strain SZ3-1 was obtained. Results showed that strain SZ3-1 not only produced less glycerol, but also increased the ethanol yield by up to 8% compared with the parent strain Z5. Further analysis suggested that the improved ethanol yield in strain SZ3-1 was mainly contributed by the enhanced ethanol tolerance of the strain. The differences in ethanol tolerance between strains Z5 and SZ3-1 were closely associated with the cell membrane fatty acid compositions and intracellular trehalose concentrations. Finally, genome rearrangements in the optimized strain were confirmed by karyotype analysis. Hence, a combination of genome shuffling and metabolic engineering is an efficient approach for the rapid improvement of yeast strains for desirable industrial phenotypes

Analysis of Clostridium beijerinckii NCIMB 8052&apos;s transcriptional response to ferulic acid and its application to enhance the strain tolerance

Background: Plant-based cellulose presents the best source of renewable sugars for biofuel production. However, the lignin associated with plant cellulose presents a hurdle as hydrolysis of this component leads to the production of inhibitory compounds, such as ferulic acid. Results: The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production, and transcriptional responses of Clostridium beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30% and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified showing significant change at each status, including ATP-binding cassette (ABC) transporters, two component system, and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up-regulated. Among these, expression of the groESL operon was induced by more than fourfold and was consequently selected to improve C. beijerinckii tolerance to ferulic acid. Real-time quantitative PCR (RT-qPCR) analysis confirmed that C. beijerinckii harboring the plasmid, pSAAT-ptb_Gro, had a two-to fivefold increased groESL operon expression during growth of these cultures. Moreover, this strain was more tolerant to ferulic acid as the growth of this recombinant strain and its bioconversion of glucose into solvents were both improved. Conclusions: Using transcriptomics, we identified numerous genes that are differentially expressed when C. beijerinckii cultures were exposed to ferulic acid for varying amounts of time. The operon expressing groESL was consistently up-regulated, suggesting that this gene cluster may contribute to strain tolerance. This was confirmed as recombinant cultures showed both an enhanced growth and solvent yield in the presence of 0.5 g/L ferulic acidopen00

Pax6 Represses Androgen Receptor-Mediated Transactivation by Inhibiting Recruitment of the Coactivator SPBP

The androgen receptor (AR) has a central role in development and maintenance of the male reproductive system and in the etiology of prostate cancer. The transcription factor Pax6 has recently been reported to act as a repressor of AR and to be hypermethylated in prostate cancer cells. SPBP is a transcriptional regulator that previously has been shown to enhance the activity of Pax6. In this study we have identified SPBP to act as a transcriptional coactivator of AR. We also show that Pax6 inhibits SPBP-mediated enhancement of AR activity on the AR target gene probasin promoter, a repression that was partly reversed by increased expression of SPBP. Enhanced expression of Pax6 reduced the amount of SPBP associated with the probasin promoter when assayed by ChIP in HeLa cells. We mapped the interaction between both AR and SPBP, and AR and Pax6 to the DNA-binding domains of the involved proteins. Further binding studies revealed that Pax6 and SPBP compete for binding to AR. These results suggest that Pax6 represses AR activity by displacing and/or inhibiting recruitment of coactivators to AR target promoters. Understanding the mechanism for inhibition of AR coactivators can give rise to molecular targeted drugs for treatment of prostate cancer