Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of Protected Area Governance in the Conservation of Mt. Marsabit Forest Ecosystem, Kenya

ABSTRACT Protected area systems (PAs) have the potential to conserve natural resources and provide social and economic benefits to local communities. Establishing and maintaining good governance and associated mechanisms is necessary for adaptive management of PAs. To test this hypothesis, we analyzed the relationships between various stakeholders and the effectiveness of PA governance of Mt. Marsabit forest ecosystem in Kenya. We used social network analysis (SNA) to assess the interactions between actors, and factor analysis to analyze the effectiveness of governance criteria. Governance of Mt. Marsabit forest ecosystem was complex with a multiplicity of stakeholders from diverse interests. Governance was moderately effective (61%) with positive indicators including the regulatory framework, delineation of areas under conservation, and reduction in poaching. The low level of interactions and associations among stakeholders suggest a weakness in the networks that may negatively affect the flow of information and other resources. This weakness was attributed to a lack of institutionalization of the links leading to poor coordination of processes. Local communities were inadequately represented in the governance of this PA despite being important actors. Our study finds that local ownership and strong linkages between actors are important ingredients for effective governance of PAs.
Soil amendment interacts with invasive grass and drought to uniquely influence aboveground versus belowground biomass in aridland restoration

Water‐holding soil amendments such as super‐absorbent polymer (SAP) may improve native species establishment in restoration but may also interact with precipitation or invasive species such as Bromus tectorum L. (cheatgrass or downy brome) to influence revegetation outcomes. We implemented an experiment at two sites in Colorado, U.S.A. , in which we investigated the interactions of drought (66% reduction of ambient rainfall), B. tectorum seed addition (BRTE, 465 seeds/m2), and SAP soil amendment (25 g/m2) on initial plant establishment and 3‐year aboveground and belowground biomass and allocation. At one site, SAP resulted in higher native seeded species establishment but only with ambient precipitation. However, by the third year, we detected no SAP effects on native seeded species biomass. Treatments interacted to influence aboveground and belowground biomass and allocation differently. At one site, a SAP × precipitation interaction resulted in lower belowground biomass in plots with SAP and drought (61.7 ± 7.3 g/m2) than plots with drought alone (91.6 ± 18.1 g/m2). At the other site, a SAP × BRTE interaction resulted in higher belowground biomass in plots with SAP and BRTE (56.6 ± 11.2 g/m2) than BRTE alone (35.0 ± 3.7 g/m2). These patterns were not reflected in aboveground biomass. SAP should be used with caution in aridland restoration because initial positive effects may not translate to long‐term benefits, SAP may uniquely influence aboveground versus belowground biomass, and SAP can interact with environmental variables to impact developing plant communities in positive and negative ways.
Inhibition of the Angiotensin I Converting Enzyme (ACE) and proteolysis of non-fat probiotic yogurt

Abstract Yogurt is an important source of many biologically active peptides with specific health benefits. The majority of the bioactive peptides produced during yogurt manufacture are related to angiotensin converting enzyme inhibitory (ACE-I) peptides. The present study evaluated the proteolysis and angiotensin converting enzyme (ACE) inhibitory activities of non-fat probiotic yogurt supplemented with sodium caseinate (0 to 4%), and Mentha piperita (peppermint) extract (0 to 0.4%) during 20 days of storage. Good correlation (R = 0.90) was found between the growth of Lactobacillus casei LFTI® L26 and ACE inhibition in all samples during the initial stages of storage, as compared to the control yogurt, with a significant (p < 0.05) decrease after storage. The results showed that the addition of sodium caseinate and peppermint extract had a significant (p < 0.05) effect on proteolysis and the viability of L. casei LFTI® L26, enhancing the ACE activity. The IC50 values of the sample containing 0.4% of peppermint and of the sample containing 4% of sodium caseinate were 0.12 and 0.02 mg/mL respectively. The results showed that the use of 4% of sodium caseinate and 0.4% of peppermint extract could provide higher probiotic viability (1.3×107cfu/g) on the 20th day of storage.
Development of Cereal Flakes from Papaya (Carica papaya L.) and it’s Quality Evaluation During Storage

In the present investigation, various treatment combinations were optimized for the preparation of papaya fruit flakes. For the standardization of papaya cereal flakes three different recipes were tried with various combinations of papaya pulp, maida flour (100 %), corn flour (100 %), maida flour and corn flour in combination (70:30) for the development of papaya cereal flakes. Papaya cereal flakes prepared by using different combinations of both flours were compared on the basis of sensory evaluation with standard recipe in which maida was used. Papaya cereal flakes (T3) prepared using papaya pulp2.5 Kg, maida and corn flour in 70:30 ratio -(220.5 +94.5) g, sucrose150 g, glucose-150 g, pectin3.65 g, water250 ml, CaCO3-3 g was rated best on the basis of sensory evaluation. Further the prepared product were packed in aluminium laminated pouches and stored for 6 months under ambient temperature conditions. The various quality characteristics such as moisture, total soluble solids, titratable acidity, ascorbic acid, total sugars, reducing sugars, ash, fibre and carotenoids, were analyzed at 0, 3 and 6 months interval. The stored papaya-cereal flakes had better quality in terms of color, flavor, texture, overall acceptability and also have better retention of all quality characteristics at ambient temperature conditions. Thus papaya-cereal flakes could be stored successfully without any significant changes in quality characteristics at ambient temperature conditions for 6 months in aluminium laminated pouches.
Time‐series observations of photosynthetic oxygen production in the subtropical western North Pacific by an underwater profiling buoy system

We conducted time‐series observations in the northwestern part of the North Pacific subtropical gyre (30°N, 145°E) from July 2012 to March 2013 using a profiling buoy system equipped with a fast repetition rate fluorometer and dissolved oxygen (DO) sensor in order to understand vertical and temporal variations in gross oxygen production (GOP) by phytoplankton and its contribution to the oxygen cycle in the upper ocean. Under stratified conditions (July–November), daily GOP slightly exceeded 2 mmol O2 m−3 d−1 and only in near‐surface waters. However, during periods of vertical mixing (December–March) when phytoplankton blooms occurred, daily GOP increased in the upper 30 m and often exceeded 5 mmol O2 m−3 d−1. The depth‐integrated daily GOP within the euphotic layer (∫GOPEL) was relatively low (84.0 ± 23.6 mmol O2 m−2 d−1) during stratification, but increased gradually with vertical mixing and reached 460 mmol O2 m−2 d−1 on 17 March 2013. Additionally, during stratified conditions, a subsurface oxygen maximum (SOM) formed below the mixed‐layer depth (MLD) because the steep density gradient constrained upward diffusion of oxygen produced below the MLD. During the period of vertical mixing, the SOM disappeared, and DO concentrations within the upper 100 m increased through both increasing ∫GOPEL and atmospheric oxygen uptake. Using our buoy observations and air–sea gas flux model, we estimated that 24% ± 7% of ∫GOPEL was emitted to the atmosphere during the stratification period, and ∫GOPEL during the mixing period was about 2.4 times the rate of oxygen uptake by the ocean from the atmosphere.
CRISPR/Cas9 mediated metabolic engineering of carbon fixation in cyanobacteria

Cyanobacteria can be used to produce various biofuels and chemicals, as so called cell factories. However, carbon ﬁxation is often a limiting step and to improve carbon ﬂux it is important to understand the control of the Calvin-Benson-Bassham cycle (Calvin cycle). This thesis suggest a way to utilize CRISPR/Cas9 to evaluate the controlling elements of the Calvin cycle. In vivo characterization of the control over carbon ﬂux can be determined by systematically changing the Ribosome Binding Site (RBS) of the enzymes in the Calvin cycle. By utilizing an engineered, ethanol producing strain of Synechocystis sp. PCC6803 ( Synechocystis ), one can correlate the change in productivity, growth rate and CO 2 consumption to the change in abundance of corresponding enzyme, thus determine the control of that enzyme. Due to time restrictions, most constructs were not ﬁnished and non of the Synechocystis strains were characterized. However, it was found that the expression of CRISPR/Cas9 editing vector appear to be toxic in Escherichia coli . Moreover, using a two vector system seem to pose a high mutational pressure in Synechocystis . Thus, this might not be an optimal approach for CRISPR/Cas9 editing in cyanobacteria.
Coral reef fish communities, diversity, and their fisheries and biodiversity status in East Africa

Coral reef fish along the East African coast were evaluated for the distinctiveness of their communities, their distributions and interactions with the environment, and their responses to management. I studied the biomass and species richness of 24 fish families at 238 unique sites in Kenya, Tanzania, and Mozambique. I identified an unfished benchmark that was associated with high biomass, high-compliance closures or low access to fishing along with 6 additional statistically different communities. In the benchmark community, biomass was dominated by snappers, surgeonfish, parrotfish, and wrasses. Of the 24 families studied, 11 declined relative to the benchmark community, with the greatest declines observed among surgeonfish, snappers, sweetlips (grunts), groupers, and triggerfish. I evaluated the community’s spatial distributions and associations of 15 of 23 environmental and human-impact variables. Fish biomass was most positively influenced by the extent of shallow water <50 m adjacent to the sites, depth, and high-compliance closures and negatively impacted by human populations within a 100 km radius of the site. Number of fish species was largely predicted by biomass with weak evidence for local environmental control. Classification of the biomass into 3 proposed management thresholds revealed that ~38% of the sites were below sustainable yields, 54% were below maximum species richness, and 92% below a proposed stable-ecosystem or conservation threshold. Therefore, increasing biomass of vulnerable taxa through fishing restrictions is recommended for maintaining sustainable fisheries, species diversity, and ecosystem services.
Fungal Community of Culturable Fungal Endophytes Associated with Cinchona calisaya Collected from Gambung, West Java, Indonesia

Previous studies regarding endophytic fungi associated with Cinchona were focused on the analysis of quinine and related fungal metabolites. In the current study, the community structure of culturable endophytic fungi associated with C. calisaya (i.e., leaf, petiole, twig, root, flower, and fruit) were analyzed and elucidated. Representative isolates from various morphotypes were identified based on a sequence generated from the Internal Transcribed Spacer (ITS) rDNA region. A total of 638 fungal strains were isolated from 700 plant segments. All isolates belong to the phylum Ascomycota and are dominated by a member of Sordariomycetes. The fungal endophyte community within C. calisaya consists of 23 known species, 10 species complexes, and 6 unidentified species. Based on the Shannon-Wiener diversity index, the leaves and fruits host the most diverse endophytic fungi, followed by twigs, petioles, and bark. Members of the genus Diaporthe are commonly found in all C. calisaya organs. Neofussicoccum sp. was only one found within twigs; the Colletotrichum gloeosporioides complex and Guignardia mangiferae were only found within leaves; the C. brasiliense complex was detected in flowers; and Fusarium oxysporum is specific to roots.
Decoding and encoding models reveal the role of the depth of processing in the brain representation of meaning

How the brain representation of conceptual knowledge vary as a function of processing goals remains unclear. We hypothesized that the brain representation of semantic categories is shaped by the depth of processing. Participants were presented with visual words during functional MRI. During shallow processing, participants had to read the items. During deep processing, they had to mentally simulate the features associated with the words. Multivariate classification, informational connectivity and encoding models were used to reveal how the depth of processing determines the brain representation of word meaning. Decoding accuracy in putative substrates of the semantic network was enhanced when the depth processing was high, and the brain representations were more generalizable in semantic space relative to shallow processing contexts. This pattern was observed even in association areas in inferior frontal and parietal cortex. Deep information processing during mental simulation also increased the informational connectivity within key substrates of the semantic network. To further examine the properties of the words encoded in brain activity, we compared computer vision models - associated with the image referents of the words - and word embeddings. Computer vision models explained more variance of the brain responses across multiple areas of the semantic network. These results indicate that the brain representation of word meaning is highly malleable by the depth of processing imposed by the task, relies on access to visual representations and is highly distributed, including prefrontal areas previously implicated in semantic control.
An Autonomous Molecular Bioluminescent Reporter (AMBER) for voltage imaging in freely moving animals

Genetically encoded reporters have greatly increased our understanding of biology, especially in neuroscience. While fluorescent reporters have been widely used, light delivery and phototoxicity have hindered their utility. Bioluminescence overcomes some of these challenges but requires the addition of an exogenous luciferin limiting its use. Using a modular approach we have engineered Autonomous Molecular BioluminEscent Reporter (AMBER), an indicator of membrane potential. Unlike other luciferase-luciferin bioluminescent systems AMBER encodes the genes to express both the luciferase and luciferin. AMBER is a voltage-gated luciferase coupling the functionalities of the Ciona voltage sensing domain (VSD) and bacterial luciferase, luxAB. When AMBER is co-expressed with the luciferin producing genes it reversibly switches the bioluminescent intensity as a function of membrane potential. Utilizing both biophysical and biochemical methods we show that unlike other voltage indicators AMBER modulates its enzymatic activity as a function of the membrane potential. AMBER shows a several fold increase in the luminescent (ΔL/L) output upon switching from off to on state when the cell is depolarized. In vivo expression of AMBER in C. elegans allowed detecting pharyngeal pumping action and mechanosensory neural activity from multiple worms simultaneously. Since we are able to report neural activity of multiple animals at the same time, we believe AMBER can be used in social behavior assays to elucidate the role of membrane potential underlying the behaviors.
Environmental Effects on Germination and Seedling Emergence of Weedy Rice

The objective of this study is to determine the germination and growth of weedy rice seedlings that were grown under four different environmental conditions simulated in either growth chamber or room conditions. Photoperiod (24 h light, 24 h dark, 12 h light-dark), drought (0, 5, 10, 20 %) and temperature (25, 30, 35, 40 °C) effects were tested in growth chamber while the flooding depth (0, 2.5, 5, 10 cm) effects was tested in room condition. Germination percentage was not significantly affected (p > 0.05) by either of the environmental factors except for flooding depth at 10 cm. Temperature treatment specifically at 30 °C showed a pronounced effect on hypocotyl length, radicle length and root-shoot ratio compared to other temperature range. Highest hypocotyl length and root-shoot ratio were recorded in 10 % drought treatment and longest radicle length obtained in control treatment. Meanwhile, a continuous dark condition in photoperiod treatment showed the highest hypocotyl length in comparison to 24 hours of light and alternate 12 hours of light and dark. Highest radicle length and root-shoot ratio were obtained in 24 hours of light and 12 hours alternate light and dark respectively. Growth of weedy rice exhibited a declining trend in increasing flooding depth. The result of this study suggests that germination was retarded by deep flooding. Temperature and flooding depth affects the vegetative growth of weedy rice the most and sustained growth was observed at higher temperature regime. The information gained from this study may be useful in assessing the growth performance of weedy rice in relation to cultivated rice, and further helps in developing effective Malaysian weedy rice control strategies.
Spatio-temporal variation of cyanobacteria and cyanotoxins in public supply reservoirs of the semi-arid region of Brazil

Cyanobacteria harmful algal blooms (CyanoHABs) have become increasingly frequent and intense in public supply reservoirs as a result of eutrophication and global climate change. The semi-arid region of Brazil has a well documented history of CyanoHABs but the underlying factors that control the excessive proliferation of these organisms and the production of their bioactive secondary metabolites are not comprehensively understood. This study aimed to identify the environmental factors that explain the spatial and temporal variations in the abundance of cyanobacteria and the concentration of cyanotoxins (microcystins, saxitoxins, and cylindrospermopsin) in semi-arid reservoirs. The following hypotheses were tested: (a) the largest biovolumes of potential toxin producing cyanobacteria occur when cyanotoxin concentrations are highest; and (b) the environmental factors that explain variations in biovolume of cyanobacteria also explain changes in cyanotoxins concentrations. Samples were taken from four reservoirs located in the Northeast region of Brazil, over a three-month period (October 2016 and February and June 2017). Of the 24 species of cyanobacteria identified, 13 were potentially toxin-producing. Physicochemical variables such as water volume of the reservoir, water transparency, soluble reactive phosphorus, and total phosphorus explained the abundance of cyanobacteria and the levels of cyanotoxins. These results corroborate the hypothesis that similar physicochemical conditions influence the abundance and diversity of cyanobacteria and cyanotoxins. Cyanobacterial blooms composed of more than one potential toxin producing species were observed in the studied reservoirs, where potential microcystin-producing species were the most common. Microcystins and saxitoxins were detected in all the reservoirs studied, while cylindrospermopsin and the cyanobacterium Cylindrospermopsis raciborskii were simultaneously recorded in only one reservoir (Camalaú Reservoir). Cylindrospermopsin was only detected in a reservoir for the first time in the State of Paraíba. Canonical redundancy analysis showed that the cyanotoxins were related to potential toxin producing species. These results corroborate the proposed hypothesis that there is a correlation between cyanotoxins and the biomass of potential producers. Also, there were situations where cyanotoxins were detected without the presence of potential producers. These results demonstrate the need for reassessment of potential toxin producing species of cyanobacteria in semi-arid reservoirs. This may lead to the identification and characterization of novel producers of these bioactive secondary metabolites.
The use of physiological, biochemical and morpho-anatomical traits in tree breeding for improved water-use efficiency of Quercus robur L.

Aim of study: In the present paper we studied the nature and level of co-dependence between leaf functional traits and intrinsic water-use efficiency (WUEi)in one-year-old Quercus roburL. seedlings, grown in a common garden experiment under moderate drought conditions. The study aimed to identify those traits that might be potentially utilized to improve leaf-level WUEi, and therefore be used in breeding programmes to enhance drought adaptation of Q. roburtree species.Area of study: The study was carried out at the common garden experiment established within UNESCO Biosphere Reserve Mura-Drava-Danube.Material and methods: The study involved one-year-old seedlings of eight half-sib lines of Q. robur. We analyzed 18 leaf parameters; i.e. physiological, biochemical, morphological and anatomical. Data were processed using multivariate statistical methods: a) principal component analysis, b) stepwise regression analysis, and c) path coefficient analysis.Main results: The results evidenced that leaf stomatal traits, particularly stomatal density (SD),and leaf dry mass per unit leaf area (LMA) were the most important traits associated closely with WUEi.Stomatal density achieved the highest score on PC1 (0.825), in which WUEihad the highest loading (0.920), as well. SDwas also included first in stepwise regression model. Research highlights: The results demonstrated that under moderate water stressWUEiin Q. robur half-sib lines were mainly the result of the plants’ structural acclimation to surrounding environmental conditions.
Global reprogramming of virulence and antibiotic resistance in Pseudomonas aeruginosa by a single nucleotide polymorphism in the elongation factor-encoding gene, fusA1

Pseudomonas aeruginosa is a common opportunistic pathogen. The organism displays elevated intrinsic antibiotic resistance and can cause life-threatening infections. The gene encoding an elongation factor, FusA1, is frequently mutated in clinical isolates of P. aeruginosa from patients with cystic fibrosis (CF). Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the aminoglycoside efflux pump, MexXY. In the current work, we isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1P443L) in which mexXY expression was increased. Through a combination of proteomic and transcriptomic analyses, we found that the fusA1 mutant also exhibited large-scale but discrete changes in the expression of key pathogenicity-associated genes. Most notably, the fusA1 mutant displayed greatly increased expression of the Type III Secretion system (T3SS), widely considered to be the most potent virulence factor in the P. aeruginosa arsenal, and also elevated expression of the Type VI Secretion (T6S) machinery. This was unexpected because expression of the T3SS is usually reciprocally coordinated with T6S system expression. The fusA1 mutant also displayed elevated exopolysaccharide production, dysregulated siderophore production, elevated ribosomal protein synthesis, and transcriptomic signatures indicative of translational stress. Each of these phenotypes (and almost all of the transcriptomic and proteomic changes associated with the fusA1 mutation) were restored to levels comparable to that in the PAO1-derived progenitor strain by expression of the wild-type fusA1 gene in trans, indicating that the mutant gene is recessive. Our data show that in addition to elevating antibiotic resistance through mexXY expression (although we also identify additional contributory resistance mechanisms), mutations in fusA1 can lead to highly-selective dysregulation of virulence gene expression.