The Effect of Dissolved Organic Carbon on Bacterial Adhesion to Conditioning Films Adsorbed on Glass from Natural Seawater Collected during Different Seasons

Adhesion of three marine bacterial strains, i.e. Marinobacter hydrocarbonoclasticus, Psychrobacter sp. and Halomonas pacifica with different cell surface hydrophobicities was measured on glass in a stagnation point flow chamber. Prior to bacterial adhesion, the glass surface was conditioned for 1?h with natural seawater collected at different seasons in order to determine the effect of seawater composition on the conditioning film and bacterial adhesion to it. The presence of a conditioning film was demonstrated by an increase in water contact angle from 15° on bare glass to 50° on the conditioned glass, concurrent with an increase in the amount of adsorbed organic carbon and nitrogen, as measured by X-ray photoelectron spectroscopy. Multiple linear regression analysis on initial deposition rates, with as explanatory variables the temperature, salinity, pH and concentration of dissolved organic carbon (DOC) of the seawater at the time of collection, showed that the concentration of DOC was most strongly associated with the initial deposition rates of the three strains. Initial deposition rates of the two most hydrophilic strains to a conditioning film, increased with the concentration of DOC in the seawater, whereas the initial deposition rate of the most hydrophobic strain decreased with an increasing concentration of DOC.     

Designing Programs for Eliminating Canine Rabies from Islands: Bali,Indonesia as a Case Study

Background

Canine rabies is one of the most important and feared zoonotic diseases in the world. In some regions rabies elimination is being successfully coordinated, whereas in others rabies is endemic and continues to spread to uninfected areas. As epidemics emerge, both accepted and contentious control methods are used, as questions remain over the most effective strategy to eliminate rabies. The Indonesian island of Bali was rabies-free until 2008 when an epidemic in domestic dogs began, resulting in the deaths of over 100 people. Here we analyze data from the epidemic and compare the effectiveness of control methods at eliminating rabies.

Methodology/Principal Findings

Using data from Bali, we estimated the basic reproductive number, R ₀, of rabies in dogs, to be ∼1·2, almost identical to that obtained in ten–fold less dense dog populations and suggesting rabies will not be effectively controlled by reducing dog density. We then developed a model to compare options for mass dog vaccination. Comprehensive high coverage was the single most important factor for achieving elimination, with omission of even small areas (<0.5% of the dog population) jeopardizing success. Parameterizing the model with data from the 2010 and 2011 vaccination campaigns, we show that a comprehensive high coverage campaign in 2012 would likely result in elimination, saving ∼550 human lives and ∼$15 million in prophylaxis costs over the next ten years.

Conclusions/Significance

The elimination of rabies from Bali will not be achieved through achievable reductions in dog density. To ensure elimination, concerted high coverage, repeated, mass dog vaccination campaigns are necessary and the cooperation of all regions of the island is critical. Momentum is building towards development of a strategy for the global elimination of canine rabies, and this study offers valuable new insights about the dynamics and control of this disease, with immediate practical relevance.     

Quantifying killing of orangutans and human-orangutan conflict in Kalimantan, Indonesia

Human-orangutan conflict and hunting are thought to pose a serious threat to orangutan existence in Kalimantan, the Indonesian part of Borneo. No data existed prior to the present study to substantiate these threats. We investigated the rates, spatial distribution and causes of conflict and hunting through an interview-based survey in the orangutan's range in Kalimantan, Indonesia. Between April 2008 and September 2009, we interviewed 6983 respondents in 687 villages to obtain socio-economic information, assess knowledge of local wildlife in general and orangutan encounters specifically, and to query respondents about their knowledge on orangutan conflicts and killing, and relevant laws. This survey revealed estimated killing rates of between 750 and 1800 animals killed in the last year, and between 1950 and 3100 animals killed per year on average within the lifetime of the survey respondents. These killing rates are higher than previously thought and are high enough to pose a serious threat to the continued existence of orangutans in Kalimantan. Importantly, the study contributes to our understanding of the spatial variation in threats, and the underlying causes of those threats, which can be used to facilitate the development of targeted conservation management.     

Enzyme logic gates for the digital analysis of physiological level upon injury

A biocomputing system composed of a combination of AND/IDENTITY logic gates based on the concerted operation of three enzymes: lactate oxidase, horseradish peroxidase and glucose dehydrogenase was designed to process biochemical information related to pathophysiological conditions originating from various injuries. Three biochemical markers: lactate, norepinephrine and glucose were applied as input signals to activate the enzyme logic system. Physiologically normal concentrations of the markers were selected as logic 0 values of the input signals, while their abnormally increased concentrations, indicative of various injury conditions were defined as logic 1 input. Biochemical processing of different patterns of the biomarkers resulted in the formation of norepi-quinone and NADH defined as the output signals. Optical and electrochemical means were used to follow the formation of the output signals for eight different combinations of three input signals. The enzymatically processed biochemical information presented in the form of a logic truth table allowed distinguishing the difference between normal physiological conditions, pathophysiological conditions corresponding to traumatic brain injury and hemorrhagic shock, and abnormal situations (not corresponding to injury). The developed system represents a biocomputing logic system applied for the analysis of biomedical conditions related to various injuries. We anticipate that such biochemical logic gates will facilitate decision-making in connection to an integrated therapeutic feedback-loop system and hence will revolutionize the monitoring and treatment of injured civilians and soldiers.     

Trichloroacetate,an inhibitor of wax biosynthesis,prevents the development of hyperhydricity in Arabidopsis seedlings

The study of allelic variations affecting organogenic capacity is not only relevant for manipulating plant traits but also to understand the fundamental mechanisms involved in plant development. Here, we report the characterization of three tomato (Solanum lycopersicum) loci (RG3C, RG7H and RG8F) whose alleles from its wild relative Solanum pennellii enhance in vitro shoot and root regeneration. S. pennellii alleles were introgressed into tomato cv. Micro-Tom (MT), creating near-isogenic lines. We evaluated the time taken for shoot induction and acquisition of competence by quantifying organogenesis after transferring explants, respectively, from the shoot-inducing medium (SIM) to the basal medium (BM) and from root-inducing medium (RIM) to the SIM. Concomitantly, we monitored the expression of key developmental genes. MT-Rg3C and MT-Rg7H started shoot induction, respectively, at 48 and 24 h earlier than MT and MT-Rg8F, while MT-Rg3C and MT-Rg8F acquired competence 24 h before MT. The impact of MT-Rg3C and MT-Rg8F in the acquisition of competence to assume different fates is consistent with their effect enhancing both shoot and root regeneration. MT-Rg7H seems to affect shoot induction specifically, which is in agreement with the enhanced expression of the shoot-related genes WUSCHEL and SHOOT MERISTEMLESS. Phenotypic characterization of greenhouse-grown plants showed that Rg3C has increased branching when compared to MT. Conversely, the normal branching observed in MT-Rg7H and MT-Rg8F indicates that adventitious in vitro shoot formation and ex vitro axillary bud formation/outgrowth are induced by different genetic pathways. These natural variations are thus useful for breeding highly regenerating varieties without undesirable effects on plant architecture.     

Can intensification reduce emission intensity of biofuel through optimized fertilizer use? Theory and the case of oil palm in Indonesia

Closing yield gaps through higher fertilizer use increases direct greenhouse gas emissions but shares the burden over a larger production volume. Net greenhouse gas (GHG) footprints per unit product under agricultural intensification vary depending on the context, scale and accounting method. Life cycle analysis of footprints includes attributable emissions due to (i) land conversion (‘fixed cost’); (ii) external inputs used (‘variable cost’); (iii) crop production (‘agronomic efficiency’); and (iv) postharvest transport and processing (‘proportional’ cost). The interplay between fixed and variable costs results in a nuanced opportunity for intermediate levels of intensification to minimize footprints. The fertilizer level that minimizes the footprint may differ from the economic optimum. The optimization problem can be solved algebraically for quadratic crop fertilizer response equations. We applied this theory to data of palm oil production and fertilizer use from 23 plantations across the Indonesian production range. The current EU threshold requiring at least 35% emission saving for biofuel use can never be achieved by palm oil if produced: (i) on peat soils, or (ii) on mineral soils where the C debt due to conversion is larger than 20 Mg C ha^?1, if the footprint is calculated using an emission ratio of N₂O–N/N fertilizer of 4%. At current fertilizer price levels in Indonesia, the economically optimized N fertilizer rate is 344–394 kg N ha^?1, while the reported mean N fertilizer rate is 141 kg N ha^?1 yr^?1 and rates of 74–277 kg N ha^?1 would minimize footprints, for a N₂O–N/N fertilizer ratio of 4–1%, respectively. At a C debt of 30 Mg C ha^?1, these values are 200–310 kg N ha^?1. Sustainable weighting of ecology and economics would require a higher fertilizer/yield price ratio, depending on C debt. Increasing production by higher fertilizer use from current 67% to 80% of attainable yields would not decrease footprints in current production conditions.     

Comparison of 2002 AECG and 2016 ACR/EULAR classification criteria and added value of salivary gland ultrasonography in a patient cohort with suspected primary Sjögren’s syndrome

Background

The objective was to evaluate concordance between 2002 American-European Consensus Group (AECG) and 2016 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) classification criteria for primary Sjögren’s syndrome (pSS) and to assess how salivary gland ultrasonography (SGUS) might improve the classification of patients.

Methods

Patients with suspected pSS underwent a standardised evaluation, including SGUS, at inclusion into the single-centre Brittany DIApSS cohort. Agreement between the two criteria sets was assessed using Cohen’s κ coefficient. Characteristics of discordantly categorised patients were detailed.

Results

We prospectively included 290 patients between 2006 and 2016, among whom 125 (43%) met ACR/EULAR criteria and 114 (39%) also met AECG criteria; thus, 11 (4%) patients fulfilled only ACR/EULAR, no patients AECG only, and 165 (57%) patients neither criteria set. Concordance was excellent (κ?=?0.92). Compared to patients fulfilling both criteria sets, the 11 patients fulfilling only ACR/EULAR criteria had similar age and symptom duration but lower frequencies of xerophthalmia and xerostomia (p?<?0.01 for each) and salivary gland dysfunction (p?<?0.01); most had systemic involvement (91%), including three (27%) with no sicca symptoms; 91% had abnormal salivary gland biopsy and 46% anti-Sjögren's-syndrome-related antigen A (anti-SSA); 64% were diagnosed with pSS by the physician. SGUS was abnormal in 12% of the 165 patients fulfilling no criteria set. Including SGUS among the ACR/EULAR criteria increased sensitivity from 87.4% to 91.1% when physician diagnosis was the reference standard.

Conclusions

Agreement between AECG and ACR/EULAR criteria sets is excellent. ACR/EULAR criteria are slightly more sensitive and classified some patients without sicca symptoms as having pSS. Including SGUS in the ACR/EULAR criteria may further improve their sensitivity.

     

Bacterial Strains Isolated from Different Niches Can Exhibit Different Patterns of Adhesion to Substrata

Various mechanisms have been demonstrated to be operative in bacterial adhesion to surfaces, but whether bacterial adhesion to surfaces can ever be captured in one generally valid mechanism is open to question. Although many papers in the literature make an attempt to generalize their conclusions, the majority of studies of bacterial adhesion comprise only two or fewer strains. Here we demonstrate that three strains isolated from a medical environment have a decreasing affinity for substrata with increasing surface free energy, whereas three strains from a marine environment have an increasing affinity for substrata with increasing surface free energy. Furthermore, adhesion of the marine strains related positively with substratum elasticity, but such a relation was absent in the strains from the medical environment. This study makes it clear that strains isolated from a given niche, whether medical or marine, utilize different mechanisms in adherence, which hampers the development of a generalized theory for bacterial adhesion to surfaces.     

Characterisation and immunolocation of an 87 kDa polypeptide associated with UDP-glucuronic acid decarboxylase activity from differentiating tobacco cells (Nicotiana tabacum L.)

UDP-glucuronic acid decarboxylase catalyses the reaction responsible for the formation of UDP-xylose and commits assimilate for the biosynthesis of cell wall polysaccharides and glycosylation of proteins. Xylose-rich polymers such as xylans are a feature of dicot secondary walls. Thus a cell culture system of tobacco transformed with the ipt gene from Agrobacterium tumefaciens for cytokinin production and which when manipulated with auxin and sucrose leads to induction of xylogenesis, has been used as a source for purification of the enzyme. UDP-glucuronic acid decarboxylase was purified by ion-exchange, gel filtration and affinity chromatography on Reactive Brown-Agarose. The native enzyme had an apparent M(r) of 220,000 which yielded a single subunit of 87,000 when analysed on SDS-PAGE using silver staining. This appears to be a novel form of the enzyme since a gene family encoding polypeptides around M(r) 40,000 with homology to the fungal enzyme also exists in plants. Using an antibody raised to the native 87 kDa form of the enzyme, this decarboxylase was localised mainly to to cambium and differentiating vascular tissue in tobacco stem, consistent with a role in the provision of UDP-xylose for the synthesis of secondary wall xylan. Further analysis using immunogold electron microscopy localised the 87 kDa UDP-glucuronic acid decarboxylase to the cytosol of developing vascular tissue.     

Regulation of CDPKs,including identification of PAL kinase,in biotically stressed cells of French bean

Changes in protein kinase activity have been investigated during the early response of suspension cultured cells of French bean to fungal elicitor. One of the kinases activated has a known target, phenylalanine ammonia-lyase (PAL), which has an important role in plant defence responses, and was purified. Kinase acivity during purification was monitored for both the PAL-derived peptide and syntide-2, which it also phosphorylated. The kinase had an M _r of 55000 on the basis of gel migration, ⁴⁵Ca²⁺ binding, autophosphorylation and phosphorylation of various substrates using in-gel assays. The kinase has been characterised with respect to kinetics and other properties in vitro and appears to be a CDPK. In-gel assays were also used to show that this kinase and a number of other CDPKs of similar M _r showed complex changes in elicitor-treated suspension-cultured cells of French bean. An activation was observed within 10 min and was maintained for up to 4 h. The time course of activation was different from MAP kinase and casein kinase assayed in the same extracts. However, at 5 min after addition of elicitor there is a transient inactivation of the CDPKs before activation. This inactivation can be mimicked by adding forskolin to the cells 30 min before elicitation, which brings about changes in the cellular pH. Forskolin potentiates the oxidative burst when elicitor is subsequently added while the CDPK cannot be activated by elicitor upon forskolin treatment. In contrast, intracellular acidification brought about by forskolin brings about slight activation of MAPkinase.