Search

Background Accurate and efficient detection of sub-microscopic malaria infections is crucial for enabling rapid treatment and interruption of transmission. Commercially available malaria LAMP kits have excellent diagnostic performance, though throughput is limited by the need to prepare samples individually. Here, we evaluate the clinical performance of a newly developed high throughput (HTP) sample processing system for use in conjunction with the Eiken malaria LAMP kit. Methods The HTP system utilised dried blood spots (DBS) and liquid whole blood (WB), with parallel sample processing of 94 samples per run. The system was evaluated using 699 samples of known infection status pre-determined by gold standard nested PCR. Results The sensitivity and specificity of WB-HTP-LAMP was 98.6% (95% CI, 95.7–100), and 99.7% (95% CI, 99.2–100); sensitivity of DBS-HTP-LAMP was 97.1% (95% CI, 93.1–100), and specificity 100% against PCR. At parasite densities greater or equal to 2 parasites/μL, WB and DBS HTP-LAMP showed 100% sensitivity and specificity against PCR. At densities less than 2 p/μL, WB-HTP-LAMP sensitivity was 88.9% (95% CI, 77.1–100) and specificity was 99.7% (95% CI, 99.2–100); sensitivity and specificity of DBS-HTP-LAMP was 77.8% (95% CI, 54.3–99.5) and 100% respectively. Conclusions The HTP-LAMP system is a highly sensitive diagnostic test, with the potential to allow large scale population screening in malaria elimination campaigns.

The Multi-Criteria Decision Analysis (MCDA) procedure was used to compare waste management options for kraft pulp mill sludge following its anaerobic digestion. Anaerobic digestion of sludge is advantageous because it produces biogas that may be used to generate electricity, heat and biofuels. However, adequate management of the digested sludge is essential. Landfill disposal is a non-sustainable waste management alternative. Kraft pulp mill digested sludge applied to land may pose risks to the environment and public health if the sludge has not been properly treated. This study is aimed to compare several recycling alternatives for anaerobically digested sludge from kraft pulp mills: land application, landfill disposal, composting, incineration, pyrolysis/gasification, and biofuel production by algae. The MCDA procedure considered nine criteria into three domains to compare digested sludge recycling alternatives in a kraft pulp mill: environmental (CO2 emission, exposure to pathogens, risk of pollution, material and energy recovery), economic (overall costs, value of products) and technical (maintenance and operation, feasibility of implementation). The most suitable management options for digested sludge from kraft pulp mills were found to be composting and incineration (when the latter was coupled with recycling ash to the cement industry). Landfill disposal was the worst option, presenting low performance in feasibility of implementation, risk of pollution, material and energy recovery.

// Lapeire Lore 1, 2 , Hendrix An 2, 3 , Lecoutere Evelyne 4 , Van Bockstal Mieke 4 , Vandesompele Jo 2, 5 , Maynard Dawn 6 , Braems Geert 7 , Van Den Broecke Rudy 7 , Muller Catherine 8 , Bracke Marc 3 , Cocquyt Veronique 1 , Denys Hannelore 1, 2 and De Wever Olivier 2, 3 1 Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium 2 Cancer Research Institute Ghent (CRIG), Ghent University Hospital, Ghent, Belgium 3 Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium 4 Department of Pathology, Ghent University Hospital, Ghent, Belgium 5 Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium 6 Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA 7 Department of Gynecology, Ghent University Hospital, Ghent, Belgium 8 Institut de Pharmacologie et de Biologie Structurale, Universite de Toulouse, UPS, Toulouse, France Correspondence to: De Wever Olivier, email: olivier.dewever@ugent.be Keywords: adipose tissue, breast cancer, proliferation, secretome, palbociclib Received: November 01, 2016 Accepted: April 17, 2017 Published: May 03, 2017 ABSTRACT Adipose tissue secretes a plethora of adipokines as evidenced by characterization of subcutaneous and visceral adipose tissue secretomes. However, adipose tissue composition and secretion pattern is depot and disease dependent, influencing the adipose tissue secretome. We investigated the secretome of cancer-associated adipose tissue (CAAT) explants from breast cancer patients and explored its role in breast cancer proliferation. CAAT proteins were identified by LC-MS/MS and human protein antibody arrays and stimulated proliferation of three breast cancer cell lines. Kinomics and transcriptomics of MCF-7 breast cancer cells treated with the secretome of CAAT revealed activation of Akt-, ERK- and JNK-pathways and differential expression of activator protein 1 (AP-1) and cAMP responsive element-binding protein (CREB) target genes. The cyclin-dependent kinase (CDK)4/6-inhibitor palbociclib significantly abrogated CAAT-enhanced breast cancer cell proliferation. Our work characterizes the specific breast CAAT protein secretome and reveals its pro-proliferative potency in breast cancer.

In the present study, we investigated the fumigant potential of five edible essential oils (EOs) against Sitophilus oryzae and their phytochemical residues in treated grains. Among the tested EOs, peppermint oil proved significantly effective (P ≤ 0.05) on S.oryzae at 400 μl/L air concentration, inducing 83 and 100% mortalities in with-food and without-food conditions respectively over 72 h exposure. In addition, it was also observed that the binary mixtures of peppermint + lemon oil (1:1 ratio) produced an equivalent effect to that of peppermint oil alone treatments. The phytochemical residue analysis by GC-MS revealed the presence of six compounds upon 72 h exposure to EOs. Further, the analysis of physico-chemical properties of the compounds indicated a positive correlation between polar surface area (PSA) and its residual nature. The residue levels of eugenol were significantly elevated corresponding to its high PSA value (29) in clove and cinnamon oils. On the other hand, the compounds with zero PSA value imparted very less or no (D-Limonene, caryophyllene, pinene and terpinolene) residues in treated grains. With respect to the most active peppermint oil, L-menthone, menthyl acetate and eucalyptol residues were at 67, 41 and 23% levels respectively. The outcome of the present study indicate the peppermint oil as a potent fumigant against S. oryzae, and although the residues of phytochemicals in treated grains is higher; they belong to the generally recognised as safe (GRAS) status leaving no harmful effect.

Despite measures to reduce disease transmission, a risk can occur when blood glucose meters (BGMs) are used on multiple individuals or by caregivers assisting a patient. The laboratory and in-clinic performance of a BGM system before and after disinfection should be demonstrated to guarantee accurate readings and reliable control of blood glucose (BG) for patients. In this study, an effective disinfection procedure, conducting wiping 10 times to assure a one minute contact time of the disinfectant on contaminated surface, was first demonstrated using test samples of the meter housing materials, including acrylonitrile butadiene styrene (ABS), polymethyl methacrylate (PMMA), and polycarbonate (PC), in accordance with ISO 15197:2013. After bench studies comprising 10,000 disinfection cycles, the elemental compositions of the disinfected ABS, PMMA, and PC samples were almost the same as in the original samples, as indicated by electron spectroscopy for chemical analysis. Subsequently, the validated disinfection procedure was then directly applied to disinfect 5 commercial BGM systems composed of ABS, PMMA, or PC to observe the effect of the validated disinfection procedure on meter accuracy. The results of HBsAg values after treatment with HBV sera and disinfectant wipes for each material were less than the LoD of each material of 0.020 IU/mL. Before and after the multiple disinfection cycles, 900 of 900 samples (100%) were within the system accuracy requirements of ISO 15197:2013. All of the systems showed high performance before and after the series of disinfection cycles and met the ISO 15197:2013 requirements. In addition, our results demonstrated multiple cleaning and disinfection cycles that represented normal use over the lifetime of a meter of 3-5 years. Our validated cleaning and disinfection procedure can be directly applied to other registered disinfectants for cleaning commercial BGM products in the future.

The objective of this study was to investigated the use of chemometric modeling of thermogravimetric (TG) data as an alternative approach to estimate the chemical and proximate (i.e. volatile matter, fixed carbon and ash contents) composition of lignocellulosic biomass. Since these properties affect the conversion pathway, processing costs, yield and / or quality of products, a capability to rapidly determine these for biomass feedstock entering the process stream will be useful in the success and efficiency of bioconversion technologies. The 38-minute long methodology developed in this study enabled the simultaneous prediction of both the chemical and proximate properties of forest-derived biomass from the same TG data. Conventionally, two separate experiments had to be conducted to obtain such information. In addition, the chemometric models constructed with normalized TG data outperformed models developed via the traditional deconvolution of TG data. PLS and PCR models were especially robust in predicting the volatile matter (R2-0.92; RPD- 3.58) and lignin (R2-0.82; RPD- 2.40) contents of the biomass. The application of chemometrics to TG data also made it possible to predict some monomeric sugars in this study. Elucidation of PC loadings obtained from chemometric models also provided some insights into the thermal decomposition behavior of the chemical constituents of lignocellulosic biomass. For instance, similar loadings were noted for volatile matter and cellulose, and for fixed carbon and lignin. The findings indicate that common latent variables are shared between these chemical and thermal reactivity properties. Results from this study buttresses literature that have reported that the less thermally stable polysaccharides are responsible for the yield of volatiles whereas the more recalcitrant lignin with its higher percentage of elementary carbon contributes to the yield of fixed carbon.

Background The definitive dietary management of propionic acidaemia (PA) is unknown although natural protein restriction with adequate energy provision is of key importance. Aim To describe European dietary practices in the management of patients with PA prior to the publication of the European PA guidelines. Methods This was a cross-sectional survey consisting of 27 questions about the dietary practices in PA patients circulated to European IMD dietitians and health professionals in 2014. Results Information on protein restricted diets of 186 PA patients from 47 centres, representing 14 European countries was collected. Total protein intake [PA precursor-free L-amino acid supplements (PFAA) and natural protein] met WHO/FAO/UNU (2007) safe protein requirements for age in 36 centres (77%). PFAA were used to supplement natural protein intake in 81% (n = 38) of centres, providing a median of 44% (14–83%) of total protein requirement. Seventy-four per cent of patients were prescribed natural protein intakes below WHO/FAO/UNU (2007) safe levels in one or more of the following age groups: 0–6 m, 7–12 m, 1–10 y, 11–16 y and > 16 y. Sixty-three per cent (n = 117) of patients were tube fed (74% gastrostomy), but only 22% received nocturnal feeds. Conclusions There was high use of PFAA with intakes of natural protein commonly below WHO/FAO/UNU (2007) safe levels. Optimal dietary management can only be determined by longitudinal, multi-centre, prospective case controlled studies. The metabolic instability of PA and small patient cohorts in each centre ensure that this is a challenging undertaking., 0, SCOPUS: ar.j, info:eu-repo/semantics/published

// Shana Claeys 1, 2 , Geertrui Denecker 1, 2 , Robrecht Cannoodt 1, 2, 3, 4, 5 , Candy Kumps 1, 6 , Kaat Durinck 1, 2 , Frank Speleman 1, 2 and Katleen De Preter 1, 2 1 Center for Medical Genetics, Ghent University, Ghent, Belgium 2 Cancer Research Institute Ghent, Ghent University, Ghent, Belgium 3 Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent, Belgium 4 Data Mining and Modelling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium 5 Department of Respiratory Medicine, Ghent University, Ghent, Belgium 6 Department of Uro-Gynaecology, Ghent University Hospital, Ghent, Belgium Correspondence to: Katleen De Preter, email: Katleen.DePreter@UGent.be Keywords: neuroblastoma; ALK; ALK inhibition; ALK signaling; dynamic Received: July 28, 2017 Accepted: October 17, 2017 Published: November 06, 2017 ABSTRACT Background: Neuroblastoma is an aggressive childhood malignancy of the sympathetic nervous system. Despite multi-modal therapy, survival of high-risk patients remains disappointingly low, underscoring the need for novel treatment strategies. The discovery of ALK activating mutations opened the way to precision treatment in a subset of these patients. Previously, we investigated the transcriptional effects of pharmacological ALK inhibition on neuroblastoma cell lines, six hours after TAE684 administration, resulting in the 77-gene ALK signature, which was shown to gradually decrease from 120 minutes after TAE684 treatment, to gain deeper insight into the molecular effects of oncogenic ALK signaling. Aim: Here, we further dissected the transcriptional dynamic profiles of neuroblastoma cells upon TAE684 treatment in a detailed timeframe of ten minutes up to six hours after inhibition, in order to identify additional early targets for combination treatment. Results: We observed an unexpected initial upregulation of positively regulated MYCN target genes following subsequent downregulation of overall MYCN activity. In addition, we identified adrenomedullin (ADM), previously shown to be implicated in sunitinib resistance, as the earliest response gene upon ALK inhibition. Conclusions: We describe the early and late effects of ALK inhibitor TAE684 treatment on the neuroblastoma transcriptome. The observed unexpected upregulation of ADM warrants further investigation in relation to putative ALK resistance in neuroblastoma patients currently undergoing ALK inhibitor treatment.

Cyanobacteria blooms are a risk to environmental health and public safety due to the potent toxins certain cyanobacteria can produce. These nuisance organisms can be removed from water bodies by biomass flocculation and sedimentation. Here, we studied the efficacy of combinations of a low dose coagulant (poly-aluminium chloride-PAC-or chitosan) with different ballast compounds (red soil, bauxite, gravel, aluminium modified zeolite and lanthanum modified bentonite) to remove cyanobacterial biomass from water collected in Funil Reservoir (Brazil). We tested the effect of different cyanobacterial biomass concentrations on removal efficiency. We also examined if zeta potential was altered by treatments. Addition of low doses of PAC and chitosan (1±8 mg Al L-1) to the cyanobacterial suspensions caused flock formation, but did not settle the cyanobacteria. When those low dose coagulants were combined with ballast, effective settling in a dose-dependent way up to 99.7% removal of the flocks could be achieved without any effect on the zeta potential and thus without potential membrane damage. Removal efficacy was influenced by the cyanobacterial biomass and at higher biomass more ballast was needed to achieve good removal. The combined coagulant-ballast technique provides a promising alternative to algaecides in lakes, ponds and reservoirs.

This study aimed to enhance hydrogen production from sugarcane syrup by biogas sparging. Two-stage continuous stirred tank reactor (CSTR) and upflow anaerobic sludge blanket (UASB) reactor were used to produce hydrogen and methane, respectively. Biogas produced from the UASB was used to sparge into the CSTR. Results indicated that sparging with biogas increased the hydrogen production rate (HPR) by 35% (from 17.1 to 23.1 L/L.d) resulted from a reduction in the hydrogen partial pressure. A fluctuation of HPR was observed during a long term monitoring because CO2 in the sparging gas and carbon source in the feedstock were consumed by Enterobacter sp. to produce succinic acid without hydrogen production. Mixed gas released from the CSTR after the sparging can be considered as bio-hythane (H2+CH4). In addition, a continuous sparging biogas into CSTR release a partial pressure in the headspace of the methane reactor. In consequent, the methane production rate is increased.

Background: Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters. Results: Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 gCOD L-1 d-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm-1), while marine conditions resembled brine waters (>47 mS cm-1). Enrichments at optimal conditions of OLR 5 gCOD L-1 d-1 and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L-1 d-1, which was later increased to OLR 10 gCOD L-1 d-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities. Conclusions: Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.

Oilseed rape straw (ORS) is a kind of biorefractory waste widely existing in the rural area of China, which is highly suitable to mix with kitchen waste (KW) and duck droppings (DD) in two-phase anaerobic digestion (AD). This research introduced the importance of KW and DD addition to improve the biogas production and biodegradation of ORS. A set of comparative experiments were conducted on two-phase mono- and co-digestion with organic load of 60 g VS/L. The total methane yield (TMY) and the biodegradation of ORS of co-digestions were obviously improving, and the synergistic effect found in the two-phase co-digestions. The optimum mixing ratio of ORS, KW and DD was 50:40:10, and the corresponding TMY and VS degradation rate of ORS were 374.5 mL/g VS and 49.7%, respectively. Addition of KW and DD maintained the pH within the optimal range for the hydrolyzing-acidification, improved the phase separation and buffering capacity of AD system.

There are two biological systems available for removing phosphorus from waste water, conventional phosphorus removal (CPR) and denitrifying phosphorus removal (DPR) systems, and each is characterized by the type of sludge used in the process. In this study, we compared the characteristics associated with the efficiency of carbon utilization between CPR and DPR sludge using acetate as a carbon source. For DPR sludge, the heat emitted during the phosphorus release and phosphorus uptake processes were 45.79 kJ/mol e- and 84.09 kJ/mol e-, respectively. These values were about 2 fold higher than the corresponding values obtained for CPR sludge, suggesting that much of the energy obtained from the carbon source was emitted as heat. Further study revealed a smaller microbial mass within the DPR sludge compared to CPR sludge, as shown by a lower sludge yield coefficient (0.05 gVSS/g COD versus 0.36 gVSS/g COD), a result that was due to the lower energy capturing efficiency of DPR sludge according to bioenergetic analysis. Although the efficiency of anoxic phosphorus removal was only 39% the efficiency of aerobic phosphorus removal, the consumption of carbon by DPR sludge was reduced by 27.8% compared to CPR sludge through the coupling of denitrification with dephosphatation.

Neuroblastoma is the most common extracranial tumor in children. Despite aggressive multimodal treatment, high-risk neuroblastoma remains a clinical challenge with survival rates below 50%. Adding targeted drugs to first-line therapy regimens is a promising approach to improve survival in these patients. TACR1 activation by substance P has been reported to be mitogenic in cancer cell lines. Tachykinin receptor (TACR1) antagonists are approved for clinical use as an antiemetic remedy since 2003. Tachykinin receptor inhibition has recently been shown to effectively reduce growth of several tumor types. Here, we report that neuroblastoma cell lines express TACR1, and that targeting TACR1 activity significantly reduced cell viability and induced apoptosis in neuroblastoma cell lines. Gene expression profiling revealed that TACR1 inhibition repressed E2F2 and induced TP53 signaling. Treating mice harboring established neuroblastoma xenograft tumors with Aprepitant also significantly reduced tumor burden. Thus, we provide evidence that the targeted inhibition of tachykinin receptor signaling shows therapeutic efficacy in preclinical models for high-risk neuroblastoma.

Artificial municipal wastewater was treated successfully by the bioaugmentation of Bacillus sp. K5 capable of simultaneous nitrification and denitrification (SND) within a sequencing batch reactor (SBR). During the long-term operation, the bioaugmentation system exhibited an excellent and steady COD and NH4+-N removal without nitrite and nitrate accumulation. The average removal efficiency for COD and NH4+-N achieved to 98% and 95%, respectively. PCR-DGGE, SEM and FISH revealed that the introduced Bacillus sp. K5 should be an important functional strain and exerted a critical influence on the structure of microbial community. qPCR analysis indicated that the strain K5 facilitated aerobic nutrients removal capabilities and SND might be the primary pathway for the nitrogen removal in the SBR. Overall, the SBR system used in our study should be very promising for the future wastewater treatment.

Contains fulltext : 182283.pdf (Publisher’s version ) (Open Access) Diversity in colorectal cancer biology is associated with variable responses to standard chemotherapy. We aimed to identify and validate DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of metastatic CRC patients. Candidate genes were selected from 389 genes involved in DNA Damage Repair by correlation analyses between gene methylation status and drug response in 32 cell lines. A large series of samples (n=818) from two phase III clinical trials was used to evaluate these candidate genes by correlating methylation status to progression-free survival after treatment with first-line single-agent fluorouracil (Capecitabine or 5-fluorouracil) or combination chemotherapy (Capecitabine or 5-fluorouracil plus irinotecan (CAPIRI/FOLFIRI)). In the discovery (n=185) and initial validation set (n=166), patients with methylated Decoy Receptor 1 (DCR1) did not benefit from CAPIRI over Capecitabine treatment (discovery set: HR=1.2 (95%CI 0.7-1.9, p=0.6), validation set: HR=0.9 (95%CI 0.6-1.4, p=0.5)), whereas patients with unmethylated DCR1 did (discovery set: HR=0.4 (95%CI 0.3-0.6, p=0.00001), validation set: HR=0.5 (95%CI 0.3-0.7, p=0.0008)). These results could not be replicated in the external data set (n=467), where a similar effect size was found in patients with methylated and unmethylated DCR1 for FOLFIRI over 5FU treatment (methylated DCR1: HR=0.7 (95%CI 0.5-0.9, p=0.01), unmethylated DCR1: HR=0.8 (95%CI 0.6-1.2, p=0.4)). In conclusion, DCR1 promoter hypermethylation status is a potential predictive biomarker for response to treatment with irinotecan, when combined with capecitabine. This finding could not be replicated in an external validation set, in which irinotecan was combined with 5FU. These results underline the challenge and importance of extensive clinical evaluation of candidate biomarkers in multiple trials.

Multiple myeloma (MM) is characterized by the accumulation of malignant plasma cells in the bone marrow (BM). Recently, several studies have highlighted the role of pathogens in either promoting or dampening malignancies of unrelated origin. Trypanosoma brucei is an extracellular protozoan parasite which causes sleeping sickness. Our group has previously demonstrated that trypanosome infection affects effector plasma B cells. Therefore, we hypothesized that T. brucei infection could have an impact on MM development. Using the immunocompetent 5T33MM model, we demonstrated a significant reduction in BM-plasmacytosis and M-protein levels in mice infected with T. brucei, resulting in an increased survival of these mice. Blocking IFN. could only partially abrogate these effects, suggesting that other mechanisms are involved in the destruction of malignant plasma cells. We found that T. brucei induces intrinsic apoptosis of 5T33MM cells in vivo, and that this was associated with reduced endogenous unfolded protein response (UPR) activation. Interestingly, pharmacological inhibition of IRE1 alpha and PERK was sufficient to induce apoptosis in these cells. Together, these results demonstrate that trypanosome infections can interfere with MM development by suppressing endogenous UPR activation and promoting intrinsic apoptosis.

In order to examine the potential for coproduct generation, we have characterised chemical compounds released by a range of alkaline and acidic aqueous pretreatments as well as the effect of these pretreatments on the saccharification ability of the lignocellulosic material. Comparative experiments were performed using three biomass types chosen for their potential as second-generation biofuel feedstocks: maize stover, miscanthus and sugarcane bagasse. The release of lignin from the feedstock correlated with the residual biomass saccharification potential, which was consistently higher after alkaline pretreament for all three feedstock types. Alkaline pretreatment released more complex mixtures of pentose and hexose sugars into the pretreatment liquor than did acid pretreatment. In addition, complex mixtures of aromatic and aliphatic compounds were released into pretreatment liquors under alkaline conditions, in a temperature-dependent manner, but far less so under acidic conditions. We show that the three feedstocks characterised interact with the pretreatment conditions in a specific manner to generate different ranges of products, highlighting the need to tailor pretreatments to both the starting feedstock and desired outcomes.

The cellulose binding domain (CBD) of cellulase binding to cellulosic materials is the initiation of a synergistic action on the enzymatic hydrolysis of the most abundant renewable biomass resources in nature. The binding of the CBD domain to cellulosic substrates generally relies on the interaction between the aromatic amino acids structurally located on the flat face of the CBD domain and the glucose rings of cellulose. In this study, we found the CBD domain of a newly cloned Penicillium crustosum endoglucanase EGL1, which was phylogenetically related to Aspergillus, Fusarium and Rhizopus, and divergent from the well-characterized Trichoderma reeseis cellulase CBD domain, contain two conserved aromatic amino acid-rich regions, Y451-Y452 and Y477-Y478-Y479, among which three amino acids Y451, Y477, and Y478 structurally sited on a flat face of this domain. Cellulose binding assays with green fluorescence protein as the marker, adsorption isotherm assays and an isothermal titration calorimetry assays revealed that although these three amino acids participated in this process, the Y451-Y452 appears to contribute more to the cellulose binding than Y477-Y478-Y479. Further glycine scanning mutagenesis and structural modelling revealed that the binding between CBD domain and cellulosic materials might be multi-amino-acids that participated in this process. The flexible poly-glucose molecule could contact Y451, Y477, and Y478 which form the contacting flat face of CBD domain as the typical model, some other amino acids in or outside the flat face might also participate in the interaction. Thus, it is possible that the conserved Y451-Y452 of CBD might have a higher chance of contacting the cellulosic substrates, contributing more to the affinity of CBD than the other amino acids.

Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their role in the molecular pathogenesis of pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1-positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. First, we used primary leukemia patient samples to identify an ETV6/RUNX1 specific expression signature consisting of 596 lncRNA transcripts. Next, integration of this lncRNA signature with RNA sequencing of BCP-ALL cell lines and lncRNA profiling of an in vitro model system of ETV6/RUNX1 knockdown, revealed that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are truly regulated by the oncogenic fusion protein. Moreover, sustained inactivation of lnc-RTN4R-1 and lnc-NKX2-3-1 in ETV6/RUNX1 positive cells caused profound changes in gene expression. All together, our study defined a unique lncRNA expression signature associated with ETV6/RUNX1-positive BCP-ALL and identified lnc-RTN4R-1 and lnc-NKX2-3-1 as lncRNAs that might be functionally implicated in the biology of this prevalent subtype of human leukemia., SCOPUS: ar.j, info:eu-repo/semantics/published

The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana. The peptidase is activated by two RING E3 ligases, Big Brother (BB) and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PROTEOLYSIS 1 (PRT1) of the N-end rule pathway. DA1 peptidase activity also cleaves the deubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22, which promote cell proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins.

Cerato-platanin (CP) is a non-catalytic, cysteine-rich protein, the first member of the cerato-platanin family. It is a single-domain protein with a double Ψ/β barrel domain resembling the D1 domain of plant and bacterial expansins. Similarly to expansins, CP shows a cell wall-loosening activity on cellulose and can be defined as an expanisin-like protein, in spite of the missing D2 domain, normally present in plant expansins. The weakening activity shown on cellulose may facilitate the CP-host interaction, corroborating the role of CP in eliciting plant defence response. Indeed, CP is an elicitor of primary defences acting as a Pathogen-Associated Molecular Patterns (PAMP). So far, structure-function relationship study has been mainly performed on the bacterial BsEXLX1 expansin, probably due to difficulties in expressing plant expansins in heterologous systems. Here, we report a subcloning and purification method of CP in the engineered E. coli SHuffle cells, which proved to be suitable to obtain the properly folded and biologically active protein. The method also enabled the production of the mutant D77A, rationally designed to be inactive. The wild-type and the mutated CP were characterized for cellulose weakening activity and for PAMP activity (i.e. induction of Reactive Oxygen Species synthesis and phytoalexins production). Our analysis reveals that the carboxyl group of D77 is crucial for expansin-like and PAMP activities, thus permitting to establish a correlation between the ability to weaken cellulose and the capacity to induce defence responses in plants. Our results enable the structural and functional characterization of a mono-domain eukaryotic expansin and identify the essential role of a specific aspartic residue in cellulose weakening.

The sustainable recovery of resources from wastewater streams can provide many social and environmental benefits. A common strategy to recover valuable resources from wastewater is to harness the products of fermentation by complex microbial communities. In these fermentation bioreactors high microbial community diversity within the inoculum source is commonly assumed as sufficient for the selection of a functional microbial community. However, variability of the product profile obtained from these bioreactors is a persistent challenge in this field. In an attempt to address this variability, the impact of inoculum on the microbial community structure and function within the bioreactor was evaluated using controlled laboratory experiments. In the course of this work, sequential batch reactors were inoculated with three complex microbial inocula and the chemical and microbial compositions were monitored by HPLC and 16S rRNA amplicon analysis, respectively. Microbial community dynamics and chemical profiles were found to be distinct to initial inoculate and highly reproducible. Additionally we found that the generation of a complex volatile fatty acid profile was not specific to the diversity of the initial microbial inoculum. Our results suggest that the composition of the original inoculum predictably contributes to bioreactor community structure and function., United States. National Institutes of Health (P30-ES002109)

Endo-s-1,4-glucanase AkEG21 belonging to glycosyl hydrolase family 45 (GHF45) is the most abundant cellulase in the digestive fluid of sea hare (Aplysia kurodai). The specific activity of this 21-kDa enzyme is considerably lower than those of other endo s-1,4-glucanases in the digestive fluid of A. kurodai, therefore its role in whole cellulose hydrolysis by sea hare is still uncertain. Although AkEG21 has a catalytic domain without a cellulose binding domain, it demonstrated stable binding to cellulose fibers, similar to that of fungal cellobiohydrolase (CBH) 1 and CBH 2, which is strongly inhibited by cellohexaose, suggesting the involvement of the catalytic site in cellulose binding. Cellulose-bound AkEG21 hydrolyzed cellulose to cellobiose, cellotriose and cellotetraose, but could not digest an external substrate, azo-carboxymethyl cellulose. Cellulose hydrolysis was considerably stimulated by the synergistic action of cellulose-bound AkEG21 and AkEG45, another s-1,4-endoglucanase present in the digestive fluid of sea hare; however no synergy in carboxymethylcellulose hydrolysis was observed. When AkEG21 was removed from the digestive fluid by immunoprecipitation, the cellulose hydrolyzing activity of the fluid was significantly reduced, indicating a critical role of AkEG21 in cellulose hydrolysis by A. kurodai. These findings suggest that AkEG21 is a processive endoglucanase functionally equivalent to the CBH, which provides a CBH-independent mechanism for the mollusk to digest seaweed cellulose to glucose.

Background Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS) is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR) assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture. Methods Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples. Results A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%). One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4–90.1%) and 62.5% (95% CI 24.5–91.5%), respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%). Among these, six were positive for a non-S. pneumoniae pathogen on culture. Conclusions Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite growth of a non-S. pneumoniae pathogen on culture. A precise definition of what constitutes a positive result is required to avoid falsely over-identifying specimens.

Malaria elimination efforts are hampered by the lack of sensitive tools to detect infections with low-level parasitemia, usually below the threshold of standard diagnostic methods, microscopy and rapid diagnostic tests. Isothermal nucleic acid amplification assays such as the loop-mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to run the test. However, the use of specialized equipment, as described by many groups, reduces the versatility of the LAMP technique as a simple tool for use in endemic countries. In this study, the use of the malachite green (MG) dye, as a visual endpoint readout, together with a simple mini heat block was evaluated for the detection of malaria parasites. The assay was performed for 1 hour at 63°C and the results scored by 3 independent human readers. The limit of detection of the assay was determined using well-quantified Plasmodium spp. infected reference samples and its utility in testing clinical samples was determined using 190 pre-treatment specimens submitted for reference diagnosis of imported malaria in the United States. Use of a simplified boil and spin methods of DNA extraction from whole blood and filter paper was also investigated. We demonstrate the accurate and sensitive detection of malaria parasites using this assay with a detection limit ranging between 1–8 parasites/μL, supporting its applicability for the detection of infections with low parasite burden. This assay is compatible with the use of a simple boil and spin sample preparation method from both whole blood and filter papers without a loss of sensitivity. The MG-LAMP assay described here has great potential to extend the reach of molecular tools to settings where they are needed.

Septic tanks are used for the removal of organic particulates in wastewaters by physical accumulation instead of through the biological production of biogas. Improved biogas production in septic tanks is crucial to increase the potential of this system for both energy generation and organic matter removal. In this study, the effect on the biogas production and biogas quality of coupling a 20 L lab-scale septic tank with a microbial electrolysis cell (MEC) was investigated and compared with a standard septic tank. Both reactors were operated at a volumetric organic loading rate of 0.5 gCOD/L d and a hydraulic retention time between 20 and 40 days using black water as an input under mesophilic conditions for a period of 3 months. The MEC-septic tank was operated at an applied voltage of 2.0 ±0.1V and the current experienced ranged from 40 mA (0.9 A/m2 projected electrode area) to 180 mA (5 A/m2 projected electrode area). The COD removal was of the order of 85% and the concentration of residual COD was not different between both reactors. Yet, the total phosphorous in the output was on average 39% lower in the MEC-septic tank. Moreover, the biogas production rate in the MEC-septic tank was a factor of 5 higher than in the control reactor and the H2S concentration in the biogas was a factor of 2.5 lower. The extra electricity supplied to the MEC-septic tank was recovered as extra biogas produced. Overall, it appears that the combination of MEC and a septic tank offers perspectives in terms of lower discharge of phosphorus and H2S, nutrient recuperation and a more reliable supply of biogas.

Mitochondrial uncoupling is implicated in many patho(physiological) states. Using confocal live cell imaging and an optical O2 sensing technique, we show that moderate uncoupling of the mitochondria with plecomacrolide Baf (bafilomycin A1) causes partial depolarization of the mitochondria and deep sustained deoxygenation of human colon cancer HCT116 cells subjected to 6% atmospheric O2. A decrease in iO2 (intracellular O2) to 0–10 μM, induced by Baf, is sufficient for stabilization of HIFs (hypoxia inducible factors) HIF-1α and HIF-2α, coupled with an increased expression of target genes including GLUT1 (glucose transporter 1), HIF PHD2 (prolyl hydroxylase domain 2) and CAIX (carbonic anhydrase IX). Under the same hypoxic conditions, treatment with Baf causes neither decrease in iO2 nor HIF-α stabilization in the low-respiring HCT116 cells deficient in COX (cytochrome c-oxidase). Both cell types display equal capacities for HIF-α stabilization by hypoxia mimetics DMOG (dimethyloxalylglycine) and CoCl2, thus suggesting that the effect of Baf under hypoxia is driven mainly by mitochondrial respiration. Altogether, by activating HIF signalling under moderate hypoxia, mitochondrial uncoupling can play an important regulatory role in colon cancer metabolism and modulate adaptation of cancer cells to natural hypoxic environments.

The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources.

Although several ADAMs (A disintegrin-like and metalloproteases) have been shown to contribute to the amyloid precursor protein (APP) metabolism, the full spectrum of metalloproteases involved in this metabolism remains to be established. Transcriptomic analyses centred on metalloprotease genes unraveled a 50% decrease in ADAM30 expression that inversely correlates with amyloid load in Alzheimer's disease brains. Accordingly, in vitro down- or up-regulation of ADAM30 expression triggered an increase/decrease in Aβ peptides levels whereas expression of a biologically inactive ADAM30 (ADAM30mut) did not affect Aβ secretion. Proteomics/cell-based experiments showed that ADAM30-dependent regulation of APP metabolism required both cathepsin D (CTSD) activation and APP sorting to lysosomes. Accordingly, in Alzheimer-like transgenic mice, neuronal ADAM30 over-expression lowered Aβ42 secretion in neuron primary cultures, soluble Aβ42 and amyloid plaque load levels in the brain and concomitantly enhanced CTSD activity and finally rescued long term potentiation alterations. Our data thus indicate that lowering ADAM30 expression may favor Aβ production, thereby contributing to Alzheimer's disease development., Highlights • By transcriptomic analyses, low levels of ADAM30 expression was observed in the brain of AD cases (compared with controls). • Activation of cathepsin D by ADAM30 is required to modulate the APP metabolism in vitro, i.e. decrease in Ab secretion. • In AD-like mice, neuronal ADAM30 expression led to lower soluble Aβ42, amyloid plaques and to rescue long term potentiation The amyloid precursor protein (APP) processing is central in the etiology of Alzheimer's disease (AD). Characterizing the actors of this metabolism is thus an important challenge. We searched for proteins involved in the APP processing and we selected the A disintegrin-like and metalloprotease 30 (ADAM30). Our results revealed an axis in APP metabolism pathway through an ADAM30-dependent cathepsin D activation. When activated following ADAM30 expression, a decrease in Aβ secretion occurred in vitro and in vivo. ADAM30 under-expression observed in AD brains and thus the impairment of the ADAM30-dependent pathway may favor Aβ peptide production and, ultimately, AD development.

Fat waste discarded from butcheries was used as a cosubstrate in the anaerobic codigestion of sewage sludge (SS). The process was evaluated under mesophilic and thermophilic conditions. The codigestion was successfully attained despite some inhibitory stages initially present that had their origin in the accumulation of volatile fatty acids (VFA) and adsorption of long-chain fatty acids (LCFA). The addition of a fat waste improved digestion stability and increased biogas yields thanks to the higher organic loading rate (OLR) applied to the reactors. However, thermophilic digestion was characterized by an effluent of poor quality and high VFA content. Results from spectroscopic analysis suggested the adsorption of lipid components onto the anaerobic biomass, thus disturbing the complete degradation of substrate during the treatment. The formation of fatty aggregates in the thermophilic reactor prevented process failure by avoiding the exposure of biomass to the toxic effect of high LCFA concentrations., This work was financially supported by the Ministerio de Economía y Competitividad through the project CTQ2015-68925-R (http://www.mineco.gob.es/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Somatic mutations found within the tyrosine kinase domain (TKD) of the human epidermal growth factor (HER) family of receptors have been implicated in the development and progression of non-small cell lung cancer (NSCLC). However, no conclusive reports have described pathogenic mutations in kinase-impaired HER3. Here, we report a case of an advanced chemotherapy-resistant NSCLC, harboring a novel HER3V855A somatic mutation homologous to the EGFRL858Ractivating mutation. Co-expression of HER3V855A and wild-type HER2 enhances ligand-induced transformation of murine and human cell lines, while HER-targeted inhibitors potently suppress mutant HER3 activity. Consistent with these observations, in silico computational modeling predicts that mutant V855A alters the kinase domain and c-terminal end of the HER3 protein. Taken together, these findings provide a basis for the clinical exploration of targeted therapies in HER3 mutant NSCLC and by extrapolation, in other cancers that more frequently carry somatic HER3 mutations. ispartof: Oncotarget vol:7 issue:3 pages:3068-83 ispartof: location:United States status: published

This study aimed to develop and test an unbiased and rapid methodology to estimate the length of external arbuscular mycorrhizal fungal (AMF) hyphae in soil. The traditional visual gridline intersection (VGI) method, which consists in a direct visual examination of the intersections of hyphae with gridlines on a microscope eyepiece after aqueous extraction, membrane-filtration, and staining (e.g., with trypan blue), was refined. For this, (i) images of the stained hyphae were taken by using a digital photomicrography technique to avoid the use of the microscope and the method was referred to as "digital gridline intersection" (DGI) method; and (ii), the images taken in (i) were processed and the hyphal length was measured by using ImageJ software, referred to as the "photomicrography-ImageJ processing" (PIP) method. The DGI and PIP methods were tested using known grade lengths of possum fur. Then they were applied to measure the hyphal lengths in soils with contrasting phosphorus (P) fertility status. Linear regressions were obtained between the known lengths (Lknown) of possum fur and the values determined by using either the DGI (LDGI) (LDGI = 0.37 + 0.97 × Lknown, r2 = 0.86) or PIP (LPIP) methods (LPIP = 0.33 + 1.01 × Lknown, r2 = 0.98). There were no significant (P > 0.05) differences between the LDGI and LPIP values. While both methods provided accurate estimation (slope of regression being 1.0), the PIP method was more precise, as reflected by a higher value of r2 and lower coefficients of variation. The average hyphal lengths (6.5-19.4 m g-1) obtained by the use of these methods were in the range of those typically reported in the literature (3-30 m g-1). Roots growing in P-deficient soil developed 2.5 times as many hyphae as roots growing in P-rich soil (17.4 vs 7.2 m g-1). These tests confirmed that the use of digital photomicrography in conjunction with either the grid-line intersection principle or image processing is a suitable method for the measurement of AMF hyphal lengths in soils for comparative investigations.

Non-native bark and ambrosia beetles represent a threat to forests worldwide. Their invasion patterns are, however, still unclear. Here we investigated first, if the spread of non-native bark and ambrosia beetles is a gradual or a discontinuous process; second, which are the main correlates of their community structure; third, whether those correlates correspond to those of native species. We used data on species distribution of non-native and native scolytines in the continental 48 USA states. These data were analyzed through a beta-diversity index, partitioned into species richness differences and species replacement, using Mantel correlograms and non-metric multidimensional scaling (NMDS) ordination for identifying spatial patterns, and regression on distance matrices to test the association of climate (temperature, rainfall), forest (cover area, composition), geographical (distance), and human-related (import) variables with β-diversity components. For both non-native bark and ambrosia beetles, β-diversity was mainly composed of species richness difference than species replacement. For non-native bark beetles, a discontinuous invasion process composed of long distance jumps or multiple introduction events was apparent. Species richness differences were primarily correlated with differences in import values while temperature was the main correlate of species replacement. For non-native ambrosia beetles, a more continuous invasion process was apparent, with the pool of non-native species arriving in the coastal areas that tended to be filtered as they spread to interior portions of the continental USA. Species richness differences were mainly correlated with differences in rainfall among states, while rainfall and temperature were the main correlates of species replacement. Our study suggests that the different ecology of bark and ambrosia beetles influences their invasion process in new environments. The lower dependency that bark beetles have on climate allowed them to potentially colonize more areas within the USA, while non-native ambrosia beetles, being dependent on rainfall, are typically filtered by the environment.

The intensive search of new and cleaner energy catches interest in recent years due to huge consumption of fossil fuels coupled with the challenge of energy and environmental sustainability. Production of renewable and environmentally benign energy from locally available raw materials is coming in the frontline. In this work, conversion of the combined biomass (cotton gin trash, cow manure, and Microalgae [Nannochloropsis oculata]) through batch pyrolysis has been investigated. The effect of temperature to the production of energy fuels such as bio-oil, char, and biogas have been simulated considering the yield and energy content as responses. Result of the investigation generally revealed that the proportions of the different biomass did not significantly affect the product yield and energy recovery. Significant effect of temperature is evident in the simulation result of energy recovery whereby maximum conversion was achieved at 400°C for char (91 wt%), 600°C for syngas (22 wt%), and 551°C for bio-oil (48 wt%). Overall energy conversion efficiency of 75.5% was obtained at 589°C in which 15.6 MJ/kg of mixed biomass will be elevated to pyrolysis products.

The fast pyrolysis behaviour of pretreated banagrass was examined at four temperatures (between 400 and 600 C) and four residence times (between ~1.2 and 12 s). The pretreatment used water washing/leaching to reduce the inorganic content of the banagrass. Yields of bio-oil, permanent gases and char were determined at each reaction condition and compared to previously published results from untreated banagrass. Comparing the bio-oil yields from the untreated and pretreated banagrass shows that the yields were greater from the pretreated banagrass by 4 to 11 wt% (absolute) at all reaction conditions. The effect of pretreatment (i.e. reducing the amount of ash, and alkali and alkali earth metals) on pyrolysis products is: 1) to increase the dry bio-oil yield, 2) to decrease the amount of undetected material, 3) to produce a slight increase in CO yield or no change, 4) to slightly decrease CO2 yield or no change, and 5) to produce a more stable bio-oil (less aging). Char yield and total gas yield were unaffected by feedstock pretreatment. Four other tropical biomass species were also pyrolyzed under one condition (450°C and 1.4 s residence time) for comparison to the banagrass results. The samples include two hardwoods: leucaena and eucalyptus, and two grasses: sugarcane bagasse and energy-cane. A sample of pretreated energy-cane was also pyrolyzed. Of the materials tested, the best feedstocks for fast pyrolysis were sugarcane bagasse, pretreated energy cane and eucalyptus based on the yields of 'dry bio-oil', CO and CO2. On the same basis, the least productive feedstocks are untreated banagrass followed by pretreated banagrass and leucaena.

An agar sediment test was developed to evaluate the suitability of organic waste streams from the food industry for recovering nutrients by the aquatic worm Lumbriculus variegatus (Lv). The effects of agar gel, sand, and food quantities in the sediment test on worm growth, reproduction, and water quality were studied. Agar gel addition ameliorated growth conditions by reducing food hydrolysis and altering sediment structure. Best results for combined reproduction and growth were obtained with 0.6% agar-gel (20 ml), 10 g. fine sand, 40 g. coarse sand, and 105 mg fish food (Tetramin). With agar gel, ingestion and growth is more the result of addition of food in its original quality. Final tests with secondary potato starch sludge and wheat bran demonstrated that this test is appropriate for the comparison of solid feedstuffs and suspended organic waste streams. This test method is expected to be suitable for organic waste studies using other sediment dwelling invertebrates.

To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved proliferation capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endodermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.

In general, in composting facilities the active, or intensive, stage of the process is done separately from the maturation stage, using a specific technology and time. The pre-composted material to be matured can contain enough biodegradable substrates to cause microbial proliferation, which in turn can cause temperatures to increase. Therefore, not controlling the maturation period during waste management at an industrial level can result in undesired outcomes. The main hypothesis of this study is that controlling the maturation stage through turning provides one with an optimized process when compared to the static approach. The waste used was sludge from a seafood-processing plant, mixed with shredded wood (1:2, v/v). The composting system consists of an intensive stage in a 600L static reactor, followed by maturation in triplicate in 200L boxes for 112 days. Two tests were carried out with the same process in reactor and different treatments in boxes: static maturation and turning during maturation when the temperature went above 55°C. PLFAs, organic matter, pH, electrical conductivity, forms of nitrogen and carbon, hydrolytic enzymes and respiratory activity were periodically measured. Turning significantly increased the duration of the thermophilic phase and consequently increased the organic-matter degradation. PCA differentiated significantly the two treatments in function of tracking parameters, especially pH, total carbon, forms of nitrogen and C/N ratio. So, stability and maturity optimum values for compost were achieved in less time with turnings. Whereas turning resulted in microbial-group stabilization and a low mono/sat ratio, static treatment produced greater variability in microbial groups and a high mono/sat ratio, the presence of more degradable substrates causes changes in microbial communities and their study during maturation gives an approach of the state of organic-matter degradation. Obtaining quality compost and optimizing the composting process requires using turning as a control mechanism during maturation.

Dried blood spot (DBS) sampling is recognized as a valuable alternative sampling strategy both in research and in clinical routine. Although many advantages are associated with DBS sampling, its more widespread use is hampered by several issues, of which the hematocrit effect on DBS-based quantitation remains undoubtedly the most widely discussed one. Previously, we developed a method to derive the approximate hematocrit from a nonvolumetrically applied DBS based on its potassium content. Although this method yielded good results and was straightforward to perform, it was also destructive and required sample preparation. Therefore, we now developed a nondestructive method which allows to predict the hematocrit of a DBS based on its hemoglobin content, measured via noncontact diffuse reflectance spectroscopy. The developed method was thoroughly validated. A linear calibration curve was established after log/log transformation. The bias, intraday and interday imprecision of quality controls at three hematocrit levels and at the lower and upper limit of quantitation (0.20 and 0.67, respectively) were less than 11%. In addition, the influence of storage and the volume spotted was evaluated, as well as DBS homogeneity. Application of the method to venous DBSs prepared from whole blood patient samples (n = 233) revealed a good correlation between the actual and the predicted hematocrit. Limits of agreement obtained after Bland and Altman analysis were -0.076 and. +0.018. Incurred sample reanalysis demonstrated good method reproducibility. In conclusion, mere scanning of a DBS suffices to derive its approximate hematocrit, one of the most important variables in DBS analysis.

This study examined the effect of debagging time on color and flavor / taste compounds in the non-red apple cultivar 'Golden Delicious' and red cultivar 'Qinguan' at mid and late stages of fruit development. Debagging briefly improved the red color in both cultivars, the peel of 'Golden Delicious' presenting pale-pink hue. However, rapid anthocyanin accumulation occurred in apple peel at a specific time (after 179 days after flowering (DAF) in 'Qinguan') and was unaltered by debagging time in the red cultivar 'Qinguan'. Furthermore, untimely debagging had a detrimental effect on the content of anthocyanin. All sugars increased and organic acids decreased in apple pulp at mid to late stages of development. Bagging treatment reduced the content of most sugars and organic acids, as well as, the overall total. However, glucose and citric acid contents were higher in bagged fruit than non-bagged fruit; the maximum occurred in T7 treatment that was no-debagging at DAF 159 / 196 ('Golden delicious' / 'Qinguan'), i.e., 24.35 and 0.07 mg g-1 FW in 'Golden delicious', and 38.86 and 0.06 mg g-1 FW in 'Qinguan', respectively. In a word, bagging treatment can alter the pattern of peel color development in apple fruit; however, it remains difficult to alter the timing of rapid anthocyanin accumulation as it is regulated solely by development. Moreover, bagging treatment reduced the total accumulation of sugars and organic acids, and even the over total in pulp, but increased the glucose and citric acid contents in apple pulp.

Highlight We identified C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) as a novel, auxin-repressed and phloem pole-expressed signal assisting in the formation of lateral roots., Roots explore the soil for water and nutrients through the continuous production of lateral roots. Lateral roots are formed at regular distances in a steadily elongating organ, but how future sites for lateral root formation become established is not yet understood. Here, we identified C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) as a novel, auxin-repressed and phloem pole-expressed signal assisting in the formation of lateral roots. In addition, based on genetic and expression data, we found evidence for the involvement of its proposed receptor, XYLEM INTERMIXED WITH PHLOEM 1 (XIP1)/CEP RECEPTOR 1 (CEPR1), during the process of lateral root initiation. In conclusion, we report here on the existence of a peptide ligand−receptor kinase interaction that impacts lateral root initiation. Our results represent an important step towards the understanding of the cellular communication implicated in the early phases of lateral root formation.

Highlight Maturation of GLV signaling peptides requires two SBT6 subtilases. SBT6 proteolytic activity is further regulated by the Serpin1 inhibitor, implying a complex network that controls cell elongation in Arabidopsis., The GOLVEN (GLV) gene family encode small secreted peptides involved in important plant developmental programs. Little is known about the factors required for the production of the mature bioactive GLV peptides. Through a genetic suppressor screen in Arabidopsis thaliana, two related subtilase genes, AtSBT6.1 and AtSBT6.2, were identified that are necessary for GLV1 activity. Root and hypocotyl GLV1 overexpression phenotypes were suppressed by mutations in either of the subtilase genes. Synthetic GLV-derived peptides were cleaved in vitro by the affinity-purified SBT6.1 catalytic enzyme, confirming that the GLV1 precursor is a direct subtilase substrate, and the elimination of the in vitro subtilase recognition sites through alanine substitution suppressed the GLV1 gain-of-function phenotype in vivo. Furthermore, the protease inhibitor Serpin1 bound to SBT6.1 and inhibited the cleavage of GLV1 precursors by the protease. GLV1 and its homolog GLV2 were expressed in the outer cell layers of the hypocotyl, preferentially in regions of rapid cell elongation. In agreement with the SBT6 role in GLV precursor processing, both null mutants for sbt6.1 and sbt6.2 and the Serpin1 overexpression plants had shorter hypocotyls. The biosynthesis of the GLV signaling peptides required subtilase activity and might be regulated by specific protease inhibitors. The data fit with a model in which the GLV1 signaling pathway participates in the regulation of hypocotyl cell elongation, is controlled by SBT6 subtilases, and is modulated locally by the Serpin1 protease inhibitor.

Highlight Strigolactones monitor lateral root development in a spatiotemporal manner by an interplay with cytokinin., Strigolactones are important rhizosphere signals that act as phytohormones and have multiple functions, including modulation of lateral root (LR) development. Here, we show that treatment with the strigolactone analog GR24 did not affect LR initiation, but negatively influenced LR priming and emergence, the latter especially near the root–shoot junction. The cytokinin module ARABIDOPSIS HISTIDINE KINASE3 (AHK3)/ARABIDOPSIS RESPONSE REGULATOR1 (ARR1)/ARR12 was found to interact with the GR24-dependent reduction in LR development, because mutants in this pathway rendered LR development insensitive to GR24. Additionally, pharmacological analyses, mutant analyses, and gene expression analyses indicated that the affected polar auxin transport stream in mutants of the AHK3/ARR1/ARR12 module could be the underlying cause. Altogether, the data reveal that the GR24 effect on LR development depends on the hormonal landscape that results from the intimate connection with auxins and cytokinins, two main players in LR development.

Second generation biofuels are derived from inedible lignocellulosic biomass of food and non-food crops. Lignocellulosic biomass is mainly composed of cell walls that contain a large proportion of cellulosic and hemicellulosic polysaccharides. An interesting route to generate biofuels and bio-based materials is via enzymatic hydrolysis of cell wall polysaccharides into fermentable sugars, a process called saccharification. The released sugars can then be fermented to fuels, e.g. by use of yeast. To test the saccharification efficiency of lignocellulosic biomass on a lab-scale, a manual saccharification protocol was established that uses only small amounts of biomass and a low concentration of enzyme. This protocol can be used for different plant species like Arabidopsis thaliana, tobacco, maize and poplar. The low enzyme concentrations make it possible to detect subtle improvements in saccharification yield and to analyze the speed of hydrolysis. Although a specific acid and alkali pretreatment were included, the saccharification step can be preceded by any other pretreatment. Because no advanced equipment is necessary, this protocol can be carried out in many laboratories to analyze saccharification yield. The protocol was initially described in Van Acker et al. (2013).

Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons.

Highlight Plant auxin efflux and influx proteins redirect the plant hormone auxin towards the feeding site upon root-knot nematode infection in Arabidopsis thaliana roots., Plant-parasitic root-knot nematodes induce the formation of giant cells within the plant root, and it has been recognized that auxin accumulates in these feeding sites. Here, we studied the role of the auxin transport system governed by AUX1/LAX3 influx proteins and different PIN efflux proteins during feeding site development in Arabidopsis thaliana roots. Data generated via promoter–reporter line and protein localization analyses evoke a model in which auxin is being imported at the basipetal side of the feeding site by the concerted action of the influx proteins AUX1 and LAX3, and the efflux protein PIN3. Mutants in auxin influx proteins AUX1 and LAX3 bear significantly fewer and smaller galls, revealing that auxin import into the feeding sites is needed for their development and expansion. The feeding site development in auxin export (PIN) mutants was only slightly hampered. Expression of some PINs appears to be suppressed in galls, probably to prevent auxin drainage. Nevertheless, a functional PIN4 gene seems to be a prerequisite for proper nematode development and gall expansion, most likely by removing excessive auxin to stabilize the hormone level in the feeding site. Our data also indicate a role of local auxin peaks in nematode attraction towards the root.

Extracts of the exuviae (cast skins) of nymphal bed bugs (Cimex lectularius) were analyzed for volatile compounds that might contribute to arrestment of adult bed bugs. Four volatile aldehydes, (E)-2-hexenal, 4-oxo-(E)-2-hexenal, (E)-2-octenal, and 4-oxo-(E)-2-octenal were consistently detected in the headspace of freshly shed exuviae regardless of the developmental stages from which the exuviae were obtained. Quantification of the aldehydes in the solvent extracts of homogenized fresh, 45- or 99-d aged 5th instar exuviae indicated that the aldehydes are present in the exuviae and dissipate over time, through evaporation or degradation. Microscopic observation of the fifth instar exuviae indicated that the dorsal abdominal glands on the exuviae maintained their pocket-like structures with gland reservoirs, within which the aldehydes might be retained. Two-choice olfactometer studies with the volatiles from exuviae or a synthetic blend mimicking the volatiles indicated that adult bed bugs tend to settle close to sources of the aldehydes. Our results imply that the presence and accumulation of bed bug exuviae and the aldehydes volatilizing from the exuviae might mediate bed bugs' interaction with their microhabitats.

Removal of pathogenic organisms from reprocessed surgical instruments is essential to prevent iatrogenic infections. Some bacteria can make persistent biofilms on medical devices. Contamination of non-disposable equipment with prions also represents a serious risk to surgical patients. Efficient disinfection of prions from endoscopes and other instruments such as high-resolution cameras remains problematic because these instruments do not tolerate aggressive chemical or heat treatments. Herein, we develop a new washing system that uses both the alkaline and acidic water produced by electrolysis. Electrolyzed acidic water, containing HCl and HOCl as active substances, has been reported to be an effective disinfectant. A 0.15% NaCl solution was electrolyzed and used immediately to wash bio-contaminated stainless steel model systems with alkaline water (pH 11.9) with sonication, and then with acidic water (pH 2.7) without sonication. Two bacterial species (Staphylococcus aureus and Pseudomonas aeruginosa) and a fungus (Candida albicans) were effectively removed or inactivated by the washing process. In addition, this process effectively removed or inactivated prions from the stainless steel surfaces. This washing system will be potentially useful for the disinfection of clinical devices such as neuroendoscopes because electrolyzed water is gentle to both patients and equipment and is environmentally sound.

PLoS one 11(1), e0147725 (2016). doi:10.1371/journal.pone.0147725, Published by PLoS, Lawrence, Kan.