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Background Brucellosis, as a serious zoonotic infectious disease, has been recognized as a re-emerging disease in the developing countries worldwide. In china, the incidence of brucellosis is increasing each year, seriously threatening the health of humans as well as animal populations. Despite a quite number of diagnostic methods currently being used for brucellosis, innovative technologies are still needed for its rapid and accurate diagnosis, especially in area where traditional diagnostic is unavailable. Methodology/Principal findings In this study, a total of 22 B cell linear epitopes were predicted from five Brucella outer membrane proteins (OMPs) using an immunoinformatic approach. These epitopes were then chemically synthesized, and with the method of indirect ELISA (iELISA), each of them displayed a certain degree of capability in identifying human brucellosis positive sera. Subsequently, a fusion protein consisting of the 22 predicted epitopes was prokaryotically expressed and used as diagnostic antigen in a newly established brucellosis testing method, nano-ZnO modified paper-based ELISA (nano-p-ELISA). According to the verifying test using a collection of sera collected from brucellosis and non-brucellosis patients, the sensitivity and specificity of multiepitope based nano-p-ELISA were 92.38% and 98.35% respectively. The positive predictive value was 98.26% and the negative predictive value was 91.67%. The multiepitope based fusion protein also displayed significantly higher specificity than Brucella lipopolysaccharide (LPS) antigen. Conclusions B cell epitopes are important candidates for serologically testing brucellosis. Multiepitope fusion protein based nano-p-ELISA displayed significantly sensitivity and specificity compared to Brucella LPS antigen. The strategy applied in this study will be helpful to develop rapid and accurate diagnostic method for brucellosis in human as well as animal populations., Author summary Brucellosis is one of the most important zoonosis in the world and has caused tremendous economic losses in agriculture and animal husbandry in many countries. Developing rapid, sensitive and specific diagnostic methods is very important for early detection and treatment of brucellosis patients. In this study, a novel diagnostic technique, nano-ZnO modified paper ELISA, was established. The antigen used in this technique was a fusion protein containing multiple B cell epitopes, which were predicted from Brucella major outer membrane proteins such as Bp26, Omp31, Omp16, Omp2b and Omp25. Comparing to traditional LPS antigen, this multiepitope based antigen displayed considerably higher sensitivity and higher specificity in laboratory. With the strategy described in this paper, more efficient epitopes and protein antigen can be identified in the future. Currently, LPS antigen is only prepared from live Brucella, while protein antigen can be produced in large quantities in prokaryotic expression system. In addition to nano-p-ELISA, this protein antigen can also be used for development other methods such as fluorescent polarization assay (FPA) and immunochromatographic assay (ICA) to meet the varied demand for brucellosis testing.

Rabies is a lethal zoonotic encephalomyelitis that causes an estimated 59,000 human deaths yearly worldwide. Although developing countries of Asia and Africa bear the heaviest burden, surveillance and disease detection in these countries is often hampered by the absence of local laboratories able to diagnose rabies and/or the difficulties of sample shipment from low-access areas to national reference laboratories. Filter papers offer a convenient cost-effective alternative for the sampling, shipment, and storage of biological materials for the diagnosis of many pathogens including rabies virus, yet the properties of diagnostic tests using this support have not been evaluated thoroughly. Sensitivity and specificity of molecular diagnosis of rabies infection using a reverse transcription followed by a hemi-nested polymerase chain reaction (RT-hn-PCR) either directly on brain tissue or using brain tissue dried on filter paper were assessed on 113 suspected field animal samples in comparison to the direct fluorescent antibody test (FAT) recommended by the World Health Organization as one of the reference tests for rabies diagnosis. Impact of the duration of the storage was also evaluated. The sensitivity and the specificity of RT-hn-PCR i) on brain tissue were 96.6% (95% CI: [88.1–99.6]) and 92.7% (95% CI: [82.4–98.0]) respectively and ii) on brain tissue dried on filter paper 100% (95% CI: [93.8–100.0]) and 90.9% (95% CI: [80.0–97.0]) respectively. No loss of sensitivity of RT-hn-PCR on samples of brain tissue dried on filter paper left 7 days at ambient temperature was detected indicating that this method would enable analyzing impregnated filter papers sent to the national reference laboratory at ambient temperature within a 1-week shipment time. It could therefore be an effective alternative to facilitate storage and shipment of samples from low-access areas to enhance and expand rabies surveillance., Author summary Dogs are responsible for 99% of human rabies deaths. Facilitating diagnostic of rabid dogs can help further identify i) people who were exposed to rabies in order to encourage them to seek post exposure prophylaxis and ii) other exposed animals to break the transmission chain (i.e. prevent them from further transmitting the virus to other people and animals). Yet, the reference diagnostic method for animal rabies requires brain samples to be collected post-mortem and shipped under temperature-controlled conditions. The shipping of such samples is complex in low-access areas, especially in low income countries, which are often those that bear the heaviest rabies burden. Filter papers offer a convenient alternative for biological sample shipment and storage. Here the efficiency of a molecular diagnostic method applied to brain tissue dried on filter paper is compared to one of the reference methods, the direct fluorescent antibody test. Our results show it has an excellent sensitivity (it does not miss any positive samples), even when filter papers are left 7 days at ambient temperature. These results let us foresee a cost-effective alternative facilitating shipment, storage and testing of samples from rabies suspected animals from low-access areas. This could considerably enhance and expand rabies surveillance in low-income countries, allowing a more comprehensive evaluation of rabies burden, and thus reinforcing arguments for allocating funds to rabies control policies.

Amphimeriasis, a fish-borne zoonotic disease caused by the liver fluke Amphimerus spp., has recently been reported as an emerging disease affecting an indigenous Ameridian group, the Chachi, living in Ecuador. The only method for diagnosing amphimeriasis was the microscopic detection of eggs from the parasite in patients' stool samples with very low sensitivity. Our group developed an ELISA technique for detection of anti-Amphimerus IgG in human sera and a molecular method based on LAMP technology (named LAMPhimerus) for specific and sensitive parasite DNA detection. The LAMPhimerus method showed to be much more sensitive than classical parasitological methods for amphimeriasis diagnosis using human stool samples for analysis. The objective of this work is to demonstrate the feasibility of using dried stool samples on filter paper as source of DNA in combination with the effectiveness of our previously designed LAMPhimerus assay for successfully Amphimerus sp. detection in clinical stool samples. A total of 102 untreated and undiluted stool samples collected from Chachi population were spread as thin layer onto common filter paper for easily transportation to our laboratory and stored at room temperature for one year until DNA extraction. When LAMPhimerus method was applied for Amphimerus sp. DNA detection, a higher number of positive results was detected (61/102; 59.80%) in comparison to parasitological methods (38/102; 37.25%), including 28/61 (45.90%) microscopy-confirmed Amphimerus sp. infections. The diagnostic parameters for the sensitivity and specificity werecalculated for our LAMPhimerus assay, which were 79.17% and 65.98%, respectively. We demonstrate, for the first time, that common filter paper is useful for easy collection and long-term storage of human stool samples for later DNA extraction and molecular analysis of human-parasitic trematode eggs. This simple, economic and easily handling method combined with the specific and sensible LAMPhimerus assay has the potential to beused as an effective molecular large-scale screening test for amphimeriasis-endemic areas.

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.

Rocky desertification is a bottleneck that reduces ecological and environmental security in karst areas. Paper mulberry, a unique deciduous tree, shows good performance in rocky desertification areas. Its resistance mechanisms are therefore of high interest. In this study, a lysine acetylation proteomics analysis of paper mulberry seedling leaves was conducted in combination with the purification of acetylated protein by high-precision nano LC-MS/MS. We identified a total of 7130 acetylation sites in 3179 proteins. Analysis of the modified sites showed a predominance of nine motifs. Six positively charged residues: lysine (K), arginine (R), and histidine (H), serine (S), threonine (T), and tyrosine (Y) occurred most frequently at the +1 position, phenylalanine (F) was both detected both upstream and downstream of the acetylated lysines; and the sequence logos showed a strong preference for lysine and arginine around acetylated lysines. Functional annotation revealed that the identified enzymes were mainly involved in translation, transcription, ribosomal structure and biological processes, showing that lysine acetylation can regulate various aspects of primary carbon and nitrogen metabolism and secondary metabolism. Acetylated proteins were enriched in the chloroplast, cytoplasm, and nucleus, and many stress response-related proteins were also discovered to be acetylated, including PAL, HSP70, and ERF. HSP70, an important protein involved in plant abiotic and disease stress responses, was identified in paper mulberry, although it is rarely found in woody plants. This may be further examined in research in other plants and could explain the good adaptation of paper mulberry to the karst environment. However, these hypotheses require further verification. Our data can provide a new starting point for the further analysis of the acetylation function in paper mulberry and other plants.

Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of 'superfolder' green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 mug/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens.

Type 1 diabetes (T1D) is increasing in incidence and predictable with measurement of serum islet autoantibodies (iAb) years prior to clinical disease onset. Identifying iAb positive individuals reduces diabetic ketoacidosis and identifies individuals for T1D prevention trials. However, large scale screening for iAb remains challenging as assays have varying sensitivities and specificities, insulin autoantibodies remain difficult to measure and venipuncture is generally required to obtain serum. We developed an approach to reliably measure all four major iAb, including insulin autoantibodies, from dried blood spots (DBS) on filter-paper. By spiking iAb positive serum into iAb negative whole blood in a dose titration, we optimized the conditions for autoantibody elution from filter paper as measured by fluid phase radioimmunoassays. After assessing stability of measuring iAb from DBS over time, we then screened iAb from DBS and the corresponding serum in new-onset T1D (n = 52), and controls (n = 72) which included first-degree relatives of T1D patients. iAb measured from eluted DBS in new-onset T1D strongly correlated with serum measurements (R2 = 0.96 for mIAA, GADA = 0.94, IA-2A = 0.85, ZnT8A = 0.82, p

In this paper, we present a facile and cost-effective method to obtain superhydrophobic filter paper and demonstrate its application for efficient water/oil separation. By coupling structurally distinct organosilane precursors (e.g., octadecyltrichlorosilane and methyltrichlorosilane) to paper fibers under controlled reaction conditions, we have formulated a simple, inexpensive, and efficient protocol to achieve a desirable superhydrophobic and superoleophilic surface on conventional filter paper. The silanized superhydrophobic filter paper showed nanostructured morphology and demonstrated great separation efficiency (up to 99.4%) for water/oil mixtures. The modified filter paper is stable in both aqueous solutions and organic solvents, and can be reused multiple times. The present study shows that our newly developed binary silanization is a promising method of modifying cellulose-based materials for practical applications, in particular the treatment of industrial waste water and ecosystem recovery.

In vitro 3D culture is an important model for tissues in vivo. Cells in different locations of 3D tissues are physiologically different, because they are exposed to different concentrations of oxygen, nutrients, and signaling molecules, and to other environmental factors (temperature, mechanical stress, etc). The majority of high-throughput assays based on 3D cultures, however, can only detect the average behavior of cells in the whole 3D construct. Isolation of cells from specific regions of 3D cultures is possible, but relies on low-throughput techniques such as tissue sectioning and micromanipulation. Based on a procedure reported previously (‘‘cells-in-gels-in-paper’’ or CiGiP), this paper describes a simple method for culture of arrays of thin planar sections of tissues, either alone or stacked to create more complex 3D tissue structures. This procedure starts with sheets of paper patterned with hydrophobic regions that form 96 hydrophilic zones. Serial spotting of cells suspended in extracellular matrix (ECM) gel onto the patterned paper creates an array of 200 micron-thick slabs of ECM gel (supported mechanically by cellulose fibers) containing cells. Stacking the sheets with zones aligned on top of one another assembles 96 3D multilayer constructs. De-stacking the layers of the 3D culture, by peeling apart the sheets of paper, ‘‘sections’’ all 96 cultures at once. It is, thus, simple to isolate 200-micron-thick cell-containing slabs from each 3D culture in the 96-zone array. Because the 3D cultures are assembled from multiple layers, the number of cells plated initially in each layer determines the spatial distribution of cells in the stacked 3D cultures. This capability made it possible to compare the growth of 3D tumor models of different spatial composition, and to examine the migration of cells in these structures.

Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a "dying" paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing "offspring". Practically, this might be used to trace the successive published milestones of a research field., SCOPUS: ar.j, info:eu-repo/semantics/published

Rapid diagnosis by using small, simple, and portable devices could represent one of the best strategies to limit the damage and contain the spread of viral, bacterial or protozoa diseases, principally when they can be transmitted by air and are highly contagious, as some respiratory viruses are. The presence of antibodies in blood or serum samples is not the best option for deciding when a person must be quarantined to stop transmission of disease, given that cured patients have antibodies, so the best diagnosis methods rely on the use of nucleic acid amplification procedures. Here we present a very simple device and detection principle, based on paper discs coupled to contactless conductivity (C4D) sensors, can provide fast and easy diagnostics that are needed when an epidemic outbreak develops. The paper device presented here solves one of the main drawbacks that nucleic acid amplification tests have when they are performed outside of central laboratories. As the device is sealed before amplification and integrally disposed in this way, amplimers release cannot occur, allowing repetitive testing in the physician’s practice, ambulances, or other places that are not prepared to avoid cross-contamination of new samples. The use of very low volume samples allows efficient reagent use and the development of low cost, simple, and disposable point-of-care diagnostic systems., Author summary In 2005, the World Health Organization (WHO) recognized Chagas Disease as a neglected tropical disease. Meanwhile the serological tests, recommended by WHO, can be performed for chronic disease diagnosis, the nucleic acid amplification tests must be performed for the detection of the acute phase of the disease. Although the existing laboratory diagnosis tests for Chagas Disease are sensitive and highly reproducible, they cannot be performed in rural, low infrastructure environments, where this disease prevails. In this sense, the use of simple and portable analytical devices may be able to offer an affordable solution to this problem, allowing fast sampling, diagnosis and treatment prescription in one simple and fast intervention, as the performed by short term medical missions. In this study we show for the first time a diagnosis test comprising low cost materials and employing a contactless and label-free conductivity detection system that is used to read the result of a nucleic acid amplification reaction. The test showed high sensitivity for Chagas Disease diagnosis showing the potential to be used in rural and low income places.

Passiflora quadrangularis L. belongs to the family Passifloraceae which bears larger fruit with edible juicy mesocarp and pulp known as a good source of phytochemicals. Cultivation and plant management practices are known to influence the phytochemical compositions of agricultural produce. This study aimed to examine the influence of the cultivation practices on the antioxidant activities and secondary metabolites of the organically and conventionally grown P. quadrangularis. Findings revealed organically treated P. quadrangularis plants showed enhancement in their antioxidant properties and secondary metabolites profiles. Among the plant parts, leaves of P. quadrangularis grown organically possessed higher antioxidant activities compared to the conventional in all assays evaluated. The antioxidant activities in the edible parts of the P. quadrangularis fruit have also been enhanced through organic cultivation with significantly higher total phenolic content and DPPH in mesocarp, and the pulp showed higher total flavonoid content, DPPH and FRAP. This observation is supported by a higher level of vitamins and secondary metabolites in the samples. The secondary metabolites profile showed mesocarps were phenolic rich, the pulps were flavonoids rich while leaves showed good composition of phenolics, flavonoids and terpenoids with outstanding antioxidant activities. The common secondary metabolites for organically produced P. quadrangularis in different plant parts include 2-isopropyl-3-methoxycinnamic acid (mesocarp and pulp), myricetin isomers (pulp and leaves), and malvidin-3-O-arabinoside isomers (pulp and leaves). This study confirmed that organic cultivated P. quadrangularis possessed higher antioxidant activities contributed by its vitamins and secondary metabolites.

Globally, the economic losses due to hard ticks infestation and the control of the associated diseases have been calculated at USD $13.9–18.7 billion per year. The economic impact is related to its direct damage to the skins, blood loss, anemia, severe immunological reactions and indirect losses that related to the effects of hemoparasites, cost of treatment for clinical cases and expenses incurred in the control of ticks. The current study evaluated the acaricidal activities of fennel Foeniculum vulgare essential oil and its main components; trans-anethole and fenchone; against R. annulatus. GC–MS analysis revealed that this oil contained 16 components representing 99.9% of the total identified compounds with E-anethole being the predominant component(64.29%), followed by fenchone (9.94%). The fennel oil and trans-anethole showed significant acaricidal activities. The LC50 of the fennel oil was attained at concentrations of 12.96% for adult ticks and 1.75% for tick larvae meanwhile the LC50 of trans-anethole was reached at concentrations of 2.36% for adult tick and 0.56% for tick larvae. On the contrary, fenchone showed no any significant adulticidal activities and its LC50 attained at a concentration of 9.11% for tick larvae. Regarding repellence activities, trans-anethole achieved 100% repellency at the concentration of 10% while fennel showed 86% repellency at the same concentration. Fenchone showed no repellency effect. Treatment of larvae with fennel, trans-anethole, and fenchone LC50 concentrations significantly inhibited the acetylcholinesterase activity. Meanwhile, glutathione s-transferase activity was significantly decreased in fennel treated larvae but no significant effect was found in the larvae of trans-anethole and fenchone groups. These results indicate that the acaricide effect of fennel oil may attributed to its high content of trans-anethole. This was supported by potent adulticidal, larvicidal, and repellency effects of trans-anethole against Rhipeciphalus annulatus tick and therefore it could be included in the list of acaricide of plant origin.

Annually, agricultural activity produces an enormous amount of plant biomass by-product. Many studies have reported the biomethane potential of agro-industrial wastes, but only a few studies have investigated applying the substrates in both batch and continuous mode. Tomato is one of the most popular vegetables globally; its processing releases a substantial amount of by-product, such as stems and leaves. This study examined the BMP of tomato plant (Solanum lycopersicum Mill. L. cv. Alfred) waste. A comparative test revealed that the BMPs of corn stover, tomato waste,and their combination were approximately the same, around 280 mL methane/g Volatile Solid. In contrast, the relative biogas production decreased in the presence of tomato waste in a continuous mesophilic anaerobic digestion system; the daily biogas productions were 860 ± 80, 290 ± 50, and 570 ± 70 mL biogas/gVolatile Solid/day in the case of corn stover, tomato waste, and their mixture, respectively. The methane content of biogas was around 46–48%. The fermentation parameters of the continuous AD experiments were optimal in all cases; thus, TW might have an inhibitory effect on the microbial community. Tomato plant materials contain e.g. flavonoids, glycoalkaloids (such as tomatine and tomatidine), etc. known as antimicrobial and antifungal agents. The negative effect of tomatine on the biogas yield was confirmed in batch fermentation experiments. Metagenomic analysis revealed that the tomato plant waste caused significant rearrangements in the microbial communities in the continuously operated reactors. The results demonstrated that tomato waste could be a good mono-substrate in batch fermentations or a co-substrate with corn stover in a proper ratio in continuous anaerobic fermentations for biogas production. These results also point to the importance of running long-term continuous fermentations to test the suitability of a novel biomass substrate for industrial biogas production.

Determining the distribution of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) in the Yangtze River has to date relied on traditional visual and counting methods, but such field surveys are time-consuming and expensive. Analyses using environmental DNA (eDNA) to investigate the presence and range of endangered aquatic species have proven to be more economical and effective detection methods, and are a non-invasive approach to sampling. A challenge of relying on eDNA for YFP monitoring is that the Yangtze River is characterized by high turbidity and a strong current. Here, we used an eDNA-based approach to estimate the presence of YFP at 18 sites in the Yangtze River in August 2017 and at an additional 11 sites in January 2018. At each sampling site, we filtered six 1 L water samples with 5 µm pore size filter paper and quantified the amount of YFP eDNA in each water sample using quantitative real-time polymerase chain reaction (qPCR). In addition, YFP eDNA was successfully detected in locations where we visually observed YFP, as well as in locations where YFP were not observed directly. We found that our eDNA-based method had higher detection rates than traditional field survey methods. Although YFP was visually observed in the Yangtze River in winter, water samples collected during the summer contained significantly higher YFP eDNA than winter water samples. Our results demonstrate the potential effectiveness of eDNA detection methods in determining the distribution of YFP in the Yangtze River.

The pre-aerobic process of coking wastewater treatment has strong capacity of decarbonization and detoxification, which contribute to the subsequent dinitrogen of non-carbon source/heterotrophic denitrification. The COD removal rate can reach > 90% in the first aerobic bioreactor of the novel O/H/O coking wastewater treatment system during long-term operation. The physico-chemical characteristics of influent and effluent coking wastewater in the first aerobic bioreactor were analyzed to examine how they correlated with bacterial communities. The diversity of the activated sludge microbial community was investigated using a culture-independent molecular approach. The microbial community functional profiling and detailed pathways were predicted from the 16S rRNA gene-sequencing data by the PICRUSt software and the KEGG database. High-throughput MiSeq sequencing results revealed a distinct microbial composition in the activated sludge of the first aerobic bioreactor of the O/H/O system. Proteobacteria, Bacteroidetes, and Chlorobi were the decarbonization and detoxification dominant phyla with the relative abundance of 84.07 ± 5.45, 10.89 ± 6.31, and 2.96 ± 1.12%, respectively. Thiobacillus, Rhodoplanes, Lysobacter, and Leucobacter were the potential major genera involved in the crucial functional pathways related to the degradation of phenols, cyanide, benzoate, and naphthalene. These results indicated that the comprehensive understanding of the structure and function diversity of the microbial community in the bioreactor will be conducive to the optimal coking wastewater treatment.

Samples of bleached kraft pine cellulosic pulp, either treated with an enzyme preparation (a Thermomyces lanuginosus xylanase, an Aspergillus sp. cellulase, and a multienzyme preparation NS-22086 containing both these activities) or untreated, were refined in a laboratory PFI mill. The treatment with cellulases contained in the last two preparations significantly improved the pulp’s susceptibility to refining (the target freeness value of 30°SR was achieved in a significantly shorter time), increased water retention value (WRV) and fines contents while the weighted average fiber length was significantly reduced. These changes of pulp parameters caused deterioration of paper strength properties. The treatment with the xylanase, which partially hydrolyzed xylan, small amounts of which are associated with cellulose fibers, only slightly loosened the structure of fibers. These subtle changes positively affected the susceptibility of the pulp to refining (refining energy was significantly reduced) and improved the static strength properties of paper. Thus, the treatment of kraft pulps with xylanases may lead to substantial savings of refining energy without negative effects on paper characteristics.

An electrochemically activated solution (ECAS), generated by electrolysis of a dilute sodium chloride solution in a four-chamber electrolytic cell (Ecas4), was tested as a sanitising aerosol in eliminating bacteria from the environment of a weaning room vacated 24-48h earlier, at a continuous flow pig farm. An ultrasonic humidifier was used to fill the environment with a fog (droplets with diameters of 1–5 μm) containing 0.25 ppm of hypochlorous acid. The weaning room was fogged for 3 min at 30 min intervals during five hours of aerosol disinfection. An innovative sample treatment with propidium monoazide dye in conjunction with cyclonic air sampling was optimised and adapted for discerning live/dead bacteria in subsequent molecular quantification steps. Without fogging, total bacterial load ranged from 5.06 ± 0.04 to 5.75 ± 0.04 Log10 CFU/m3. After the first hour of fogging, a 78% total bacterial reduction was observed, which further increased to > 97% after the second hour, > 99.4% after the third and 99.8% after the fourth hour, finally resulting in a 99.99% reduction from the farm environment over five hours. Unlike the current formaldehyde spray disinfection protocol, which requires a long empty period because of its hazardous properties, this economically viable and environmentally friendly disinfection protocol may significantly lower downtime. Moreover, ECAS fogging can be easily adapted to a variety of applications, including the elimination of pathogens from livestock farm air environment for disease prevention, as well as decontamination after disease outbreaks. Refereed/Peer-reviewed

The arthropod melanization immune response is activated by extracellular protease cascades predominantly comprised of CLIP-domain serine proteases (CLIP-SPs) and serine protease homologs (CLIP-SPHs). In the malaria vector, Anopheles gambiae, the CLIP-SPHs SPCLIP1, CLIPA8, and CLIPA28 form the core of a hierarchical cascade downstream of mosquito complement that is required for microbial melanization. However, our understanding of the regulatory relationship of the CLIP-SPH cascade with the catalytic CLIP-SPs driving melanization is incomplete. Here, we report on the development of a novel screen to identify melanization pathway components based on the quantitation of melanotic mosquito excreta, eliminating the need for microdissections or hemolymph enzymatic assays. Using this screen, we identified CLIPC9 and subsequent functional analyses established that this protease is essential for the melanization of both Escherichia coli and the rodent malaria parasite Plasmodium berghei. Mechanistically, septic infection with E. coli promotes CLIPC9 cleavage and both full-length and cleaved CLIPC9 localize to this bacterium in a CLIPA8-dependent manner. The steady state level of CLIPC9 in the hemolymph is regulated by thioester-containing protein 1 (TEP1), suggesting it functions downstream of mosquito complement. In support, CLIPC9 cleavage is inhibited following SPCLIP1, CLIPA8, and CLIPA28 knockdown positioning it downstream of the CLIP-SPH cascade. Moreover, like CLIPA8 and CLIPA28, CLIPC9 processing is negatively regulated by serine protease inhibitor 2 (SRPN2). This report demonstrates how our novel excretion-based approach can be utilized to dissect the complex protease networks regulating mosquito melanization. Collectively, our findings establish that CLIPC9 is required for microbial melanization in An. gambiae and shed light on how the CLIP-SPH cascade regulates this potent immune response., Author summary Mosquito vector competence for Plasmodium, antifungal defense, and lifespan are all influenced by the melanization response. Despite its importance, our understanding of the proteins comprising the An. gambiae melanization cascade is incomplete. To streamline the discovery of melanization pathway components in this disease vector, we developed a screening method that is able to identify proteins with far fewer mosquitoes than other approaches. This technique facilitated our discovery that the serine protease CLIPC9 is required for the melanization of E. coli bacteria and malaria parasites. CLIPC9 activation and localization to bacteria is regulated by members of the CLIPA subfamily, highlighting that these serine protease homologs broadly regulate the melanization immune response. Traditionally viewed as ‘co-factors’ for the prophenoloxidase activating CLIPBs, this work demonstrates that CLIPAs can also control the activation of the catalytic proteases driving melanization. This work identifies a new player in the melanization hierarchy and provides the field with an efficient approach for dissecting the complex protease cascades controlling this important immune response.

The current technologies of algal biofuels production and wastewater treatment (e.g., aerobic) process are still in question, due to the significant amount of fresh water and nutrients requirements for microalgae cultivation, and negative energy balance in both processes, especially when considered in the context of developing counties around the world. In this research, a simplistic sustainable approach of algal biofuels production from wastewater was proposed using a Hybrid Anaerobic Baffled Reactor (HABR) and Photobioreactor (PBR) system. The study suggests that the HABR was capable of removing most of the organic and solid (>90% COD and TSS removal) from wastewater, and produced a healthy feedstock (high N: P = 3:1) for microalgae cultivation in PBRs for biofuels production. A co-culture of Chlorella vulgaris, Chlorella sorokiniana, and Scenedesmus simris002 showed high lipid content up to 44.1%; and the dominant FAMEs composition (C16-C18) of 87.9% in produced biofuels. Perhaps, this proposed low-cost technological approach (e.g., HABR-PBR system) would connect the currently broken link of sustainable bioenergy generation and wastewater treatment pathway for developing countries.

A bioflocculant (MBFA18) was produced by Aspergillus niger (A18) using potato starch wastewater (PSW) as nutrients. The cultivation processes and flocculating treatment for PSW purification were systematically studied. The flocculating rate of the MBFA 18 achieved 90.06% (kaolin clay) under the optimal cultivation condition (PSW with 5950 mg/L COD, 20 g/L glucose, 0.2 g/L urea and without phosphorus source addition and pH adjustment). Furthermore, effects of flocculant dosage, initial pH, coagulant aid (CaCl2) addition and sedimentation time on the PSW treatment were discussed and studied in detail. The optimum flocculation treatment conditions were determined according to the treatment efficiency, cost and flocculation conditions. During the PSW treatment, 2 mL/L bioflocculant (1.89 g/L) dosage and 0.5 mol/L coagulant aid addition were applied without pH adjustment and 91.15% COD and 60.22% turbidity removal rate could be achieved within 20 min. The comparative study between the bioflocculant and conventional chemical flocculants showed excellent flocculating efficiency of MBFA 18 with lower cost (4.7 yuan/t), which indicated that the bioflocculant MBFA 18 produced in PSW substrate has a great potential to be an alternative flocculant in PSW treatment.

Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.

Efficient conversion of cellulosic sugars in cellulosic hydrolysates is important for economically viable production of biofuels from lignocellulosic biomass, but the goal remains a critical challenge. The present study reports a new approach for simultaneous fermentation of cellobiose and xylose by using the co-culture consisting of recombinant Saccharomyces cerevisiae specialist strains. The co-culture system can provide competitive advantage of modularity compared to the single culture system and can be tuned to deal with fluctuations in feedstock composition to achieve robust and cost-effective biofuel production. This study characterized fermentation kinetics of the recombinant cellobiose-consuming S. cerevisiae strain EJ2, xylose-consuming S. cerevisiae strain SR8, and their co-culture. The motivation for kinetic modeling was to provide guidance and prediction of using the co-culture system for simultaneous fermentation of mixed sugars with adjustable biomass of each specialist strain under different substrate concentrations. The kinetic model for the co-culture system was developed based on the pure culture models and incorporated the effects of product inhibition, initial substrate concentration and inoculum size. The model simulations were validated by results from independent fermentation experiments under different substrate conditions, and good agreement was found between model predictions and experimental data from batch fermentation of cellobiose, xylose and their mixtures. Additionally, with the guidance of model prediction, simultaneous co-fermentation of 60 g/L cellobiose and 20 g/L xylose was achieved with the initial cell densities of 0.45 g dry cell weight /L for EJ2 and 0.9 g dry cell weight /L SR8. The results demonstrated that the kinetic modeling could be used to guide the design and optimization of yeast co-culture conditions for achieving simultaneous fermentation of cellobiose and xylose with improved ethanol productivity, which is critically important for robust and efficient renewable biofuel production from lignocellulosic biomass.

Ricin is a highly-toxic compound derived from castor plant beans. Several incidents involving contamination of residences and buildings due to ricin production or dissemination have occurred in recent years. The goal of this study was to determine whether ricin bioactivity could be attenuated in reasonable time via simple modifications of the indoor environment. Attenuation was assessed on six different materials as a function of temperature, relative humidity (RH), and contact time, using both a pure and crude preparation of the toxin. Ricin bioactivity was quantified via a cytotoxicity assay, and attenuation determined as the difference in ricin recovered from test and positive controls. The results showed that pure ricin could be attenuated successfully, while the crude ricin was generally more persistent and results more variable. We found no significant attenuation in crude ricin after two weeks at typical indoor environmental conditions, except on steel. Attenuation mostly improved with increasing temperature, but the effect of RH varied. For pure ricin, heat treatments at 40°C for 5 days or 50°C for 2–3 days achieved greater than 96% attenuation on steel. In contrast, appreciable recovery of the crude ricin preparation still occurred at 40°C after two weeks.

The increasing water crisis makes fresh water a valuable resource, which must be used wisely. However, with growing population and inefficient waste treatment systems, the amount of wastewater dispelled in rivers is increasing abominably. Utilizing this freely available waste-water along with biodiesel industry waste- crude glycerol for bio-hydrogen production is being reported here. The bacterial cultures of Bacillus thuringiensis strain EGU45 and Bacillus amyloliquefaciens strain CD16 produced2.4–3.0 L H2/day/L feed during a 60 days continuous culture system at hydraulic retention time of 2 days. An average H2 yield of 100–120 L/L CG was reported by the two strains. Recycling of the effluent by up to 25% resulted in up to 94% H2 production compared to control.

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.

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.

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.

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.

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.

To learn how the endogenous polyphenols may play a role in fruit ripening and senescence, apple pulp discs were used as a model to study the influences of chlorogenic acid (CHA, a major polyphenol in apple pulp) on fruit ripening and senescence. Apple ('Golden Delicious') pulp discs prepared from pre-climacteric fruit were treated with 50 mg L(-1) CHA and incubated in flasks with 10 mM MES buffer (pH 6.0, 11% sorbitol). Compared to the control samples, treatment with CHA significantly reduced ethylene production and respiration rate, and enhanced levels of firmness and soluble solids content of the pulp discs during incubation at 25°C. These results suggested that CHA could retard senescence of the apple pulp discs. Proteomics analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry (MALDI-TOF/TOF) revealed that the expressions of several key proteins correlated to fruit ripening and senescence were affected by the treatment with CHA. Further study showed that treating the pulp discs with CHA remarkably reduced levels of lipoxygenase, β-galactosidase, NADP-malic enzyme, and enzymatic activities of lipoxygenase and UDP-glucose pyrophosphorylase, all of which are known as promoters of fruit ripening and senescence. These results could provide new insights into the functions of endogenous phenolic compounds in fruit ripening and senescence.

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.

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.

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.

Endocrine disrupting chemicals (EDCs) are environmental contaminants causing increasing concerns due to their toxicity, persistence and ubiquity. In the present study, degradative capabilities of Trametes versicolor, Pleurotus ostreatus and Phanerochaete chrysosporium to act on five EDCs, which represent different classes of chemicals (phenols, parabens and phthalate) and were first applied as single compounds, were assessed. T. versicolor was selected due to its efficiency against target EDCs and its potentialities were exploited against a mixture of EDCs in a cost-effective bioremediation process. A fed-batch approach as well as a starvation strategy were applied in order to reduce the need for input of 'fresh' biomass, and avoid the requirement for external nutrients. The fungus was successfully operated in two different bioreactors over one week. Semi-batch cultures were carried out by daily adding a mixture of EDCs to the bioreactors in a total of five consecutive degradation cycles. T. versicolor was able to efficiently remove all compounds during each cycle converting up to 21 mg L-1 day-1 of the tested EDCs. The maintained ability of T. versicolor to remove EDCs without any additional nutrients represents the main outcome of this study, which enables to forecast its application in a water treatment process.

This work evaluated the effect of cocoa pulp as a malt adjunct on the parameters of fermentation for beer production on a pilot scale. For this purpose, yeast isolated from the spontaneous fermentation of cachaça (SC52), belonging to the strain bank of the State University of Feira de Santana-Ba (Brazil), and a commercial strain of ale yeast (Safale S-04 Belgium) were used. The beer produced was subjected to acceptance and purchase intention tests for sensorial analysis. At the beginning of fermentation, 30% cocoa pulp (adjunct) was added to the wort at 12°P concentration. The production of beer on a pilot scale was carried out in a bioreactor with a 100-liter capacity, a usable volume of 60 liters, a temperature of 22°C and a fermentation time of 96 hours. The fermentation parameters evaluated were consumption of fermentable sugars and production of ethanol, glycerol and esters. The beer produced using the adjunct and yeast SC52 showed better fermentation performance and better acceptance according to sensorial analysis.

Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks. © 2012 Çetinkol et al.

Industrial oil spills into aquatic environments can have catastrophic environmental effects. First responders to oil spills along the coast of the Gulf of Mexico in the southern United States have used spunbond nylon fabric bags and fences to separate spilled oil and oil waste from contaminated water. Low area mass density spunbond nylon is capable of sorbing more than 16 times its mass in low viscosity crude oil and more than 26 times its mass in higher viscosity gear lube oil. Nylon bags separated more than 95% of gear lube oil contaminate from a 4.5% oil-in-water emulsion. Field testing of spunbond nylon fences by oil spill first responders has demonstrated the ability of this material to contain the oily contaminate while allowing water to flow through. We hypothesize that the effectiveness of nylon as an oil filter is due to the fact that it is both more oleophilic and more hydrophilic than other commonly used oil separation materials. The nylon traps oil droplets within the fabric or on the surface, while water droplets are free to flow through the fabric to the water on the opposite side of the fabric.

This paper describes a method for reliably identifying saccharide materials in paintings. Since the 3(rd) millennium B.C., polysaccharide materials such as plant gums, sugar, flour, and honey were used as binding media and sizing agents in paintings, illuminated manuscripts, and polychrome objects. Although it has been reported that plant gums have a stable composition, their identification in paint samples is often doubtful and rarely discussed. Our research was carried out independently at two different laboratories: the Getty Conservation Institute in Los Angeles, USA (GCI) and the Department of Chemistry and Industrial Chemistry of the University of Pisa, Italy (DCCI). It was shown in a previous stage of this research that the two methods give highly comparable data when analysing both reference paint samples and paint layers from art objects, thus the combined data was used to build a large database. In this study, the simultaneous presence of proteinaceous binders and pigments in fresh and artificially aged paint replicas was investigated, and it highlighted how these can affect the sugar profile of arabic, tragacanth, and fruit tree gums. The environmental contamination due to sugars from various plant tissues is also discussed. The results allowed the development of a new model for the reliable identification of saccharide binders in paintings based on the evaluation of markers that are stable to ageing and unaffected by pigments. This new model was applied to the sugar profiles obtained from the analysis of a large number of samples from murals, easel paintings, manuscripts, and polychrome objects from different geographical areas and dating from the 13(th) century BC to the 20(th) century AD, thus demonstrating its reliability.

Choice tests are a standard method to determine preferences in bio-assays, e.g. for food types and food additives such as bait attractants and toxicants. Choice between food additives can be determined only when the food substrate is sufficiently homogeneous. This is difficult to achieve for wood eating organisms as wood is a highly variable biological material, even within a tree species due to the age of the tree (e.g. sapwood vs. heartwood), and components therein (sugar, starch, cellulose and lignin). The current practice to minimise variation is to use wood from the same tree, yet the variation can still be large and the quantity of wood from one tree may be insufficient. We used wood samples of identical volume from multiple sources, measured three physical properties (dry weight, moisture absorption and reflected light intensity), then ranked and clustered the samples using fuzzy c-means clustering. A reverse analysis of the clustered samples found a high correlation between their physical properties and their source of origin. This suggested approach allows a quantifiable, consistent, repeatable, simple and quick method to maximize control over similarity of wood used in choice tests. © 2014 Oberst et al.

The symport of lactose and H+ is an important physiological process in E. coli, for it is closely related to cellular energy supply. In this paper, the symport of H+ and lactose by E. coli LacY protein is computationally simulated using a newly proposed cotransport model that takes the "leakage" phenomenon (uncoupled sugar translocation) into account and also satisfies the static head equilibrium condition. Then, we study the equilibrium properties of this cotransport process including equilibrium solution and the time required to reach equilibrium state, when varying the parameters of the initial state of cotransport system. It can be found that in the presence of leakage, H+ and lactose will reach their equilibrium state separately, but the intensity of "leakage" has almost no effect on the equilibrium solution, while the stronger leakage is, the shorter the time required for H+ and lactose to reach equilibrium. For E. coli cells with different periplasm and cytoplasm volumes, when cotransport is performed at constant initial particle concentration, the time for cytoplasm pH to be stabilized increases monotonically with the periplasm to cytoplasm volume ratio. For a certain E. coli cell, as it continues to lose water and contract, the time for cytoplasm pH to be stabilized by cotransport also increases monotonically when the cell survives. The above phenomena and other findings in this paper may help us to not only further validate or improve the model, but also deepen our understanding of the cotransport process of E. coli LacY protein., 10 figures

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention (a python package) and https://github.com/EESI/seq2att (a command line tool)., Author summary Microbiomes are communities of microscopic organisms found everywhere, including on and in the human body. For example, the gut microbiome plays an important role in digestion, and changes in composition are associated with changes in health or disease, e.g., inflammatory bowel disease (IBD). Today, microbiome composition is often obtained from high-throughput sequencing, which generates many short DNA reads from multiple organisms in a sample. In this paper, we present a novel deep learning framework, Read2Pheno, to predict phenotype from all the reads in a set of biological samples. An attention mechanism allows visualization of specific subregions (sets of bases) which are important in classifying the reads according to phenotype or taxon labels. We evaluate the framework on sequencing data for 16S rRNA genes, genetic markers used to identify microbial taxonomy. We show that Read2Pheno performs comparably as conventional methods on three distinct data sets from the American Gut Project, IBD patients and controls, and a comprehensive taxonomic database. Moreover, Read2Pheno results can be readily interpreted—e.g., to identify regions of the 16S rRNA gene to target for PCR diagnostics—without additional pre/post-processing steps that can introduce complexity and error.

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology., Author summary The cell’s most important pieces of machinery are large complexes of proteins often along with nucleic acids. From the ribosome, to CRISPR-Cas9, to transcription factors and DNA-wrangling proteins like the SMC-Kleisins, these complexes allow organisms to replicate and enable cells to respond to environmental cues. Computer simulation is a key technology that can be used to connect physical theories with biological reality. Unfortunately, the time and length scales accessible to molecular simulation have not kept pace with our ambition to study the cell’s molecular factories. Many simulation codes also unfortunately remain effectively locked away from the user community who need to modify them as more of the underlying physics is learned. In this paper, we present OpenAWSEM and Open3SPN2, two new easy-to-use and easy to modify implementations of efficient and accurate coarse-grained protein and DNA simulation forcefields that can now be run hundreds of times faster than before, thereby making studies of large biomolecular machines more facile.

Replication of DNA is an essential process in all domains of life. A protein often involved without exception in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize conservation of protein sequence among sliding clamps. In this paper we have used PSI blast to the second interation in NCBI to show a statistically significant sequence homology betweenPyrococcus furiosusPCNA andKallipyga gabonensisbeta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.

Fin-tech is an emerging field, inspiring revolutionary innovations in the financial field. It may initiate the evolutionary episode of the financial research, where volatility forecasting is a crucial topic in finance. For forecasting volatility, GARCH model is a prevailing model, however, further improvement of the GARCH model is still challenging. In this paper, we demonstrate how Fintech can play a part in volatility forecasting by employing a metaheuristic procedure called Genetic Programming. On the basis, we are able to develop a new volatility forecasting model, which can beat GARCH family models (including GARCH, IGARCH and TGARCH models) in a significant way. Since genetic programming is an evolutionary algorithm based on the principles of natural selection, this innovative work will be a breakthrough point in the financial area. The innovation of this paper demonstrates how GP technology can be applied in the financial field, attempting to explore the volatility forecasting area from the combination of new technology and finance, known as fintech. More importantly, when the formula of volatility forecasting is unknown as we introduce a new factor, namely, the liquidity factor, we unveil that how GP method can be helpful in determining the specific volatility forecasting model format. We thereby exhibit the liquidity effects on volatility forecasting filed from the fintech perspective.

In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various applications have been developed based on the efficient urease that can induce the precipitation of calcium carbonate. However, the metabolic mechanism related to biomineralization of S. pasteurii has not been clearly elucidated. The process of bacterial culture and biomineralization consumes a large amount of urea or ammonium salts, which are usually used as agricultural fertilizers, not to mention probable environmental pollutions caused by the excessive use of these raw materials. Therefore, it is urgent to reveal the mechanism of nitrogen utilization and metabolism of S. pasteurii. In this paper, we compared the growth and gene expression of S. pasteurii under three different culture conditions through transcriptome analyses. GO and KEGG analyses revealed that both ammonium and urea were direct nitrogen sources of S. pasteurii, and the bacteria could not grow normally in the absence of ammonium or urea. To the best of our knowledge, this paper is the first one to reveal the nitrogen utilization mechanism of S. pasteurii through transcriptome methods. Furthermore, the presence of ammonium might promote the synthesis of intracellular ATP and enhance the motility of the bacteria. There should be an ATP synthesis mechanism associated with urea hydrolysis catalyzed by urease in S. pasteurii.

Current image encryption methods have many shortcomings for the medical image encryption with high resolution, strong correlation and large storage space, and it is difficult to obtain reliable clinically applicable medical images. Therefore, this paper proposes a medical image encryption algorithm based on a new five-dimensional three-leaf chaotic system and genetic operation. And the dynamic analysis of the phase diagram and bifurcation diagram of the five-dimensional three-leaf chaotic system selected in this paper is carried out, and NIST is used to test the randomness of its chaotic sequence. This algorithm follows the diffusion-scrambling framework, especially using the principle of DNA recombination combined with the five-dimensional three-leaf chaotic system to generate a chaotic matrix that participates in the operation. The bit-level DNA mutation operation is introduced in the diffusion, and the scrambling and diffusion effects have been further improved. Algorithm security and randomness have been enhanced. This paper evaluates the efficiency of this algorithm for medical image encryption in terms of security analysis and time performance. Security analysis is carried out from key space, information entropy, histogram, similarity between decrypted image and original image, PSNR, correlation, sensitivity, noise attack, cropping attack and so on. Perform time efficiency analysis from the perspective of time performance. The comparison between this algorithm and the experimental results obtained by some of the latest medical image encryption algorithms shows that this algorithm is superior to the existing medical image encryption algorithms to a certain extent in terms of security and time efficiency.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus poses serious threats to the global public health and leads to worldwide crisis. No effective drug or vaccine is readily available. The viral RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target. A hybrid drug screening procedure was proposed and applied to identify potential drug candidates targeting RdRp from 1906 approved drugs. Among the four selected market available drug candidates, Pralatrexate and Azithromycin were confirmed to effectively inhibit SARS-CoV-2 replication in vitro with EC50 values of 0.008μM and 9.453 μM, respectively. For the first time, our study discovered that Pralatrexate is able to potently inhibit SARS-CoV-2 replication with a stronger inhibitory activity than Remdesivir within the same experimental conditions. The paper demonstrates the feasibility of fast and accurate anti-viral drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19., Author summary Currently, a novel coronavirus called SARS-COV-2 is spreading across many parts of the world. Unfortunately, there is still a lack of effective drugs against the virus. Additionally, it usually takes much longer time to develop a new drug using traditional methods. Thus, it is now better to rely on some alternative methods to develop drugs that can treat such a disease effectively. In this paper, we have proposed a deep learning and molecular dynamics simulation based hybrid drug screening procedure for identifying potential drug candidates targeting RdRp from 1906 market available drugs. Our screening have successfully identified a FDA-approved drug called Pralatrexate that strongly inhibits the replication of 2019-nCoV in vitro with EC50 values of 0.008μM. This work demonstrated the feasibility of accurate virtual drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19.