Serial Transfer Research Articles

A discrete state Markov chain model and decomposition solution method for the transient behaviour of buffered long serial transfer lines

As demand for greater manufacturing efficiency over shorter production runs in serial manufacturing lines increase, models for transient behaviour are required for insight into short-term production operation and control. This paper proposes a method to model the discrete time transient behaviour of paced long serial transfer lines with finite buffers. The method provides for the solution of lines comprised of machines that represent a variety of complex discrete state behaviours. The solution decouples the line into two-machine, one buffer models and adds external starvation and blockage coupling states and harmonizes the system behaviour by solving for transition probabilities into these external states with optimization. The efficacy of the approach is illustrated with three examples, a twenty-machine serial line with geometric machine behaviour, a twenty-machine serial line with complex machine behaviour, and the design of a transient line for a CONWIP strategy.

Synthetic symbiosis between a cyanobacterium and a ciliate toward novel chloroplast-like endosymbiosis

Chloroplasts are thought to have co-evolved through endosymbiosis, after a cyanobacterial-like prokaryote was engulfed by a eukaryotic cell; however, it is impossible to observe the process toward chloroplasts. In this study, we constructed an experimental symbiosis model to observe the initial stage in the process from independent organisms to a chloroplast-like organelle. Our system of synthetic symbiosis is capable of long-term coculture of two model organisms: a cyanobacterium (Synechocystis sp. PCC6803) as a symbiont and a ciliate (Tetrahymena thermophila) as a host with endocytic ability. The experimental system was clearly defined, because we used a synthetic medium and the cultures were shaken to avoid spatial complexity. We determined the experimental conditions for sustainable coculture, by analyzing population dynamics using a mathematical model. We experimentally demonstrated that the coculture was sustainable for at least 100 generations, through serial transfers. Moreover, we found that cells isolated after the serial transfer improved the probability of coexistence of both species without extinction in re-coculture. The constructed system will be useful for understanding the initial stage of primary endosymbiosis from cyanobacteria to chloroplasts, i.e., the origin of algae and plants.

In Vitro Transcription/Translation-Coupled DNA Replication through Partial Regeneration of 20 Aminoacyl-tRNA Synthetases.

The in vitro reconstruction of life-like self-reproducing systems is a major challenge in in vitro synthetic biology. Self-reproduction requires regeneration of all molecules involved in DNA replication, transcription, and translation. This study demonstrated the continuous DNA replication and partial regeneration of major translation factors, 20 aminoacyl-tRNA synthetases (aaRS), in a reconstituted transcription/translation system (PURE system) for the first time. First, we replicated each DNA that encodes one of the 20 aaRSs through aaRS expression from the DNA by serial transfer experiments. Thereafter, we successively increased the number of aaRS genes and achieved simultaneous, continuous replication of DNA that encodes all 20 aaRSs, which comprised approximately half the number of protein factors in the PURE system, except for ribosomes, by employing dialyzed reaction and sequence optimization. This study provides a step-by-step methodology for continuous DNA replication with an increasing number of self-regenerative genes toward self-reproducing artificial systems.

Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers.

Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.

Understanding cellular growth strategies via optimal control.

Evolutionary prediction and control are increasingly interesting research topics that are expanding to new areas of application. Unravelling and anticipating successful adaptations to different selection pressures becomes crucial when steering rapidly evolving cancer or microbial populations towards a chosen target. Here we introduce and apply a rich theoretical framework of optimal control to understand adaptive use of traits, which in turn allows eco-evolutionarily informed population control. Using adaptive metabolism and microbial experimental evolution as a case study, we show how demographic stochasticity alone can lead to lag time evolution, which appears as an emergent property in our model. We further show that the cycle length used in serial transfer experiments has practical importance as it may cause unintentional selection for specific growth strategies and lag times. Finally, we show how frequency-dependent selection can be incorporated to the state-dependent optimal control framework allowing the modelling of complex eco-evolutionary dynamics. Our study demonstrates the utility of optimal control theory in elucidating organismal adaptations and the intrinsic decision making of cellular communities with high adaptive potential.

Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction.

Adaptive laboratory evolution (ALE) is a useful experimental methodology for fundamental scientific research and industrial applications to create microbial cell factories. By using ALE, cells are adapted to the environment that researchers set based on their objectives through the serial transfer of cell populations in batch cultivations or continuous cultures and the fitness of the cells (i.e., cell growth) under such an environment increases. Then, omics analyses of the evolved mutants, including genome sequencing, transcriptome, proteome and metabolome analyses, are performed. It is expected that researchers can understand the evolutionary adaptation processes, and for industrial applications, researchers can create useful microorganisms that exhibit increased carbon source availability, stress tolerance, and production of target compounds based on omics analysis data. In this review article, the methodologies for ALE in microorganisms are introduced. Moreover, the application of ALE for the creation of useful microorganisms as cell factories has also been introduced.

In-Situ Monitoring of Reciprocal Charge Transfer and Losses in Graphene-Silicon CCD Pixels

Charge-coupled devices (CCD) allow imaging by photodetection, charge integration, and serial transfer of the stored charge packets from multiple pixels to the readout node. The functionality of CCD can be extended to the non-destructive and in-situ readout of the integrated charges by replacing metallic electrodes with graphene in the metal-oxide-semiconductors (MOS) structure of a CCD pixel. The electrostatic capacitive coupling of graphene with the substrate allows the Fermi level tuning that reflects the integrated charge density in the depletion well. This work demonstrates the in-situ monitoring of the serial charge transfer and interpixel transfer losses in a reciprocating manner between two adjacent Gr-Si CCD pixels by benefitting the electrostatic and gate-to-gate couplings. We achieved the maximum charge transfer efficiency (CTE) of 92.4%, which is mainly decided by the inter-pixel distance, phase clock amplitudes, switching slopes, and density of surface defects. The discussion on overcoming transfer losses and improving CTE by realizing a graphene-electron multiplication CCD is also presented. The proof of the concept of the in-situ readout of the out-of-plane avalanche in a single Gr-Si CCD pixel is also demonstrated, which can amplify the photo packet in a pre-transfer manner.

Occurrence and Biological Cost of mcr-1-Carrying Plasmids Co-harbouring Beta-Lactamase Resistance Genes in Zoonotic Pathogens from Intensive Animal Production.

Colistin is classified as a high-priority critical antimicrobial by the World Health Organization (WHO). A better understanding of the biological cost imposed by mcr-plasmids is paramount to comprehending their spread and may facilitate the decision about the ban of colistin in livestock. This study aimed to assess the prevalence of mcr and ESBL genes from 98 Escherichia coli and 142 Salmonella enterica isolates from food-producing animals and the impact of the mcr-1 acquisition on bacterial fitness. Only mcr-1 was identified by multiplex PCR (mcr-1 to mcr-10) in 15.3% of E. coli. Colistin MICs ranged between 8–32 mg/L. In four isolates, blaTEM-1, blaCTX-M-1, and blaCTX-M-15 co-existed with mcr-1. The IncH12, IncHI1, IncP, IncN, and IncI plasmids were transferred by conjugation to E. coli J53 at frequencies of 10−7 to 10−2 cells/recipient. Growth kinetics assays showed that transconjugants had a significantly lower growth rate than the recipient (p < 0.05), and transconjugants’ average growth rate was higher in the absence than in the presence of colistin (1.66 versus 1.32 (p = 0.0003)). Serial transfer assay during 10 days demonstrated that plasmid retention ranged from complete loss to full retention. Overall, mcr-1-bearing plasmids impose a fitness cost, but the loss of plasmids is highly variable, suggesting that other factors beyond colistin pressure regulate the plasmid maintenance in a bacterial population, and colistin withdrawal will not completely lead to a decrease of mcr-1 levels.

Diploid-associated adaptation to chronic low-dose UV irradiation requires homologous recombination in Saccharomyces cerevisiae.

Ultraviolet-induced DNA lesions impede DNA replication and transcription and are therefore a potential source of genome instability. Here, we performed serial transfer experiments on nucleotide excision repair-deficient (rad14Δ) yeast cells in the presence of chronic low-dose ultraviolet irradiation, focusing on the mechanisms underlying adaptive responses to chronic low-dose ultraviolet irradiation. Our results show that the entire haploid rad14Δ population rapidly becomes diploid during chronic low-dose ultraviolet exposure, and the evolved diploid rad14Δ cells were more chronic low-dose ultraviolet-resistant than haploid cells. Strikingly, single-stranded DNA, but not pyrimidine dimer, accumulation is associated with diploid-dependent fitness in response to chronic low-dose ultraviolet stress, suggesting that efficient repair of single-stranded DNA tracts is beneficial for chronic low-dose ultraviolet tolerance. Consistent with this hypothesis, homologous recombination is essential for the rapid evolutionary adaptation of diploidy, and rad14Δ cells lacking Rad51 recombinase, a key player in homologous recombination, exhibited abnormal cell morphology characterized by multiple RPA-yellow fluorescent protein foci after chronic low-dose ultraviolet exposure. Furthermore, interhomolog recombination is increased in chronic low-dose ultraviolet-exposed rad14Δ diploids, which causes frequent loss of heterozygosity. Thus, our results highlight the importance of homologous recombination in the survival and genomic stability of cells with unrepaired lesions.

Visual recognition in rhesus monkeys requires area TE but not TEO.

The primate visual system is often described as a hierarchical feature-conjunction pathway, whereby each level represents an increasingly complex combination of image elements, culminating in the representation of whole coherent images in anterior inferior temporal cortex. Although many models of the ventral visual stream emphasize serial feedforward processing ((Poggio T, Mutch J, Leibo J, Rosasco L, Tacchetti A. The computationalmagic of the ventral stream: sketch of a theory (and why some deep architectures work). TechRep MIT-CSAIL-TR-2012-035. MIT CSAIL, Cambridge, MA. 2012); (Yamins DLK, DiCarlo JJ. Eight open questions in the computational modeling of higher sensory cortex. Curr Opin Neurobiol. 2016:37:114-120.)), anatomical studies show connections that bypass intermediate areas and that feedback to preceding areas ((Distler C, Boussaoud D, Desimone R, Ungerleider LG. Cortical connections of inferior temporal area TEO in macaque monkeys. J Comp Neurol. 1993:334(1):125-150.); (Kravitz DJ, Saleem KS, Baker CI, Mishkin M. A new neural framework for visuospatial processing. Nat Rev Neurosci. 2011:12(4):217-230.)). Prior studies on visual discrimination and object transforms also provide evidence against a strictly feed-forward serial transfer of information between adjacent areas ((Kikuchi R, Iwai E. The locus of the posterior subdivision of the inferotemporal visual learning area in the monkey. Brain Res. 1980:198(2):347-360.); (Weiskrantz L, Saunders RC. Impairments of visual object transforms in monkeys. Brain. 1984:107(4):1033-1072.); (Kar K, DiCarlo JJ. Fast recurrent processing via ventrolateral prefrontal cortex is needed by the primate ventral stream for robust Core visual object recognition. Neuron. 2021:109(1):164-176.e5.)). Thus, we sought to investigate whether behaviorally relevant propagation of visual information is as strictly sequential as sometimes supposed. We compared the accuracy of visual recognition after selective removal of specific subregions of inferior temporal cortex-area TEO, area TE, or both areas combined. Removal of TEO alone had no detectable effect on recognition memory, whereas removal of TE alone produced a large and significant impairment. Combined removal of both areas created no additional deficit relative to removal of TE alone. Thus, area TE is critical for rapid visual object recognition, and detailed image-level visual information can reach area TE via a route other than through TEO.

The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution.

The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the haploid state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. Mutation frequencies were highly repeatable among replicates, suggesting that selection was the cause of the observed allele frequency changes. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.

Broadband Graphene Field-Effect Coupled Detectors: From Soft X-Ray to Near-Infrared

Here, we report a broadband graphene-silicon field-effect coupled detector (FCD) sensitive to photons spanning from soft X-ray to Near-Infrared region. Unlike traditional charge-coupled devices (CCD) relying on serial charge transfer between potential wells, the FCD integrates photo-sensing, charge integration, field-effect amplification, and random readout in one pixel. The charge integration in the potential well of the semiconductor substrate and field-effect coupled amplification in graphene transistor result in a highly sensitive broadband response. In the X-ray region, the device displays a high sensitivity of 1088 CGy <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">air</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−2</sup> and a fast response time < ~5 ms. Linear array imaging reveals the potential of our devices for array-based broadband imaging. Our FCD offers a viable strategy to monolithically integrate 2D materials into conventional solid-state imaging technology, exploring the next-generation broadband photodetectors for high-quality imaging and super vision technology.

Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods.

ABSTRACTThe complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities.IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.

In Vitro Evolution of Specific Phages Infecting the Fish Pathogen Flavobacterium psychrophilum.

Flavobacterium psychrophilum is the causative agent of the bacterial cold-water disease and rainbow trout fry syndrome. Owing to the issues associated with increasing use of antibiotics to control the diseases, phage therapy has been proposed as an alternative method to control Flavobacterium infection within the industry. We explored two simple and fast in vitro strategies for the isolation of evolved F. psychrophilum phages, using three well-characterized phages FpV4, FpV9, and FPSV-S20. During in vitro serial transfer experiments, 12 evolved phages were selected 72-96 h after phage exposure in the first or second week. Phenotype analysis showed improvement of host range and efficiency of plating and adsorption constants. Comparative genomic analysis of the evolved phages identified 13 independent point mutations causing amino acid changes mostly in hypothetical proteins. These results confirmed the reliability and effectivity of two strategies to isolate evolved F. psychrophilum phages, which may be used to expand phage-host range and target phage-resistant pathogens in phage therapy applications against Flavobacterium infections.

Firmware-based Capacitor and Equivalent Series Resistance (ESR) Meter

This paper presents the development of a capacitor ESR meter, which covers capacitance and ESR measurements as well as the interrelationship of the constituent parts/circuits. The idea is to keep the hardware design simple, transferring the complexity to firmware which controls the hardware. In particular, it uses automatic functions controlled by relays thus there is no need for switches and its automatic calibration ensures there is no need for menus. This work covers voltmeter function, C/R time constant function and ESR function using Arduino Uno boards. Each firmware code was developed one after the other, starting with the voltmeter function then C/R time constant function and finally ESR function. Results were checked by serial data transfer from Arduino Uno board to the laptop that is running the Arduino compiler with terminal. One Arduino Nano interface was constructed to interface the project shield. The firmware was developed to provide the voltmeter function, C/R time constant function and ESR function. An organic light-emitting diode (OLED) display was used to show measurement results. Logic control was added to provide the required functions to work as intended, as well as an automatic short circuit detection at DUT terminals firmware which includes a calibration cycle. Conventional ESR meters are usually have complex hardware, in contrast the design presented in this work shifts the focus to the firmware so that hardware is uncomplicated. This reduces the cost that typically comes with more hardware components. Keywords : Capacitor, ESR Meter, C-R Time Constant, Arduino, OLED Display, Calibration DOI: 10.7176/CEIS/13-1-02 Publication date: January 31 st 2022

X-ray Crystallography: Seeding Technique with Cytochrome P450 Reductase.

Cytochrome P450 reductase (CPR) is a multi-domain protein that acts as a redox partner of cytochrome P450s. The CPR contains a flavin adenine dinucleotide (FAD)-binding domain, a flavin mononucleotide (FMN)-binding domain, and a connecting domain. To achieve catalytic events, the FMN-binding domain needs to move relative to the FAD-binding domain, and this high flexibility complicates structural determination in high-resolution by X-ray crystallography. Here, we demonstrate a seeding technique of sorghum CPR crystals for resolution improvement, which can be applied to other poorly diffracting protein crystals. Protein expression is completed using an E. coli cell line with a high protein yield and purified using chromatography techniques. Crystals are screened using an automated 96-well plating robot. Poorly diffracting crystals are originally grown using a hanging drop method from successful trials observed in sitting drops. A macro seeding technique is applied by transferring crystal clusters to fresh conditions without nucleation to increase crystal size. Prior to diffraction, a dehydration technique is applied by serial transfer to higher precipitant concentrations. Thus, an increase in resolution by 7 Å is achieved by limiting the inopportune effects of the flexibility inherent to the domains of CPR, and secondary structures of SbCPR2c are observed. Graphical abstract.

Design and Construction of a Smart-home Automation System (SHAS) using Nodemcu and Google Assistant

This paper presents the design and construction of a smart-home automation system using nodeMCU and Google assistant. The device consist of Enhanced Universal Synchronous Asynchronous Receiver Transmitter (EUSART) module that contains all clock generators, shift registers and data buffers necessary to perform an input or output serial data transfer independently of the device program execution. The NodeMCU (ESP8266) Wi-fi Shield connected the microcontroller to the provided Wi-fi network. The Arduino and MPLAB Programming Interface with the help of PICKit3 were used to run the code on PIC16F877A. Home appliances were controlled via a web page created using IFTTT for the voice command and the Blynk app for controlling hardware remotely and also display sensor data. IFTTT is a simple to use internet service that easily enables IoT devices to GET and POST data. The device was constructed based on low cost and reliable home controlled monitoring system for accessing and controlling electronics appliances remotely using any Smart phone with access to Google assistance or Computer web application. The device was test under different electronics appliances with different voltage capacities and was found efficient. Therefore, this device when used is capable of improving the living standard at home, reduces human effort, save energy and time thus make homes have sufficient automation.

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

BackgroundEfficient use of glucose and xylose is a key for the economic production of lignocellulosic biofuels and biochemicals, and different recombinant strains have been constructed for xylose utilization including those using Zymomonas mobilis as the host. However, the xylose utilization efficiency still needs to be improved. In this work, the strategy of combining metabolic engineering and adaptive laboratory evolution (ALE) was employed to develop recombinant Z. mobilis strains that can utilize xylose efficiently at high concentrations, and NGS-based genome resequencing and RNA-Seq transcriptomics were performed for strains evolved after serial transfers in different media to understand the impact of xylose and differences among strains with different xylose-utilization capabilities at molecular level.ResultsHeterologous genes encoding xylose isomerase and xylulokinase were evaluated, which were then introduced into xylose-utilizing strain Z. mobilis 8b to enhance its capacity of xylose utilization. The results demonstrated that the effect of three xylose isomerases on xylose utilization was different, and the increase of copy number of xylose metabolism genes can improve xylose utilization. Among various recombinant strains constructed, the xylose utilization capacity of the recombinant strain 8b-RsXI-xylB was the best, which was further improved through continuous adaption with 38 transfers over 100 days in 50 g/L xylose media. The fermentation performances of the parental strain 8b, the evolved 8b-S38 strain with the best xylose utilization capability, and the intermediate strain 8b-S8 in different media were compared, and the results showed that only 8b-S38 could completely consume xylose at 50 g/L and 100 g/L concentrations. In addition, the xylose consumption rate of 8b-S38 was faster than that of 8b at different xylose concentrations from 50 to 150 g/L, and the ethanol yield increased by 16 ~ 40%, respectively. The results of the mixed-sugar fermentation also demonstrated that 8b-S38 had a higher xylose consumption rate than 8b, and its maximum ethanol productivity was 1.2 ~ 1.4 times higher than that of 8b and 8b-S8. Whole-genome resequencing identified three common genetic changes in 8b-S38 compared with 8b and 8b-S8. RNA-Seq study demonstrated that the expression levels of genes encoding chaperone proteins, ATP-dependent proteases, phage shock proteins, ribosomal proteins, flagellar operons, and transcriptional regulators were significantly increased in xylose media in 8b-S38. The up-regulated expression of these genes may therefore contribute to the efficient xylose utilization of 8b-S38 by maintaining the normal cell metabolism and growth, repairing cellular damages, and rebalancing cellular energy to help cells resist the stressful environment.ConclusionsThis study provides gene candidates to improve xylose utilization, and the result of expressing an extra copy of xylose isomerase and xylulokinase improved xylose utilization also provides a direction for efficient xylose-utilization strain development in other microorganisms. In addition, this study demonstrated the necessity to combine metabolic engineering and ALE for industrial strain development. The recombinant strain 8b-S38 can efficiently metabolize xylose for ethanol fermentation at high xylose concentrations as well as in mixed sugars of glucose and xylose, which could be further developed as the microbial biocatalyst for the production of lignocellulosic biofuels and biochemicals.

Design of a Low‐Cost Electrical Resistivity Meter for Near Surface Surveys

AbstractA programmable automated electrical resistivity meter was designed and constructed. The device was created to perform near surface studies, particularly for archaeogeophysical target characterization. Real field and laboratory model studies can be performed changing the current input of the device. The equipment consists of two independent devices, each one with its own microcontroller platform. They are interconnected through serial data transfer protocol. The first device, works as a resistivity meter where the ABMN electrode positions are programmed and permits the interaction with the user. The second one, connects the current and voltage channels to the programmed electrode positions. A physical model and field measurements were performed with different electrode configurations such as Dipole‐Dipole, Werner‐Schlumberger and Wenner γ112 in order to verify the performance of the automated electrical resistivity meter. The measurements give mean relative standard deviation values between 0.6% and 5.5% and data inversion convergence between 1.3% and 7.2%. Even though this open source and low cost electrical resistivity meter was design primarily for archaeogeophysical studies, it could be adapted to other geophysical issues such as contamination plumes detection and characterization, tunnel detection, etc.

Microbial dechlorination of polychrolinated biphenyls

Polychlorinated biphenyls (PCBs) are organic xenobiotics contaminating environment for at least 50 years. They could be eventually eliminated by various organisms under different conditions. The degree of chlorine substitution per biphenyl molecule influences biodegradability which decreases with increasing chlorination. Our work is focused on the PCBs biodegradation under anaerobic conditions. The suitable high chlorinated biphenyls are converted via reductive dechlorination to the chlorinated biphenyls with lower extent of chlorine, which could be eventually fully mineralized by aerobic bacteria. Microbial consortium was isolated from sediment of Strážský Creek (located near by plant producing PCBs in the past). This consortium was able to dechlorinate polychlorinated biphenyls under anoxic conditions. The effectiveness of this process was tested under different cultivation condition – different energetic sources (Aroclor 1248 or Aroclor 1260 or Delor 103 or Delor 106), addition of potential electron donors (pyruvate, lactate or acetate with hydrogen) and further if there is necessary to add yeast extract into fresh low sulphur cultivation media.&#x0D; Our microbial consortia so far do not need supplementation by non-contaminated sediment to maintain dechlorination activity. Addition of yeast extract is non essential, but needs to be further proved in serial transfers. In all cases (except acetate without yeast extract) dechlorination proceeds at meta- and flanked paraposition.