A fast-flexible strategy based approach to solving employee scheduling problem considering soft work time.

Employee scheduling aims to assign employees to shifts to satisfy daily workload and constraints. Some employee scheduling problems and their variants have been proven NP-hard, and a series of works have been done. However, the existing algorithms consider the fixed work time, which may cause plenty of overstaffing and understaffing phenomenons. Hence, this paper proposes a fast-flexible strategy based approach (FFS) to solve it. FFS introduces the idea of soft work time, which allows the work time of employees can be adjusted in a range. Based on this, we set the flextime strategy to decide the specific work time of each employee every day. Besides, FFS adopts a pairwise-allocated strategy and proficiency average matrix to boost its efficiency and effectiveness. Finally, the extensive experimental evaluation shows that FFS is more effective and efficient than the baselines for solving the employee scheduling problem considering soft work time.

Development of a flow cytometry-based plating-free system for strain engineering in industrial fungi.

Recent technical advances regarding filamentous fungi have accelerated the engineering of fungal-based production and benefited basic science. However, challenges still remain and limit the speed of fungal applications. For example, high-throughput technologies tailored to filamentous fungi are not yet commonly available for genetic modification. The currently used fungal genetic manipulations are time-consuming and laborious. Here, we developed a flow cytometry-based plating-free system to directly screen and isolate the transformed protoplasts in industrial fungi Myceliophthora thermophila and Aspergillus niger. This system combines genetic engineering via the 2A peptide and the CRISPR-Cas9 system, strain screening by flow cytometry, and direct sorting of colonies for deep-well-plate incubation and phenotypic analysis while avoiding culturing transformed protoplasts in plates, colony picking, conidiation, and cultivation. As a proof of concept, we successfully applied this system to generate the glucoamylase-hyperproducing strains MtYM6 and AnLM3 in M. thermophila and A. niger, respectively. Notably, the protein secretion level and enzyme activities in MtYM6 were 17.3- and 25.1-fold higher than in the host strain. Overall, these findings suggest that the flow cytometry-based plating-free system can be a convenient and efficient tool for strain engineering in fungal biotechnology. We expect this system to facilitate improvements of filamentous fungal strains for industrial applications. KEY POINTS: • Development of a flow cytometry-based plating-free (FCPF) system is presented. • Application of FCPF system in M. thermophila and A. niger for glucoamylase platform. • Hyper-produced strains MtYM6 and AnLM3 for glucoamylase production are generated.

Production and use of immobilized lipases in/on nanomaterials: A review from the waste to biodiesel production.

As a highly efficient and environmentally friendly biocatalyst, immobilized lipase has received incredible interest among the biotechnology community for the production of biodiesel. Nanomaterials possess high enzyme loading, low mass transfer limitation, and good dispersibility, making them suitable biocatalytic supports for biodiesel production. In addition to traditional nanomaterials such as nano­silicon, magnetic nanoparticles and nano metal particles, novel nanostructured forms such as nanoflowers, carbon nanotubes, nanofibers and metal-organic frameworks (MOFs) have also been studied for biodiesel production in the recent years. However, some problems still exist that need to be overcome in achieving large-scale biodiesel production using immobilized lipase on/in nanomaterials. This article mainly presents an overview of the current and state-of-the-art research on biodiesel production by immobilized lipases in/on nanomaterials. Various immobilization strategies of lipase on various advanced nanomaterial supports and its applications in biodiesel production are highlighted. Influential factors such as source of lipase, immobilization methods, feedstocks, and production process are also critically discussed. Finally, the current challenges and future directions in developing immobilized lipase-based biocatalytic systems for high-level production of biodiesel from waste resources are also recommended.

Physiological and Metabolic Responses of a Novel Dunaliella salina Strain to Myo-inositol1.

Dunaliella salina is well known for its ability to accumulate large amounts of ß-carotene. Myo-inositol (MI) enhances the biomass production of D. salina, but the underlying mechanisms were unclear. The present study showed that the concentration of exogenous MI decreased gradually and reached a constant level at the 4th day of cultivation. MI enhanced the contents of total colored carotenoids and the activity of photosystem II. Metabolic profiles were significantly changed after the addition of exogenous MI, as revealed by multivariate statistical analysis. The metabolites could be categorized into four groups based on the relative levels in different samples. Exogenous MI increased the levels of most detected sugars, amino acids, and total saturated and unsaturated fatty acids. Based on the physiological and metabolic analyses, a hypothetical growth-promoting model that MI promotes the growth of D. salina TG by increasing the levels of key metabolites and possibly enhancing photosynthesis, was proposed. This study provides valuable information for understanding the growth-promoting mechanisms of MI in D. salina from the metabolic perspective.

Comparative proteomic analysis of Nostoc flagelliforme reveals the difference in adaptive mechanism in response to different ultraviolet-B radiation treatments.

Nostoc flagelliforme is a pioneer organism in the desert and highly resistant to ultraviolet B (UV-B) radiation, while the involved adaptive mechanism has not been fully explored yet. To elucidate the responsive mechanism, two doses of UV-B radiation (low: 1 W/m2 and high: 5 W/m2) were irradiated for 6 h and 48 h, respectively, and their effects on global metabolism in N. flagelliforme were comprehensively investigated. In this study, we used iTRAQ-based proteomic approach to explore the proteomes of N. flagelliforme, and 151, 172, 124 and 148 differentially expressed proteins were identified under low and high UV-B doses for 6 h and 48 h, respectively. Functional classification analysis showed these proteins were mainly involved in photosynthesis, amino acid metabolism, antioxidant activity and carbohydrate metabolism. Further analysis revealed that UV-B imposed restrictions on primary metabolism including photosynthesis, Calvin cycle, and amino acid metabolism, and cells started defense mechanism through repair of DNA and protein damage, increasing antioxidant activity, and accumulating extracellular polysaccharides to minimize the damage. Moreover, high UV-B dose imposed more severe restrictions and activated stronger defense mechanism compared with low dose. The results would improve the understanding of molecular mechanisms of UV-B-stress adaption in N. flagelliforme.

The physiological responses of terrestrial cyanobacterium Nostoc flagelliforme to different intensities of ultraviolet-B radiation.

Nostoc flagelliforme is a pioneer organism in the desert and exerts important ecological functions. The habitats of N. flagelliforme are characterized by intense solar radiation, while the ultraviolet B (UV-B) tolerance has not been fully explored yet. To evaluate the physiological responses of N. flagelliforme to UV-B radiation, three intensities (1 W m-2, 3 W m-2 and 5 W m-2) were used, and the changes in photosynthetic pigments, cell morphology, mycosporine-like amino acids (MAAs) synthesis and cell metabolism were comparatively investigated. Under high UV-B intensity or long term radiation, chlorophyll a, allophycocyanin and phycocyanin were greatly decreased; scanning electron microscope observations showed that cell morphology significantly changed. To reduce the damage, cells synthesized a large amount of carotenoid. Moreover, three kinds of MAAs were identified, and their concentrations varied with the changes of UV-B intensity. Under 1 W m-2 radiation, cells synthesized shinorine and porphyra-334 against UV-B, while with the increase of intensity, more shinorine turned into asterine-330. Metabolite profiling revealed the contents of some cytoprotective metabolites were greatly increased under 5 W m-2 radiation. The principal component analysis showed cells exposed to UV-B were metabolically distinct from the control sample, and the influence on metabolism was particularly dependent on intensity. The results would improve the understanding of physiological responses of N. flagelliforme to UV-B radiation and provide an important theoretical basis for applying this organism to control desertification.

Study on community structure of microbial consortium for the degradation of viscose fiber wastewater.

BACKGROUND: Enrichment culture was applied to obtain microbial consortium from activated sludge samples collected from biodegradation system, a chemical fiber plant in Hebei Province, China. Bacterial composition and community dynamic variation were assessed employing denaturing gradient gel electrophoresis fingerprinting technology based on amplified 16S rRNA genes in the entire process of enrichment culture for viscose fiber wastewater. RESULTS: Four bacteria named as VF01, VF02, VF03, and VF04 were isolated from the microbial consortium adopting the spray-plate method. The DNA bands of these four bacteria were corresponded to the predominant DNA bands in the electrophoresis pattern. VF01, VF02, VF03, and VF04 were phylogenetically closed to Bacillus licheniformis, Bacillus subtilis, Paracoccus tibetensis, and Pseudomonas sp. by sequence analysis, respectively. The degradation effects for CODCr of single isolated strain, mixed strains, and microbial consortium (VF) originally screened from viscose fiber wastewater were determined. The degradation ability was as follows: microbial consortium (VF) > mixed strains > single isolated strain. Microbial consortium (VF) showed the optimum degradation rate of CODCr of 87% on 14th day. Degradation of pollutants sped up by bio-augmentation of four strains. The molecular weight distribution of organic matter showed that viscose fiber wastewater contained a certain amount of large molecular organic matter, which could be decomposed into smaller molecular substances by microbial consortium (VF). CONCLUSIONS: The microbial consortium (VF) obtained from enrichment culture exhibited great potential for CODCr degradation. The screened strains had bio-augmentation functions and the addition of a mixture of four bacteria could speed up the degradation rate of pollutants.

Analysis of the Physiological and Molecular Responses of Dunaliella salina to Macronutrient Deprivation.

The halotolerant chlorophyte Dunaliella salina can accumulate up to 10% of its dry weight as ß-carotene in chloroplasts when subjected to adverse conditions, including nutrient deprivation. However, the mechanisms of carotenoid biosynthesis are poorly understood. Here, the physiological and molecular responses to the deprivation of nitrogen (-N), sulfur (-S), phosphorus (-P) and different combinations of those nutrients (-N-P, -N-S, -P-S and -N-P-S) were compared to gain insights into the underlying regulatory mechanisms of carotenoid biosynthesis. The results showed that both the growth and photosynthetic rates of cells were decreased during nutrient deprivation, accompanied by lipid globule accumulation and reduced chlorophyll levels. The SOD and CAT activities of the cells were altered during nutrient deprivation, but their responses were different. The total carotenoid contents of cells subjected to multiple nutrient deprivation were higher than those of cells subjected to single nutrient deprivation and non-stressed cells. The ß-carotene contents of cells subjected to -N-P, -N-S and -N-P-S were higher than those of cells subjected to single nutrient deprivation. Cells subjected to sulfur deprivation accumulated more lutein than cells subjected to nitrogen and phosphorous deprivation. In contrast, no cumulative effects of nutrient deprivation on the transcription of genes in the carotenogenic pathway were observed because MEP and carotenogenic pathway genes were up-regulated during single nutrient deprivation but were downregulated during multiple nutrient deprivation. Therefore, we proposed that the carotenoid biosynthesis pathway of D. salina is regulated at both the transcriptional and posttranscriptional levels and that a complex crosstalk occurs at the physiological and molecular levels in response to the deprivation of different nutrients.

Bacterial Species and Biochemical Characteristic Investigations of Nostoc flagelliforme Concentrates during its Storage.

Preservation of fresh algae plays an important role in algae seed subculture and aquaculture. The determination and examination of the changes of cell viability, composition, and bacterial species during storage would help to take suitable preservation methods to prolong the preservation time of fresh algae. Nostoc flagelliforme is a kind of edible cyanobacterium with important herbal and dietary values. This article investigated the changes of bacterial species and biochemical characteristics of fresh N. flagelliforme concentrate during natural storage. It was found that the viability of cells decreased along with the storage time. Fourteen bacteria strains in the algae concentrate were identified by PCR-DGGE and were grouped into four phyla, including Cyanobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among them, Enterococcus viikkiensis may be a concern in the preservation. Eleven volatile organic compounds were identified from N. flagelliforme cells, in which geosmin could be treated as an indicator of the freshness of N. flagelliforme. The occurrence of indole compound may be an indicator of the degradation of cells.

Comparison of bacterial community structures of terrestrial cyanobacterium Nostoc flagelliforme in three different regions of China using PCR-DGGE analysis.

Filamentous Nostoc flagelliforme form colloidal complex, with beaded cells interacting with other bacteria embedded in the complex multilayer sheath. However, the species of bacteria in the sheath and the interaction between N. flagelliforme and associated bacteria remain unclear. In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities of N. flagelliforme from three regions of China. DGGE patterns showed variations in all samples, exhibiting 25 discrete bands with various intensities. The diversity index analysis of bands profiles suggested the high similarity of bacterial communities to each other but also the dependence of microbial composition on each location. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Cyanobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, of which Cyanobacteria was dominant, followed the Proteobacteria. Members of the genus Nostoc were the most abundant in all samples. Rhizobiales and Actinobacteria were identified, whereas, Craurococcus, Caulobacter, Pseudomonas, Terriglobus and Mucilaginibacter were also identified at low levels. Through comparing the bacterial composition of N. flagelliforme from different regions, it was revealed that N. flagelliforme could facilitate the growth of other microorganisms including both autotrophic bacteria and heterotrophic ones and positively contributed to their harsh ecosystems. The results indicated N. flagelliforme played an important role in diversifying the microbial community composition and had potential application in soil desertification.

The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome.

BACKGROUND: Gene gain and loss frequently occurs in the cyanobacterium Prochlorococcus, a phototroph that numerically dominates tropical and subtropical open oceans. However, little is known about the stabilization of its core genome, which contains approximately 1250 genes, in the context of genome streamlining. Using Prochlorococcus MED4 as a model organism, we investigated the constraints on core genome stabilization using transcriptome profiling. RESULTS: RNA-Seq technique was used to obtain the transcriptome map of Prochlorococcus MED4, including operons, untranslated regions, non-coding RNAs, and novel genes. Genome-wide expression profiles revealed that three factors contribute to core genome stabilization. First, a negative correlation between gene expression levels and protein evolutionary rates was observed. Highly expressed genes were overrepresented in the core genome but not in the flexible genome. Gene necessity was determined as a second powerful constraint on genome evolution through functional enrichment analysis. Third, quick mRNA turnover may increase corresponding proteins' fidelity among genes that were abundantly expressed. Together, these factors influence core genome stabilization during MED4 genome evolution. CONCLUSIONS: Gene expression, gene necessity, and mRNA turnover contribute to core genome maintenance during cyanobacterium Prochlorococcus genus evolution.

Transcriptome analysis of Chlamydomonas reinhardtii during the process of lipid accumulation.

Algae are potential candidates for biodiesel production; thus, it is important to gain insight into the molecular mechanism of their lipid metabolism. Time-course transcriptome analyses were carried out during the lipid biosynthesis and accumulation processes of the model green alga Chlamydomonas reinhardtii using the Illumina RNA-seq platform. Transcriptome results indicated that over 2500 genes are upregulated or during lipid accumulation compared to log phase growth. As a proof of principle, two of the enzymes required for lipid metabolism that were significantly up-regulated during lipid accumulation, Lyso-Phosphatidic Acid Acyltransferase (LPAAT), diacylglycerol acyltransferase (DAGAT) were knocked down using artificial microRNAs. Neutral lipid production decreased in strains knocked down in expression of the lpaat and dagat genes. In addition, forty-one transcription factors were up- or down-regulated during the lipid accumulation process. This transcriptome data will be useful for engineering economic algae species aimed at biodiesel production.