Fungal Diversity Profiles in Pit Mud Samples from Chinese Strong-Flavour Liquor Pit.

Pit mud, a specific fermented soil, is an essential material for the fermentation of Chinese strong-flavour liquor. However, few studies to date have sought to characterize the spatial profiles of pit mud fungal communities in fermentation cellars from Chinese strong-flavour liquor distilleries. In this analysis, differences in fungal community structures and physicochemical properties in pit mud samples from different spatial positions within fermentation cellars were analyzed, revealing unique characteristic multidimensional pit mud fungal community profiles. Penicillium roqueforti, Pichia kudriavzevii, Aotearoamyces nothofagi, Penicillium robsamsonii, Alternaria arborescens, Trichosporon insectorum, Seltsamia ulmi, Trichosporon coremiiforme, Malassezia restricta were dominant in the pit mud samples form the upper cellar wall, whereas Metarhizium frigidum, Calonectria pseudoreteaudii, Penicillium clavigerum, Fusarium equiseti, Simplicillium chinense, Aspergillus intermedius, Trichosporon coremiiforme, Fusarium circinatum, Alternaria radicina, Aspergillus heterocaryoticus were predominant in the middle cellar wall. Alternaria radicina, Cladosporium chasmanthicola, Alternaria helianthiinficiens, Penicillium argentinense, Antarctomyces psychrotrophicus, and Trichosporon inkin are majorly present in the down cellar wall layer. Bipolaris axonopicola, Ramgea ozimecii, Penicillium argentinense, Calonectria queenslandica, Metarhizium robertsii, and Penicillium roqueforti were identified as the dominant fungi in pit mud samples from the cellar bottom. Additionally, Alternaria destruens and Alternaria doliconidium are present at notably high levels in all layers of pit mud samples. Moisture, pH, PO43-, acetic acid, humus, K+, Mg2+, Ca2+, butyric acid, and caproic acid levels in these different pit mud positions exhibited a rising incremental pattern from the upper wall layer to the bottom layer, whereas lactic acid levels were significantly lower in the bottom pit mud layer relative to these other layers. Moisture, pH, and NH4+-N were identified as the three most significant factors associated with fungal community composition through a redundancy analysis. Overall, these findings may offer a theoretical foundation for future efforts to improve or standardize artificial pit mud.

Enhanced production of cordycepic acid from Cordyceps cicadae isolated from a wild environment.

Cordyceps acid is an active component of Cordyceps cicadae and has a variety of medicinal uses, including anti-tumor effects, the prevention of cerebral hemorrhaging and myocardial infarction, and the inhibition of a wide range of bacteria. The objectives of this study were to identify C. cicadae fungi and optimize the culture conditions to obtain a high yield of cordycepic acid. First, a wild C. cicadae was identified by morphological observation and rDNA sequence analysis. Secondly, the optimal fermentation conditions were determined using a single-factor method, a Plackett-Burman design, and a Box-Behnken response surface. Finally, using the yield of fruit bodies and the content of cordyceps acid as indices, combined with a single-factor experiment and a response surface design, the best combination of conditions for cultivation was determined. The results showed that the best combination was as follows: sucrose 2%, tryptone 2%, KH2PO4 0.4%, MgSO4·7H2O 0.4%, an initial pH of the fermentation liquid of 7.0, 5% inoculum, fermentation for 4.5 d, a ratio of medium to liquid of 1:1.7, illumination intensity 150 Lux, illumination time 15 h per day, and 70% humidity. The content of cordycepic acid in the fruiting bodies developed in cultivation was 2.07-fold higher than that in the wild C. cicadae. This study provides a theoretical basis for the large-scale cultivation of C. cicadae with a high concentration of cordycepic acid.

Yeasts from Chinese strong flavour Daqu samples: isolation and evaluation of their potential for fortified Daqu production.

In total, 16 yeast were isolated from Chinese strong flavour Daqu samples and underwent RAPD analysis and identification. Totally, 11 different species were identified among these isolates including Saccharomyces cerevisiae, Hanseniaspora vineae, Pichia kluyveri, Trichosporon asahii, Wickerhamomyces anomalus, Kluyveromyces lactis, Yarrowia lipolytica, Wickerhamomyces mori, Galactomyces geotrichum, Dabaryomyces hansenii, and Saccharomyces kudriavzevii. To understand the impact of these yeast strains on the quality and flavour of Daqu, we then assessed volatile compounds associated with Daqu samples fermented with corresponding strains. These analyses revealed strain YE006 exhibited the most robust ability to produce ethanol via fermentation but yielded relatively low quantities of volatile compounds, whereas strain YE010 exhibited relatively poor fermentation efficiency but produced the greatest quantity of volatile compounds. These two yeast strains were then utilized in a mixed culture to produce fortified Daqu, with the optimal inoculum size being assessed experimentally. These analyses revealed that maximal fermentation, saccharifying, liquefying, and esterifying power as well as high levels of volatile compounds were achieved when using a 2% inoculum composed of YE006/YE010 at a 1:2 (v/v) ratio. When the liquor prepared using this optimized fortified Daqu was compared to unfortified control Daqu, the former was found to exhibit significantly higher levels of flavour compounds and better sensory scores. Overall, our findings may provide a reliable approach to ensuring Daqu quality and improving the consistency and flavour of Chinese strong-flavour liquor through bioaugmentation.

CRMarker: A manually curated comprehensive resource of cancer RNA markers.

Biomolecular markers have extremely important value for cancer research and treatment. However, as far as we know, there are still no searchable and predictable resources focusing on multiple classes of RNA molecular markers in cancers. Herein, we developed CRMarker, a manually curated comprehensive repository of cancer RNA markers. In the current release, CRMarker v1.1 consists of 5489 "known" cancer RNA markers based on 8756 valid publications in PubMed, including 2878 mRNAs (genes), 1314 miRNAs, 1097 lncRNAs and 200 circRNAs, and involving two functional molecules (diagnosis and prognosis), 21 organisms and 154 cancers. The search results provided by the database are comprehensive, including 11 items such as RNA molecule expression and risk level, type of tissue or sample, cancer subtype, reference type, etc. Moreover, CRMarker also provides more than 18,000 potential cancer RNA markers, which are predicted based on "guilt-by-association" analysis of the above-mentioned "known" RNA markers and three molecular interaction networks, and survival analysis of 18 gene expression data sets with survival data. CRMarker v1.1 has a friendly interface and is freely available online at http://crmarker.hnnu.edu.cn/. We aim to build a comprehensive platform that is convenient for cancer researchers and clinicians to inquire and retrieve.

Quantification and evolution of mitochondrial genome rearrangement in Amphibians.

BACKGROUND: Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS: Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION: It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.

Development of Chinese chestnut whiskey: yeast strains isolation, fermentation system optimization, and scale-up fermentation.

In this study, we used Chinese chestnut as the main raw material to develop a novel type of whiskey. First, 16 yeasts were isolated and identified for producing aroma using olfactory plate assay. Of these, we screened nine yeast strains based on their fermentation capacity, aroma profile, and sensory evaluation. The results demonstrated the combination of strains HN006 (Saccharomyces cerevisiae) and HN010 (Wickerhamomyces anomalus) provided satisfactory wine fermentation with an interesting flavor profile, as strain HN010 was highly aromatic and had elevated sensory scores with comparatively low ethanol yield, while strain HN006 had a poor flavor profile but produced the largest amount of ethanol. Subsequently, we co-cultured strains HN006 and HN010 to optimize the fermentation system. The results revealed the following optimum parameters: a mixed inoculum of 6% (v/v) at an HN006/HN010 ratio of 1:2 (v/v), a raw material ratio of 5:3:2 (chestnut: malt: glutinous rice), and yeast extract concentration of 6 g/L. Additionally, this fermentation system was successfully scaled-up to a 1000 L pilot-scale system. The results of this study showed that strains HN006 and HN010 could be used as alternatives for whiskey fermentation, as well as provided a generalized experimental scheme to assess other microorganisms.

Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome.

Prognostic gene signatures are critical in cancer prognosis assessments and their pinpoint treatments. However, their network properties remain unclear. Here, we obtained nine prognostic gene sets including 1439 prognostic genes of different cancers from related publications. Four network centralities were used to examine the network properties of prognostic genes (PG) compared with other gene sets based on the Human Protein Reference Database (HPRD) and String networks. We also proposed three novel network measures for further investigating the network properties of prognostic gene sets (PGS) besides clustering coefficient. The results showed that PG did not occupy key positions in the human protein interaction network and were more similar to essential genes rather than cancer genes. However, PGS had significantly smaller intra-set distance (IAD) and inter-set distance (IED) in comparison with random sets (p-value < 0.001). Moreover, we also found that PGS tended to be distributed within network modules rather than between modules (p-value < 0.01), and the functional intersection of the modules enriched with PGS was closely related to cancer development and progression. Our research reveals the common network properties of cancer prognostic gene signatures in the human protein interactome. We argue that these are biologically meaningful and useful for understanding their molecular mechanism.

Heat shock pretreatment induced cadmium resistance in the nematode Caenorhabditis elegans is depend on transcription factors DAF-16 and HSF-1.

Cadmium (Cd) exposure poses a serious environmental problem due to the metal's bioaccumulation and difficult to eliminate from body. Understanding the mechanisms of Cd detoxification and resistance can provide insights into methods to protect against the damaging effects of the heavy metal. In the present study, we found that heat shock (HS) pretreatment increased Cd resistance of the nematode Caenorhabditis elegans by reducing the bagging phenotype and protecting the integrity of the intestinal barrier. HS pretreatment increased the expression of heat shock protein-16.2 (HSP-16.2) prior to Cd exposure, and HS-induced Cd resistance was absent in worms with hsp-16.2 loss-of-function mutation. Worm strain with daf-2(e1370) mutation presented enhanced HS-induced Cd resistance, which was eliminated in worm strains of daf-16(mu86) and hsf-1(sy441). HS pretreatment increased DAF-16 nuclear localization and HSF-1 granule formation prior to Cd exposure. DAF-16 and HSF-1 was essential in reducing bagging formation and protecting the integrity of intestinal barrier after HS pretreatment. In conclusion, the present study demonstrated that HS-induced Cd resistance in C. elegans is regulated by the DAF-16/FOXO and HSF-1 pathways through regulation of HSP-16.2 expression.

Main parameters and the dynamics of volatile compounds during the fermentation of Chinese Mao-tofu from Huangshan region.

The physico-chemical parameters and kinetics of the volatile compounds during the fermentation of Chinese Mao-tofu was investigated. The levels of water soluble proteins, amino nitrogen and acidity increased gradually throughout the fermentation process, while that of reducing sugars peaked after 2 days before gradually declining. The protease activity increased significantly and reached the maximum levels at day 3, then it slightly decreased. The hardness and firmness decreased during the first 3 days, but both increased subsequently. The viscosity and adhesiveness was inversely related to the hardness and firmness. Forty-four volatile compounds were identified and quantified. Correlation analysis revealed significant correlation of the content of water soluble proteins and amino nitrogen with most volatile compounds. Acidity levels were positively correlated with that of ethyl caproate and hexyl alcohol, and negatively with 2-methyl butyric acid, palmitic acid, ethyl laurate, 1-octen-3-ol and 1-nonanol. Reducing sugar content was also positively correlated with ethyl caproate.

Improvement of the aroma of lily rice wine by using aroma-producing yeast strain Wickerhamomyces anomalus HN006.

A fruity aroma-producing yeast strain was isolated with the aim of improving the aroma of fermented lily rice wine, and identified as Wickerhamomyces anomalus HN006. In addition, the effects of adding solid residues of previous fermentation cycles, and of fungus α-amylase and W. anomalus HN006 supplementation on the biochemical parameters of lily rice wine were evaluated. The optimum quality of the wine, in terms of ethanol and residual sugar content, acidity levels and aroma, was obtained with 5% (w/v) solid residue addition, and supplementation with 10 U/g fungal α-amylase and 2% (v/v) W. anomalus inoculum on the 4th day of fermentation. Volatile compound profiles, the total amount of amino acids and the sensory characteristics of the lily rice wines produced by the two fermentation processes were also evaluated and compared. The lily rice wine obtained from our optimized experimental technology produced higher amounts of some esters, free fatty acids, alcohols, aldehydes, ketones, alkenes, volatile phenol and thiazole, in addition to higher total amino acid content and sensory scores compared to the traditionally brewed wine. Our process resulted in an intensification and improvement of lily rice wine aroma.

Improvement of caproic acid production in a Clostridium kluyveri H068 and Methanogen 166 co-culture fermentation system.

The aim of this study was to develop a bioprocess capable of producing caproic acid using a binary fermentation system consisting of Clostridium kluyveri H068 and Methanogen 166 which could then be applied to the brewing of Chinese strong flavor liquor. We initially explored the mechanism by which the Methanogen 166 strain facilitates caproic acid accumulation, revealing its ability to convert accumulated H2 that is produced by C. kluyveri H068 into methane, thereby eliminating the hydrogen-mediated feedback inhibition that normally constrains C. kluyveri H068 and thus enhancing caproic acid production. In addition, laboratory experiments were conducted to optimize this binary fermentation system, allowing us to determine that the optimum conditions for caproic acid production are a mixed inoculum size of 10% with a C. kluyveri H588/Methanogen 166 inoculation ratio of 2:1 (v/v), a sodium acetate concentration of 20 g/L, a 4% ethanol content (v/v), and a yeast extract concentration of 10 g/L. We further scaled this optimized condition up to use in a 1000 L fermenter and the obtained caproic acid broth was subjected to pit-entry fermentation. Our results demonstrated that this pit-entry fermentation approach was an efficient means of improving the quality of Chinese strong flavor liquor.

Improvement of kojic acid production in Aspergillus oryzae B008 mutant strain and its uses in fermentation of concentrated corn stalk hydrolysate.

A strain designated M866, producing kojic acid with a high yield, was obtained by combining induced mutation using ion beam implantation and ethyl methane sulfonate treatment of a wild type strain of Aspergillus oryzae B008. The amount of kojic acid produced by the strain M866 in a shaking flask was 40.2 g/L from 100 g/L of glucose, which was 1.7 times higher than that produced by wild strain (23.58 g/L). When the mixture of glucose and xylose was used as carbon source, the resulting kojic acid production was raised with the increasing of glucose ratios in the mixture. With concentrations of glucose at 75 g/L and xylose at 25 g/L mixed in the medium, the production of kojic acid reached 90.8 %, which was slightly lower than with glucose as the sole source of carbon. In addition, the kojic acid fermentation of the concentrated hydrolysate from corn stalk was also investigated in this study, the maximum concentration of kojic acid accumulated at the end of the fermentation was 33.1 g/L and this represents the yield based on reducing sugar consumed and the overall productivity of 0.36 g/g and 0.17 g/L/h, respectively.

Pilot-scale production of fuel ethanol from concentrated food waste hydrolysates using Saccharomyces cerevisiae H058.

The aim of this study was to develop a bioprocess to produce ethanol from food waste at laboratory, semipilot and pilot scales. Laboratory tests demonstrated that ethanol fermentation with reducing sugar concentration of 200 g/L, inoculum size of 2 % (Initial cell number was 2 × 106 CFU/mL) and addition of YEP (3 g/L of yeast extract and 5 g/L of peptone) was the best choice. The maximum ethanol concentration in laboratory scale (93.86 ± 1.15 g/L) was in satisfactory with semipilot scale (93.79 ± 1.11 g/L), but lower than that (96.46 ± 1.12 g/L) of pilot-scale. Similar ethanol yield and volumetric ethanol productivity of 0.47 ± 0.02 g/g, 1.56 ± 0.03 g/L/h and 0.47 ± 0.03 g/g, 1.56 ± 0.03 g/L/h after 60 h of fermentation in laboratory and semipilot fermentors, respectively, however, both were lower than that (0.48 ± 0.02 g/g, 1.79 ± 0.03 g/L/h) of pilot reactor. In addition, simple models were developed to predict the fermentation kinetics during the scale-up process and they were successfully applied to simulate experimental results.

Fed batch enzymatic saccharification of food waste improves the sugar concentration in the hydrolysates and eventually the ethanol fermentation by Saccharomyces cerevisiae H058

The enzymatic hydrolysis of food waste by commercially available enzymes and the subsequent ethanol fermentation of the hydrolysates by Saccharomyces cerecisiae H058 were studied in this work. The optimum batch enzymatic conditions were found to be saccharification pH of 4.5, temperature of 55!, glucoamylase concentration of 120 u/g, α-amylase concentration of 10 u/g, solid-liquid ratio of 1: 0.75 (w/w). Fed batch hydrolysis process was started with a solid-liquid ratio of 1: 1 (w/w), with solid food waste added at time lapse of 2 h to get a final solid-liquid ratio of 1: 0.5 (w/w). After 4 h of reaction, the reducing sugar concentration reached 194.43 g/L with a enzymatic digestibility of 93.12%. Further fermentation of the batch and fed batch enzymatic hydrolysates, which contained reducing sugar concentration of 131.41 and 194.43 g/L respectively, was performed using Saccharomyces cerevisiae H058, 62.93 and 90.72 g/L ethanol was obtained within 48 h.

Ethanol production from concentrated food waste hydrolysates with yeast cells immobilized on corn stalk.

The aim of the present study was to examine ethanol production from concentrated food waste hydrolysates using whole cells of S. cerevisiae immobilized on corn stalks. In order to improve cell immobilization efficiency, biological modification of the carrier was carried out by cellulase hydrolysis. The results show that proper modification of the carrier with cellulase hydrolysis was suitable for cell immobilization. The mechanism proposed, cellulase hydrolysis, not only increased the immobilized cell concentration, but also disrupted the sleek surface to become rough and porous, which enhanced ethanol production. In batch fermentation with an initial reducing sugar concentration of 202.64 ± 1.86 g/l, an optimal ethanol concentration of 87.91 ± 1.98 g/l was obtained using a modified corn stalk-immobilized cell system. The ethanol concentration produced by the immobilized cells was 6.9% higher than that produced by the free cells. Ethanol production in the 14th cycle repeated batch fermentation demonstrated the enhanced stability of the immobilized yeast cells. Under continuous fermentation in an immobilized cell reactor, the maximum ethanol concentration of 84.85 g/l, and the highest ethanol yield of 0.43 g/g (of reducing sugar) were achieved at hydraulic retention time (HRT) of 3.10 h, whereas the maximum volumetric ethanol productivity of 43.54 g/l/h was observed at a HRT of 1.55 h.