Functional roles and engineering strategies to improve the industrial functionalities of lactic acid bacteria during food fermentation.

In order to improve the flavor profiles, food security, probiotic effects and shorten the fermentation period of traditional fermented foods, lactic acid bacteria (LAB) were often considered as the ideal candidate to participate in the fermentation process. In general, LAB strains possessed the ability to develop flavor compounds via carbohydrate metabolism, protein hydrolysis and amino acid metabolism, lipid hydrolysis and fatty acid metabolism. Based on the functional properties to inhibit spoilage microbes, foodborne pathogens and fungi, those species could improve the safety properties and prolong the shelf life of fermented products. Meanwhile, influence of LAB on texture and functionality of fermented food were also involved in this review. As for the adverse effect carried by environmental challenges during fermentation process, engineering strategies based on exogenous addition, cross protection, and metabolic engineering to improve the robustness and of LAB were also discussed in this review. Besides, this review also summarized the potential strategies including microbial co-culture and metabolic engineering for improvement of fermentation performance in LAB strains. The authors hope this review could contribute to provide an understanding and insight into improving the industrial functionalities of LAB.

Expanding roles of circRNAs in cardiovascular diseases.

CircRNAs are a class of single-stranded RNAs characterized by covalently looped structures. Emerging advances have promoted our understanding of circRNA biogenesis, nuclear export, biological functions, and functional mechanisms. Roles of circRNAs in diverse diseases have been increasingly recognized in the past decade, with novel approaches in bioinformatics analysis and new strategies in modulating circRNA levels, which have made circRNAs the hot spot for therapeutic applications. Moreover, due to the intrinsic features of circRNAs such as high stability, conservation, and tissue-/stage-specific expression, circRNAs are believed to be promising prognostic and diagnostic markers for diseases. Aiming cardiovascular disease (CVD), one of the leading causes of mortality worldwide, we briefly summarize the current understanding of circRNAs, provide the recent progress in circRNA functions and functional mechanisms in CVD, and discuss the future perspectives both in circRNA research and therapeutics based on existing knowledge.

Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.).

BACKGROUND: The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.). RESULTS: Here, the comprehensive identification and a comparative analysis of P450 superfamily members were conducted in cultivated and wild pear genomes. In total, 338, 299 and 419 P450 genes were identified in Chinese white pear, European pear and the wild pear, respectively. Based on the phylogenetic analyses, pear P450 genes were divided into ten clans, comprising 48 families. The motif and gene structure analyses further supported this classification. The expansion of the pear P450 gene family was attributed to whole-genome and single-gene duplication events. Several P450 gene clusters were detected, which have resulted from tandem and proximal duplications. Purifying selection was the major force imposed on the long-term evolution of P450 genes. Gene dosage balance, subfunctionalization and neofunctionalization jointly drove the retention and functional diversification of P450 gene pairs. Based on the association analysis between transcriptome expression profiles and flavonoid content during fruit development, three candidate genes were identified as being closely associated with the flavonoid biosynthesis, and the expression of one gene was further verified using qRT-PCR and its function was validated through transient transformation in pear fruit. CONCLUSIONS: The study results provide insights into the evolution and biological functions of P450 genes in pear.

Protein regulator of cytokinesis 1: a potential oncogenic driver.

Protein regulator of cytokinesis 1 (PRC1) is involved in cytokinesis. Growing evidence suggests the association of PRC1 with multiple cancers. Here, we unveil that, in 28 cancer types, PRC1 is higher expressed in tumor tissues than in non-malignant tissues. Overexpression of PRC1 indicates unfavorable prognostic value, especially in ACC, LGG, KIRP, LICH, LUAD, MESO, PAAD, SARC and UCEC, while methylation of the PRC1 gene at sites associated with its inactivation has a favorable prognostic value in ACC, KIRP, LUAD, MESO, KIRP and LGG. Differentially expressed genes (DEGs) associated with high (> median) PRC1 expression contribute to key signaling pathways related with cell cycle, DNA damage and repair, EMT, cell migration, invasion and cell proliferation in most cancer types. More specifically, the DEGs involved in RAS/RAF/MAPK, PI3K/AKT, WNT, NOTCH, TGF-ß, integrin, EMT process, focal adhesion, RHO GTPase-related pathway or microtubule cytoskeleton regulation are upregulated when PRC1 expression is above median, as confirmed for most cancers. Most importantly, high expression of PRC1 appears to be associated with an overabundance of poor-prognosis TH2 cells. Furthermore, positive correlations of PRC1 and some immune checkpoint genes (CD274, CTLA4, HAVCR2, LAG3, PDCD1, PDCD1LG2, TIGIT, and CD86) were observed in several cancers, especially BLCA, BRCA, KIRC, LUAD, LIHC, PRAD and THCA. These findings plead in favor of further studies validating the diagnostic and prognostic impact of PRC1 as well as the elaboration of pharmacological strategies for targeting PRC1.

Gut Bacterial Diversity of Insecticide-Susceptible and Insecticide-Resistant Megalurothrips usitatus (Thysanoptera: Thripidae) and Elucidation of Their Putative Functional Roles.

The gut bacterial microbiota of insects plays a crucial role in physiological, metabolic, and innate immune processes. In the current study, the gut bacterial communities of an insecticide-susceptible (IS), and a resistant (IR) population of a major legume pest, Megalurothrips usitatus (Bagnall), were evaluated. The 16S rDNA V3 + V4 regions of M. usitatus infected with Beauveria brongniartii along with the intestinal flora of both populations were sequenced based on a High-throughput sequencing platform. Toxicological bioassays revealed that the IR population exhibited resistance to acetamiprid and B. brongniartii isolate SB010 at levels of 138.0-fold and 55.6-fold higher, respectively, compared to the IS population. Through 16S High-throughput sequencing, the results indicate that both resistant populations, as well as B. brongniartii infestation, reduce the number of species of M. usitatus gut microbes. Using KEGG function prediction, it was found that most intestinal bacteria were involved in various metabolic activities, and the abundance of resistant populations was higher than that of sensitive populations. The bacteria in the gut of M. usitatus are mainly involved in various metabolic activities to achieve the degradation of B. brongniartii. This study provides valuable insights into the interaction between gut bacteria, insecticide resistance, and Beauveria. brongniartii infection in Megalurothrips usitatus, which can help inform future pest control strategies.

Universal Stress Proteins: From Gene to Function.

Universal stress proteins (USPs) exist across a wide range of species and are vital for survival under stressful conditions. Due to the increasingly harsh global environmental conditions, it is increasingly important to study the role of USPs in achieving stress tolerance. This review discusses the role of USPs in organisms from three aspects: (1) organisms generally have multiple USP genes that play specific roles at different developmental periods of the organism, and, due to their ubiquity, USPs can be used as an important indicator to study species evolution; (2) a comparison of the structures of USPs reveals that they generally bind ATP or its analogs at similar sequence positions, which may underlie the regulatory role of USPs; and (3) the functions of USPs in species are diverse, and are generally directly related to the stress tolerance. In microorganisms, USPs are associated with cell membrane formation, whereas in plants they may act as protein chaperones or RNA chaperones to help plants withstand stress at the molecular level and may also interact with other proteins to regulate normal plant activities. This review will provide directions for future research, focusing on USPs to provide clues for the development of stress-tolerant crop varieties and for the generation of novel green pesticide formulations in agriculture, and to better understand the evolution of drug resistance in pathogenic microorganisms in medicine.

Nutritional and Functional Roles of Phytase and Xylanase Enhancing the Intestinal Health and Growth of Nursery Pigs and Broiler Chickens.

This review paper discussed the nutritional and functional roles of phytase and xylanase enhancing the intestinal and growth of nursery pigs and broiler chickens. There are different feed enzymes that are currently supplemented to feeds for nursery pigs and broiler chickens. Phytase and xylanase have been extensively studied showing consistent results especially related to enhancement of nutrient digestibility and growth performance of nursery pigs and broiler chickens. Findings from recent studies raise the hypothesis that phytase and xylanase could play functional roles beyond increasing nutrient digestibility, but also enhancing the intestinal health and positively modulating the intestinal microbiota of nursery pigs and broiler chickens. In conclusion, the supplementation of phytase and xylanase for nursery pigs and broiler chickens reaffirmed the benefits related to enhancement of nutrient digestibility and growth performance, whilst also playing functional roles benefiting the intestinal microbiota and reducing the intestinal oxidative damages. As a result, it could contribute to a reduction in the feed costs by allowing the use of a wider range of feedstuffs without compromising the optimal performance of the animals, as well as the environmental concerns associated with a poor hydrolysis of antinutritional factors present in the diets for swine and poultry.

An Update of Lectins from Marine Organisms: Characterization, Extraction Methodology, and Potential Biofunctional Applications.

Lectins are a unique group of nonimmune carbohydrate-binding proteins or glycoproteins that exhibit specific and reversible carbohydrate-binding activity in a non-catalytic manner. Lectins have diverse sources and are classified according to their origins, such as plant lectins, animal lectins, and fish lectins. Marine organisms including fish, crustaceans, and mollusks produce a myriad of lectins, including rhamnose binding lectins (RBL), fucose-binding lectins (FTL), mannose-binding lectin, galectins, galactose binding lectins, and C-type lectins. The widely used method of extracting lectins from marine samples is a simple two-step process employing a polar salt solution and purification by column chromatography. Lectins exert several immunomodulatory functions, including pathogen recognition, inflammatory reactions, participating in various hemocyte functions (e.g., agglutination), phagocytic reactions, among others. Lectins can also control cell proliferation, protein folding, RNA splicing, and trafficking of molecules. Due to their reported biological and pharmaceutical activities, lectins have attracted the attention of scientists and industries (i.e., food, biomedical, and pharmaceutical industries). Therefore, this review aims to update current information on lectins from marine organisms, their characterization, extraction, and biofunctionalities.

Collagenic architecture and morphotraits in a marine basal metazoan as a model for bioinspired applied research.

In some Porifera (Demospongiae: Keratosa), prototypes of the connective system are almost exclusively based on collagenic networks. We studied the topographic distribution, spatial layout, microtraits, and/or morphogenesis of these collagenic structures in Ircinia retidermata (Dictyoceratida: Irciniidae). Analyses were carried out on a clonal strain from sustainable experimental mariculture by using light and scanning electron microscopy. Histology revealed new insights on the widely diversified and complex hierarchical assemblage of collagenic structures. Key evolutionary novelties in the organization of sponge connective system were found out. The aquiferous canals are shaped as corrugate-like pipelines conferring plasticity to the water circulation system. Compact clusters of elongated cells are putatively involved in a nutrient transferring system. Knob-ended filaments are characterized by a banding pattern and micro-components. Ectosome and outer endosome districts are the active fibrogenetic areas, where exogenous material constitutes an axial condensation nucleus for the ensuing morphogenesis. The new data can be useful to understand not only the evolutionary novelties occurring in the target taxon but also the morpho-functional significance of its adaptive collagenic anatomical traits. In addition, data may give insights on both marine collagen sustainable applied researches along with evolutionary and phylogenetic analyses, thus highlighting sponges as a key renewable source for inspired biomaterials. Therefore, we also promote bioresources sustainable exploitation with the aim to provide new donors of marine collagen, thereby supporting conservation of wild populations/species.

Advances in the functional roles of N6-methyladenosine modification in cancer progression: mechanisms and clinical implications.

N6-methyladenosine (m6A), the methylation targeting the N6 position of adenosine, is the most common internal modification of mRNA in eukaryotes. Considering the roles of m6A in regulating gene expression, the investigation of m6A roles in the biological processes including cell renewal, differentiation, apoptosis, and invasion of cancer cells has become a hot research topic. There are three kinds of protein involved in m6A regulation. The methyltransferases and demethylases cooperatively regulate the m6A levels, while the m6A reading proteins recognize the m6A sites and mediate multiple m6A-dependent biological functions including mRNA splicing, transfer, translation, and degradation. At present, a large number of studies have found that the changes of m6A levels in tumor cells play a very important role in the occurrence and development of tumors, as well as metastasis and invasion of tumor cells. This review summarizes the different roles of m6A modification in the occurrence and development of various cancers, and discusses the possibility of choosing the m6A related proteins as potential therapeutic targets.

Quantifying production rates and size fractions of parrotfish-derived sediment: A key functional role on Maldivian coral reefs.

Coral reef fish perform numerous important functional roles on coral reefs. Of these, carbonate sediment production, as a by-product of parrotfish feeding, is especially important for contributing to reef framework construction and reef-associated landform development. However, only limited data exist on: (i) how production rates vary among reef habitats as a function of parrotfish assemblages, (ii) the relative importance of sediment produced from eroded, reworked, and endogenous sources, or (iii) the size fractions of sediment generated by different parrotfish species and size classes. These parameters influence not only overall reef-derived sediment supply, but also influence the transport potential and depositional fate of this sedimentary material. Here, we show that parrotfish sediment production varies significantly between reef-platform habitats on an atoll-margin Maldivian reef. Highest rates of production (over 0.8 kg m-2 year-1) were calculated in three of the eight platform habitats; a rubble-dominated zone, an Acropora spp. dominated zone, and a patch reef zone. Habitat spatial extent and differences in associated parrotfish assemblages strongly influenced the total quantities of sediment generated within each habitat. Nearly half of total parrotfish sediment production occurred in the rubble habitat, which comprised only 8% of the total platform area. Over 90% of this sedimentary material originated from eroded reef framework as opposed to being reworked existing or endogenously produced sediment, and comprised predominantly coral sands (predominantly 125-1000 µm in diameter). This is comparable to the dominant sand types and size fractions found on Maldivian reef islands. By contrast, nearly half of the sediment egested by parrotfish in the Acropora spp. dominated and patch reef habitats resulted from reworked existing sediments. These differences between habitats are a result of the different parrotfish assemblages supported. Endogenous carbonate production was found to be insignificant compared to the quantity of eroded and reworked material. Our findings have important implications for identifying key habitats and species which act as major sources of sediment for reef-island systems.

Functional roles of ants in a temperate grassland.

Ants in temperate grasslands are consumers and ecosystem engineers, influencing biodiversity and potentially grassland productivity. However, the effects of ant exclusion or suppression on resource removal and the biological community in temperate grasslands have yet to be fully explored. We conducted ant-suppression experiments and evaluated the effects of ants on ground-dwelling arthropod communities in the field by using pitfall and bait traps. In the laboratory, we evaluated the effects of ants on the ant-attended aphid Aphis rumicis, which is a honeydew resource for ants, and the slug (Deroceras laeve), an aphid predator. Aboveground arthropod communities were not affected by the ant-suppression treatment. However, slugs (D. laeve and Ambigolimax valentianus) visited bait resources more frequently in the ant-suppression treatment area. In the ant-absence condition in the laboratory experiment, there were fewer aphids on the plants compared to the ant-presence condition owing to predation by D. laeve. Our results suggest that ant abundance in temperate grasslands influences the predation activity of slugs toward honeydew sources such as aphids.

The comprehensive landscape of miR-34a in cancer research.

MicroRNA-34 (miR-34) plays central roles in human diseases, especially cancers. Inactivation of miR-34 is detected in cancer cell lines and tumor tissues versus normal controls, implying its potential tumor-suppressive effect. Clinically, miR-34 has been identified as promising prognostic indicators for various cancers. In fact, members of the miR-34 family, especially miR-34a, have been convincingly proved to affect almost the whole cancer progression process. Here, a total of 512 (miR-34a, 10/21), 85 (miR-34b, 10/16), and 114 (miR-34c, 10/14) putative targets of miR-34a/b/c are predicted by at least ten miRNA databases, respectively. These targets are further analyzed in gene ontology (GO), KEGG pathway, and the Reactome pathway dataset. The results suggest their involvement in the regulation of signal transduction, macromolecule metabolism, and protein modification. Also, the targets are implicated in critical signaling pathways, such as MAPK, Notch, Wnt, PI3K/AKT, p53, and Ras, as well as apoptosis, cell cycle, and EMT-related pathways. Moreover, the upstream regulators of miR-34a, mainly including transcription factors (TFs), lncRNAs, and DNA methylation, will be summarized. Meanwhile, the potential TF upstream of miR-34a/b/c will be predicted by PROMO, JASPAR, Animal TFDB 3.0, and GeneCard databases. Notably, miR-34a is an attractive target for certain cancers. In fact, miR-34a-based systemic delivery combined with chemotherapy or radiotherapy can more effectively control tumor progression. Collectively, this review will provide a panorama for miR-34a in cancer research.

Structural and physicochemical characterisation and antioxidant activity of an α-D-glucan produced by sourdough isolate Weissella cibaria MED17.

An exopolysaccharide (EPS) producer slimy-mucoid type colony was isolated from sourdough and identified as Weissella cibaria MED17. The 1H and 13C NMR spectra of EPS MED17 demonstrated that this EPS was a dextran type glucan ((1 â†’ 6)-linked α-D-glucose core structure) containing (1 â†’ 3)-linked α-D-glucose branches and proportion of (1 â†’ 6)-linked α-D-glucose units to (1 â†’ 3)-linked α-D-glucose units was 94.3:5.7%. The FTIR analysis also confirmed the (1 â†’ 6)-linked α-D-glucose linkage. A high level of thermal stability was observed for glucan MED17 as no degradation up to 300 °C was observed by TGA and DSC analysis. The XRD analysis of glucan MED17 showed its semi- crystalline nature and its compact sheet-like morphology was observed by SEM analysis. Finally, antioxidant characteristics of glucan MED17 were determined by ABTS and DPPH radical scavenging activity tests that revealed a moderate antioxidant activity of glucan MED17. These findings show potential techno-functional characteristics of glucan MED17.

Selective pressures of heavy metals on microbial community determine microbial functional roles during composting: Sensitive, resistant and actor.

Heavy metals (HM) pollution exerts an effect on microbial community composition and structure during composting, the way how microbial community responses to HM pressure is remain poorly understood though. The aim of this study was to explore functional roles of microorganisms based on selective pressures of HM (Cu, Zn and Cd). The results of microbial resistance showed that the toxicity of metals to microorganisms were Cu > Zn > Cd during composting. Cu and Zn were more toxic for microorganisms during composting when compared with Cd. However, microorganisms had a longer lag period to grow under Zn stress through microbial tolerance determination. In addition, the microbial catalase activity generally decreased and protease activity generally increased, thus microorganisms became more adaptable to HM stress during composting. The experimental results confirmed the existence of sensitive, resistant and actor microorganisms during beef cattle and chicken manures composting. Ultimately, the resistant, sensitive and actor microorganisms at genus level were distinguished under HM pressure based on the network analysis and structural equation models, including 85 resistant microorganisms, 5 sensitive microorganisms and 6 actor microorganisms. This would be helpful to understand the microbial succession process under HM stress and identify functional strains of HM remediation.

Interconnectedness of the Grinnellian and Eltonian Niche in Regional and Local Plant-Pollinator Communities.

Understanding the causes and consequences of coexistence and thus biodiversity is one of the most fundamental endeavors of ecology, which has been addressed by studying species' requirements and impacts - conceptualized as their Grinnellian and Eltonian niches. However, different niche types have been mostly studied in isolation and thus potential covariation between them remains unknown. Here we quantified the realized Grinnellian niche (environmental requirements), the fundamental (morphological phenotype) and realized Eltonian niche (role in networks) of plant and pollinator taxa at a local and regional scale to investigate the interconnectedness of these niche types. We found a strong and scale-independent co-variation of niche types suggesting that taxa specialized in environmental factors are also specialized in their position in trait spaces and their role in bipartite networks. The integration of niche types thus will help to detect the true causes for species distributions, interaction networks, as well as the taxonomic and functional diversity of communities.

The Physiological Functions of Universal Stress Proteins and Their Molecular Mechanism to Protect Plants From Environmental Stresses.

Since the original discovery of a Universal Stress Protein (USP) in Escherichia coli, a number of USPs have been identified from diverse sources including archaea, bacteria, plants, and metazoans. As their name implies, these proteins participate in a broad range of cellular responses to biotic and abiotic stresses. Their physiological functions are associated with ion scavenging, hypoxia responses, cellular mobility, and regulation of cell growth and development. Consistent with their roles in resistance to multiple stresses, USPs show a wide range of structural diversity that results from the diverse range of other functional motifs fused with the USP domain. As well as providing structural diversity, these catalytic motifs are responsible for the diverse biochemical properties of USPs and enable them to act in a number of cellular signaling transducers and metabolic regulators. Despite the importance of USP function in many organisms, the molecular mechanisms by which USPs protect cells and provide stress resistance remain largely unknown. This review addresses the diverse roles of USPs in plants and how the proteins enable plants to resist against multiple stresses in ever-changing environment. Bioinformatic tools used for the collection of a set of USPs from various plant species provide more than 2,100 USPs and their functional diversity in plant physiology. Data from previous studies are used to understand how the biochemical activity of plant USPs modulates biotic and abiotic stress signaling. As USPs interact with the redox protein, thioredoxin, in Arabidopsis and reactive oxygen species (ROS) regulates the activity of USPs, the involvement of USPs in redox-mediated defense signaling is also considered. Finally, this review discusses the biotechnological application of USPs in an agricultural context by considering the development of novel stress-resistant crops through manipulating the expression of USP genes.

Insect community composition and functional roles along a tropical agricultural production gradient.

High intensity agricultural production systems are problematic not only for human health and the surrounding environment, but can threaten the provision of ecosystem services on which farm productivity depends. This research investigates the effects of management practices in Costa Rica on on-farm insect diversity, using three different types of banana farm management systems: high-input conventional system, low-input conventional system, and organic system. Insect sampling was done using pitfall and yellow bowl traps, left for a 24-h period at two locations inside the banana farm, at the edge of the farm, and in adjacent forest. All 39,091 individual insects were classified to family level and then morphospecies. Insect species community composition and diversity were compared using multivariate statistics with ordination analysis and Monte Carlo permutation testing, and revealed that each of the management systems were significantly different from each other for both trap types. Insect diversity decreased as management intensity increased. Reduced insect diversity resulted in fewer functional groups and fewer insect families assuming different functions essential to ecosystem health. Organic farms had similar species composition on the farm compared to adjacent forest sites, whereas species composition increasingly differed between farm and forest sites as management intensity increased. We conclude that while organic production has minimal impact on insect biodiversity, even small reductions in management intensity can have a significantly positive impact on on-farm insect biodiversity and functional roles supported.

LRIG proteins in glioma: Functional roles, molecular mechanisms, and potential clinical implications.

Gliomas are the most common intracranial tumors of the nervous system. These tumors are characterized by unlimited cell proliferation and excessive invasiveness. Despite the advances in diagnostic imaging, microneurosurgical techniques, radiation therapy, and chemotherapy, significant increases in the progression free survival of glioma patients have not been achieved. Improvements in our understanding of the molecular subtypes of gliomas and the underlying alterations in specific signaling pathways may impact both the diagnosis and the treatment strategies for patients with gliomas. Growth factors and their corresponding receptor tyrosine kinases are associated with oncogenesis and development of tumors in numerous human cancer types, including glioma. Leucine-rich repeats and immunoglobulin-like domains (LRIG) are integral membrane proteins which contain three vertebrate members including LRIG1, LRIG2 and LRIG3. They mainly function as regulators of growth factor signaling. Specifically, LRIG1 has been identified as a tumor suppressor in human cancers. In contrast, LRIG2 appears to function as a tumor promoter, while LRIG3 appears to have a function similar to that of LRIG1. In the present review, we summarize the functional roles, molecular mechanisms, and clinical perspectives of LRIG proteins in gliomas and propose that these proteins may be useful in the future as targets for treatment and prognostication in glioma patients.