Genetic Information Processing Research Articles

Gene Regulation in and out of Equilibrium.

Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.

Responses of rhizosphere soil bacteria to 2-year tillage rotation treatments during fallow period in semiarid southeastern Loess Plateau.

BackgroundSoil compaction can be mitigated by deep tillage and subsoiling practices following a long period of no-tillage. Fallow tillage rotation methods are frequently used to improve water availability in the soils of the southeastern Loess Plateau region of China. Rhizosphere soil bacteria are ecologically important for the transformation of matter and energy in the plant root system and can be influenced by tillage rotation treatments. However, the effect of tillage rotations on the bacterial community and structure of rhizosphere soil is not well understood.MethodsA two-year field experiment was conducted with four tillage rotation treatments, including subsoil–subsoil (SS-SS), subsoil–deep tillage (SS-DT), deep tillage–deep tillage (DT-DT), and the control treatment of no-tillage–no-tillage (NT-NT). Our study was conducted during wheat’s fallow period to investigate the abundance, diversity, and functions of rhizosphere soil bacteria using high-throughput sequencing technology.ResultsOur results showed that tillage rotation methods significantly influenced the bacterial diversity and composition of the rhizosphere soil in the plough layer (20–40 cm depth) by altering the moisture content of the soil. The metabolism, environmental information processing, and genetic information processing of the bacteria in the rhizosphere soil were affected. The most abundant phyla across all samples were Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Bacteroidetes, Gemmatimonadetes, Frimicutes, Chloroflexi, Nitrospirae, and Verrucomicrobia, which are classic bacterial decomposers in soil. The bacterial diversity and composition was similar for treatments causing higher soil perturbation (SS-DT and DT-DT), which disrupted the balance between aerobic and anaerobic bacteria. The less disruptive tillage methods (SS-SS and NT-NT), preserved the integrity of the soil bacteria. However, the NT-NT treatment may have led to soil compaction, particularly in the 20–40 cm layer. These results suggested that SS-SS was the most effective tillage rotation practice to accumulate soil moisture, maintain the balance between aerobic and anaerobic bacteria, and to enhance the metabolic capacity of rhizosphere soil bacteria. This method may have a significant impact on the sustainable development and farming practices of dryland agriculture.

Adverse physiological and molecular level effects of polystyrene microplastics on freshwater microalgae

Microplastics have aroused widespread concern because of their adverse effects on aquatic organisms. However, the underlying toxicity mechanisms have not been examined in detail. This study investigated the interactions between polystyrene microplastics (PS-MPs) and the model freshwater microalgae Euglena gracilis. The results of transmission electron microscopy showed that the vacuoles of microalgae were induced after 24 h exposure to 1 mg/L PS-MPs (5 μm and 0.1 μm). Furthermore, PS-MPs significantly (p < 0.05) reduced pigment contents. Moreover, superoxide dismutase activities were significantly (p < 0.05) induced in all PS-MPs treated groups. Peroxidase activities were also significantly (p < 0.05) affected by two sizes of PS-MPs (5 μm and 0.1 μm), indicating that oxidative stress was induced after exposure to PS-MPs. At the molecular level, PS-MPs dysregulated the expression of genes involved in cellular processes, genetic information processing, organismal systems, and metabolisms. The KCS gene and the CTR1 gene may be key pathways to induce adverse effects on the E. gracilis after exposure to 5 μm PS-MPs. These findings will help to elucidate the underlying molecular mechanism of microplastics toxicity on freshwater organisms.

Captivity Influences Gut Microbiota in Crocodile Lizards (Shinisaurus crocodilurus).

Captivity is an important measure for conservation of an endangered species, and it is becoming a hot topic in conservation biology, which integrates gut microbiota and endangered species management in captivity. As an ancient reptile, the crocodile lizard (Shinisaurus crocodilurus) is facing extreme danger of extinction, resulting in great significance to species conservation in the reserve. Thus, it is critical to understand the differences in gut microbiota composition between captive and wild populations, as it could provide fundamental information for conservative management of crocodile lizards. Here, fecal samples of crocodile lizards were collected from two wild and one captive populations with different ages (i.e., juveniles and adults) and were analyzed for microbiota composition by 16S ribosomal RNA (rRNA) gene amplicon sequencing. This study showed that the lizard gut microbiota was mainly composed of Firmicutes and Proteobacteria. The gut microbiota composition of crocodile lizard did not differ between juveniles and adults, as well as between two wild populations. Interestingly, captivity increased community richness and influenced community structures of gut microbiota in crocodile lizards, compared with wild congeners. This was indicated by higher abundances of the genera Epulopiscium and Glutamicibacter. These increases might be induced by complex integration of simple food resources or human contact in captivity. The gut microbiota functions of crocodile lizards are primarily enriched in metabolism, environmental information processing, genetic information processing, and cellular processes based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This study provides fundamental information about the gut microbiota of crocodile lizards in wild and captive populations. In the future, exploring the relationship among diet, gut microbiota, and host health is necessary for providing animal conservation strategies.

Gut Microbiome Reveals Specific Dysbiosis in Primary Osteoporosis.

Object: Primary osteoporosis (PO) is the most common bone disease, which is characterized by decreased bone mass, damage of bone tissue microstructure, increased bone fragility, and is prone to fracture. Gut microbiome may be involved in bone metabolism of PO through gut–brain axis regulation of immune system and endocrine system, however, the specific mechanism is still unclear. The purpose of this study was to characterize the gut microbiome of patients with PO and its possible role in the occurrence and development of the disease.Methods: Fecal samples were collected from 48 PO patients and 48 healthy controls (HC). The composition of gut microbiome community was analyzed by 16s rDNA amplification sequencing, and the difference of gut microbiome composition between PO patients and HC individuals was compared. PICRUSt was also used to predict the biological function of gut microbiome in patients with PO, and to explore its possible role in the occurrence and development of this disease. The classification model is constructed by random forest algorithm so as to screen the key biomarkers.Result: The diversity of gut microorganisms in PO patients was significantly higher than that in HC group (p < 0.05) and there was significant difference in microbial composition in PO group. The abundance of Dialister (0.036 vs. 0.004, p < 0.001) and Faecalibacterium (0.331 vs. 0.132, p < 0.001) were significantly enriched which were the key flora related to PO. Although no significant correlation between bone mineral density and the richness of microbial communities are found, PICRUST results show that there are a wide range of potential pathways between gut microbiome and PO patients, including genetic information processing, metabolism, environmental information processing, cellular processes, human diseases, and organic systems. Notably, the discriminant model based on dominant microflora can effectively distinguish PO from HC (AUC = 93.56).Conclusions: The findings show that PO is related to the change of gut microbiome, especially the enriched Dialister and Faecalibacterium genera, which give new clues to understand the disease and provide markers for the diagnosis and new strategies for intervention treatment of the disease.

Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa.

It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of thethree primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.

Low-gossypol cottonseed protein concentrate used as a replacement of fish meal for juvenile hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂): Effects on growth performance, immune responses and intestinal microbiota

The use of low-gossypol cottonseed protein concentrate (CPC) as a replacement for fishmeal (FM) in the juvenile hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) was investigated concerning differences in growth performance, immune response, and intestinal microbiota among the dietary treatments. Hybrid grouper were fed a diet (isonitrogenous and isolipidic) with FM or FM replaced with either 20% (CPC20), 40% (CPC40) or 60% CPC (CPC60) for 10 weeks. At the end of the study, there were no significant differences in the weight gain rate, specific growth rate, survival rate, and feed intake of fish among the groups. However, the feed conversion ratio of fish in the CPC-containing groups was higher than that in the FM group and was significantly higher in the CPC40 and CPC60 group. The levels of immunity-related enzyme activities and gene expression in the fish intestine were also investigated. In the CPC-containing groups, the lysozyme activity and immunoglobulin M levels were significantly increased, while the superoxide dismutase and catalase activities were significantly reduced compared to the FM group. The mRNA expression of innate immune genes (MHC-II-β, TLR22, TNF-α1, IL-6, IFN-γ, and IL-10) of the distal intestine (DI) was significantly increased in CPC-fed fish; however, there was no significant change in the TGF-β1 expression. The bacterial community in the DI was analyzed by Next-Generation Sequencing, which showed no significant difference in alpha diversity among the four diet groups. At the family level, the relative abundance of Burkholderiaceae was significantly higher in the CPC20 group compared to the FM group, while the relative abundance of Bacteroidales S24–7 group and Lachnospiraceae was significantly higher in the FM group. The functional prediction of the microbiota indicated that the pathways of amino acid metabolism, xenobiotics biodegradation and metabolism were significantly more abundant in the CPC-containing groups than the FM group. In contrast, the pathways associated with genetic information processing (translation, replication and repair) were more prevalent in the FM group. These results demonstrated that although dietary CPC replacement of levels up to 60% did not significantly alter the growth performance in hybrid grouper, the immune responses were adversely influenced. Replacing FM with CPC had an important impact on microbial profiles but not on diversity.

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.1EX9Jugkb3j7HLsLG9gAj8Video abstract.

Root transcriptome profiling of contrasting wheat genotypes provides an insight to their adaptive strategies to water deficit

Water deficit limits plant growth and productivity in wheat. The effect of water deficit varies considerably in the contrasting genotypes. This study attempted comparative transcriptome profiling of the tolerant (Abura) and susceptible (AUS12671) genotypes under PEG-simulated water stress via genome-wide RNA-seq technology to understand the dynamics of tolerance mechanism. Morphological and physiological analyses indicated that the tolerant genotype Abura had a higher root growth and net photosynthesis, which accounted for its higher root biomass than AUS12671 under stress. Transcriptomic analysis revealed a total of 924 differentially expressed genes (DEGs) that were unique in the contrasting genotypes under stress across time points. The susceptible genotype AUS12671 had slightly more abundant DEGs (505) than the tolerant genotype Abura (419). Gene ontology enrichment and pathway analyses of these DEGs suggested that the two genotypes differed significantly in terms of adaptive mechanism. Predominant upregulation of genes involved in various metabolic pathways was the key adaptive feature of the susceptive genotype AUS12671 indicating its energy-consuming approach in adaptation to water deficit. In contrast, downregulation the expression of genes of key pathways, such as global and overview maps, carbohydrate metabolism, and genetic information processing was the main strategy for the tolerant genotype Abura. Besides, significantly higher number of genes encoding transcription factors (TF) families like MYB and NAC, which were reported to be associated with stress defense, were differentially expressed in the tolerant genotype Abura. Gene encoding transcription factors TIFY were only differentially expressed between stressed and non-stressed conditions in the sensitive genotype. The identified DEGs and the suggested differential adaptive strategies of the contrasting genotypes provided an insight for improving water deficit tolerance in wheat.

Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans

BackgroundBarnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the intertidal zone and shallow waters, but a few species inhabit the deep-sea floor. It is of interest to investigate how such sessile crustaceans became adapted to extreme deep-sea environments. We sequenced the transcriptomes of a deep-sea barnacle, Glyptelasma gigas collected at a depth of 731 m from the northern area of the Zhongjiannan Basin, and a shallow-water coordinal relative, Octolasmis warwicki. The purpose of this study was to provide genetic resources for investigating adaptation mechanisms of deep-sea barnacles.ResultsTotals of 62,470 and 51,585 unigenes were assembled for G. gigas and O. warwicki, respectively, and functional annotation of these unigenes was made using public databases. Comparison of the protein-coding genes between the deep- and shallow-water barnacles, and with those of four other shallow-water crustaceans, revealed 26 gene families that had experienced significant expansion in G. gigas. Functional annotation showed that these expanded genes were predominately related to DNA repair, signal transduction and carbohydrate metabolism. Base substitution analysis on the 11,611 single-copy orthologs between G. gigas and O. warwicki indicated that 25 of them were distinctly positive selected in the deep-sea barnacle, including genes related to transcription, DNA repair, ligand binding, ion channels and energy metabolism, potentially indicating their importance for survival of G. gigas in the deep-sea environment.ConclusionsThe barnacle G. gigas has adopted strategies of expansion of specific gene families and of positive selection of key genes to counteract the negative effects of high hydrostatic pressure, hypoxia, low temperature and food limitation on the deep-sea floor. These expanded gene families and genes under positive selection would tend to enhance the capacities of G. gigas for signal transduction, genetic information processing and energy metabolism, and facilitate networks for perceiving and responding physiologically to the environmental conditions in deep-sea habitats. In short, our results provide genomic evidence relating to deep-sea adaptation of G. gigas, which provide a basis for further biological studies of sessile crustaceans in the deep sea.

A formulated diet improved digestive capacity, immune function and intestinal microbiota structure of juvenile hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) when compared with chilled trash fish

The effects of two diets on the growth, intestinal microbiota, digestive enzymes, immunity-related enzymes and gene expression were assessed in the juvenile hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂). Hybrid grouper were fed either a formulated diet (FM group) or chilled trash fish (CTF group). Following a 10-week feeding study, the results showed that the final weight, weight gain rate, specific growth rate and survival rate of fish were not significantly different between the groups. However, bio-economic analysis of the feeds showed that the profit from fish in the FM group was significantly higher than from the CTF group. In addition, digestive enzyme (trypsin and pepsin) activities in fish were significantly higher in the FM group, while lysozyme activity was significantly higher in the CTF group. Levels of complement component 4 (C4) and immunoglobulin M (IgM) in fish serum were significantly lower in FM group fish, while complement component 3 (C3) levels were higher in FM group fish. In the fish intestine, IgM levels were significantly higher in the FM group, while lysozyme activity and C3 and C4 levels were higher in the CTF group. The expression of innate immune genes (MHC II β and TLR22) and inflammatory cytokines (IL-1β, IL-6, IL-10, TNF α1 and IFN γ) were significantly lower in the FM group. The bacterial community of the distal intestine was analyzed by Next-Generation Sequencing. At the phylum level, the relative abundance of Acidobacteria was significantly lower in the FM group, while the abundance of Bacteroidetes was lower in the CTF group. At the family level, the relative abundance of Flavobacterium was significantly lower in the FM group, while the abundance of Bacteroidales_S24-7_group and Lachnospiraceae was lower in the CTF group. The most significantly changed pathways between the two groups were metabolism and genetic information processing. The overall results showed that feed bio-economics, digestive capacity, and immunity of hybrid grouper were superior in the FM group compared to the CTF group.

Microbial community composition, co-occurrence network pattern and nitrogen transformation genera response to biochar addition in cattle manure-maize straw composting

A better understanding of the microbial group influencing nitrogen (N) dynamics and cycling in composting matrix is critical in achieving good management to alleviate N loss and improve final compost quality. This study investigated the bacterial composition, structure, co-occurrence network patterns and topological roles of N transformation in cattle manure-maize straw composting using high-throughput sequencing. The two treatments used in this experiment were cattle manure and maize straw mixture (CM) and CM with 10% biochar addition (CMB). In both treatments, the bacterial community composition varied during composting and the major phyla included Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes and Chloroflexi. The phyla Actinobacteria and Proteobacteria were more abundant in CMB treatment while Firmicutes was abundant in CM piles. The metabolic functional profiles of bacteria was predicted using the “phylogenetic investigation of communities by reconstruction of unobserved states” (PICRUSt) which revealed that except for cellular processes pathway, CMB had slight higher abundance in metabolism, genetic information processing and environmental information processing than the CM. Pearson correlation revealed more significant relationship between the important bacteria communities and N transformation in CMB piles compared with CM. Furthermore, network pattern analysis revealed that the bacterial networks in biochar amended piles are more complex and harbored more positive links than that of no biochar piles. Corresponding agreement of multivariate analyses (correlation heatmap, stepwise regression, Path and network analyses) revealed that Psychrobacter, Thermopolyspora and Thermobifida in CM while Corynebacterium_1, Thermomonospora and Streptomyces in CMB were key bacterial genera affecting NH4+-N, NO3−-N and total nitrogen (TN) transformation respectively during composting process. These results provide insight into nitrogen transformation and co-occurrence patterns mediating microbes and bacterial metabolism which could be useful in enhancing compost quality and mitigating N loss during composting.

Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes.

Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus

Hyphae of filamentous fungi undergo polar extension, bifurcation and hyphal fusion to form reticulating networks of mycelia. Hyphal fusion or anastomosis, a ubiquitous process among filamentous fungi, is a vital strategy for how fungi expand over their substrate and interact with or recognise self- and non-self hyphae of neighbouring mycelia in their environment. Morphological and genetic characterisation of anastomosis has been studied in many model fungal species, but little is known of the direct proteomic response of two interacting fungal isolates. Agaricus bisporus, the most widely cultivated edible mushroom crop worldwide, was used as an in vitro model to profile the proteomes of interacting cultures. The globally cultivated strain (A15) was paired with two distinct strains; a commercial hybrid strain and a wild isolate strain. Each co-culture presented a different interaction ranging from complete vegetative compatibility (self), lack of interactions, and antagonistic interactions. These incompatible strains are the focus of research into disease-resistance in commercial crops as the spread of intracellular pathogens, namely mycoviruses, is limited by the lack of interhyphal anastomosis. Unique proteomic responses were detected between all co-cultures. An array of cell wall modifying enzymes, plus fungal growth and morphogenesis proteins were found in significantly (P < 0.05) altered abundances. Nitrogen metabolism dominated in the intracellular proteome, with evidence of nitrogen starvation between competing, non-compatible cultures. Changes in key enzymes of A. bisporus morphogenesis were observed, particularly via increased abundance of glucanosyltransferase in competing interactions and certain chitinases in vegetative compatible interactions only. Carbohydrate-active enzyme arsenals are expanded in antagonistic interactions in A. bisporus. Pathways involved in carbohydrate metabolism and genetic information processing were higher in interacting cultures, most notably during self-recognition. New insights into the differential response of interacting strains of A. bisporus will enhance our understanding of potential barriers to viral transmission through vegetative incompatibility. Our results suggest that a differential proteomic response occurs between A. bisporus at strain-level and findings from this work may guide future proteomic investigation of fungal anastomosis.

Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus.

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.

Characterization of the milk fat globule membrane proteome in colostrum and mature milk of Xinong Saanen goats

Xinong Saanen goat milk is a major source of milk in the Chinese dairy industry. Milk fat globule membrane (MFGM) proteomes of goat colostrum and mature milk were analyzed and compared using proteomic technology. A total of 543 and 585 proteins were identified in goat colostrum and mature milk, respectively. Functional category analyses revealed that most of the MFGM proteins in both colostrum and mature milk were related to phosphoprotein and acetylation. The biological process of translation, cellular component of extracellular exosome, and molecular function of poly(A) RNA binding were the main gene ontology annotations of both colostrum and mature milk. Pathways associated with disease and genetic information processing involved large number of proteins in colostrum and mature milk, and more metabolism-related pathways were observed in mature milk. Protein-protein interaction network analyses showed that ribosome was abundant in both colostrum and mature milk. Colostrum showed more functions associated with protein processing in the endoplasmic reticulum, whereas mature milk had more oxidative phosphorylation functions. The results could provide further understanding of the unique biological properties of MFGM proteins of goat colostrum and mature milk.

Does a Ribosome Really Read? On the Cognitive Roots and Heuristic Value of Linguistic Metaphors in Molecular Genetics. Part 2

We discuss the role of linguistic metaphors as a cognitive frame for the understanding of genetic information processing. The essential similarity between language and genetic information processing has been recognized since the very beginning, and many prominent scholars have noted the possibility of considering genes and genomes as texts or languages. Most of the core terms in molecular biology are based on linguistic metaphors. The processing of genetic information is understood as some operations on text – writing, reading and editing and their specification (encoding/decoding, proofreading, transcription, translation, reading frame). The concept of gene reading can be traced from the archaic idea of the equation of Life and Nature with the Book. Thus, the genetics itself can be metaphorically represented as some operations on text (deciphering, understanding, code-breaking, transcribing, editing, etc.), which are performed by scientists. At the same time linguistic metaphors portrayed gene entities also as having the ability of reading. In the case of such “bio-reading” some essential features similar to the processes of human reading can be revealed: this is an ability to identify the biochemical sequences based on their function in an abstract system and distinguish between type and its contextual tokens of the same type. Metaphors seem to be an effective instrument for representation, as they make possible a two-dimensional description: biochemical by its experimental empirical results and textual based on the cognitive models of comprehension. In addition to their heuristic value, linguistic metaphors are based on the essential characteristics of genetic information derived from its dual nature: biochemical by its substance, textual (or quasi-textual) by its formal organization. It can be concluded that linguistic metaphors denoting biochemical objects and processes seem to be a method of description and explanation of these heterogeneous properties.

Rhizosphere Bacterial Community Structure and Predicted Functional Analysis in the Water-Level Fluctuation Zone of the Danjiangkou Reservoir in China During the Dry Period.

The water-level fluctuation zone (WLFZ) is a transitional zone between terrestrial and aquatic ecosystems. Plant communities that are constructed artificially in the WLFZ can absorb and retain nutrients such as nitrogen (N) and phosphorus (P). However, the microbial community composition and function associated with this process have not been elucidated. In this study, four artificially constructed plant communities, including those of herbs (Cynodon dactylon and Chrysopogon zizanioides), trees (Metasequoia glyptostroboides), and shrubs (Salix matsudana) from the newly formed WLFZ of the Danjiangkou Reservoir were evaluated. The bacterial community compositions were analyzed by 16S rRNA gene sequencing using a MiSeq platform, and the functions of these communities were assessed via Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. The results showed that the bacterial communities primarily comprised 362 genera from 24 phyla, such as Proteobacteria, Acidobacteria, Actinobacteria, and Gemmatimonadetes, showing the richness of the community composition. Planting altered the bacterial community composition, with varying effects observed among the different plant types. The bacterial community functional analysis revealed that these bacteria were primarily associated with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, and environmental information processing) with 34 subfunctions, showing the richness of community functions. The planting of M. glyptostroboides, S. matsudana, and C. dactylon improved the metabolic capabilities of bacterial communities. N- and P-cycling gene analysis showed that planting altered the N- and P-cycling metabolic capacities of soil bacteria. The overall N- and P-metabolic capacity was highly similar between C. dactylon and C. zizanioides samples and between S. matsudana and M. glyptostroboides samples. The results of this study provide a preliminary analysis of soil bacterial community structure and function in the WLFZ of the Danjiangkou Reservoir and provides a reference for vegetation construction in this zone.

Modelling the Genetic Information Processes of a Genetically Minimal Cell

Modelling the Genetic Information Processes of a Genetically Minimal Cell

Modelling the Nucleotide Metabolic Network of a Genetically Minimal Cell

Determination of the fundamental principles governing bacterial cellular behavior has been a goal since the discovery of the cell. To get at the fundamental principles, not only is an understanding of how cellular networks operate, but also how the individual networks control and communicate with one another. In this study, we aim to elucidate the function of the nucleotide metabolic network in governing DNA replication and transcription. Ordinarily the intrinsically complex nature of bacteria hinders fundamental investigations of their behavior, however this complexity has been relatively simplified using a genetically minimized organism. JCVI-syn3A is a synthetically constructed bacterium with a 543 kbp genome containing 493 genes. Previously published work, Breuer et al. eLife 2019, reported on the pathways in the metabolic networks of JCVI-syn3A along with genome-scale proteomics and gene essentiality studies. The essential nucleotide metabolic network was established to be a series of salvage pathways capable of transporting in nucleobases and nucleosides and then converting them to the final products, either NTPs or dNTPs. The network is made up of 62 reactions coded by 27 genes. The nucleotide metabolic network functions as the connection between the metabolic networks and the genetic information processing of the cell, and must be able to meet the demands of the cell. To construct the model, kinetic parameters have been developed from proteomics and metabolomics data, thermodynamics calculations, and the literature when necessary. The resulting model was capable of meeting cellular demands for DNA and RNA production.