The impact of admission diagnosis on gastric emptying in critically ill patients

Introduction Disturbed gastric emptying (GE) occurs commonly in critically ill patients. Admission diagnoses are believed to influence the incidence of delayed GE and subsequent feed intolerance. Although patients with burns and head injury are considered to be at greater risk, the true incidence has not been determined by examination of patient groups of sufficient number. This study aimed to evaluate the impact of admission diagnosis on GE in critically ill patients. Methods A retrospective review of patient demographics, diagnosis, intensive care unit (ICU) admission details, GE, and enteral feeding was performed on an unselected cohort of 132 mechanically ventilated patients (94 males, 38 females; age 54 ± 1.2 years; admission Acute Physiology and Chronic Health Evaluation II [APACHE II] score of 22 ± 1) who had undergone GE assessment by 13C-octanoic acid breath test. Delayed GE was defined as GE coefficient (GEC) of less than 3.20 and/or gastric half-emptying time (t50) of more than 140 minutes. Results Overall, 60% of the patients had delayed GE and a mean GEC of 2.9 ± 0.1 and t50 of 163 ± 7 minutes. On univariate analysis, GE correlated significantly with older age, higher admission APACHE II scores, longer length of stay in ICU prior to GE measurement, higher respiratory rate, higher FiO2 (fraction of inspired oxygen), and higher serum creatinine. After these factors were controlled for, there was a modest relationship between admission diagnosis and GE (r = 0.48; P = 0.02). The highest occurrence of delayed GE was observed in patients with head injuries, burns, multi-system trauma, and sepsis. Delayed GE was least common in patients with myocardial injury and non-gastrointestinal post-operative respiratory failure. Patients with delayed GE received fewer feeds and stayed longer in ICU and hospital compared to those with normal GE. Conclusion Admission diagnosis has a modest impact on GE in critically ill patients, even after controlling for factors such as age, illness severity, and medication, which are known to influence this function.Nam Q Nguyen, Mei P Ng, Marianne Chapman, Robert J Fraser and Richard H Hollowa

Identification of a Latitude Gradient in the Prevalence of Primary Biliary Cholangitis

Introduction: The prevalence of primary biliary cholangitis (PBC) reported in different countries varies significantly and seems to have a latitudinal gradient with the highest prevalence reported in higher latitudes, as has been observed with other autoimmune diseases. This study aimed to determine whether there is a latitudinal gradient of PBC prevalence in Australia using 2 methods of case ascertainment.Methods: We investigated the latitudinal variation of PBC prevalence across the states and territories of Australia (latitudinal range 18.0°-42.7°S) using pathology-based (private pathology antimitochondrial antibody results and PBC-specific prescription databases (prescriptions for ursodeoxycholic acid, the only publicly subsidized treatment for this disease).Results: PBC prevalence was significantly positively associated with latitude, and the postcodes in the highest quintile of latitude (encompassing the south coastal areas of the Australian mainland and Tasmania; latitude range -37.75° to -42.72°) had a prevalence estimate that was 1.78 times higher using the pathology-based prevalence estimation than those in the lowest quintile (encompassing tropical and southern Queensland; latitude range -18.02° to -27.59°). Comparing prevalence estimates between states/territories, the result was 2.53 and 2.21 times higher in Tasmania compared with Queensland when using the pathology-based and prescription-based methods, respectively.Discussion: Using 2 different case-ascertainment methods, we have demonstrated that prevalence estimates of PBC vary significantly with latitude in Australia. Further studies are needed to determine whether factors such as variations in ultraviolet radiation exposure and/or vitamin D levels are responsible for this observation and to investigate the latitudinal prevalence of PBC in other populations

Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass.

BackgroundTrichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression.ResultsBy analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates.ConclusionOur data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes

Identification of a gene encoding the last step of the L-rhamnose catabolic pathway in Aspergillus niger revealed the inducer of the pathway regulator

In fungi, L-rhamnose (Rha) is converted via four enzymatic steps into pyruvate and L-lactaldehyde, which enter central carbon metabolism. In Aspergillus niger, only the genes involved in the first three steps of the Rha catabolic pathway have been identified and characterized, and the inducer of the pathway regulator RhaR remained unknown. In this study, we identified the gene (lkaA) involved in the conversion of L-2-keto-3-deoxyrhamnonate (L-KDR) into pyruvate and L-lactaldehyde, which is the last step of the Rha pathway. Deletion of lkaA resulted in impaired growth on L-rhamnose, and potentially in accumulation of L-KDR. Contrary to Delta lraA, Delta lrlA and Delta lrdA, the expression of the Rha-responsive genes that are under control of RhaR, were at the same levels in Delta lkaA and the reference strain, indicating the role of L-KDR as the inducer of the Rha pathway regulator.Peer reviewe

Corrigendum to "Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens" [J. Biotechnol. 380 (2020) 35-39].

In Section 3.1 of the Results and Discussion, it should have stated 100 μM and not 50 μM for the concentration of the aromatic compounds. The correct concentration was stated in the Materials and Methods and the error only occurred in the Results and Discussion section. The authors would like to apologize for any inconvenience caused

Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate in lignin synthesis. Filamentous fungi are able to degrade cinnamic acid through multiple metabolic pathways. One of the best studied pathways is the non-oxidative decarboxylation of cinnamic acid to styrene. In Aspergillus niger, the enzymes cinnamic acid decarboxylase (CdcA, formally ferulic acid decarboxylase) and the flavin prenyltransferase (PadA) catalyze together the non-oxidative decarboxylation of cinnamic acid and sorbic acid. The corresponding genes, cdcA and padA, are clustered in the genome together with a putative transcription factor previously named sorbic acid decarboxylase regulator (SdrA). While SdrA was predicted to be involved in the regulation of the non-oxidative decarboxylation of cinnamic acid and sorbic acid, this was never functionally analyzed. In this study, A. niger deletion mutants of sdrA, cdcA, and padA were made to further investigate the role of SdrA in cinnamic acid metabolism. Phenotypic analysis revealed that cdcA, sdrA and padA are exclusively involved in the degradation of cinnamic acid and sorbic acid and not required for other related aromatic compounds. Whole genome transcriptome analysis of ΔsdrA grown on different cinnamic acid related compounds, revealed additional target genes, which were also clustered with cdcA, sdrA, and padA in the A. niger genome. Synteny analysis using 30 Aspergillus genomes demonstrated a conserved cinnamic acid decarboxylation gene cluster in most Aspergilli of the Nigri clade. Aspergilli lacking certain genes in the cluster were unable to grow on cinnamic acid, but could still grow on related aromatic compounds, confirming the specific role of these three genes for cinnamic acid metabolism of A. niger.Peer reviewe

Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity

Next to d-glucose, the pentoses l-arabinose and d-xylose are the main monosaccharide components of plant cell wall polysaccharides and are therefore of major importance in biotechnological applications that use plant biomass as a substrate. Pentose catabolism is one of the best-studied pathways of primary metabolism of Aspergillus niger, and an initial outline of this pathway with individual enzymes covering each step of the pathway has been previously established. However, although growth on l-arabinose and/or d-xylose of most pentose catabolic pathway (PCP) single deletion mutants of A. niger has been shown to be negatively affected, it was not abolished, suggesting the involvement of additional enzymes. Detailed analysis of the single deletion mutants of the known A. niger PCP genes led to the identification of additional genes involved in the pathway. These results reveal a high level of complexity and redundancy in this pathway, emphasizing the need for a comprehensive understanding of metabolic pathways before entering metabolic engineering of such pathways for the generation of more efficient fungal cell factories.Peer reviewe

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Funding Information: The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 . CK, EB was supported by a grant of the Applied and Engineering Sciences division of NWO , and the Technology Program of the Ministry of Economic Affairs 016.130.609 to RPdV. PD was supported by a grant of the Netherlands Scientific Organization NWO 824.15.023 to RPdV. The Academy of Finland grant no. 308284 to MRM is acknowledged. Publisher Copyright: © 2021 The Author(s)Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.Peer reviewe