Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms

Colorectal cancer affects the colon or rectum and is a common global health issue, with 1.1 million new cases occurring yearly. The study aimed to identify gene signatures for the early detection of CRC using machine learning (ML) algorithms utilizing gene expression data. The TCGA-CRC and GSE50760 datasets were pre-processed and subjected to feature selection using the LASSO method in combination with five ML algorithms: Adaboost, Random Forest (RF), Logistic Regression (LR), Gaussian Naive Bayes (GNB), and Support Vector Machine (SVM). The important features were further analyzed for gene expression, correlation, and survival analyses. Validation of the external dataset GSE142279 was also performed. The RF model had the best classification accuracy for both datasets. A feature selection process resulted in the identification of 12 candidate genes, which were subsequently reduced to 3 (CA2, CA7, and ITM2C) through gene expression and correlation analyses. These three genes achieved 100% accuracy in an external dataset. The AUC values for these genes were 99.24%, 100%, and 99.5%, respectively. The survival analysis showed a significant logrank p-value of 0.044 for the final gene signatures. The analysis of tumor immunocyte infiltration showed a weak correlation with the expression of the gene signatures. CA2, CA7, and ITM2C can serve as gene signatures for the early detection of CRC and may provide valuable information for prognostic and therapeutic decision making. Further research is needed to fully understand the potential of these genes in the context of CRC

Assessment of the effects of liquid and granular fertilizers on maize yield in Rwanda

Maize (Zea mays L.) is the most widely grown cereal in the world, accounting for 1,116.34 MT of production in 2019/2020. In Africa, this crop represented approximately 56% of the total cultivated area from 1990 to 2005. About 50% of the African population depends on maize as a staple food and source of carbohydrates, protein, iron, vitamin B, and minerals. Lately, maize has become a cash crop which contributes to the improvement of farmers' livelihoods. For example, the Strategic Plan for Agricultural Transformation (SPAT) III outlined that fertilizer availability in Rwanda should increase to 55,000 MT per year, while fertilizer use should increase from 30 kg/ha in 2013 to 45 kg/ha for the 2017/18 cropping season. Only inorganic fertilizers are currently being used in maize production in Rwanda. This research was conducted to assess the effects of liquid (CBX: Complete Biological Extract) and granular fertilizers on maize crop yields in Rwanda. The study was conducted in the fields of the Rwanda Agriculture and Animal Resources Development Board (Rubona Station) during the 2018/2019 cropping season. Analysis of variance (ANOVA) was used to determine whether differences between treatments were statistically significant, with the threshold for statistical significance set at p < 0.05. Aboveground biomass differed significantly between treatments, with maximum and minimum values of 11,475 kg and 7,850 kg, respectively, being observed. Furthermore, the harvest index differed significantly between treatments, with minimum and maximum values of 0.2136 and 0.33, respectively, being observed. Grain yield also differed significantly between treatments, with the highest value (3,053 kg/ha) observed for a treatment which applied liquid and granular fertilizer at equal proportions (treatment 8), and the lowest one was found in treatment 3 with 1,852 kg/ha. In this study, the gap between the lowest and highest grain yields was about 39.3%. In conclusion, the combination of organic liquid fertilizer and granular fertilizer can significantly increase the grain yield of maize in Rwanda

A thermostable organic solvent-tolerant lipase from Brevibacillus sp.: production and integrated downstream processing using an alcohol-salt-based aqueous two-phase system

Lipases are used for the synthesis of different compounds in the chemical, pharmaceutical, and food industries. Most of the reactions are carried out in non-aqueous media and often at elevated temperature, requiring the use of organic solvent-tolerant thermostable lipases. However, most known lipases are not stable in the presence of organic solvents and at elevated temperature. In this study, an organic solvent-tolerant thermostable lipase was obtained from Brevibacillus sp. SHI-160, a moderate thermophile isolated from a hot spring in the East African Rift Valley. The enzyme was optimally active at 65 degrees C and retained over 90% of its activity after 1 h of incubation at 70 degrees C. High lipase activity was measured in the pH range of 6.5 to 9.0 with an optimum pH of 8.5. The enzyme was stable in the presence of both polar and non-polar organic solvents. The stability of the enzyme in the presence of polar organic solvents allowed the development of an efficient downstream processing using an alcohol-salt-based aqueous two-phase system (ATPS). Thus, in the presence of 2% salt, over 98% of the enzyme partitioned to the alcohol phase. The ATPS-recovered enzyme was directly immobilized on a solid support through adsorption and successfully used to catalyze a transesterification reaction between paranitrophenyl palmitate and short-chain alcohols in non-aqueous media. This shows the potential of lipase SHI-160 to catalyze reactions in non-aqueous media for the synthesis of valuable compounds. The integrated approach developed for enzyme production and cheap and efficient downstream processing using ATPS could allow a significant reduction in enzyme production costs. The results also show the potential of extreme environments in the East African Rift Valley as sources of valuable microbial genetic resources for the isolation of novel lipases and other industrially important enzymes

Assessment of the effects of liquid and granular fertilizers on maize yield in Rwanda

Maize (Zea mays L.) is the most widely grown cereal in the world, accounting for 1,116.34 MT of production in 2019/2020. In Africa, this crop represented approximately 56% of the total cultivated area from 1990 to 2005. About 50% of the African population depends on maize as a staple food and source of carbohydrates, protein, iron, vitamin B, and minerals. Lately, maize has become a cash crop which contributes to the improvement of farmers' livelihoods. For example, the Strategic Plan for Agricultural Transformation (SPAT) III outlined that fertilizer availability in Rwanda should increase to 55,000 MT per year, while fertilizer use should increase from 30 kg/ha in 2013 to 45 kg/ha for the 2017/18 cropping season. Only inorganic fertilizers are currently being used in maize production in Rwanda. This research was conducted to assess the effects of liquid (CBX: Complete Biological Extract) and granular fertilizers on maize crop yields in Rwanda. The study was conducted in the fields of the Rwanda Agriculture and Animal Resources Development Board (Rubona Station) during the 2018/2019 cropping season. Analysis of variance (ANOVA) was used to determine whether differences between treatments were statistically significant, with the threshold for statistical significance set at p < 0.05. Aboveground biomass differed significantly between treatments, with maximum and minimum values of 11,475 kg and 7,850 kg, respectively, being observed. Furthermore, the harvest index differed significantly between treatments, with minimum and maximum values of 0.2136 and 0.33, respectively, being observed. Grain yield also differed significantly between treatments, with the highest value (3,053 kg/ha) observed for a treatment which applied liquid and granular fertilizer at equal proportions (treatment 8), and the lowest one was found in treatment 3 with 1,852 kg/ha. In this study, the gap between the lowest and highest grain yields was about 39.3%. In conclusion, the combination of organic liquid fertilizer and granular fertilizer can significantly increase the grain yield of maize in Rwanda

Optimization of Culture Conditions and Production of Bio-Fungicides from Trichoderma Species under Solid-State Fermentation Using Mathematical Modeling

Agro-industrial wastes suitable for economical and high mass production of novel Trichoderma species under solid-state fermentation were identified by optimizing the culture conditions using a mathematical model and evaluating the viability of the formulated bio-product. Fourteen inexpensive, locally available, organic substrates and cereals were examined using a one-factor-at-a-time experiment. The fungus colonized nearly all substrates after 21 days of incubation, although the degree of colonization and conidiation varied among the substrates. A mixture of wheat bran and white rice (2:1 w/w) was found to support maximum growth of T. asperellum AU131 (3.2 x 10(7) spores/g dry substrate) and T. longibrachiatum AU158 (3.5 x 10(7) spores/g dry substrate). Using a fractional factorial design, the most significant growth factors influencing biomass production were found to be temperature, moisture content, inoculum concentration, and incubation period (p <= 0.05). Analysis of variance of a Box-Behnken design showed that the regression model was highly significant (p <= 0.05) with F-values of 10.38 (P = 0.0027, T. asperellum AU131) and 12.01 (p < 0.0017, T. longibrachiatum AU158). Under optimal conditions, maximum conidia yield of log(10) (8.6) (T. asperellum AU131) and log(10)(9.18) (T. longibrachiatum) were obtained. For wettable powder Trichoderma species formulations, it was possible to maintain conidial viability at room temperature (25 degrees C) for eight months at concentrations above 10(6) CFU/g

Effect of Biochar and Microbial Inoculation on P, Fe, and Zn Bioavailability in a Calcareous Soil

To identify effective ways of increasing the yield of crops grown in nutrient-poor calcareous soils, the combined effects of biochar addition and inoculation with plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on wheat growth and soil properties were investigated under rhizobox conditions. Measured soil properties included pH, electrical conductivity (EC), organic matter content (OM), the availability of P, Fe, and Zn in the rhizosphere, and the uptake of these elements by plants. Combined biochar addition and microbial inoculation were shown to significantly increase the concentration of available forms of P, Fe, and Zn in the soil when compared to non-biochar treatments. The highest soil pH (7.82) was observed following biochar addition without microbial inoculation. The EC following biochar addition and PGPR inoculation was significantly higher than the other treatments, and the soil OM content was highest when combining AMF inoculation with biochar addition. The available P content after AMF inoculation combined with biochar addition was 27.81% higher than the control conditions, and AMF inoculation increased Fe and Zn bioavailability by factors of 2.38 and 1.29, respectively, when combined with biochar addition relative to AMF inoculation alone. The simultaneous biochar addition and PGPR inoculation significantly increased P uptake by the plants. The highest shoot Fe and Zn uptake rates were observed after a simultaneous application of biochar and PGPR inoculation. Under these conditions, shoot uptake was higher than seen when combining biochar addition with AMF inoculation by factors of 1.64 and 1.21, respectively. In general, it can be concluded that combining inoculation with growth-promoting bacteria and biochar addition can effectively improve nutrient availability to plant and soil conditions

Biological management of coffee wilt disease (Fusarium xylarioides) using antagonistic Trichoderma isolates

Coffee wilt disease (CWD) is a serious threat to the food security of small-scale farmers in Ethiopia, causing significant reductions in coffee yield. Currently, there are no effective control measures available against the causative agent of CWD, Fusarium xylarioides. The main objective of this study was therefore to develop, formulate, and evaluate a range of biofungicides against F. xylarioides, derived from Trichoderma species and tested under in vitro, greenhouse, and field conditions. In total, 175 Trichoderma isolates were screened as microbial biocontrol agents against F. xylarioides. The efficacy of two biofungicide formulations, wettable powder and water dispensable granules, were tested on the susceptible Geisha coffee variety in three different agro-ecological zones in southwestern Ethiopia over three years. The greenhouse experiments were set up using a complete block design, while in the field a randomized complete block design was used, with twice yearly applications of biofungicide. The test pathogen spore suspension was applied to the coffee seedlings by soil drenching, and the subsequent incidence and severity of CWD evaluated annually. The mycelial growth inhibition profiles of the Trichoderma isolates against F. xylarioides ranged from 44.5% to 84.8%. In vitro experiments revealed that T. asperelloides AU71, T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The greenhouse study indicated that wettable powder (WP) of T. asperellum AU131 had the highest biocontrol efficacy (84.3%), followed by T. longibrachiatum AU158 (77.9%) and T. asperelloides AU71 (71.2%); they also had a significant positive impact on plant growth. The pathogen-treated control plants had a disease severity index of 100% across all the field experiments, and of 76.7% in the greenhouse experiments. In comparison to untreated controls, the annual and cumulative disease incidence over the three years of the study period varied from 46.2 to 90%, 51.6 to 84.5%, and 58.2 to 91%, at the Teppi, Gera and Jimma field experimental locations. Overall, the greenhouse and field experiments and in vitro assays support the biocontrol potential of Trichoderma isolates, and T. asperellum AU131 and T. longibrachiatum AU158 in particular are recommended for the management of CWD under field conditions

Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance

MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance

Antifungal compounds, GC-MS analysis and toxicity assessment of methanolic extracts of Trichoderma species in an animal model

Fungi of the genus Trichoderma have been marketed for the management of diseases of crops. However, some Trichoderma species may produce toxic secondary metabolites and it should receive due attention to ensure human safety. In this study, we investigated the in vitro antagonistic potential of T. asperellum AU131 and T. longibrachiatum AU158 as microbial biocontrol agents (MBCAs) against Fusarium xylarioides and the associated antagonistic mechanism with bioactive substances. Swiss albino mice were used to evaluate the in vivo toxicity and pathogenicity of T. asperellum AU131 and T. longibrachiatum AU158 methanolic extracts and spore suspensions, respectively, in a preliminary safety assessment for use as biofungicides. Gas Chromatography-Mass Spectrometry (GC-MS) was used to profile volatile organic metabolites (VOCs) present in the methanolic extracts. The agar diffusion assay of the methanolic extracts from both T. asperellum AU131 and T. longibrachiatum AU158 were effective at a concentration of 200 mu g/mL (1x10(7) spores/mL), causing 62.5%, and 74.3% inhibition, respectively. A GC-MS analysis of methanolic extracts from both bioagents identified 23 VOCs which classified as alcohols, acids, sesquiterpenes, ketones and aromatic compounds. The oral administration of methanolic extracts and spore suspensions of each Trichoderma species to female Swiss albino mice over 14 days did not show any significant signs of toxicity, mortality or changes to body weight. It can be concluded that the tested spore suspensions and methanolic extracts were not pathogenic or toxic, respectively, when administered to Swiss albino mice at various doses

Comparison of two commercial recirculated aquacultural systems and their microbial potential in plant disease suppression

Background: Aquaponics are food production systems advocated for food security and health. Their sustainability from a nutritional and plant health perspective is, however, a significant challenge. Recirculated aquaculture systems (RAS) form a major part of aquaponic systems, but knowledge about their microbial potential to benefit plant growth and plant health is limited. The current study tested if the diversity and function of microbial communities in two commercial RAS were specific to the fish species used (Tilapia or Clarias) and sampling site (fish tanks and wastewaters), and whether they confer benefits to plants and have in vitro antagonistic potential towards plant pathogens. Results: Microbial diversity and composition was found to be dependent on fish species and sample site. The Tilapia RAS hosted higher bacterial diversity than the Clarias RAS; but the later hosted higher fungal diversity. Both Tilapia and Clarias RAS hosted bacterial and fungal communities that promoted plant growth, inhibited plant pathogens and encouraged biodegradation. The production of extracellular enzymes, related to nutrient availability and pathogen control, by bacterial strains isolated from the Tilapia and Clarias systems, makes them a promising tool in aquaponics and in their system design. Conclusions: This study explored the microbial diversity and potential of the commercial RAS with either Tilapia or Clarias as a tool to benefit the aquaponic system with respect to plant growth promotion and control of plant diseases