Genome-wide analyses of Bacillus amyloliquefaciens strains provide insights into their beneficial role on plants

The innate immunity system of plants provides a basal defence barrier to most microorganisms. However, many plant pathogens have evolved to overcome this defence. Certain bacteria in the PGPB (plant growth promoting bacteria) category that improve plant growth have also been found to improve plant defence against insect pests and pathogens. Some bacteria of the genus Bacillus are known to be associated with plant roots, and have potential as possible biocontrol agents and biofertilizers in agriculture. For instance, Bacillus amyloliquefaciens subsp. plantarum strains can support plant growth and protection to stress after developing physical and biochemical contacts with plants. This thesis provides detailed descriptions of the genomic structure of three B. amyloliquefaciens subsp. plantarum strains with ability to promote plant growth and to suppress disease from several pathogens. The Bacillus genomes contain the basic genetic traits required for survival in the rhizosphere and plant growth promotion including chemotaxis and motility, root colonization, and biosynthesis of phytohormones. Besides growth promotion, the genomes have the capability to encode several antibacterial and antifungal compounds that effectively protect plant from pathogenic microorganisms. Several of the predicted traits were confirmed by experimental analysis. Genome-wide comparative analysis of the Bacillus strains indicates that the genomes are very similar although variation has been observed in phenotypes associated with plant growth promotion and disease suppression. A possible explanation could be mutations in one or more putative genes. Genomic comparison with other non-plant associated Bacillus species indicates the genomic polymorphism has a crucial role in loss and gain of function in the two groups of Bacillus species

Whole genome assembly, annotation and bioinformatics analysis of Bacillus amyloliquefaciens strain UCMB5113"

Bacillus amyloliquefaciens strain UCMB5113 is a Gram negative rhizo-bacterium, that produces antimicrobial compounds and induce plant basal defense with unknown genetic mechanism that suppress soil-borne plants and pathogens. Paired-end reads of length 75 bp with insert size of ~230 bp were sequenced from the genome of UCMB5113 by Illumina multiplex technology. Reference-guided assembly of the paired-end reads was performed using Bacillus amyloliquefaciens FZB42 as reference sequence which was found to be closely related to UCMB5113 strain. A draft of UCMB5113 genome obtained after mapping the reads with reference sequence containing 4,169 genes excluding 90 tRNA and 29 rRNA genes. The draft genome of UCMB5113 harbors cluster of genes, which were found in B. amyloliquefaciens FZB42 and involved in synthesis of secondary metabolites like surfactin, fengycin, bacillomycinD, bacillibactin, and bacilysin, by pathways not involving ribosomes. Initial analysis reveals that UCMB5113 genome lacks an operon NRS involved in synthesis of putative secondary metabolite. The determination of draft genome sequence of UCMB5113 provided very basic analysis of set of genes involved in plant bacterium interaction and plant growth and protection. Further analysis is required to understand the genetic mechanism of interaction and protection mediated by CMB5113

Mediating Role of Death Anxiety between Supernatural Beliefs and Life Satisfaction among Muslim Adults

The belief in supernatural forces is so pervasive in Pakistani society that it is nearly universal among illiterate and semi-literate people. Few literate individuals also subscribe to the idea of supernatural beings and entities. Such beliefs may invoke anxieties resulting in reduced satisfaction with life. In the current study, a cross-sectional survey of Muslim people was used to examine the potential mediation effect of death anxiety between supernatural beliefs and life satisfaction. A purposive sample (N = 220; with equal representation of both genders) of adults was recruited from different areas of district Sargodha. The supernatural Belief Scale, Arabic Scale of Death Anxiety, and Satisfaction with Life Scale were employed for assessing supernatural belief, death anxiety, and life satisfaction, respectively. Path analysis in Amos revealed the positive direct effect of supernatural belief on death anxiety and the negative direct effect of death anxiety on life satisfaction. Supernatural beliefs also demonstrated a negative indirect effect on life satisfaction through death anxiety. Overall, we found that individuals with supernatural beliefs were more likely to feel death anxiety, which might make them less satisfied with their life. Clinicians and mental health practitioners must envisage such therapeutic strategies as could counter the supernatural beliefs of the clients so that they might enjoy a more fulfilling and satisfying life

Role of Mindfulness and Psychological Wellbeing Between External Locus of Control and Depression: A Moderated Mediation Model

The present research aimed at examining the role of mindfulness and psychological wellbeing in the relationship between external locus of control and depression. Five Facet Mindfulness Questionnaire (Baer, 2003), Ryff Scale of Wellbeing (Ryff, 1989), DAAS Depression Subscale (Lovibond & Lovibond, 1995), and Rotter’s Locus of Control Scale (Rotter, 1966) were administered on a convenient sample of three hundred and four (N=304) adults of Sargodha city (Punjab, Pakistan) to operationalize mindfulness, psychological wellbeing, depression, and external locus of control respectively. Results revealed that external locus of control had positive relationship with mindfulness whereas mindfulness and psychological wellbeing were negatively related with depression. Mindfulness fully mediated between external locus of control and depression. Psychological wellbeing moderated between mindfulness and depression by dampening their negative relationship. Moderated mediation analysis was undertaken through PROCESS macro for SPSS (Hayes, 2013), which revealed that conditional indirect relationship of external locus of control with depression was significant only at lower to moderate levels of psychological wellbeing. Implications of the study and suggestions for further research were discussed

Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions

An Improved Correlation to Investigate the Effect of Chemical Additives on the Mobility Ratio of Two-Phase Flow

World energy demand continues to increase, as they evolve, and developing countries consume more energy to keep their rising factories going. A significant portion of the energy demand is supplied by fossil fuels, especially crude oil. Therefore, in order to satisfy the world's energy demand, oil reserves and oil production capability must be increased. This objective can be accomplished by enhancing the recovery efficiency of the existing generating or mature reservoirs through the application of increased oil recovery. The injection of fluids into oil reservoirs has the purpose of supplementing natural energy and is used in some cases to engage with the reservoir's rock/oil system, standardizing for oil recovery, such as lower interfacial stress, oil swelling, reduction of oil viscosity and adjustment of wettability. Subject to comprehensive studies, in heavy oil reservoirs, polymer injection is not dependent on large technological instruments, requiring only mixing and filtration equipment, except for those already used for traditional water injections. In addition, polymers are non-toxic and corrosive and can produce desirable mobility ratios. The implementation of this approach decreases the output ratio of water to oil, thus decreasing operating. In the present work, thirty-five data points from experimental work had been investigated to develop a new correlation for viscosity of water by using the suitable program. It was analyzed the influence of the polymer additives on the mobility ratio, temperature and concentration effect on mobility ratio, and viscosity altering with the additives have been investigated. The results of the correlation showed acceptable agreement between the observed and predicted viscosity values. As a contrast to the polymer additives approach, pure water was proposed

Identification of Transmission Routes of Campylobacter and On-Farm Measures to Reduce Campylobacter in Chicken

An in-depth analysis was performed on Swedish broiler producers that had delivered chickens with Campylobacter to slaughter over several years, in order to identify possible transmission routes and formulate effective measures to prevent chickens being colonized with Campylobacter. Between 2017 and 2019, 626 samples were collected at farm level and Campylobacter was isolated from 133 (21.2%). All C. jejuni and C. coli isolated from these samples were whole-genome sequenced, together with isolates from the corresponding cecum samples at slaughter (n = 256). Core genome multi-locus sequence typing (cgMLST) analysis, using schemes consisting of 1140 and 529 genes for C. jejuni and C. coli, respectively, revealed that nearby cattle, contaminated drinking water, water ponds, transport crates, and parent flocks were potential reservoirs of Campylobacter. A novel feature compared with previous studies is that measures were implemented and tested during the work. These contributed to a nationwide decrease in Campylobacter-positive flocks from 15.4% in 2016 to 4.6% in 2019, which is the lowest ever rate in Sweden. To conclude, there are different sources and routes of Campylobacter transmission to chickens from different broiler producers, and individual measures must be taken by each producer to prevent Campylobacter colonization of chickens

Microbial profiling of amniotic fluid, umbilical blood ad placenta of the foaling mare

The presence of a microbiome/microbiota in the placenta is hotly debated. In previous studies, the presence of bacteria in equine amniotic fluid and umbilical blood was independent of foal health. The objective of the present study was to determine if the same bacteria are present in the equine placenta as in amniotic fluid and umbilical blood. Samples were obtained from 24 parturient mares and foals. Placental bacterial DNA was extracted, and the microbiome was identified using 16S rRNA sequencing. All amniotic fluid samples contained some polymorphonucleocytes; bacteria were isolated from four samples. Aerobic or anaerobic growth was found in 18 and 3 umbilical blood samples, respectively. Serum amyloid A wa

TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3′-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr’s performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.publishedVersio

EpiCass And CassavaNet4Dev Advanced Bioinformatics Workshop

EpiCass and CassavaNet4Dev are collaborative projects funded by the Swedish Research Council between the Swedish University of Agriculture (SLU) and the International Institute of Tropical Agriculture (IITA). The projects aim to investigate the influence of epigenetic changes on agricultural traits such as yield and virus resistance while also providing African students and researchers with advanced bioinformatics training and opportunities to participate in big data analysis events. The first advanced bioinformatics training workshop took place from May 16th to May 18th, 2022, followed by an online mini-symposium titled “Epigenetics and crop improvement” on May 19th. The symposium featured international speakers covering a wide range of topics related to plant epigenetics, cassava viral diseases, and cassava breeding strategies. A new online and on-site teaching model was developed for the three-day workshop to ensure maximum student participation across Western, Eastern, and Southern Africa. Initially planned in Nigeria, Kenya, Ethiopia, Tanzania, and Zambia, the workshop ultimately focused on Nigeria, Kenya, and Ethiopia due to a lack of qualified candidates in the other countries. Each classroom hosted 20 to 25 students, with at least one bioinformatician present for support. The classrooms were connected via video conferencing, whereas teachers located in different places in Africa and Europe joined the video stream to conduct teaching sessions. The workshop was divided into theoretical classes and hands-on sessions, where participants could run data analysis with support from online teachers and local bioinformaticians. To enable participants to run guided, CPU and RAM-intensive data analysis workflows and overcome local computing and internet access restrictions, a system of virtual machines (VMs) hosted in the cloud was developed. The teaching platform provided teaching and exercise materials to support the use of the VMs. Some students could not run heavy data analysis workflows due to unforeseen restrictions in the cloud. Currently, these issues have been solved and in the future all participants will have the opportunity to run the analysis steps independently in the cloud using the protocols hosted on the teaching platform