Parent Organism Research Articles

Bringing Calm to Antibiotic Stewardship: Customizing and Automating Antibiogram Creation at a Multi-Hospital Institution

Abstract We sought to automate antibiogram creation at our multi-hospital institution with custom features including transparency into data filtering, expanding the granularity to include multi-resistant organisms, and additional conditional formatting based on sensitivity percentages. We automated creation of the antibiogram using a python framework with embedded SQL scripts. The sensitivity data for isolates from the prior year was retrieved from our lab information system. It was filtered to include only inpatient, emergency department, and observation patients across all seven hospitals in our system. Additionally, the data was filtered to only include the first organism per patient per year. Finally, organisms meeting specific sensitivity criteria (i.e. methicillin resistant Staphylococcus aureus) were included as separate rows beneath the parent organism. This data was inserted into an excel workbook with customized formatting to include the institutional logo, coloring based on sensitivity percentages, and customizable comments. Each of these steps are easily editable year-to-year to allow for changing requirements. At each step of filtering, the integrity of the data was extensively validated to make sure it was performing as intended. The antibiograms are generated within a few minutes in a fully automated manner (Figure 1). These will be distributed systemwide after review by the Medical Microbiology directors and Antimicrobial Stewardship Committee in January of each year. The code was made in an easily editable, modular way such that requests for additional separation of organisms by sensitivity, removing drugs not pertinent to our formulary, and editing what organisms appear is easily managed by the informatics team on a year-to-year basis.

Intergenerational neurotoxicity of polystyrene nanoplastics in offspring mice is mediated by dysfunctional microbe-gut-brain axis

Nanoplastics (NPs) are ubiquitous in daily life, posing potential risks to the environment and human. While their negative effects on parental organisms have been extensively studied, intergenerational effects are still in the early stages of investigation. Here, we aimed to investigate the impact of maternal exposure to an environmentally relevant level of polystyrene NPs (PSNPs, 100 nm) during gestation and lactation (∼32 days, 50 μg/mouse/day) on neurotoxicity mediated by the microbe-gut-brain axis in offspring mice. Maternal PSNPs exposure significantly increased brain TNF-α level and microglia by 1.43 and 1.48 folds respectively, compared to control, accompanied by nuclear pyknosis and cell vacuolization in cortex and hippocampus. Targeted neurotransmitter metabolomics analysis revealed dysregulation in dopamine and serotonin metabolism. Specifically, dopamine levels increased significantly from 0.007 ng/L to 0.015 ng/L, while N-acetylseroton and 3,4-dihydroxyphenylacetic acid decreased significantly from 0.002 and 0.929 ng/L to 0.001 and 0.680 ng/L, respectively. Through a combination of 16S rRNA sequencing and biochemical analysis, we discovered that maternal PSNPs exposure led to a depletion of anti-inflammatory bacteria and an enrichment of pro-inflammatory bacteria resulting in intestinal barrier damage, elevated levels of lipopolysaccharide in blood, and subsequent activation of neuroinflammation. Meanwhile, gut bacteria dysbiosis interfered with communication between gut and brain by dysregulating neurotransmitter synthesis, as evidenced by significant associations between neurotransmitter-related bacteria (Akkermansia, Family_XIII_AD3011_group, Lachnoclostridium) and dopamine/serotonin related metabolites. Furthermore, transcriptional alterations in dopamine and serotonin related pathways were observed in the enteric nervous system, suggesting abnormal signal transduction from gut to brain contributes to neurotoxicity. This study provides new insights into NPs-induced neurotoxicity within the context of microbe-gut-brain axis and highlights the risk of cerebral dysfunction in offspring with maternal NPs exposure.

Diverse YqeK Diadenosine Tetraphosphate Hydrolases Control Biofilm Formation in an Iron-Dependent Manner

YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity and disrupted biofilm formation. Ap4A thus plays a central role in bacterial physiology and metabolism, and its hydrolysis by YqeK is intimately linked to the ability of these microbes to cope with stress. Although YqeK is reported to hydrolyze Ap4A under aerobic conditions, all four existing crystal structures reveal an active site that consists of a diiron center, portraying a cryptic chemical nature for the active metallocofactor. This study examines two YqeK proteins from two ecologically diverse parent organisms: the obligate anaerobe Clostridium acetobutylicum and the facultative aerobe Bacillus halodurans. Both enzymes utilize Fe-based cofactors for catalysis, while under ambient or oxidative conditions, Bh YqeK hydrolyzes Ap4A more efficiently compared to Ca YqeK. This redox-dependent activity difference stems from the following two molecular mechanisms: the incorporation of mixed-metal, Fe-based bimetallic cofactors, in which the second metal is redox inert (i.e., Fe–Zn) and the upshift of the Fe–Fe cofactor reduction potentials. In addition, three strictly conserved, positively charged residues vicinal to the active site are critical for tuning Ap4A hydrolysis. In conclusion, YqeK is an Fe-dependent phosphohydrolase that appears to have evolved to permit Ap4A hydrolysis under different environmental niches (aerobic vs. anaerobic) by expanding its cofactor configuration and O2 tolerance.

Improved production of RNA-inhibiting antimicrobial peptide by Bacillus licheniformis MCC 2514 facilitated by a genetic algorithm optimized medium.

One of the significant challenges during the purification and characterization of antimicrobial peptides (AMPs) from Bacillus sp. is the interference of unutilized peptides from complex medium components during analytical procedures. In this study, a semi-synthetic medium was devised to overcome this challenge. Using a genetic algorithm, the production medium of AMP is optimized. The parent organism, Bacillus licheniformis MCC2514, produces AMP in very small quantities. This AMP is known to inhibit RNA biosynthesis. The findings revealed that lactose, NH4Cl and NaNO3 were crucial medium constituents for enhanced AMP synthesis. The potency of the AMP produced was studied using bacterium, Kocuria rhizophila ATCC 9341. The AMP produced from the optimized medium was eightfold higher than that produced from the unoptimized medium. Furthermore, activity was increased by 1.5-fold when cultivation conditions were standardized using the optimized medium. Later, AMP was produced in a 5 L bioreactor under controlled conditions, which led to similar results as those of shake-flask production. The mode of action of optimally produced AMP was confirmed to be inhibition of RNA biosynthesis. Here, we demonstrate that improved production of AMP is possible with the developed semi-synthetic medium recipe and could help further AMP production in an industrial setup.

A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections

Nanopore metagenomics has been used for infectious disease diagnosis for bacterial pathogens. However, this technology currently lacks comprehensive performance studies in clinical settings for simultaneous detection of bacteria, fungi, and viruses. We developed a dual-process of Nanopore sequencing for one sample, with unbiased metagenomics in Meta process and target enrichment in Panel process (Nanopore Meta-Panel process, NanoMP) and prospectively enrolled 450 respiratory specimens from multiple centers. The filter system of pathogen detection was established with machine learning and receiver operator characteristic (ROC) curve to optimize the detection accuracy based on orthogonal test of 21 species. Antimicrobial resistance (AMR) genes were identified based on the Comprehensive Antibiotic Resistance Database (CARD) and single-nucleotide polymorphism matrix. Our approach showed high sensitivity in Meta process, with 82.9%, 88.7%, and 75.0% for bacteria, fungi (except Aspergillus), and Mycobacterium tuberculosis groups, respectively. Moreover, target amplification improved the sensitivity of virus (>80.0% vs. 39.4%) and Aspergillus (81.8% vs. 42.3%) groups in Panel process compared with Meta process. Overall, NanoMP achieved 80.2% sensitivity and 98.8% specificity compared with the composite reference standard, and we were able to accurately detect AMR genes including blaKPC-2, blaOXA-23 and mecA and distinguish their parent organisms in patients with mixed infections. We combined metagenomic and enriched Nanopore sequencing for one sample in parallel. Our NanoMP approach simultaneously covered bacteria, viruses and fungi in respiratory specimens and demonstrated good diagnostic performance in real clinical settings. National Key Research and Development Program of China and National Natural Science Foundation of China.

Rubredoxin Protein Scaffolds Sourced from Diverse Environmental Niches as an Artificial Hydrogenase Platform.

Nickel-substituted rubredoxin (NiRd) from Desulfovibrio desulfuricans has previously been shown to act as both a structural and functional mimic of the [NiFe] hydrogenase. However, improvements both in turnover frequency and overpotential are needed to rival the native [NiFe] hydrogenase enzymes. Characterization of a library of NiRd mutants with variations in the secondary coordination sphere suggested that protein dynamics played a substantial role in modulating activity. In this work, rubredoxin scaffolds were selected from diverse organisms to study the effects of distal sequence variation on catalytic activity. It was found that though electrochemical catalytic activity was only slightly impacted across the series, the Rd sequence from a psychrophilic organism exhibited substantially higher levels of solution-phase hydrogen production. Additionally, Eyring analyses suggest that catalytic activation properties relate to the growth temperature of the parent organism, implying that the general correlation between the parent organism environment and catalytic activity often seen in naturally occurring enzymes may also be observed in artificial enzymes. Selecting protein scaffolds from hosts that inhabit diverse environments, particularly low-temperature environments, represents an alternative approach for engineering artificial metalloenzymes.

The weathering process of carbonatite: weathering time.

Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established. In this study, we selected abandoned carbonatite tombstones commonly found in the karst region of southwest China for investigation, using the date when the tombstones were erected as the onset of weathering. Chemical weathering indices were used to evaluate the weathering degree of different oxide contents produced by the carbonatite weathering process. In order to explore the weathering characteristics over time, the relationship between weathering duration and weathering degree was established. The results showed the following: (1) magnesium (Mg), aluminum (Al), silicon (Si), iron (Fe), titanium (Ti) are gradually enriched in the carbonatite regolith, and calcium (Ca) is gradually reduced. (2) The chemical indices of alteration (CIA), leaching coefficient (Lc), alumina-to-calcium ratio (AC) and mobiles index (Imob) can be successfully used for evaluation of the weathering degree of the carbonatite in different weathering time periods. (3) During the weathering of carbonatite, the weathering rate is a logarithmic function of time. Our research shows that over a period of more than 100 years of weathering, the carbonatite weathering process is characterized by fast weathering rates and low weathering degree in the early stages, but slow weathering rates in the later stages.

Wildcat Strike and Collective Bargaining Outcome of Petroleum Marketing Companies in Rivers State, Nigeria

Union strike strategy and collective bargaining outcome are integral parts of industrial democracy. The purpose of this study was to investigate the relationship between wildcat strike and measures of collective bargaining outcome (Terms/conditions of employment, Workplace rules and grievance procedures) as elements of industrial democracy of petroleum marketing companies in Rivers State, Nigeria. The population of the study consists of all the 10 petroleum marketing companies under the petroleum downstream sector in Rivers State, Nigeria, while the sample size is the same as the population because it qualified as small. The correlation survey approach was adopted. The structured questionnaire was developed and 102 copies distributed to managers and union leaders of the 10 petroleum marketing companies in Rivers State, Nigeria. 93 copies were retrieved representing 91.18 percent but 88 copies were usable and represent 94.62 percent. Instruments for the study were tested using the convergence validity test and Cronbach alpha tool for validity and reliability respectively. Analysis included four stages. Bivariate hypotheses were tested using Spearman’s rank order correlation coefficient and the multivariate; using the bootstrapping tool. Results from the study show that there exist strong positive and significant relationship amongst wildcat strike and measures of collective bargaining outcome. The results also show that the environment is the parent organism and wildcat strike is the signal that alerts it to intervene and forestall or correct intolerable practices in industry. The study concludes that wildcat strike is the way of influencing or coercing management to the bargaining table when it does not want to; and an action to ensure timely and proper implementation of collective agreement. The study recommends that better and regular workers-management meetings should be enshrined, the study also recommends co-authorship of workplace rules between unions and managements, and that companies should resort to internal and external laid down procedures for settling disputes.

A genome-wide RNAi screen for genes important for proliferation of cultured Drosophila cells at low temperature identifies the Ball/VRK protein kinase

A change in ambient temperature is predicted to disrupt cellular homeostasis by affecting all cellular processes in an albeit non-uniform manner. Diffusion is generally less temperature-sensitive than enzymes, for example, and each enzyme has a characteristic individual temperature profile. The actual effects of temperature variation on cells are still poorly understood at the molecular level. Towards an improved understanding, we have performed a genome-wide RNA interference screen with S2R + cells. This Drosophila cell line proliferates over a temperature range comparable to that tolerated by the parental ectothermic organism. Based on effects on cell counts and cell cycle profile after knockdown at 27 and 17 °C, respectively, genes were identified with an apparent greater physiological significance at one or the other temperature. While 27 °C is close to the temperature optimum, the substantially lower 17 °C was chosen to identify genes important at low temperatures, which have received less attention compared to the heat shock response. Among a substantial number of screen hits, we validated a set successfully in cell culture and selected ballchen for further evaluation in the organism. This gene encodes the conserved metazoan VRK protein kinase that is crucial for the release of chromosomes from the nuclear envelope during mitosis. Our analyses in early embryos and larval wing imaginal discs confirmed a higher requirement for ballchen function at temperatures below the optimum. Overall, our experiments validate the genome-wide screen as a basis for future characterizations of genes with increased physiological significance at the lower end of the readily tolerated temperature range.

REGRESSION MODEL OF TOPOGRAPHY WITH THE DISTRIBUTION OF SELECTED SOIL PROPERTIES IN NORTHEAST AKWA IBOM STATE, NIGERIA

Regression model of topography with the distribution of selected soil properties in Northeast Akwa Ibom State, Nigeria was carried out. The aim was to establish a regression model of topography with the distribution of selected soil properties in Northeast Akwa Ibom State for soil properties predictions and management. Topographic map (or elevation map) of the study area was generated from digital elevation model (DEM) at 30m resolution acquired from United State Geological Survey (USGS). It was classified into three elevation classes of lower elevation (0-50 masl), middle elevation (50-100 masl) and higher elevation (100-150 masl) to guide field sampling. With the aid of Global Positioning System (GPS), the classes obtained from topographic map were cross-checked (ground-truthing) in the field. Modified Conditioned Latin Hypercube Sampling Method was used in selecting observation points. Each observation point was purposively selected to fall within the classes of topographic map to give a good coverage of both feature space (classes of topographic map) and geographical space (study area). A total of 120 soil samples were collected at a depth of 0-30cm and 30-60 cm using soil auger. The samples were taken to the laboratory for analysis. The results revealed variation in soil properties among the three topographic classes under study. Sand fraction was significantly higher (p > 0.05) in lower elevation than other elevation classes while silt and clay fractions were significantly higher (p > 0.05) in the middle and higher elevations than lower elevation in the study area. Soil pH was significantly higher (p > 0.05) (slightly acid) in the lower elevation than middle and higher elevations (moderately acid). Electrical conductivity and base saturation were significantly higher (p > 0.05) in the lower elevation than middle and higher elevations. Organic carbon, total N, ECEC, exchangeable Mg and exchangeable K were significantly higher (p > 0.05) in the middle elevation than that of lower and higher elevations. Available P of higher elevation was significantly higher (p > 0.05) than that of lower and middle elevations. The study also showed that topography accounted for 3 % variation of sand and silt fractions; 5 % variation of clay fraction and 4 % variation of soil pH. Topography also explained 19 % variation of available P, 8.4 % variation of exchangeable K and 5.5 % variation of organic carbon and total N in the study area. The remaining fractions of variation may be attributed to other factors of soil formation such as parent material, climate, organism and time.

Doubled Haploids: Contributions of Poland’s Academies in Recognizing the Mechanism of Gametophyte Cell Reprogramming and Their Utilization in Breeding of Agricultural and Vegetable Species

Abstract Diverse processes leading to doubled haploid (DH) plant production, such as microspore embryogenesis, gynogenesis, and distant hybridization followed by genome elimination, are based on the unique ability of plant cells to form haploid embryos without fertilization. All of these are possible because of various in vitro culture systems that enable the growth and development of tissues or single cells outside of the parental organism. The possibility of re-directing cell development from its original pathway to embryogenesis brings several benefits to many research areas, but the most important is the possibility of its implementation in breeding programs. This review summarizes the achievements of Polish research groups in studies of the mechanisms of haploid/DH embryo development and demonstrates the practical applications of these systems in basic studies and plant breeding. It shows the results of studies on economically important crops including barley ( Hordeum vulgare L.), oilseed rape ( Brassica napus L.), triticale (× Triticosecale Wittm.), oat ( Avena sativa L.), rye ( Secale cereale L.), sugar beet ( Beta vulgaris ssp. vulgaris L.), and some vegetable species, including carrot ( Daucus carota L.), onion ( Allium cepa L.), red beet ( Beta vulgaris L.), and members of the Brassicaceae.

Vibrio cholerae V-cGAP3 Is an HD-GYP Phosphodiesterase with a Metal Tunable Substrate Selectivity.

Cyclic dinucleotides (CDNs) are signaling molecules involved in the immune response and virulence factor production. CDN cellular levels are fine-tuned by metal-dependent phosphodiesterases (PDEs), among which HD-GYPs make up a subclass of the larger HD-domain protein superfamily. The human pathogen Vibrio cholerae (Vc) encodes nine HD-GYPs, one of which is V-cGAP3 (or VCA0931). V-cGAP3 acts on c-di-GMP and 3'3'c-GAMP, and this activity is related to bacterial infectivity. However, the extant chemical makeup of the V-cGAP3 cofactor and steady state parameters have not been established. Employing electron paramagnetic resonance and Mössbauer spectroscopy in tandem with elemental analyses and activity assays, we demonstrate that V-cGAP3 coordinates different dimetal cofactors with variable activities. MnII and FeII afford c-di-GMP hydrolysis with the highest observed rates, while c-GAMP hydrolysis is selectively dependent on Mn. V-cGAP3 has a single functional domain, and this simple architecture allows us to examine the roles of characteristic conserved residues in catalysis. Substitution of the adjacent to the active site GYP residue triad and the specifically conserved in HD-domain PDEs fifth histidine ligand (i.e., H371 in V-cGAP3) with alanines severely compromises CDN hydrolysis but only modestly affects cofactor incorporation. Our data are consistent with V-cGAP3 being the major regulator of 3'3'c-GAMP hydrolysis in Vc and delineate the importance of specific residues in tuning activity in HD-GYPs in general. We propose that HD-GYPs exhibit diversity in their metallocofactors and substrates, which may serve to increase their functional potential in regulatory pathways or allow for PDE activity upon adaptation of the parent organism to diverse environmental niches.

PROPERTIES OF SOILS ALONG A TOPOSEQUENCE UNDERLAIN BY COARSE GRAINED GRANITE GNEISS IN IFE AREA SOUTH WEST NIGERIA

Research has shown that soil profiles are influenced by five separate, yet interacting factors: parent material, climate, topography, organisms and time which give soil profiles their distinctive character. Topography however, plays a major role in the variation of soil properties and nutrient distribution along a non-uniform agricultural landscape. This study was conducted to investigate the effects of topography on chemical properties of soil underlain by coarse grained granite gneiss at the teaching and research farm of Obafemi Awolowo University Ile Ife. Three profile pits was established at different physiographic positions along a toposequence (upper, middle and lower positions) were considered for this study. A total of eleven (11) samples were collected for routine laboratory analysis from the established horizons. The results revealed that the clay content increased with increase in profile depth while sand content decreases. Organic matter content was relatively low 0.2 – 1.35%, a result of continuous cultivation in the area. The values of available P (1.29 – 5.40ppm) showed that it is inadequate for crop production. The pH, exchangeable cations and exchangeable acidity values fluctuate across the pedons under investigation. The correlation between slope position and chemical properties showed that no singular property consistently showed the same level of significance on the entire slope.
 For effective management of the soils, organic inputs and usage of vegetal cover such as planting of cowpea and other crawling plants of economic importance should be adopted to assist in improving the organic matter content, conservation management practices should also be employed to prevent rapid soil degradation across the topography.

The possible modes of microbial reproduction are fundamentally restricted by distribution of mass between parent and offspring

Multiple modes of asexual reproduction are observed among microbial organisms in natural populations. These modes are not only subject to evolution, but may drive evolutionary competition directly through their impact on population growth rates. The most prominent transition between two such modes is the one from unicellularity to multicellularity. We present a model of the evolution of reproduction modes, where a parent organism fragments into smaller parts. While the size of an organism at fragmentation, the number of offspring, and their sizes may vary a lot, the combined mass of fragments is limited by the mass of the parent organism. We found that mass conservation can fundamentally limit the number of possible reproduction modes. This has important direct implications for microbial life: For unicellular species, the interplay between cell shape and kinetics of the cell growth implies that the largest and the smallest possible cells should be rod shaped rather than spherical. For primitive multicellular species, these considerations can explain why rosette cell colonies evolved a mechanistically complex binary split reproduction. Finally, we show that the loss of organism mass during sporulation can explain the macroscopic sizes of the formally unicellular microorganism Myxomycetes plasmodium. Our findings demonstrate that a number of seemingly unconnected phenomena observed in unrelated species may be different manifestations of the same underlying process.

Mouldy Matriarchs and Dangerous Daughters

Mouldy Matriarchs and Dangerous Daughters

The Human Impact on All Soil-Forming Factors during the Anthropocene.

Soil-the thin outer skin of the Earth's land-is a critical and fragile natural resource. Soil is the basis for almost all global agriculture and the medium in which most terrestrial biological activity occurs. Here, we reconsider the five forming factors of soil originally suggested more than a century ago (parent material, time, climate, topography, and organisms) and updated over the years to add human activity as the sixth forming factor. We demonstrate how present anthropogenic activity has become the leading component influencing each one of the original forming factors. We thus propose that, starting from the Anthropocene, human activity should no longer be considered as a separate forming factor but rather a main driving force of each of the five original ones. We suggest that the importance of soil and the strong direct and indirect effects of anthropogenic factors on soil-forming factors should be considered together to ensure sustainability of this critical resource.

The role of soils in habitat creation, maintenance and restoration.

Soils are the fundament of terrestrial ecosystems. Across the globe we find different soil types with different properties resulting from the interacting soil forming factors: parent material, climate, topography, organisms and time. Here we present the role of soils in habitat formation and maintenance in natural systems, and reflect on how humans have modified soils from local to global scale. Soils host a tremendous diversity of life forms, most of them microscopic in size. We do not yet know all the functionalities of this diversity at the level of individual taxa or through their interactions. However, we do know that the interactions and feedbacks between soil life, plants and soil chemistry and physics are essential for soil and habitat formation, maintenance and restoration. Moreover, the couplings between soils and major cycles of carbon, nutrients and water are essential for supporting the production of food, feed and fibre, drinking water and greenhouse gas balances. Soils take thousands of years to form, yet are lost very quickly through a multitude of stressors. The current status of our soils globally is worrisome, yet with concerted action we can bend the curve and create win–wins of soil and habitat conservation, regeneration and sustainable development.This article is part of the theme issue ‘The role of soils in delivering Nature's Contributions to People’.

Evaluating pedogenesis and soil Atterberg limits for inducing landslides in the Western Ghats, Idukki District of Kerala, South India

In the Western Ghats of India, the soil properties, particularly Atterberg limits, are of relevance to the landslides. Pedogenic processes in the Western Ghats and plateaus on it are regulated by parent materials, relief (topography), organisms, climate, and time. In this study, the five major soils found within the mid-part of the Western Ghats in the Idukki district of Kerala, Southern India was analyzed for elucidating physical, chemical, and geotechnical properties (Atterberg limits) on landslides potentiality or slope failure processes. The result reveals that the highly weathered lateritic soils noted with lower KCl pH (3.6–4.6), low-cation exchange capacity (3.1 to 19.6 cmol( +) kg−1), low-effective cation exchange capacity (0.8 to 10.7 cmol( +) kg−1) and a negative ∆pH value indicate the presence of variable charge minerals such as amorphous sesquioxides. The variable ranking of random forest revealed that the soil Atterberg limits were significantly influenced by Citrate Bicarbonate Dithionite (CBD) iron, sand fractions, and organic carbon. The layer of porous sandy soils showed lower Atterberg limits due to accentuate with clay matter, whereas the illuvial layer (Bt) have noted as higher Atterberg limits that lead to potentially collapsing gullies or triggering mass movement during heavy rainfall followed by intensive runoff due to instability of soil mass within proxy of the steeply sloping surface. Soil geotechnical properties such as liquid limit, plastic limit, and plasticity index are the main characteristics that decide the slope stability and failure in various parts of the study area, whereas the soil profile morphometry has significantly associated with the occurrence of landslides with the plastic limit value between 28.01 and 40.48. It was noticed that the failed slopes have a higher value than stable slopes along with the hill-range topography, with soil particle sizes range of silt and clay (8.79 to 36.17 and 22.31 to 57.74%) with the measurement of liquid limit (40.05 to 68.4), plastic limit (24.2 to 43.94), and plasticity index (7.81 to 24.8). This indicates that the pedogenesis of the weathering profile of soils have significantly influenced the Atterberg limits that triggering slope failure or landslides along the gullies and weathered lateritic uplands.

Naming of parts: the use of fossil-taxa in palaeobotany

Fossil plants are extinct plants whose remains (referred to as plant fossils) are found preserved in sedimentary deposits. Plant fossils are classified using fossil-taxa as defined in the International Code of Nomenclature. Fossil-taxa differ conceptually from taxa of living plants in that they often do not refer to whole organisms, but to the remains of one or more parts of the parent organism, in one or more preservational states. There can be complications when two parts of a plant are shown to be connected, or when two preservational states are correlated, and to avoid disrupting the wider palaeobotanical taxonomy it is often best to keep the fossil-taxa separate. Extinct fossil plants reconstructed by piecing together the plant fossils are best not given formal Linnean taxonomic names. There can also be problems using living plant taxa for fossils, even when there is a close morphological similarity of particular plant parts. Fossil-taxa for different plant parts can reflect different taxonomic ranks of the parent plants so care must be taken when using such taxa in floristic or phylogenetic studies. Because of taphonomic factors, a number of “artificial” fossil-taxa have proved useful, despite that they do not fully reflect the systematic positions of the parent plants.

A Budding Relationship: Bacterial Extracellular Vesicles in the Microbiota-Gut-Brain Axis.

The discovery of the microbiota-gut-brain axis has revolutionized our understanding of systemic influences on brain function and may lead to novel therapeutic approaches to neurodevelopmental and mood disorders. A parallel revolution has occurred in the field of intercellular communication, with the realization that endosomes, and other extracellular vesicles, rival the endocrine system as regulators of distant tissues. These two paradigms shifting developments come together in recent observations that bacterial membrane vesicles contribute to inter-kingdom signaling and may be an integral component of gut microbe communication with the brain. In this short review we address the current understanding of the biogenesis of bacterial membrane vesicles and the roles they play in the survival of microbes and in intra and inter-kingdom communication. We identify recent observations indicating that bacterial membrane vesicles, particularly those derived from probiotic organisms, regulate brain function. We discuss mechanisms by which bacterial membrane vesicles may influence the brain including interaction with the peripheral nervous system, and modulation of immune activity. We also review evidence suggesting that, unlike the parent organism, gut bacteria derived membrane vesicles are able to deliver cargo, including neurotransmitters, directly to the central nervous system and may thus constitute key components of the microbiota-gut-brain axis.