The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.
Sukhen Goswami, Md. Masum Billah, Md Sabbir Hossen
et al.
Riverbank erosion, driven by natural processes and human activities, poses significant socio-environmental challenges in Bangladesh. This study investigated the geomorphic evolution and socioeconomic impacts of riverbank erosion along the Sandhya River in Babuganj Upazila, Barishal, Bangladesh. The primary aim was to assess how natural processes and human interventions, such as sand mining and infrastructure development, have altered the river morphology and affected local communities. Landsat imagery from 1980 to 2023, with a 10-year interval, was analyzed to assess key geomorphic indices—sinuosity, channel width, widening rate, and migration rate using remote sensing, geographic information systems (GIS), and field surveys. The results indicate significant geomorphic transformation, with sinuosity varying between 1.01 and 2.08, with a post-2000 increase in channel widening (up to 27 m/year) linked to intensified sand mining and brickfield expansion. Mid-channel bar formation, absent before 2000, reached 4.0 km2 by 2023, affecting flow patterns. The widening rate shifted from a maximum of 19 m/year (1980–2000, pre-sand mining) to 27 m/year (2000–2023, post-sand mining), with a peak near Doarika Bridge, which increased the vulnerability of the Barishal Airport area, averaging 3.65 m/year. Socioeconomic surveys (n = 154) reveal severe livelihood disruption: 65 % of lost land was agricultural, 73 % of affected households migrated to urban centers, and 45 % fell into debt. The most affected areas were Dehergati, Rahamatpur, Rakudia, and Kedarpur, emphasizing the need for capacity building. The study concludes that integrated geomorphic restoration and community resilience planning are urgently needed to address erosion-driven displacement and economic vulnerability in the region.
Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.
Barometric levelling, traditionally employed in aviation, parachute jumping, and mountain climbing, has undergone a transformative shift with the technological advancement of state-of-the-art atmospheric pressure sensors. This evolution has rendered these sensors more accurate and affordable, broadening their applications within the realm of Intelligent Systems. The integration of barometric altimeter modules into electronic devices, coupled with GNSS and mapping systems, has significantly enhanced their versatility, making them complementary components in various consumer electronics like smartphones, watches, sports bands, bicycle computers, and motor vehicle tracking devices. Moreover, they play a pivotal role in emerging technologies such as drone mapping projects and modelling. This because of their capabilities of measuring elevations in GNSS denied areas such as caves, canyons, and tunnels. The significance of barometric levelling lies in its capacity to determine relative elevation between two points through the measurement of atmospheric pressure. This technique leverages the fact that atmospheric pressure decreases with increasing altitude, enabling the calculation of elevation differences by comparing pressure readings at different locations.<br />In this study, 25 elevations within a 3 km radius were independently measured using barometric levelling, highlighting its practical usage. These elevations ranged from 2 m to 140 m. Readings of time of measurements, temperature, air pressure, and humidity were taken at each of these stations and were synchronized with the readings obtained from a fixed reference station of known elevation. The measurements at this reference station were carried out with an instrument with data logging capabilities, able to record relevant weather data at pre-established intervals of time without human intervention. The results of these measurements were compared to fixed reference stations of known elevation, and the subsequent differences were analysed. The study employed a portable weather monitoring instrumentation with data logging capabilities, emphasizing the importance of automated data collection practices. The comparison of the 25 elevation readings with true elevations, determined by conventional surveying methods, revealed an RMSE of +/- 0.49 meters, affirming the accuracy of barometric levelling.<br />Additionally, a distance-dependent test demonstrated a predictable decrease in positional accuracy as the distance from a reference base station increased, providing valuable insights into the system's limitations. The barometric levelling tests presented here offer results that can inform future applications. The conclusions and recommendations derived from this study provide guidance for optimizing the use of barometric levelling within the broader landscape of Intelligent Systems.
Human infections with the H7N9 influenza virus have been eliminated in China through vaccination of poultry; however, the H7N9 virus has not yet been eradicated from poultry. Carefully analysis of H7N9 viruses in poultry that have sub-optimal immunity may provide a unique opportunity to witness the evolution of highly pathogenic avian influenza virus in the context of vaccination. Between January 2020 and June 2023, we isolated 16 H7N9 viruses from samples we collected during surveillance and samples that were sent to us for disease diagnosis. Genetic analysis indicated that these viruses belonged to a single genotype previously detected in poultry. Antigenic analysis indicated that 12 of the 16 viruses were antigenically close to the H7-Re4 vaccine virus that has been used since January 2022, and the other four viruses showed reduced reactivity with the vaccine. Animal studies indicated that all 16 viruses were nonlethal in mice, and four of six viruses showed reduced virulence in chickens upon intranasally inoculation. Importantly, the H7N9 viruses detected in this study exclusively bound to the avian-type receptors, having lost the capacity to bind to human-type receptors. Our study shows that vaccination slows the evolution of H7N9 virus by preventing its reassortment with other viruses and eliminates a harmful characteristic of H7N9 virus, namely its ability to bind to human-type receptors.
The Loess Plateau in China is renowned for its dense gullies and complex terrain, with drastic changes primarily due to soil erosion and human activities, significantly affecting the evolution of the ecological environment. The complex terrains and dense vegetation make precise terrain measurement and modeling challenging. Although the development of Unmanned Aerial Vehicle (UAV) light detection and ranging (LiDAR) scanning and photogrammetry technologies has improved data acquisition precision, relying solely on one remote sensing technology struggles with accurately extracting bare earth information. This study adopted a method that fuses UAV lidar scanning with aerial photogrammetric imagery, generating detailed lidar point cloud data that includes coordinate, reflectance, true color, and texture information to enhance data classifiability and interpretability. Subsequently, a point cloud classification model based on the Transformer architecture (Stratified Transformer) is introduced to intelligently complete the initial ground point cloud extraction in complex gully terrains. Further, to address residual non-ground noise in the initial ground point clouds, a new point cloud classification optimization algorithm (MDD, Multi-scale C2M Distance Difference) is proposed. This algorithm, based on the characteristics of discrete and non-continuous with the ground surface of the noisy point clouds, effectively eliminates the discrete noisy point clouds by analyzing the distances between the point clouds and TINs (Triangular Irregular Networks) of different scales and their differences. This study effectively addresses the technical challenges of ground point cloud extraction in the mixed environment of complex terrain and vegetation, solving the problem of precise terrain measurement and intelligent data processing in complex gully terrains, and offering new technical pathways for detecting geomorphological changes.
Laura Kienzle, Stefano Bettinazzi, Thierry Choquette
et al.
Abstract Background Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. Results We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. Conclusions Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.