Jingtao Lilue, André Corvelo, Jèssica Gómez-Garrido
et al.
Abstract Background The cotton rat (Sigmodon hispidus), a rodent species native to the Americas, has emerged as a valuable laboratory model of infections by numerous human pathogens including poliovirus and respiratory syncytial virus (RSV). Results Here we report the first reference assembly of the cotton rat genome organized at a chromosomal level, providing annotation of 24,878 protein-coding genes. Data from PCR-free whole genome sequencing, linked-read sequencing, and RNA sequencing from pooled cotton rat tissues were analyzed to assemble and annotate this novel genome sequence. Spectral karyotyping data using fluorescent probes derived from mouse chromosomes facilitated the assignment of cotton rat orthologs to syntenic chromosomes, comprising 25 autosomes and a sex chromosome in the haploid genome. Comparative phylome analysis revealed both gains and losses of numerous genes including immune defense genes against pathogens. We identified thousands of recently retrotransposed L1, SINE B2, and ERV elements, revealing widespread genomic insertions unique to this species. Conclusions We anticipate that annotation and characterization of the first chromosome-level cotton rat genome assembly as described here will enable and accelerate ongoing investigations into its host defenses against viral and other pathogens, genome biology, and mammalian evolution.
This study investigates the historical evolution and current trends of brain drain from Turkey to the United States and Europe. Beginning in the 1960s, this migration has undergone significant transformations driven by socioeconomic and political shifts. Using data from TurkStat, the U.S. Department of Justice and Eurostat, the study highlights key developments such as the rise in H-1B and Green Card applications to the United States in the 1990s and the structured focus of Europe’s Blue Card program on skilled labor. Migration to the United States is primarily associated with technological, scientific, and academic opportunities, whereas Europe’s migration policies have evolved from labor agreements to selective skilled migration programs. This study comprehensively analyzes these dynamics, offering insights into how international opportunities have historically shaped Turkey’s skilled workforce. It concludes with policy recommendations emphasizing academic collaborations, incentives for diaspora engagement and sustainable strategies to mitigate human capital losses and strengthen Turkey’s global competitiveness.
Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea
et al.
Abstract Background Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. Results To address this, we devise an approach to search for lineage-specific selection on three critical steps in transcriptional regulation: chromatin activity, transcription factor binding, and chromosomal looping. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Conclusions Overall, our study indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.
Abstract Human adenoviruses (HAdVs) are highly contagious and have significant clinical implications in the pediatric population. In the present study, we employed a combination of long-read sequencing and short-read sequencing to accurately reconstruct 32 genomes of HAdVs. The phylogenetic analyses based on the whole genome and genes revealed distinct sub-clusters within HAdV-B and -E. For HAdV-C, the phylogenetic trees constructed from hexon, fiber, and E3 gene sequences consistently matched the whole-genome phylogeny, reflecting the high sequence diversity in these regions. Notably, in regions with high sequence diversity, we observed a higher number of recombination breakpoints and lower GC content. Additionally, the E4 gene region of HAdV-C exhibited a Ka/Ks ratio > 1, indicating that positive selection may be driving the fixation of advantageous mutations. These genetic characterization analyses are crucial for enhancing future surveillance of HAdVs, facilitating a more strategic and proactive approach to monitoring their evolution, diversity, and epidemiological trends.
Sajedeh Nasr Esfahani, Yi Zheng, Auriana Arabpour
et al.
Abstract Primordial germ cells (PGCs) are the embryonic precursors of sperm and eggs. They transmit genetic and epigenetic information across generations. Given the prominent role of germline defects in diseases such as infertility, detailed understanding of human PGC (hPGC) development has important implications in reproductive medicine and studying human evolution. Yet, hPGC specification remains an elusive process. Here, we report the induction of hPGC-like cells (hPGCLCs) in a bioengineered human pluripotent stem cell (hPSC) culture that mimics peri-implantation human development. In this culture, amniotic ectoderm-like cells (AMLCs), derived from hPSCs, induce hPGCLC specification from hPSCs through paracrine signaling downstream of ISL1. Our data further show functional roles of NODAL, WNT, and BMP signaling in hPGCLC induction. hPGCLCs are successfully derived from eight non-obstructive azoospermia (NOA) participant-derived hPSC lines using this biomimetic platform, demonstrating its promise for screening applications.
A carbonate build-up or reef is a thick carbonate deposit consisting of mainly skeletal remains of organisms that can be large enough to develop a favourable topography. Delineation of such geologic features provides important input in understanding the basin's evolution and petroleum prospects. Here, we introduce a new attribute called the Reef Cube (RC) meta-attribute that has been computed by fusing several other seismic attributes that are characteristics of the reef through a supervised machine-learning algorithm. The neural learning resulted in a minimum nRMS error of 0.28 and 0.30 and a misclassification percentage of 1.13% and 1.06% for the train and test data sets. The Reef Cube meta-attribute has efficiently captured the anatomy of carbonate reef buried at ∼450 m below the seafloor from high-resolution 3D seismic data in the NW shelf of Australia. The novel approach not only picks up the subsurface architecture of the carbonate reef accurately but also accelerates the process of interpretation with a much-reduced intervention of human analysts. This can be efficiently suited for delimiting any subsurface geologic feature from a large volume of surface seismic data.
Alexander L. Starr, David Gokhman, Hunter B. Fraser
Abstract Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis-regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical organoids, we identify signatures of lineage-specific selection on genes related to saccharide metabolism, neurodegeneration, and primary cilia. We also highlight cis-regulatory divergence in CUX1 and EDNRB that may shape the trajectory of human brain development.
Protected areas (PAs) are globally important environmental management tools against the effects of human activities, as they support the conservation of marine biodiversity, habitats, ecosystems and the processes within them, as well as resources in a broad sense. However, the application of Ecosystem Services (ESs) research in the environmental management of PAs has not been elucidated and it still has obvious shortcomings. Here, we present the first systematic review of studies that have assessed the application of ES research in PAs, evaluated the beneficial evidence of using ES for PA management, and identified research gaps to be addressed for future work. The majority of the 84 studies examined were conducted in Europe (44.44%) and Asia (30.77%), and they primarily examined cultural and provisioning ESs. Most case studies focused on methodological design and lacked an understanding of the spatial and temporal evolution patterns of ESs and of the interaction between ESs and management decisions in PAs. Future studies of PAs should (1) identify the main ESs provided, (2) improve ESs assessment methods and data acquisition capabilities, and (3) assess how pressures from outside the boundaries of PAs affect their ability to maintain biodiversity and ESs in the long term.
Summary: Human respiratory viruses are of vastly different virulence, giving rise to symptoms ranging from common cold to severe pneumonia or even death. Although this most likely impacts molecular evolution of the corresponding viruses, the specific differences in their evolutionary patterns remain largely unknown. By comparing structural and nonstructural genes within respiratory viruses, greater similarities in codon usage bias (CUB) between nonstructural genes and humans were observed in weakly virulent viruses, whereas in strongly virulent viruses, it was structural genes whose CUBs were more similar to that of humans. Further comparisons between genomes of weakly and strongly virulent coronaviruses revealed greater similarities in CUBs between strongly virulent viruses and humans. Finally, using phylogenetic independent contrasts, dissimilation of viral CUB from that of humans was observed in SARS-CoV-2. Our work revealed distinct CUB evolutionary patterns between weakly and strongly virulent viruses, a previously unrecognized interaction between CUB and virulence in respiratory viruses
The immune system is highly networked and complex, which is continuously changing as encountering old and new pathogens. However, reductionism-based researches do not give a systematic understanding of the molecular mechanism of the immune response and viral pathogenesis. Here, we present HUMPPI-2022, a high-quality human protein-protein interaction (PPI) network, containing > 11,000 protein-coding genes with > 78,000 interactions. The network topology and functional characteristics analyses of the immune-related genes (IRGs) reveal that IRGs are mostly located in the center of the network and link genes of diverse biological processes, which may reflect the gene pleiotropy phenomenon. Moreover, the virus-human interactions reveal that pan-viral targets are mostly hubs, located in the center of the network and enriched in fundamental biological processes, but not for coronavirus. Finally, gene age effect was analyzed from the view of the host network for IRGs and virally-targeted genes (VTGs) during evolution, with IRGs gradually became hubs and integrated into host network through bridging functionally differentiated modules. Briefly, HUMPPI-2022 serves as a valuable resource for gaining a better understanding of the composition and evolution of human immune system, as well as the pathogenesis of viruses.
Boubacar SOLLY, EL HADJI Balla DIEYE, Oumar SY
et al.
Context and background
In the classified and managed forests of Upper-Casamance, the vegetation cover is undergoing significant changes. The result is a strong tendency to convert forest into savannah and cultivation areas, which goes against the policy of classification and management of forests.
Objectives
This study analyzes the changes in vegetation cover in classified and managed forests in Upper-Casamance between 1965 and 2018 to help politicians in their decision-making.
Methodology
It focused on six forest areas that reflect the evolution of plant cover in Haute-Casamance, including three classified (Pata, Kantora and Dabo) and three developed (Saré Bidji, Medina Salam Dingha and Bonconto). The approach used is based on a visual interpretation, from Corona 1965 and Sentinel 2 imagery from 2018, of land use trends and vegetation changes.
Results
The results indicated a great variability in plant cover depending on the area, the geographical position of these perimeters in the study area, and anthropogenic pressure. With the exception of the classified forest of Dabo located in the south, the forests of the classified domain (Pata and Kantora which are exposed in the north) have experienced a greater conversion of plant cover. They are also more affected by human actions than the forests in the managed area. Likewise, the managed forest of Medina Salam Dingha, located a little further north, has undergone a greater conversion of vegetation than those reserved a little more in the south. Moreover, in the managed forest of Bonconto, the tendency is to regenerate the vegetation cover. These different trends in vegetation raise the issue of the current status of certain classified forests and the importance of forest management.
Introduction: The evolution in the approach to human resource development in enterprises is progressively heading towards systemic integration with the overall strategy of organization. This entails the need to develop methods for measurement of the maturity level in the HRD area. Models used in practice are universal and flexible at their core, leaving quite a wide field for interpretation, what at the same time hinders their effective use. Research aim: The aim of the research was a practical verification of the J. Burgoyone Model, in the view of Matthews, Megginson, Surtees (2008), where the aforementioned model is used as a tool for assessment of the maturity level of systemic solutions in the area of human resources development in SMEs. The research problem was formulated in the form of a question whether the use of J. Burgoyone's Model in practice can effectively support the process of building a long-term human resource development strategy in small and medium-sized enterprises. Research method: Analytical process qualifies as a diagnostic research and was conducted in SME-type enterprises between 2019-2021. For this purpose, an original questionnaire was used (HRD Audit in A. Różański's organization - version 2018). Results: The analysis confirmed that HRD tools are used intuitively and are not systemically integrated in SME-type organizations. It is then again confirmed through the diversified level of advancement in terms of undertaken activities in various functional areas. Conclusions: The conducted analysis have shown that the use of the J. Burgoyone Model (and its subsequent adaptations) to assess the level of HRD maturity in SMEs additionaly requires the usage of „the second dimension of the assessment”, in this case the refinement of functional areas based on certain concepts (e.g. systematic approach to training, Sloman 2007). This type of operation enables of the advancement level in particular functional areas. In practice, this enables precise planning of activities supporting the identification of the subsequent steps in the process of integrating HRD with the process of building an overall organizational strategy.
As a uniquely human behavior, language is crucial to our understanding of ourselves and of the world around us. Despite centuries of research into how languages have historically developed and how people learn them, fully understanding the origin and evolution of language remains an ongoing challenge. In parallel, researchers have studied the divergence of birdsong in vocal-learning songbirds to uncover broader patterns of cultural evolution. One approach to studying cultural change over time, adapted from biology, focuses on the transmission of socially learned traits, including language, in a population. By studying how learning and the distribution of cultural traits interact at the population level, we can better understand the processes that underlie cultural evolution. Here, we take a two-fold approach to understanding the cultural evolution of vocalizations, with a focus on the role of the learner in cultural transmission. First, we explore previous research on the evolution of social learning, focusing on recent progress regarding the origin and ongoing cultural evolution of both language and birdsong. We then use a spatially explicit population model to investigate the coevolution of culture and learning preferences, with the assumption that selection acts directly on cultural phenotypes and indirectly on learning preferences. Our results suggest that the spatial distribution of learned behaviors can cause unexpected evolutionary patterns of learning. We find that, intuitively, selection for rare cultural phenotypes can indirectly favor a novelty-biased learning strategy. In contrast, selection for common cultural phenotypes leads to cultural homogeneity; we find that there is no selective pressure on learning strategy without cultural variation. Thus, counterintuitively, selection for common cultural traits does not consistently favor conformity bias, and novelty bias can stably persist in this cultural context. We propose that the evolutionary dynamics of learning preferences and cultural biases can depend on the existing variation of learned behaviors, and that this interaction could be important to understanding the origin and evolution of cultural systems such as language and birdsong. Selection acting on learned behaviors may indirectly impose counterintuitive selective pressures on learning strategies, and understanding the cultural landscape is crucial to understanding how patterns of learning might change over time.