Abstract Agricultural heritage systems, a paradigm of harmonious symbiosis between humans and the natural environment, contain rich biodiversity and embody distinctive cultural values and historical significance. Macro-level spatial analysis is essential to understand agricultural heritage systems. This study is based on 188 China’s Important Agricultural Heritage Systems (CIAHS) (2013–2023), utilizing spatial analysis methods such as the nearest neighbor index, standard deviational ellipse, kernel density analysis, and Geodetector to examine the spatial distribution characteristics and influencing factors of CIAHS. The results show an uneven distribution of CIAHS, characterized by significant regional discrepancies and an overall clustered spatial pattern. This pattern can be attributed to the combined effects of natural environmental factors (e.g., temperature, precipitation, topography, and water resources) and human environmental factors (e.g., economy, population, transportation, government response, and residents’ attention), which interact synergistically. Among these factors, government response, temperature, and residents’ attention play relatively greater roles in shaping the overall pattern. The study of the spatial distribution characteristics and influencing factors of CIAHS will enhance the understanding of the geographical evolution and regional variations of these resources, thus providing a scientific basis for their preservation and sustainable development.
IntroductionBrucella canis is a zoonotic pathogen that infects both dogs and humans, yet its evolutionary and phylogenetic characteristics are poorly understood.MethodsHere, we comprehensively characterized an isolated strain of B. canis through integrated bacteriological, comparative genomic, and whole-genome sequencing-based core genome single-nucleotide polymorphism (WGS-cgSNP) analyses.ResultsB. canis YN20042 was isolated from a febrile patient (38 °C) with sweating and fatigue. The culture exhibited rough, grayish white, sticky, and opaque colonies. The isolate was identified as Brucella strain by a BCSP-31 polymerase chain reaction (PCR) assay, which yielded an amplicon of the expected 223-bp size, and was classified as a B. canis strain by conventional biotyping. The patient reported frequent contact with dogs and livestock. The strain showed a 99.99% average nucleotide identity to the B. canis reference strain ATCC 23365 (GCA_000018525.1). An in silico multilocus sequence typing (MLST) analysis showed that the strain belonged to sequence type 21, which was consistent with its classification within B. canis. The genome of strain YN20042 exhibited strong synteny with the reference strain and showed no detectable structural variations. It harbored 12 predicted virulence factors encompassing 71 associated genes, although it notably lacked the wbpL gene but contained a Brucella suis mprF gene. A further analysis identified predicted mutations in key virulence genes (eryA, pagN, bmaC, cfa1, and cfa2) and predicted multiple horizontally acquired genes, collectively suggesting a complex evolutionary trajectory involving both gene variants and potential recombination events. A WGS-SNP analysis revealed that YN20042 clustered closely with strains isolated from Zhejiang and Beijing, indicating a high degree of genetic relatedness.ConclusionThe first isolation of B. canis in the region expands the local spectrum of pathogenic Brucella and highlights the substantial infection risk for individuals with close dog and livestock contact. Enhanced surveillance, targeted screening of high-risk populations, and public health education are necessary to mitigate the risk of B. canis transmission.
Laura Deelen, Zoe H Mitchell, Martina Demurtas
et al.
Abstract Craniofacial development is evolutionarily conserved, yet subtle changes in its regulatory network drive species-specific traits. Transposable elements (TEs) contribute to genome evolution, but their role in cranial neural crest cells (CNCCs) remains unclear. Here, we investigate the domestication of hominoid-specific TEs (LTR5Hs and SVAs) as enhancers during human CNCC specification, a process critical for vertebrate craniofacial development. Using human iPSC-derived CNCCs, we identified ~515 hominoid-specific TEs functioning as enhancers, including ~250 human-specific, predominantly LTR5Hs. These elements are enriched for CNCC coordinator motifs, are bound by the CNCC signature factor TWIST1, and their enhancer activity appears largely CNCC-specific. CRISPR-interference targeting ~75% of these active TEs led to widespread transcriptional dysregulation of genes involved in neural crest migration, and two orthogonal functional assays confirmed that CNCC migration is impaired upon TE repression. Finally, genes near human-specific TEs showed higher expression in human CNCCs compared to chimpanzee CNCCs, but TE repression restored gene expression to chimpanzee levels. These findings highlight how young TEs were domesticated to fine-tune CNCC regulatory networks, potentially contributing to lineage-specific craniofacial evolution.
Our goal is to evaluate the use of ultrasound to detect small regions of increased vascular density and altered blood flow and to quantify small changes in these parameters due to effects of new anti-angiogenic drugs. Regions containing intravascular contrast agents are identified using a new ultrasound strategy that combines subharmonic and phase inversion imaging. The contrast agent is repeatedly destroyed in order to estimate the time required for local replenishment. Parameters are estimated based on this strategy and include measures of the spatial extent of flow, the spatial integral of flow, and the time required for 80% replenishment. In a study of 25 tumors, we first demonstrate that regions of viable tumor as small as 1 mm, as verified by histology, can be detected and show similar morphology to images acquired with computed tomography (CT). The spatial mapping of vessels with ultrasound is superior to contrast enhanced computed tomography due to the intravascular distribution of ultrasound contrast agents. Estimation of the time to 80% replenishment was conducted on kidney and tumor data and is a robust parameter not altered by attenuation. Mean times to 80% replenishment of 1–5 s were estimated for the kidney cortex and mean times of 6–14 s were observed for viable tumor tissue. This broad range of replenishment times is indicative of abnormal tumor vascular density and tortuosity. Changes in flow parameters with anti-angiogenic therapy are significant beginning at 48 hours post-treatment.
The rate of progression to disease varies considerably among individuals infected with human immunodeficiency virus-type 1 (HIV-1). Analyses of semiannual blood samples obtained from six infected men showed that a rapid rate of CD4 T cell loss was associated with relative evolutionary stasis of the HIV-1 quasispecies virus population. More moderate rates of CD4 T cell loss correlated with genetic evolution within three of four subjects. Consistent with selection by the immune constraints of these subjects, amino acid changes were apparent within the appropriate epitopes of human leukocyte antigen class I-restricted cytotoxic T lymphocytes. Thus, the evolutionary dynamics exhibited by the HIV-1 quasispecies virus populations under natural selection are compatible with adaptive evolution.
Magdalena Blanz, Magdalena Blanz, Magdalena Blanz
et al.
IntroductionStable sulfur isotope ratios (δ34S) in bone collagen are often employed to study the consumption of marine and freshwater fish, wetland grazing, marine foraging patterns, and the possible geographic origins of food sources. However, a recent small-scale crop experiment showed that biofertilisation with seaweed can elevate δ34S in Celtic beans by ca. 10 ‰. Consumption of this food could erroneously suggest a marine diet and therefore has important implications for the reconstruction of past diets and dietary origins. However, limited research has so far been undertaken on cereals.MethodsTo address this issue, a large-scale field trial was undertaken on the Orkney Islands, whereby bere barley (a Scottish landrace, Hordeum vulgare L.) was biofertilised with seaweed at different dosages (25 t/ha, 50 t/ha), with a mineral NPK fertiliser, and left unfertilised as a control.ResultsThe total barley biomass yield was higher and barley grains were enlarged following all fertilisation treatments compared to the control barley. Barley grain and straw from seaweed-fertilised crops had more elevated δ34S values by around 2–3 ‰ compared to unfertilised plants, while the NPK-fertilised grains and plants had δ34S values 1 ‰ lower.DiscussionThese results confirm previous hypotheses that seaweed fertilisation can elevate cereal δ34S values. The comparatively small δ34S difference between control and seaweed fertilised crops in this field trial is likely due to background elevated δ34S values in the soil (+12.7 ‰), which in turn may be due to long-term exposure to oceanic-influenced rain and sea spray and/or possible historical application of seaweed, or the underlying bedrock composition. The results of this study show that seaweed fertilisation can increase barley grain sizes and δ34S values, and thus should be considered when reconstructing land management and dietary practices in the archaeological record.
Chien-Hsiang Lin, Siao-Man Wu, Chia-Yen Lin
et al.
Abstract Understanding the diversity of deep-sea fish fauna based on otoliths in the tropical and subtropical West Pacific has been limited, creating a significant knowledge gap regarding regional and temporal variations in deep-sea fish fauna. To address this gap, we collected a total of 122 bulk sediment samples from the Lower Pliocene Gutingkeng Formation in southwestern Taiwan to reconstruct the otolith-based fish fauna. Using planktonic foraminiferal biostratigraphy, we determined the age of the samples to be 5.6 to 3.1 Ma. A total of 8314 otoliths were assigned to 64 different taxa from 33 families, including the discovery of one new genus, Gutingichthys gen. nov., and three new species: Benthosema duanformis sp. nov., Benthosema parafibulatum sp. nov., and Gutingichthys changi sp. nov. Comparisons with other regional otolith-based assemblages highlighted the exceptional diversity of our collection, making it the most diverse fossil fish fauna reported from Taiwan to date. Otolith diversity analysis revealed very few taxa were dominant in the assemblage, particularly the mesopelagic Myctophidae, with a wide variety of minor taxa. The co-occurrence of shallow-water elements suggests episodic storm events as a potential source. The predominance of deep-sea and oceanic fishes indicated an outer-shelf to upper slope environment, resembling the modern outer-shelf and upper slope fish fauna in the region. Our findings suggest an early establishment and persistent presence of the mesopelagic fish community since the Early Pliocene. Further investigations of the Upper Miocene and Pleistocene sections of the Gutingkeng Formation would provide valuable insights into the evolution of deep-sea fish fauna in the area. ZooBank LSID: urn:lsid:zoobank.org:pub:7A336FC7-0D9A-4D17-B212-0B51427945DD.
The dramatic changes brought by the relationship between humans and their natural environments by different human activities such as the exploitation of natural resources and use of fossil fuels threatens humanity at large. Beside considerable disagreements on when Anthropocene began, it is considered an epochal transformation linked to deterioration of global ecologies, loss of biodiversity and environmental degradation. Environmental anthropologists are contributing both theoretically and by important ethnographic insights in analyzing and understanding the consequences of climate changes in socio-ecological systems worldwide. In this article we provide an overview of main theoretical contributions during the development of environmental anthropology as a discipline. In addition, we highlight the possible Cultural Evolution theory (CE) contribution in climate changes consequences to a socio-ecological system.