ICDP workshop on the Lake Tanganyika Scientific Drilling Project: a late Miocene–present record of climate, rifting, and ecosystem evolution from the world's oldest tropical lake

The Neogene and Quaternary are characterized by enormous changes in global climate and environments, including global cooling and the establishment of northern high-latitude glaciers. These changes reshaped global ecosystems, including the emergence of tropical dry forests and savannahs that are found in Africa today, which in turn may have influenced the evolution of humans and their ancestors. However, despite decades of research we lack long, continuous, well-resolved records of tropical climate, ecosystem changes, and surface processes necessary to understand their interactions and influences on evolutionary processes. Lake Tanganyika, Africa, contains the most continuous, long continental climate record from the mid-Miocene (∼10 Ma) to the present anywhere in the tropics and has long been recognized as a top-priority site for scientific drilling. The lake is surrounded by the Miombo woodlands, part of the largest dry tropical biome on Earth. Lake Tanganyika also harbors incredibly diverse endemic biota and an entirely unexplored deep microbial biosphere, and it provides textbook examples of rift segmentation, fault behavior, and associated surface processes. To evaluate the interdisciplinary scientific opportunities that an ICDP drilling program at Lake Tanganyika could offer, more than 70 scientists representing 12 countries and a variety of scientific disciplines met in Dar es Salaam, Tanzania, in June 2019. The team developed key research objectives in basin evolution, source-to-sink sedimentology, organismal evolution, geomicrobiology, paleoclimatology, paleolimnology, terrestrial paleoecology, paleoanthropology, and geochronology to be addressed through scientific drilling on Lake Tanganyika. They also identified drilling targets and strategies, logistical challenges, and education and capacity building programs to be carried out through the project. Participants concluded that a drilling program at Lake Tanganyika would produce the first continuous Miocene–present record from the tropics, transforming our understanding of global environmental change, the environmental context of human origins in Africa, and providing a detailed window into the dynamics, tempo and mode of biological diversification and adaptive radiations.© Author(s) 2020. This open access article is distributed under the Creative Commons Attribution 4.0 License

Coupling coordination degree between social-economic development and water environment: A case study of Taihu lake basin, China

Exploring the coupled and coordinated development of social-ecological systems is an important basis for promoting integrated watershed management. Based on the framework of the social-ecological system of lake water environment governance, this study builds an evaluation index system for quantifying the coupling and coordination of the social-ecological system, selects the representative key variables in each component of the social-ecological system, and evaluates the coupling and coordination changes in the social-ecological system of Taihu lake water environment governance from 1987 to 2020. This study uses the coupling coordination degree model (CCDM) and the obstacle degree model (ODM) to reveal the dynamic relationship between the coupling degree (CD), the coupling coordination degree (CCD), and their obstacle factors of the social-ecological system of lake water environment governance. The results show that: (1) The comprehensive social system development level shows an uptrend, while ecological subsystem shows a decreasing and then increasing trend. With the development of social economy, water environment has experienced the process of deterioration followed by recovery. (2) CD and CCD both show a downward trend first and then an upward trend. CD ranges from 0.71 to 0.98, its status had fluctuated between high-quality coupling stage and break-in stage. CCD ranges from 0.42 to 0.58, its status had fluctuated between near maladjustment recession and critical coordination stage. (3) The average obstacle degrees of the ecosystem and the social system are 0.51 and 0.49, the strong human activity interference in the social system and the vulnerability of the ecosystem and uncertainty jointly affects the CCD. Therefore, to improve the CCD of the social-ecological system of lake water environment governance, it is recommended that attention should be paid to the use and treatment of water resources in the process of social and economic development of the basin, and the amount of external pollution into the lake should be controlled in many ways. This study can help to understand the coupled social-ecological system interactions of Taihu lake water environment governance and provide a scientific basis for decision-makers

Urban forestry and greening strategies: the case of Nanjing, China

published_or_final_versionGeography and GeologyDoctoralDoctor of Philosoph

Integrated Application of SWAT and L-THIA Models for Nonpoint Source Pollution Assessment in Data Scarce Regions

Nonpoint source pollution (NPS) has become the most important reason for the deterioration of water quality, while relevant studies are often limited to African river and lake basins with insufficient data. Taking the Simiyu catchment of the Lake Victoria basin as the study area, we set up a NPS model based on the soil and water assessment tool (SWAT). Furthermore, the rationality of this model is verified with the field-measured data. The results manifest that: (1) the temporal variation of NPS load is consistent with the variation pattern of rainfall, the average monthly output of total nitrogen (TN) and total phosphorus (TP) in the rainy season was 1360.6 t and 336.2 t, respectively, while in the dry season was much lower, only 13.5 t and 3.0 t, respectively; (2) in view of spatial distribution among 32 sub-basins, TN load ranged from 2.051 to 24.288 kg/ha with an average load of 12.940 kg/ha, and TP load ranged from 0.263 to 8.103 kg/ha with an average load of 3.321 kg/ha during the 16-month study period; (3) Among the land use types, the cropland contributed the highest proportion of TN and TP pollution with 50.28% and 76.29%, respectively, while the effect of forest on NPS was minimal with 0.05% and 0.02% for TN and TP, respectively. (4) Moreover, the event mean concentration (EMC) values of different land use types have been derived based on the SWAT model, which are key parameters for the application of the long-term hydrological impact assessment (L-THIA) model. Therefore, this study facilitates applying the L-THIA model to other similar data-deficient catchments in view of its relatively lower data requirement

Morphological Characteristics of Informal Settlements and Strategic Suggestions for Urban Sustainable Development in Tanzania: Dar es Salaam, Mwanza, and Kigoma

Rapid urbanization in developing countries has been accompanied by the spread of informal settlements, which is particularly prominent in sub-Saharan Africa. These settlements have become an important supplement to the inadequate formal housing supply in cities, and their spontaneously formed spatial patterns have important influences on sustainable development. In this study, qualitative and quantitative approaches were used to examine the morphological characteristics of informal settlements in Tanzania and the associated influences on urban development. Geographic spatial analyses, landscape pattern indices, and mathematical statistics, along with quick assessments, group discussions, and key informant interviews, were used to obtain detailed information on the spatial forms of informal settlements. The results indicate that the form of the settlements does not conform to the social, economic, or environmental characteristics of sustainable development. The disordered expansion of single-layered buildings with a single function, irregular road networks in poor condition, and a lack of consideration and protection of the ecological environment were found to negatively impact urban function and sustainable development. However, the structure and form of informal settlements could, in addition to formalization projects, be optimized to drive sustainable and socioeconomic development goals as well as environmental conservation

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

INTRODUCTION Genome-wide association studies (GWASs) have identified thousands of loci associated with neurodevelopmental and psychiatric disorders, yet our lack of understanding of the target genes and biological mechanisms underlying these associations remains a major challenge. GWAS signals for many neuropsychiatric disorders, including autism spectrum disorder, schizophrenia, and bipolar disorder, are particularly enriched for gene-regulatory elements active during human brain development. However, the lack of a unified population-scale, ancestrally diverse gene-regulatory atlas of human brain development has been a major obstacle for the functional assessment of top loci and post-GWAS integrative analyses. RATIONALE To address this critical gap in knowledge, we have uniformly processed and systematically characterized gene, isoform, and splicing quantitative trait loci (cumulatively referred to as xQTLs) in the developing human brain across 672 unique samples from 4 to 39 postconception weeks spanning European, African-American, and Latino/admixed American ancestries). With this expanded atlas, we sought to specifically localize the timing and molecular features mediating the greatest proportion of neuropsychiatric GWAS heritability, to prioritize candidate risk genes and mechanisms for top loci, and to compare with analogous results using larger adult brain functional genomic reference panels. RESULTS In total, we identified 15,752 genes harboring a gene, isoform and/or splicing cis-xQTL, including 49 genes associated with four large, recurrent inversions. Highly concordant effect sizes were observed across populations, and our diverse reference panel improved resolution to fine-map underlying candidate causal regulatory variants. Substantially more genes were found to harbor QTLs in the first versus second trimester of brain development, with a notable drop in gene expression and splicing heritability observed from 10 to 18 weeks coinciding with a period of rapidly increasing cellular heterogeneity in the developing brain. Isoform-level regulation, particularly in the second trimester, mediated a greater proportion of heritability across multiple psychiatric GWASs compared with gene expression regulation. Through colocalization and transcriptome-wide association studies, we prioritized biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, with >2-fold more colocalizations observed compared with larger adult brain functional genomic reference panels. We observed convergence between common and rare-variant associations, including a cryptic splicing event in the high-confidence schizophrenia risk gene SP4. Finally, we constructed a comprehensive set of developmentally regulated gene and isoform coexpression networks harboring unique cell-type specificity and genetic enrichments. Leveraging this cell-type specificity, we identified >8000 module interaction QTLs, many of which exhibited additional GWAS colocalizations. Overall, neuropsychiatric GWASs and rare variant signals localized more strongly within maturing excitatory- and interneuron-associated modules compared with those enriched for neural progenitor cell types. Results can be visualized at devbrainhub.gandallab.org. CONCLUSION We have generated a large-scale, cross-population resource of gene, isoform, and splicing regulation in the developing human brain, providing comprehensive developmental and cell-type-informed mechanistic insights into the genetic underpinnings of complex neurodevelopmental and psychiatric disorders

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Performance of a modular ton-scale pixel-readout liquid argon time projection chamber

The Module-0 Demonstrator is a single-phase 600 kg liquid argon time projection chamber operated as a prototype for the DUNE liquid argon near detector. Based on the ArgonCube design concept, Module-0 features a novel 80k-channel pixelated charge readout and advanced high-coverage photon detection system. In this paper, we present an analysis of an eight-day data set consisting of 25 million cosmic ray events collected in the spring of 2021. We use this sample to demonstrate the imaging performance of the charge and light readout systems as well as the signal correlations between the two. We also report argon purity and detector uniformity measurements, and provide comparisons to detector simulations

Supernova Pointing Capabilities of DUNE

International audienceThe determination of the direction of a stellar core collapse via its neutrino emission is crucial for the identification of the progenitor for a multimessenger follow-up. A highly effective method of reconstructing supernova directions within the Deep Underground Neutrino Experiment (DUNE) is introduced. The supernova neutrino pointing resolution is studied by simulating and reconstructing electron-neutrino charged-current absorption on $^{40}$Ar and elastic scattering of neutrinos on electrons. Procedures to reconstruct individual interactions, including a newly developed technique called ``brems flipping'', as well as the burst direction from an ensemble of interactions are described. Performance of the burst direction reconstruction is evaluated for supernovae happening at a distance of 10 kpc for a specific supernova burst flux model. The pointing resolution is found to be 3.4 degrees at 68% coverage for a perfect interaction-channel classification and a fiducial mass of 40 kton, and 6.6 degrees for a 10 kton fiducial mass respectively. Assuming a 4% rate of charged-current interactions being misidentified as elastic scattering, DUNE's burst pointing resolution is found to be 4.3 degrees (8.7 degrees) at 68% coverage