Bostonia: The Boston University Alumni Magazine. Volume 11

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Modelling biological N fixation and grass-legume dynamics with process-based biogeochemical models of varying complexity

This work was conducted by the Models4Pastures consortium project under the auspices of FACCE-JPI. Funding was provided by: the New Zealand Government to support the objectives of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases; AgResearch’s Strategic Science Investment Fund as a contribution to the Forages for Reduced Nitrate Leaching (FRNL) research programme; the input of UK partners was funded by DEFRA and also contributes to the RCUK-funded projects: N-Circle (BB/N013484/1), UGRASS (NE/M016900/1) and GREENHOUSE (NE/K002589/1). R.M. Rees and C.F.E. Topp also received funding from the Scottish Government Strategic Research Programme. Lutz Merbold and Kathrin Fuchs acknowledge funding received for the Swiss contribution to Models4Pastures (FACCE-JPI project, SNSF funded contract: 40FA40_154245/1) and for the Doc.Mobility fellowship (SNSF funded project: P1EZP2_172121). Lorenzo Brilli, Camilla Dibari and Marco Bindi acknowledge funding received from the Italian Ministry of Agricultural Food and Forestry Policies (MiPAAF).Peer reviewedPublisher PD

Quantifying the habitat and zoogeomorphic capabilities of spawning European barbel Barbus barbus, a lithophilous cyprinid

Suitable gravel availability is critical for the spawning success of lithophilous fishes, including redd builders. Redd construction during spawning can alter substrate characteristics, thereby influencing hydraulic conditions and sediment transport, highlighting the importance of spawning as a zoogeomorphic activity. Here, interactions between redd‐building fish and their spawning environment were investigated for European barbel Barbus barbus with a comparative approach across three English rivers: Teme (western), Great Ouse (eastern) and Idle (central). Sediment characteristics of spawning habitats were similar across the rivers, including subsurface fine sediment (<2 mm) content (≈20% dry weight), but elevated subsurface silt content and coarser surface sediments were found in the river Teme. Water velocities were similar at spawning sites despite differences in channel width and depth. Redds were characterized by a pit and tailspill, with no differences in surface grain‐size characteristics between these and the surrounding riverbed, but with topographic alteration (dimensions and tailspill amplitude) in line with those of salmonids. Estimates of the fraction of the bed that spawning barbel were capable of moving exceeded 97% in all rivers. Estimated reproductive potential varied significantly between the rivers Idle and Teme (3,098 to 9,715 eggs/m2), which was largely due to differences in barbel lengths affecting fecundity. Larger barbel, capable of producing and depositing more eggs, but in more spatially extensive redds, meaning fewer redds per given surface area of riverbed. Predictions of barbel egg mortality based on sand content were low across both rivers. The effects of silt on barbel egg and larvae development are unknown, but the levels detected here would significantly impact salmon egg mortality. Similarities in fish length to redd area and the size of moveable grains by spawning barbel and salmon suggest they have similar geomorphic effects on sediments, although fine sediment tolerance is highly divergent

Greenhouse gas and ammonia emission mitigation priorities for UK policy targets

Publication history: Accepted - 16 March 2023; Published online - 6th May 2023.Agriculture is essential for providing food and maintaining food security while concurrently delivering multiple other ecosystem services. However, agricultural systems are generally a net source of greenhouse gases and ammonia. They, therefore, need to substantively contribute to climate change mitigation and net zero ambitions. It is widely acknowledged that there is a need to further reduce and mitigate emissions across sectors, including agriculture to address the climate emergency and emissions gap. This discussion paper outlines a collation of opinions from a range of experts within agricultural research and advisory roles following a greenhouse gas and ammonia emission mitigation workshop held in the UK in March 2022. The meeting identified the top mitigation priorities within the UK’s agricultural sector to achieve reductions in greenhouse gases and ammonia that are compatible with policy targets. In addition, experts provided an overview of what they believe are the key knowledge gaps, future opportunities and co-benefits to mitigation practices as well as indicating the potential barriers to uptake for mitigation scenarios discussed.This work was supported with funding from the Scottish Government Strategic Research Programme (2022−2027, C2-1 SRUC) and Biotechnology and Biological Sciences Research Council (BBSRC) (BBS/E/C/000I0320 and BBS/E/C/000I0330). We also acknowledge support from UKRI-BBSRC (UK Research and Innovation-Biotechnology and Biological Sciences Research Council) via grants BBS/E/C/000I0320 and BBS/E/C/000I0330, and Rothamsted Research Science Initiative Catalyst Award supported by BBSRC

Patient-derived xenograft (PDX) models in basic and translational breast cancer research

Patient-derived xenograft (PDX) models of a growing spectrum of cancers are rapidly supplanting long-established traditional cell lines as preferred models for conducting basic and translational preclinical research. In breast cancer, to complement the now curated collection of approximately 45 long-established human breast cancer cell lines, a newly formed consortium of academic laboratories, currently from Europe, Australia, and North America, herein summarizes data on over 500 stably transplantable PDX models representing all three clinical subtypes of breast cancer (ER+, HER2+, and "Triple-negative" (TNBC)). Many of these models are well-characterized with respect to genomic, transcriptomic, and proteomic features, metastatic behavior, and treatment response to a variety of standard-of-care and experimental therapeutics. These stably transplantable PDX lines are generally available for dissemination to laboratories conducting translational research, and contact information for each collection is provided. This review summarizes current experiences related to PDX generation across participating groups, efforts to develop data standards for annotation and dissemination of patient clinical information that does not compromise patient privacy, efforts to develop complementary data standards for annotation of PDX characteristics and biology, and progress toward "credentialing" of PDX models as surrogates to represent individual patients for use in preclinical and co-clinical translational research. In addition, this review highlights important unresolved questions, as well as current limitations, that have hampered more efficient generation of PDX lines and more rapid adoption of PDX use in translational breast cancer research

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century