Precautionary principle or evidence-based conservation? Assessing the information content of threat data for the Yangtze finless porpoise

Conservation management requires evidence, but robust data on key parameters such as threats are often unavailable. Conservation-relevant insights might be available within datasets collected for other reasons, making it important to determine the information content of available data for threatened species and identify remaining data-gaps before investing time and resources in novel data collection. The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) has declined severely across the middle-lower Yangtze, but multiple threats exist in this system and the relative impact of different anthropogenic activities is unclear, preventing identification of appropriate mitigation strategies. Several datasets containing information on porpoises or potential threats are available from past boat-based and fishing community surveys, which might provide novel insights into causes of porpoise mortality and decline. We employed multiple analytical approaches to investigate spatial relationships between live and dead porpoises and different threats, reproductive trends over time, and sustainable offtake levels, to assess whether evidence-based conservation is feasible under current data availability. Our combined analyses provide new evidence that mortality is spatially associated with increased cargo traffic; observed mortality levels (probably a substantial underestimate of true levels) are unsustainable; and population recruitment is decreasing, although multiple factors could be responsible (pollutants, declining fish stocks, anthropogenic noise, reduced genetic diversity). Available data show little correlation between patterns of mortality and fishing activity even when analyzed across multiple spatial scales; however, interview data can be affected by multiple biases that potentially complicate attempts to reconstruct levels of bycatch, and new data are required to understand dynamics and sustainability of porpoise-fisheries interactions. This critical assessment of existing data thus suggests that in situ porpoise conservation management must target multiple co-occurring threats. Even limited available datasets can provide new insights for understanding declines, and we demonstrate the importance of an integrative approach for investigating complex conservation problems and maximizing evidence in conservation planning for poorly known taxa

Photosynthetic adaptation strategies in peppers under continuous lighting: insights into photosystem protection

Energy efficient lighting strategies have received increased interest from controlled environment producers. Long photoperiods (up to 24 h - continuous lighting (CL)) of lower light intensities could be used to achieve the desired daily light integral (DLI) with lower installed light capacity/capital costs and low electricity costs in regions with low night electricity prices. However, plants grown under CL tend to have higher carbohydrate and reactive oxygen species (ROS) levels which may lead to leaf chlorosis and down-regulation of photosynthesis. We hypothesize that the use of dynamic CL using a spectral change and/or light intensity change between day and night can negate CL-injury. In this experiment we set out to assess the impact of CL on pepper plants by subjecting them to white light during the day and up to 150 µmol m-2 s-1 of monochromatic blue light at night while controlling the DLI at the same level. Plants grown under all CL treatments had similar cumulative fruit number and weight compared to the 16h control indicating no reduction in production. Plants grown under CL had higher carbohydrate levels and ROS-scavenging capacity than plants grown under the 16h control. Conversely, the amount of photosynthetic pigment decreased with increasing nighttime blue light intensity. The maximum quantum yield of photosystem II (Fv/Fm), a metric often used to measure stress, was unaffected by light treatments. However, when light-adapted, the operating efficiency of photosystem II (ΦPSII) decreased and non-photochemical quenching (NPQ) increased with increasing nighttime blue light intensity. This suggests that both acclimated and instantaneous photochemistry during CL can be altered and is dependent on the nighttime light intensity. Furthermore, light-adapted chlorophyll fluorescence measurements may be more adept at detecting altered photochemical states than the conventional stress metric using dark-adapted measurements

Mitigating the effect of shipping on freshwater megafauna: the case study of the Yangtze finless porpoise

Shipping has increasingly become a major threat to cetaceans due to its direct effect (e.g. ship strikes) and indirect effects (e.g. noise and habitat displacement). Most previous studies have focused on the deleterious effects of shipping traffic on marine species, while the effect of shipping on freshwater cetaceans has received little attention. The Yangtze River is a major trade artery in China, and shipping traffic there caused deaths of the now-extinct Yangtze river dolphin or baiji (Lipotes vexillifer). Here, we examine the distributional overlap of another cetacean species, the critically endangered Yangtze finless porpoise (Neophocoena asiaorientalis asiaorientalis) and cargo ships in a busy section of Yangtze River from Ezhou to Zhenjiang City. We use vessel-based survey data from 2006, 2012, and 2017 to quantify the distribution of porpoise. We use satellite images to quantify the distribution of cargo vessels travelling upstream. Most porpoise were concentrated within 300 m of the river banks. Shipping increased by 65% from 2006 to 2017, and ~ 60% of the upstream vessels was also within 300 m of the banks. This increase in shipping may have caused an observed shift in porpoise distribution away from the banks after 2006. Enhanced enforcement of existing shipping regulations that limit vessels to established shipping lane and set refuges in the side channels could help reduce the distributional overlap of porpoise and ships and aid in porpoise conservation. This could be applied and benefit the cetacean conservation under continued growth of shipping in rivers

Peptides encoded by short ORFs control development and define a new eukaryotic gene family

Despite recent advances in developmental biology and in genomics, key questions remain regarding the organisation of cells into embryos. One possibility is that novel types of genes might await discovery and could provide some of the answers. Genome annotation depends strongly on comparison with previously known gene sequences, and so genes having previously uncharacterised structure and function can be missed. Here we present the characterisation of tarsal-less, a new such type of gene. Tarsal-less has two unusual features: first, it contains more than one coding unit, a structure more similar to some bacterial genes. Second, it codes for small peptides rather than proteins, and in fact these peptides represent the smallest gene products known to date. Functional analysis of this gene in the fruitfly Drosophila shows that it has important functions throughout development, including tissue morphogenesis and pattern formation. We identify genes similar to tarsal-less in other species, and thus define a tarsal-less-related gene family. We expect that a combination of bioinformatic and functional methods, such as the ones we use in this study, will identify and characterize more genes of this type. Potentially, thousands of such new genes may exist

Imperial trophy or island relict? A new extinction paradigm for Père David's deer: a Chinese conservation icon

The file attached is the Published/publisher’s pdf version of the article

A Schwarz lemma for K\"ahler affine metrics and the canonical potential of a proper convex cone

This is an account of some aspects of the geometry of K\"ahler affine metrics based on considering them as smooth metric measure spaces and applying the comparison geometry of Bakry-Emery Ricci tensors. Such techniques yield a version for K\"ahler affine metrics of Yau's Schwarz lemma for volume forms. By a theorem of Cheng and Yau there is a canonical K\"ahler affine Einstein metric on a proper convex domain, and the Schwarz lemma gives a direct proof of its uniqueness up to homothety. The potential for this metric is a function canonically associated to the cone, characterized by the property that its level sets are hyperbolic affine spheres foliating the cone. It is shown that for an $n$-dimensional cone a rescaling of the canonical potential is an $n$-normal barrier function in the sense of interior point methods for conic programming. It is explained also how to construct from the canonical potential Monge-Amp\`ere metrics of both Riemannian and Lorentzian signatures, and a mean curvature zero conical Lagrangian submanifold of the flat para-K\"ahler space.Comment: Minor corrections. References adde

Histone Acetylation-Mediated Regulation of the Hippo Pathway

The Hippo pathway is a signaling cascade recently found to play a key role in tumorigenesis therefore understanding the mechanisms that regulate it should open new opportunities for cancer treatment. Available data indicate that this pathway is controlled by signals from cell-cell junctions however the potential role of nuclear regulation has not yet been described. Here we set out to verify this possibility and define putative mechanism(s) by which it might occur. By using a luciferase reporter of the Hippo pathway, we measured the effects of different nuclear targeting drugs and found that chromatin-modifying agents, and to a lesser extent certain DNA damaging drugs, strongly induced activity of the reporter. This effect was not mediated by upstream core components (i.e. Mst, Lats) of the Hippo pathway, but through enhanced levels of the Hippo transducer TAZ. Investigation of the underlying mechanism led to the finding that cancer cell exposure to histone deacetylase inhibitors induced secretion of growth factors and cytokines, which in turn activate Akt and inhibit the GSK3 beta associated protein degradation complex in drug-affected as well as in their neighboring cells. Consequently, expression of EMT genes, cell migration and resistance to therapy were induced. These processes were suppressed by using pyrvinium, a recently described small molecule activator of the GSK 3 beta associated degradation complex. Overall, these findings shed light on a previously unrecognized phenomenon by which certain anti-cancer agents may paradoxically promote tumor progression by facilitating stabilization of the Hippo transducer TAZ and inducing cancer cell migration and resistance to therapy. Pharmacological targeting of the GSK3 beta associated degradation complex may thus represent a unique approach to treat cancer. © 2013 Basu et al

The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure

Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. To address this, quantitative analysis of single cell responses can help characterise the redundancy within gene families. We developed high-throughput quantitative imaging of stomatal closure, a response of plant guard cells, and performed a reverse genetic screen in a group of Arabidopsis mutants to five stimuli. Focussing on the intersection between guard cell signalling and the endomembrane system, we identified eight clusters based on the mutant stomatal responses. Mutants generally affected in stomatal closure were mostly in genes encoding SNARE and SCAMP membrane regulators. By contrast, mutants in RAB5 GTPase genes played specific roles in stomatal closure to microbial but not drought stress. Together with timed quantitative imaging of endosomes revealing sequential patterns in FLS2 trafficking, our imaging pipeline can resolve non-redundant functions of the RAB5 GTPase gene family. Finally, we provide a valuable image-based tool to dissect guard cell responses and outline a genetic framework of stomatal closure. This article is protected by copyright. All rights reserved

RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether

Long-distance RNA transport enables local protein synthesis at metabolicallyactive sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules “hitchhike” on moving lysosomes. In vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS) mutations impair RNA granule transport in neurons by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS