Patterns of richness across forest beetle communities—A methodological comparison of observed and estimated species numbers

Abstract Species richness is a frequently used measure of biodiversity. The compilation of a complete species list is an often unattainable goal. Estimators of species richness have been developed to overcome this problem. While the use of these estimators is becoming increasingly popular, working with the observed number of species is still common practice. To assess whether patterns of beetle communities based on observed numbers may be compared among each other, we compared patterns from observed and estimated numbers of species for beetle communities in the canopy of the Leipzig floodplain forest. These patterns were species richness and the number of shared species among three tree species and two canopy strata. We tested the applicability of the asymptotic Chao1 estimator and the estimate provided by the nonasymptotic rarefaction–extrapolation method for all tree species and both upper canopy and lower canopy. In the majority of cases, the ranking patterns of species richness for host tree species and strata were the same for the observed and estimated number of species. The ranking patterns of the number of species shared among host tree species and strata, however, were significantly different between observed and estimated values. Our results indicate that the observed number of species under‐represents species richness and the number of shared species. However, ranking comparisons of published patterns based on the number of observed species may be acceptable for species richness but likely not reliable for the number of shared species. Further studies are needed to corroborate this conclusion. We encourage to use estimators and to provide open access to data to allow comparative assessments

Production of Se-methylselenocysteine in transgenic plants expressing selenocysteine methyltransferase

Background: It has become increasingly evident that dietary Se plays a significant role in reducing the incidence of lung, colorectal and prostate cancer in humans. Different forms of Se vary in their chemopreventative efficacy, with Se-methylselenocysteine being one of the most potent. Interestingly, the Se accumulating plant Astragalus bisulcatus (Two-grooved poison vetch) contains up to 0.6% of its shoot dry weight as Se-methylselenocysteine. The ability of this Se accumulator to biosynthesize Se-methylselenocysteine provides a critical metabolic shunt that prevents selenocysteine and selenomethionine from entering the protein biosynthetic machinery. Such a metabolic shunt has been proposed to be vital for Se tolerance in A. bisulcatus. Utilization of this mechanism in other plants may provide a possible avenue for the genetic engineering of Se tolerance in plants ideally suited for the phytoremediation of Se contaminated land. Here, we describe the overexpression of a selenocysteine methyltransferase from A. bisulcatus to engineer Se-methylselenocysteine metabolism in the Se non-accumulator Arabidopsis thaliana (Thale cress). Results: By over producing the A. bisulcatus enzyme selenocysteine methyltransferase in A. thaliana, we have introduced a novel biosynthetic ability that allows the non-accumulator to accumulate Se-methylselenocysteine and γ-glutamylmethylselenocysteine in shoots. The biosynthesis of Se-methylselenocysteine in A. thaliana also confers significantly increased selenite tolerance and foliar Se accumulation. Conclusion: These results demonstrate the feasibility of developing transgenic plant-based production of Se-methylselenocysteine, as well as bioengineering selenite resistance in plants. Selenite resistance is the first step in engineering plants that are resistant to selenate, the predominant form of Se in the environment.Danielle R Ellis, Thomas G Sors, Dennis G Brunk, Carrie Albrecht, Cindy Orser, Brett Lahner, Karl V Wood, Hugh H Harris, Ingrid J Pickering and David E Sal

Implantable Photonic Neural Probes with 3D-Printed Microfluidics and Applications to Uncaging

Advances in chip-scale photonic-electronic integration are enabling a new generation of foundry-manufacturable implantable silicon neural probes incorporating nanophotonic waveguides and microelectrodes for optogenetic stimulation and electrophysiological recording in neuroscience research. Further extending neural probe functionalities with integrated microfluidics is a direct approach to achieve neurochemical injection and sampling capabilities. In this work, we use two-photon polymerization 3D printing to integrate microfluidic channels onto photonic neural probes, which include silicon nitride nanophotonic waveguides and grating emitters. The customizability of 3D printing enables a unique geometry of microfluidics that conforms to the shape of each neural probe, enabling integration of microfluidics with a variety of existing neural probes while avoiding the complexities of monolithic microfluidics integration. We demonstrate the photonic and fluidic functionalities of the neural probes via fluorescein injection in agarose gel and photoloysis of caged fluorescein in solution and in flxed brain tissue

A Path Algorithm for Constrained Estimation

Many least squares problems involve affine equality and inequality constraints. Although there are variety of methods for solving such problems, most statisticians find constrained estimation challenging. The current paper proposes a new path following algorithm for quadratic programming based on exact penalization. Similar penalties arise in $l_1$ regularization in model selection. Classical penalty methods solve a sequence of unconstrained problems that put greater and greater stress on meeting the constraints. In the limit as the penalty constant tends to $\infty$, one recovers the constrained solution. In the exact penalty method, squared penalties are replaced by absolute value penalties, and the solution is recovered for a finite value of the penalty constant. The exact path following method starts at the unconstrained solution and follows the solution path as the penalty constant increases. In the process, the solution path hits, slides along, and exits from the various constraints. Path following in lasso penalized regression, in contrast, starts with a large value of the penalty constant and works its way downward. In both settings, inspection of the entire solution path is revealing. Just as with the lasso and generalized lasso, it is possible to plot the effective degrees of freedom along the solution path. For a strictly convex quadratic program, the exact penalty algorithm can be framed entirely in terms of the sweep operator of regression analysis. A few well chosen examples illustrate the mechanics and potential of path following.Comment: 26 pages, 5 figure

“Upload Your Impact”: Can Digital Enclaves Enable Participation in Racialized Markets?

Copyright © The Author(s) 2022. Ethno-racial minorities are often racialized and consequently excluded from various consumption contexts. Racialized market actors strive to overcome exclusion and gain participation in markets; however, these efforts are often insufficient because they cannot create equitable access to market resources, fair opportunities for voice, and empowerment to shape market practices. Our research identifies digital enclave movements as a unique means by which racialized market actors redirect their resources and mobilize digital network tools to participate in markets. Using a qualitative study of the digital enclave #MyBlackReceipt, we explore tactics supporting the formation and sustenance of digital enclaves and how they support participation in markets. We identify five tactics that racialized market actors employ to foster digital enclaves and enhance market participation: legitimizing, delimitating, vitalizing, manifesting, and bridging. Last, we provide recommendations for policymakers on how to support and foster more equitable participation of ethnic minority groups in markets while addressing the risks of radicalization and the backlash related to enclaves

Lysosomes in iron metabolism, ageing and apoptosis

The lysosomal compartment is essential for a variety of cellular functions, including the normal turnover of most long-lived proteins and all organelles. The compartment consists of numerous acidic vesicles (pH ∼4 to 5) that constantly fuse and divide. It receives a large number of hydrolases (∼50) from the trans-Golgi network, and substrates from both the cells’ outside (heterophagy) and inside (autophagy). Many macromolecules contain iron that gives rise to an iron-rich environment in lysosomes that recently have degraded such macromolecules. Iron-rich lysosomes are sensitive to oxidative stress, while ‘resting’ lysosomes, which have not recently participated in autophagic events, are not. The magnitude of oxidative stress determines the degree of lysosomal destabilization and, consequently, whether arrested growth, reparative autophagy, apoptosis, or necrosis will follow. Heterophagy is the first step in the process by which immunocompetent cells modify antigens and produce antibodies, while exocytosis of lysosomal enzymes may promote tumor invasion, angiogenesis, and metastasis. Apart from being an essential turnover process, autophagy is also a mechanism by which cells will be able to sustain temporary starvation and rid themselves of intracellular organisms that have invaded, although some pathogens have evolved mechanisms to prevent their destruction. Mutated lysosomal enzymes are the underlying cause of a number of lysosomal storage diseases involving the accumulation of materials that would be the substrate for the corresponding hydrolases, were they not defective. The normal, low-level diffusion of hydrogen peroxide into iron-rich lysosomes causes the slow formation of lipofuscin in long-lived postmitotic cells, where it occupies a substantial part of the lysosomal compartment at the end of the life span. This seems to result in the diversion of newly produced lysosomal enzymes away from autophagosomes, leading to the accumulation of malfunctioning mitochondria and proteins with consequent cellular dysfunction. If autophagy were a perfect turnover process, postmitotic ageing and several age-related neurodegenerative diseases would, perhaps, not take place

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

A proteomics analysis identifies one third of the predicted Toxoplasma gondii proteins and integrates proteomics and genomics data to refine genome annotation

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach