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Biology subjects

Beyer, N.

Publications and source records attributed to Beyer, N..

2 recordsLinked to original sources

Deep Learning-Based Methods for Automated Estimation of Insect Length, Volume, and Biomass

We present InsectMorphoAI, an open-source, user-friendly software package that automates the measurement of insects from 2D images. The software addresses the need for high-throughput, non-invasive alternatives to laborious and often destructive manual measurement methods. InsectMorphoAI provides two analysis modes: a rapid, general-purpose method using oriented bounding boxes for linear length estimation across diverse taxa, and a high-precision, taxon-specific instance segmentation method for detailed curvilinear length, volume, and biomass estimation. We demonstrate the softwares accuracy, showing that the volume estimates from the segmentation module are strongly correlated with dry weight (R = 0.907), and the general length module achieves a mean absolute error corresponding to ~2.3% of the average specimen length. InsectMorphoAI is distributed with a graphical user interface and is freely available, with straightforward installation via a Docker container or a native Python environment. By streamlining data acquisition, InsectMorphoAI facilitates the integration of detailed trait data into large-scale ecological research, from biodiversity monitoring to functional trait analysis.

bioinformatics↗

Experimental and theoretical aspects of Golden Gate Assembly assays

Molecular cloning, a routine yet essential technique, relies heavily on efficient ligation, which can be significantly improved using Golden Gate Assembly (GGA). A key component of GGA is the use of type IIS enzymes, which uniquely cleave downstream of their recognition sequences to generate various overhangs, including non-palindromic ones. Recent advancements in GGA include the development of newly engineered enzymes with enhanced activity. Additionally, high-throughput GGA assays, which allow for the simultaneous study of all possible overhangs, have identified optimal GGA substrates with high efficiencies and fidelities, greatly facilitating the design of complex assemblies. Interestingly, these assays reveal unexpected correlations between ligation efficiencies and overhang stabilities. One hypothesis for this observation is that newly hydrolyzed DNA fragments with strong overhangs can readily re-ligate, thereby slowing down the overall process. In this paper, we employ a combination of gel electrophoresis and numerical calculations to test this hypothesis, ultimately determining that it does not hold true under the conditions established by conventional GGA assays. Using an assembly of 10 fragments, we demonstrate that strong overhangs yield higher GGA efficiency, while weak overhangs result in lower efficiency. These findings enable us to propose optimal overhangs for efficient GGA assays, significantly increasing yield.

molecular biology↗