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Three-dimensional CAD model of the robotic system used for acquiring samples from bacterial swarms

This CAD model shows the robotic sampling system that was used in the scientific article "Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations" by the following authors: Hannah Jeckel*, Kazuki Nosho*, Konstantin Neuhaus, Alasdair D. Hastewell, Dominic J. Skinner, Dibya Saha, Niklas Netter, Nicole Paczia, Jörn Dunkel, Knut Drescher. The symbol "*" indicates an equal contribution.  The CAD model consists of 81 individual files in IPT or IAM format, which need to be loaded together into a AutoDesk Inventor to be viewed. We used AutoDesk Inventor 2021 to create and view this CAD model.

opencc-by-4.0Apr 2023View details →

Figure 1 in Length-weight relationship, sex ratio, and diet of three fish species (Actinopterygii: Teleostei) in streams of the Pomba River basin, Paraíba do Sul river drainage, Southeastern Brazil

Figure 1. Volumetric frequency (Vi%) of food items identified in the diet of D. intermedius (A), A. paraibae (B) and H. punctatus (C) in streams in the Pomba River basin, Brazil, from October to December 2018.

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Three-dimensional mandibular kinematics of mastication in the marsupial Didelphis virginiana

Didelphis virginiana (the Virginia opossum) is often used as an extant model for understanding feeding behavior in Mesozoic mammaliaforms, primarily due to their morphological similarities, including an unfused mandibular symphysis and tribosphenic molars. However, the 3D jaw kinematics of opossum chewing have not yet been fully quantified. We used biplanar videofluoroscopy and the X-Ray Reconstruction of Moving Morphology workflow to quantify mandibular kinematics in four wild-caught opossums feeding on hard (almonds) and soft (cheese cubes) foods. These data were used to test hypotheses regarding the importance of roll versus yaw in chewing by early mammals, and the impact of food material properties (FMPs) on jaw kinematics. The magnitude of roll exceeds that of yaw, but both are necessary for tooth-tooth or tooth-food-tooth contact between complex occlusal surfaces. We confirmed the utility of the four vertical kinematic gape cycle phases identified in tetrapods but we further defined two more in order to capture non-vertical kinematics. Statistical tests support the separation of chew cycle phases into two functional groups: occlusal and non-occlusal phases. The separation of slow close into two (occlusal) phases gives quantitative kinematic support for the long-hypothesized multifunctionality of the tribosphenic molar.

opencc-zeroAug 2023View details →

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Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species

Infection tolerance in rodents was examined by injecting single-dose lipopolysaccharide (LPS) to induce inflammation in Peromyscus leucopus (LL stock), the white-footed deermouse also reservoir for Lyme disease and Mus musculus (outbred CD-1 breed), the house mouse, and Rattus norvegicus, the brown rat (Fischer strain). Reaction to LPS was analyzed in the blood of challenged rodents and compared to control animals. As natural reservoirs of zoonoses deermice show significant anti-inflammatory response as described in "An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin" (<a href="https://doi.org/10.1128/mBio.00588-21)" rel="noopener">https://doi.org/10.1128/mBio.00588-21)</a>. The project and the description of the samples are described under the following NCBI BioProjects: PRJNA975149 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149" rel="noopener">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149)</a> for mouse and deermouse and PRJNA973677 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)" rel="noopener">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)</a>. This project is a follow-up project focusing on the transcriptomic analysis of the whole blood bulk RNA-seq and further analysis of differentially expressed genes (DEG) between the treatment arm and controls. Complete fold change and false discovery rate for all three rodent species used for the current Dryad set are previously published (<a href="https://doi.org/10.7280/D1470Z">https://doi.org/10.7280/D1470Z</a>). Here we report that deermice tolerance to infection is partly due to lower expression of interferon-gamma in comparison to mice and rats.

opencc-zeroAug 2023View details →

Fig. 17–20 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 17–20. Leucopholis ratcliffei sp. nov., holotype, ♂ (UNSM). 17. Habitus, dorsal aspect.18. Metaventral process, dorsal aspect. 19. Male genitalia, dorsal aspect. 20. Male genitalia, lateral aspect.

Fig. 15–16. Leucopholis semperi Brenske, 1896. 15 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 15–16. Leucopholis semperi Brenske, 1896. 15. Neotype, ♂ (MNHN), metaventral process, dorsal aspect. 16. Nontypes, ♀♀, dorsal aspect (photograph of Brenske's non-type series from ZMHB courtesy of Dr Joachim Willers).

Fig. 7–10 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 7–10. Leucopholis bezdeki sp. nov., holotype, ♂ (PNM). 7. Habitus, dorsal aspect. 8. Metaventral process, dorsal aspect. 9. Male genitalia, dorsal aspect. 10. Male genitalia, lateral aspect.

Fig. 4–6 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 4–6. Leucopholis stainesi sp. nov., holotype, ♂ (PNM). 4. Elytron, dorsal aspect. 5. Male genitalia, dorsal aspect. 6. Male genitalia, lateral aspect.

Fig. 1–3 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 1–3. Leucopholis stainesi sp. nov., holotype, ♂ (PNM). 1. Habitus, dorsal aspect. 2. Metaventral process, dorsal aspect. 3. Elytron, anterior margin and anterior angle.

Fig. 11–14. Leucopholis semperi Brenske, 1896 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 11–14. Leucopholis semperi Brenske, 1896, neotype, ♂ (MNHN). 11. Habitus, dorsal aspect. 12. Metaventral process, dorsal aspect. 13. Male genitalia, dorsal aspect. 14. Male genitalia, lateral aspect.

Fig. 21 in Three new species of the genus Leucopholis Dejean, 1833 (Coleoptera, Scarabaeidae, Melolonthinae, Leucopholini) from the Philippines and designation of a neotype for L. semperi Brenske, 1896

Fig. 21. Geographical distribution map of genus Leucopholis Dejean, 1833 in the Philippines. (Map courtesy of Dr Sheryl A. Yap of IWEP-UPLB, Los Baños, Laguna, unpublished thesis 2004).

opencc-zeroSep 2023View details →

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Functional traits of young seedlings predict trade-offs in seedling performance in three neotropical forests

<ol> <li>Understanding the mechanisms that promote the coexistence of hundreds of species over small areas in tropical forest remains a challenge. Many tropical tree species are presumed to be functionally equivalent shade-tolerant species that differ in performance trade-offs between survival in shade and the ability to quickly grow in sunlight.</li> <li>Variation in plant functional traits related to resource acquisition is thought to predict variation in performance among species, perhaps explaining community assembly across habitats with gradients in resource availability. Many studies have found low predictive power, however, when linking trait measurements to species demographic rates.</li> <li>Seedlings face different challenges recruiting on the forest floor and may exhibit different traits and/or performance trade-offs than older individuals face in the eventual adult niche. Seed mass is the typical proxy for seedling success, but species also differ in cotyledon strategy (reserve vs photosynthetic) or other seedling traits. These can cause species with the same average seed mass to have divergent performance in the same habitat.</li> <li>We combined long-term studies of seedling dynamics with functional trait data collected at a standard developmental stage in three diverse neotropical forests to ask whether variation in coordinated suites of traits predicts variation among species in demographic performance.</li> <li>Across hundreds of species in Ecuador, Panama, and Puerto Rico, we found seedlings displayed correlated suites of leaf, stem, and root traits, which strongly correlated with seed mass and cotyledon strategy. Variation among species in seedling functional traits, seed mass, and cotyledon strategy were strong predictors of trade-offs in seedling growth and survival.</li> <li>Our findings highlight the importance of cotyledon strategy in addition to seed mass as a key component of seed and seedling biology. These results also underscore the importance of matching the ontogenetic stage of the trait measurement to the stage of demographic dynamics.</li> <li> Synthesis: With strikingly consistent patterns across three tropical forests, we find strong evidence for the promise of functional traits to provide mechanistic links between seedling form and demographic performance. </li> </ol>

FIGURE 34 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 34 Photos of localities. A) the habitat of M. flavitibius, Arailer (Armenia), rich mesophilous mountain grasslands, 2100 m asl., B) the joint habitat of M. brevis and M. flavitibius, Boghaqar (Armenia), edges of deciduous mountain forest with shrubs and grasslands, 1340–1400 m asl, C) The habitat of M. brevis, Tsghuk (Armenia). Subalpine meadows, ruderal vegetation (herbaceous legumes, Carduus) on roadsides. 2100 m asl, D) the habitat of M. aberrans, Vršac Mountains, 300 m asl., Serbia. PHOTO BY GRIGORY POPOV (A-C) AND TAMARA TOT (D).

FIGURE 33 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 33 Maximum Likelihood tree based on the General Time Reversible model constructed by MEGA version 7.0. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.9228)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 63.3530 % sites). Bootstrap support values (≥50) are shown near nodes.

FIGURE 32 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 32 Holotype of Merodon brevis, male. A) metafemur and metatibia of the left leg, lateral view, B) male genitalia, lateral view, C) metafemur and metatibia of the right leg, lateral view, D) male genitalia, ventral view.

FIGURE 30 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 30 Body parts of Merodon brevis. A) metaleg of male, lateral view, B) metaleg of female, lateral view, C) thorax of male, lateral view.

FIGURE 29 A in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 29 A) Merodon brevis, head of male, lateral view, B) M. brevis, head of female, lateral view, C) M. aberrans, antenna of male, lateral view, D) M. brevis, antenna of male, lateral view, E) M. retectus sp. nov., antenna of male, lateral view, F) M. aberrans, antenna of female, lateral view, G) M. brevis, antenna of female, lateral view, H) M. retectus sp. nov., antenna of female, lateral view. Abbreviations: x, distance from top of basoflagellomere and most prominent point of pedicel; y, width of basoflagellomere at level of base of arista.

FIGURE 26 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 26 Male genitalia of Merodon retectus sp. nov. A) epandrium, lateral view, B) epandrium, ventral view, C) hypandrium, lateral view. Abbreviations: al, anterior surstyle lobe; c, cercus; il, interior accessory lobe of posterior surstyle lobe; l, lingula; pl, posterior surstyle lobe.

FIGURE 31 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 31 Male genitalia of Merodon brevis. A) epandrium, lateral view, B) epandrium, ventral view, C) hypandrium, lateral view. Abbreviations: al, anterior surstyle lobe; c, cercus; il, interior accessory lobe of posterior surstyle lobe; l, lingula; pl, posterior surstyle lobe.

FIGURE 24 in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

FIGURE 24 Body parts of Merodon retectus sp. nov., male. A) abdomen, dorsal view, B) abdomen, lateral view, C) thorax, lateral view.