Musculoskeletal morphology of the pelvis and pelvic fins in the lungfish Protopterus annectens

The West African lungfish (Protopterus annectens) performs benthic, pelvic fin‐driven locomotion with gaits common to tetrapods, the sister group of the lungfishes. Features of P. annectens movement are similar to those of modern tetrapods and include use of the distal region of the pelvic fin as a “foot,” use of the fin to lift the body above the substrate and rotation of the fin around the joint with the pelvis. In contrast to these similarities in movement, the pelvic fins of P. annectens are long, slender structures that are superficially very different from tetrapod limbs. Here, we describe the musculoskeletal anatomy of the pelvis and pelvic fins of P. annectens with dissection, magnetic resonance imaging, histology and 3D‐reconstruction methods. We found that the pelvis is embedded in the hypaxial muscle by a median rostral and two dorsolateral skeletal projections. The protractor and retractor muscles at the base of the pelvic fin are fan‐shaped muscles that cup the femur. The skeletal elements of the fin are serially repeating cartilage cylinders. Along the length of the fin, repeating truncated cones of muscles, the musculus circumradialis pelvici, are separated by connective tissue sheets that connect the skeletal elements to the skin. The simplicity of the protractor and retractor muscles at the base of the fin is surprising, given the complex rotational movement those muscles generate. In contrast, the series of many repeating segmental muscles along the length of the fin is consistent with the dexterity of bending of the distal limb. P. annectens can provide a window into soft‐tissue anatomy and sarcopterygian fish fin function that complements the fossil data from related taxa. This work, combined with previous behavioral examination of P. annectens, illustrates that fin morphologies that do not appear to be capable of walking can accomplish that function, and may inform the interpretation of fossil anatomical evidence. J. Morphol. 275:431–441, 2014. © 2013 Wiley Periodicals, Inc.     

Molecular weight and symmetry of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

The molecular weight and polypeptide chain stoichiometry of the native pyruvate dehydrogenase multienzyme complex from Escherichia coli were determined by independent techniques. The translational diffusion coefficient (D^o_20,w) of the complex was measured by laser light intensity fluctuation spectroscopy and found to be 0.90 (±0.02) × 10^?11m²/s. When this was combined in the Svedberg equation with the measured sedimentation coefficient (s^o_20,w = 60.2 (±0.4) S) and partial specific volume ($\text{v}\text{?}\text{= 0.735 (±0.01)}\text{ml/g}$), the molecular weight of the intact native complex was calculated to be 6.1 (±0.3) × 10⁶. The polypeptide chain stoichiometry (pyruvate decarboxylase: lipoate acetyltransferase: lipoamide dehydrogenase) of the same sample of pyruvate dehydrogenase complex was measured by the radioamidination technique of Bates et al. (1975) and found to be 1.56:1.0:0.78.From this stoichiometry and the published polypeptide chain molecular weights estimated by sodium dodecyl sulphate/polyacrylamide gel electrophoresis, a minimum chemical molecular weight of 283,000 was calculated. This structure must therefore be repeated approximately 22 times to make up the native complex, a number which is in good agreement with the expected repeat of 24 times if the lipoate acetyltransferase core component has octahedral symmetry. It is consistent with what appears in the electron microscope to be trimer-clustering of the lipoate acetyltransferase chains at the corners of a cube. It rules out any structure based on 16 lipoate acetyltransferase chains comprising the enzyme core.The preparation of pyruvate dehydrogenase complex was polydisperse: in addition to the major component, two minor components with sedimentation coefficients (s^o_20,w) of 90.3 (±0.9) S and 19.8 (±0.3) S were observed. Together they comprised about 17% of the total protein in the enzyme sample. Both were in slowly reversible equilibrium with the major 60.2 S component but appeared to be enzymically active in the whole complex reaction. The faster-sedimenting species is probably a dimer of the complex, whereas the slower-sedimenting species has the properties of an incomplete aggregate of the component enzymes of the complex based on a trimer of the lipoate acetyltransferase chain.     

SARS-CoV-2 variants reveal features critical for replication in primary human cells

Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 [COVID-19]) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.

SARS-CoV-2 variants have appeared throughout the emergence of the current COVID-19 pandemic. In this study, characterization of a panel of infectious SARS-CoV-2 isolates in primary human respiratory cells allows the identification of important sequence features that contribute to virus replication.     

Optimization of Single- and Dual-Color Immunofluorescence Protocols for Formalin-Fixed,Paraffin-Embedded Archival Tissues

Performance of immunofluorescence staining on archival formalin-fixed paraffin-embedded human tissues is generally not considered to be feasible, primarily due to problems with tissue quality and autofluorescence. We report the development and application of procedures that allowed for the study of a unique archive of thymus tissues derived from autopsies of individuals exposed to atomic bomb radiation in Hiroshima, Japan in 1945. Multiple independent treatments were used to minimize autofluorescence and maximize fluorescent antibody signals. Treatments with NH₃/EtOH and Sudan Black B were particularly useful in decreasing autofluorescent moieties present in the tissue. Deconvolution microscopy was used to further enhance the signal-to-noise ratios. Together, these techniques provide high-quality single- and dual-color fluorescent images with low background and high contrast from paraffin blocks of thymus tissue that were prepared up to 60 years ago. The resulting high-quality images allow the application of a variety of image analyses to thymus tissues that previously were not accessible. Whereas the procedures presented remain to be tested for other tissue types and archival conditions, the approach described may facilitate greater utilization of older paraffin block archives for modern immunofluorescence studies.     

Vulnerability of macronutrients to the concurrent effects of enhanced temperature and atmospheric pCO<Subscript>2</Subscript> in representative shelf sea sediment habitats

Fundamental changes in seawater carbonate chemistry and sea surface temperatures associated with the ocean uptake of anthropogenic CO₂ are accelerating, but investigations of the susceptibility of biogeochemical processes to the simultaneous occurrence of multiple components of climate change are uncommon. Here, we quantify how concurrent changes in enhanced temperature and atmospheric pCO₂, coupled with an associated shift in macrofaunal community structure and behavior (sediment particle reworking and bioirrigation), modify net carbon and nutrient concentrations (NH₄-N, NO_x-N, PO₄-P) in representative shelf sea sediment habitats (mud, sandy-mud, muddy-sand and sand) of the Celtic Sea. We show that net concentrations of organic carbon, nitrogen and phosphate are, irrespective of sediment type, largely unaffected by a simultaneous increase in temperature and atmospheric pCO₂. However, our analyses also reveal that a reduction in macrofaunal species richness and total abundance occurs under future environmental conditions, varies across a gradient of cohesive to non-cohesive sediments, and negatively moderates biogeochemical processes, in particular nitrification. Our findings indicate that future environmental conditions are unlikely to have strong direct effects on biogeochemical processes but, particularly in muddy sands, the abundance, activity, composition and functional role of invertebrate communities are likely to be altered in ways that will be sufficient to regulate the function of the microbial community and the availability of nutrients in shelf sea waters.     

Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding

Nigeria is the world’s largest cassava producer, hosting a diverse array of cassava farmers and processors. Cassava breeding programs prioritize “common denominator” traits in setting breeding agendas, to impact the largest possible number of people through improved varieties. This approach has been successful, but cassava adoption rates are less than expected, with room for improvement by integrating traits in demand by farmers and processors. This paper aims to inform breeding priority setting, by examining trait and varietal preferences of men and women cassava farmer/processors. Men and women in eight communities in Southwest and Southeast Nigeria were consulted using mixed methods. Women and men had significantly different patterns of cassava use in the Southwest. Fifty-five variety names were recorded from the communities demonstrating high genetic diversity maintained by growers, especially in the Southeast. High yield, early maturity, and root size were most important traits across both regions, while traits women and men preferred followed gender roles: women prioritized product quality/cooking traits, while men placed higher priority on agronomic traits. Trait preference patterns differed significantly between the Southeast and Southwest, and showed differentiation based on gender. Patterns of access to stem sources were determined more by region and religion than gender.