The Making of a Flight Feather: Bio-architectural Principles and Adaptation.

The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations. In rachidial ridges, epidermal progenitors generate cortex and medullary keratinocytes, guided by Bmp and transforming growth factor ß (TGF-ß) signaling that convert rachides into adaptable bilayer composite beams. In barb ridges, epidermal progenitors generate cylindrical, plate-, or hooklet-shaped barbule cells that form fluffy branches or pennaceous vanes, mediated by asymmetric cell junction and keratin expression. Transcriptome analyses and functional studies show anterior-posterior Wnt2b signaling within the dermal papilla controls barbule cell fates with spatiotemporal collinearity. Quantitative bio-physical analyses of feathers from birds with different flight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be achieved and may inspire future composite material designs. VIDEO ABSTRACT.

Symbiosis between Cretaceous dinosaurs and feather-feeding beetles.

Extant terrestrial vertebrates, including birds, have a panoply of symbiotic relationships with many insects and arachnids, such as parasitism or mutualism. Yet, identifying arthropod-vertebrate symbioses in the fossil record has been based largely on indirect evidence; findings of direct association between arthropod guests and dinosaur host remains are exceedingly scarce. Here, we present direct and indirect evidence demonstrating that beetle larvae fed on feathers from an undetermined theropod host (avian or nonavian) 105 million y ago. An exceptional amber assemblage is reported of larval molts (exuviae) intimately associated with plumulaceous feather and other remains, as well as three additional amber pieces preserving isolated conspecific exuviae. Samples were found in the roughly coeval Spanish amber deposits of El Soplao, San Just, and Peñacerrada I. Integration of the morphological, systematic, and taphonomic data shows that the beetle larval exuviae, belonging to three developmental stages, are most consistent with skin/hide beetles (family Dermestidae), an ecologically important group with extant keratophagous species that commonly inhabit bird and mammal nests. These findings show that a symbiotic relationship involving keratophagy comparable to that of beetles and birds in current ecosystems existed between their Early Cretaceous relatives.

MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations.

The preprocessed initial files that feed the molecular dynamics (MD) simulation packages dramatically influence the outcome of the simulations. However, the popular MD simulation packages depend, to a great extent, on the user's experience in the preparation of MD simulation systems. In this work, we present an easy-to-use tool called MDBuilder, a PyMOL plugin that assists researchers in building the starting structures for multiple popular MD simulation packages. MDBuilder is not only designed to assist MD beginners to overcome the steep learning curve by providing a menu-oriented, point-and-click user graphic interface (GUI), but also to provide an alternative way to prepare the input files for some highly scalable CHARMM force field-based MD simulation packages. The platform-independent GUI is implemented as a PyMOL plugin using the Python language, and it has been tested on Windows and Linux platforms. The source code and documentation of MDBuilder can be downloaded freely from https://github.com/HuiLiuCode/MDBuilder under the GNU General Public License.

Mitigating the impact of blood shortages in England.

The supply of blood components and products in sufficient quantities is key to any effective health care system. This report describes the challenges faced by the English blood service, NHS Blood and Transplant (NHSBT), towards the end of the COVID-19 pandemic, which in October 2022 led to an Amber Alert being declared to hospitals indicating an impending blood shortage. The impact on the hospital transfusion services and clinical users is explained. The actions taken by NHSBT to mitigate the blood supply challenges and ensure equity of transfusion support for hospitals in England including revisions to the national blood shortage plans are described. This report focuses on the collaboration and communication between NHSBT, NHS England (NHSE), Department of Health and Social Care (DHSC), National Blood Transfusion Committee (NBTC), National Transfusion Laboratory Managers Advisory Group for NBTC (NTLM), National Transfusion Practitioners Network, the medical Royal Colleges and clinical colleagues across the NHS.

Group mating in Cretaceous water striders.

Fossilized mating insects are irreplaceable material for comprehending the evolution of the mating behaviours and life-history traits in the deep-time record of insects as well as the potential sexual conflict. However, cases of mating pairs are particularly rare in fossil insects, especially aquatic or semi-aquatic species. Here, we report the first fossil record of a group of water striders in copulation (including three pairs and a single adult male) based on fossils from the mid-Cretaceous of northern Myanmar. The new taxon, Burmogerris gen. nov., likely represents one of the oldest cases of insects related to the marine environment, such as billabongs formed by the tides. It exhibits conspicuous dimorphism associated with sexual conflict: the male is equipped with a specialized protibial comb as a grasping apparatus, likely representing an adaptation to overcome female resistance during struggles. The paired Burmogerris show smaller males riding on the backs of the females, seemingly recording a scene of copulatory struggles between the sexes. Our discovery reveals a mating system dominated by males and sheds light on the potential sexual conflicts of Burmogerris in the Cretaceous. It indicates the mating behaviour remained stable over long-term geological time in these water-walking insects.

Probing calmodulin-NO synthase interactions via site-specific infrared spectroscopy: an introductory investigation.

Calmodulin (CaM) binds to a linker between the oxygenase and reductase domains of nitric oxide synthase (NOS) to regulate the functional conformational dynamics. Specific residues on the interdomain interface guide the domain-domain docking to facilitate the electron transfer in NOS. Notably, the docking interface between CaM and the heme-containing oxygenase domain of NOS is isoform specific, which is only beginning to be investigated. Toward advancing understanding of the distinct CaM-NOS docking interactions by infrared spectroscopy, we introduced a cyano-group as frequency-resolved vibrational probe into CaM individually and when associated with full-length and a bi-domain oxygenase/FMN construct of the inducible NOS isoform (iNOS). Site-specific, selective labeling with p-cyano-L-phenylalanine (CNF) by amber suppression of CaM bound to the iNOS has been accomplished by protein coexpression due to the instability of recombinant iNOS protein alone. We introduced CNF at residue 108, which is at the putative CaM-heme (NOS) docking interface. CNF was also introduced at residue 29, which is distant from the docking interface. FT IR data show that the 108 site is sensitive to CaM-NOS complex formation, while insensitivity to its association with the iNOS protein or peptide was observed for the 29 site. Moreover, narrowing of the IR bands at residue 108 suggests the C≡N probe experiences a more limited distribution of environments, indicating side chain restriction apparent for the complex with iNOS. This initial work sets the stage for residue-specific characterizations of structural dynamics of the docked states of NOS proteins.

Amber coloured plasma-Case for illustration.

INTRODUCTION: Abnormal colour of plasma is infrequently identified during processing of blood and blood components. Common reasons include haemolysis, medications or diet related. Sometimes, the aetiology is unknown. It is a dilemma for every transfusion specialist encountering this situation. Effort should be made to find the aetiology of discolouration of plasma, so that the blood donor can be suitably advised, and a decision can be made regarding the use of blood products. MATERIALS AND METHODS: We encountered two cases of orange coloured (amber coloured) plasma in our regular blood donors. All the common reasons for abnormal plasma discolouration were evaluated, including the donor's medication and diet. Spectrophotometry along with Liquid Chromatography-Mass Spectrometry (LC-MS) in both the positive and negative ion modes with literature search helped in arriving at a conclusion. RESULTS: Haemolysis was ruled out by estimation of plasma haemoglobin. Spectrophotometric analysis of the coloured plasma samples showed a peak, which was absent in normal coloured plasma. This was further investigated using Liquid Chromatography-Mass Spectrometry (LC-MS) in both the positive and negative ion modes. There was no significant difference between the coloured and normal samples in the positive ion mode. But in the negative ion mode, there was a peak observed at 110.5 and 191 m/z value in the profile of the coloured samples in comparison with the normal sample. Literature review shows the peak was corresponding to the presence of quinic acid residues-a substance found in coffee, and potentially excreted into the plasma of an individual with high coffee consumption. CONCLUSION: Reporting unusual causes associated with plasma discolouration is important. Present guidelines forbid issue of abnormal coloured blood and blood components for transfusion. Further such reports are necessary to confirm the safety of recipients receiving such units. This is the first case report to our knowledge of quinic acid discolouring blood products.

Interaction between spiders and ticks-ancient arthropod predatory behavior?

Ticks are ectoparasite vectors of pathogens affecting human and animal health worldwide. Rational integration of different control interventions including plant-derived repellents and acaricides, management of natural predators, and vaccines is required for innovative approaches to reduce the risks associated with ticks and tick-borne diseases. How tick populations are naturally controlled is always a question. Tick interactions with other arthropods including predators evolved from ancient times. In this study, Cretaceous (ca. 100 Mya) Burmese amber inclusions were identified as probably related to Compluriscutula vetulum (Acari: Ixodida: Ixodidae) tick larvae and spider silk. As illustrated in this study, ancient interactions between ticks and spiders may support arthropod predatory behavior as a natural control intervention. Rational integrative management of different tick control interventions including natural predators under a One Health perspective will contribute to effectively and sustainably reducing the risks associated with ticks and tick-borne diseases.

Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber.

BACKGROUND: Ponerine ants are almost exclusively predatory and comprise many of the largest known ant species. Within this clade, the genus Neoponera is among the most conspicuous Neotropical predators. We describe the first fossil member of this lineage: a worker preserved in Miocene-age Dominican amber from Hispaniola. RESULTS: Neoponera vejestoria sp. nov. demonstrates a clear case of local extinction-there are no known extant Neoponera species in the Greater Antilles. The species is attributable to an extant and well-defined species group in the genus, which suggests the group is older than previously estimated. Through CT scan reconstruction and linear morphometrics, we reconstruct the morphospace of extant and fossil ants to evaluate the history and evolution of predatory taxa in this island system. CONCLUSIONS: The fossil attests to a shift in insular ecological community structure since the Miocene. The largest predatory taxa have undergone extinction on the island, but their extant relatives persist throughout the Neotropics. Neoponera vejestoria sp. nov. is larger than all other predatory ant workers known from Hispaniola, extant or extinct. Our results empirically demonstrate the loss of a functional niche associated with body size, which is a trait long hypothesized to be related to extinction risk.

A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.

Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-ß (Aß42), an IDP, with and without disulfide bonds at different resolutions. Our results clearly show that the addition of a disulfide bond decreases the ß-content of Aß42; however, it increases the tendency of the monomeric Aß42 to form fibril-like conformations, explaining the various aggregation rates observed in experiments. Moreover, analysis of the monomeric Aß42 compactness, secondary structure content, and comparison between calculated and experimental chemical shifts demonstrates that all three methods provide a reasonable choice to study IDPs; however, coarse-grained approaches may lack some atomistic details, such as secondary structure recognition, due to the simplifications used. In general, this study not only explains the role of disulfide bonds in Aß42 but also provides a step-by-step protocol for setting up, conducting, and analyzing molecular dynamics (MD) simulations, which is adaptable for studying other biomacromolecules, including folded and disordered proteins and peptides.

Unveiling deception: Characterizing false amber necklace messages on Facebook.

BACKGROUND: Messages promoting the benefits of amber necklaces for children are common on social media, despite their health risks. AIM: This study characterized Facebook posts with false content about the efficacy of amber necklaces in teething. DESIGN: A sample of 500 English-language Facebook posts was analyzed by two investigators to determine the motivations, author's profile, and sentiments of posts. Latent Dirichlet Allocation topic modeling was used to identify salient terms and topics. An intertopic distance map was created to calculate the topic similarity. These data were analyzed using descriptive analysis, the Mann-Whitney U test, Cramer's V test, and multiple logistic regression models, regarding the time since initial posting and interaction metrics. RESULTS: Most posts were made by business profiles and expressed positive sentiments, with social, psychological, and financial motivations. The posts were categorized into the topics "giveaway," "healing features," and "sales." Overperforming scores and total interaction increased with time since the initial posting. Posts with links had higher overperforming scores. CONCLUSION: The findings suggest that Facebook posts about the efficacy of amber necklaces in teething are motivated by financial interests, using psychological and social mechanisms to achieve greater interaction with their target audience.

Unjustified use of amber necklaces for teething symptoms alleviation: Succinic acid release underperforms compared with natural skin bacteria production.

BACKGROUND: There is limited evidence of succinic acid release from amber necklace that justifies its biological plausibility. AIM: This study aimed to evaluate the release of succinic acid from Baltic amber beads in the presence of Staphylococcus epidermidis. DESIGN: The Baltic amber beads from the necklace were stratified according to their weight (average 0.05 g ± 0.067). Subsequently, the beads (n = 8) were submerged in 0.9% buffered saline (Control) or brain-heart infusion culture medium in the presence of a commercial strain of S. epidermidis, a resident skin bacterium incubated at 37°C for 24 h or 7 days. The samples were centrifuged, and the supernatants were analyzed by 1H Nuclear Magnetic Resonance. Multivariate analyses were adopted using the sparse partial least squares discriminant analysis method (p < .05). RESULTS: The group incubated with saline solution showed small release of succinic acid only after 7 days. In the groups with S. epidermidis, the release of succinic acid was observed in the both presence and absence of amber beads, indicating that succinic acid is a product released by bacteria. CONCLUSIONS: It was found that amber beads do not exhibit the ability to release expressive succinic acid, especially in a short period of time, which does not justify their use in infants. The most production of succinic acid is tributed to S. epidermidis.

Ancestral archaea expanded the genetic code with pyrrolysine.

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNAPyl) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNAPyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNAPyl and reveal the emergence of tRNAPyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNAPyl species with the more common G73-containing tRNAPyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

Amber Light Control of Peptide Secondary Structure by a Perfluoroaromatic Azobenzene Photoswitch.

The incorporation of photoswitches into the molecular structure of peptides and proteins enables their dynamic photocontrol in complex biological systems. Here, a perfluorinated azobenzene derivative triggered by amber light was site-specifically conjugated to cysteines in a helical peptide by perfluoroarylation chemistry. In response to the photoisomerization (trans→cis) of the conjugated azobenzene with amber light, the secondary structure of the peptide was modulated from a disorganized into an amphiphilic helical structure.

A tRNAModification-based strategy for Identifying amiNo acid Overproducers (AMINO).

Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and marker genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries of Escherichia coli and Corynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.

Too early for the ferry: The biogeographic history of the Assamiidae of southeast Asia (Chelicerata: Opiliones, Laniatores).

Opiliones (harvestmen) have come to be regarded as an abundant source of model groups for study of historical biogeography, due to their ancient age, poor dispersal capability, and high fidelity to biogeographic terranes. One of the least understood harvestman groups is the Paleotropical Assamiidae, one of the more diverse families of Opiliones. Due to a labyrinthine taxonomy, poorly established generic and subfamilial boundaries, and the lack of taxonomic keys for the group, few efforts have been undertaken to decipher relationships within this arachnid lineage. Neither the monophyly of the family, nor its exact placement in the harvestman phylogeny, have been established. Here, we assessed the internal phylogeny of Assamiidae using a ten-locus Sanger dataset, sampling key lineages putatively ascribed to this family for five of the ten markers. Our analyses recovered Assamiidae as a monophyletic group, in a clade with the primarily Afrotropical Pyramidopidae and the southeast Asian Beloniscidae. Internal relationships of assamiids disfavored the systematic validity of subfamilies, with biogeography reflecting much better phylogenetic structure than the existing higher-level taxonomy. To assess whether the Asian assamiids came to occupy Indo-Pacific terranes via rafting on the Indian subcontinent, we performed divergence dating to infer the age of the family. Our results show that Indo-Pacific clades are ancient, originating well before the Cretaceous and therefore predate a vicariant mechanism commonly encountered for Paleotropical taxa.

How to study a highly toxic protein to bacteria: A case of voltage sensor domain of mouse sperm-specific sodium/proton exchanger.

Heterologous expression systems have been used as a powerful experimental strategy to study the function of many proteins, particularly ion transporters. For this experiment, it is fundamental to prepare an expression vector encoding a protein of interest. However, we encountered problems in vector preparation of the voltage sensor domain (VSD) of murine sperm-specific Na+/H+ exchanger (sNHE) due to its severe toxicity to bacteria. We overcame the problems by insertion of an amber stop codon or a synthetic intron into the coding sequence of the VSD in the expression vectors. Both methods allowed us to express the protein of interest in HEK293 cells (combined with a stop codon suppression system for amber codon). The VSD of mouse sNHE generates voltage-dependent outward ionic currents, which is a probable cause of toxicity to bacteria. We propose these two strategies as practical solutions to study the function of any protein toxic to bacteria.

Amber Light Emitting Samarium Incorporated Barium Cerate Perovskite with 100% Color Purity for Pharmaceutical Industry.

Numerous structural and conductive properties of barium cerate (BC) make this material a promising candidate for energy storage applications. In this work, we demonstrated that BC can be proficiently functionalized by incorporating trivalent samarium ions to give rise to optical properties. Single-phased BaCeO3:Sm3+ (BCS) phosphors were synthesized by gel combustion technique followed by calcination. The crystal structure, optical properties, and prospective applications in LEDs were investigated systematically. By linking the information acquired from the diffuse reflectance spectra with that of the PL spectra, we better understood the electronic level structure and energy transfer mechanism. Fine yellow-orange luminescence with 100% color purity (CP) and lower Correlated Color Temperature (CCT) has been achieved via energization at 348 nm wavelength. The x = 0.02 Sm3+ has been identified as the optimized content for the luminescence with a quantum efficiency of 34.2%. Obtained yellow-orange coordinates (0.564, 0.435) are proximate to commercialized L3 rank amber LED (Nichia corporation). The present results signify that UV light can suitably energize the BCS phosphor to get monochromatic amber light which can be used to guard medications during manufacture and storage.

Synthesis and structure-activity relationship of kujigamberol B, a dinorlabdane diterpenoid isolated from an ancient Kuji amber.

The versatile methodology was developed for synthesizing kujigamberol B, a dinorlabdane diterpenoid isolated from the methanol extract of Kuji amber. A highly efficient intramolecular cyclization is followed by a Sonogashira-coupling reaction during the total synthesis. The synthesized compounds were evaluated for the growth-restoring activity against the mutant yeast (zds1Δ erg3Δ pdr1Δ pdr3Δ) and for the degranulation of RBL-2H3 cells. We found that in both activities, primary alcohol and secondary alcohol analogs are as active as kujigamberol B.

Determination of Anthracene Derivatives in Baltic Amber Using SERS.

The article describes the results of Raman spectroscopy and SERS for the study of fluorescent components of Baltic amber via the extraction method. Using SERS, it was possible to confirm the presence of anthracene derivatives in amber: tetracene and benzanthracene. It has been shown that SERS methods are effective for the detection of aromatic compounds; they increase the registered Raman signal and make it possible to identify peaks characteristic of the compounds under study. By combining experimental methods with DFT simulations, anthracene derivatives were modeled and confirmed to be present in the structure of Baltic amber. A combination of the proposed methods can be used to distinguish between different types of amber and isolate the necessary amber components. The obtained results are promising for compiling spectral maps of ambers for their possible classification by their place of origin.