ALBERT

Description: Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.

Description: Local extinction and undetected presence are two very different biological phenomena, but they can be challenging to differentiate. Stochastic environments hamper the development of standardized monitoring schemes for wildlife, and make it more challenging to plan and evaluate the success of conservation efforts. To avoid reintroductions of species at risk that could jeopardize extant populations, managers attempting translocation events require a higher level of confidence that a failure to confirm presence represents a true absence. For many pond breeding amphibians, monitoring of the breeding population occurs indirectly through larval surveys. Larval development and successful recruitment only occurs after a sequence of appropriate environmental conditions, thus it is possible for a breeding population of adults to exist at a site but for detectability of the species to be functionally zero. We investigate how annual variability in detection influences long-term monitoring efforts of Reticulated Flatwoods Salamanders (Ambystoma bishopi) breeding in 29 wetlands in Florida. Using 8 years of historic dip net data, we simulate plausible monitoring scenarios that incorporate environmental stochasticity into estimates of detection probability. We found that annual variation in environmental conditions precluded a high degree of certainty in predicting site status for low-intensity monitoring schemes. Uncertainty was partly alleviated by increasing survey effort, but even at the highest level of sampling intensity assessed, multiple years of monitoring are required to confidently determine presence/absence at a site. Combined with assessments of habitat quality and landscape connectivity, our results can be used to identify sites suitable for reintroduction efforts. Our methodologies can be generally applied to increase the effectiveness of surveys for diverse organisms for which annual variability in detectability is known.

Description: Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Microbial enzymes are known to contribute to fermentation; however, not much is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to improve the quality, consistency, and safety of the Budu products. In this study, we collected 60 samples from 20 bottles of Budu produced by seven manufacturers. We analyzed their microbiota using V3–V4 16S rRNA amplicon sequencing when we first opened the bottle (month 0), as well as 3 and 7 months post-opening (months 3 and 7). Tetragenococcus was the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such as Staphylococcus, Acinetobacter, Halanaerobium and Bacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genus Chromobacterium at month 7. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared to Tetragenococcus-dominated samples; these two pathways are fundamental to fermentation quality and health attributes of fish sauce. Among the non-Tetragenococcus-dominated samples, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa. Our results demonstrated that the utility of 16S sequencing to assess batch variation in fermented food production. The distinct microbiota was shown to correlate with characteristic metagenome function including functions potentially related to fermented food nutrition and quality.

Description: The genus Cornus is known for its complicated taxonomy and extreme polymorphism. Currently, dogwoods are classified into four morphological groups reflected in four phylogenetic clades: blue- or white-fruited dogwoods (BW), cornelian cherries (CC), big-bracted dogwoods (BB), and dwarf dogwoods (DW). The present study is a continuation of a series of papers that started with the examination of the endocarp morphological diversity among BW species. The endocarps of 22 Cornus species were studied according to their morphology, internal structure, and sculpture; the aim was to evaluate the taxonomic importance of the examined characters and check whether endocarp differentiation supports the published phylogenies, according to which the relationships within the genus are indicated as (BW(CC(DW-BB))). Among the quantitative characters, the endocarp’s length, thickness, and width, its length/width ratio, and the number of vascular bundles on its surface were considered taxonomically important. Regarding the qualitative characters, the taxonomic significance of the stone shape, the endocarp apex and base outline, the position of vascular bundles on the endocarp surface, and the presence of the apical cavity and distinct furrow on the endocarp side walls was proved. Additionally, the uniform qualitative characters having a 100% share of a given character state were identified. Cornelian cherries and dwarf dogwoods were characterised by the presence of four uniform characters. In the big-bracted group, two uniform characters were found. Blue- or white-fruited species were the most heterogeneous, with no uniform characters. Regarding the endocarp’s internal structure, the presence of secretory cavities in the endocarp wall and in the septa, the presence of crystals in the outer endocarp, the number of cell layers in the transition sclereid zone, and the primary and secondary sculptures were found to be taxonomically significant. Additionally, the comparative analyses of dogwood endocarps found the following parameters to be useful: the germination valve thickness, the ratio of endocarp wall thickness to endocarp diameter, and the septum’s width and structure. Due to the great differentiation of the examined characters, it was difficult to verify the research hypothesis unambiguously. The calculated similarity coefficients of the endocarps’ qualitative and quantitative characters revealed the highest morphological similarity of endocarps between DW and BB groups, supporting the phylogenetic relationships based on molecular evidence. The number of vascular bundles on the endocarp surface was the character that supported this similarity the most. The similarity coefficients calculated separately for qualitative characters showed the closest similarity between groups CC-DW. However, these results do not directly reflect any of the published phylogenies.

Description: Background This study assessed the associations of metabolic obesity phenotypes with the risk of atrial fibrillation (Afib). Methods This prospective cohort study categorized Taiwanese adults according to their body mass index (BMI) and metabolic health status at baseline. We assigned the participants to the underweight (BMI 〈 18.5 kg/m2), normal weight (BMI = 18.5–23.9 kg/m2), and overweight/obesity groups (BMI ≥ 24 kg/m2). Metabolically healthy was defined as absence of hypertension, diabetes, and hyperlipidemia and the presence of healthy metabolic profiles. Results In total, 5,742 adults were included. During a median follow-up of 13.7 years, 148 patients developed Afib. Compared to the metabolically healthy normal weight group, the risk of Afib was significantly higher than those in the metabolically unhealthy overweight/obesity (hazard ratio = 2.20, 95% confidence interval [1.12–4.33]) and metabolically unhealthy normal weight groups (HR = 2.64, 95% CI [1.34–5.17]). Additionally, the point estimate suggested a 1.97-fold greater risk among the metabolically healthy overweight/obesity group, although this difference was not significant given the wide confidence interval (HR = 1.97, 95% CI [0.80–4.86]). Conclusion Our results demonstrated the relationships of metabolic health and weight regarding the risk of Afib in Taiwanese adults. The Afib risk among metabolic and obesity phenotypes is associated with a metabolically unhealthy status. A trend toward a higher Afib risk with obesity among metabolically healthy subjects was observed. However, the result was not robust and it still suggested further study.

Description: The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.

Description: Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.

Description: Sea turtles are threatened by climate change and human activity, and their global populations continue to decline sharply. The Chinese government encourages artificial breeding of sea turtles to reduce the use of wild populations. However, artificial breeding of sea turtles is still fairly difficult, and some facilities may illegally purchase wild turtle eggs and then sell incubated turtles by marketing them as artificially bred turtles, which adds another threat to an already endangered species. Therefore, it is necessary to find a reliable method to distinguish the authenticity of artificially bred individuals. In this study, we investigated a turtle farm in southern China, that contained more than 400 green turtles, which were claimed to have been bred in captivity. Parentage testing of turtles from this farm was successfully conducted using two nuclear microsatellites combined with a mitochondrial D-loop DNA marker. Genetic matching of all 19 adults and randomly selected 16 juvenile turtles revealed that none of the juvenile turtles had a matching parent combination among the adult turtles. Therefore, we speculated that the green turtles in this farm were from the wild and that their origin of birth was mainly the Sulu Sea. The methods and molecular markers used in this study could be a reference for rapid authenticity testing of green turtles in future forensic enforcement and population management.

Description: Background Radioresistance is still the major cause of radiotherapy failure and poor prognosis in patients with non-small cell lung cancer (NSCLC). Apatinib (AP) is a highly selective inhibitor of vascular endothelial growth factor receptor 2 (VEGFR2). Whether and how AP affects radiosensitivity in NSCLC remains unknown. The present study aimed to explore the radiosensitization effect of AP in NSCLC and its underlying mechanism as a radiosensitizer. Methods The NSCLC cell lines A549 and LK2 were treated with AP, ionizing radiation (IR), or both AP and IR. Expression of VEGFR2 was analyzed by western blot and RT-PCR. Cell proliferation was measured using CCK-8 and colony formation assays. Apoptosis and cell cycle distribution in NSCLC cells were analyzed by flow cytometry. Nuclear phosphorylated histone H2AX foci immunofluorescence staining was performed to evaluate the efficacy of the combination treatment. Western blot was used to explore the potential mechanisms of action. Results AP inhibited cell proliferation in a dose- and time-dependent manner. Flow cytometry analysis indicated that AP significantly increased radiation-induced apoptosis. Colony formation assays revealed that AP enhanced the radiosensitivity of NSCLC cells. AP strongly restored radiosensitivity by increasing IR-induced G2/M phase arrest. AP effectively inhibited repair of radiation-induced DNA double-strand breaks. Western blot analysis showed that AP enhanced radiosensitivity by downregulating AKT and extracellular signal-regulated kinase (ERK) signaling. Conclusion Our findings suggest that AP may enhance radiosensitivity in NSCLC cells by blocking AKT and ERK signaling. Therefore, AP may be a potential clinical radiotherapy synergist and a novel small-molecule radiosensitizer in NSCLC. Our study fills a gap in the field of anti-angiogenic drugs and radiosensitivity.

Description: The first appearance of Fusarium head blight (FHB)—and the beginning of scientific research of this disease—occurred the Far East region of Russia at the end of the 19th century. In the summer of 2019, in the Amur region, which comprises 60–70% of grain production in the Russian Far East, flooding caused a state of emergency. The quality of wheat and barley grains grown under natural conditions of FHB outbreaks, including grain infection, fungal species composition, DNA content of F. graminearum and chemotypes, and the presence of various mycotoxins, was studied. Fusarium infection rates reached extremely high percentages, 51–98%, the majority of which were F. graminearum infections. The amount of F. graminearum DNA in wheat grain samples was higher than in the barley grain samples and averaged 6.1 and 2.1 pg/ng, respectively. The content of deoxynivalenol (DON) in the wheat samples reached 13,343 ppb and in barley reached 7,755 ppb. A multilocus genotyping assay was conducted on the partially sequenced fragments of the translation elongation factor EF-1a, ammonium ligase gene, reductase gene, and 3-O-acetyltransferase gene in 29 Fusarium graminearum sensu lato strains from the grain harvested in the Amur region. All strains from the Far East region were characterized as F. graminearum sensu stricto; 70% were the 15-AcDON chemotype, while the other strains were the 3-AcDON chemotype. According to the results, after 140 years of study of FHB, we are still not very successful in controlling this disease if conditions are favorable for pathogen development. Even at present, some of the grain harvested must be destroyed, as high contamination of mycotoxins renders it unusable.