Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

Structural Features and Digestibility of Corn Starch With Different Amylose Content

In this study, the in vitro digestibility of corn starch with different amylose content was determined. The results showed that waxy corn starch (WCS) and corn starch (CS) have the highest digestibility, while high amylose corn starch (HACS) has a higher content of resistant starch (RS). Besides being related to amylose content, RS content is also closely related to particle shape, debranched fine structure, molecular structure, and semi-crystalline structure. HACS can maintain a complete particle structure after gelatinization and enzymolysis; differential scanning calorimetry showed a positive correlation between gelatinization enthalpy and RS content. As the amylose content increased, the content of fa (DP 6–12) decreased, while the content of fb2 (DP 25–36) and fb3 (DP ≥ 37) increased, which in-turn decreased the cluster polymer formed by short branch chains, and the formation of more hydrogen bonds between long chain branches improved starch stability. D, which characterizes the compactness of starch semi-crystalline structure, increased with the increase of RS content. HACS 60 with the highest RS content had a unique surface fractal structure between 7.41 < d (2π/q) < 10.58 nm, indicating that the dense structure is effective in maintaining the RS content.

Effect of the Crack Tip Bifurcation on the Plasticity-Induced Fatigue Propagation in Metallic Materials

This article deals with the influence of the crack path branching (at the micro level) on the plasticity-induced fatigue crack growth. With regard to this, a modeling by means of the finite element method was performed considering a cracked panel subjected to tension with different symmetric and asymmetric configurations of the bifurcated crack tip. The results show the appearance of a retardation effect in the growth rate of the bifurcated crack in relation to the growth rate of the fully straight crack in different cases studied, namely: (i) if the two branches of the bifurcation have different initial projected length, the propagation rate is greater at the crack tip corresponding to the long-branch than that of the short-branch, and the long-branch growth rate increases with the decrease of the initial branch angle and of the initial projected short-branch length and with the increase of the intensity of fatigue; (ii) if the two branches of the bifurcation have identical initial projected length, the retardation effect depends on the initial distance between the two bifurcated crack tips, the growth rate going up with the decrease of such a distance and with the increase of the fatigue intensity.

Evidence for Range Expansion and Origins of an Invasive Hornet Vespa bicolor (Hymenoptera, Vespidae) in Taiwan, with Notes on Its Natural Status

The invasive alien species (IAS) Vespa bicolor is the first reported hornet that has established in Taiwan and is concerning as they prey on honeybee Apis mellifera, which leads to colony losses and public concerns. Thus, the aim of this study was to assess the current status of V. bicolor abundance, dispersal, and impact and to trace the origins of Taiwan’s V. bicolor population. Our studies took place in five areas in northern to central Taiwan. We used mtDNA in the phylogenetic analyses. Field survey and ecological niche modeling (ENM) were used to understand the origins and current range of the invasive species. Two main subgroups of V. bicolor in the phylogenetic tree were found, and a clade with short branch lengths in Southeastern China and Taiwan formed a subgroup, which shows that the Taiwan population may have invaded from a single event. Evidence shows that V. bicolor is not a severe pest to honeybees in the study area; however, using ENM, we predict the rapid dispersion of this species to the cooler and hilly mountain areas of Taiwan. The management of V. bicolor should also involve considering it a local pest to reduce loss by beekeepers and public fear in Taiwan. Our findings highlight how the government, beekeepers, and researchers alike should be aware of the implications of V. bicolor’s rapid range expansion in Taiwan, or in other countries.

Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi

The zoosporic obligate endoparasites, Olpidium, hold a pivotal position to the reconstruction of the flagellum loss in fungi, one of the key morphological transitions associated with the colonization of land by the early fungi. We generated genome and transcriptome data from non-axenic zoospores of Olpidium bornovanus and used a metagenome approach to extract phylogenetically informative fungal markers. Our phylogenetic reconstruction strongly supported Olpidium as the closest zoosporic relative of the non-flagellated terrestrial fungi. Super-alignment analyses resolved Olpidium as sister to the non-flagellated terrestrial fungi, whereas a super-tree approach recovered different placements of Olpidium, but without strong support. Further investigations detected little conflicting signal among the sampled markers but revealed a potential polytomy in early fungal evolution associated with the branching order among Olpidium, Zoopagomycota and Mucoromycota. The branches defining the evolutionary relationships of these lineages were characterized by short branch lengths and low phylogenetic content and received equivocal support for alternative phylogenetic hypotheses from individual markers. These nodes were marked by important morphological innovations, including the transition to hyphal growth and the loss of flagellum, which enabled early fungi to explore new niches and resulted in rapid and temporally concurrent Precambrian diversifications of the ancestors of several phyla of fungi.

Revising transcriptome assemblies with phylogenetic information

A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.

Correlations Between Parental Lines and Indica Hybrid Rice in Terms of Eating Quality Traits

In this study, by analyzing the relationship between hybrid combinations and parental lines, we found that the eating quality traits of hybrid combinations were determined by both parents. The sterile lines determined the overall eating quality characteristics of the hybrid combinations. For the same sterile line, there were some correlations between the hybrid combinations and restorer lines in terms of taste value, rapid visco analyzer breakdown and setback values, apparent amylose content, and cooked rice hardness and stickiness. Analysis of the starch fine structure between hybrid combinations and their restorer lines demonstrated positive correlations between them in terms of short-branch amylopectin chains and amylose. Moreover, different allelic combinations of the Wx gene showed different genetic effects on the eating quality traits of hybrid rice. Overall, this study provides a framework for the development of hybrid rice with superior eating quality.

The Arterial Vascularization of the Small and Large Intestine in Adult Male Turkeys (Meleagris gallopavo)

The aim of this study was to reveal the blood supply of the intestinal tract in male adult turkey. Five healthy birds were collected from local suppliers at Baaqoba province. All birds were euthanized and their coelomic cavity was dissected. The descending aorta was cannulated and injected with colored latex, and then the course of arteries along the intestinal tract investigated. Small intestine received the blood by celiac artery, cranial and caudal mesenteric artery. Celiac was split into two branches right and left, the right branch of celiac artery supplied the proventriculus, gizzard, duodenum, pancreas, jejunum and distal part of ileum and cecum while left branch supply the stomach. The crania mesenteric artery nourished the terminal parts of duodenum, jejunum ileum and cranial part of the two ceca, on the other hand. Caudal mesenteric artery was the third artery that supplied the intestine which was short branch originated from descending aorta and divided into two groups cranial groups supplied distal part of ileum and base of ceca while the caudal groups supplied the rectum and cloaca and anastomosed with cranial mesenteric artery. Form the above results, it was concluded that the small and large intestine are nourished by the three major arteries namely Celiac, Cranial and Caudal mesenteric arteries and its branches.

Cephalometric features of connective tissue dysplasia manifestation in children and adolescents

Relevance. The high prevalence of dysplastic disorders involving connective tissue, and its negative effecton the development of dentoalveolar anomalies, carious and non-carious lesions of the teeth, periodontopathy, temporomandibular joint issues in the child population, lay the basis for improving diagnostics algorithms. Enhancing the already available standards is of greatest importance for children at the initial stages of diagnostics when evaluating the external signs of dysplastic disorders.Purpose – improving diagnostics algorithms for connective tissue dysplasia (CTD) in children in primary dental care facilities based on the evaluation of external phenotype signs and maxillofacial morphological features.Materials and methods. Depending on the external phenotype manifestations severity, as well as on laboratory, clinical and instrumental signs, the 92 children with CTD were divided into groups with mild, moderate and severe degrees of undifferentiated dysplasia. Gnathometric and biometric examinations of the maxillofacial area were performed through traditional methods, whereas the diagnosis was set following the generally accepted classifications. The diagnosis confirmation implied evaluation through cone beam computed imaging.Results. The nature and the intensity of morphofunctional disorders in the craniofacial structures (“small” stigmas) depend on the severity of connective tissue dysplastic disorders.Conclusions. The change direction vector in the facial and brain parts of cranium in children with CTD is aimed at increasing hypoplastic tendencies and dolichocephalia, proof to that being the following constitutional and morphological features: the prevalence of the vertical type of face skeleton growth over the horizontal and neutral ones; a convex face profile with a disproportionate general heights of the face skeleton; reduction of latitudinal with an increase in altitude facial parameters; a narrow short branch of the lower jaw; the upper jaw displaced downwards and forward; a decrease in the size of the apical basis of the lower dentition, the lower jaw body, as well as the height and width of the lower jaw branches.

ILS-Aware Analyses of Retroelement Insertions in the Anomaly Zone

A major shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting (ILS). Coalescence methods explicitly address this problem, but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescence methods, retroelement insertions have emerged as powerful phylogenomic markers for species tree estimation. We show that two recently proposed methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the species tree under the multispecies coalescent model, with retroelement insertions following a neutral infinite sites model of mutation. The accuracy of these and other methods for inferring species trees with retroelements has not been assessed in simulation studies. We simulate retroelements for four different species trees, including three with short branch lengths in the anomaly zone, and assess the performance of eight different methods for recovering the correct species tree. We also examine whether ASTRAL_BP recovers accurate internal branch lengths for internodes of various lengths (in coalescent units). Our results indicate that two recently proposed ILS-aware methods, ASTRAL_BP and SDPquartets, as well as the newly proposed ASTRID_BP, always recover the correct species tree on data sets with large numbers of retroelements even when there are extremely short species-tree branches in the anomaly zone. Dollo parsimony performed almost as well as these ILS-aware methods. By contrast, unordered parsimony, polymorphism parsimony, and MDC recovered the correct species tree in the case of a pectinate tree with four ingroup taxa in the anomaly zone, but failed to recover the correct tree in more complex anomaly-zone situations with additional lineages impacted by extensive incomplete lineage sorting. Camin-Sokal parsimony always reconstructed an incorrect tree in the anomaly zone. ASTRAL_BP accurately estimated branch lengths when internal branches were very short as in anomaly zone situations, but branch lengths were upwardly biased by more than 35% when species tree branches were longer. We derive a mathematical correction for these distortions, assuming the expected number of new retroelement insertions per generation is constant across the species tree. We also show that short branches do not need to be corrected even when this assumption does not hold; therefore, the branch lengths estimates produced by ASTRAL_BP may provide insight into whether an estimated species tree is in the anomaly zone.