Molecular studies of cotton fiber initiation

textCotton fiber development is a fundamental biological phenomenon. In spite of its economical importance, a large proportion of cotton fiber initiation is unknown. A naked seed mutant (N1N1) was compared with its isogenic lines of cotton (Gossypium hirsutum, TM-1) using a 70-mer oligonucleotide microarray that contained 1,536 features designed from a subset of cotton fiber ESTs. Statistical analysis and quantitative RT-PCR identified 23 "fiber-associated" genes. The annotation suggested that the temporal regulation of genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. To get a large view of fiber initiation, a new cotton oligonucleotide microarray was developed containing sequences from an ovule EST library from Gossypium hirsutum L. T̲M̲-1 immature o̲vules (GH_TMO), a set from Jonathan Wendel's lab at Iowa State University, and the pilot set of oligos used for previous study. Global gene expression studies were performed with microdissected fiber initials (or epidermis) and inner ovules to investigate fiber preferentially expressed genes. Laser capture microdissection and antisense RNA (aRNA) amplification allowed us to collect fiber initials (0 DPA and 2 DPA) or epidermal layers (-2 DPA) from whole ovule tissues. The gene expression profiles of fiber initials showed up-regulation of fiber proteins, myb transcription factors, and hormonal regulators as well as trichome related factors during fiber initiation. In each developmental stage, different sets of gene categories in molecular function or biological processes were over- or under-represented, suggesting temporal regulation of genes during fiber development. One of the possible "fiber associated genes" found in microarray analyses, RD22 like gene (GhRDL), was highly enriched in the epidermis of cotton ovules during fiber initiation. The function of GhRDL was studied with the Arabidopsis trichome system which shares many similarities with fiber development. Overexpression of 35S::GhRDL into Arabidopsis thaliana Columia-0 induced seed hairs (or seed trichomes) and pRDL:GUS was localized in Arabidopsis seeds. This suggests that GhRDL plays an important role in the seed trichome development and can be a key player in cell differentiation and fiber development.Plant Biolog

Towards the Human Global Context: Does the Vision-Language Model Really Judge Like a Human Being?

As computer vision and NLP make progress, Vision-Language(VL) is becoming an important area of research. Despite the importance, evaluation metrics of the research domain is still at a preliminary stage of development. In this paper, we propose a quantitative metric "Equivariance Score" and evaluation dataset "Human Puzzle" to assess whether a VL model is understanding an image like a human. We observed that the VL model does not interpret the overall context of an input image but instead shows biases toward a specific object or shape that forms the local context. We aim to quantitatively measure a model's performance in understanding context. To verify the current existing VL model's capability, we sliced the original input image into pieces and randomly placed them, distorting the global context of the image. Our paper discusses each VL model's level of interpretation on global context and addresses how the structural characteristics influenced the results

Phytochemical analyses and inheritance of resistance to TEV (Tobacco Etch Virus) in pepper (Capsicum spp.)

Due to the character of the original source materials and the nature of batch digitization, quality control issues may be present in this document. Please report any quality issues you encounter to [email protected], referencing the URI of the item.Includes bibliographical references (leaves 44-54).Issued also on microfiche from Lange Micrographics.Peppers, Capsicum spp., were grown under 3 different locations for phytochemical analyses. They were produced in the greenhouse at College Station and under the field conditions at Uvalde and Weslaco, TX. Among the pepper samples grown in the greenhouse at College Station, Fidel, C 127, and Golden Peproncini 263 showed high beta-carotene, Sweet Jalapeǫ 82, Tropic Bell and PI 357509 had high lutein. Zeaxanthin content was relatively high in MJ 201 and Ancho at College Station. Flavonoid analyses revealed that Banana Supreme and PI 357509 contained high quercetin levels and Fidel contained high luteolin levels. Among the samples grown under field conditions at Uvalde, Grande had high beta-carotene and lutein, MJ 201 had high zeaxanthin. Flavonoid contents were highest in Banana Supreme. Banana Supreme and Jaloro showed high beta-carotene and zeaxanthin contents at Weslaco, and Orange Habanero showed high lutein. In the flavonoid analysis, PI 357509 had a high content of quercetin and Rio Grande Gold and Banana Supreme had high contents of luteolin. The pepper samples grown in the greenhouse at College Station showed relatively high amounts of carotenoids compared to the field grown samples, but there was no significant difference in the flavonoid contents. Two different F₂ populations (PI 238061þ PI 260488, and PI 238061þ Guadeloupe) were inoculated with Tobacco Etch Virus (TEV) and tested by ELISA. ELISA results were close to a 3:1 ratio for one family which support the possibility that the gene for resistance to TEV could be a single dominant gene. The imperfect segregation ratios on the other family may be due to the fact that it is derived from an interspecific cross

Investigating Designed Protein Nanocages as a Modular Platform for Synthetic Biology

Protein nanocages are abundant throughout nature, comprising many different shapes, sizes, and functions. However, despite their wide variety, these assemblies share key features, including a modifiable exterior surface, interior volume, and subunit-subunit interfaces. These characteristics, in conjunction with general stability and monodispersity, confer on nanocages an incredible capacity for synthetic biology applications. Already, both natural and designed protein nanocages have demonstrated exciting potential in therapeutics, imaging, and materials. The primary focus of the dissertation is to explore the utility of protein nanocages as modular molecular delivery platforms. In the first chapter, I briefly review prior works that have studied protein nanocages as potential molecular carriers and delivery vehicles. The most prominent natural cages featured in the literature, ranging from small ferritins to large virus-like particles, are discussed. These examples encompass applications such as small molecule loading and delivery to more complex chemical and/or genetic modifications. The emergence of designed nanocages as an alternative to evolved nanocages for synthetic biology is also discussed. However, despite these incredible advances, the general lack of specificity and modularity in protein cage-based encapsulation and delivery systems remains an ongoing challenge. In the second chapter, I present the ligand-operable cage (LOC), a new type of protein cage that can “open” in response to a specific ligand. These designs aim to address the lack of a modular nanocage platform with a target-based disassembly mechanism. Uniquely, the opening mechanism of LOCs relies on the spatial orientation of surface-fused adaptors. In this study, we fused designed ankyrin repeat proteins (DARPins) to the surface of two different nanocages, sulfur oxygenase-reductase and the previously designed T33-51 cage. We also developed two readout assays indicating successful nanocage disassembly: one based on fluorescence unquenching of an encapsulated fluorophore, and one based on a split-NanoLuc luciferase assay. In the third chapter, I discuss the design of three new cages to: 1) demonstrate the modularity of the LOC platform, and 2) explore their ability to bind cancer targets. The LOC variants, all based on the same T33-51 core, were designed to bind either BARD1, BRCA1, or KRAS, which are all prominently implicated in cancer. We modeled the overall structure of these designs and their adaptor orientations using AlphaFold-based ColabFold. We discuss the synthesis and purification of these LOC variants, characterize their assembly, and show preliminary results from target-triggered disassembly experiments. In the fourth chapter, I aim to develop a combinatorial DNA-triggered bioswitch incorporating a protein nanocage. In a prior study, a NanoLuc-Cy3 BRET-beacon was designed to turn “on” or “off” in response to an oligonucleotide (ODN) trigger. We sought to expand this existing modular bioswitch by conditionally encapsulating the target ODN (i.e., the bioswitch trigger) inside of a ligand-operable cage. In this manner, we could add an additional layer of modular control over the on-off state of the BRET-beacon. We detail the experimental scheme of this combinatorial switch, the synthesis of its components, and results from initial experiments. In conclusion, the dissertation demonstrates the utility of protein nanocages as modular platforms for synthetic biology applications. Though prior works have exceptionally leveraged evolved cages, such as ferritin, VLPs, and other nonviral cages for molecular storage and delivery, we sought to address the general lack of a target-based, modular system. To this end, we demonstrate that our first LOC designs successfully released an encapsulated cargo upon specific target-binding using fluorescent and luminescent readout assays. Furthermore, we generated additional LOC variants that aimed to bind cancer-relevant proteins. Finally, we integrated a designed nanocage with a modular DNA sensor to create a combinatorial bioswitch. Taken together, these results, in consideration of experimental challenges and future directions, have exciting implications for future synthetic biology applications using protein nanocages

Factors That Affect Suicidal Attempt Risk Among Korean Elderly Adults: A Path Analysis

Objectives: Among the Korean elderly (those 65 years of age and older), the suicide rate is 80.3/100 000 people, which is ten times higher than the Organization for Economic Cooperation and Development average. Because South Korea is rapidly becoming an aging population, this high elderly suicidal rate will only get worse. Although the size of the elderly suicide problem is quite large, previous research in South Korea has surveyed restricted areas and not the entire country. Even though the factors that affect elderly suicide are complicated, there has been little research into these influencing factors. Thus, this research uses the national survey data (Community Health Survey) that was obtained in 2009. Additionally, we analyze factors affecting elderly suicidal ideation and attempts as well as the paths of these effects. Methods: Community Health Survey data obtained by the Korea Centers for Disease Control and Prevention in 2009 was used for this study. We additionally examined the factors that affect suicide with chi-squared tests, t-tests, Pearson’s correlation test, and path analysis. Results: Depressive symptoms and suicidal ideation are the only factors that directly affect suicidal attempts. Demographic, behavioral, and physical activity factors have indirect effects on suicidal attempts. Conclusions: Depression has the strongest influence on suicidal ideation and attempts. Demographic, behavioral, and physical activity factors affect suicidal attempts mostly through depressive symptoms. In addition, there is a path that suggests that demographic, behavioral, and physical activity factors affect suicidal attempts not through depression symptoms but only through suicidal ideation. This means that the elderly who do not have depression symptoms attempt suicide according to their own situations and characteristics

Integrated Analysis of Permeability Reduction Caused by Polymer Retention for Better Understanding Polymer Transport

Polymer retention is one of the most important factors to govern polymer propagation through porous media, determining whether successful or not. The focus of previous studies has been limited to polymer concentration loss caused by the retention; not only change in polymer concentration, but also reduction in reservoir permeability is the main issue for theoretical transport study. Due to the lack of accuracy of Langmuir isotherm describing the polymer retention mechanisms, this study proposes a new type of matching interpretation method to correlate the permeability reduction factors from experiments to permeability. In order to solve the problem of poorly matching results between estimation and observation, use of nonadsorptive constant conditionally selected in matching process was made. Based on the threshold permeability reduction factors, approximate critical permeability can be calculated to which nonadsorptive constant would be applied. Results showed significant improvements in the estimation of permeability reduction for both low and high permeability cores. In addition, effects of permeability reduction on polymer transport in field scale were analyzed using the proposed matching model. Thus, not only does this interpretation method help to evaluate prediction for accurate flow behavior, but also unwanted risk can be evaluated

Efficient Path Generation and Tracking Control for Autonomous Vehicles

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