From buds to shoots: insights into grapevine development from the Witch's Broom bud sport.

BACKGROUND: Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch's Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch's Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch's Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets. RESULTS: The Dakapo and Merlot cases of Witch's Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch's Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968-974 unique genetic mutations in our two Witch's Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch's Broom impacting the gene GSVIVG01008260001. CONCLUSIONS: The Witch's Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch's Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and Ravaz index.

Annual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were collected at the beginning (1995 to 1999) and end (2017 to 2020) of the lifetime of a vineyard initially planted in 1991 and removed in 2021. X-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number using a negative exponential model. Early and late wood ring widths, cambium width, and scion trunk radius were correlated with 27 traits. Modeling of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay of later rings, consistently shortening ring width throughout the lifetime of the vine. Ravaz index, juice pH, photosynthetic assimilation and transpiration rates, and instantaneous water use efficiency are correlated with scion trunk radius. Ultimately, our research indicates that rootstocks modulate secondary growth over years, altering physiology and agronomic traits. Rootstocks act in similar but distinct ways from climate to modulate ring width, which borrowing techniques from dendrochronology, can be used to monitor both genetic and environmental effects in woody perennial crop species.

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography.

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (µCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30-90 µm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

The shape of things to come: Topological data analysis and biology, from molecules to organisms.

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features-connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub-disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data-driven era where the meaningful interpretation of large data sets is a limiting factor.

Transitioning a Nonclinical House Administrator to a Nurse-Led Hospital Operations Role.

Nurse leaders must utilize diverse operational skills in today's healthcare delivery system. Thus, the purposes of this article are to describe 1 institution's experience in expanding the role of a nonclinical house administrator to a nurse-led Hospital Operations Administrator team. The skills reflective of the American Organization of Nurse Executives competencies needed to successfully implement the newly configured role are discussed. The expansion of this role has been beneficial in showcasing the unique contributions of nurse leaders.

Cerebrospinal fluid flow in foramen magnum: temporal and spatial patterns at MR imaging in volunteers and in patients with Chiari I malformation.

PURPOSE: To measure spatial and temporal variations in cerebrospinal fluid (CSF) flow through the cardiac cycle and throughout the subarachnoid space at magnetic resonance (MR) imaging in volunteer subjects with no known neurologic or spinal problems and in patients with Chiari I malformation. MATERIALS AND METHODS: A cardiac-gated phase-contrast MR technique was used to acquire images at 14 time points evenly spaced through the cardiac cycle in 10 volunteers and eight patients with Chiari I malformation. Instantaneous CSF velocities were displayed as temporal and spatial plots and examined for homogeneity, differences between flow anterior and flow posterior to the spinal cord, synchronous bidirectional flow, and equivalence of the caudad flow and craniad flow in each voxel. Indexes for flow homogeneity, synchronous bidirectional flow, and preferential flow direction were calculated, and differences between the patient and volunteer groups were tested for significance with a t test of the means. RESULTS: In volunteers, diastolic velocity peaked in two regions in the anterior paramedial subarachnoid space. Patients had greater inhomogeneity of flow than volunteers. They had substantially increased flow (jets) in the anterior paramedial locations. Synchronous bidirectional flow was seen in six of the patients and in none of the volunteers. Cephalad flow in the jets or nodes (P =.05), proportion of cephalad and caudad flow in the anterior compartment (P <.005 for both), and the fraction of voxels with flow directionality (P =.03) differed significantly between patients and volunteers. CONCLUSION: CSF flow in symptomatic patients with Chiari I malformation, unlike that in volunteer subjects, is characterized by flow jets, regions with a preponderance of flow in one direction, and synchronous bidirectional flow.

Role of the corpus callosum in functional connectivity.

BACKGROUND AND PURPOSE: Regional cerebral blood flow fluctuates synchronously in corresponding brain regions between the hemispheres. This synchrony implies neuronal connections between brain regions. The synchrony of blood flow changes is defined operationally as functional connectivity. Our purpose was to measure functional connectivity in patients with corpus callosal agenesis, in whom the interhemispheric connectivity is hypothetically diminished. METHODS: In three patients with agenesis of the corpus callosum, functional MR imaging was performed while patients performed text-listening and finger-tapping tasks. Functional images were also acquired while the patients performed no specific task (resting state). Regions of activation temporally correlated with the performance of the tasks were identified by cross-correlating the task data with a reference function. Voxel clusters (seed voxels) that corresponded to regions of activation in the task-activation data set were selected in the resting data set. All the voxels in the resting 3D data set that had a correlation coefficient exceeding 0.4 were identified. The number of these voxels in the ipsilateral and contralateral hemispheres was tabulated. RESULTS: In all patients, technically adequate functional MR and functional connectivity MR maps were obtained. For both tasks, activation was found in both hemispheres. For all of the seed voxels, significantly more functionally connected voxels were found in the ipsilateral hemisphere than in the contralateral hemisphere. For most seed voxels, no functionally connected voxels were found in the contralateral hemisphere. CONCLUSION: Interhemispheric functional connectivity in the motor and auditory cortices is diminished in patients with agenesis of the corpus callosum compared with that of healthy subjects.

Comparison of independent component analysis and conventional hypothesis-driven analysis for clinical functional MR image processing.

BACKGROUND AND PURPOSE: With independent component analysis (ICA), regions of activation can be identified on functional MR (fMR) images without a priori knowledge of expected hemodynamic responses. The purpose of this study was to compare the results of fMR imaging data processed with spatial ICA with results obtained with conventional hypothesis-driven analysis. METHODS: Eleven patients with focal cerebral lesions and one with agenesis of the corpus callosum were enrolled. Each patient performed text-listening, finger-tapping, and word-generation tasks. Conventional activation maps were generated by fitting time courses of each voxel to a boxcar reference function. Maps were created from the same image data with ICA techniques. To compare the maps, a concurrence ratio (CR) (number of voxels activated on both maps to number of voxels activated on either map) was calculated. RESULTS: In the ICA analysis, maps with appropriate spatial and temporal features for auditory, sensorimotor, or language cortices were identified in most patients. Images processed with ICA resembled images processed with conventional means. In patients who moved or performed the task incorrectly, ICA produced a map that resembled the expected activation pattern but differed from the conventional image. CRs averaged 70% for all comparisons in the 12 patients. CONCLUSION: fMR imaging maps for auditory, sensorimotor, and language tasks produced with ICA and conventional techniques were similar in most cases. Differences were consistent with the particular characteristics of the method. In data sets corrupted by motion or incorrect task performance, ICA may produce more accurate maps.