SpykProps: an imaging pipeline to quantify architecture in unilateral grass inflorescences

BACKGROUND

Inflorescence properties such length, spikelet number, and their spatial distribution across the rachis, are fundamental indicators of seed productivity in grasses and have been a target of selection throughout domestication and crop improvement. However, quantifying such complex morphology is laborious, time-consuming, and commonly limited to human-perceived traits. These limitations can be exacerbated by unfavorable trait correlations between inflorescence architecture and seed yield that can be unconsciously selected for. Computer vision offers an alternative to conventional phenotyping, enabling higher throughput and reducing subjectivity. These approaches provide valuable insights into the determinants of seed yield, and thus, aid breeding decisions.

RESULTS

Here, we described SpykProps, an inexpensive Python-based imaging system to quantify morphological properties in unilateral inflorescences, that was developed and tested on images of perennial grass (Lolium perenne L.) spikes. SpykProps is able to rapidly and accurately identify spikes (RMSE < 1), estimate their length (R2 = 0.96), and number of spikelets (R2 = 0.61). It also quantifies color and shape from hundreds of interacting descriptors that are accurate predictors of architectural and agronomic traits such as seed yield potential (R2 = 0.94), rachis weight (R2 = 0.83), and seed shattering (R2 = 0.85).

CONCLUSIONS

SpykProps is an open-source platform to characterize inflorescence architecture in a wide range of grasses. This imaging tool generates conventional and latent traits that can be used to better characterize developmental and agronomic traits associated with inflorescence architecture, and has applications in fields that include breeding, physiology, evolution, and development biology.

Recovery after chronic stress within spatial reference and working memory domains: correspondence with hippocampal morphology

Chronic stress results in reversible spatial learning impairments in the Morris water maze that correspond with hippocampal CA3 dendritic retraction in male rats. Whether chronic stress impacts different types of memory domains, and whether these can similarly recover, is unknown. This study assessed the effects of chronic stress with and without a post-stress delay to evaluate learning and memory deficits within two memory domains, reference and working memory, in the radial arm water maze (RAWM). Three groups of 5-month-old male Sprague-Dawley rats were either not stressed [control (CON)], or restrained (6 h/day for 21 days) and then tested on the RAWM either on the next day [stress immediate (STR-IMM)] or following a 21-day delay [stress delay (STR-DEL)]. Although the groups learned the RAWM task similarly, groups differed in their 24-h retention trial assessment. Specifically, the STR-IMM group made more errors within both the spatial reference and working memory domains, and these deficits corresponded with a reduction in apical branch points and length of hippocampal CA3 dendrites. In contrast, the STR-DEL group showed significantly fewer errors in both the reference and working memory domains than the STR-IMM group. Moreover, the STR-DEL group showed better RAWM performance in the reference memory domain than did the CON group, and this corresponded with restored CA3 dendritic complexity, revealing long-term enhancing actions of chronic stress. These results indicate that chronic stress-induced spatial working and reference memory impairments, and CA3 dendritic retraction, are reversible, with chronic stress having lasting effects that can benefit spatial reference memory, but with these lasting beneficial effects being independent of CA3 dendritic complexity.

Histopathological alterations and induction of cytochrome P-450 1A in the liver and gills of the gilthead seabream (Sparus aurata) exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

The toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been demonstrated in the seabream Sparus aurata specimens. Liver presented hepatocytic alterations, with an increase of lipid droplets and glycogen granules. Ultrastructural modifications of hepatocytes included RER fractionation, glycogen augmentation, as well as a rise in the number of lipid droplets, vacuoles and secondary lysosomes. In the gills, secondary lamellar epithelium showed hyperplasia, hypertrophy and lamellar fusion on the edge of the filaments. At the end of the exposure period (1 pg1(-1) TCDD for 20 days), some organelles in epithelial cells of the secondary lamellae and the tubular system of the chloride cells appeared altered. In the liver of TCDD-exposed specimens, immunoreactive cytochrome P-450 1A was concentrated close to the cytoplasmic and nuclear membranes, and positive granules were also evident throughout cytoplasm of the hepatocytes. Significant cytochrome P-450 staining was especially evident in endothelium of the hepatic vascular system. At the beginning of the exposure (1 pg 1(-1) TCDD, for 5 and 10 days), cytochrome P-450 immunostaining was observed in the cytoplasm of scarce hepatic cells and after 20 days of treatment, specific immunostained cytoplasmic granules were detected in most hepatocytes. In gills of TCDD-treated specimens, pillar-endothelial cells showed a cytochrome P-450 1A immunostaining concentrated close to the base of gill filaments and dispersed through the gill lamellae. There was also significant cytochrome staining of the endothelium of the branchial vascular system. However, no cytochrome immunoreactivity was observed in epithelial-respiratory cells.

Immunohistochemical distribution of cytochrome P4501A in larvae and fingerlings of the Siberian sturgeon, Acipenser baeri

In this paper we investigate by means of immunohistochemistry, the tissue distribution of constitutive cytochrome P4501A (CYPIA), from hatching until 30 days posthatching in developing Siberian sturgeon, Acipenser baeri. For this purpose, a polyclonal (BN-1) antiserum developed against a conservative sequence of piscine CYP1A and a monoclonal (C10-7) antiserum directed against cod CYP1A were used on paraffin-embedded samples. From hatching onwards, distinct CYP1A immunoreactivity was distinctly observed in the following tissues and cells: envelope of oil droplets, matrix and syncytium of the yolk-sac, sinusoids, biliary epithelial cells and hepatocytes. In the digestive tract, buccopharyngeal, oesophageal, gastric and intestinal epithelia, as well as the cytoplasm and brush border of enterocytes were CYP1A-positive. Interestingly, gastric glands and melanin-plug present within lumen of the digestive system were strongly immunoreactive. Kidney (epithelia of renal tubules), gills (pillar and endothelial cells), skin (epithelial cells), muscle fibres of heart and eye (retina) were positive. In brain, we observed a strong CYP1A staining in the developing telencephalon and especially in olfactory system, as well as in those nerve fibres running ventrally toward the posterior brain. A strong CYP1A staining was observed in vascular endothelia of all organs/tissues, especially in the liver. In general, the intensity of CYP1A immunostaining increased during larval development, suggesting besides its known metabolic function (endogenous and/or exogenous), a possible participation of this heme-protein in control of cell division, regulation of growth and differentiation.

Immunocytochemical distribution of cytochrome P4501A (CYP1A) in developing gilthead seabream, Sparus aurata

CYP1A is a major inducible enzyme in the metabolism of xenobiotic substrates. In this paper we investigate by means of immunohistochemistry, the tissue distribution of constitutive cytochrome P4501A (CYP1A) during the period of endogenous nutrition (from hatching until day 4) in developing gilthead seabream, Sparus aurata larvae. For this purpose, a polyclonal antiserum (BN-1, Biosense Laboratories) directed against conserved piscine CYP1A sequences was used on paraffin-embedded sections from seabream larvae. From hatching onward, CYP1A immunoreactivity was observed in the following tissues and cells: syncytial, oil-globule envelopes and matrix of the yolk-sac, kidney (epithelia of renal tubules), cardiac muscle cells, skin epidermal cells, troncal musculature, enterocytes of different intestinal regions, goblet cells of the bucco-pharyngeal region, gill epithelial cells and the endothelia of the vascular system of various tissues (especially from liver and brain). Moreover, eye (retina), olfactory epithelium and some positive nerve fibers located in the proximity of the olfactory bulbs and running ventrally toward the posterior brain were strongly CYP1A immunoreactive. In general, the intensity of immunostaining increased with larval development.

Functional complementation of the radiation-sensitive mutant M10 cell line by human chromosome 5

The mouse lymphoma (L5178Y) cell mutant M10 is defective in rejoining DNA double-strand breaks and is hypersensitive to ionizing radiation. The introduction of human chromosome 5 into M10 cells by microcell mediated chromosome transfer complemented the ionizing-radiation hypersensitivity defect of this cell line. The presence of chromosome 5 in the microcell hybrids was shown using PCR with chromosome-specific primers and fluorescence in situ hybridization. From this data we conclude that the gene that corrects the radiation hypersensitivity of M10 cells is located on chromosome 5 and tentatively assigned to the 5q14 to 5pter region. We designate this gene XRCC4L.

Migratory behaviors of alveolar macrophages during the alveolar clearance of light to heavy burdens of particles

We investigated the unstimulated and stimulated migratory activities of lavaged alveolar macrophages (AMs) in vitro over the course of alveolar clearance of three different mass lung burdens of microspheres. Our intent was to uncover potentially important relationships between the migratory behaviors of the AM and the retention kinetics of particles. Groups of adult, male Fischer-344 rats were intratracheally instilled with approximately 86 micrograms (low burden, LB), approximately 1 mg (medium burden, MB), or approximately 3.7 mg (high burden, HB) of polystyrene microspheres (2.13 microns diameter), or with carrier vehicle (phosphate buffered saline, PBS) alone. The lung retention kinetics of the particles were determined over an approximately 170 day period. On days 14, approximately 57, and approximately 85, lavaged AMs were assessed for their abilities to migrate through 5-microns pore membranes in response to inactivated rat serum (unstimulated condition) and yeast-activated rat serum (stimulated condition). The retention characteristics of the three burdens could be satisfactorily described by two-component, negative exponential equations. The kinetics of retention of the LB and MB were similar, although some evidence indicated the MB slightly retarded the lung clearance process. Deposition of the HB resulted in more marked prolongations of both the early, more rapid, and the slower, longer term components of alveolar clearance. The unstimulated migration indices of AMs from the particle-instilled lungs were generally not significantly different from those of AMs from PBS-instilled lungs except for a significant increase in the migration indices of LB AMs at the last assay time. The stimulated migration indices of MB and HB AMs were significantly decreased on assay days 14 and approximately 57. On day approximately 85, however, the migration indices of LB, MB, and HB AMs were all increased above the PBS AMs. Comparisons of the frequency distributions of particles in the unstimulated and stimulated AM that migrated to those in corresponding parent AM populations consistently indicated a preferential migration of particle-free AMs and of AMs with lesser loads of microspheres. The overall results of this study suggest that the unstimulated and stimulated migratory activities of particle-laden AMs are depressed in vitro. Our results also suggest that the migratory activities of generally particle-free AMs may be enhanced over a prolonged period of time following the deposition of particles in the lung.