Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture.

Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic, and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell-type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response nonredundancy. Using causative gene network inference to compare the genes regulated in different cell types and during responses to nitrogen and a biotic interaction, we found that common transcriptional modules often regulate the same gene families but control different individual members of these families, specific to response and cell type. This reinforces that the activity of a gene cannot be defined simply as molecular function; rather, it is a consequence of spatial location, expression timing, and environmental responsiveness.

Transient Anomalous Diffusion MRI in Excised Mouse Spinal Cord: Comparison Among Different Diffusion Metrics and Validation With Histology.

Neural tissue is a hierarchical multiscale system with intracellular and extracellular diffusion compartments at different length scales. The normal diffusion of bulk water in tissues is not able to detect the specific features of a complex system, providing nonlocal, diffusion measurement averaged on a 10-20 µm length scale. Being able to probe tissues with sub-micrometric diffusion length and quantify new local parameters, transient anomalous diffusion (tAD) would dramatically increase the diagnostic potential of diffusion MRI (DMRI) in detecting collective and sub-micro architectural changes of human tissues due to pathological damage. In DMRI, the use of tAD parameters quantified using specific DMRI acquisition protocols and their interpretation has often aroused skepticism. Although the derived formulas may accurately fit experimental diffusion-weighted data, the relationships between the postulated dynamical feature and the underlying geometrical structure remains elusive, or at most only suggestive. This work aimed to elucidate and validate the image contrast and information that can be obtained using the tAD model in white matter (WM) through a direct comparison between different diffusion metrics and histology. Towards this goal, we compared tAD metrics extracted from pure subdiffusion (α-imaging) and super-pseudodiffusion (γ-imaging) in excised mouse spinal cord WM, together with T2 and T2* relaxometry, conventional (normal diffusion-based) diffusion tensor imaging (DTI) and q-space imaging (QSI), with morphologic measures obtained by optical microscopy, to determine which structural and topological characteristics of myelinated axons influenced tAD contrast. Axon diameter (AxDiam), the standard deviation of diameters (SD ax.diam ), axonal density (AxDens) and effective local density (ELD) were extracted from optical images in several WM tracts. Among all the diffusion parameters obtained at 9.4 T, γ-metrics confirmed a strong dependence on magnetic in-homogeneities quantified by R2* = 1/T2* and showed the strongest associations with AxDiam and ELD. On the other hand, α-metrics showed strong associations with SD ax.diam and was significantly related to AxDens, suggesting its ability to quantify local heterogeneity degree in neural tissue. These results elucidate the biophysical mechanism underpinning tAD parameters and show the clinical potential of tAD-imaging, considering that both physiologic and pathologic neurodegeneration translate into alterations of WM morphometry and topology.

Evidence for overestimation of the prevalence of malignancy in indeterminate thyroid nodules classified as Bethesda category III.

BACKGROUND: Several recent analyses of indeterminate thyroid nodules classified as Bethesda III (follicular lesion of undetermined significance) have reported considerably greater rates of malignancy than those initially reported by the Bethesda System for Reporting Cytopathology (BSRTC). These values, however, may be overestimates owing to several sources of bias, such as referral, selection, and publication biases. Our aim was to analyze the prevalence of malignancy in Bethesda III and IV thyroid nodules in a comprehensive health system less prone to institutional referral bias, excluding incidental carcinomas, and we examine the literature for publication bias. METHODS: We performed a retrospective analysis with pathologic re-review of 119 patients with Bethesda III/IV cytology undergoing surgery in a comprehensive health system by examining patient and nodule characteristics. A review of the literature was performed and analyzed for publication bias. RESULTS: The malignancy rate in resected thyroid nodules was 13% (6/48) for Bethesda III and 28% (20/71) for Bethesda IV. There were 9 of 119 patients (8%) with incidental microcarcinomas. Age <30 years was associated with an increased risk of malignancy (odds ratio, 25.8; P = .005). Sex, nodule size, and ultrasonographic features were not associated with risk of malignancy. Analysis of the literature was indicative of publication bias for Bethesda III cohorts, with reported rates positively skewed (P = .039). CONCLUSION: In a comprehensive health system, the rate of malignancy in Bethesda III nodules was similar to the range reported by the BSRTC. Recent reports of greater rates of malignancy may be attributable to institutional referral patterns, operative selection, inclusion of incidental microcarcinomas, and publication bias.

Postsplenectomy immunodepression and its implications: an underestimated problem.

The most important sequelae of splenectomy is immunity depression. This study, conducted in three phases, was aimed at confirming this clinical condition. Data from our phase 1 study clearly show that patients undergoing splenectomy for trauma are in a critical condition because of a latent immunodeficiency shown by skin tests (ST) and in vitro evaluation of the aspecific immune activity. Because the in vitro study of the unspecific immunity that we used seems to be more expensive and complicated than ST, the aim of the phase 2 study was to compare the efficacy and the limits of the two assays (ST versus in vitro study) in detecting the immunodeficiency status of the splenectomized patient. The aim of the phase 3 study was to ascertain whether postsplenectomy immunodeficiency could be a consequence of an altered equilibrium between the lymphocyte subpopulations T helper (Th)1/Th2, evaluated by serum dosage of interferon-gamma and interleukin-4.

Diagnosing and treating Sphincter of Oddi dysfunction: a critical literature review and reevaluation.

Sphincter of Oddi dysfunction is a pathologic syndrome, without considering etiology, physiopathology, or anatomic aspects of the condition. The clinical manifestations of the syndrome may be a consequence of an "organic stenosis" of the tract or a consequence of "abnormal motility" of the sphincter. Until some years ago, the gold standard technique for studying and treating this pathologic condition was endoscopic retrograde cholangiopancreatography. Two criteria for defining patients in the Milwaukee classification are related to this procedure. The Milwaukee classification was introduced to use clinical and radiologic criteria to define patients with Sphincter of Oddi dysfunction to choose the best treatment. Subsequently, great emphasis has been placed on manometry of the sphincter performed by endoscopic cannulation. The enormous increase of cholecystectomies by means of laparoscopic technique has increased the number of patients who return to their reference-surgeon with a post-cholecystectomy pain and possible Sphincter of Oddi dysfunction. The aim of this paper is to review the literature and to evaluate an up-to-date flow chart for diagnosing and treating the syndrome by using alternative diagnostic procedures that are less invasive than endoscopic retrograde cholangiopancreatography.

Contractility in vitro and mitochondrial response in small and large rabbit bowel after anastomosis.

Leakage of a large bowel anastomosis remains the most serious postoperative complication in gastrointestinal surgery. In a recent experimental study we found that surgically induced hypoxia resulted in more derangement of a variety of biochemical markers in the large bowel (LB) than in the small bowel (SB). We explored the question of whether spontaneous and agonist-induced contractility of SB and LB muscle strips was influenced by surgical procedures and how contractility was related to energetic oxidative metabolism capacity in smooth muscle mitochondria. Sixty male New Zealand rabbits were operated on under general anesthesia. Segments of ileum and colon were resected from each rabbit, and an end-to-end anastomosis was constructed. A representative subset of segments from SB (n = 14) and LB (n = 14) at time 0 was used as controls. Tracts containing an anastomosis were resected at days 2, 7, and 14 after operation. At each time point, 20 segments adjacent to the anastomosis of both SB and LB were used for tensiometric and biochemical studies. Tensiometric studies demonstrated modifications in the smooth muscle function at both the acute and chronic stages with intestinal inflammation that may contribute to surgical stress-associated abnormal motility. Biochemical data showed that the respiratory capacity of the resected LB was more impaired than that of the SB. In both SB and LB, changes in respiratory activity preceded tensiometric changes. Thus abnormalities of contractility after surgical stress are more evident in LB than SB in segments adjacent to the anastomoses. This could be the consequence of abnormal biochemical changes, as adenosine triphosphate (ATP) is required for membrane potential maintenance, calcium homeostasis, and actin-myosin interactions.