Simulated bipolar cells in fovea of human retina

This static bipolar cell (BC) model of the human fovea is based on a number of reasonable assumptions. The human fovea is directly responsible for visual acuity and color vision. The fovea can be considered as having two parts; a central fovea with only red- and green-sensitive cones and a parafovea with blue-sensitive cones added to the other two. A cone mosaic can be precisely organized spatially into unit hexagons that specify inputs to horizontal cells (HC) and BCs. The retina up to and including BCs is piece-wise linear, i.e. at a given steady-state adapting light intensity BC outputs are linear functions of the physical image. BC centers receive inputs directly from weighted cones, while antagonistic surrounds receive inverted inputs from HCs. Appropriate optical and chromatic filtering due to the eye that are taken from human data are incorporated into the model. Chromatic aberrations are simulated by three separate point spread functions that also are taken from human data. Automatic gain control of cones is a function of intensity and wavelength of the steady adapting light.The major part of this work was done while the author was a Senior Research Associate of the National Research Council, USA     

Simulated bipolar cells in fovea of human retina

The static model developed in Part I is used to study spectral responses of C-type bipolar cells (BC). Once unique loci are adjusted to their proper wavelengths, and with a specified set of absorption spectra for cones, spectral responses of C-type BCs are dependent on only the balance between BC receptive field center and surround responses. This is true regardless of cone mosaic or BC receptive field organization. The unique yellow loci for the r-g channel is set at 576.7 nm while the unique green locus for the blue-center BC is set at 517.7 nm. A unique orange locus for a combined r-g and bl-y channels is set at 600 nm by multiplying the blue-center BC response spectra by a factor of six before adding to the r-g channel.     

A role for the chaperone Hsp70 in the regulation of border cell migration in the Drosophila ovary

Unravelling the molecular mechanisms that govern cell migration is of great importance towards understanding both normal embryogenesis and physiological and pathological processes occurring in the adult. Migration of border cells (BCs) during Drosophila oogenesis provides a simple and attractive model in which to address this problem. Here, we show that the molecular chaperone Hsp70 is required for BC migration. Thus, BCs lacking all Hsp70 genes present in the fly genome fail to reorganize their actin cytoskeleton, resulting in migration defects. Similar defects are found when the Hsp70 co-chaperone DnaJ-1, the Drosophila homolog of the human Hsp40, is overexpressed specifically in BCs. In addition, we provide biochemical and genetic evidence for an interaction between DnaJ-1 and PDGF/VEGF receptor (PVR), which is also required for actin-mediated BC migration. Furthermore, our results showing that PVR also interacts genetically with Hsp70 suggest that a mechanism by which the DnaJ-1/Hsp70 chaperone complex regulates BC migration is by modulating PVR function.     

Simulated bipolar cells in fovea of human retina

Fourier analysis is used to study resolution of images processed by the matrix of simulated red-center (BCR) and green-center (BCG) bipolar cells (BC) of the human central fovea. Simulated achromatic and chromatic sine and square waves, and a two-bar stimulus are used to activate the BCs. Due to the "honeycomb" packing of the cones and BC matrices Fourier transforms are computed row by row using a one-dimensional FFT. Resolution computed by the Fourier transform is compared with the resolution index (RI), which is a method for determining resolution based on two-point discrimination in the space domain. In general the harmonic with the maximum amplitude gives the best correlation with RI for the three stimuli. Amplitudes at all spatial frequencies are enhanced by increasing the number of cycles in the sine and square wave gratings. Results with simulated BCs compare favorably with human and macaque psychophysics measuring contrast sensitivity. Square wave gratings are better than sine wave greetings for studying resolution.     

Mono-N-Methylation of 1,2,3,4-Tetrahydro-β-Carbolines in Brain Cytosol: Absence of Indole Methylation

In an accompanying report we demonstrated enzyme activity in guinea pig brain cell nuclei that catalyzes S-adenosylmethionine (SAM)-dependent N-methylations of heteroaromatic beta-carbolines (BCs) on the 2[beta]-nitrogen and subsequently on the 9[indole]-nitrogen, ultimately yielding N2,N9-dimethylated BCs. Presented here are the results of a parallel study of the N-methylation of 1,2,3,4-tetrahydro-BCs (THBCs), which form endogenously via condensations of tryptophan and its derived indoles with carbonyl compounds or, like their BC oxidation products, are environmental constituents and plant alkaloids. THBCs were enzymatically methylated on the 2[beta]-nitrogen by [3H]-SAM in undialyzed homogenates of rat or guinea pig brain, but [3H]methyl transfer to the 9[indole]-nitrogen was not observed. The structure of the 2[beta]-methyl THBC product was verified with capillary gas chromatography-mass spectrometry. Furthermore, whereas BC N-methylation was largely particulate and displayed micromolar Km values for BC substrate, THBC 2[beta]-N-methylation activity was cytosolic and displayed a relatively high (millimolar) Km for THBC substrate. The N-methylation of THBCs may be due to cytosolic N-methyltransferases that others have studied using different azaheterocyclics. Our overall studies indicate that N2,N9-dimethylated BCs could be unique neurotoxic factors that are bioactivated within brain by sequential N-methylations of BCs. These results suggest the possibility of an additional route to the putative 2,9-dimethylated toxins involving, as a first step, 2[beta]-N-methylation of environmental or endogenously derived THBCs in the brain and perhaps other organs.     

Morphogenesis and proliferation in mono- and organotypic co-cultures of primary human periodontal ligament fibroblasts and alveolar bone cells

Cells of the periodontal ligament and the alveolar bone lie in close vicinity in the periodontium. The goal of this study was to create an in vitro model to facilitate the study of the morphogenesis and proliferation of these two cell types under more in-vivo-like conditions. This was accomplished by the generation of organotypic co-cultures of primary human periodontal ligament fibroblasts (PDL) and alveolar bone cells (BC) and matched mono-cultures after 1, 2 and 3 weeks. Indirect immunofluorescence (IIF) for vimentin indicated that PDL cells exhibited sustained stratification only in the presence of BC cells, suggesting an important role for BCs in maintaining the stratification of PDL cells. In mono-cultures, only BC cells showed progressing stratification. They also displayed the most pronounced contraction of the cell culture matrix. Moreover, Ki-67 antigen detection by IIF revealed that these features coincided with cell proliferation localized on the matrix surface at the onset of cell stratification. These findings suggest that, in addition to proliferation, a further prerequisite for stratification may be cell migration. Furthermore, the maintained cell stratification, proliferation, and compartmentalization noted for PDL cells in organotypic co-cultures and BCs in mono-cultures can only be observed in a three-dimensional culture system. Thus, our system represents a novel experimental tool to further elucidate the underlying mechanisms of the growth and differentiation of PDL and bone tissue.     

The correlations between HPV16 infection and expressions of c-erbB-2 and bcl-2 in breast carcinoma

Breast carcinoma (BC) is a prevalent malignant tumour occurring in women. Many studies have indicated the role of human papilloma virus type 16 (HPV16) in the pathogenesis of BC; however, the correlations of HPV16 infection with the clinicopathologic features of BC and the expressions of c-erbB-2 and bcl-2 have not yet been elucidated. In this study, HPV16 was detected by amplifying the HPV16 E6 gene by the polymerase chain reaction method, and the expressions of c-erbB-2 and bcl-2 in 40 BCs and 20 normal breast tissue samples, obtained from Shaanxi Province, were examined using the streptavidin-peroxidase method with monoclonal antibodies specific to c-erbB-2 and bcl-2. The infection rate of HPV16 E6 and the positive expression rate of c-erbB-2 were significantly higher in the BCs than in the normal tissues (HPV16 E6: 60% vs. 5%; c-erbB-2: 42.5% vs. 5%, P < 0.05). However, the positive expression rate of bcl-2 was significantly lower in the BCs than in the normal tissues (67.5% vs. 95%, P < 0.05). The infection rate of HPV16 did not correlate with any of the pathological features observed (P > 0.05). HPV16 infection correlated with bcl-2 expression (P = 0.015) but not with c-erbB-2 expression (P = 0.747) in the BCs. Interestingly, HPV16 infection correlated with bcl-2 expression in grade I BCs (P = 0.018) but not in grade II–III BCs (P = 0.633). Our data suggest that HPV16 infection is correlated with bcl-2 expression in BCs.     

Detection of Human Papillomavirus DNA in Patients with Breast Tumor in China

The presence of HPV in breast tissue and the potential causal association between human papillomavirus (HPV) and breast cancer (BC) remains controversial. The aim of the present study was to compare the HPV prevalence in BC tissues, adjacent normal breast tissues and breast benign disease tissues and to investigate the possible association between HPV and breast tumor development in Chinese women. Paraffin-embedded specimens from 187 pairs of BCs including tumor and normal breast tissue adjacent to tumors and 92 breast benign lesions between June 2009 and July 2014 were investigated by nested polymerase chain reaction (PCR) and type-specific PCR, respectively. With strictly quality control, HPV positive infection was detected in three BC tissues. No HPV positive infection was detected in all normal breast tissue adjacent to tumors and benign breast tissues. Through our detailed analysis, rare HPV infection in this study suggests that HPV might not be associated with BC progression.     

The Prostate Basal Cell (BC) Heterogeneity and the p63-Positive BC Differentiation Spectrum in Mice

The prostate epithelium is composed of basal (BC), luminal (LEC), and neuroendocrine (NEC) cells. It is unclear how many subtypes of BCs in the prostate and which subtype of BCs contains the main stem cell niche in the adult prostate. Here we report seven BC subpopulations according to their p63, cytokeratin 14 (K14) and K5 expression patterns, including p63-positive/K14-negative/K5-negative (p63+/K14-/K5-), p63-/K14+/K5-, p63-/K14-/K5+, p63+/K14+/K5-, p63+/K14-/K5+, p63-/K14+/K5+, and p63+/K14+/K5+ BCs. We generated a p63-CreERT2 knock-in mouse line that expresses tamoxifen-inducible Cre activity in the p63-expressing cells, including the prostate BCs. We then crossbred this line with ROSA26R mice, and generated p63-CreERT2×ROSA26R bi-genic mice harboring the Cre-activated β-galactosidase reporter gene. We treated these bi-genic mice with tamoxifen to mark the p63+ BCs at different ages or under different hormonal conditions, and then traced the lineage differentiation of these genetically labeled BCs. We discovered that these p63+ BCs contain self-renewable stem cells in culture and efficiently differentiated into LECs, NECs and BCs in the postnatal, adult and re-generating mouse prostates. Therefore, BC population contains heterogeneous BCs that express different combinations of the p63, K14 and K5 differentiation markers. Because K14+ and K5+ BCs were previously shown to be extremely inefficient to produce LECs in adulthood, we propose that the p63+/K5-/K14- subpopulation of BCs contains most stem-like cells, especially in adult animals.     

Root border cell development is a temperature-insensitive and Al-sensitive process in barley

In vivo and in vitro experiments showed that border cell (BC) survival was dependent on root tip mucigel in barley (Hordeum vulgare L. cv. Hang 981). In aeroponic culture, BC development was an induced process in barley, whereas in hydroponic culture, it was a kinetic equilibrium process during which 300-400 BCs were released into water daily. The response of root elongation to temperatures (10-35 degrees C) was very sensitive but temperature changes had no great effect on barley BC development. At 35 degrees C, the root elongation ceased whereas BC production still continued, indicating that the two processes might be regulated independently under high temperature (35 degrees C) stress. Fifty microM Al could inhibit significantly BC development by inhibiting pectin methylesterase activity in the root cap of cv. 2000-2 (Al-sensitive) and cv. Humai 16 (Al-tolerant), but 20 microM Al could not block BC development in cv. Humai 16. BCs and their mucigel of barley had a limited role in the protection of Al-induced inhibition of root elongation, but played a significant role in the prevention of Al from diffusing into the meristems of the root tip and the root cap. Together, these results suggested that BC development was a temperature-insensitive but Al-sensitive process, and that BCs and their mucigel played an important role in the protection of root tip and root cap meristems from Al toxicity.     

Novel S-Adenosylmethionine-Dependent Indole-N-Methylation of β-Carbolines in Brain Particulate Fractions

Guinea pig brain S-adenosylmethionine (SAM)-dependent N-methyltransferase activity toward physiologically relevant beta-carboline (BC) substrates was examined with reverse-phase HPLC and radiochemical detection. Representative BCs, norharman and harmine, were enzymatically methylated on the 2[beta]-nitrogen by [3H]CH3-SAM in undialyzed homogenates to yield 2[beta]-methylated BCs and subsequently on the 9[indole]-nitrogen to generate 2,9-dimethylated BC products. This may be the first account of mammalian indole N-methyl transfer. There was no HPLC evidence for 9-methyl BC or (from carbon methylation) 2,6-dimethyl BC products. Capillary gas chromatography-mass spectrometry analysis confirmed the structures of the 2,9-dimethyl and 2-methyl products of norharman. The 2[beta]- and 9[indole]-N-methylation activities were mainly in the nuclear fractions and were negligible in undialyzed cytosol. This differs from the cytosolic SAM-dependent N-methylations reported with other azaheterocyclics, including 1,2,3,4-tetrahydro-BCs. The involvement of a single enzyme was suggested because the two N-methyl transfers with BC substrate had similar subcellular activity patterns, regional brain distributions, and Km and Vmax values. Sequential N-methylation of various BCs that have been observed in vivo may be a unique route to centrally retained N2,N9-dimethylated beta-carbolinium ions. Because they resemble the synthetic parkinsonian toxicant, N-methyl-4-phenylpyridinium, with respect to structure and neurotoxic activity, such "bioactivated" carbolinium ions could be endogenous causative factors in Parkinson's disease.     

QCT/FEA predictions of femoral stiffness are strongly affected by boundary condition modeling

Quantitative computed tomography-based finite element models of proximal femora must be validated with cadaveric experiments before using them to assess fracture risk in osteoporotic patients. During validation, it is essential to carefully assess whether the boundary condition (BC) modeling matches the experimental conditions. This study evaluated proximal femur stiffness results predicted by six different BC methods on a sample of 30 cadaveric femora and compared the predictions with experimental data. The average stiffness varied by 280% among the six BCs. Compared with experimental data, the predictions ranged from overestimating the average stiffness by 65% to underestimating it by 41%. In addition, we found that the BC that distributed the load to the contact surfaces similar to the expected contact mechanics predictions had the best agreement with experimental stiffness. We concluded that BC modeling introduced large variations in proximal femora stiffness predictions.     

Cross-species scRNA-seq reveals the cellular landscape of retina and early alterations in type 2 diabetes mice

Single-cell RNA sequencing (scRNA-seq) analysis have provided an unprecedented resolution for the studies on diabetic retinopathy (DR). However, the early changes in the retina in diabetes remain unclear. A total of 8 human and mouse scRNA-seq datasets, containing 276,402 cells were analyzed individually to comprehensively delineate the retinal cell atlas. The neural retinas were isolated from the type 2 diabetes (T2D) and control mice, and scRNA-seq analysis was conducted to evaluate the early effects of diabetes on the retina. Bipolar cell (BC) heterogeneity were identified. We found some stable BCs across multiple datasets, and explored their biological functions. A new RBC subtype (Car8_RBC) in the mouse retina was validated using the multi-color immunohistochemistry. AC149090.1 was significantly upregulated in the rod cells, ON cone BCs (CBCs), OFF CBCs, and RBCs in T2D mice. Additionally, the interneurons, especially BCs, were the most vulnerable cells to diabetes by integrating scRNA-seq and genome-wide association studies (GWAS) analyses. In conclusion, this study delineated a cross-species retinal cell atlas and uncovered the early pathological alterations in the retina of T2D mice.     

Effect of Soil pH Increase by Biochar on NO,N2O and N2 Production during Denitrification in Acid Soils

Biochar (BC) application to soil suppresses emission of nitrous- (N₂O) and nitric oxide (NO), but the mechanisms are unclear. One of the most prominent features of BC is its alkalizing effect in soils, which may affect denitrification and its product stoichiometry directly or indirectly. We conducted laboratory experiments with anoxic slurries of acid Acrisols from Indonesia and Zambia and two contrasting BCs produced locally from rice husk and cacao shell. Dose-dependent responses of denitrification and gaseous products (NO, N₂O and N₂) were assessed by high-resolution gas kinetics and related to the alkalizing effect of the BCs. To delineate the pH effect from other BC effects, we removed part of the alkalinity by leaching the BCs with water and acid prior to incubation. Uncharred cacao shell and sodium hydroxide (NaOH) were also included in the study. The untreated BCs suppressed N₂O and NO and increased N₂ production during denitrification, irrespective of the effect on denitrification rate. The extent of N₂O and NO suppression was dose-dependent and increased with the alkalizing effect of the two BC types, which was strongest for cacao shell BC. Acid leaching of BC, which decreased its alkalizing effect, reduced or eliminated the ability of BC to suppress N₂O and NO net production. Just like untreated BCs, NaOH reduced net production of N₂O and NO while increasing that of N₂. This confirms the importance of altered soil pH for denitrification product stoichiometry. Addition of uncharred cacao shell stimulated denitrification strongly due to availability of labile carbon but only minor effects on the product stoichiometry of denitrification were found, in accordance with its modest effect on soil pH. Our study indicates that stimulation of denitrification was mainly due to increases in labile carbon whereas change in product stoichiometry was mainly due to a change in soil pH.     

Simplified boundary conditions alter cortical-trabecular load sharing at the distal radius; A multiscale finite element analysis

High-resolution peripheral quantitative computed tomography (HR-pQCT) derived micro-finite element (FE) modeling is used to evaluate mechanical behavior at the distal radius microstructure. However, these analyses typically simulate non-physiologic simplified platen-compression boundary conditions on a small section of the distal radius. Cortical and trabecular regions contribute uniquely to distal radius mechanical behavior, and various factors affect these regions distinctly. Generalized strength predictions from standardized platen-compression analyses may not adequately capture region specific responses in bone. Our goal was to compare load sharing within the cortical-trabecular compartments between the standardized platen-compression BC simulations, and physiologic BC simulations using a validated multiscale approach. Clinical- and high-resolution images were acquired from nine cadaveric forearm specimens using an HR-pQCT scanner. Multiscale FE models simulating physiologic BCs, and micro-FE only models simulating platen-compression BCs were created for each specimen. Cortical and trabecular loads (N) along the length of the distal radius micro-FE section were compared between BCs using correlations. Principal strain distributions were also compared quantitatively. Cortical and trabecular loads from the platen-compression BC simulations were strongly correlated to the physiologic BC simulations. However, a 30% difference in cortical loads distally, and a 53% difference in trabecular loads proximally was observed under platen BC simulations. Also, distribution of principal strains was clearly different. Our data indicated that platen-compression BC simulations alter cortical-trabecular load sharing. Therefore, results from these analyses should be interpreted in the appropriate mechanical context for clinical evaluations of normal and pathologic mechanical behavior at the distal radius.     

Human DNA polymerase lambda functionally and physically interacts with proliferating cell nuclear antigen in normal and translesion DNA synthesis

Proliferating cell nuclear antigen (PCNA) has been shown to interact with a variety of DNA polymerases (pol) such as pol delta, pol epsilon, pol iota, pol kappa, pol eta, and pol beta. Here we show that PCNA directly interacts with the newly discovered pol lambda cloned from human cells. This interaction stabilizes the binding of pol lambda to the primer template, thus increasing its affinity for the hydroxyl primer and its processivity in DNA synthesis. However, no effect of PCNA was detected on the rate of nucleotide incorporation or discrimination efficiency by pol lambda. PCNA was found to stimulate efficient synthesis by pol lambda across an abasic (AP) site. When compared with pol delta, human pol lambda showed the ability to incorporate a nucleotide in front of the lesion. Addition of PCNA led to efficient elongation past the AP site by pol lambda but not by pol delta. However, when tested on a template containing a bulky DNA lesion, such as the major cisplatin Pt-d(GpG) adduct, PCNA could not allow translesion synthesis by pol lambda. Our results suggest that the complex between PCNA and pol lambda may play an important role in the bypass of abasic sites in human cells.     

Delineation by fluorescence in situ hybridization of a single hemizygous chromosomal region associated with aposporous embryo sac formation in Pennisetum squamulatum and Cenchrus ciliaris

Apomixis is a means of asexual reproduction by which plants produce embryos without meiosis and fertilization; thus the embryo is of clonal, maternal origin. We previously reported molecular markers showing no recombination with the trait for aposporous embryo sac development in Pennisetum squamulatum and Cenchrus ciliaris, and the collective single-dose alleles defined an apospory-specific genomic region (ASGR). Fluorescence in situ hybridization (FISH) was used to confirm that the ASGR is a hemizygous genomic region and to determine its chromosomal position with respect to rDNA loci and centromere repeats. We also documented chromosome transmission from P. squamulatum in several backcrosses (BCs) with P. glaucum using genomic in situ hybridization (GISH). One to three complete P. squamulatum chromosomes were detected in BC(6), but only one of the three hybridized with the ASGR-linked markers. In P. squamulatum and in all BCs examined, the apospory-linked markers were located in the distal region of the short arm of a single chromosome. All alien chromosomes behaved as univalents during meiosis and segregated randomly in BC(3) and later BC generations, but presence of the ASGR-carrier chromosome alone was sufficient to confer apospory. FISH results support our hypotheses that hemizygosity, proximity to centromeric sequences, and chromosome structure may all play a role in low recombination in the ASGR.     

Notch-dependent differentiation of adult airway basal stem cells

The epithelium lining the airways of the adult human lung is composed of ciliated and secretory cells together with undifferentiated basal cells (BCs). The composition and organization of this epithelium is severely disrupted in many respiratory diseases. However, little is known about the mechanisms controlling airway homeostasis and repair after epithelial damage. Here, we exploit the mouse tracheobronchial epithelium, in which BCs function as resident stem cells, as a genetically tractable model of human small airways. Using a reporter allele we show that the low level of Notch signaling at steady state is greatly enhanced during repair and the generation of luminal progenitors. Loss-of-function experiments show that Notch signaling is required for the differentiation, but not self-renewal, of BCs. Moreover, sustained Notch activation in BCs promotes their luminal differentiation, primarily toward secretory lineages. We also provide evidence that this function of Notch signaling is conserved in BCs from human airways.     

Are T cells at the origin of B cell lymphomas?

Lymphoma pathogenesis is at least in some cases related to transformed B cells (BCs) arising from germinal centre reactions (GCRs). In this article possible deregulations of GCRs are investigated using in silico simulations. It is found that the final differentiation of BCs as regulated by helper T cells (TCs) is the best candidate mechanism for such a deregulation. This shifts the paradigm of BC lymphoma pathogenesis from BC transformations to an emphasized role of TC-BC interactions.