CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells

Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions can play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore, not suitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, that reconstructs structural ensembles based on Hi-C data and identifies significant many-body interactions. For a diverse set of highly-active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase-accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.

“In-silico studies of facilitated VEGF(s) – VEGFR(s) bindings for assessment of Lysine as an indirect Low-Mol-Wt angiogen: Experimental validation of a potential synthetic Low-Mol-Wt angiogen”

In-vivo angiogenesis process is highly conserved and is mediated through a family of peptides having VEGF-A as the lead member. A respective receptor family comprising of members VEGFR-1, 2, 3 gets expressed on the endothelial cell membrane of the vascular bed in ischemic zone along with parallel expressions of VEGF-A, B, C, D and PlGF. Degree of ischaemia is the main regulator of these coupled expressions of angiogenic peptides/factors (AFs) and respective receptor(s) for a paracrine angiogenic process to take place. Physiological angiogenesis in intrauterine growth phase is the lead process in foetal growth, organogenesis and cellular specialization. Post birth and with aging, this process gets gradually inefficient and slow. In the present in-silico study, all angiogenic factors and receptor species are examined as for their binding stability in basal unaided condition and in presence of a possible Low-Mol-Wt linkage molecule–Lysine. Also a Lysine analogue 1,6-diaminohexanoic acid has been examined for its angiogenic potential both in dry docking experiment and in cell culture assay.

Morphological Characteristics and In Situ Auxin Production during the Histogenesis of Staminate Flowers in Precocious Walnut

Monoclonal anti-indole acetic acid antibodies were used to monitor the temporal and spatial pattern of auxin during staminate flower differentiation in walnut (Juglans regia) cultivars Liaoning 1 and Liaoning 3. The relationship between morphological characteristics and histological structure was established. Seven stages of differentiation were recognized based on the visibility and color of the squama, bract, perianth, and rachis as follows: Stage 1, several bract primordia were present in the squama with catkins protruding from the squama as the only externally visible portion of the floret (Stage 1); the bract became externally visible, and the floret, perianth, and stamen primordia formed basipetally (Stage 2); the length of catkins were elongated, only bracts visible and getting brown (Stage 3); the bracts were brown and wrapped tightly, cellular specialization occurred to form a central core containing reproductive cells and tapetal cells that differentiated (Stage 4); the perianth became visible externally, reproductive cells and tapetal cells separated from the exterior layers of the anther wall (Stage 5); the anther walls were reduced to two cell layers (epidermis and endothecium) as the anthers became visible and matured (Stage 6); and the anther turned black, dehisced, and released its pollen grains (Stage 7). The histological differentiation of the flowers was related to auxin. The auxin signal was strongest in the shoot apical meristem (SAM) during bract primordia differentiation; thus, the SAM may be a site of auxin production. When the floral organs began centralized differentiation, auxin was distributed mainly in the differentiating tissues. Our findings indicate that a high level of auxin may strongly affect morphogenesis. Additionally, the tapetal and reproductive cells that arise during cellular specialization may be important for auxin production. The distribution of auxin was centralized in germ pores at the pollen grain surface, indicating that a high level of auxin induces pollen germination.

Asymmetric distribution of metals in the Xenopus laevis oocyte: a synchrotron X-ray fluorescence microprobe study

The asymmetric distribution of many components of the Xenopus oocyte, including RNA, proteins, and pigment, provides a framework for cellular specialization during development. During maturation, Xenopus oocytes also acquire metals needed for development, but apart from zinc, little is known about their distribution. Synchrotron X-ray fluorescence microprobe was used to map iron, copper, and zinc and the metalloid selenium in a whole oocyte. Iron, zinc, and copper were asymmetrically distributed in the cytoplasm, while selenium and copper were more abundant in the nucleus. A zone of high copper and zinc was seen in the animal pole cytoplasm. Iron was also concentrated in the animal pole but did not colocalize with zinc, copper, or pigment accumulations. This asymmetry of metal deposition may be important for normal development. Synchrotron X-ray fluorescence microprobe will be a useful tool to examine how metals accumulate and redistribute during fertilization and embryonic development.

External Morphological Characteristics for Histogenesis in Pecan Anthers

External “morphological characteristics of catkins from one protogynous (`Stuart') and one protandrous (`Desirable') cultivar of pecan [Carya illinoensis Wangenh.) C. Koch] were examined to define markers of cellular differentiation in the anthers. The angle between the catkin rachis and the bract, visibility of the bracteole, rachis, and anther, and anther color proved to be markers by which development could be categorized into five stages. `Stuart' catkins with bracts as the only externally visible portion of the floret (Stage I) commonly had two locules in each anther lobe. When bracteoles became externally visible (Stage II), cellular specialization had occurred to form a central core containing reproductive cells and tapetal cells differentiated and separated from the exterior layers of the anther wall. Disintegration of tapetal cells and thickening of endothecium eel! walls occurred as the angle between the rachis and bract increased to 45° (Stage III). The anther wall was reduced to only two cell layers, epidermis and endothecium, as the anthers became visible (Stage IV). The pollen grains were mature when the anthers developed a yellowish tinge (Stage V) just before anther dehiscence. Tapetal cells had developed distinguishing traits in anthers of Stage I `Desirable' catkins and endothecial cells of Stage II. Internal anther development was similar for both cultivars from Stages III-V. Trichomes, a common feature-on the surface of the staminate floral parts, became less dense with proximity of the floral parts to the interior of the floret and with catkin maturity.