Intragene higher order repeats in neuroblastoma breakpoint family genes distinguish humans from chimpanzees

Much attention has been devoted to identifying genomic patterns underlying the evolution of the human brain and its emergent advanced cognitive capabilities, which lie at the heart of differences distinguishing humans from chimpanzees, our closest living relatives. Here, we identify two particular intragene repeat structures of noncoding human DNA, spanning as much as a hundred kilobases, that are present in human genome but are absent from the chimpanzee genome and other nonhuman primates. Using our novel computational method Global Repeat Map, we examine tandem repeat structure in human and chimpanzee chromosome 1. In human chromosome 1, we find three higher order repeats (HORs), two of them novel, not reported previously, whereas in chimpanzee chromosome 1, we find only one HOR, a 2mer alphoid HOR instead of human alphoid 11mer HOR. In human chromosome 1, we identify an HOR based on 39-bp primary repeat unit, with secondary, tertiary, and quartic repeat units, fully embedded in human hornerin gene, related to regenerating and psoriatric skin. Such an HOR is not found in chimpanzee chromosome 1. We find a remarkable human 3mer HOR organization based on the ~1.6-kb primary repeat unit, fully embedded within the neuroblastoma breakpoint family genes, which is related to the function of the human brain. Such HORs are not present in chimpanzees. In general, we find that human-chimpanzee differences are much larger for tandem repeats, in particularly for HORs, than for gene sequences. This may be of great significance in light of recent studies that are beginning to reveal the large-scale regulatory architecture of the human genome, in particular the role of noncoding sequences. We hypothesize about the possible importance of human accelerated HOR patterns as components in the gene expression multilayered regulatory network.     

The Cenomanian–Turonian boundary in the northwestern part of the Adriatic Carbonate Platform (Ćićarija Mtn., Istria,Croatia): characteristics and implications

The Cenomanian–Turonian boundary (CTB) in the ?i?arija Mountain region (northern Istria, Croatia) is characterized by calcisphere limestone successions with a firmground and glauconite horizon, bioturbated intervals, tempestites, and slumped structures as well as microbially laminated and organic-rich interbeds deposited in the northwestern part of the intra-Tethyan Adriatic Carbonate Platform (AdCP). Compilation of the results from three studied sections (Vodice–Jelovica, Martinjak and Planik) of litho-, bio-, and microfacies analyses, X-ray diffraction, SEM, EDS, and stable isotope analyses allowed reconstruction of marine paleoenvironmental conditions during this time period. Shallow-marine carbonate deposits of the Milna Formation underlie a drowned-platform succession of the Sveti (Sv.) Duh Formation. The contact between these two formations is sharp and commonly marked by slumped deposits. The Sv. Duh Formation consists of about 100 m of calcisphere wackestone enriched in organic matter. The results of preliminary δ¹³C and δ¹⁸O stable isotope analyses indicate the influence of the global Oceanic Anoxic Event (OAE2) on the deposition of this carbonate succession. Anoxic and hypoxic conditions in the water column lead to major changes in the shallow-marine carbonate system of the AdCP. Numerous benthic foraminifera declined during that time, but planktonic foraminifera and calcareous dinoflagellates diversified and expanded greatly. The results of this research provide new insights into the character of the CTB interval in this part of the Tethyan realm. Local and regional synsedimentary tectonics combined with global upper Cretaceous sea-level dynamics allows the correlation of the investigated deeper-marine lithostratigraphic units with OAE2.     

Effect of Blood Vessel Segmentation on the Outcome of Electroporation-Based Treatments of Liver Tumors

Electroporation-based treatments rely on increasing the permeability of the cell membrane by high voltage electric pulses applied to tissue via electrodes. To ensure that the whole tumor is covered with sufficiently high electric field, accurate numerical models are built based on individual patient anatomy. Extraction of patient''s anatomy through segmentation of medical images inevitably produces some errors. In order to ensure the robustness of treatment planning, it is necessary to evaluate the potential effect of such errors on the electric field distribution. In this work we focus on determining the effect of errors in automatic segmentation of hepatic vessels on the electric field distribution in electroporation-based treatments in the liver. First, a numerical analysis was performed on a simple ''sphere and cylinder'' model for tumors and vessels of different sizes and relative positions. Second, an analysis of two models extracted from medical images of real patients in which we introduced variations of an error of the automatic vessel segmentation method was performed. The results obtained from a simple model indicate that ignoring the vessels when calculating the electric field distribution can cause insufficient coverage of the tumor with electric fields. Results of this study indicate that this effect happens for small (10 mm) and medium-sized (30 mm) tumors, especially in the absence of a central electrode inserted in the tumor. The results obtained from the real-case models also show higher negative impact of automatic vessel segmentation errors on the electric field distribution when the central electrode is absent. However, the average error of the automatic vessel segmentation did not have an impact on the electric field distribution if the central electrode was present. This suggests the algorithm is robust enough to be used in creating a model for treatment parameter optimization, but with a central electrode.     

Bone morphogenetic protein (BMP)1-3 enhances bone repair

Members of the astacin family of metalloproteinases such as human bone morphogenetic protein 1 (BMP-1) regulate morphogenesis by processing precursors to mature functional extracellular matrix (ECM) proteins and several growth factors including TGFβ, BMP2, BMP4 and GFD8. We have recently discovered that BMP1-3 isoform of the Bmp-1 gene circulates in the human plasma and is significantly increased in patients with acute bone fracture. We hypothesized that circulating BMP1-3 might have an important role in bone repair and serve as a novel bone biomarker. When administered systemically to rats with a long bone fracture and locally to rabbits with a critical size defect of the ulna, recombinant human BMP1-3 enhanced bone healing. In contrast, neutralization of the endogenous BMP1-3 by a specific polyclonal antibody delayed the bone union. Invitro BMP1-3 increased the expression of collagen type I and osteocalcin in MC3T3-E₁ osteoblast like cells, and enhanced the formation of mineralized bone nodules from bone marrow mesenchymal stem cells. We suggest that BMP1-3 is a novel systemic regulator of bone repair.     

Cell prestress. II. Contribution of microtubules

The tensegritymodel hypothesizes that cytoskeleton-based microtubules (MTs) carrycompression as they balance a portion of cell contractile stress. Totest this hypothesis, we used traction force microscopy to measuretraction at the interface of adhering human airway smooth muscle cellsand a flexible polyacrylamide gel substrate. The prediction is that ifMTs balance a portion of contractile stress, then, upon theirdisruption, the portion of stress balanced by MTs would shift to thesubstrate, thereby causing an increase in traction. Measurements weredone first in maximally activated cells (10 µM histamine) and thenagain after MTs had been disrupted (1 µM colchicine). We found that after disruption of MTs, traction increased on average by ~13%. Because in activated cells colchicine induced neither an increase inintracellular Ca²⁺ nor an increase in myosin light chainphosphorylation as shown previously, we concluded that the observedincrease in traction was a result of load shift from MTs to thesubstrate. In addition, energy stored in the flexible substrate wascalculated as work done by traction on the deformation of thesubstrate. This result was then utilized in an energetic analysis. Weassumed that cytoskeleton-based MTs are slender elastic rods supportedlaterally by intermediate filaments and that MTs buckle as the cellcontracts. Using the post-buckling equilibrium theory of Euler struts,we found that energy stored during buckling of MTs was quantitativelyconsistent with the measured increase in substrate energy afterdisruption of MTs. This is further evidence supporting the idea thatMTs are intracellular compression-bearing elements.

     

A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly

The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a “basal body”, a lock-nut structure spanning both bacterial membranes, and a “needle” that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.     

Multiple primary melanoma: epidemiological and prognostic implications; analysis of 36 cases

Patients who are already diagnosed with cutaneous melanoma are at increased risk of developing another primary melanoma. The occurrence of multiple primary melanoma is a rare phenomenon, varying in frequency, with an estimated incidence ranging from 0.2% to 8.6%. The authors are presenting data on the patients with multiple primary melanoma from the Croatian Referral Melanoma Centre. The clinical, histological and epidemiological characteristics of 36 (3.6%) patients, identified from 991 patients with histologically confirmed melanoma, are analyzed in this study. Twenty-eight of the patients (78%) had two primary melanomas, six had three melanomas (16.7%) and two (5,6%) had four melanomas. Diagnosis was established synchronously in 11 patients (30%) and, in the rest of the patients, time interval between the diagnosis of the first and second melanoma varied from 1 month to the longest interval of 16 years. However, the majority of subsequent melanomas were removed within 2 years of the initial operation. The mean Breslow's thickness of the first melanoma was significantly higher than the mean Breslow's thickness of the second primary melanoma. The proportion of in situ to invasive melanomas was greater for the second melanomas compared with the first melanomas. Therefore, we emphasize the importance of regular follow-up as well as the education in regular self--skin examinations in melanoma patients in order to detect subsequent primary melanomas in the early phase.