Intrinsically bent DNA sites in the <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> third chromosome amplified domain

Bent DNA sites promote the curvature of DNA in both eukaryotic and prokaryotic chromosomes. Here, we investigate the localization and structure of intrinsically bent DNA sites in the extensively characterized Drosophila melanogaster third chromosome DAFC-66D segment (Drosophila amplicon in the follicle cells). This region contains the amplification control element ACE3, which is a replication enhancer that acts in cis to activate the major replication origin ori-β. Through both electrophoretic and in silico analysis, we have identified three major bent DNA sites in DAFC-66D. The bent DNA site (b1) is localized in the ACE3 element, whereas the other two bent DNA sites (b2 and b3) are localized in the ori-β region. Four additional bent DNA sites were identified in the intron of the S18 gene and near the TATA box of the S15, S19, and S16 genes. The identification of DNA bent sites in genomic regions previously characterized as functionally relevant for DNA amplification further supports a function for DNA bent sites in DNA replication in eukaryotes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sizzled-Tolloid Interactions Maintain Foregut Progenitors by Regulating Fibronectin-Dependent BMP Signaling

The liver, pancreas, and lungs are induced from endoderm progenitors by a series of dynamic growth factor signals from the mesoderm, but how the temporal-spatial activity of these signals is controlled is poorly understood. We have identified an extracellular regulatory loop required for robust bone morphogenetic protein (BMP) signaling in the Xenopus foregut. We show that BMP signaling is required to maintain foregut progenitors and induce expression of the secreted frizzled related protein Sizzled (Szl) and the extracellular metalloprotease Tolloid-like 1 (Tll1). Szl negatively regulates Tll activity to control deposition of a fibronectin (FN) matrix between the mesoderm and endoderm, which is required to maintain BMP signaling. Foregut-specific Szl depletion results in a loss of the FN matrix and failure to maintain robust pSmad1 levels, causing a loss of foregut gene expression and organ agenesis. These results have implications for BMP signaling in diverse contexts and the differentiation of foregut tissue from stem cells.     

Validating the use of stereo‐video cameras to conduct remote measurements of sea turtles

Point 1: Stereo‐video camera systems (SVCSs) are a promising tool to remotely measure body size of wild animals without the need for animal handling. Here, we assessed the accuracy of SVCSs for measuring straight carapace length (SCL) of sea turtles.Point 2: To achieve this, we hand captured and measured 63 juvenile, subadult, and adult sea turtles across three species: greens, Chelonia mydas (n = 52); loggerheads, Caretta caretta (n = 8); and Kemp''s ridley, Lepidochelys kempii (n = 3) in the waters off Eleuthera, The Bahamas and Crystal River, Florida, USA, between May and November 2019. Upon release, we filmed these individuals with the SVCS. We performed photogrammetric analysis to extract stereo SCL measurements (eSCL), which were then compared to the (manual) capture measurements (mSCL).Point 3: mSCL ranged from 25.9 to 89.2 cm, while eSCL ranged from 24.7 to 91.4 cm. Mean percent bias of eSCL ranged from −0.61% (±0.11 SE) to −4.46% (±0.31 SE) across all species and locations. We statistically analyzed potential drivers of measurement error, including distance of the turtle to the SVCS, turtle angle, image quality, turtle size, capture location, and species.Point 4: Using a linear mixed effects model, we found that the distance between the turtle and the SVCS was the primary factor influencing measurement error. Our research suggests that stereo‐video technology enables high‐quality measurements of sea turtle body size collected in situ without the need for hand‐capturing individuals. This study contributes to the growing knowledge base that SVCS are accurate for body size measurements independent of taxonomic clade.     

The effect of a GnRH agonist on follicular dynamics and response to FSH stimulation in prepubertal calves

Endocrine control of follicular growth was determined by observing the left ovary of prepubertal calves previously treated with a potent GnRH agonist for 13 days. The ovarian response to hormonal stimulation was determined using the right ovaries of the same animals. Three-month-old crossbred calves were assigned to one of the two following treatment groups: 1) saline control for 13 days, with purified porcine FSH for the last 3 days (n = 5); and 2) GnRHa for 13 days, with purified porcine FSH for the final 3 days (n = 5). The left ovaries were removed from all calves after 10 days, and the right ovaries were removed at the end of treatment. Plasma concentrations of FSH, LH and oestradiol-17 beta were followed up during the GnRHa and pFSH treatments. The maximum macroscopic diameter of the F1 follicle, as determined by daily ultrasonography, did not differ between GnRHa-treated calves (from 6.6 to 10.4 mm) and the saline control calves (from 6.7 to 10.3 mm). Histological analysis of the ovaries showed that the number of follicles > 0.40 mm in diameter varied greatly for calves of the two groups (from 11 to 220 at 10 days). GnRHa significantly increased the mean number of follicles (total and nonatretic) of size class > 5.4 mm as compared to saline control calves (P < 0.05). The FSH treatment significantly increased the mean number of follicles 3.00-5.4 and > 5.4 mm in diameter (P < 0.05), with no change in the number of follicles smaller than 3.00 mm. The rate of atresia of large follicles (3.01-5.40 mm) was significantly reduced by purified porcine FSH treatment in both groups (P < 0.05). In no case did the GnRHa induce ovulation or luteinization of follicles. The LH and FSH concentrations increased transiently after GnRHa treatment on the first day, but afterwards, both hormones increased to only one sixth of what was observed after the initial GnRHa injection treatment. This increase in LH and FSH was observed 1 h after GnRHa treatment on each consecutive day of the experiment and were significantly different in the control group (0 h versus 1 h versus 2 h x saline control versus GnRH agonists groups; P < 0.01). During the superovulatory treatment, FSH concentrations peaked at around 0.70 ng.mL-1 in both saline- and GnRHa-treated groups on the first day but on the last day of surovulatory treatment, FSH concentrations were higher in GnRHa agonist-treated calves than in the control calves (day 11 versus day 12 versus day 13 x saline control versus GnRH agonist treatment groups; P < 0.01). LH profiles were unchanged by surovulatory treatment. Concentrations of oestradiol-17 beta increased significantly over the three days (P < 0.001) of the superovulatory treatments in both groups (P < 0.01). These results indicate that GnRH agonist treatment allows recruited antral follicles to pursue their growth during the early selection process via sustained FSH and LH secretion allowing more than a single large follicle to maintain their growth without going to atresia.     

Cytokine profiles of HeLa and human diploid cells induced by different fractions of Vibrio parahaemolyticus cultures exposed to stress conditions

Vibrio (V.) parahaemolyticus is an aquatic halophilic bacteria which produces gastroenteritis and in rare cases septicaemia after the consumption of raw or under-cooked contaminated seafood.The severity of diarrheal illness caused by this bacterium is closely related to the presence of two types of hemolysins (the thermostable direct hemolysin-TDH and TDH related hemolysin-TRH) and also of type III secretion system (TTSS) proteins. The TTSS type 1 induces a wide array of effects on infected HeLa cells such as autophagy, oncosis, cell rounding and lysis. Previous studies have shown that heat shock proteins have the ability to stimulate the production of interleukins in different cellular cultures. In our studies we have stimulated two cellular lines (HeLa and human diploid cells) with different V. parahaemolyticus culture fractions in order to observe the effect on cytokines production. Thus, the purpose of this study was to analyze the expression of IL-1, IL-2, IL-4, IL-6, IL-10 and TNF-alpha induced by the cell treatment with total cellular lysate, periplasmic fractions and culture supernatants extracted from V. parahaemolyticus exposed to normal and also to stress conditions. The ELISA assay of the cytokine profile of the HeLa and HDC cell lines stimulated with different bacterial fractions revealed that in the V. parahemolyticus cultures submitted to osmotic and heat shock stress are accumulating factors (probably heat shock proteins) which are exhibiting immunomodulatory activity, responsible for the induction of a pro-inflammatory response associated with increased levels of IL-6 and TNF-alpha expression, however balanced by the stimulation of the anti-inflammatory cytokine IL-4 synthesis.     

Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors

Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1′ pocket.     

Structure Analysis of Two <Emphasis Type="Italic">Toxoplasma gondii</Emphasis> and <Emphasis Type="BoldItalic">Neospora caninum</Emphasis> Satellite DNA Families and Evolution of Their Common Monomeric Sequence

A family of repetitive DNA elements of approximately 350 bp—Sat350—that are members of Toxoplasma gondii satellite DNA was further analyzed. Sequence analysis identified at least three distinct repeat types within this family, called types A, B, and C. B repeats were divided into the subtypes B1 and B2. A search for internal repetitions within this family permitted the identification of conserved regions and the design of PCR primers that amplify almost all these repetitive elements. These primers amplified the expected 350-bp repeats and a novel 680-bp repetitive element (Sat680) related to this family. Two additional tandemly repeated high-order structures corresponding to this satellite DNA family were found by searching the Toxoplasma genome database with these sequences. These studies were confirmed by sequence analysis and identified: (1) an arrangement of AB1CB2 350-bp repeats and (2) an arrangement of two 350-bp-like repeats, resulting in a 680-bp monomer. Sequence comparison and phylogenetic analysis indicated that both high-order structures may have originated from the same ancestral 350-bp repeat. PCR amplification, sequence analysis and Southern blot showed that similar high-order structures were also found in the Toxoplasma-sister taxon Neospora caninum. The Toxoplasma genome database ( ) permitted the assembly of a contig harboring Sat350 elements at one end and a long nonrepetitive DNA sequence flanking this satellite DNA. The region bordering the Sat350 repeats contained two differentially expressed sequence-related regions and interstitial telomeric sequences.     

DNA double-strand breaks, recombination and synapsis: the timing of meiosis differs in grasshoppers and flies

The temporal and functional relationships between DNA events of meiotic recombination and synaptonemal complex formation are a matter of discussion within the meiotic field. To analyse this subject in grasshoppers, organisms that have been considered as models for meiotic studies for many years, we have studied the localization of phosphorylated histone H2AX (gamma-H2AX), which marks the sites of double-strand breaks (DSBs), in combination with localization of cohesin SMC3 and recombinase Rad51. We show that the loss of gamma-H2AX staining is spatially and temporally linked to synapsis, and that in grasshoppers the initiation of recombination, produced as a consequence of DSB formation, precedes synapsis. This result supports the idea that grasshoppers display a pairing pathway that is not present in other insects such as Drosophila melanogaster, but is similar to those reported in yeast, mouse and Arabidopsis. In addition, we have observed the presence of gamma-H2AX in the X chromosome from zygotene to late pachytene, indicating that the function of H2AX phosphorylation during grasshopper spermatogenesis is not restricted to the formation of gamma-H2AX foci at DNA DSBs.     

Synthesis and structural characterization of two new polynuclear metal thiosaccharinates: Hexakis(thiosaccharinato)hexasilver(I) and tetrakis(thiosaccharinato)tetracopper(I)

The title compounds, for short Ag₆(tsac)₆ (1) and [Cu₄(tsac)₄(MeCN)₂] · 2MeCN (2), were prepared by the reaction of thiosaccharin with Ag(I) or Cu(II) salts in different solvents. The new complexes were characterized by FT-IR, Raman, UV-Vis and NMR spectroscopy. Their crystal and molecular structures were determined by X-ray diffraction methods. The structures were solved from 1621 (1) and 7080 (2) reflections with I > 2σ(I) and refined to agreement R1-factors of 0.0261 (1) and 0.0456 (2). Ag₆(tsac)₆ molecule derives from the clustering of six Ag(tsac) moieties related to each other through the crystallographic 3-bar (S₆) symmetry operations of the space group. This results in a highly regular molecular structure where the silver atoms are at the corners of an octahedral core slightly compressed along one of its three-fold axis [inter-metallic Ag?Ag contacts of 3.1723(4) and 3.1556(4) Å]. The six thiosaccharinate ligands bridge neighboring Ag atoms along the C₃-axis through Ag-N bonds [d(Ag-N) = 2.285(2) Å] at one end and bifurcated Ag-S(thione)-Ag bonds [Ag-S distances of 2.4861(7) and 2.5014(8) Å] at the other end. In contrast, the 2 compound is arranged in the lattice as an irregular tetrameric copper complex [Cu₄(tsac)₄(MeCN)₂] where the metals show different environments. Two copper ions are four-fold coordinated to three tsac ions through the N-atom of one tsac [Cu-N distances of 2.112(3) and 2.064(3) Å] and the thione sulfur atom of the other two [Cu-S distances in the range from 2.284(1) to 2.358(1) Å] and to a MeCN solvent molecule [Cu-N distances of 1.983(4) and 2.052(3) Å]. The other two copper ions are in three-fold environment, one trans-coordinated to two tsac ions [Cu-N distances of 1.912(3) and 1.920(3) Å] and to the thione S-atom of a third ligand [d(Cu-S) = 2.531(1) Å], the other one to the thione sulfur atom of three tsac ligands [Cu-S distances in the range from 2.229(1) to 2.334(1) Å]. The clustering renders the metals to short distances from each other, the shorter Cu?Cu distance being 2.6033(7) Å, as to presume the existence of weak inter-metallic interaction within the cluster.