High-throughput thermal stability assessment of DNA hairpins based on high resolution melting

On the basis of high-resolution melting, a high-throughput approach to measure melting temperatures (T_ms) of short DNA hairpins was developed. With this method, T_ms of thousands of triloop, tetraloop, and pentaloop hairpins involving various loop sequences and various closing base pairs (cbp) were obtained in hours. The stability of triloop hairpins decreased with the change of cbp (5′–3′) in the order of c-g > g-c > t-a ≥ a-t, showing that the cbp of 5′-Pyr-Pur-3′ (Pyr = pyrimidine, Pur = purine) contributed more stability than 5′-Pur-Pyr-3′. For tetraloop hairpins, GNNA, GNAB, and CNNG (N = A, G, C, or T; B = G, C, or T) were found to be highly stable irrespective of the cbp type. TNNA was also stable in both g-c and a-t families, while CGNA only in the c-g family. Pentaloop hairpins of cTGNAGg, cGNYNAg (Y = T or C) and cCGNNAg were exceptionally stable motifs. In most cases, pyrimidine-rich loops were more favorable to stabilize the whole structure than purine-rich ones. The present approach showed a good performance in assessing the thermal stability of large amounts of DNA hairpins comprehensively. These data are useful to understand the sequence dependence of the stability of DNA secondary structures and promising to improve the structure simulation by consummating basic databases.     

Determination of endogenous faecal phosphorus loss in goats

Four black Liuyang wether goats were fed with corn stover and concentrate formulated to contain four levels of dietary phosphorus (P), including 0.129, 0.140, 0.162 and 0.180% of P. In a 4 × 4 Latin square experiment the endogenous faecal P loss was determined by the regression technique and the substitution method. Treatment effects on faecal and urinary P output, apparent P digestibility and P retention, and saliva P secretion were not significant. A linear relationship was observed between apparent faecal digestible P (Y, g/kg DMI) and P intake (X, g/kg DMI), which was described by the equation: Y = 0.4799X ?0.9209, r² = 0.9869, (p < 0.05). The true P digestibility determined by the regression technique and the substitution method amounted to 48.0 and 48.9%, respectively; the recorded endogenous faecal P losses were 0.92 and 0.93 g/kg DMI, respectively. The study demonstrated the potential of the regression method as well as the substitution method for estimation of true P digestibility and endogenous faecal P losses in goats.     

Historical introduction,geographical distribution,and biological characteristics of alien plants in China

Using the published literature and records, this study investigated the historical introduction, geographical distribution, and biological characteristics of 404 alien plants in 32 provinces (including municipalities) in China. The results showed that three fifths of the alien plants was introduced for intentional purposes, and the introduction of alien plants increased with time from 139 BC to the current time, especially during historical events that played an important part in the process of introduction. The geographical distribution of alien plant species tended to decrease from the south and the east to the north and the west. Annual average precipitation (Y = 7.51X + 7.05, R² = 0.67) and temperature (Y = 0.07X + 41.54, R² = 0.67) had a linear relationship with alien plant introduction throughout China. Furthermore, population density and economic conditions also affected and promoted plant invasions in China. The life forms were well adapted to regional precipitation and temperature, but different life forms of alien plants were not consistent with the distribution tendency based on the quantity of alien plants. There was a higher percentage of annual and biennial plants in the northern provinces (e.g. 66.7 and 15.7% in Inner Mongolia), whereas there were more perennial and woody plant species in the southern provinces (e.g. 37.0 and 21.2% in Hainan). Family characteristics could not accurately predict plant invasions; however, predictions based on genera were acceptable. In addition, the origin of alien plants can also predict the distribution and potential risk of invasions. Thus, our study investigated the factors affecting plant invasions in order to provide information on the prevention and control of alien plants.     

Theoretical study of noncovalent interactions in XCN···YO<Subscript>2</Subscript>H (X = F,Cl, Br,I; Y = P,As, Sb) complexes

Noncovalent interactions in XCN···YO₂H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or dual interactions. An examination of binding distances and interaction energies suggested that π-hole bonds are more stable than the other interactions. Molecular electrostatic potentials, electron densities, second-order stabilization energies, and electron density differences were computed to study the character of these interactions.     

Synthesis and Biological Activity of N-Sulfonyltripeptides with C-Terminal Arginine as Potential Serine Proteases Inhibitors

Tripeptides of the general X-SO₂-d-Ser-AA-Arg-CO-Y formula, where X = α-tolyl, p-tolyl, 2,4,6-triisopropylphenyl; AA = alanine, glycine, norvaline and Y = OH, NH-(CH₂)₅NH₂ were obtained and tested for their effect on the amidolytic activities of urokinase, thrombin, trypsin, plasmin, t-PA and kallikrein. The most active compound towards urokinase was PhCH₂SO₂-d-Ser-Gly-Arg-OH with K_i value 5.4 μM and the most active compound toward thrombin was PhCH₂SO₂-d-Ser-NVa-Arg-OH with K_i value 0.82 μM. The peptides were nontoxic against porcine erythrocytes in vitro. PhCH₂SO₂-d-Ser-Gly-Arg-OH showed cytotoxic effect against DLD cell lines with IC₅₀ values of 5 μM. For the highly selective determination of the interaction of some of the synthesised acids of tripeptides with urokinase and plasmin the Surface Plasmon Resonance Imaging sensor has been applied. These compounds bind to urokinase and plasmin in 0.05 mM concentration.     

Alleviation of metal and BTEX inhibition on BTEX degradation using PVA-immobilized degrader: kinetic model of BTEX degradation

Alleviation of metal inhibition on BTEX degradation using PVA-immobilized degrader (Mycobacterium sp. CHXY119) was investigated. When BTEX of 29 mg L^?1 [B:T:E:X = 1:1:1:1 (mg)] was used, more than 99 % of BTEX was simultaneously degraded by the free cells within 170 h. In contrast, BTEX of 114–172 mg L^?1 seriously inhibited degradation. High concentrations of metals (Mn²⁺: 15, Ni²⁺: 10, and Zn²⁺: 10 mg L^?1) also strongly inhibited BTEX degradation by the free cells at BTEX of 29 mg L^?1. Immobilization of degraders alleviated the inhibition of BTEX and heavy metals at high concentrations. A modified non-competitive inhibition model well described the BTEX degradation by the free and immobilized cells in the absence and presence of metal ions (R ² = 0.92–0.99). The above results provide valuable information on treatment of metal-BTEX co-contaminated wastewater by the immobilized degrader.     

Influenza della temperatura sullo sviluppo della “Dicranophora fulva„ Schröter

Abstract

Karyotype features and microsporogenesis of Tripogandra diuretica (Mart.) Handlos and Tripogandra glandulosa (Seub.) Rohw. from 15 NE Argentina accessions are analysed via classical cytogenetics, CMA/DA/DAPI and Ag-NOR. The karyotype of T. glandulosa (2n = 2x = 16; 2m + 6sm + 8st) is bimodal (A ₂ = 0.37; R = 2.65) and asymmetrical (A ₁ = 0.63; i = 26.06; r > 2 = 0.88) (3B-Stebbins) with a genome size of 33.28 μm; two pairs are satellited, CMA+ and NOR-actives. Another four CMA+ loci and DAPI+ universal centromeric heterochromatin occur. Microsporogenesis is normal (pollen viability short stamens = 97.8%; large = 96.7%), meiotic behaviour is regular and chromosomes pair as 8II. The karyotype of T. diuretica (2n = 8x = 64; 8m + 24sm + 32st) is bimodal (A ₂ = 0.27; R = 2.54) and asymmetrical (A ₁ = 0.60; i = 27.32; r > 2 = 0.88) (3B-Stebbins); additionally, two pairs are satellited. Microsporogenesis is normal (short stamens = 77.8%; large = 68.5%), except for micronuclei and low pollen viability in some accessions. Meiotic behaviour is regular with 32II, acting as a cytological diploid, however the arrangement of the haploid karyotype suggests that T. diuretica, which also exhibits a reduction of the genome size (18.58 μm), constitutes an auto-octoploid taxa. Additionally, both species share cytological features common to karyotype orthoselection.     

Karyotype analysis and DNA content in some species of Chrysolaena (Vernonieae,Asteraceae)

Cytogenetic characterization by karyotyping and determination of DNA content by flow cytometry of five species of Chrysolaena (Vernonieae, Asteraceae) was performed. This is the first study of nuclear DNA content realized in the genus. The 2C-values were compared with the ploidy level and the total karyotype length (TKL) of each species. Mitotic analysis revealed a base chromosome number x = 10 for all entities and different ploidy levels, from diploid (2n = 2x = 20) to octoploid (2n = 8x = 80). All species showed bimodal karyotypes composed of metacentric and submetacentric chromosomes. The average chromosome size (ML) varied from 1.86 μm to 2.70 μm, while the TKL ranged from 18.65 μm to 80.55 μm. The intrachromosomal asymmetry index (A₁) varied from 0.27 to 0.38, while the interchromosomal asymmetry index (A₂) ranged from 0.19 to 0.25. A new cytotype is reported for the first time for C. propinqua. Accessory chromosomes found in C. verbascifolia, C. cognata, C. flexuosa, and C. propinqua are also reported as new.     

In ovo silver nanoparticle supplementation for improving the post-hatch immunity status of broiler chickens

Silver nanoparticles (AgNano) are known for their unique physical, chemical and biological properties, enabling cell penetration and anti-inflammatory response. In Experiment 1, the effect of an in ovo administration of AgNano (15 µg/egg; n = 360) at different incubation times (d 7 and d 18) on hatchability parameters was explored. In Experiment 2, post-hatch performance of broilers (42 d, n = 250) was studied after in ovo AgNano administration: Group T1 remained un-injected, Group T2 was the sham control and Groups T3, T4 and T5 were injected with 12.5, 25 and 50 µg AgNano, respectively, at 18 d of incubation. Chick weight, chick to egg weight ratio and hatchability as well average daily gain, average daily feed intake and feed conversion ratio were similar in all treatment groups. No variation was seen in the weight of thymus; however, the bursa and spleen weight was increased (p < 0.05) in Groups T4 and T5 in comparison to Group T1. The in vivo immune response to phytohaemagglutinin-P was increased in Group T3 in comparison to Groups T1 and T2 (p < 0.05), while the response to sheep red blood cells was increased in all AgNano-treated groups in comparison with Group T1 (p < 0.01). The expression of toll-like receptors 2 and 4 genes was up-regulated in AgNano groups in comparison with Groups T1 and T2 (p < 0.01). In summary, an in ovo supplementation of AgNano carried out at d 18 of incubation is effective and modulates the post-hatch immune response without affecting the hatchability, growth and other performance parameters in broilers.     

The novel human MRC1 gene polymorphisms are associated with susceptibility to pulmonary tuberculosis in Chinese Uygur and Kazak populations

The MRC1 gene, encoding the human mannose receptor (MR), is a member of the C-type lectin receptors family. MR can recognize and bind to Mycobacterium tuberculosis by the extracellular structure, and play a role in antigen-presenting and maintaining a stable internal environment. This study aimed to investigate potential associations of SNPs in exon 7 of the MRC1 gene with pulmonary tuberculosis (TB). G1186A, G1195A, T1212C, C1221G, C1303T and C1323T were genotyped using PCR and DNA sequencing in 595 Chinese Uygur and 513 Kazak subjects. In the Uygur, the frequency of allele G (P = 0.031, OR = 1.29, 95 % CI = 1.02–1.62) and AA genotype (P = 0.033, OR = 1.64, 95 % CI = 1.04–2.60) for G1186A was lower in the pulmonary TB than healthy control and were significantly correlated with pulmonary TB. After adjustment for age and gender, G1186A was found to be additive models in association with pulmonary TB (P = 0.04, OR = 1.27, 95 % CI = 1.01–1.60). By calculating linkage disequilibrium, the frequency of haplotype GGTCCT (P = 0.032, OR = 0.75, 95 % CI = 0.57–0.97) and GGTCCC (P = 0.044, OR = 0.57, 95 % CI = 0.33–0.99) was significantly associated with pulmonary TB. No association was found between other SNPs and pulmonary TB. In the Kazak, all SNPs were not associated with pulmonary TB. Our results suggest that genetic factors play an important role in susceptibility to pulmonary TB at the individual level, and provide an experimental basis to clarify the pathogenesis of pulmonary TB.     

Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases

Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. ΔG values were ?15.82(12), ?3.66(12), and ?12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (r = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.     

Design,synthesis, MTT assay,DNA interaction studies of platinum(II) complexes

The square planar Pt(II) complexes of the type [Pt(Lⁿ)(Cl₂)] (where Lⁿ = L^1?3 = thiophene-2-carboxamide derivatives and L^4?6 = thiophene-2-carbothioamide derivatives) have been synthesized and characterized by physicochemical and various spectroscopic studies. MIC method was employed to inference the antibacterial potency of complexes in reference to free ligands and metal salt. Characteristic binding constant (K_b) and binding mode of complexes with calf thymus DNA (CT-DNA) were determined using absorption titration (0.76–1.61 × 10⁵ M^?1), hydrodynamic chain length assay and fluorescence quenching analysis, deducing the partial intercalative mode of binding. Molecular docking calculation displayed free energy of binding in the range of –260.06 to –219.63 kJmol^?1. The nuclease profile of complexes towards pUC19 DNA shows that the complexes cleave DNA more efficiently compared to their respective metal salt. Cytotoxicity profile of the complexes on the brine shrimp shows that all the complex exhibit noteworthy cytotoxic activity with LC₅₀ values ranging from 7.87 to 15.94 μg/mL. The complexes have been evaluated for cell proliferation potential in human colon carcinoma cells (HCT 116) and IC₅₀ value of complexes by MTT assay (IC₅₀ = 125–1000 μg/mL).     

Ewing Sarcoma: influence of TP53 Arg72Pro and MDM2 T309G SNPs

The Ewing Sarcoma is an important tumor of bone and soft tissue. The SNPs Arg72Pro of TP53 and T309G of MDM2 have been associated with many cancer types and have been differently distributed among populations worldwide. Based on a case–control design, this study aimed to assess the role of these SNPs in 24 Ewing Sarcoma patients, compared to 91 control individuals. DNA samples were extracted from blood and genotyped for both SNPs by PCR–RFLP and confirmed by DNA sequencing. The results showed an association between the G allele of the T309G and Ewing Sarcoma (P = 0.02). Comparing to the TT carriers, the risk of G allele carriers was 3.35 (95 % CI = 1.22–9.21) with P = 0.02. At the genotypic level, an association of the TT genotype with the control group (P = 0.03) was found. Comparing to the TT genotype, the risk of TG and GG was 2.97 (95 % CI = 1.03–8.58) with P = 0.04 and 5.00 (95 % CI = 1.23–20.34) with P = 0.02, respectively. No associations regarding the Arg72Pro SNP were found. Considering that the T309G has been associated with several types of cancer, including sarcomas, our results indicate that this SNP may also be important to Ewing Sarcoma predisposition.     

Chronotype and depressive symptoms in students: An investigation of possible mechanisms

ABSTRACT

Individuals with an evening chronotype are at increased risk of experiencing emotional problems, including depressive symptoms. However, the mechanisms underlying these associations remain unclear. The present study aimed to determine whether poor sleep quality, substance use and cognitive emotion regulation difficulties – which have been implicated in the etiology of depression – mediate the relationship between chronotype and depressive symptoms in a student sample, which was assessed cross-sectionally and after 1 year. A total of 742 Dutch students (75% women, mean age 21.4 ± 2.9 years) completed the Quick Inventory of Depressive Symptomatology, the Morningness-Eveningness Questionnaire, the Pittsburgh Sleep Quality Index, a questionnaire assessing alcohol, caffeine, tobacco and cannabis use, the Cognitive Emotion Regulation Questionnaire and the Behavioral Inhibition/Activation Scale. A subsample (n = 115) was assessed 1 year later with the same questionnaires. Cross-sectional analyses showed that evening chronotype was associated with more depressive symptoms, adjusted for age and gender (β = ?0.082, p = 0.028). The relationship between eveningness and depressive symptoms was mediated by sleep quality, alcohol consumption and the cognitive emotion regulation strategies of self-blame and positive reappraisal. In longitudinal analyses, eveningness at baseline predicted more depressive symptoms at follow-up, adjusted for age and gender (β = ?0.29, p = 0.002); after additional adjustment for baseline depressive symptoms, chronotype remained a significant predictor of depressive symptoms at T2 (β = ?0.16, t = ?2.01, p = 0.047). Only poor sleep quality at follow-up was a significant mediator of this relationship. Even though the effect is small in terms of explained variance, eveningness is related to depressive symptoms and this relationship is mediated by poor sleep quality, also in a prospective design. Self-blame and reduced positive reappraisal are correlated with eveningness. Further research is needed to assess the efficacy of chronotherapeutic interventions for the prevention of depression, in addition to sleep education and cognitive approaches.     

Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface

Ar–CF₄ intermolecular interaction potential is studied by ab initio calculations at the MP2 and CCSD(T) levels of theory containing the so-called bond functions ({3s3p2d1f} basis set was chosen) both with and without a correction for the basis-set superposition error. The calculations were performed with Dunning's correlation consistent basis sets (aug-cc-pVXZ, X = D, T, Q, 5) to extrapolate the Ar–CF₄ potential energy minimum and intermolecular distance to their complete basis set (CBS) limits. It is shown that the addition of bond functions results in a dramatic improvement in the convergence of the calculated interaction energies at the MP2/aug-cc-pVTZ level. The MP2/{3s3p2d1f}-aug-cc-pVTZ potential energy surface even approaches the CCSD(T)/aug-cc-pVQZ potential energy surface. The potential energy minima and the intermolecular distances are both significantly closer to the CBS limit when using the bond functions, and it implies that adding bond functions in the calculation has a great effect on the interaction energies. We also find that with bond functions included in the CCSD(T)/aug-cc-pVDZ model chemistry, the potential energy minima are extremely close to the CBS limit and are better than the CCSD(T)/aug-cc-pVQZ values. Several levels of theory described in the text were used to determine pairwise analytic potential energy surfaces for Ar+CF₄. The analytic potential energy surfaces are in very good agreement with the ab initio values.     

Sex change and sequential hermaphroditism in Tegillarca granosa (Bivalvia: Arcidae)

This study aimed to confirm sex change in Tegillarca granosa to determine whether this species is a sequential hermaphrodite. Samples of bivalves were divided into two groups, namely, a 1+ year class (14 months) and a 2+ year class (26 months), for analysis. At the beginning of the study, 44.3% of T. granosa were female, and after one year, this increased to 53.9% in the same population. The increase of females in the population was greater in the 1+ year class (12.3%), when compared with the 2+ year class (6.5%). Overall, a sex change ratio of 15.1% (n = 104/688) was recorded for T. granosa. The sex change ratio of the 1+ year class (17.8%) was higher than that of the 2+ year class (12.1%), and displayed the tendency of being higher in the males (21.2%), than the females (6.2%). The results of this study indicate that T. granosa is a sequential hermaphrodite.     

PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis,Binding Properties,and Enzymatic Stability

Abstract

Three chimeric dimer synthons (oeg_t^NHT, oeg_up^NHT and oeg_uh^NHT) containing thymine (t), 5-(l-propynyl)-uracil (up) and 5-(1-hexyn-1-yl)-uracil (uh) PNA units with N-(2-hydroxyethyl)glycine (oeg) backbone were synthesized in solution and incorporated into T₂₀ oligonucleotide analogues, using standard P-amidite chemistry. Insertion of dimer blocks led to destabilization of duplexes with dA₂₀ target. The smallest T _m drops were found for chimeras containing oeg_up^NHT dimers. Incorporation of the chimeric synthons into the 3′-end of T₂₀ brought about growing resistance to 3′-exonucleolytic (SV PDE) cleavage in the order of oeg_t^NHT < oeg_up^NHT < oeg_uh^NHT. Due to different endonuclease activities of 3′- and 5′-exonucleases applied, placing of five consecutive dimers at the 5′-terminus resulted in a relatively smaller, but also side-chain dependent, stabilization towards the hydrolysis by 5′-exonuclease (BS PDE). Neither exonucleases (SV and BS PDE) nor an endonuclease (Nuclease P₁) could hydrolyse the unnatural phosphodiester bond linking the 3′-OH of thymidine to the terminal OH of N-(2-hydroxyethyl)glycine PNA backbone.