Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species Microlepia matthewii.

Introduction: Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. Methods: We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. Results and discussion: The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.

The identity of Hypolepis robusta, as a new synonym of Hypolepis alpina (Dennstaedtiaceae), based on morphology and DNA barcoding and the new distribution.

Based on field observations and examinations of herbarium specimens (including type material), consulting the original literature and molecular phylogenetic analysis of the rbcL and trnL-F sequences, it is concluded that Hypolepis robusta is conspecific with Hypolepis alpina and is here formally treated as a synonym of it. Additionally H. alpina is reported with new distribution records in Guangdong, Guangxi and the Hainan Island of China, respectively.

Hiya: A new genus segregated from Hypolepis in the fern family Dennstaedtiaceae, based on phylogenetic evidence and character evolution.

The relationship of Hypolepis brooksiae, H. nigrescens, and H. scabristipes to the remainder of Hypolepis (Dennstaedtiaceae) has been questioned by previous authors based on their unique combination of morphological characters and different base chromosome number. Using four chloroplast genes including rbcL, atpA, rpL6, and rps4-trnS intergenic spacer (IGS) from 32 samples, representing 24 species of Dennstaedtiaceae, we recovered a clade comprising H. brooksiae and H. nigrescens, distinct from the remaining species of Hypolepis. This clade is resolved as sister to the clade comprising Blotiella, Paesia and Histiopteris. We reconstructed ancestral states of 16 morphological characters and found that this clade is distinguished by indeterminate, scandent leaves exhibiting rhythmic growth, provided with recurved black-tipped prickles, and stipule-like pinnules that protect the emerging crosier and pinnae departures, rachis-costa architecture where the adaxial sulcus is confluent with the next lower order, and a base chromosome number of x = 29. In light of this molecular and morphological evidence, we describe a new genus, Hiya, and provide nomenclatural combinations to accommodate the three known species segregated from Hypolepis: Hiya brooksiae, Hiya nigrescens, and Hiya scabristipes.

Complexation of Lysozyme with Sodium Poly(styrenesulfonate) via the Two-State and Non-Two-State Unfoldings of Lysozyme.

To provide an in-depth understanding of the complexation mechanism of protein and polyelectrolyte, a heating-cooling-reheating protocol was employed to study the unfolding and refolding behaviors of a model protein, lysozyme, in the presence of a negatively charged polyelectrolyte, sodium poly(styrenesulfonate) (PSS). It was found that, with elevated PSS concentration, a new state (state I) was first formed via a "two-state" conversion process and this state could further convert to a completely unfolded state (state II) via a "non-two-state" conversion. This non-two-state conversion process occurs without the coexistence of states I and II but involves the formation of various intermediate unfolded protein structures. Different from the pure lysozyme that exhibited refolding upon cooling from its heat-denatured state, lysozyme in state I could undergo unfolding upon heating but no refolding upon cooling, while lysozyme in state II did not undergo unfolding or refolding upon thermal treatments. In addition, the effects of ionic strength and molecular weight of polyelectrolyte on the unfolding and refolding behaviors of lysozyme were also investigated. The present work provides a better understanding of the principles governing protein-polyelectrolyte interactions and may have implications for the fabrication of biocolloids and biofilms.

Hydrogen-bonding interactions between [BMIM][BF4] and acetonitrile.

In this work, the interactions between a representative imidazolium-based ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) and acetonitrile (CH3CN) were investigated in detail using attenuated total reflection infrared spectroscopy (ATR-IR), hydrogen nuclear magnetic resonance ((1)H NMR), and density functional theory calculations. The main conclusions are: (1) a number of species in the [BMIM][BF4]-CH3CN mixtures were identified with the help of excess infrared spectroscopy and quantum chemical calculations. The dilution process of the ionic liquid by acetonitrile was found to be the transformation from ion clusters to ion pairs. (2) The solvent molecules cannot break apart the strong Coulombic interaction between [BMIM](+) and [BF4](-) but can break apart the ion cluster into an ion pair within the concentration range investigated. The strength of hydrogen bonds between the C-Hs of [BMIM](+) and the N of acetonitrile is enhanced during the dilution process. (3) The methyl group of CH3CN locates above/below the imidazolium ring in the solution. These in-depth studies on the properties of the ionic liquid-acetonitrile mixed solvents may shed light on exploring their applications as reaction media in electrochemistry and chemical synthesis.

Fibrillar seeds alleviate amyloid-ß cytotoxicity by omitting formation of higher-molecular-weight oligomers.

Amyloid-ß (Aß) peptides can exist in distinct forms including monomers, oligomers and fibrils, consisting of increased numbers of monomeric units. Among these, Aß oligomers are implicated as the primary toxic species as pointed by multiple lines of evidence. It has been suggested that toxicity could be rendered by the soluble higher-molecular-weight (high-n) Aß oligomers. Yet, the most culpable form in the pathogenesis of Alzheimer's disease (AD) remains elusive. Moreover, the potential interaction among the insoluble fibrils that have been excluded from the responsible aggregates in AD development, Aß monomers and high-n oligomers is undetermined. Here, we report that insoluble Aß fibrillar seeds can interact with Aß monomers at the stoichiometry of 1:2 (namely, each Aß molecule of seed can bind to two Aß monomers at a time) facilitating the fibrillization by omitting the otherwise mandatory formation of the toxic high-n oligomers during the fibril maturation. As a result, the addition of exogenous Aß fibrillar seeds is seen to rescue neuronal cells from Aß cytotoxicity presumably exerted by high-n oligomers, suggesting an unexpected protective role of Aß fibrillar seeds.

In situ unfolded lysozyme induces the lipid lateral redistribution of a mixed lipid model membrane.

Redistribution of charged lipids induced by polyelectrolytes is an intriguing phenomenon. Proteins, due to their nature as polyelectrolytes, should also have this capacity. But their highly ordered structures may bring about more complex mechanisms. We studied the interaction between positively charged lysozyme and liposomes consisting of neutral dipalmitoylphosphatidylcholine (DPPC) and negatively charged dioleoylphosphatidylglycerol (DOPG). Interestingly, the enrichment of DOPG cannot be induced by the native and ex situ unfolded (unfolded in the absence of liposomes) lysozyme, but requires that lysozyme undergo an in situ unfolding process (unfolding in the presence of liposomes). These observations suggest that, for proteins, the capacity to induce lipid redistribution relies on not only the net charges but also the spatial distribution of the charges. During the in situ unfolding process, lysozyme reorganizes its structure into a specially unfolded structure that is rich in flat ß-sheets and more "rigid" in the presence of lipid membrane. This special spatial structure changes the charge distribution and is advantageous to the protein-membrane electrostatic interaction and thus can induce lipid redistribution.

Stepwise ordering of imidazolium-based cationic surfactants during cooling-induced crystallization.

Surfactants bearing imidazolium cations represent a new class of building blocks in molecular self-assembly. These imidazolium-based cationic surfactants can exhibit various morphologies during phase transformations. In this work, we studied the self-assembly and phase behavior of 1-hexadecyl-3-methylimidazolium chloride (C(16)mimCl) aqueous dispersions (0.5-10 wt %) by using isothermal titration calorimetry, differential scanning calorimetry, synchrotron small- and wide-angle X-ray scattering, freeze-fracture electron microscopy, optical microscopy, electrical conductance, and Fourier transform infrared spectroscopy. It was found that C(16)mimCl in aqueous solutions can form two different crystalline phases. At higher C(16)mimCl concentrations (>6 wt %), the initial spherical micelles convert directly to the stable crystalline phase upon cooling. At lower concentrations (0.5 or 1 wt %), the micelles first convert to a metastable crystalline phase upon cooling and then transform to the stable crystalline phase upon further incubation at low temperature. The electrical conductance measurement reveals that the two crystalline phases have similar surface charge densities and surface curvatures. Besides, the microscopic and spectroscopic investigations of the two crystalline phases suggest that the metastable crystalline phase has preassembled morphology and a preordered submolecular packing state that contribute to the final stable crystalline structure. The formation of a preordered structure prior to the final crystalline state deepens our understanding of the crystallization mechanisms of common surfactants and amphiphilic ionic liquids and should thus be widely recognized and explored.

Denaturation behaviors of two-state and non-two-state proteins examined by an interruption-incubation protocol.

We established an interruption-incubation protocol to study the denaturation and aggregation behaviors of two-state and non-two-state proteins, represented by hen egg-white lysozyme (lysozyme) and bovine serum albumin (BSA), by differential scanning calorimetry (DSC) and Fourier-transform infrared (FTIR) spectroscopy. After incubation at selected interrupting temperatures (T(int)), the onset temperature (T(onset)) and denaturation temperature (T(d)) of the reheating scans were found to pose distinct contrasts between the two proteins. BSA shows increasing T(onset) and T(d) as T(int) increases, whereas lysozyme exhibits invariable T(onset) and T(d). After long-time incubation, the reheating scans of BSA still show residual peaks in the DSC curves. Moderate aggregation upon incubation restricts the refolding of the thermodynamically stable unfolding intermediates in the denaturation of BSA. On the contrary, prolonged incubation at selected T(int) causes complete denaturation of lysozyme. The results were also supported by FTIR experiments. It is concluded that the variable T(onset) and T(d) indicate the unfolding of the "trapped" intermediates in the second heating scans, and the invariable T(onset) and T(d) values indicate the nonexistence of such intermediates. The examination of two additional proteins, ribonuclease A and γ-globulin, shows a similar phenomenon. The results may represent the general features of two-state and non-two-state denaturations and the protocol would serve to study protein denaturation cooperativity.

Unfolding and refolding details of lysozyme in the presence of ß-casein micelles.

In this work, we selected a small globular protein, lysozyme, to study how it unfolds and refolds in the presence of micelles composed of the unstructured ß-casein proteins by using microcalorimetry and circular dichroism spectroscopy. It was found that a partially unfolded structure of lysozyme starts to form when the ß-casein/lysozyme molar ratio is above 0.7, and the structure forms exclusively when the ß-casein/lysozyme molar ratio is above 1.6. This partially unfolded state of lysozyme loses most of its tertiary structure and after heating, the denatured lysozyme molecules are trapped in the charged coatings of ß-casein micelles and cannot refold upon cooling. The thus obtained protein complex can be viewed as a kind of special polyelectrolyte complex micelle. The net charge ratios of the two proteins and the ionic strength of the dispersions can significantly modulate the electrostatic and hydrophobic interactions between the two proteins. Our present work may have implications for the nanoparticle protein engineering therapy in the biomedicine field and may provide a better understanding of the principles governing the protein-protein interactions. Besides, the heating-cooling-reheating procedure employed in this work can also be used to study the unfolding and refolding details of the target protein in other protein-protein, protein-polymer and protein-small solute systems.

Mechanism of the fast exchange between bound and free guests in cucurbit[7]uril-guest systems.

The fast exchange is found to be due to the mismatch between the hydrophobic interaction inside the CB[7] cavity and the ion-dipole/hydrogen-bonding interactions in the port region of the CB[7]. This mismatch also induces the multi-step separation process between guest and CB[7] molecules, as elucidated by molecular dynamics simulation.

Infrared spectroscopy reveals the nonsynchronicity phenomenon in the glassy to fluid micellar transition of DSPE-PEG2000 aqueous dispersions.

One challenging question regarding the phase transition mechanism of amphiphiles is to seek the roles individual groups/portions of the amphiphilic molecule play during the transformation. To address this question, we selected a poly(ethylene glycol)-grafted phospholipid, distearoylphosphatidylethanolamine-N-[methoxy(poly(ethylene glycol))-2000] (DSPE-PEG2000), to study its glassy to fluid micellar phase transition by using differential scanning calorimetry and Fourier transform infrared (FTIR) spectroscopy. FTIR results revealed that during the glassy to fluid micellar transition, the lipid acyl tails have evident conformational rearrangements but undergo only slight modifications in the packing state. For the lipid interface region, small changes in the hydration state of C=O groups were observed, whereas for the lipid headgroups (NHCO and PO(4)(-)), their conformation and hydration states remain unchanged. Thus, the head, the interface, and the tail regions of DSPE-PEG2000 molecules change nonsynchronously during the transition. As to the bulky PEG corona residing at the outer micellar surface, no evident hydration state change was observed upon heating, and its behavior is almost the same as that of the hydrated free PEG2000 molecules. Such a nonsynchronous change in different parts of the self-assembled amphiphilic aggregates undergoing phase transition could be a common phenomenon that needs to be widely recognized.

Nonsynchronicity phenomenon observed during the lamellar-micellar phase transitions of 1-stearoyllysophosphatidylcholine dispersed in water.

Knowledge on the synchronicity or cooperativity of changes in different parts of the amphiphilic molecules is important to understand the molecular mechanisms of phase transformations of self-assembled aggregates. A long-standing and challenging question is to understand the roles individual groups/portions in an amphiphilic molecule play during phase transitions. To address this question, we selected a lysophospholipid, 1-stearoyllysophosphatidylcholine (SLPC), to study the transition mechanisms between its lamellar phase and micellar phase by using differential scanning calorimetry, small-angle X-ray scattering, Fourier transform infrared spectroscopy, and two-dimensional correlation analysis. It was found that during the lamellar to micellar transition the interfacial C=O groups and the lipid acyl tails change evidently with the former changing a little earlier, but the lipid headgroups remain unchanged in the hydration and conformation state. This means that the head, interface, and tail of SLPC molecules change nonsynchronously. Moreover, the results show that the lamellar to micellar transition is initiated by the interfacial groups. The molecular mechanism of the slow formation kinetics of the lamellar state from the micellar state was also discussed in the context of the nonsynchronicity phenomenon. The markedly different behaviors of the head and interface/tail groups during phase transitions are explained as the retention of the intermolecular attractive forces between the neighboring polar headgroups of the amphiphiles.

Expression and DNA binding activity of the tomato transcription factor RIN (ripening inhibitor).

Recently, we have found that the accumulation of ripening inhibitor (RIN) protein increased gradually during tomato fruit ripening. Here, the recombinant protein was expressed in Escherichia coli and affinity-purified. The DNA binding activity of renatured RIN protein was tested by electrophoretic mobility shift assay. The results indicated that an optimal expression and purification system was suitable for obtaining active RIN with DNA binding activity.