Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).

BACKGROUND: Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS: In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS: The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery.

DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.

Amyloidogenic and non-amyloidogenic molten globule conformation of ß-lactoglobulin in self-crowded regime.

Molecular insights on the ß-lactoglobulin thermal unfolding and aggregation are derived from FTIR and UV Resonance Raman (UVRR) investigations. We propose an in situ and in real-time approach that thanks to the identification of specific spectroscopic markers can distinguish the two different unfolding pathways pursued by ß-lactoglobulin during the conformational transition from the folded to the molten globule state, as triggered by the pH conditions. For both the investigated pH values (1.4 and 7.5) the greatest conformational variation of ß-lactoglobulin occurs at 80 °C and a high degree of structural reversibility after cooling is observed. In acidic condition ß-lactoglobulin exposes to the solvent its hydrophobic moieties in a much higher extent than in neutral solution, resulting on a highly open conformation. Moving from the diluted to the self-crowded regime, the solution pH and consequently the different molten globule conformation select the amyloid or non-amyloid aggregation pathway. At acidic condition the amyloid aggregates form during the heating cycle leading to the formation of transparent hydrogel. On the contrary, in neutral condition the amyloid aggregates never form. Information on the secondary structure conformational change of ß-lactoglobulin and the formation of amyloid aggregates are obtained by FTIR spectroscopy and are related to the information of the structural changes localized around the aromatic amino acid sites by UVRR technique. Our results highlight a strong involvement of the chain portions where tryptophan is located on the formation of amyloid aggregates.

Multi-length scale structural investigation of lysozyme self-assembly.

Reactive amyloid oligomers are responsible for cytotoxicity in amyloid pathologies and because of their unstable nature characterizing their behavior is a challenge. The physics governing the self-assembly of proteins in crowded conditions is extremely complex and its comprehension, despite its paramount relevance to understanding molecular mechanisms inside cells and optimizing pharmaceutical processes, remains inconclusive. Here, we focus on the amyloid oligomerization process in self-crowded lysozyme aqueous solutions in acidic conditions. We reveal that the amyloid oligomers form at high protein concentration and low pH. Through multi-length scale spectroscopic investigations, we find that amyloid oligomers can further interconnect with each other by weak and non-specific interactions forming an extended network that leads to the percolation of the whole system. Our multi-length scale structural analysis follows the thermal history of amyloid oligomers from different perspectives and highlights the impact of hierarchical self-assembly of biological macromolecules on functional properties.

Temperature Dependence of Spin-Phonon Coupling in [VO(acac)2]: A Computational and Spectroscopic Study.

Molecular electronic spins are good candidates as qubits since they are characterized by a large tunability of their electronic and magnetic properties through a rational chemical design. Coordination compounds of light transition metals are promising systems for spin-based quantum information technologies, thanks to their long spin coherence times up to room temperature. Our work aims at presenting an in-depth study on how the spin-phonon coupling in vanadyl-acetylacetonate, [VO(acac)2], can change as a function of temperature using terahertz time-domain spectroscopy and density functional theory (DFT) calculations. Powder THz spectra were recorded between 10 and 300 K. The temperature dependence of vibrational frequencies was then accounted for in the periodic DFT calculations using unit-cell parameters measured at two different temperatures and the optimized ones, as usually reported in the literature. In this way, it was possible to calculate the observed THz anharmonic frequency shift with high accuracy. The overall differences in the spin-phonon coupling magnitudes as a function of temperature were also highlighted showing that the computed trends have to be ascribed to the anisotropic variation of cell parameters.

Exploring the Organometallic Route to Molecular Spin Qubits: The [CpTi(cot)] Case.

The coherence time of the 17-electron, mixed sandwich complex [CpTi(cot)], (η8 -cyclooctatetraene)(η5 -cyclopentadienyl)titanium, reaches 34 µs at 4.5 K in a frozen deuterated toluene solution. This is a remarkable coherence time for a highly protonated molecule. The intramolecular distances between the Ti and H atoms provide a good compromise between instantaneous and spin diffusion sources of decoherence. Ab initio calculations at the molecular and crystal packing levels reveal that the characteristic low-energy ring rotations of the sandwich framework do not yield a too detrimental spin-lattice relaxation because of their small spin-phonon coupling. The volatility of [CpTi(cot)] and the accessibility of the semi-occupied, non-bonding d z 2 orbital make this neutral compound an ideal candidate for single-qubit addressing on surface and quantum sensing in combination with scanning probe microscopy.

Pressure Effects on Water Dynamics by Time-Resolved Optical Kerr Effect.

Despite water being the most common and most widely studied substance in the world, it still presents unknown aspects. In particular, water shows several thermodynamic and dynamical anomalies in the liquid and supercooled metastable phases, and the natures of these phases are still hotly debated. Here, we report measurements of water using the optical Kerr effect as a function of pressure along two isotherms, at 273 K from 0.1 to 750 MPa and at 297 K from 0.1 to 1350 MPa, reaching the supercooled metastable phase. The structural relaxation and the low frequency vibrational dynamics of water show a peculiar pressure dependence similar to that of other dynamical properties. The data analysis suggests the presence in the water phase diagram of a crossover area that divides two regions characterized by different dynamic regimes, which appear to be related to two liquid forms, one dominated by the high density water and the other by the low density water.

A non-traditional approach to cryopreservation by ultra-rapid cooling for human mesenchymal stem cells.

Cryopreservation is the most common method for long-term cell storage. Successful cryopreservation of cells depends on optimal freezing conditions, freezer storage and a proper thawing technique to minimize the cellular damage that can occur during the cryopreservation process. These factors are especially critical for sensitive stem cells with a consequential and significant impact on viability and functionality. Until now, slow-freezing has been the routine method of cryopreservation but, more recently rapid-cooling techniques have also been proposed. In this study, an ultra-rapid cooling technique [1] was performed for the first time on human mesenchymal stem cells and the effectiveness evaluated in comparison with the conventional slow-freezing procedure. A thin nylon-membrane carrier was used combined with different cryoprotective agents: dimethyl sulfoxide, ethylene glycol and/or trehalose. Various aspects of the low cryoprotective doses and the ultra-rapid cooling procedure of the human mesenchymal stem cells were examined including: the physical properties of the nylon-support, cells encumbrance, viability, proliferation and differentiation. The expression of cell surface markers and apoptosis were also investigated. The study used an ultra-rapid cooling/warming method and showed an overall cell integrity preservation (83-99%), with no significant differences between dimethyl sulfoxide or ethylene glycol treatment (83-87%) and a substantial cell viability of 68% and 51%, respectively. We confirmed a discrepancy also observed by other authors in cell viability and integrity, which implies that caution is necessary when assessing and reporting cell viability data.

First-Principles Investigation of Spin-Phonon Coupling in Vanadium-Based Molecular Spin Quantum Bits.

Paramagnetic molecules can show long spin-coherence times, which make them good candidates as quantum bits (qubits). Reducing the efficiency of the spin-phonon interaction is the primary challenge toward achieving long coherence times over a wide temperature range in soft molecular lattices. The lack of a microscopic understanding about the role of vibrations in spin relaxation strongly undermines the possibility of chemically designing better-performing molecular qubits. Here we report a first-principles characterization of the main mechanism contributing to the spin-phonon coupling for a class of vanadium(IV) molecular qubits. Post-Hartree-Fock and density functional theory methods are used to determine the effect of both intermolecular and intramolecular vibrations on modulation of the Zeeman energy for four molecules showing different coordination geometries and ligands. This comparative study provides the first insight into the role played by coordination geometry and ligand-field strength in determining the spin-lattice relaxation time of molecular qubits, opening an avenue to the rational design of new compounds.

Time-domain THz spectroscopy of the characteristics of hydroxyapatite provides a signature of heating in bone tissue.

Because of the importance of bone in the biomedical, forensic and archaeological contexts, new investigation techniques are constantly required to better characterize bone ultrastructure. In the present paper, we provide an extended investigation of the vibrational features of bone tissue in the 0.1-3 THz frequency range by time-domain THz spectroscopy. Their assignment is supported by a combination of X-ray diffraction and DFT-normal modes calculations. We investigate the effect of heating on bone tissue and synthetic calcium-phosphates compounds with close structure and composition to bone mineral, including stoichiometric and non-stoichiometric hydroxyapatite (HA), tricalcium phosphate, calcium pyrophosphate and tetracalcium phosphate. We thus demonstrate that the narrow vibrational mode at 2.1 THz in bone samples exposed to thermal treatment above 750 °C arises from a lattice mode of stoichiometric HA. This feature is also observed in the other synthetic compounds, although weaker or broader, but is completely smeared out in the non-stoichiometric HA, close to natural bone mineral composition, or in synthetic poorly crystalline HA powder. The THz spectral range therefore provides a clear signature of the crystalline state of the investigated bone tissue and could, therefore be used to monitor or identify structural transitions occurring in bone upon heating.

Scaling Up Electronic Spin Qubits into a Three-Dimensional Metal-Organic Framework.

Practical implementation of highly coherent molecular spin qubits for challenging technological applications, such as quantum information processing or quantum sensing, requires precise organization of electronic qubit molecular components into extended frameworks. Realization of spatial control over qubit-qubit distances can be achieved by coordination chemistry approaches through an appropriate choice of the molecular building blocks. However, translating single qubit molecular building units into extended arrays does not guarantee a priori retention of long quantum coherence and spin-lattice relaxation times due to the introduced modifications over qubit-qubit reciprocal distances and molecular crystal lattice phonon structure. In this work, we report the preparation of a three-dimensional (3D) metal-organic framework (MOF) based on vanadyl qubits, [VO(TCPP-Zn2-bpy)] (TCPP = tetracarboxylphenylporphyrinate; bpy = 4,4'-bipyridyl) (1), and the investigation of how such structural modifications influence qubits' performances. This has been done through a multitechnique approach where the structure and properties of a representative molecular building block of formula [VO(TPP)] (TPP = tetraphenylporphyrinate) (2) have been compared with those of the 3D MOF 1. Pulsed electron paramagnetic resonance measurements on magnetically diluted samples in titanyl isostructural analogues revealed that coherence times are retained almost unchanged for 1 with respect to 2 up to room temperature, while the temperature dependence of the spin-lattice relaxation time revealed insights into the role of low-energy vibrations, detected through terahertz spectroscopy, on the spin dynamics.

Structural Effects on the Spin Dynamics of Potential Molecular Qubits.

Control of spin-lattice magnetic relaxation is crucial to observe long quantum coherence in spin systems at reasonable temperatures. Such a control is most often extremely difficult to achieve, because of the coexistence of several relaxation mechanisms, that is direct, Raman, and Orbach. These are not always easy to relate to the energy states of the investigated system, because of the contribution to the relaxation of additional spin-phonon coupling phenomena mediated by intramolecular vibrations. In this work, we have investigated the effect of slight changes on the molecular structure of four vanadium(IV)-based potential spin qubits on their spin dynamics, studied by alternate current (AC) susceptometry. The analysis of the magnetic field dependence of the relaxation time correlates well with the low-energy vibrational modes experimentally detected by time-domain THz spectroscopy. This confirms and extends our preliminary observations on the role played by spin-vibration coupling in determining the fine structure of the spin-lattice relaxation time as a function of the magnetic field, for S = 1/2 potential spin qubits. This study represents a step forward in the use of low-energy vibrational spectroscopy as a prediction tool for the design of molecular spin qubits with long-lived quantum coherence. Indeed, quantum coherence times of ca. 4.0-6.0 µs in the 4-100 K range are observed for the best performing vanadyl derivatives identified through this multitechnique approach.

Spin Dynamics and Low Energy Vibrations: Insights from Vanadyl-Based Potential Molecular Qubits.

Here we report the investigation of the magnetization dynamics of a vanadyl complex with diethyldithiocarbamate (Et2dtc-) ligands, namely [VO(Et2dtc)2] (1), in both solid-state and frozen solution. This showed an anomalous and unprecedentedly observed field dependence of the relaxation time, which was modeled with three contributions to the relaxation mechanism. The temperature dependence of the weight of the two processes dominating at low fields was found to well correlate with the low energy vibrations as determined by THz spectroscopy. This detailed experimental comparative study represents a fundamental step to understand the spin dynamics of potential molecular quantum bits, and enriches the guidelines to design molecule-based systems with enhanced quantum coherence.

Pfeiffer syndrome: literature review of prenatal sonographic findings and genetic diagnosis.

PURPOSE: Pfeiffer syndrome (PS) is an autosomal dominant disorder caused by mutations in FGFR1 and FGFR2 genes. Given its wide range of clinical expression and severity, early prenatal diagnosis is difficult and genetic counseling is desirable. We report a literature review of all prenatal diagnosis of PS and a case report, with a focused description of ultrasound findings. METHODS: After literature search, we selected 14 studies of antenatal diagnosis of PS. Prenatal ultrasound findings, outcome, maternal and obstetrical data and genetic tests were recorded and analyzed. RESULTS: A total of 18 cases including the one we present were selected. Among the most frequent sonographic features, skull shape anomalies were evident in 72.2% of cases, nasal abnormalities in 50%, proptosis and hypertelorism in 44.4% and frontal bossing in 22.2%. Thumbs' anomalies were present in 33.3% of cases and toes' abnormalities in 38.9%. In all cases, postnatal or postmortem examination confirmed the prenatal diagnosis of PS. CONCLUSIONS: We provide a literature review of prenatal diagnosis of PS to identify ultrasound features that may be supportive in the diagnosis of this rare disease, helping in making a differential diagnosis with the other possible craniosynostosis syndromes and in suggesting gene molecular testing.

Wharton's jelly mesenchymal stromal cells have contrasting effects on proliferation and phenotype of cancer stem cells from different subtypes of lung cancer.

Studies on the role of multipotent mesenchymal stromal cells (MSC) on tumor growth have reported both a tumor promoting and a suppressive effect. The aim of the present study was to determine the effect of MSC isolated from Wharton's jelly of umbilical cord (WJMSC) on lung cancer stem cells (LCSC) derived from human lung tumors: two adenocarcinomas (AC) and two squamous cell carcinomas (SCC). LCSC derived from SCC and AC expressed, to varying extents, the more relevant stem cell markers. The effect of WJMSC on LCSC was investigated in vitro using conditioned medium (WJ-CM): a proliferation increase in AC-LCSC was observed, with an increase in the ALDH+ and in the CD133+ cell population. By contrast, WJ-CM hampered the growth of SCC-LCSC, with an increase in the pre-G1 phase indicating the induction of apoptosis. Furthermore, the ALDH+ and CD133+ population was also reduced. In vivo, subcutaneous co-transplantation of AC-LCSC/WJMSC generated larger tumors than AC-LCSC alone, characterized by an increased percentage of CD133+ and CD166+ cells. By contrast, co-transplantation of WJMSC and SCC-LCSC did not affect the tumor size. Our results strongly suggest that WJMSC exert, both in vitro and in vivo, contrasting effects on LCSC derived from different lung tumor subtypes.

Vibrational Spectroscopy and Dynamics of Water.

We present an overview of recent static and time-resolved vibrational spectroscopic studies of liquid water from ambient conditions to the supercooled state, as well as of crystalline and amorphous ice forms. The structure and dynamics of the complex hydrogen-bond network formed by water molecules in the bulk and interphases are discussed, as well as the dissipation mechanism of vibrational energy throughout this network. A broad range of water investigations are addressed, from conventional infrared and Raman spectroscopy to femtosecond pump-probe, photon-echo, optical Kerr effect, sum-frequency generation, and two-dimensional infrared spectroscopic studies. Additionally, we discuss novel approaches, such as two-dimensional sum-frequency generation, three-dimensional infrared, and two-dimensional Raman terahertz spectroscopy. By comparison of the complementary aspects probed by various linear and nonlinear spectroscopic techniques, a coherent picture of water dynamics and energetics emerges. Furthermore, we outline future perspectives of vibrational spectroscopy for water researches.

Prenatal diagnosis of proximal focal femoral deficiency: Literature review of prenatal sonographic findings.

Proximal focal femoral deficiency (PFFD) is a rare musculoskeletal malformation that occurs in 0.11-0.2 per 10,000 live births. This congenital anomaly involves the pelvis and proximal femur with widely variable manifestations, from mild femoral shortening and hypoplasia to the absence of any functional femur and acetabular aplasia. Prenatal diagnosis of PFFD is still a challenge, but early recognition of this malformation could provide useful information to both parents and physicians concerning management and therapeutic planning. For this review, we analyzed all the cases of prenatally diagnosed PFFD that were reported in the literature from 1990 to 2014 and provide a description of the most common prenatal sonographic findings.

A comparative study on bulk and nanoconfined water by time-resolved optical Kerr effect spectroscopy.

The low frequency (nu < 500 cm(-1)) vibrational spectra of hydrated porous silica are specifically sensitive to the hydrogen bond interactions and provide a wealth of information on the structural and dynamical properties of the water contained in the pores of the matrix. We investigate systematically this spectral region for a series of Vycor porous silica samples (pore size approximately equal 4 nm) at different levels of hydration, from the dry matrix to completely filled pores. The spectra are obtained as the Fourier transforms of time-resolved heterodyne detected optical Kerr effect (HD-OKE) measurements. The comparison of these spectra with that of bulk water enables us to separately extract and analyze the spectral contributions of the first and second hydration layers, as well as that of bulk-like inner water. We conclude that the extra water entering the pores above approximately equal 10% water/silica weight ratio behaves very similarly to bulk water. At lower levels of hydration, corresponding to two complete superficial water layers or less, the H-bond bending and stretching bands, characteristic of the tetrahedral coordination of water in the bulk phase, progressively disappear: clearly in these conditions the H-bond connectivity is very different from that of liquid water. A similar behavior is observed for the structural relaxation times measured from the decay of the time-dependent HD-OKE signal. The value for the inner water is very similar to that of the bulk liquid; that of the first two water layers is definitely longer by a factor approximately equal 4. These findings should be carefully taken into account when employing pore confinement to extend towards lower temperatures the accessible temperature range of supercooled water.

Fetal hyperechogenic bowel may indicate congenital cytomegalovirus disease responsive to immunoglobulin therapy.

OBJECTIVE: To determine whether fetal hyperechogenic bowel is associated with a poor outcome with or without immunoglobulin therapy. METHODS: Sixteen pregnant women whose 17 fetuses had hyperechogenic bowel were followed by a protocol of offering additional serologic testing, amniocentesis, hyperimmunoglobulin (HIG), serial ultrasounds, and evaluation of their children. RESULTS: Of 17 fetuses with hyperechogenic bowel, 13 showed hyperechogenic bowel as a single or first ultrasound sign compared to four who showed it concomitantly or after other ultrasound abnormalities appeared (P = 0.02). Of the 17 fetuses with hyperechogenic bowel, nine were treated with HIG. Eight of the nine were normal at birth and during a follow-up of 3-8 years. One treated fetus is deaf at 4 years of age. A significantly different result (P < 0.0004) occurred among seven untreated fetuses who were each severely affected at 2-7 years of age, and the remaining one died soon after preterm birth. Among seven of nine fetuses (77.8%) of treated mothers the fetal hyperechogenic bowel resolved after HIG administration. There were no significant differences between treated and untreated fetuses for gestational age at maternal infection, gestational age at birth, and birth weight. CONCLUSION: Hyperechogenic bowel may be a marker of congenital cytomegalovirus (CMV) disease, which may be prevented by HIG.

Reverse end-diastolic flow in a fetus with a rare liver malformation: a case report.

INTRODUCTION: We describe a case of early and persistent reverse end-diastolic flow in the middle cerebral artery in a fetus with severe ascites. These features are associated with a rare liver malformation known as ductal plate malformation. CASE PRESENTATION: A 28-year-old Caucasian woman was referred to our high-risk obstetric unit at 24 weeks' gestation for fetal ascites detected during a routine ultrasound examination. During her hospitalization we performed medical investigations, including a fetal paracentesis, to detect the etiology of fetal ascites. The cause of fetal ascites (then considered non-immune or idiopathic) was not evident, but a subsequent ultrasound examination at 27 weeks' gestation showed a reverse end-diastolic flow in the middle cerebral artery without any other Doppler abnormalities. A cesarean section was performed at 28 weeks' gestation because of the compromised fetal condition. An autopsy revealed a rare malformation of intrahepatic bile ducts known as ductal plate malformation. CONCLUSION: Persistent reverse flow in the middle cerebral artery should be considered a marker of adverse pregnancy outcome. We recommend careful ultrasound monitoring in the presence of this ultrasonographic sign to exclude any other cause of increased intracranial pressure. To better understand the nature of these ultrasonographic signs, additional reports are deemed necessary. In fact in our case, as confirmed by histopathological examination, the fetal condition was extremely compromised due to failure of the fetal liver. Ductal plate malformation altered the liver structures causing hypoproteinemia and probably portal hypertension. These two conditions therefore explain the severe hydrops that compromised the fetal situation.