Discrete Species Research Articles

A morphologically cryptic salamander reveals additional hidden diversity: evidence for ancient genetic divergence in Webster’s salamander, Plethodon websteri

We investigated the genetic diversity and phylogenetic structure of Webster’s salamander (Plethodon websteri), an understudied species of conservation concern and one of the first morphologically cryptic salamander species described solely on the basis of molecular techniques. Using a combination of mitochondrial and microsatellite data, we discovered significant genetic differentiation across the known distribution (ɸST > 0.868 and FST = 0.261−0.652, p < 0.001), and identified at least two highly divergent clades. These clades, referenced herein as the Semlitsch and Type Locality clades, are of late Miocene origin (approximately 5.3 million years old) and are composed of several geographically and genetically distinct populations. Together, our observations suggest that previously unrecognized species-level diversity may exist in P. websteri, with populations potentially representing distinct but undescribed taxa. We hypothesize that divergence within P. websteri likely resulted from a culmination of radical changes in climate, hydrology, and geology over deep time. Moreover, our results add to mounting evidence suggesting that P. websteri does not belong within the P. welleri group, but instead forms its own discrete species complex separate and genetically distant from P. welleri. This study provides a starting point for future work and reiterates that relationships among, and species-level diversity within, eastern species of Plethodon require additional investigation and potential reevaluation.

Asymptotic Behavior of Discrete Time Fuzzy Single Species Model

This work is concerned with the qualitative behavior of discrete time single species model with fuzzy environment xn+1=xnexp⁡A-Bxn, n=0,1,2,…, where xn denotes the number of individuals of generation n, A is the intrinsic growth rate, and B is interpreted as the carrying capacity of the surrounding environment. xn is a sequence of positive fuzzy number. A,B and the initial value x0 are positive fuzzy numbers. Applying difference of Hukuhara (H-difference), the existence, uniqueness of the positive solution, and global asymptotic behavior of all positive solution with the model are obtained. Moreover a numerical example is presented to show the effectiveness of theoretic results obtained.

HDL modification: recent developments and their relevance to atherosclerotic cardiovascular disease.

In the last 2 years, significant advances in the understanding of HDL particle structure and the associations between particle structure, function, and atherosclerosis have been made. We will review and provide clinical and epidemiological context to these recent advances. Several recent studies have analyzed the associations between HDL particle size distribution, number, and particle function and specific environmental, behavioral, and pharmacologic exposures. Detailed phenotyping of HDL-associated protein complements, particularly apolipoproteins, strongly suggests structural subspecies of HDL exist with differential associations with HDL function and ASCVD risk. The recent data on biological and structural variation in HDL suggests the existence of relatively discrete particle species, which share a similar structure and function. We propose that the classical taxonomy that clusters HDL particles by cholesterol content is incomplete. Detailed phenotyping of HDL subspecies in clinical and epidemiological research may yield insights into new risk markers and biochemical pathways that could provide targets for atherosclerotic cardiovascular disease (ASCVD) therapy and prevention in the future.

Synthesis and Structural Characterization of a Series of One-Dimensional Heteronuclear Dirhodium-Silver Coordination Polymers.

Herein, we describe the preparation of heteronuclear dirhodium-silver complexes by reaction between molecular Rh(II)-Rh(II) compounds [Rh2(μ-O2CR)4L2] (R = Me, Ph (1), CH2OEt (2); L = solvent molecules) with paddlewheel structure and PPh4[Ag(CN)2]. One-dimensional coordination polymers of (PPh4)n[Rh2(μ-O2CR)4Ag(CN)2]n (R = Me (3), Ph (4), CH2OEt (5)) formula have been obtained by replacement of the two labile molecules in the axial positions of the paddlewheel structures by a [Ag(CN)2]− bridging unit. The crystal structures of 3–5 display a similar arrangement, having anionic chains with a wavy structure and bulky (PPh4)+ cations placed between the chains. The presence of the (PPh4)+ cations hinders the existence of intermolecular Ag-Ag interactions although several C-H····π interactions have been observed. A similar reaction between [Rh2(μ-O2CCMe3)4(HO2CCMe3)2] and PPh4[Ag(CN)2] led to the molecular compound (PPh4)2{Rh2(μ-O2CCMe3)4[Ag(CN)2]2} (6) by replacement of the axial HO2CCMe3 ligands by two [Ag(CN)2]− units. The trimethylacetate ligand increases the solubility of the complex during the crystallization favouring the formation of discrete heteronuclear species.

Observations on some Actinoporellas (Chlorophyta, Polyphysaceae). Revision of the Jacques Emberger Collection. Part 1

On the occasion of the inventory of the J. Emberger Collection, specimens from the Lower Cretaceous (Valanginian and Hauterivian) of Algeria, which are referable to the genus Actinoporella (Gumbel in Alth) and which were earlier identified to its type-species A. podolica (Alth) by Conrad et al., are re-examined. They correspond to two discrete species, one of which could be a junior synonym of A. podolica, a synonymy that remains pending because it would require a new sampling at the original locality in western Ukraine some 140 years after the original specimens, now lost, were collected. Regarding their age ascription, they are Tithonian and/or Berriasian in age, i.e., latest Jurassic (sensu Oppel) in age, not earliest Cretaceous. In addition to these two Actinoporellas, a third discrete species, initially described as Clypeina nigra (Conrad & Peybernes), but later referred to the genus Actinoporella, is revised. New data justify its re-ascription to the genus Bakalovaella Bucur. Finally, it is now confirmed that both the Polyphysaceae and the modern Dasycladaceae derive from the Diploporaceae either directly or indirectly through the ancestral Dasycladaceae.

New data on some type-species of Maastrichtian-Paleocene Dasycladales (Green algae) from Iran. Part I. Pseudocymopolia Elliott, 1970

Pseudocymopolia anadyomenea, the type-species of the genus, was described by ELLIOTT (1959) from the Maastrichtian of Iraq. Besides the type-locality, it was also recorded from the upper Maastrichtian Tarbur Formation of Iran, from Afghanistan and Tibet. A rich but moderately preserved material is analyzed herein, evidencing the presence of two discrete species: P. anadyomenea and P. acuta n. sp. The new species is characterized by its thallus morphology displaying tapering, keeled segment margins. Besides the morphology, both are also distinguished by biometric parameters such as the outer diameter (D), inner diameter (d), and the d/D ratio. All other Lower Cretaceous species of Pseudocymopolia as well as the Maastrichtian P. anadyomenea have rounded segment margins. Both taxa from the Tarbur Formation occur in inner platform quiet water depositional settings whereas the Lower Cretaceous representatives typically characterize platform margin deposits.

Phase Control of Ferromagnetic Copper(II) Carbonate Coordination Polymers through Reagent Concentration

A significant degree of control over the dimensionality and magnetic connectivity of CuII carbonate coordination polymers is achieved through varying the concentration of ammonia in the reactant solution. Higher concentration leads to a two‐dimensional ferromagnetic [Cu3(2,4′‐bipy)6(CO3)2]n2n+ kagome structure while lower concentration develops a ferromagnetic [Cu(2,4′‐bipy)2(H2O)2][Cu(2,4′‐bipy)2(CO3)2] chain (where 2,4′‐bipy = 2,4′‐bipyridine). The carbonate anion in the structures arises from the fixation of atmospheric CO2 by the basic ammonia solution. Modelling the magnetic susceptibility of 1 and 2 reveals ferromagnetic interactions with J/kB = +28.1 K for 1 and +13.99 K for 2. (H = –J). The use of a monodentate polypyridine ligand results in the suppression of the superexchange pathway between layers in 1, removing the metamagnetic behaviour seen in related compounds where a ditopic ligand presents the ability for the layer to couple antiferromagnetically. Attempts to substitute 2,4′‐bipy for 4‐(N,N‐dimethylamino)pyridine (4‐dmap) result in a discrete species [Cu(4‐ampy)4](ClO4)2 (3).

Orientation of AgI Ions in Coordination Architectures through Ligand Conformation and Anion Binding: from Polymeric Chains to Discrete Squares

Five new complexes containing AgI salts and the ligand 3,4‐dipyridyl ketone (L34) were synthesized and characterized, namely {[AgL34]ClO4}∞ (1), {[AgL34]BF4}∞ (2), {AgL34NO3}∞ (3), {AgL34CF3CO2}∞ (4) and [AgL34CF3SO3]4 (5). Both the anion and the ligand conformation were found to affect the structure packing. This set of 1:1 M/L structures demonstrated the role of anion binding and ligand conformation in determining the molecular architecture; the increasing alignment of cations in neighboring M‐L chains in structures 1–4 can be attributed to the anions' ability to coordinate to AgI cations. The conformation of the ligand was shown to determine whether a discrete or polymeric architecture formed. In complexes 1–4 the N3py atom was in a cis orientation, with 1 and 2 forming offset chains held together in 2‐D sheets. The anion in 3 helped link 1‐D chains together to form double chains with the double chains offset in the 2‐D sheet. Complex 4 was present as a 2‐D sheet, with the bifurcating CF3CO2– anion causing the alignment of the AgI cations within the sheet. Complex 5 was the only discrete species, with L34 adopting a trans arrangement and acting as corner pieces of a molecular square. DFT calculations showed that the two conformations of the free ligand had a difference in energy of only 2.1 kJ mol–1.

Gut microbiota-dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes.

We hypothesized that the gut microbiota influences survival of murine cardiac allografts through modulation of immunity. Antibiotic pretreated mice received vascularized cardiac allografts and fecal microbiota transfer (FMT), along with tacrolimus immunosuppression. FMT source samples were from normal, pregnant (immune suppressed), or spontaneously colitic (inflammation) mice. Bifidobacterium pseudolongum (B. pseudolongum) in pregnant FMT recipients was associated with prolonged allograft survival and lower inflammation and fibrosis, while normal or colitic FMT resulted in inferior survival and worse histology. Transfer of B. pseudolongum alone resulted in reduced inflammation and fibrosis. Stimulation of DC and macrophage lines with B. pseudolongum induced the antiinflammatory cytokine IL-10 and homeostatic chemokine CCL19 but induced lesser amounts of the proinflammatory cytokines TNFα and IL-6. In contrast, LPS and Desulfovibrio desulfuricans (D. desulfuricans), more abundant in colitic FMT, induced a more inflammatory cytokine response. Analysis of mesenteric and peripheral lymph node structure showed that B. pseudolongum gavage resulted in a higher laminin α4/α5 ratio in the lymph node cortical ridge, indicative of a suppressive environment, while D. desulfuricans resulted in a lower laminin α4/α5 ratio, supportive of inflammation. Discrete gut bacterial species alter immunity and may predict graft outcomes through stimulation of myeloid cells and shifts in lymph node structure and permissiveness.

Configurational and Conformational Equilibria of N6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA.

The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.

Synthesis and structural characterization of isothiocyanato-4-methoxypyridine-cobalt(II) complexes with diverse geometries and a bridged 1D coordination polymer showing metamagnetic transition

Three cobalt(II) isothiocyanato complexes with 4-methoxypyridine (4-MOP) as a co-ligand have been synthesized: catena-[Co(4-MOP)2(μ1,3-NCS)2] (1), trans-[Co(4-MOP)4(NCS)2] (2), and [Co(4-MOP)2(NCS)2] (3) and structurally characterized by IR, UV–Vis spectroscopy and single crystal X-ray diffraction. The complexes 2 and 3 are discrete monomeric species with octahedral and tetrahedral geometries, respectively whereas the catena-[Co(4-MOP)2(μ1,3-NCS)2] (1) is featuring a polymeric 1D system with doubly bridging NCS− groups through the terminals N- and S-donor atoms in a trans octahedral geometry. The thermoanalytical behavior of 1–3 is reported. Magnetic susceptibility of the bridged-isothiocyanato coordination polymer 1 was studied down to a temperature of 2 K and at various magnetic dc and ac fields. These measurements indicate a metamagnetic transition in 1.

Abrupt Spin Crossover Behavior in a Linear N1,N2-Triazole Bridged Trinuclear Fe(II) Complex

The synthesis, structures and magnetic properties of a new trinuclear spin crossover complex [FeII3(pyrtrz)6(TsO)6]·10H2O·2CH3OH (C2) and its analogue binuclear [FeII2(pyrtrz)5(SCN)4]·7H2O (C1), are reported here. These two compounds are synthesized based on the pyrrolyl functionalized Schiff base 1,2,4-triazole ligand 4-((1H-pyrrol-2-yl)methylene-amino)-4H-1,2,4-triazole (pyrtrz), which represent rare discrete multi-nuclear species, with µ2-N1,N2-triazole bridges linking the FeII centers. DC magnetic susceptibility measurements revealed an abrupt single-step spin crossover (SCO) behavior for compound 2 on the central FeII site and single-crystal X-ray diffraction (173 K) showed that this compound crystallizes in the monoclinic space group (P21/c), and multiple intramolecular interactions were found responsible for the abrupt transition. Compound 1 is a binuclear complex with thiocyanate as terminal ligands. This compound stays in high spin state over the whole temperature range and displays weak antiferromagnetic exchange coupling.

A hybrid droplet vaporization-chemical surrogate approach for emulating vaporization, physical properties, and chemical combustion behavior of multicomponent fuels

The complex nature of multicomponent aviation fuels presents a daunting task for accurately simulating combustion behavior without incurring impractical computational costs. To reduce computation time, chemical fuel surrogates comprised of only a few species are used to emulate the combustion of complex pre-vaporized fuels. These surrogates are often unable to match the vaporization behavior and physical properties of the real fuel and fail to capture the effect of preferential vaporization on combustion behavior. Therefore, a computationally efficient, hybrid droplet vaporization-chemical surrogate approach has been developed which emulates both the physical and chemical properties of a multicomponent kerosene fuel. The droplet vaporization/physical portion of the hybrid uses the Coupled Algebraic–Direct Quadrature Method of Moments with delumping to accurately solve for the evolution of every discrete species in a vaporizing fuel droplet with the computational efficiency of a continuous thermodynamic model. The chemical surrogate portion of the hybrid is linked to the vaporization model using a functional group matching method, which creates an instantaneous surrogate composition to match the distribution of chemical functional groups (CH2, (CH2)n, CH3 and Benzyl-type) in the vaporization flux of the full fuel. The result is a hybrid method which can accurately and efficiently predict time-dependent, distillation-resolved combustion property targets of the vaporizing fuel and can be used to investigate the effects of preferential vaporization on combustion behavior.

Integrating morphological characters, molecular markers, and distribution patterns to assess the identity of Blepharis species from Jordan

BackgroundBlepharis constitutes an important part of the vegetation of the Jordanian arid and semi-arid regions, yet whether one or more species of this genus occurs in the Jordanian area is uncertain. We addressed this question by assessing morphological characters and testing Inter-Simple Sequence Repeat (ISSR) markers from three populations of Blepharis: two northern (lower slopes of Kufranjah valley and the Dead Sea region) and one southern (Wadi al Yutm).ResultsShoots from randomly chosen Blepharis plants were harvested from each of the three populations for morphological and molecular analyses. In the northern populations, spikes were lax and bract width was significantly shorter than length of the longest lateral spine compared to the southern population. A multivariate linear discriminant analysis distinguished the northern populations from the southern one by internode length, bract width, longest lateral spine length, and bract width to spine length ratio. The ISSR analysis revealed that 44 markers across eight primers were polymorphic with major allele frequency of 83.6% and an average of 5.5 polymorphic markers per primer. The genetic resemblance among individuals ranged from 0.27 to 0.96. The three Blepharis populations were accordingly clustered into two distinct groups, similar to the analysis of morphological differences and corresponding with the “northern” and “southern” population designations.ConclusionsOur results strongly indicate the occurrence of two discrete Blepharis species in Jordan and reject the hypothesis that the genus is represented by only one species. We propose that the Blepharis species in Jordan are B. attenutata Napper (represented by the northern populations) and B. ciliaris (L.) B. L. Burtt (represented by the southern population). These findings are important for informing and revising floristic work within the region and an updated key has been included in our findings.

Divergence in tissue-specific expression patterns of genes associated with the terpeniod biosynthesis in two oregano species Origanum vulgare L., and Origanum majorana

Oregano (Origanum vulgare) and marjoram (O. majorana) are two discrete (in terms of sensory characteristics) species within the genus Origanum (Lamiaceae). Their aroma, flavor, and pharmaceutical value are a result of their essential oils, which comprise mainly of monoterpenes and sesquiterpenes. Marjoram is rich in bicyclic monoterpene cis-sabinene hydrate derived from the biosynthetic “sabinyl” pathway while the phenolic monoterpene carvacrol, arising from the “cymyl” pathway, is the distinctive feature of oregano. To investigate differences between the terpene biosynthetic pathways of both species, we identified key enzymes of terpene biosynthesis from the two species of genus Origanum. The heterologous expression of these enzymes showed that each formed multiple mono- or sesquiterpene products and, in combination, were responsible for the direct production of almost all terpenes found in Origanum essential oils. The correlation between essential oil composition and relative terpene synthase transcript concentrations in O. vulgare and O. majorana demonstrated that monoterpene synthase activity is predominantly regulated at the level of transcription and that the phenolic monoterpene alcohol thymol is derived from α-terpinene, the product of a single monoterpene synthase. The combination of heterologously expressed terpene synthases for in vitro assays resulted in blends of mono- and sesquiterpene products that strongly resembled those found in vivo, indicating that terpene synthase expression levels directly control the composition of the essential oils. These results will facilitate the metabolic engineering, directed breeding of Origanum cultivars with higher quantities of essential oils, and improved oil compositions.

New diagnostic SNP molecular markers for the Mytilus species complex

The development of diagnostic markers has been a long-standing interest of population geneticists as it allows clarification of taxonomic uncertainties. Historically, there has been much debate on the taxonomic status of species belonging to the Mytilus species complex (M. edulis, M. galloprovincialis and M. trossulus), and whether they are discrete species. We analysed reference pure specimens of M. edulis, M. galloprovincialis and M. trossulus, using Restriction site associated DNA (RAD) sequencing and identified over 6,000 SNP markers separating the three species unambiguously. We developed a panel of diagnostic SNP markers for the genotyping of Mytilus species complex as well as the identification of hybrids and interspecies introgression events in Mytilus species. We validated a panel of twelve diagnostic SNP markers which can be used for species genotyping. Being able to accurately identify species and hybrids within the Mytilus species complex is important for the selective mussel stock management, the exclusion of invasive species, basic physiology and bio-diversity studies.

Analysing Multivariate Spatial Point Processes with Continuous Marks: A Graphical Modelling Approach

SummaryThis paper discusses the application of graphical modelling in the statistical analysis of marked point patterns. We consider a multivariate planar point process with quantitative marks. After a survey of statistical methods for marked point processes, a new graphical model is presented. The sub‐processes of marked points with identical discrete marks are identified with nodes of a graph, which is used to describe aspects of the spatial relationship: If two sub‐patterns are similar, then an arc is made between the corresponding nodes. Similarity is defined based on spectral densities, which makes the computations efficient. The resulting graph presents all these pairwise similarities simultaneously. We demonstrate the application of our method in the analysis of a multi‐species forest, where the points are tree locations, the discrete marks tree species and the quantitative marks are the diameters at breast height.

Spatial Coordination of Cooperativity in Silica-Supported Cu/TEMPO/Imidazole Catalytic Triad

Multifunctional catalysts obtained by the covalent immobilization of discrete molecular species on porous supports represent a unique approach to emulate some of the design principle and performances of enzymes. However, it is decisive in such systems to control the stoichiometry, spatial distribution, and proximity between the grafted catalytic centers to satisfy the chemical and geometrical requirements for cooperativity. Here, we present strategies to optimize the activity of a catalytic triad on mesoporous silica particles in the representative aerobic oxidation of benzyl alcohol and show that, in contrast with the more-traditional mixed-monolayer approach, activity can be amplified by tuning the spatial distribution of the co-catalysts to maximize the probability of full synergistic pairings.

Cross-coupling of dissimilar ketone enolates via enolonium species to afford non-symmetrical 1,4-diketones.

Due to their closely matched reactivity, the coupling of two dissimilar ketone enolates to form a 1,4-diketone remains a challenge in organic synthesis. We herein report that umpolung of a ketone trimethylsilyl enol ether (1 equiv) to form a discrete enolonium species, followed by addition of as little as 1.2–1.4 equivalents of a second trimethylsilyl enol ether, provides an attractive solution to this problem. A wide array of enolates may be used to form the 1,4-diketone products in 38 to 74% yield. Due to the use of two TMS enol ethers as precursors, an optimization of the cross-coupling should include investigating the order of addition.

A Persulfide Donor Responsive to Reactive Oxygen Species: Insights into Reactivity and Therapeutic Potential

AbstractPersulfides (RSSH) have been hypothesized as critical components in sulfur‐mediated redox cycles and as potential signaling compounds, similar to hydrogen sulfide (H2S). Hindering the study of persulfides is a lack of persulfide‐donor compounds with selective triggers that release discrete persulfide species. Reported here is the synthesis and characterization of a ROS‐responsive (ROS=reactive oxygen species), self‐immolative persulfide donor. The donor, termed BDP‐NAC, showed selectivity towards H2O2 over other potential oxidative or nucleophilic triggers, resulting in the sustained release of the persulfide of N‐acetyl cysteine (NAC) over the course of 2 h, as measured by LCMS. Exposure of H9C2 cardiomyocytes to H2O2 revealed that BDP‐NAC mitigated the effects of a highly oxidative environment in a dose‐dependent manner over relevant controls and to a greater degree than common H2S donors sodium sulfide (Na2S) and GYY4137. BDP‐NAC also rescued cells more effectively than a non‐persulfide‐releasing control compound in concert with common H2S donors and thiols.