Basal Positions Research Articles

Regional distribution of diffuse fibrosis in the basal and mid-ventricular AHA segments in patients with type 2 diabetes

Abstract Introduction Cardiovascular magnetic resonance (CMR) research including from our research group, has documented that patients (pts.) with type 2 diabetes (DM2) even without symptoms exhibit subtle to moderately increased myocardial extracellular volume (ECV). ECV is an imaging biomarker of diffuse fibrosis. Also, our prior research has revealed a prevalence of approx. 10% for non-ischemic late gadolinium enhancement (LGE). Intriguingly, these LGE lesions manifested in a distinct pattern, situated in the basal lateral or infero-lateral positions. We postulate that these lesions may represent the end-stage of severe diffuse fibrosis, potentially influenced by factors such as increased shear wall stress. Purpose To investigate if pts. with DM2 with known high global ECV had higher regional ECV in the basal and lateral or infero-lateral AHA segments compared to other segments. Method A case-control study of 20 healthy controls, 20 pts. with DM2 with low ECV (ECV<28%), 20 pts. with DM2 with high ECV (ECV>29%), and 20 pts. with DM2 with non-ischemic LGE (LGE+). Pts. were identified from a cross-sectional cohort of pts. with DM2. All subjects underwent physical examination and extensive CMR with T1 mapping before and after gadolinium contrast, and myocardial perfusion at rest and during adenosine stress. The regional ECV values for the basal and the mid-ventricular short axis slide were analysed using the AHA segments model: segments 1 to 12. Results All groups (grp.) had comparable age and sex distribution. In the DM2 grp. there was a difference between the no. of pts. with DM2 duration >10 years (low ECV 11(55%), high ECV 12(60%), LGE+ 16(80%), however statistically significant. Global ECV were: Controls (mean±sd) 26.7±1.6%, Low ECV 26.3±1.4%, High ECV 32.0±2.9%, LGE+ 29.5±2.6%, p<0.001. Control subjects had regional ECV between 24.4±2% to 27.3±2% (p<0.001), highest values in the septum. The DM2 grp. with low ECV had regional ECV values of 24.5±3% to 29.2±4%, highest values in the basal inferior and septal parts (segments 2-4). The high ECV grp. had regional ECV values between 28.3±4% and 35.3±6 % with very high values in the basal and the mid-ventricular septum, inferior, and inferolateral part (segments 2-5 and 8-11). The DM2 group LGE+ had values between 26.6±3% and 34.5±7%, highest values in the basal slice in the septum, inferior, and infero-lateral parts (segments 2-5). We found no significant difference in the regional myocardial perfusion reserve index. Conclusion This evidence indicates that diffuse fibrosis in DM2 cardiomyopathy tends to concentrate in the septum and inferolateral regions. However, among pts. with non-ischemic LGE lesions, we observed normal ECV in the anterior segments, in contrast to the high ECV group where all segments exceeded normal levels, albeit with notable regional variations. Subsequent investigations should prioritize uncovering the underlying reasons for this specific regional distribution of diffuse fibrosis.AHA segments 1-12 mapsAHA segments 1-12 maps

Barriers to Early Progress in Adult Cochlear Implant Outcomes.

Adult cochlear implant (CI) recipients obtain varying levels of speech perception from their device. Adult CI users adapt quickly to their CI if they have no peripheral "bottom-up" or neurocognitive "top-down" limiting factors. Our objective here was to understand the influence of limiting factors on the progression of sentence understanding in quiet and in noise, initially and over time. We hypothesized that the presence of limiting factors, detected using a short test battery, would predictably influence sentence recognition with practical consequences. We aimed to validate the test battery by comparing the presence of limiting factors and the success criteria of >90% sentence understanding in quiet 1 month after activation. The study was a single-clinic, cross-sectional, retrospective design incorporating 32 adult unilateral Nucleus CI users aged 27 to 90 years (mean = 70, SD = 13.5). Postoperative outcome was assessed through sentence recognition scores in quiet and in varying signal to noise ratios at 1 day, 1 to 2 months, and up to 2 years. Our clinic's standard test battery comprises physiological and neurocognitive measures. Physiological measures included electrically evoked compound action potentials for recovery function, spread of excitation, and polarity effect. To evaluate general cognitive function, inhibition, and phonological awareness, the Montreal Cognitive Assessment screening test, the Stroop Color-Word Test, and tests 3 and 4 of the French Assessment of Reading Skills in Adults over 16 years of age, respectively were performed. Physiological scores were considered abnormal, and therefore limiting, when total neural recovery periods and polarity effects, for both apical and basal electrode positions, were >1.65 SDs from the population mean. A spread of excitation of >6 electrode units was also considered limiting. For the neurocognitive tests, scores poorer than 1.65 SDs from published normal population means were considered limiting. At 1 month, 13 out of 32 CI users scored ≥90% sentence recognition in quiet with no significant dependence on age. Subjects with no limiting peripheral or neurocognitive factors were 8.5 times more likely to achieve ≥90% score in quiet at 1 month after CI switch-on (p = 0.010). In our sample, we detected 4 out of 32 cases with peripheral limiting factors that related to neural health or poor electrode-neural interface at both apical and basal positions. In contrast, neurocognitive limiting factors were identified in 14 out of 32 subjects. Early sentence recognition scores were predictive of long-term sentence recognition thresholds in noise such that limiting factors appeared to be of continuous influence. Both peripheral and neurocognitive processing factors affect early sentence recognition after CI activation. Peripheral limiting factors may have been detected less often than neurocognitive limiting factors because they were defined using sample-based criteria versus normal population-based criteria. Early performance was generally predictive of long-term performance. Understanding the measurable covariables that limit CI performance may inform follow-up and improve counseling. A score of ≥90% for sentence recognition in quiet at 1 month may be used to define successful progress; whereas, lower scores indicate the need for diagnostic testing and ongoing rehabilitation. Our findings suggest that sentence test scores as early as 1 day after activation can provide vital information for the new CI user and indicate the need for rehabilitation follow-up.

Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes.

The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae.

Environmental and seed-position effects on viability and germination of buried seeds of an invasive diaspore-heteromorphic annual grass.

Environmental factors, such as temperature and moisture, and plant factors, such as seed position on the mother plant, can affect seed viability and germination. However, little is known about the viability and germination of seeds in different positions on the mother plant after burial in soil under natural environmental conditions. Here, diaspores from three positions on a compound spike and seeds from two/three positions in a diaspore of the invasive diaspore-heteromorphic annual grass Aegilops tauschii were buried at four depths for more than 2 years (1-26 months) under natural conditions and viability and germination monitored monthly. Viability of seeds in each diaspore/seed position decreased as burial depth and duration increased and was associated with changes in soil temperature and moisture. Germination was highest at 2 cm and lowest at 10 cm soil depths, with peaks and valleys in autumn/spring and winter/summer, respectively. Overall, seeds in distal diaspore and distal seed positions had higher germination percentages than those in basal diaspore and basal seed positions, but basal ones lived longer than distal ones. Chemical content of fresh diaspores/seeds was related to diaspore/seed position effects on seed germination and viability during burial. We conclude that seeds in distal diaspores/seed positions have a 'high risk' strategy and those in basal positions a 'low risk' strategy. The two risk strategies may act as a bet-hedging strategy that spreads risks of germination failure in the soil seed bank over time, thereby facilitating the survival and invasiveness of A. tauschii.

Electrically Evoked Auditory Brainstem Response Using Extracochlear Stimulation at Different Cochlear Sites: A Comparison With Intracochlear Stimulation.

The distribution and extent of excitable spiral ganglion neurons (SGNs) have been investigated using the electrically evoked auditory brainstem response (EABR) during preoperative and perioperative periods. In this study, we investigated the EABR with extracochlear stimulation (eEABR) as a preoperative test to estimate these factors. Sixteen male Sprague-Dawley rats were used in this study. Experiments were conducted in nine rats with normal hearing and seven rats that were partially deafened with ouabain treatment. Each experiment involved the following steps: extracochlear stimulating electrode placement at three different sites along the axis of the cochlea and eEABR recordings; cochleostomy and four-channel intracochlear array implantation, followed by EABR recordings with various electrode pair combinations; and after electrophysiological measurements, harvest of the cochleae for histopathological evaluation. The slope characteristics of the amplitude growth function measured from eEABR and EABR, frequency-specific auditory thresholds, and the density of SGNs were compared. Similar trends were observed in slope changes on different sites of stimulation with both types of stimulation in normal-hearing animals-specifically, a monotonically increasing slope with increasing distance between bipolar pairs. In addition, eEABR slopes showed significant correlations with EABR slopes when the expected cochlear regions of stimulation were similar in normal-hearing animals. In partially deaf animals, the auditory thresholds at several frequencies had a significant correlation with the eEABR slopes of each extracochlear electrode at the apical, middle, and basal cochlear positions. This indicated that increasing the regions of cochlear stimulation had a differential impact on eEABR slopes, depending on the neural conditions. Our results indicated that eEABR slopes showed significant spatial correlations with the functionality of the auditory nerve. Therefore, eEABR tests at various cochlear positions might be used for estimating the extent of excitable SGNs in cochlear implant candidates prior to implantation.

Chemoprotective effect of arbutin on azoxymethane-induced aberrant crypt foci in rat colon via modulation of PCNA/Bax protein.

Arbutin is utilized in traditional remedies to cure numerous syndromes because of its anti-microbial, antioxidant, and anti-inflammatory properties. This study aimed to evaluate chemopreventive effects of arbutin on azoxymethane (AOM)-induced colon aberrant crypt foci (ACF) in rats. Five groups of rats were used: normal control group (rats injected hypodermically with sterile phosphate-buffered saline once per week for two weeks) and groups 2-5, which were subcutaneously inoculated with 15 mg/kg AOM once a week for two weeks. AOM control and 5-fluorouracil (5-FU) control groups were fed 10% Tween orally daily for 8 weeks using a feeding tube. The treated groups were fed 30 and 60 mg/kg arbutin every day for 2 months. ACF from the AOM control group had aberrant nuclei in addition to multilayered cells and an absence of goblet cells. The negative control group displayed spherical cells and nuclei in basal positions. Histological examination revealed a reduced number of AFC cells from colon tissues of the 5-FU reference group. Arbutin-fed animals showed down-regulation of proliferating cell nuclear antigen (PCNA) and up-regulation of Bax protein compared to AOM control. Rats fed with arbutin displayed a significant increase of superoxide dismutase (SOD) and catalase (CAT) activities in colon tissue homogenates compared to the AOM control group. In conclusion, arbutin showed therapeutic effects against colorectal cancer, explained by its ability to significantly decrease ACF, down-regulate PCNA protein, and up-regulate Bax protein. In addition, arbutin significantly increased SOD and CAT, and decreased malondialdehyde (MDA) levels, which might be due to its anti-proliferative and antioxidant properties.

57Fe nuclear resonance vibrational spectroscopic studies of tetranuclear iron clusters bearing terminal iron(iii)-oxido/hydroxido moieties.

57Fe nuclear resonance vibrational spectroscopy (NRVS) has been applied to study a series of tetranuclear iron ([Fe4]) clusters based on a multidentate ligand platform (L3-) anchored by a 1,3,5-triarylbenzene linker and pyrazolate or (tertbutylamino)pyrazolate ligand (PzNH t Bu-). These clusters bear a terminal Fe(iii)-O/OH moiety at the apical position and three additional iron centers forming the basal positions. The three basal irons are connected with the apical iron center via a μ4-oxido ligand. Detailed vibrational analysis via density functional theory calculations revealed that strong NRVS spectral features below 400 cm-1 can be used as an oxidation state marker for the overall [Fe4] cluster core. The terminal Fe(iii)-O/OH stretching frequencies, which were observed in the range of 500-700 cm-1, can be strongly modulated (energy shifts of 20-40 cm-1 were observed) upon redox events at the three remote basal iron centers of the [Fe4] cluster without the change of the terminal Fe(iii) oxidation state and its coordination environment. Therefore, the current study provides a quantitative vibrational analysis of how the remote iron centers within the same iron cluster exert exquisite control of the chemical reactivities and thermodynamic properties of the specific iron site that is responsible for small molecule activation.

Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus

BackgroundEllobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.Methods and resultsPCR amplification of the putative mtDNA CytB-D-loop fragment using ‘universal’ primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, ‘haplotype B’ was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.ConclusionsNumerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.

Effect of Ni/Mo on the preparation of non-loaded NiMoSx catalysts and the hydrogenation performance of coal tar

Efficient and clean utilization of coal tar is one of the key technologies for efficient and clean utilization of coal. Molybdenum disulfide has been favored for its superior catalytic hydrogenation of poor-quality oil. Molybdenum disulfide catalysts doped with different contents of nickel were synthesized by a two-step method. By SEM, XRD, Raman analyses, and other analyses. non-loaded NiMoSx-0.1 catalysts with larger lateral dimensions, fewer layers, and the appearance of specific active sites at both Basal and Edge positions were synthesized when Ni/Mo = 0.1 compared to undoped molybdenum disulfide. When Ni/Mo is continuously increased, the conversion of the intermediate MoS4-xOx is severely affected, which decreases the amount of MoS2 generated and increases the number of MoS2 layers and transverse dimensions. NiMoSx-0.1 promotes the conversion of CA to CN and enhances the hydrogenation and cracking of coal tar. The total gasoline and diesel content of the hydrotreating product was increased by 13.6 % with no coke production, in addition to the viscosity, density, and average molecular mass decreasing by 90 %, 5 %, and 33 %, respectively.

Diversity of Wolbachia infection and its influence on mitochondrial DNA variation in the diamondback moth, Plutella xylostella

Plutella xylostella is a pest that severely damages cruciferous vegetables worldwide and has been shown to be infected with the maternally inherited bacteria Wolbachia, with the main infected strain was plutWB1. In this study, we performed a large-scale global sampling of P. xylostella and amplified 3 mtDNA genes of P. xylostella and 6 Wolbachia genes to analyze the infection status, diversity of Wolbachia in P. xylostella, and its effect on mtDNA variation in P. xylostella. This study provides a conservative estimate of Wolbachia infection rates in P. xylostella, which was found to be 7% (104/1440). The ST 108 (plutWB1) was shared among butterfly species and the moth species P. xylostella, revealing that Wolbachia strain plutWB1 acquisition in P. xylostella may be through horizontal transmission. The Parafit analyses indicated a significant association between Wolbachia and Wolbachia-infected P. xylostella individuals, and individuals infected with plutWB1 tended to cluster in the basal positions of the phylogenetic tree based on the mtDNA data. Additionally, Wolbachia infections were associated with increased mtDNA polymorphism in the infected P. xylostella population. These data suggest that Wolbachia endosymbionts may have a potential effect on mtDNA variation of P. xylostella.

Effect of nodal cutting position and plant growth regulator on bud sprouting of Dendrocalamus giganteus Wall. Ex Munro in Uganda

Dendrocalamus giganteus Wall. Ex Munro (giant bamboo) is one of the most economically important bamboo species globally. However, propagation of Dendrocalamus giganteus from seed is hampered by the duration it takes to flower – making the large-scale production of planting stock for this valuable species untenable. This study was conducted under greenhouse conditions to determine the optimal doses of indole-3-butyric acid (IBA) and culm cutting position to propagate D. giganteus. Cuttings from the top, middle and basal culm positions were treated with different concentrations of Indole-3-Butyric Acid (0.6 %, 0.8 % and 1.0 %) and a control with distilled water. A mixture of top forest soil and sand in a ratio of 2:1 was used as a growth medium. The experiment was set up in a Complete Randomized Factorial Design (CRFD). Cuttings were monitored for the number of bud sprouts over 18 weeks. Results indicated that cuttings’ position and concentration of IBA greatly influenced the sprouting of D. giganteus. The highest bud sprouts were obtained for 0.6 % IBA and cuttings from the basal position. Bud sprouting was lowest in the control and cuttings from the top position. We conclude that while propagating D. giganteus by culm cuttings, basal cuttings and 0.6 % IBA should be encouraged.

Gujaratia indica, the oldest artiodactyl (Mammalia) from South Asia: new dental material and phylogenetic relationships

Diacodexeids are widely considered to be a paraphyletic group consisting of the oldest and most primitive artiodactyls that made their sudden appearance in all northern continents around the Palaeocene–Eocene boundary. In South Asia, the first record of artiodactyls is marked by the appearance of Gujaratia indica from the early Ypresian (∼55 Ma) Cambay Shale of the Vastan lignite mine, India, which is slightly younger than the oldest artiodactyls from Europe and North America. Here we describe new dental material of G. indica, documenting associated upper dentition, including P4, a new locus. Gujaratia (including G. pakistanensis and G. indica) is clearly distinct from all known diacodexeids in having the most triangular upper molars and lower molars with weaker paraconids. Cladistic analysis performed to assess the phylogenetic relationships of Gujaratia with other diacodexeids, dichobunoids, raoellids and pakicetids shows that Gujaratia is monophyletic while Diacodexis and Diacodexeidae are strongly polyphyletic. Gujaratia is found to be closer to the North American diacodexeids and D. gigasei and D. morrisi from Europe, which form a paraphyletic group. The European Diacodexis represents an unnatural grouping with D. antunesi being most closely related to a clade comprising dichobunids and homacodontids, and D. gazini and D. varleti occupying basal positions in a clade comprising raoellids and pakicetids. Dichobunidae is also recovered as a polyphyletic group whereas Homacodontidae is paraphyletic. Raoellids and pakicetids, long considered to be endemic to the Indian subcontinent, are monophyletic and without close affinities to Gujaratia, and appear to be more closely allied to some European dichobunoids, e.g., D. gazini, necessitating a reappraisal of current ideas about artiodactyl origins.

Biogeographic role of the Indonesian Seaway implicated by colonization history of purpleback flying squid, Sthenoteuthis oualaniensis (Lesson, 1830), in the Indo-Pacific Ocean

As a bio]diversity hotspot, the East Indies (Coral) Triangle possesses the highest biodiversity on the earth. However, evolutionary hypotheses around this area remain controversial; e.g., center of origin, center of accumulation, and center of overlap have been supported by different species. This study aims to answer the evolutionary influence of the Indonesian Seaway on the biodiversity of the Coral Triangle by recovering the evolutionary origins of a wide-ranging ommastrephid squid (Sthenoteuthis oualaniensis) based on integrated molecular and oceanographic clues from the Indo-Pacific. Three new clades were revealed; viz., clade I from the South China Sea, clade II from the northern East Indian Ocean, and clade III from the southern East Indian Ocean. These two Indian Ocean clades formed a monophyly closely related to clade IV from the Central-Southeast Pacific. Clade VI from the central Equatorial Pacific and clade V from the northern Eastern Pacific sit in basal positions of phylogenetic trees. Ancestral Sthenoteuthis was inferred to have originated from the Atlantic Ocean and sequentially dispersed to the northern East Pacific, central Equatorial Pacific, and West Pacific through the open Panama Seaway and being transported by westward North Equatorial Current. The East Indian Ocean was likely colonized by an ancestral population of clade IV from the Southeast Pacific. Westward South Equatorial Circulation could have promoted transoceanic migration of S. oualaniensis through the wide paleo-Indonesian Seaway. Sea level regression since the Miocene and the closure of the Indonesian Seaway at 4–3 Ma were responsible for the population genetic differentiation of S. oualaniensis in the Indo-Pacific. Therefore, the Indonesian Gateway played an important role in influencing marine organisms’ migration and population differentiation through controlling and reorganizing circulations in the Indo-Pacific.

Structural conformation and coordination architecture investigation in the solvent induced cis Cu(II) complex containing fluorine-substituted β-diketonate ligand

The modification in structural conformation, coordination bonds, and hydrogen bonding has been investigated in the solvent-induced Cu(II) complex with 4,4,4-Trifluoro-1-phenyl-1,3-butanedione. A new β-diketone-based Cu(II) complex [Cu(TFPB)2(DMSO)] has been identified and structurally characterized. Single-crystal X-ray diffraction analysis revealed that the [Cu(TFPB)2(DMSO)] (complex 1) is crystallized in triclinic (P1¯) and complex [Cu(TFPB)2] (complex 2), which was reported earlier, is in the monoclinic (P21/n) system. The Cu(II) complex with coordinated solvent (complex 1) features a five-coordination with doubly chelated -O donors of β-diketone in basal positions and the oxygen atom of DMSO solvent supplementing the fifth coordination site. The coordination geometry around the metal centre is described as a slightly distorted square pyramidal with the trigonality index τ5 of 0.0586. While in solvent-free complex (complex 2), two β-diketone molecules are coordinated to a central Cu(II) ion in a basal position to form a perfect square planar geometry with τ4 of zero. Interestingly, the oxygen donors of β-diketone in complex 1 are inclined in a cis configuration, whereas in complex 2, they are aligned in a trans configuration. The changes in molecular orbital energies and reactive chemical descriptors in the solvent-induced complexes were studied by the electronic structure method. A relatively lower energy gap value is observed for the trans (3.1119 eV) form than cis (3.2186 eV). In addition, molecular docking analysis was performed to investigate the influence of structural variation of complexes on the binding modes and protein-ligand interactions with the penicillin-binding protein 2.

Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar.

In Madagascar, the house mouse (Mus musculus) is widely believed to have colonized with human activities and is now one of the most abundant rodents on the island. However, its genetic background at the genomic level remains unclear, and clarifying this would help us to infer the timing of introduction and route of migration. In this study, we determined the whole-genome sequences of five Madagascar house mice captured from an inland location in Madagascar. We examined the genetic background of samples by analyzing the mitochondrial and autosomal genomes. We confirmed that the mitochondrial genome lineages of collected samples formed a single clade placed at one of the most basal positions in the Mus musculus species. Autosomal genomic sequences revealed that these samples are most closely related to the subspecies M. m. castaneus (CAS), but also contain a genetic component of the subspecies M. m. domesticus (DOM). The signature of a strong population bottleneck 1,000-3,000 years ago was observed in both mitochondrial and autosomal genomic data. In a comparison with global samples of M. musculus, the Madagascar samples showed strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal and insular regions, with divergence time estimated as around 4,000 years ago. These findings support the proposition that the ancestors of these animals started to colonize the island with human agricultural activity and experienced a complex history during their establishment.

Seed position in spikelet as a contributing factor to the success of the winter annual invasive grass Aegilops tauschii.

Seed position – dependent effects on seed dormancy/germination are well documented at the inflorescence/infructescence level, but less is known about seeds at different positions within a dispersal unit. For the invasive winter annual grass Aegilops tauschii, we quantified morphology, mass and dormancy/germination of seeds from basal (1), middle (2), and distal (3) positions in two spikelet types (Left and Right). We also investigated seedling emergence, survival, plant size and seed production of plants from seeds in different spikelet positions of two spikelet types under different soil nutrient and water conditions. We found that these seed, seedling and plant traits performed as mirror images between the Left and Right spikelet types. The middle seed was significantly the longest and had the maximum mass, while the basal seed was the shortest and had medium mass. Middle seeds had the highest increase in mass during imbibition and the highest germination percentages and rates, while basal seeds had the lowest. Seedling emergence and survival, plant size and seed production for each position of seeds were highest in the added fertilizer combined with regular watering treatment and lowest in the no fertilizer combined with natural moisture, while height of plants derived from the middle and the distal seeds was significantly higher than that of plants derived from the basal seeds under all soil nutrient and water conditions. Seedling survival, number of tillers per plant and seed production per plant from the middle and distal seeds were significantly lower than those from basal seeds under all soil nutrient and water treatments. The considerable variation in seedling emergence and survival, plant size and seed production between seeds in different positions in the spikelet results in much flexibility in all stages of the life cycle, thereby likely contributing to the invasiveness of A. tauschii.

Reevaluation of the phylogenetic relationships among Neotomini rodents (Hodomys, Neotoma, and Xenomys) and comments on the woodrat classification.

The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.

Tissue and salinity specific Na+/Cl\u2212 cotransporter (NCC) orthologues involved in the adaptive osmoregulation of sea lamprey (Petromyzon marinus)

Two orthologues of the gene encoding the Na+-Cl− cotransporter (NCC), termed ncca and nccb, were found in the sea lamprey genome. No gene encoding the Na+-K+-2Cl− cotransporter 2 (nkcc2) was identified. In a phylogenetic comparison among other vertebrate NCC and NKCC sequences, the sea lamprey NCCs occupied basal positions within the NCC clades. In freshwater, ncca mRNA was found only in the gill and nccb only in the intestine, whereas both were found in the kidney. Intestinal nccb mRNA levels increased during late metamorphosis coincident with salinity tolerance. Acclimation to seawater increased nccb mRNA levels in the intestine and kidney. Electrophysiological analysis of intestinal tissue ex vivo showed this tissue was anion absorptive. After seawater acclimation, the proximal intestine became less anion absorptive, whereas the distal intestine remained unchanged. Luminal application of indapamide (an NCC inhibitor) resulted in 73% and 30% inhibition of short-circuit current (Isc) in the proximal and distal intestine, respectively. Luminal application of bumetanide (an NKCC inhibitor) did not affect intestinal Isc. Indapamide also inhibited intestinal water absorption. Our results indicate that NCCb is likely the key ion cotransport protein for ion uptake by the lamprey intestine that facilitates water absorption in seawater. As such, the preparatory increases in intestinal nccb mRNA levels during metamorphosis of sea lamprey are likely critical to development of whole animal salinity tolerance.

Small intestinal mucosal cells in piglets fed with probiotic and zinc: a qualitative and quantitative microanatomical study.

Probiotics and zinc are commonly used and beneficial in pig production. This work aimed to assess the effects of probiotic and zinc on the mucosal cells of the small intestine in respect to digestive capacity and immunity in pre- and post-weaned piglets. Eighteen Large White Yorkshire piglets were divided equally into control and treatment groups. The piglets were maintained in standard management conditions and were weaned at 28 days of age. The treatment group of piglets fed a mixture of probiotics orally at 1.25 × 109 CFU/day and zinc at 2000 ppm/day from birth to 10 days of age. At three different age-groups viz. day 20 (pre-weaning) and, day 30 and day 60 (post-weaning), the animals were sacrificed. For histomorphology, the tissue samples were processed and stained with Mayer's haematoxylin and eosin for routine study, combined periodic acid-Schiff-Alcian blue for mucopolysaccharides and Masson-Hamperl argentaffin technique for argentaffin cells. The stained slides were observed under the microscope. The samples were processed as per the standard procedure for scanning and transmission electron microscopy. The statistical analysis of the data using the appropriate statistical tests was also conducted. The mucosal epithelium of villi and crypts were lined by enterocytes, goblet cells, argentaffin cells, microfold (M-cell) cells, tuft cells and intraepithelial lymphocytes. The multipotent stem cells were located at the crypt base. The length of the enterocyte microvilli was significantly longer (p < 0.05) in the treatment group of piglets. The number of different types of goblet cells and argentaffin cells was more in treated piglets irrespective of segments of intestine and age. The intraepithelial lymphocytes were located in apical, nuclear and basal positions in the lining epithelium of both villus tip and base with their significant increase in the treatment group of piglets. The transmission electron microscopy revealed the frequent occurrence of tuft cells in the lining mucosa of the small intestine in treated piglets. Dietary supplementation of probiotic and zinc induced the number of different mucosal cells of villi and crypts in the small intestine that might suggest the greater absorptive capacity of nutrients and effective immunity in critical pre and post-weaned piglets.

Phylogenetic Signal and Bias in Paleontology.

An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA data sets usually increases congruence of resulting topologies to the well-corroborated tree, but this varies among morphological data sets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artifacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. [Concatenation; fossilization; morphology; parsimony; systematics; taphonomy; total-evidence.]