Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae,Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae‐zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3‐rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3‐rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3‐rpl16 spacer, shows greater variation between ssp. fragile and novae‐zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae‐zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re‐evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.     

Duality of interaction outcomes in a plant–frugivore multilayer network

In plant–animal interactions, species are commonly labeled as either mutualists or antagonists, based on the most common, most studied, or most easily observed outcome. Nevertheless, evidence from simple systems comprising 2–4 species suggests that those labels are an oversimplification: individual species often function in both roles, either simultaneously or at different places or times. We include both mutualistic and antagonistic interactions between mammals and seeds in a multilayer network, to explore for the first time the community‐level consequences of the dual roles played by some species. We tested whether negative and positive interactions within a plant–frugivore network are separated into different modules, or whether they overlap due to the presence of frugivores that both kill and disperse seeds. The frugivorous diets of nonvolant small mammals were studied at one dry tropical forest site in southeastern Brazil by analyzing fecal samples from individuals captured in live traps. Seed viability was assessed with a tetrazolium test to determine the outcome of those interactions, as estimated by whether or not seeds survived gut passage. Interactions were analyzed as a weighted multilayer network, subdivided into one potentially mutualistic (live seeds deposited) and one antagonistic (dead seeds deposited) layer. The two layers had similar structure with high overlap between them. Some mammal species exhibited highly central, dual roles, acting both as antagonists and mutualists, in many cases of the same plant species. Dispersal service by most of these small mammals is accompanied by seed destruction, suggesting that the selective pressures exerted by those animals on the plants is much more complex than often assumed. Our results demonstrate that the complexity of plant–frugivore networks can not be fully understood without proper incorporating measures of seed fate following gut passage.     

Traditions,beliefs and indigenous technologies in connection with the edible longhorn grasshopper <Emphasis Type="Italic">Ruspolia differens</Emphasis> (Serville 1838) in Tanzania

Background

Edible insects are an important source of food to many African populations. The longhorn grasshopper, Ruspolia differens (Serville 1838), commonly known as senene in Tanzania is one of the most appreciated edible insects by societies around Lake Victoria crescent. Senene is primarily an essential treat for the tribes around the lake, e.g., the Haya of Tanzania, Luo of Kenya and Baganda of Uganda. Despite its importance as a food item and appreciation as a delicacy, there are few studies dealing with culture, beliefs and indigenous technology in connection with the senene. The main objective of this study was to survey indigenous technologies, processing methods and traditions in relation to senene consumption among the Haya tribe in Kagera region of Tanzania.

Methods

Our ethnographic study was conducted through semi-structured interviews. A total of 51 locals, 26 females and 25 males aged 21 to 60 years were interviewed (with 3 female and 7 male key informants among them). Questions focused on cultures, beliefs and traditions towards senene consumption. Processing, preservation and shelf-life as well as nutritional knowledge were also investigated.

Results

Harvesting for household consumption was mainly done through wild collection. Traditionally made traps were mostly used for commercial harvesting. Deep frying was the most preferred processing method while smoking was the most preferred preservation method, with shelf-life of up to 12 months. Interesting traditions and taboos associated with senene consumption were identified, with men monopolising the insects as food by declaring the insects taboo for women and children. Deep fried senene in locally packed containers were mostly sold by street vendors, but also available from a variety of stores and supermarkets.

Conclusion

Beyond being just an important traditional delicacy, senene is becoming increasingly popular, providing opportunity for local businesses. Indigenous technologies for harvesting, processing and preserving senene exist, but must be improved to meet food processing standards, thereby promoting commercialization. This carries economic potential essential for improving incomes and livelihoods of women and smallholder farmers, improving household level food security.

     

Haplotype-specific <Emphasis Type="Italic">MAPT</Emphasis> exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders

Background

Genome wide association studies have identified microtubule associated protein tau (MAPT) H1 haplotype single nucleotide polymorphisms (SNPs) as leading common risk variants for Parkinson’s disease, progressive supranuclear palsy and corticobasal degeneration. The MAPT risk variants fall within a large 1.8 Mb region of high linkage disequilibrium, making it difficult to discern the functionally important risk variants. Here, we leverage the strong haplotype-specific expression of MAPT exon 3 to investigate the functionality of SNPs that fall within this H1 haplotype region of linkage disequilibrium.

Methods

In this study, we dissect the molecular mechanisms by which haplotype-specific SNPs confer allele-specific effects on the alternative splicing of MAPT exon 3. Firstly, we use haplotype-hybrid whole-locus genomic MAPT vectors studies to identify functional SNPs. Next, we characterise the RNA-protein interactions at two loci by mass spectrometry. Lastly, we knockdown candidate splice factors to determine their effect on MAPT exon 3 using a novel allele-specific qPCR assay.

Results

Using whole-locus genomic DNA expression vectors to express MAPT haplotype variants, we demonstrate that rs17651213 regulates exon 3 inclusion in a haplotype-specific manner. We further investigated the functionality of this region using RNA-electrophoretic mobility shift assays to show differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213 and rs1800547 and subsequently identified candidate trans-acting splicing factors interacting with these functional SNPs sequences by RNA-protein pull-down experiment and mass spectrometry. Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrate a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion.

Conclusions

We identified common splice factors hnRNP F and hnRNP Q regulating the haplotype-specific splicing of MAPT exon 3 through intronic variants rs1800547 and rs17651213. This work demonstrates an integrated approach to characterise the functionality of risk variants in large regions of linkage disequilibrium.

     

High‐Temperature Treatment of Li‐Rich Cathode Materials with Ammonia: Improved Capacity and Mean Voltage Stability during Cycling

Li‐rich electrode materials of the family x Li₂MnO₃·(1?x )LiNi_a Co_b Mn_c O₂ (a + b + c = 1) suffer a voltage fade upon cycling that limits their utilization in commercial batteries despite their extremely high discharge capacity, ≈250 mA h g^?1. Li‐rich, 0.35Li₂MnO₃·0.65LiNi_0.35Mn_0.45Co_0.20O₂, is exposed to NH₃ at 400 °C, producing materials with improved characteristics: enhanced electrode capacity and a limited average voltage fade during 100 cycles in half cells versus Li. Three main changes caused by NH₃ treatment are established. First, a general bulk reduction of Co and Mn is observed via X‐ray photoelectron spectroscopy and X‐ray absorption near edge structure. Next, a structural rearrangement lowers the coordination number of Co? O and Mn? O bonds, as well as formation of a surface spinel‐like structure. Additionally, Li⁺ removal from the bulk causes the formation of surface LiOH, Li₂CO₃, and Li₂O. These structural and surface changes can enhance the voltage and capacity stability of the Li‐rich material electrodes after moderate NH₃ treatment times of 1–2 h.     

Arctic ground squirrel neuronal progenitor cells resist oxygen and glucose deprivation-induced death

AIM: To investigate the influence of ischemia/reperfusion on arctic ground squirrel(AGS) neuronal progenitor cells(NPCs), we subjected these cultured cells to oxygen and glucose deprivation.METHODS: AGS NPCs were expanded and differentiated into NPCs and as an ischemia vulnerable control, commercially available human NPCs(hNPCs) were seeded from thawed NPCs. NPCs, identified by expression of TUJ1 were seen at 14-21 d in vitro(DIV). Cultures were exposed to control conditions, hypoxia, oxygen and glucose deprivation or glucose deprivation alone or following return to normal conditions to model reperfusion. Cell viability and death were assessed from loss of ATP as well as from measures of alamarB lue~ and lactate dehydrogenase in the media and from counts of TUJ1 positive cells using immunocytochemistry. Dividing cells were identified by expression of Ki67 and phenotyped by double labeling with GFAP, MAP2 ab or TUJ1. RESULTS: We report that when cultured in NeuraLife~(TM), AGS cells remain viable out to 21 DIV, continue to express TUJ1 and begin to express MAP2 ab. Viability of hN PCs assessed by fluorescence alamarB lue(arbitrary units) depends on both glucose and oxygen availability [viability of hNPCs after 24 h oxygen glucose deprivation(OGD) with return of oxygen and glucose decreased from 48151 ± 4551 in control cultures to 43481 ± 2413 after OGD, P 0.05]. By contrast, when AGS NPCs are exposed to the same OGD with reperfusion at 14 DIV, cell viability assessed by alamar Blue increased from 165305 ± 11719 in control cultures to 196054 ± 13977 after OGD. Likewise AGS NPCs recovered ATP(92766 ± 6089 in control and 92907 ± 4290 after modeled reperfusion; arbitrary luminescence units), and doubled in the ratio of TUJ1 expressing neurons to total dividing cells(0.11 ± 0.04 in control cultures vs 0.22 ± 0.2 after modeled reperfusion, P 0.05). Maintaining AGS NPCs for a longer time in culture lowered resistance to injury, however, did not impair proliferation of NPCs relative to other cell lineages after oxygen deprivation followed by re-oxygenation.CONCLUSION: Ischemic-like insults decrease viability and increase cell death in cultures of human NPCs. Similar conditions have less affect on cell death and promote proliferation in AGS NPCs.     

Synthesis of a novel superabsorbent hydrogel by copolymerization of acrylamide and cashew gum modified with glycidyl methacrylate

Novel superabsorbent hydrogels were manufactured using chemically modified cashew gum (CGMA) and acrylamide (AAm) as reactants. The route for the synthesis was feasible due to the incorporation of glycidyl methacrylate (GMA) into structure of cashew gum (CG) to form the cashew gum-methacrylated (CGMA), in an appropriate mixture water-DMSO, as solvent, and using TEMED as catalyst. Thereafter, the CGMA was copolymerized with AAm yielding (CGMA-co-AAm) hydrogels. The main characteristics of raw and the modified materials are reported in this paper. ¹³C NMR, ¹H NMR and FTIR spectroscopies confirmed the incorporation of vinyl groups, from GMA, into CG structure. By the spectrophotometry analyses, it was found that, ca. 82% of GMA was incorporated to the CG after 24 h of reaction. The cross-linking of CGMA or co-polymerization of CGMA with acrylamide leads to a hydrogel formation. Their gelation was characterized by FT-IR analysis. Alkaline hydrolysis at 40 °C for 3 and 4.5 h increased the water uptake (WU) capacity. Hydrolyzed CGMA-co-AAm hydrogels present higher values of WU (up to 1500) and may be classified as water superabsorbent material. Applications in agriculture, as soil conditioner, and in biomedical field, as biomaterial (scaffold) are being investigated.     

Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.