Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 10⁵ to 8.9 × 10⁵ copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 × 10³ to 2.6 × 10⁴, 7.4 × 10² to 1.4 × 10³, 2.5 × 10² to 6.4 × 10³, and 1.2 × 10³ to 5.5 × 10³, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.     

Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence

Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter‐ and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3–V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%–30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by‐product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans‐generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM.     

Lifetime inbreeding depression in a leaf beetle

Ongoing habitat loss and fragmentation result in rapid population size reductions, which can increase the levels of inbreeding. Consequently, many species are threatened by inbreeding depression, a loss of individual fitness following the mating of close relatives. Here, we investigated inbreeding effects on fitness‐related traits throughout the lifetime of the mustard leaf beetle (Phaedon cochleariae) and mechanisms for the avoidance of inbreeding. Previously, we found that these beetles have family‐specific cuticular hydrocarbon profiles, which are likely not used as recognition cue for precopulatory inbreeding avoidance. Thus, we examined whether adult beetles show postcopulatory inbreeding avoidance instead. For this purpose, we determined the larval hatching rate of eggs laid by females mated sequentially with two nonsiblings, two siblings, a nonsibling, and a sibling or vice versa. The beetles suffered from inbreeding depression throughout their entire ontogeny, as evinced by a prolonged larval development, a decreased larval and adult survival and a decreased reproductive output of inbred compared to outbred individuals. The highest larval hatching rates were detected when females were mated with two nonsiblings or first with a sibling and second with a nonsibling. Significantly lower hatching rates were measured in the treatments with a sibling as second male. Thus, the results do not support the existence of postcopulatory inbreeding avoidance in P. cochleariae, but revealed evidence for second male sperm precedence. Consequently, an alternative strategy to avoid inbreeding costs might exist in this beetle, such as a polyandrous mating system, potentially coupled with a specific dispersal behavior.     

Response of obligate heterozygotes for phytosterolemia to a low-fat diet and to a plant sterol ester dietary challenge

Twelve obligate heterozygotes from two kindreds were ascertained through phytosterolemic probands homozygous for molecular defects in the ATP binding cassette (ABC) half transporter, ABCG8. The response of these heterozygotes to a Step 1 diet low in fat, saturated fat, and cholesterol, and to 2.2 g daily of plant sterols (as esters) was determined in Protocol I (16 weeks) and Protocol II (28 weeks) during three consecutive feeding periods: Step 1/placebo spread; Step 1/plant sterol spread; and Step 1/placebo spread (washout). At baseline, half the heterozygotes had moderate dyslipidemia and one-third had mildly elevated campesterol and sitosterol levels. On the Step 1/placebo spread, mean LDL cholesterol decreased significantly, 11.2% in Protocol I (n = 12), and 16.0% in Protocol II (n = 7). Substitution with plant sterol spread produced a significant treatment effect on LDL levels in Protocols I and II. Conversely, the mean levels of campesterol and sitosterol increased 119% and 54%, respectively, during the use of plant sterol spread for 6 weeks in Protocol I, an effect mirrored for 12 weeks in Protocol II. During the placebo spread washouts, LDL levels increased, while those of plant sterols decreased to baseline levels in both protocols. In conclusion, phytosterolemic heterozygotes respond well to a Step 1 diet, and their response to a plant sterol ester challenge appears similar to that observed in normals.     

1,1-Organoboration of tri-1-alkynyltin compounds: novel triorganotin cations, stannoles, 3-stannolenes and 1-stanna-4-bora-2,5-cyclohexadienes

Tri-1-alkynyltin compounds [R²Sn(CCR¹)₃ (1), R² = Me, R¹ = Me (a), ⁿBu (b), ^tBu (c), Me₃Si (d), 1-(1-cyclohexenyl) (e); R² = Et, R¹ = Me (a(Et)), ⁿBu (b(Et)), ^tBu (c(Et)), SiMe₃ (d(Et)); R² = ⁿBu, R¹ = Me (a(Bu)), ⁿBu (b(Bu))] were prepared, and their reactivity towards trialkylboranes Et₃B (2) and ⁱPr₃B (3) in 1,1-organoboration reactions was studied. The first step in each reaction is an intermolecular 1,1-alkytoboration. Afterwards, intramolecular 1,1-vinyloboration or 1,1-alkyloboration compete with further intermolecular 1,1-alkyloboration. Various triorganotin cations (4-7), stabilized by intramolecular side-on coordination to the CC bond of an alkynylborate moiety, were detected as highly fluxional intermediates prior to rearrangement into heterocyclic systems such as stannoles (9-11), 1-stanna-4-bora-2, 5-cyclohexadienes (8, 12). The reactions between 1a or 1a(Bu) and an excess of Et₃B (2) afford the tris(alkenyl)tin compounds 13 via threefold intermolecular 1, 1-ethyloboration. 13 rearrange to the 3-stannolenes (14a or 14a(Bu)). The intermediates and final products were characterized by multinuclear one- and two-dimensional ¹H, ¹¹B, ¹³C, ²⁹Si and ¹¹⁹Sn NMR.     

Highly efficient CRISPR-Cas9-mediated gene knockout in primary human B cells for functional genetic studies of Epstein-Barr virus infection

Gene editing is now routine in all prokaryotic and metazoan cells but has not received much attention in immune cells when the CRISPR-Cas9 technology was introduced in the field of mammalian cell biology less than ten years ago. This versatile technology has been successfully adapted for gene modifications in human myeloid cells and T cells, among others, but applications to human primary B cells have been scarce and limited to activated B cells. This limitation has precluded conclusive studies into cell activation, differentiation or cell cycle control in this cell type. We report on highly efficient, simple and rapid genome engineering in primary resting human B cells using nucleofection of Cas9 ribonucleoprotein complexes, followed by EBV infection or culture on CD40 ligand feeder cells to drive in vitro B cell survival. We provide proof-of-principle of gene editing in quiescent human B cells using two model genes: CD46 and CDKN2A. The latter encodes the cell cycle regulator p16^INK4a which is an important target of Epstein-Barr virus (EBV). Infection of B cells carrying a knockout of CDKN2A with wildtype and EBNA3 oncoprotein mutant strains of EBV allowed us to conclude that EBNA3C controls CDKN2A, the only barrier to B cell proliferation in EBV infected cells. Together, this approach enables efficient targeting of specific gene loci in quiescent human B cells supporting basic research as well as immunotherapeutic strategies.     

Better safe than sorry: The response to a simulated predator and unfamiliar scent by the European hare

Predator presence can create a “landscape of fear,” which is defined as the spatially explicit distribution of perceived predation risk as seen by prey. Prey species can alter their behavior and space use as a response to increased predation risk, which might be traded off with energetic requirements. Thus, whether or not an anti-predator behavior is performed might depend on the perceived risk. In this study, we investigated the behavioral and spatial response of the European hare (Lepus europaeus) toward the presence of a predator scent, using red fox (Vulpes vulpes) scat, an unfamiliar control scent (butyric acid), and a true control (no scent). We collected data on hare activity times and behavior using 50 camera trap locations and spatial data using GPS telemetry (30,481 GPS positions of 12 hares). Hares showed spatial anti-predator behaviors within their home range, for example, the local avoidance of areas treated with scent and remaining further from field edges, in response to sympatric predator scent and partly also in response to unfamiliar butyric acid. Conversely, more costly anti-predator behaviors, that is, increased vigilance at the expense of foraging, were only shown in response to the predator scent. Our results suggest that prey species respond flexibly toward scent cues, utilizing less costly anti-predator behaviors independent of the perceived threat, whereas costly anti-predator responses are only used in the presence of “real” threat. Further, our findings emphasize that a combination of camera trap and GPS data can provide detailed information on animal behavior and space use, and caution that interpretation of one data source alone might lead to incomplete conclusions.     

AFX1 and p54 nrb : fine mapping, genomic structure, and exclusion as candidate genes of X-linked dystonia parkinsonism

We have mapped AFX1 and p54 ^nrb to a yeast artificial chromosome (YAC) contig of Xq13.1 that harbors the X-linked dystonia parkinsonism (XDP) locus DYT3. AFX1 is flanked by loci DXS7116 and Il2Rγ, and p54 ^nrb by loci DXS6673E and DXS7120. The exon-intron structure of both genes was analyzed. AFX1 is composed of three exons with most of exon 3 being untranslated. p54 ^nrb is made up of 12 exons ranging in size from 40 bp to 1227 bp. The start codon is in exon 3 and the stop codon in exon 12. Both genes are expressed in the brain, among other tissues. AFX1 and p54 ^nrb were excluded as candidates of DYT3 by sequencing of the exons and the flanking intronic sequences in an XDP patient and a control, and by Northern blot analysis. Received: 27 June 1997 / Accepted: 3 July 1997