Preliminary evaluation of non-native rainbow trout (Oncorhynchus mykiss) impact on the Cederberg ghost frog (Heleophryne depressa) in South Africa’s Cape Fold Ecoregion

We evaluated the impact of non-native rainbow trout Oncorhynchus mykiss on a population of endemic Cedarberg ghost frog Heleophryne depressa in the upper Krom River (Olifants-Doring River Catchment, Cape Fold Ecoregion). We compared H. depressa abundance (using kick-sampling and underwater video analysis) and environmental conditions between sites above and below a waterfall that marks the upper distribution limit of O. mykiss. Heleophryne depressa abundance was significantly greater above the waterfall than that below it, and, because there was no significant difference in measured environmental variables, O. mykiss presence is identified as the most likely explanation for the observed decrease in H. depressa abundance.     

LARVAL X‐RAY IRRADIATION INFLUENCES PROTEIN EXPRESSION IN PUPAE OF THE ORIENTAL FRUIT FLY,BACTROCERA DORSALIS

The sterile insect technique (SIT) was developed to eradicate the new world screwworm from the southern United States and Mexico, and became a component of many area‐wide integrated pest management programs, particularly useful in managing tephritid fruit flies. SIT is based on the idea of rearing and sterilizing male pests, originally by ionizing radiation, and then releasing into field, where they compete for and mate with wild females. Mating with sterile males leads to reduced fecundity to lower pest populations. There are concerns with the use and distribution of radioisotopes for SIT programs, which have led to developing X‐ray irradiation protocols to sterilize insects. We considered the possibility that X‐ray irradiation exerts sublethal impacts aside form sterilizing insects. Such effects may not be directly observable, which led us to the hypothesis that X‐ray irradiation in one life stage creates alterations in biological fitness and protein expression in the subsequent stage. We tested our hypothesis by irradiating larvae of Bactrocera dorsalis. There are two major points. One, exposing larvae to X‐ray treatments led to reduced adult emergence, fecundity, fertility, and flight capacity from the corresponding pupae and emerged adults. Two, the X‐ray treatments led to substantial expression changes in 27 pupal proteins. We assorted the 67 spots representing these proteins into three groups, metabolism, development, and structure. Our interpretation is these X‐ray induced changes in biological performance and protein expression indicate their adult counterparts may be disabled in their abilities to successfully compete for and mate wild females in native habitats.     

Fine mapping of an H-2Kk restricted cytotoxic T lymphocyte epitope in SV40 T antigen by using in-frame deletion mutants and a synthetic peptide

The CTL response to SV40 in C3H/HeJ mice is directed against the tumor (T) Ag and is H-2Kk restricted. CTL specific for both the amino terminus (residues 1-271) and the carboxyl terminus (residues 512-708) of the T Ag molecule have been detected, and we have previously cloned CTL of both specificities. In this paper we show that the panel of 10 CTL clones specific for the C-terminal region includes clones specific for three different epitopes, termed C1, C2, and C3. Epitopes C1 and C2 are conserved in the T Ag of the related papova viruses BK and SA12, and only epitopes C2 and C3 are present on SV40 transformed targets bearing the Kk mutant Kkml. Epitopes C1 and C2 were mapped to residues 563-576 by using in-frame deletion mutants of SV40 T antigen, and all clones specific for these two epitopes can lyse Kk bearing target cells in the presence of a synthetic peptide comprising residues 559-576. Kk and Kkml differ at residue 152, which is located in the Ag-binding pocket. Because epitopes C1 and C2 can be formed by the same antigenic peptide, but epitope C1 is not present on SV40 transformed Kkml cells, epitopes C1 and C2 must differ in the contribution made by residue 152 of the MHC class I molecule. These data show that CTL epitopes on transformed cells can be made up of Ag fragments, and strengthen the idea that this is a general phenomenon for both class I and class II restricted T cell epitopes.     

Large-scale genetic census of an elusive carnivore,the European wildcat (<Emphasis Type="Italic">Felis s. silvestris</Emphasis>)

The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently.     

Metal contamination and human health risk associated with the consumption of Labeo rosae from the Olifants River system,South Africa

The Olifants River, a tributary of the Limpopo River system, is one of the most polluted rivers in South Africa. In May 2011 the concentrations of metals in fish muscle tissue from two impoundments, Loskop and Flag Boshielo dams, on the Olifants River were measured and a human health risk assessment conducted to investigate whether it was safe to consume Labeo rosae from these impoundments. Labeo rosae is one of the most common pan fish in these impoundments and is readily available to rural communities. Metals are accumulating in the muscle tissue of L. rosae even although the fish populations appear to be healthy. At Loskop Dam all L. rosae analysed exceeded the recommended hazard quotient (HQ) of 1 for antimony, and less than 50% exceeded that for lead. At Flag Boshielo Dam, the recommended HQ was exceeded for lead in less than 50% of L. rosae analysed, and more than 50% exceeded that for antimony. The weekly consumption of 150?g of L. rosae muscle tissue from these impoundments may pose an unacceptable health risk to rural communities.     

Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1

Correction to: EMBO Reports (2019) 20: e47074. DOI 10.15252/embr.201847074 | Published online 6 May 2019The authors noticed that the control and disease labels had been inverted in their data analysis resulting in publication of incorrect data in Figure 1C. The corrected figure is displayed below. This change affects the conclusions as detailed below. The authors apologize for this error and any confusion it may have caused.In the legend of 1C, change from, “Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows increased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.Open in a separate windowFigure 1CCorrected Open in a separate windowFigure 1COriginal To, "Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows decreased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.In abstract, change from, “Here, we report increased IMP1 expression in patients with Crohn''s disease and ulcerative colitis”.To, “Here, we report increased IMP1 expression in adult patients with Crohn''s disease and ulcerative colitis”.In results, change from, “Consistent with these findings, analysis of published the Pediatric RISK Stratification Study (RISK) cohort of RNA‐sequencing data 38 from pediatric patients with Crohn''s disease (CD) patients revealed that IMP1 is upregulated significantly compared to control patients and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.To, “Contrary to our findings in colon tissue from adults, analysis of published RNA‐sequencing data from the Pediatric RISK Stratification Study (RISK) cohort of ileal tissue from children with Crohn’s disease (CD) 38 revealed that IMP1 is downregulated significantly compared to control patients in the RISK cohort and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.In discussion, change from, “Indeed, we report that IMP1 is upregulated in patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.To “Indeed, we report that IMP1 is upregulated in adult patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.     

Genome Sequence of a Cellulose-Producing Bacterium,Gluconacetobacter hansenii ATCC 23769

The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for studying cellulose synthesis. We have determined the genome sequence of strain ATCC 23769.Plants produce cellulose, an unbranched chain of β-1,4-linked glucose units, as a structural polysaccharide. It is the most abundant polymer on earth, recently receiving much interest due to its potential use as a feedstock for bioethanol. Bacteria also produce cellulose. Among these, Gluconacetobacter hansenii (previously named Acetobacter xylinus) (4) has been extensively characterized and is a model system for cellulose biosynthesis (1, 2, 7). G. hansenii produces extracellular cellulose that is devoid of lignin or hemicellulose, making it an excellent source for pure cellulose. A lack of a completely sequenced genome for this organism has been a limiting factor in identifying other key proteins involved in cellulose synthesis.The whole-genome sequencing of G. hansenii ATCC 23769 was performed using the 454 FLX-Titanium pyrosequencing technology (5). A combinatorial sequencing approach using 489,201 reads obtained from the shotgun library and 195,088 reads from an 8-kb pair end library (3) produced a total of 221,294,116 bp. These reads were assembled using the Newbler assembler, producing 88 large contigs (>500 bp) and a chromosome-sized scaffold of 3,646,142 bp with an average coverage of ×50.5. This scaffold contained exclusively chromosomal DNA and no plasmid sequences. The gaps in the large scaffold were filled by primer walking and subsequent sequencing of the PCR products. The resulting high-quality draft assembly, consisting of a large scaffold with 71 contigs, was annotated using the Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) service of the National Institute of Biotechnology Information (NCBI).The chromosomal sequence of G. hansenii 23769 contains 3,547,122 bp, with a G+C content of 59%. The genome contains 3,351 genes, of which 3,308 are protein-encoding genes, accounting for 84% of the genome. There are 43 genes for tRNAs and 2 rRNA loci. The genes encoding proteins involved in cellulose synthesis are in an operon consisting of acsAB (GXY_04277), acsC (GXY_04282), and acsD (GXY_04292), as previously shown by Saxena et al. (7). Interestingly, there are two additional copies of acsAB, GXY_08864 and GXY_14452, which share 69% and 72% sequence identity, respectively, with the acsAB genes in the operon; the deduced amino acid sequences are 40% and 46% identical, respectively, with that deduced from acsAB in the operon. There are also two additional copies of acsC, GXY_08869 and GXY_014472, which share 72% and 65% DNA sequence identity, respectively, with the acsC gene in the operon; the deduced amino acid sequences share 28% and 30% amino acid identity, respectively, with that deduced from acsC. acsAB (GXY_08864) and acsC (GXY_08869) are only 17 bp apart, less than the distance (66 bp) between the acsAB and acsC genes in the operon. acsAB (GXY_14452) and acsC (GXY_14472) are separated by 3,299 bp, with three genes in between. However, acsD is present only in the operon, not duplicated elsewhere in the genome. The genome also contains three genes encoding diguanylate cyclase, as previously reported by Tal et al. (8). Diguanylate cyclase catalyzes the formation of cyclic di-GMP, a second messenger in bacteria that functions as an allosteric activator of cellulase synthase AcsAB (6).