High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences (“markers”) and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred     

Ethacrynic acid analogues lacking the α,β-unsaturated carbonyl unit—Potential anti-metastatic drugs

A series of ethacrynic acid analogues, lacking the α,β-unsaturated carbonyl unit, was synthesized and subsequently evaluated for their ability to inhibit the migration of human breast cancer cells, MCF-7/AZ. Several of the analogues were already active in the low micromolar range, whereas ethacrynic acid itself shows no potential to inhibit the migration of these cancer cells. Preliminary studies show that the presence of one or more methoxy groups at the phenyl ring of ethacrynic acid is important in order for the ethacrynic acid analogues to demonstrate an inhibitory effect on the migration.     

Trade-offs underlying polyphagy in a facultative ant-tended florivorous butterfly: the role of host plant quality and enemy-free space

The underlying mechanisms mediating the use of multiple host plants were investigated in Parrhasius polibetes (Lycaenidae), a florivorous and facultative myrmecophilous butterfly. Plant traits such as presence of ant–treehopper associations as a source of enemy-free space, flower bud dimensions, toughness, thickness, trichomes, and the corresponding performance and wear of P. polibetes mandibles were examined for three natural hosts: Schefflera vinosa (Araliaceae), Pyrostegia venusta (Bignoniaceae) and Luehea grandiflora (Malvaceae). Parasitism levels of larvae found on the three hosts were also determined. Almost all Luehea had ant–treehopper associations, and all larvae found on this host were non-parasitized. Parasitism was low in larvae found on Schefflera, half of which hosted ant–treehopper associations. No ant–treehopper association was found on Pyrostegia, where parasitism was significantly higher compared to other hosts. In the laboratory, P. polibetes performed well on Schefflera, followed by Pyrostegia. No larvae survived when fed with Luehea. Flower buds of Luehea were thicker and tougher than those of Schefflera and Pyrostegia. Indeed, mandibles of larvae reared on Luehea showed substantial wear, whereas those reared either on Schefflera or Pyrostegia presented no significant damage. Additionally, we suggest that co-occurrence with ant–treehopper associations on a plant provides parasitoid-free space for P. polibetes larvae. Our results support the hypothesis that ecological trade-offs among host plants (i.e., food quality and enemy-free space) promote polyphagy in natural populations of P. polibetes. Host morphological traits seem to play a relevant role in P. polibetes performance. To our knowledge, this is the first report showing the costs of polyphagy in a myrmecophilous butterfly.     

Rectogerochammina eugubina nov. gen., nov. sp., a new agglutinated foraminifer from the Upper Cretaceous of Gubbio, Italy

We describe the new agglutinated foraminiferal genus and species Rectogerochammina eugubina nov. gen., nov. sp. from the Upper Cretaceous Scaglia Rossa Formation of the Umbria-Marche Basin in Italy. The genus differs from Gerochammina (Neagu, 1990) in the presence of a terminal uniserial part.     

Role of Purα in the cellular response to ultraviolet-C radiation

Purα is a nucleic acid-binding protein with DNA-unwinding activity, which has recently been shown to have a role in the cellular response to DNA damage. We have investigated the function of Purα in Ultraviolet-C (UVC) radiation-induced DNA damage and nucleotide excision repair (NER). Mouse embryo fibroblasts from PURA^-/- knockout mice, which lack Purα, showed enhanced sensitivity to UVC irradiation as assessed by assays for cell viability and clonogenicity compared to Purα positive control cultures. In reporter plasmid reactivation assays to measure the removal of DNA adducts induced in vitro by UVC, the Purα-negative cells were less efficient in DNA damage repair. Purα-negative cells were also more sensitive to UVC-induced DNA damage measured by Comet assay and showed a decreased ability to remove UVC-induced cyclobutane pyrimidine dimers. In wild-type mouse fibroblasts, expression of Purα is induced following S-phase checkpoint activation by UVC in a similar manner to the NER factor TFIIH. Moreover, co-immunoprecipitation experiments showed that Purα physically associates with TFIIH. Thus, Purα has a role in NER and the repair of UVC-induced DNA damage.Key words: purα, ultraviolet radiation, DNA damage, DNA repair, nucleotide excision repair, TFIIH     

Expression of proopiomelanocortin, proenkephalin and prodynorphin genes in porcine theca and granulosa cells

Previous studies have demonstrated the presence of endogenous opioid peptides (EOP) in the ovary and suggested their implication in local interactions within ovarian structures. Nevertheless, data pertaining to the expression of genes, coding for the opioid precursors, in ovarian cells are still rudimentary and not available for the pig. The study was undertaken to test whether genes of the opioid precursors - proopiomelanocortin (POMC), proenkephalin (PENK) and prodynorphin (PDYN) - are expressed in non-treated and gonadotropin-treated theca and granulosa cells isolated from ovarian follicles of the pig. The cells were isolated from small (days 15-16 of the estrous cycle) and large (days 19-20) porcine follicles. Dispersed cells were cultured in Eagle's medium under the water saturated atmosphere of 95% air and 5% CO(2), in the presence or absence of respective gonadotropin; theca cells with LH (100 ng/ml) and granulosa cells with FSH (100 ng/ml). Following 24h-incubation, the cells were harvested and the total RNA was isolated. The expression of genes coding for opioid precursors was estimated by the semi-quantitative RT-PCR technique involving co-amplification of the target cDNA (POMC, PENK or PDYN) and control cDNA (beta-actin or 18S rRNA). Specificities of PCR products were confirmed by Southern analysis and sequencing. In theca cells the expression of opioid precursors appeared to be gonadotropin-dependent except for PENK in the cells isolated from large follicles. In turn, granulosa cells exhibited the expression of POMC and PENK genes independently on treatment with FSH. This gonadotropin induced the expression of PDYN gene in granulosa cells isolated from small and large follicles and significantly increased POMC mRNA content in the cells from the large ones. The present studies indicate that porcine follicular cells (especially granulosa cells) may produce opioid peptides and that gonadotropins may modulate gene expression of their precursors in these cells. Moreover, our results support a participation of opioid peptides in the local regulations within ovarian follicle.     

Occurrence of Lepidopterism caused by the moth Hylesia nigricans (Berg) (Lepidoptera: Saturniidae) in Rio Grande do Sul State, Brazil

Lepidopterism by Hylesia nigricans (Berg) moth is recorded for the first time in southern Brazil. Preventive strategies of control are proposed based on information on the biology and ecology of this moth.