Bird community composition across an Andean tree‐line ecotone

Few studies have found strong evidence to suggest that ecotones promote species richness and diversity. In this study we examine the responses of a high‐Andean bird community to changes in vegetation and topographical characteristics across an Andean tree‐line ecotone and adjacent cloud forest and puna grassland vegetation in southern Peru. Over a 6‐month period, birds and vegetation were surveyed using a 100 m fixed‐width Distance Sampling point count method. Vegetation analyses revealed that the tree‐line ecotone represented a distinctive high‐Andean vegetation community that was easily differentiated from the adjacent cloud forest and puna grassland based on changes in tree‐size characteristics and vegetation cover. Bird community composition was strongly seasonal and influenced by a pool of bird species from a wider elevational gradient. There were also clear differences in bird community measures between tree‐line vegetation, cloud forest and puna grassland with species turnover (β‐diversity) most pronounced at the tree‐line. Canonical Correspondence Analysis revealed that the majority of the 81 bird species were associated with tree‐line vegetation. Categorizing patterns of relative abundance of the 42 most common species revealed that the tree‐line ecotone was composed primarily of cloud forest specialists and habitat generalists, with very few species from the puna grassland. Only two species, Thlypopsis ruficeps and Anairetes parulus, both widespread Andean species more typical of montane woodland vegetation edges, were categorized as ecotone specialists. However, our findings were influenced by significant differences in species detectability between all three vegetation communities. Our study highlights the importance of examining ecotones at an appropriate spatial and temporal scale. Selecting a suitable distance between sampling points based on the detection probabilities of the target bird species is essential to obtain an unbiased picture of how ecotones influence avian richness and diversity.     

Caffeine: cardiorespiratory effects and tissue protection in animal models

The aim of this review is to analyze the cardiorespiratory and tissue-protective effects of caffeine in animal models. Peer-reviewed literature published between 1975 and 2021 was retrieved from CAB Abstracts, PubMed, ISI Web of Knowledge, and Scopus. Extracted data were analyzed to address the mechanism of action of caffeine on cardiorespiratory parameters (heart rate and rhythm), vasopressor effects, and some indices of respiratory function; we close this review by discussing the current debate on the research carried out on the effects of caffeine on tissue protection. Adenosine acts through specific receptors and is a negative inotropic and chronotropic agent. Blockage of its cardiac receptors can cause tachycardia (with arrhythmogenic potential) due to the intense activity of β1 receptors. In terms of tissue protection, caffeine inhibits hyperoxia-induced pulmonary inflammation by decreasing proinflammatory cytokine expression in animal models. The protection that caffeine provides to tissues is not limited to the CNS, as studies have demonstrated that it generates attenuation of inflammatory effects in pulmonary tissue. It inhibits the effects of some pro-inflammatory cytokines and prevents functional and structural changes.     

Evidence of hexaploid karyotype in shortnose sturgeon

A karyotype analysis by several staining techniques was carried out on triplicate samples of the shortnose sturgeon, Acipenser brevirostrum. The chromosome number was found to be 2n = 372 +/- 6. A representative karyotype of 374 chromosomes was composed of 178 metacentrics/submetacentrics and 196 telocentrics/acrocentrics and microchromosomes. The signals of fluorescent in situ hybridization (FISH) with a HindIII satellite DNA probe were visible on 14 chromosomes. The signals obtained with a PstI satellite DNA probe appeared on 12 chromosomes. The FISH with a 5S rDNA probe revealed fluorescent signals on 6 chromosomes. These last results, compared with 2 signals in species with about 120 chromosomes and 4 in species with 240, support the hypothesis that A. brevirostrum is a hexaploid species, probably of hybrid origin. Based on these results, we propose a model explaining speciation events occurring in sturgeons by hybridization, genome duplication, and diploidization.     

Residues of Heat-Labile Enterotoxin Involved in Bacterial Cell Surface Binding

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of traveler''s diarrhea worldwide. One major virulence factor released by this pathogen is the heat-labile enterotoxin LT, which upsets the balance of electrolytes in the intestine. After export, LT binds to lipopolysaccharide (LPS) on the bacterial surface. Although the residues responsible for LT''s binding to its host receptor are known, the portion of the toxin which mediates LPS binding has not been defined previously. Here, we describe mutations in LT that impair the binding of the toxin to the external surface of E. coli without altering holotoxin assembly. One mutation in particular, T47A, nearly abrogates surface binding without adversely affecting expression or secretion in ETEC. Interestingly, T47A is able to bind mutant E. coli expressing highly truncated forms of LPS, indicating that LT binding to wild-type LPS may be due primarily to association with an outer core sugar. Consequently, we have identified a region of LT distinct from the pocket involved in eukaryotic receptor binding that is responsible for binding to the surface of E. coli.Enterotoxigenic Escherichia coli (ETEC), a common etiologic agent behind traveler''s diarrhea, is also a significant cause of mortality worldwide (38). Many strains of ETEC elaborate a virulence factor called heat-labile enterotoxin or LT (34). LT is an AB₅ toxin, consisting of a single A subunit, LTA, and a ring of five B subunits, LTB (33). LTB mediates the toxin''s binding properties, and LTA ADP ribosylates host G proteins, increasing levels of cyclic AMP and causing the efflux of electrolytes and water into the intestinal lumen (27, 35). Each subunit of LT is translated separately from a bicistronic message and then transported to the periplasm, where holotoxin assembly spontaneously occurs (16). Subsequent export into the extracellular milieu is carried out by the main terminal branch of the general secretory pathway (31, 36).LT binds eukaryotic cells via an interaction between LTB and host gangliosides, primarily the monosialoganglioside GM₁ (35). The binding site for GM₁, situated at the interface of two B subunits, has been identified by crystallography (26). GM₁ binding can be strongly impaired by a point mutation in LTB that converts Gly-33 to an aspartic acid residue (37). LT is highly homologous to cholera toxin (CT), both in sequence and structure (7, 35), contributing to ETEC''s potentially cholera-like symptoms (39).Previous work in our lab has demonstrated that LT possesses an additional binding capacity beyond its affinity for host glycolipids: the ability to associate with lipopolysaccharide (LPS) on the surface of E. coli (20). LPS, the major component of the outer leaflet of the gram-negative outer membrane, consists of a characteristic lipid moiety, lipid A, covalently linked to a chain of sugar residues (30). In bacteria like E. coli, this sugar chain can be further divided into an inner core oligosaccharide of around five sugars, an outer core of four to six additional sugars, and in some cases a series of oligosaccharide repeats known as the O antigen. Lipid A itself cannot inhibit binding of soluble LT to cells containing full-length or truncated LPS, indicating that the LT-LPS interaction involves sugar residues on the surface of E. coli (19). The addition of the inner core sugar 3-deoxy-d-manno-octulosonic acid (Kdo) is the minimal lipid A modification required for LT binding, although longer oligosaccharide chains are preferred, and expression of a kinase that phosphorylates Kdo abrogates binding by LT (19). Competitive binding assays and microscopy with fluorescently labeled ETEC vesicles show that binding to GM₁ and LPS can occur at the same time, revealing that the binding sites are distinct (20, 23). In contrast to LT''s ability to bind to the surface of ETEC, CT (or LT, when expressed heterologously) cannot bind Vibrio cells, presumably because Kdo is phosphorylated in Vibrio spp. (5).As a result of the LT-LPS surface interaction, over 95% of secreted LT is found associated with E. coli outer membrane vesicles (OMVs), rather than being secreted solubly (20). OMVs are spherical structures, 50 to 200 nm in diameter, that are derived from the outer membrane but also enclose periplasmic components (24). As such, active LT is found both on the surface of an OMV and within its lumen (21). ETEC releases a large amount of OMVs (40), and these vesicles may serve as vehicles for delivery of LT to host cells.Recent work by Holmner et al. has uncovered a third binding substrate for LT: human blood group A antigen (17, 18). This interaction was noted previously as a novel binding characteristic of artificially constructed CT-LT hybrid molecules, but it has now been shown to occur with wild-type LT as well (17, 18). LTB binding to sugar residues in the receptor molecule occurs at a site that is separate from the GM₁-binding pocket, in the same region we proposed was involved in LPS binding (17, 19). While the severity of cholera disease symptoms has been linked to blood type (14), the effects of blood type on ETEC infection are less clear. However, it has been demonstrated that LT can use A antigen as a functional receptor in cultured human intestinal cells (11, 12), and one recent cohort study found an increased prevalence of ETEC-based diarrhea among children with A or AB blood type (29).We set out to generate a mutation in LT that reduces its LPS binding without adversely affecting its expression, secretion, or toxicity. In this work, we present the discovery of point mutations in LTB that impair its interactions with the bacterial surface. Examination of these mutations reveals an LPS binding pocket which shares residues with the blood sugar pocket. Binding studies of mutants to bacteria with truncated LPS provide a better understanding of the roles that inner and outer core sugars play in toxin binding, and expression, secretion, and toxicity studies demonstrate which mutant is a particularly good candidate for future research. These binding mutants may lead to further discovery of the role that surface binding plays in the pathogenesis associated with ETEC infection.     

Long-term exposure of Boeckellagibbosa (Copepoda, Calanoida) to in situ levels of solar UVB radiation

1. The freshwater calanoid copepod Boeckella gibbosa is typical of high elevation lakes and ponds in Patagonia (Argentina). Previous studies have shown that this species is highly tolerant to short-term exposure to natural and artificial UVB radiation, and that its tolerance is due to photoreactivation by longer wavelength radiation. In this study, we investigate the potential sublethal effects of solar radiation after prolonged exposure.
2. We incubated B. gibbosa at 1 m depth in oligotrophic Lake Toncek for 24 days. The incubation chambers were 1.2 l acrylic cylinders covered with appropriate filters in order to obtain three radiation treatments: visible radiation only, visible radiation + UVA and visible radiation + UVA + UVB.
3. The three treatments did not differ significantly in variables considered as indicators of survival (number of individuals), reproduction (proportion of ovigerous females, clutch size) and development (instar composition). Although resistance to solar UVB radiation is certainly a requisite to live in transparent high elevation habitats, the fact of being effectively exposed to natural levels of UVB radiation does not seem to have measurable consequences on an already adapted species, such as B. gibbosa     

Differentiation of strains and isolates of chicken reovirus using PCR and heteroduplex mobility assay in amplified cDNA

The method of chicken reovirus strain differentiation was worked out on the basis of RT-PCR and heteroduplex mobility assay (HMA). The S3 gene cDNA (633-896 b.p.) of some Russian and Italian chicken reovirus isolates was amplified by RT-PCR. The analysis of these cDNA samples was carried out by HMA. The relation between nucleotide differences and relative mobility of compared cDNA heteroduplex was reflected by the regression curve. The equation of linear regression was derived (y = 91.726-0.89x; where y is the level of nucleotide difference of compared cDNA (%), x is the relative mobility of compared cDNA heteroduplex (%)). This method made it possible to take correct results within 5-35% of nucleotide difference in heteroduplex sequences.     

The Polymerase η Translesion Synthesis DNA Polymerase Acts Independently of the Mismatch Repair System To Limit Mutagenesis Caused by 7,8-Dihydro-8-Oxoguanine in Yeast

Reactive oxygen species are ubiquitous mutagens that have been linked to both disease and aging. The most studied oxidative lesion is 7,8-dihydro-8-oxoguanine (GO), which is often miscoded during DNA replication, resulting specifically in GC → TA transversions. In yeast, the mismatch repair (MMR) system repairs GO·A mismatches generated during DNA replication, and the polymerase η (Polη) translesion synthesis DNA polymerase additionally promotes error-free bypass of GO lesions. It has been suggested that Polη limits GO-associated mutagenesis exclusively through its participation in the filling of MMR-generated gaps that contain GO lesions. In the experiments reported here, the SUP4-o forward-mutation assay was used to monitor GC → TA mutation rates in strains defective in MMR (Msh2 or Msh6) and/or in Polη activity. The results clearly demonstrate that Polη can function independently of the MMR system to prevent GO-associated mutations, presumably through preferential insertion of cytosine opposite replication-blocking GO lesions. Furthermore, the Polη-dependent bypass of GO lesions is more efficient on the lagging strand of replication and requires an interaction with proliferating cell nuclear antigen. These studies establish a new paradigm for the prevention of GO-associated mutagenesis in eukaryotes.Eukaryotic genome stability can be compromised by changes at the nucleotide level, alterations in chromosome structure, or changes in chromosome number. Although such changes are responsible for many human diseases, including cancer, a low level of instability is necessary to provide the raw material for evolutionary processes. Changes at the nucleotide level generally occur during replication, either as errors made when copying an undamaged DNA template or during the bypass of DNA lesions. Many types of DNA lesions are due to reactive oxygen species (ROS), which are generated by exposure to physical and chemical mutagens, as well as by normal metabolic processes, such as aerobic respiration (12, 32). Although cells contain multiple antioxidants and other proteins that protect the genome from oxidative damage, ROS have been implicated as causal agents of many diseases and of aging (11, 50).The most common oxidized DNA lesion is 7,8-dihydro-8-oxoguanine, which is referred to here as a GO lesion. The mutagenic potential of this lesion is due to miscoding during DNA synthesis, with replicative DNA polymerases usually misinserting adenine across from the lesion to generate GO·A mispairs and ultimately GC → TA transversions (49). Studies examining the crystal structure of T7 DNA polymerase complexed with a GO·C base pair or a GO·A mispair indicate the basis of this mutagenic specificity. Whereas the GO·C structure physically resembles that of a mismatch, the GO·A mispair structurally resembles a normal Watson-Crick base pair and therefore is likely to escape polymerase-associated proofreading activity (6). A GO-containing nucleotide triphosphate (8-oxo-dGTP) can also be used by DNA polymerases during DNA synthesis, leading specifically to AT > CG transversion events (7).There are three major proteins in Escherichia coli that work independently to prevent GO-associated mutagenesis: MutM (Fpg), MutY, and MutT (36). MutM is a DNA glycosylase that removes GO lesions in the GO·C base pairs created by oxidation of guanine in normal G·C base pairs, while MutY is an adenine-DNA glycosylase that removes adenines from the GO·A mispairs created by incorporation of adenine opposite a GO lesion. If DNA replication occurs before MutM can remove the GO lesion from a GO·C base pair, the lesion will likely generate a GO·A mispair, which is then subjected to the A-specific activity of the MutY protein. Once MutY removes the adenine from the newly synthesized strand, a cytosine can be inserted opposite the lesion, giving MutM another opportunity to excise the GO base. MutT is an 8-oxo-dGTPase that degrades 8-oxo-dGTP, thereby greatly reducing its incorporation into DNA. The postreplicative mismatch repair (MMR) pathway has also been implicated in preventing GO-associated mutagenesis in E. coli by functioning as an alternative to MutY or by helping MutY identify and remove mismatched adenines from GO·A mispairs (3, 60).In the yeast Saccharomyces cerevisiae, the Ogg1 protein is the functional homolog of MutM (55) and thus removes GO lesions that are base paired with cytosine. The MMR machinery is functionally analogous to the MutY protein (37), excising adenines that are inserted opposite GO lesions during DNA replication. The mismatch recognition MutSα complex (a heterodimer of the Msh2 and Msh6 proteins) specifically recognizes GO·A mispairs and initiates removal of the portion of the newly synthesized strand containing the adenine (37). A homolog of MutT has yet to be identified in yeast, although one does exist in mammalian cells (23). It is possible that the MutT homolog has eluded discovery either because it is essential, because there is a redundant activity, or because 8-oxo-dGTP is not a significant mutagen in yeast.A third mechanism that limits GO-associated mutagenesis in yeast involves the translesion synthesis (TLS) polymerase, polymerase η (Polη), which is a member of the Y family of DNA polymerases and is encoded by the RAD30 gene (18, 61). Y family polymerases have a large active-site pocket that can accommodate structurally deformed bases, enabling them to insert a nucleotide opposite a lesion (29). Not only is such lesion bypass potentially error prone, the larger active-site pocket of TLS polymerases imparts very low fidelity when copying undamaged DNA. Polη, for example, is error prone when bypassing some lesions, such as abasic sites (17), but has relatively high fidelity when bypassing GO lesions, usually inserting a cytosine across from the lesion (18, 61). At GO lesions, Polη is 10-fold more accurate and efficient than Polδ (34). When given an undamaged DNA template, however, the base substitution error frequency of Polη in vitro is 3 orders of magnitude greater than that of a typical replicative polymerase (35). In addition to Polη, there are two other TLS polymerases in S. cerevisiae (Polζ and Rev1), but neither has been implicated in the bypass of GO lesions (10, 48).The most straightforward way for Polη to be involved in GO bypass would be for it to be recruited when a replicative polymerase stalls or leaves behind a gap. The replication-blocking potential of GO lesions, however, is unclear. Some in vitro studies have shown that replicative DNA polymerases stall or pause when encountering a template GO lesion (18, 47), but other studies have suggested that this is not the case (49). The currently accepted model is that Polη is specifically recruited to fill the gaps generated by MMR when it initiates correction of GO·A mispairs (18, 54). This model of MMR-Polη cooperation in preventing GO-associated mutagenesis is based on epistasis analysis performed using the CAN1 forward mutation assay (18). Although the relationship between msh2 and rad30 was concluded to be epistatic, the data are also consistent with an additive relationship and, hence, potentially independent roles of Msh2 and Polη in limiting GO-associated mutagenesis. How and why the MMR pathway might specifically recruit a generally error-prone polymerase to fill the gaps in what is normally an extremely accurate repair process is not obvious.In the present study, a SUP4-o forward-mutation system was used to reexamine the relationship between MMR and Polη in preventing GO-associated mutagenesis in yeast. To enhance the accumulation of GO lesions, all experiments were conducted in mutants defective in removing GO from GO·C base pairs (an ogg1 background). In addition, both msh2 and msh6 mutants were analyzed. In an msh6 background, loss of the MutSα heterodimer eliminates the correction of GO·A mispairs, while retention of MutSβ (a heterodimer of Msh2 and Msh3) allows continued correction of most insertion-deletion loops. Finally, mutation spectra, as well as mutation rates, were considered in order to focus specifically on GC → TA mutations. The results reported here demonstrate that Polη can function independently of MMR to prevent GO-associated mutagenesis, presumably through its ability to bypass these lesions in an error-free manner. The data further indicate that the Polη-dependent bypass of GO lesions is more efficient on the lagging strand of replication and that it requires interaction with proliferating cell nuclear antigen (PCNA).     

Disease development of Pythium root rot in bulbous Iris and Crocus

Iris bulbs and Crocus corms were planted at two planting dates in sandy soil infested with Pythium spp. At monthly intervals during the growing season root rot infection was assessed over 3 consecutive years and disease development curves were predicted for both crops. The disease development was remarkably different for Iris and Crocus and the curve shape was determined by the crop rather than by the Pythium species. Planting date had a significant effect on disease development in both crops. No correlation was found between disease development and soil temperature.