Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching

Fluorescence of 2-aminopurine (2AP)-substituted A-site and acrylamide quenching were used to study the interactions of paromomycin and neamine with the decoding region of 16S rRNA. The results reveal that paromomycin binding to the A-site RNA leads to increased exposure of residue A1492. In contrast, neamine has little effect on the solvent accessibility of A1492. Electrospray ionization mass spectrometry was used to compare the affinity of paromomycin with the A-site and 2-AP-substituted A-site RNAs.     

Y-SNP haplogroups related to the Yqh+ heteromorphism in the Mexican northwestern population

Morphological variation of the Y chromosome has been observed in different populations. This variation is mostly related to the heteromorphic Yq12 band, which is composed of a variable block of constitutive heterochromatin. The Yqh+ heteromorphism has a worldwide frequency of 2.85% and is considered clinically innocuous. The aim of this study was to identify the ancestry of the Yqh+ heteromorphism present in individuals from western Mexico. For this purpose, 17 Y-chromosome single nucleotide polymorphisms were analysed by multiplex polymerase chain reaction and SNaPshot assays. In 28 Yqh+ males, only five haplogroups were observed; with a haplogroup diversity of 0.4841 ± 0.1094, which was less than that observed in a study of unselected Mexican mestizo population. Differences were specifically conferred by the high frequencies of haplogroups R1b1 and P*(xQ,R), and by the absence of the Amerindian haplogroup Q (Q*(xQ1a3a) plus Q1a3a) from the Yqh+ group. This study suggests a post-1492 incorporation for Yqh+ chromosomes into the Mexican northwestern population.     

Environmental Factors Influencing Hairy-Nosed Wombat Abundance in Semi-Arid Rangelands

Understanding environmental factors influencing the abundance of species is important for developing strategies to manage wildlife effectively. Long-term studies provide the most reliable information upon which to base management decisions. This is particularly important when considering threatening processes, like drought and climate change, and a species' future security. We collected data on abundance of southern hairy-nosed wombats (Lasiorhinus latifrons) on Kooloola Station in South Australia's Murraylands during nightly spot-lighting excursions in winter and spring between 1993 and 2014. Wombat numbers declined significantly after the early-mid 1990s, and were lowest in 2002–2003 in the middle of the millennium drought (late 1996–mid-2010). Despite an observed decline in grazing competition from domestic sheep and rabbits (Oryctolagus cunniculus) after 2003 and above-average rainfall in 5 of the next 11 years, the wombat population failed to recover to early–mid-1990s levels, remaining at approximately 50% of estimated abundance pre-drought. The study provides evidence that rainfall has a significant effect on southern hairy-nosed wombat population size, most likely through improvements in the availability of palatable plant species. Historical information suggests that there was a change in the grass and herbaceous layer on Kooloola Station in the mid-1970s from a pasture dominated by summer-germinating native grass and forb species, the natural diet of the southern hairy-nosed wombat, to one dominated by winter-germinating introduced weeds. Several consecutive years of above-average rainfall are needed before effective wombat population increase occurs and the size of yearly winter and spring rainfall events is strongly linked to population trends the following year. Historical information and first-hand observations suggest that dietary components (either native grasses or introduced weed species) and level of grazing competition may also interact to affect wombat survival and population recovery from drought, although this requires further testing. Together with rainfall, these factors have important implications to develop appropriate conservation and management strategies for this species in a changing climate likely to be dominated by increased drought frequency and duration. © 2020 The Wildlife Society.     

Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae

Streptococcus pneumoniae open reading frame SP1492 encodes a surface protein that contains a novel conserved domain similar to the repeated fragments of mucin-binding proteins from lactobacilli and lactococci. To investigate the functional role(s) of this protein and its potential adhesive properties, the surface-exposed region of SP1492 was expressed in Escherichia coli, purified to homogeneity, and partially characterized by biophysical and immunological methods. Circular dichroism and sedimentation measurements confirmed that SP1492 is an all-beta protein that exists in solution as a monomer. The SP1492 protein has been shown to be expressed by S. pneumoniae and was experimentally localized to its surface. The protein functional domain binds to mucins II and III from porcine stomach and to purified submaxillary bovine gland mucin. It appears to be one of the very few unambiguous pneumococcal adhesin molecules known to date. A hypothetical model constructed by ab initio techniques predicts a novel beta-sandwich protein structure.     

Life history and phenology of the eucalyptus psyllid, Ctenarytaina eucalypti in Ireland

During the early 1990s, the eucalyptus psyllid, Ctenarytaina eucalypti Maskell, was accidentally introduced into Ireland and began to threaten economically a newly developing ornamental foliage production industry based in the south west. The life cycle of the psyllid was studied at three field sites in Co. Kerry. The psyllid exhibited a complex seasonal population dynamic suggesting that two, largely overlapping population cohorts over‐winter as eggs and nymphs, respectively, in a state of reduced development or temporary dormancy. The duration of this dormancy is short. Evidence of a resumption of activity was monitored at all sites in early February with increasing adult numbers and renewed egg laying being seen before any significant rise in temperatures. This strongly suggests that retarded development, and resumption of psyllid activity in early spring, are at least partially consequences of the changing nutritional quality of the food plant, probably mediated by changing day length. As a consequence of seasonally inhibited development, individual egg and nymphal over‐wintering cohorts probably alternate in the completion of two or three generations per growing season. Analysis of psyllid numbers on shoot samples showed that greater population densities were found on shoots at the top of the food plant compared with lower‐placed shoots. Evidence was also found that the distribution of nymphal instars changed seasonally, probably in response to population density and increased competition for preferred feeding sites. Overall psyllid abundance, and the finer details of seasonal population dynamics, varied between plantations. In the absence of effective predation or parasitism by indigenous natural enemies, these differences were also likely to be due to variation in nutritional quality of the host plant and may be influenced by crop husbandry factors such as the timing and severity of crop pruning.     

Understanding Fluctuations in Bobcat Harvest at the Northern Limit of Their Range

ABSTRACT In Quebec, Canada, harvest of bobcats (Lynx rufus) started to decline in 1985 and by 1991, harvest seasons were closed due to concerns of a perceived population decline. Since the closing of harvest season in 1991, the average temperature has increased, snow quantity has decreased, and important changes in agriculture and forest management have occurred. In light of changing conditions, the situation of Quebec bobcats needed reassessment. Thus, we analyzed harvest data to clarify the current status of bobcat populations in Quebec. From 1980 to 1991, bobcat harvest in Quebec was strongly correlated with bobcat harvest in Maine (USA), Nova Scotia (Canada), Ontario (Canada), and Vermont (USA). Extrapolations of harvest in Quebec relative to harvest in Maine, Ontario, Vermont, and Nova Scotia suggested an increase in number of bobcats after 1991. Mass of male and female bobcats before 1991 was less than mass of animals captured after 1991. Percentage of juveniles in the reported harvest before 1991 was higher than after 1991. However, percentage of males and litter sizes in the harvest did not differ before and after 1991. The geographic distribution of bobcats captured has gradually expanded after the closure of the harvest season. Our findings suggest that bobcat populations in Quebec have recovered from the 1985–1991 decline, and that the harvest season for this species could resume. This study also illustrates how managers can rely on data from neighboring jurisdiction to manage species when local harvest data is unavailable.     

Temperature,predator–prey interaction strength and population stability

Warming could strongly stabilize or destabilize populations and food webs by changing the interaction strengths between predators and their prey. Predicting the consequences of warming requires understanding how temperature affects ingestion (energy gain) and metabolism (energy loss). Here, we studied the temperature dependence of metabolism and ingestion in laboratory experiments with terrestrial arthropods (beetles and spiders). From this data, we calculated ingestion efficiencies (ingestion/metabolism) and per capita interaction strengths in the short and long term. Additionally, we investigated if and how body mass changes these temperature dependencies. For both predator groups, warming increased metabolic rates substantially, whereas temperature effects on ingestion rates were weak. Accordingly, the ingestion efficiency (the ratio of ingestion to metabolism) decreased in all treatments. This result has two possible consequences: on the one hand, it suggests that warming of natural ecosystems could increase intrinsic population stability, meaning less fluctuations in population density; on the other hand, decreasing ingestion efficiencies may also lead to higher extinction risks because of starvation. Additionally, predicted long‐term per capita interaction strengths decreased with warming, which suggests an increase in perturbation stability of populations, i.e., a higher probability of returning to the same equilibrium density after a small perturbation. Together, these results suggest that warming has complex and potentially profound effects on predator–prey interactions and food‐web stability.     

Degradation of Fumonisin B1 by a Bacterial Strain Isolated from Soil

A mixed microbial culture degrading fumonisin B l was obtained from soil samples using an enrichment culture procedure. A bacterial isolate from the enrichment culture (strain NCB 1492) degraded fumonisin B1 after incubation for 3 h, as indicated by TLC and HPLC analysis. On the basis of the sequence analysis of 16S rDNA, strain NCB 1492 was related to the Delftia/Comamonas group. Thin-layer chromatographic analysis indicated the presence of metabolites in the NCB 1492 culture filtrates after degradation of fumonisin B1 supplied as sole carbon and nitrogen source in phosphate buffer. Four metabolites were identified by mass spectrometry analysis.     

Flipping of the Ribosomal A-Site Adenines Provides a Basis for tRNA Selection

Ribosomes control the missense error rate of ~ 10^− 4 during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near-cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3 kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4 kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA–tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA.     

Modelling the population dynamics of <Emphasis Type="Italic">Daphnia obtusa</Emphasis> (Kurz) in Lake Orta (N. Italy) under pre- and post-liming conditions

A mathematical matrix model was formulated to investigate the response of Daphnia obtusa population dynamics to the changes in the water chemistry of Lake Orta before and after the liming operation. Model parameters were estimated from experimental laboratory data. Model analysis showed that water chemistry changes induced by liming affected mainly egg survival and predicted the highest population growth at pH␣6. Whereas increased egg mortality heavily inhibits population growth rate, the model still predicts a long term tendency of the population to increase in number. However, both before and after the liming operation due to high food availability in the laboratory, egg production was higher under all experimental conditions than in the field. When food limitation is accounted for and more realistic, field based estimates of egg production are used, the model predicts the extinction of D. obtusa population in the lake. This suggests that the effects of water chemistry changes on egg mortality had a critical role in the disappearance of D. obtusa from Lake Orta and may even adequately explain the extinction of this population.     

A peptide sequence controls the physical properties of nanoparticles formed by peptide-polymer conjugates that respond to a protein kinase a signal

We previously reported that poly(N-isopropylacrylamide) grafted with Peptide 1 (-GLRRASLG) and poly(ethylene glycol) changed its physical properties in response to an intracellular protein phosphorylation signal, protein kinase A (PKA) (Katayama, Y. et al. (2001) Macromolecules 34, 905). In this study, we investigated the effect of changing peptide structure on the lower critical solution temperature (LCST) of peptide-polymer conjugates, before and after phosphorylation with PKA. For Peptide 2 (Ac-LRRASL-), which has a formal net charge of +2 at physiological pH, the LCST of the conjugate decreased on phosphorylation. In contrast, the LCSTs of the conjugates with Peptide 3 (-ALRRASLE) and Peptide 4 (Ac-DWDALRRASL-), which have neutral net charges, were greatly increased. This suggests that the LCST of the polymer was mainly governed by two factors: the change in hydration around the polymer chain and the interpeptide electrostatic repulsion, resulting from phosphorylation. These polymers have potential for use as drug capsules that respond to cellular conditions.     

Population effects of increased climate variation

Global circulation models predict and numerous observations confirm that anthropogenic climate change has altered high-frequency climate variability. However, it is not yet well understood how changing patterns of environmental variation will affect wildlife population dynamics and other ecological processes. Theory predicts that a population's long-run growth rate is diminished and the chance of population extinction is increased as environmental variation increases. This results from the fact that population growth is a multiplicative process and that long-run population growth rate is the geometric mean of growth rates over time, which is always less than the arithmetic mean. However, when population growth rates for unstructured populations are related nonlinearly to environmental drivers, increasing environmental variation can increase a population's long-run growth rate. This suggests that patterns of environmental variation associated with different aspects of climate change may affect population dynamics in different ways. Specifically, increasing variation in rainfall might result in diminished long-run growth rates for many animal species while increasing variation in temperature might result in increased long-run growth rates. While the effect of rainfall is theoretically well understood and supported by data, the hypothesized effect of temperature is not. Here, I analyse two datasets to study the effect of fluctuating temperatures on growth rates of zooplankton. Results are consistent with the prediction that fluctuating temperatures should increase long-run growth rates and the frequency of extreme demographic events.     

Mother's death and child survival: the case of early Quebec

The aim of this paper is to account for the effect of mother's death on child survival in a historical population. Using comprehensive data on the early French Canadian population of Quebec, evidence is provided for a higher risk of dying for motherless children that remains significant over all childhood and long after the death of the mother. The specific effect of the loss of maternal care was estimated by comparing mortality before and after mother's death, furnishing a means to control for family heterogeneity. No differential in investment between genders was detected before age 3, but older girls suffered a three-fold higher susceptibility to mother's death than their male counterparts. This suggests that grown-up girls assuming the responsibilities of the missing mother had a lower chance of survival.     

日粮中添加鱼油后肉牛瘤胃细菌区系的变化

目的：研究肉牛日粮中添加2%鱼油后瘤胃细菌区系的变化。方法：分别于添加鱼油前后取瘤胃液提取总DNA,根据细菌通用引物27F/1492R扩增16S rDNA基因序列,分别构建2个16S rDNA基因文库;从每个文库中各随机挑取384个克隆,对阳性克隆用HhaⅠ进行限制性片段长度多态性（RFLP）分析、聚类,取各RFLP类群中的代表克隆进行16S rDNA序列测定,构建系统发育树,研究细菌区系多样性的变化。结果：添加鱼油前、后,文库的RFLP图谱分别可以分成74和41个RFLP类群;添加鱼油前后的优势菌群均为噬纤维菌-屈挠杆菌-拟杆菌（CFB）和低（G＋C）含量的革兰阳性菌（LGCGPB）,但添加鱼油后文库中LGCGPB比例降低,而且未检测到纤维菌门细菌;有50%～60%的测定序列与GenBank数据库中的序列相似性高于97%,90%以上为未培养的细菌;添加鱼油后瘤胃细菌的多样性减少。结论：日粮添加鱼油后CFB比例增高但多样性下降,LGCGPB、纤维杆菌比例下降,这一结果为调控瘤胃发酵提供了依据。     

Threshold levels of generalist predation determine consumer response to resource pulses

Many ecological systems are characterized by brief periods of increased resource availability called resource pulses. Empirical studies suggest that some populations of primary consumers grow rapidly in response to resource pulses, but others instead remain at low abundance despite increases in resource availability. Previous theory suggests that the lack of increase in primary consumers might be due to predators, which can respond to increased prey density both numerically, by increasing their own population, and functionally, by killing prey at a faster rate. The complexity of potential population responses to resource pulses can be assessed with simulations, but analytical conditions determining when one observes qualitatively distinct dynamics have yet to be identified. Here we use a graphical method based on a bifurcation diagram to derive the conditions leading to qualitatively distinct steady state and transient prey population dynamics as levels of predation (abundance and diversity) vary. When predation thresholds are crossed, consumer populations respond numerically to increases in their resources and provide a secondary resource pulse to their predators and parasites. These community dynamics have broad implications for the impact of changing predator communities on insect and rodent population outbreaks, which are economically and epidemiologically important.     

Genetic and plastic responses of a northern mammal to climate change

Climate change is predicted to be most severe in northern regions and there has been much interest in to what extent organisms can cope with these changes through phenotypic plasticity or microevolutionary processes. A red squirrel population in the southwest Yukon, Canada, faced with increasing spring temperatures and food supply has advanced the timing of breeding by 18 days over the last 10 years (6 days per generation). Longitudinal analysis of females breeding in multiple years suggests that much of this change in parturition date can be explained by a plastic response to increased food abundance (3.7 days per generation). Significant changes in breeding values (0.8 days per generation), were in concordance with predictions from the breeder's equation (0.6 days per generation), and indicated that an evolutionary response to strong selection favouring earlier breeders also contributed to the observed advancement of this heritable trait. The timing of breeding in this population of squirrels, therefore, has advanced as a result of both phenotypic changes within generations, and genetic changes among generations in response to a rapidly changing environment.     

Examining natural population growth from near extinction: the case of the Antarctic fur seal at the South Shetlands,Antarctica

This study examined the recovery process of an Antarctic fur-seal population, starting from minimal numbers after commercial exploitation to the now largest breeding population in the South Shetland Archipelago, Cape Shirreff and San Telmo Islets. It used direct census data from 20 breeding seasons (including 11 consecutive years) that spanned over 45 years. Since early population estimates, pup production increased at an intrinsic rate of ca. 20% which, during the last decade, dramatically slowed to 4.6%. The population-change trajectory is currently converging into a tightly bounded oscillation around an apparent equilibrium (carrying capacity), which is an order of magnitude lower than those levels before exploitation began. This pattern suggests the onset of an alternative stable state and highlights the far-reaching implications of strong and large-scale perturbations on marine systems.     

BROWN ROOT ROT OF TOMATOES

Population counts and nutritional grouping of bacteria from a tomato-sick soil showed that steaming greatly reduced the population and the percentage of group I bacteria (i.e. those able to use inorganic nitrogen). The numbers subsequently increased, and by the time tomatoes were planted, the distribution of nutritional groups approximated to that in unsteamed soil. Rhizosphere and root-surface population numbers did not differ widely in steamed and unsteamed soils. The nutritional groups in soil before planting differed much more between samples from steamed soil with a changing population, than from soil unsteamed for 3 years. Groups I and II (bacteria requiring amino acids) were higher in unsteamed, cropped soil than in steamed soil, and were dominant in rhizosphere and root-surface populations. Group I increased on the root surface in unsteamed soil from July to October, whereas group II increased on root surfaces in steamed soil. Group V (bacteria requiring soil extract) was less frequent on the root surface than in soil from plots unsteamed for 1 year, but more frequent on the root surface than in soil unsteamed for 3 years.