Autophagy is required for necrotic cell death in Caenorhabditis elegans

Autophagy is the main process for bulk protein and organelle recycling in cells under extracellular or intracellular stress. Deregulation of autophagy has been associated with pathological conditions such as cancer, muscular disorders and neurodegeneration. Necrotic cell death underlies extensive neuronal loss in acute neurodegenerative episodes such as ischemic stroke. We find that excessive autophagosome formation is induced early during necrotic cell death in C. elegans. In addition, autophagy is required for necrotic cell death. Impairment of autophagy by genetic inactivation of autophagy genes or by pharmacological treatment suppresses necrosis. Autophagy synergizes with lysosomal catabolic mechanisms to facilitate cell death. Our findings demonstrate that autophagy contributes to cellular destruction during necrosis. Thus, interfering with the autophagic process may protect neurons against necrotic damage in humans.     

Influence of antibiotics on bacterial load and sperm parameters during short-term preservation of collared peccary semen

Studies on semen and sperm cells are critical to develop assisted reproductive technologies for the conservation of the collared peccary. The objective of the study was to compare the effect of different antibiotics on the bacterial load and sperm quality during short-term storage of peccary semen. Fresh semen samples from 10 males were extended in Tris-egg yolk or Tris-Aloe vera supplemented with streptomycin-penicillin (SP; 1 mg/mL - 1000 IU/mL or 2 mg/mL - 2000 IU/mL) or gentamicin (30 µg/mL or 70 µg/mL) before storage at 5°C. Bacterial load and sperm motility, membrane integrity and function, mitochondrial activity, and morphology, were evaluated at different time points for 36 h. The SP and gentamicin treatments concentration inhibited (p < 0.05) bacterial growth for 36 h regardless of the extender. Compared to the other treatments, Tris-egg yolk plus 70 µg/mL gentamicin maintained the sperm parameters for longer, including total motility (41.9 ± 6.1%) at 24 h, and membrane integrity (58.3 ± 2.1%) at 36 h. In contrast, the highest SP concentration in both extenders impaired sperm membrane integrity at 36 h (p < 0.05). For the liquid storage of collared peccary semen, it therefore is recommended to use Tris extender supplemented with egg yolk and gentamicin (70 µg/mL).     

Trends in Energy Intake in U.S. between 1977 and 1996: Similar Shifts Seen across Age Groups

Objective: To determine the trends in locations and food sources of Americans stratified by age group for both total energy and the meal and snack subcomponents. Research Methods and Procedures: Nationally representative data was taken from the 1977 to 1978 Nationwide Food Consumption Survey and the 1989 to 1991 and 1994 to 1996 (and 1998 for children age 2 through 9) Continuing Surveys of Food Intake by Individuals. The sample consisted of 63,380 individuals, age 2 and up. For each survey year, the percentage of total energy intake from meals and snacks was calculated separately for 2‐ to 18‐year‐olds, 19‐ to 39‐year‐olds, 40‐ to 59‐year‐olds, and those 60 years and older. The percentage of energy intake by location (at‐home consumption or preparation, vending, store eaten out, restaurant/fast‐food, and school) and by specific food group was computed for all age groups separately. Results: The trends in location and food sources were almost identical for all age groups. Key dietary behavior shifts included greater away‐from‐home consumption; large increases in total energy from salty snacks, soft drinks, and pizza; and large decreases in energy from low‐ and medium‐fat milk and medium‐ and high‐fat beef and pork. Discussion: Total energy intake has increased over the past 20 years, with shifts away from meals to snacks and from at‐home to away‐from‐home consumption. The similarity of changes across all age groups furthers the assertion that broad‐based environmental changes are needed to improve the diets of Americans.     

Host-use pattern of the shrimp <Emphasis Type="Italic">Periclimenes paivai</Emphasis> on the scyphozoan jellyfish <Emphasis Type="Italic">Lychnorhiza lucerna</Emphasis>: probing for territoriality and inferring its mating system

In symbiotic crustaceans, host-use patterns vary broadly. Some species inhabit host individuals solitarily, other species live in heterosexual pairs, and even other species live in aggregations. This disparity in host-use patterns coupled with considerable differences in host ecology provide opportunities to explore how environmental conditions affect animal behavior. In this study, we explored whether or not symbiotic crustaceans inhabiting relatively large and structurally complex host species live in aggregations. We expected Periclimenes paivai, a small caridean shrimp that lives among the tentacles of the large and morphologically complex scyphozoan jellyfish Lychnorhiza lucerna, to live in groups given that the host traits above constraint host-monopolization behaviors by symbiotic crustaceans. We described the population distribution of P. paivai during a bloom of L. lucerna near the mouth of the Paraíba River estuary in Paraíba, Brazil. The population distribution of P. paivai did not differ statistically from a random Poisson distribution. Male shrimps were most often found dwelling on the surface of L. lucerna individuals as small groups (2–4 individuals), in agreement with expectations. Periclimenes paivai is a sexually dimorphic species with males attaining smaller average body sizes than females and exhibiting no elaborated weaponry (claws). Females, but not males, experience positive allometry in cheliped size and were found living solitarily in small but not large host individuals. The above suggest that females might be territorial or that they might be competing for resources (i.e., food) likely expected to impact their reproductive output. Our results agree, but only partially, with the idea that large and morphologically complex host species should harbor non-territorial gregarious symbiotic crustaceans. Symbiotic crustaceans represent excellent models to improve our understanding about the conditions driving the social behavior of marine organisms.     

Cell polarity protein Spa2P associates with proteins involved in actin function in Saccharomyces cerevisiae

Spa2p is a nonessential protein that regulates yeast cell polarity. It localizes early to the presumptive bud site and remains at sites of growth throughout the cell cycle. To understand how Spa2p localization is regulated and to gain insight into its molecular function in cell polarity, we used a coimmunoprecipitation strategy followed by tandem mass spectrometry analysis to identify proteins that associate with Spa2p in vivo. We identified Myo1p, Myo2p, Pan1p, and the protein encoded by YFR016c as proteins that interact with Spa2p. Strikingly, all of these proteins are involved in cell polarity and/or actin function. Here we focus on the functional significance of the interactions of Spa2p with Myo2p and Myo1p. We find that localization of Spa2GFP to sites of polarized growth depends on functional Myo2p but not on Myo1p. We also find that Spa2p, like Myo2p, cosediments with F-actin in an ATP-sensitive manner. We hypothesize that Spa2p associates with actin via a direct or indirect interaction with Myo2p and that Spa2p may be involved in mediating polarized localization of polarity proteins via Myo2p. In addition, we observe an enhanced cell-separation defect in a myo1spa2 strain at 37 degrees C. This provides further evidence that Spa2p is involved in cytokinesis and cell wall morphogenesis.     

Preserved left ventricular structure and function in mice with cardiac sympathetic hyperinnervation

Cardiac-specific overexpression of nerve growth factor (NGF), a neurotrophin, leads to sympathetic hyperinnervation of heart. As a consequence, adverse functional changes that occur after chronically enhanced sympathoadrenergic stimulation of heart might develop in this model. However, NGF also facilitates synaptic transmission and norepinephrine uptake, effects that would be expected to restrain such deleterious outcomes. To test this, we examined 5- to 6-mo-old transgenic (TG) mice that overexpress NGF in heart and their wild-type (WT) littermates using echocardiography, invasive catheterization, histology, and catecholamine assays. In TG mice, hypertrophy of the right ventricle was evident (+67%), but the left ventricle was only mildly affected (+17%). Left ventricular (LV) fractional shortening and fractional area change values as indicated by echocardiography were similar between the two groups. Catheterization experiments revealed that LV +/-dP/dt values were comparable between TG and WT mice and responded similarly upon isoproterenol stimulation, which indicates lack of beta-adrenergic receptor dysfunction. Although norepinephrine levels in TG LV tissue were approximately twofold those of WT tissue, TG plasma levels of the neuronal norepinephrine metabolite dihydroxyphenylglycol were fivefold those of WT plasma. A greater neuronal uptake activity was also observed in TG LV tissue. In conclusion, overexpression of NGF in heart leads to sympathetic hyperinnervation that is not associated with detrimental effects on LV performance and is likely due to concomitantly enhanced norepinephrine neuronal uptake.     

The affinity of the dynein microtubule-binding domain is modulated by the conformation of its coiled-coil stalk

The microtubule-binding domain (MTBD) of dynein is separated from the AAA (ATPase with any other activity) core of the motor by an approximately 15-nm stalk that is predicted to consist of an antiparallel coiled coil. However, the structure of this coiled coil and the mechanism it uses to mediate communication between the MTBD and ATP-binding core are unknown. Here, we sought to identify the optimal alignment between the hydrophobic heptad repeats in the two strands of the stalk coiled coil. To do this, we fused the MTBD of mouse cytoplasmic dynein, together with 12-36 residues of its stalk, onto a stable coiled-coil base provided by Thermus thermophilus seryl-tRNA synthetase and tested these chimeric constructs for microtubule binding in vitro. The results identified one alignment that yielded a protein displaying high affinity for microtubules (2.2 microM). The effects of mutations applied to the MTBD of this construct paralleled those previously reported (Koonce, M. P., and Tikhonenko, I. (2000) Mol. Biol. Cell 11, 523-529) for an intact dynein motor unit in the absence of ATP, suggesting that it resembles the tight binding state of native intact dynein. All other alignments showed at least 10-fold lower affinity for microtubules with the exception of one, which had an intermediate affinity. Based on these results and on amino acid sequence analysis, we hypothesize that dynein utilizes small amounts of sliding displacement between the two strands of its coiled-coil stalk as a means of communication between the AAA core of the motor and the MTBD during the mechanochemical cycle.     

Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice

Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.     

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low‐copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome‐wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome‐wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova , we conclude that there are two genetically distinct O. rufipogon groups, Ruf‐I and Ruf‐II. The two groups exhibit a clinal variation pattern generally from north‐east to south‐west. Different from many earlier studies, Ruf‐I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf‐II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.