Epidemiological Characterization of Influenza A(H1N1)pdm09 Cases from 2009 to 2010 in Baguio City,the Philippines

Background

Baguio City, Philippines experienced its first influenza A(H1N1)pdm09 [A(H1)pdm09] case in May 2009. In spite of numerous reports describing the epidemiological and clinical features of A(H1)pdm09 cases, there are no studies about A(H1)pdm09 epidemiology in the Philippines, where year-round influenza activity was observed.

Objectives

We aimed to investigate the epidemiological and clinical features of A(H1)pdm09 in pandemic and post-pandemic periods.

Methods

Data were collected under enhanced surveillance of influenza-like illness (ILI) and severe acute respiratory infection (SARI) from January 2009 to December 2010. RT-PCR was used to detect A(H1)pdm09, following the protocol of the United States Centers for Disease Control and Prevention. The reproduction number was computed as a simple exponential growth rate. Differences in proportional and categorical data were examined using chi-square test or Fishers’ exact test.

Results and Conclusions

The outbreak was observed from week 25 to 35 in 2009 and from week 24 to 37 in 2010. The highest proportion of cases was among children aged 5–14 years. The number of ILI outpatients was 2.3-fold higher in 2009 than in 2010, while the number of inpatients was 1.8-fold higher in 2009. No significant difference in gender was observed during the two periods. The clinical condition of all patients was generally mild and self-limiting, with only 2 mortalities among inpatients in 2009. The basic reproduction number was estimated as 1.16 in 2009 and 1.05 in 2010 in the assumption of mean generation time as 2.6 days. School children played a significant role in facilitating influenza transmission.     

Pathogenesis of a Thai strain of white spot syndrome virus (WSSV) in juvenile, specific pathogen-free Litopenaeus vannamei

White spot syndrome virus (WSSV) causes disease and mortality in cultured and wild shrimp. A standardized WSSV oral inoculation procedure was used in specific pathogen-free (SPF) Litopenaeus vannamei (also called Penaeus vannamei) to determine the primary sites of replication (portal of entry), to analyze the viral spread and to propose the cause of death. Shrimp were inoculated orally with a low (10(1.5) shrimp infectious dose 50% endpoint [SID50]) or a high (10(4) SID50) dose. Per dose, 6 shrimp were collected at 0, 6, 12, 18, 24, 36, 48 and 60 h post inoculation (hpi). WSSV-infected cells were located in tissues by immunohistochemistry and in hemolymph by indirect immunofluorescence. Cell-free hemolymph was examined for WSSV DNA using 1-step PCR. Tissues and cell-free hemolymph were first positive at 18 hpi (low dose) or at 12 hpi (high dose). With the 2 doses, primary replication was found in cells of the foregut and gills. The antennal gland was an additional primary replication site at the high dose. WSSV-infected cells were found in the hemolymph starting from 36 hpi. At 60 hpi, the percentage of WSSV-infected cells was 36 for the epithelial cells of the foregut and 27 for the epithelial cells of the integument; the number of WSSV-infected cells per mm2 was 98 for the gills, 26 for the antennal gland, 78 for the hematopoietic tissue and 49 for the lymphoid organ. Areas of necrosis were observed in infected tissues starting from 48 hpi (low dose) or 36 hpi (high dose). Since the foregut, gills, antennal gland and integument are essential for the maintenance of shrimp homeostasis, it is likely that WSSV infection leads to death due to their dysfunction.     

Soil and vegetation development during early succession on restored coal wastes: a six-year permanent plot study

Plant and Soil - Little is known about how soil parameters change during early stages of revegetation dynamics on newly-restored coal mines, particularly in a Mediterranean climate. Our aim was to...     

Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies

There is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30–48 h. Photosynthesis and quantum yield peaked at subjective noon, and non‐photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light‐harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non‐stressed plants maximize photosynthesis.     

Soil drying procedure affects the DNA quantification of <Emphasis Type="Italic">Lactarius vinosus</Emphasis> but does not change the fungal community composition

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.     

The importance of topography and climate on short-term revegetation of coal wastes in Spain

The initial colonization phase is the crucial start point for succession and therefore for restoration. However, little is known about abiotic factors that influence the early stages of revegetation dynamics on restored coal mines, particularly in a Mediterranean climate. This information is crucial for improving our ability to reclaim land despoiled by mining. Here, we characterized the short-term plant community development in the first 3 years after hydroseeding on a topographically diverse reclaimed open-pit coal mines in Spain. Topography influenced both community composition and diversity producing different trajectories between the three different aspects (north-facing, south-facing, flat). Hydroseeded species provided most of the initial vegetation cover, which brought about most of the compositional differences between these aspects. We also found that the changing climate through the growing season also influenced floristic composition and diversity. Summer drought reduced the cover of hydroseeded perennial species and allowed native species to colonize. These results emphasize the need to take topography into account when developing reclamation management plans in Mediterranean ecosystems, and an acknowledgement that climate might drive the succession in the desired direction, hence increasing success in restoring mining impacts.     

Vegetation succession on reclaimed coal wastes in Spain: the influence of soil and environmental factors

Question: How is vegetation succession on coal mine wastes under a Mediterranean climate affected by the restoration method used (topsoil addition or not)? How are plant successional processes influenced by local landscape and soil factors? Location: Reclaimed coal mines in the north of Palencia province, northern Spain (42°47′‐42°50′ N, 4°32′‐4°53′ W). Methods: In Jun–Jul 2008, vascular plant species cover was monitored in 31 coal mines. The mines, which had been restored using two restoration methods (topsoil addition or not), comprised a chronosequence of different ages from 1 to 40 yr since restoration started. Soil and environmental factors at each mine were monitored and related to species cover using a combination of ordination methods and Huisman–Olff–Fresco modeling. Results: Plant succession was affected by restoration method . Where topsoil was added, succession was influenced by age since restoration and soil pH. Where no topsoil was added, soil factors seem to arrest succession. Vegetation composition on topsoiled sites showed a gradient with age, from the youngest, with early colonizing species, to oldest, with an increase in woody species. Vegetation on non‐topsoiled sites comprised mainly early‐successional species. Response to age and pH of 37 species found on topsoiled mines is described. Conclusions: Restoration of coal mines under this Mediterranean climate can be relatively fast if topsoil is added, with a native shrub community developing after 15 yr. However, if topsoil is not used, it takes more than 40 yr. For topsoiled mines, the species found in the different successional stages were identified, and their tolerance to soil pH was derived. This information will assist future restoration projects in the area.     

Alk3 controls nephron number and androgen production via lineage-specific effects in intermediate mesoderm

The mammalian kidney and male reproductive system are both derived from the intermediate mesoderm. The spatial and temporal expression of bone morphogenetic protein (BMP) 2 and BMP4 and their cognate receptor, activin like kinase 3 (ALK3), suggests a functional role for BMP-ALK3 signaling during formation of intermediate mesoderm-derivative organs. Here, we define cell autonomous functions for Alk3 in the kidney and male gonad in mice with CRE-mediated Alk3 inactivation targeted to intermediate mesoderm progenitors (Alk3(IMP null)). Alk3-deficient mice exhibit simple renal hypoplasia characterized by decreases in both kidney size and nephron number but normal tissue architecture. These defects are preceded by a decreased contribution of Alk3-deleted cells to the metanephric blastema and reduced expression of Osr1 and SIX2, which mark nephron progenitor cells. Mutant mice are also characterized by defects in intermediate mesoderm-derived genital tissues with fewer mesonephric tubules and testicular Leydig cells, epithelial vacuolization in the postnatal corpus epididymis, and decreased serum testosterone levels and reduced fertility. Analysis of ALK3-dependent signaling effectors revealed lineage-specific reduction of phospho-p38 MAPK in metanephric mesenchyme and phospho-SMAD1/5/8 in the testis. Together, these results demonstrate a requirement for Alk3 in distinct progenitor cell populations derived from the intermediate mesoderm.     

Effects of fire regime shift in Mediterranean Basin ecosystems: changes in soil seed bank composition among functional types

We studied the soil seed bank in a possible scenario of fire regime shift and asked: (1) Does high fire frequency impact the density of seeds stored, species richness and evenness? (2) Overall, does high fire frequency produce changes in the presence–absence and abundance of species? The study was implemented in a Mediterranean Basin ecosystem in plots with increasing fire frequency (unburned, burned once and burned twice in the last 66 years). The number of seeds increased with fire frequency for all life forms (shrub, scrub, perennial forb, annual forb and perennial graminoid). Species richness of annual forbs also increased. Evenness of shrubs diminished because the number of seeds in all the species decreased, except C. albidus, which increased. Overall, differences in the abundance of species were found, mainly by depleting shrubs and increasing forbs. There were no differences in the presence–absence data. In conclusion, high fire frequencies act as a filtering factor for species of a larger size and advanced maturity age. In contrast, life forms of small size and rapid onset of reproductive maturity can be enhanced. This community conversion from woody to herbaceous soil seed banks is fundamental to identify vegetation changes in future regimes of high fire frequency.