Can we rely on forest reserves for primate conservation?

Tropical forests contain much of the world's biodiversity, yet their rate of decline is increasing. The strategy most frequently used to protect this biodiversity is to make parks and reserves. While there is a great deal of research on the effectiveness of parks for protecting biodiversity, there is little research on how well extractive reserves conserve biodiversity. Here, we evaluate the effectiveness of four forest reserves in western Uganda at maintaining populations of primates and compare census data from the reserves to data from the neighbouring well‐protected Kibale National Park. The relative abundance of the five most common primates in the park was approximately four times that of the forest reserves. In the forest reserves, evidence of new human encroachment was seen every 500 m, while in the park it was seen every 100,000 m. Two recommendations emerge from our research: (i) for forest reserves, such as those studied here, to have conservation value for primates, extraction must be reduced and (ii) until the long‐term viability of the populations in forest reserves can be ascertained, they should not be considered in estimates of the sizes of endangered species protected ranges.     

Cord-factor analogs: synthesis of 6,6'-di-O-mycoloyl- and -corynomycoloyl-(alpha-D-galactopyranosyl alpha-D-galactopyranoside)

Appropriate solvolysis of 2,3,2',3'-tetra-O-benzyl-4,6,4', 6'-tetra-O-mesyl-alpha,alpha-trehalose gave 2,3,2',3' -tetra-O-benzyl-(alpha-D-galactopyranosyl alpha-D-galactopyranoside) (2). Selective tosylation or mesylation of 2 respectively gave the 6, 6'-ditosylate (3) and 6,6'-dimesylate (4), the structures of which were confirmed by the 1H-n.m.r. spectra of the corresponding 4,4'-di-O-acetyl derivatives. Treatment of 3 with potassium mycolate in toluene, and subsequent hydrogenolysis, gave the 6'-mycolate 6-tosylate derivative. Treatment of 3 with potassium mycolate or potassium corynomycolate in hexamethylphosphoric triamide, followed by catalytic hydrogenolysis, yielded the respective cord-factor analogs 6,6'-di-O-mycoloyl-(alpha-D-galactopyranosyl alpha-D-galactopyranoside) and 6,6'-di-O-corynomycoloyl-(alpha-D-galactopyranosyl alpha-D-galactopyranoside). The same 6,6'-diesters were obtained from the 6,6'-dimesylate 4. Putative 4,6-anhydro-6'-monomycolates are also described.     

High-elevation mountain hemlock growth as a surrogate for cool-season precipitation in Crater Lake National Park,USA

Snow dominates the hydrology and climate of the United States’ central Pacific Coast, but because local measurements of snowpack and winter precipitation often extend back only a few decades, observations by themselves are not adequate to describe potential amplitude of wintertime conditions. Here we present a set of updated and extended mountain hemlock (Tsuga mertensiana [Bong.] Carr.) tree-ring width records from Crater Lake National Park, Oregon, and use these data to make inferences about snowpack prior to the start of instrumental monitoring. In July and August 2013, we collected cores from 228 trees at seven high-elevation hemlock stands that surround the crater’s rim. The oldest tree had an inner ring date of CE 1474, and the longest ring-width chronology maintained a satisfactory common signal back to the middle of the 16th century. The growth of high-elevation mountain hemlock is strongly and inversely related to cool-season precipitation, making these records some of the most southerly examples of a robust inverse cool-season moisture signal in North American tree rings. The growth of these snow-limited forests does not appear to have been affected by the substantial decline in spring snowpack observed in the past two decades across the broader Cascade Range, and we did not find any indication of changing relationships between tree growth and either monthly or seasonal winter precipitation since the early 1990s. The exceptional three-year sequence in Crater Lake tree rings between CE 1809 and 1811, which includes the narrowest ring since CE 1540 and anatomical abnormalities produced by cold weather, leads us to conclude that 1809–1810 was the most snowy and severe winter to affect south-central Oregon during the past four and a half centuries.     

Esophageal squamous cell carcinoma and adenocarcinoma in Malaysia – Pooled data from upper gastrointestinal centers in a multiethnic Asian population

BackgroundEsophageal cancer is the sixth leading cause of cancer death worldwide with considerable geographical histological variation There is a paucity of data in esophageal cancer in demographics, histology, and survival among the multi-ethnic Malaysian population. This paper is a review of esophageal cancer epidemiology and survival among esophageal cancer patients from data collected by the Malaysian Upper Gastrointestinal Surgical Society.MethodsThis is a multicenter retrospective observational study of esophageal cancer patients from six upper gastrointestinal surgical centers in Malaysia between 2005 and 2019. Patient characteristics, histological type and stage were compared and survival analyzed.ResultsThere were 820 patients with esophageal cancer included, where 442 (53.9 %) cases had squamous cell carcinoma (SCC) and 378 (46.1 %) had adenocarcinomas (AC). Malays were the predominant ethnicity with AC (66.7 %) while Indians were the ethnic majority (74.6 %) with SCC. Majority of patients (56.8 %) presented as stage IV disease. Overall, the 1-, 3-, and 5-years’ survival were 35.8 %, 13.8 % and 11.0 %, respectively. Surgical resection with curative intent yielded the best 5-year survival (29.4 %). Intervention in stage IV AC yielded superior survival when compared to SCC (median survival, 7.9 months vs 4.8 months; p, 0.018) Our series demonstrated an increase in AC to SCC over the last 15 years.ConclusionsThere was an ethnic preponderance seen between different histology in this region, not previously discussed. An increase in AC was observed over the last 15 years. Late diagnosis seen in most patients imparts poor prognosis as curative surgery affords the best outcome.     

Northern bobwhite response to Conservation Reserve Program habitat and landscape attributes

The northern bobwhite (Colinus virginianus; hereafter bobwhite) has experienced substantial population declines in recent decades in the United States, and especially in Maryland and Delaware. The United States Department of Agriculture's Conservation Reserve Program (CRP) could provide additional habitat for bobwhites, leading to an increase in bobwhite abundance. I investigated if bobwhite abundance was related to the percent cover of CRP land and landscape attributes in local landscapes on Maryland's Eastern Shore and Delaware. Observers conducted bobwhite point transect surveys at 113 locations during the breeding seasons of 2006–2007, and I calculated landscape metrics for 500-m radius landscapes centered on each point transect location. Most CRP land in the study landscapes was planted to herbaceous vegetation. Bobwhite abundance was strongly positively associated with percent cover of CRP land in the landscape but was not strongly related to percent cover of agriculture or forest or to landscape patch density. These results suggest that the CRP has created additional habitat for bobwhites in Maryland and Delaware and that landscapes with greater proportions of herbaceous CRP practices support more bobwhites. © 2012 The Wildlife Society.     

Emergence,evolution, and vaccine production approaches of SARS-CoV-2 virus: Benefits of getting vaccinated and common questions

The emergence of coronavirus disease 2019 (COVID-19) pandemic in Wuhan city, China at the end of 2019 made it urgent to identify the origin of the causal pathogen and its molecular evolution, to appropriately design an effective vaccine. This study analyzes the evolutionary background of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or SARS-2) in accordance with its close relative SARS-CoV (SARS-1), which was emerged in 2002. A comparative genomic and proteomic study was conducted on SARS-2, SARS-1, and Middle East respiratory syndrome coronavirus (MERS), which was emerged in 2012. In silico analysis inferred the genetic variability among the tested viruses. The SARS-1 genome harbored 11 genes encoding 12 proteins, while SARS-2 genome contained only 10 genes encoding for 10 proteins. MERS genome contained 11 genes encoding 11 proteins. The analysis also revealed a slight variation in the whole genome size of SARS-2 comparing to its siblings resulting from sequential insertions and deletions (indels) throughout the viral genome particularly ORF1AB, spike, ORF10 and ORF8. The effective indels were observed in the gene encoding the spike protein that is responsible for viral attachment to the angiotensin-converting enzyme 2 (ACE2) cell receptor and initiating infection. These indels are responsible for the newly emerging COVID-19 variants αCoV, βCoV, γCoV and δCoV. Nowadays, few effective COVID-19 vaccines developed based on spike (S) glycoprotein were approved and become available worldwide. Currently available vaccines can relatively prevent the spread of COVID-19 and suppress the disease. The traditional (killed or attenuated virus vaccine and antibody-based vaccine) and innovated vaccine production technologies (RNA- and DNA-based vaccines and viral vectors) are summarized in this review. We finally highlight the most common questions related to COVID-19 disease and the benefits of getting vaccinated.     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Planning connectivity at multiple scales for large mammals in a human-dominated biodiversity hotspot

Connectivity for large mammals across human-altered landscapes results from movement by individuals that can be described via nested spatial scales as linkages (or zones or areas) with compatible land use types, constrictions that repeatedly funnel movement (as corridors) or impede it (as barriers), and the specific paths (or routes) across completely anthropogenic features (such as highways). Mitigation to facilitate animal movement through such landscapes requires similar attention to spatial scale, particularly when they involve complex topography, diverse types of human land use, and transportation infrastructure. We modeled connectivity for Asian elephant (Elephas maximus) and gaur (Bos gaurus) in the Shencottah Gap, a multiple-use region separating two tiger reserves in the Western Ghats, India. Using 840 km of surveys for animal signs within a region of 621 km², we modeled landscape linkages via resource selection functions integrated across two spatial resolutions, and then potential dispersal corridors within these linkages using circuit theoretical models. Within these corridors, we further identified potential small-scale movement paths across a busy transportation route via least-cost paths and evaluated their viability. Both elephants and gaur avoided human-dominated habitat, resulting in broken connectivity across the Shencottah Gap. Predicted corridor locations were sensitive to analysis resolution, and corridors derived from scale-integrated habitat models correlated best with habitat quality. Less than 1% of elephant and gaur detections occurred in habitat that was poorer in quality than the lowest-quality component of the movement path across the transportation route, suggesting that connectivity will require habitat improvement. Only 28% of dispersal corridor area and 5% of movement path length overlapped with the upper 50% quantile of the landscape linkage; thus, jointly modeling these three components enabled a more nuanced evaluation of connectivity than any of them in isolation.