SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia

The B.1.1.529 Omicron variant of SARS-CoV-2 is rapidly spreading, displacing the globally prevalent Delta variant. Before December 16, 2021, community transmission had already been observed in tens of countries globally. However, in Russia, all reported cases had been sporadic and associated with travel. Here, we report an Omicron outbreak at a students’ dormitory in Saint Petersburg, Russia. Out of the 462 sampled residents of the dormitory, 206 (44.6%) tested PCR positive, and 159 (77.1%) of these infections carried the S:ins214EPE insertion, indicating that they were of the Omicron strain. 104 (65%) of Omicron-positive patients have been vaccinated and/or reported previous covid-19. Whole genome sequencing confirmed that the outbreak is caused by the Omicron variant. Phylogenetic analysis showed that the outbreak has a single origin, and belongs to the S:346K sublineage of Omicron which may be characterized by an increased rate of spread, compared to other Omicron sublineages. The rapid spread of Omicron in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.

Lanskap Agrowisata Kopi Sumedang Sebagai Kolaborasi Peningkatan Perkebunan Rakyat Dan Perlindungan Lahan Danau Sunyayuri

called Kopi Buhun. Buhun Coffee is a type of Arabica coffee which is a single origin "special tea coffee". In developing Buhun coffee, land is needed that can be planted with coffee. This land is not only a coffee plantation but can become a tourist attraction that can educate, increase recreation and protect the environment besides that it can economically increase the income of residents around agrotourism. In general, the land of Lake Sunyayuri, Cimarias Village, Pamulihan District, Sumedang Regency is an area that has the potential to become a tourist spot with an artificial lake, and a panoramic view of the hills surrounding the lake with a beautiful and calming atmosphere. The productivity of Indonesian coffee is still low compared to the potential that can be increased. The need for plantation land, especially coffee, is still lacking. Utilization of abandoned forest areas in areas with coffee potential can still be carried out, including utilizing the Pamulihan Cekdam area. What is the form of the Sumedang Coffee Agrotourism design in utilizing the existing potential into plantation tourism that provides interesting tourist experiences, recreational facilities, and social interaction as well as coffee education for visitors and the community about how to cultivate coffee from nurseries to products that can be enjoyed and provide a source of income for local communities while preserving the environment?

SCIENTIFIC LINGUISTICS, A NEVER-ENDING HISTORY

1866 was a turning point in scientific linguistics when the Linguistic Society of Paris banned all papers and presentations on the origin of language. De Saussure locked up the debate with two concepts, diachrony and synchrony. I intend to examine the emergence of the hypothesis of a single origin of human articulated languages, in Africa first, and then Black Africa. The phylogenic approach of biological studies has today spread to linguistics. Sally McBrearty rejected the idea of a Neolithic revolution. Consequently, Black Africa became a major field of archaeological research. Yuval Noah Harari stating the existence of a symbolic revolution around 70,000 years ago, rejected Black Africa along with the Americas, and the Denisovans. Asia has become a major archaeological field. Julien d’Huy implements phylogenetic arborescent technique to the study of myths. The oldest form of a myth is not the origin of it. In oral civlizations some literate individual had to tell the story behind representations for the people to understand, appreciate, and remember them. I will then consider structural linguistics (Noam Chomsky & Universal Grammar). UG has never been able to develop semantics within its own system (Generative Semantics & George Lakoff). Science is always a temporarily approximate vision of what it considers. First, what any science explores is constantly evolving following phylogenic dynamics that are contained in the very objects of such scientific studies. Second, any new knowledge appearing in the field concerned causes a complete restructuration of what we knew before.

Chemical characteristics of Indonesian single-origin cocoa beans and the effect of tempering treatments on dark chocolate - a preliminary study

The aim of this study was to investigate the effect of geographical origin on the chemical characteristics of cocoa beans and to determine the effect of tempering treatment on the glossiness of dark chocolate. In this study, three roasted single-origin cocoa nibs, i.e., single-origin Kulon Progo, Aceh, and Gunung Kidul, were analysed to determine their moisture content, ash, crude protein, total fat, and pH value, as well as their sensory properties. Kulon Progo cocoa nibs were mostly preferred and further processed into dark chocolate using three tempering variations and analysed to determine their glossiness, texture, and colour. The glossiness level of dark chocolates under different tempering treatments was ranked using RedJade Sensory Software. Data were analysed using Minitab 17.0 Statistical Software. The results show that single-origin cocoa beans from Kulon Progo had the lowest moisture content (1.33 ± 0.015 %) and the highest fat content (54.01 ± 0.434 %). Dark chocolate tempered at 50:32:27:32°C had the most preferred glossy appearance (2.59 out of 3.00).

Assessing wild genetic background and parental effects on size of growth hormone transgenic coho salmon

Experiments examining potential impacts of growth hormone (GH) transgenesis in fish typically use a single source strain, and do not address potential differential impacts in strains of different genetic backgrounds. Here, we examine the effects of differing genetic backgrounds when reared in culture on the growth of transgenic and non-transgenic coho salmon (Oncorhynchus kisutch) produced by mating sires from different rivers with transgenic dams from a single origin. We found a significant difference in size between offspring of sires originating from various river systems in British Columbia. This difference was independent of differences between transgenotypes (i.e., transgenic vs. non-transgenic offspring). However, the effects of strain or sire were relatively small compared to the effects of the transgene, which were consistent regardless of sire origin. Thus, results derived from studies of GH transgenic fish from a single source population can provide useful information for assessments of GH transgenic salmon from other systems. This has important implications for examining potential risks from introgression of a transgene into different populations.

Transcriptome phylogenies support ancient evolutionary transitions in bioluminescence traits of cypridinid ostracods

Bioluminescence evolved many times independently, leading to dramatic effects on ecosystems by influencing communication both within and between species. One origin of bioluminescence is within cypridinid ostracods. Bioluminescent cypridinids probably all use light as an anti-predator display, while a subset that diversified in the Caribbean also use light for courtship signaling. Despite their importance for understanding the evolution of bioluminescence, very little molecular phylogenetic data are available for cypridinids and the timing of evolutionary transitions of luminous traits is poorly understood. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. Our results strongly support previous hypotheses of a single origin of bioluminescent courtship signaling, nested within a single origin of bioluminescence, and the secondary loss of courtship signaling in Vargula tsujii. We propose the name Luminini for the Tribe of bioluminescent cypridinids and Luxorina for the Sub-tribe of cypridinids with courtship signaling. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved at least 151 Million Years Ago (MYA) and cypridinid bioluminescence originated at least 197 MYA, making it one of the oldest documented origins of bioluminescence. The molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence.

Single Origin Coffee Aroma: From Optimized Flavor Protocols and Coffee Customization to Instrumental Volatile Characterization and Chemometrics

In this study, the aroma profile of 10 single origin Arabica coffees originating from eight different growing locations, from Central America to Indonesia, was analyzed using Headspace SPME-GC-MS as the analytical method. Their roasting was performed under temperature–time conditions, customized for each sample to reach specific sensory brew characteristics in an attempt to underline the customization of roast profiles and implementation of separate roastings followed by subsequent blending as a means to tailor cup quality. A total of 138 volatile compounds were identified in all coffee samples, mainly furan (~24–41%) and pyrazine (~25–39%) derivatives, many of which are recognized as coffee key odorants, while the main formation mechanism was the Maillard reaction. Volatile compounds’ composition data were also chemometrically processed using the HCA Heatmap, PCA and HCA aiming to explore if they meet the expected aroma quality attributes and if they can be an indicator of coffee origin. The desired brew characteristics of the samples were satisfactorily captured from the volatile compounds formed, contributing to the aroma potential of each sample. Furthermore, the volatile compounds presented a strong variation with the applied roasting conditions, meaning lighter roasted samples were efficiently differentiated from darker roasted samples, while roasting degree exceeded the geographical origin of the coffee. The coffee samples were distinguished into two groups, with the first two PCs accounting for 73.66% of the total variation, attributed mainly to the presence of higher quantities of furans and pyrazines, as well as to other chemical classes (e.g., dihydrofuranone and phenol derivatives), while HCA confirmed the above results rendering roasting conditions as the underlying criterion for differentiation.

The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production

Steroid and hopanoid biomarkers can be found in ancient rocks and may give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is complicated by losses and horizontal gene transfers, and appears to be widely misinterpretted. Here, I have added sequences from additional key species, and re-analysis of the phylogeny of SHC and OSC indicates a single origin of both enzymes among eukaryotes. This pattern is best explained by vertical inheritance of both enzymes from a bacterial ancestor, followed by widespread loss of SHC, and two subsequent HGT events to ferns and ascomycetes. Thus, the last common ancestor of eukaryotes would have been bifunctional for both sterol and hopanoid production. Later enzymatic innovations allowed diversification of sterols in eukaryotes. Contrary to previous interpretations, the LCA of eukaryotes potentially would have been able to produce hopanoids as a substitute for sterols in anaerobic conditions. Without invoking any other metabolic demand, the LCA of eukaryotes could have been a facultative aerobe, living in unstable conditions with respect to oxygen level.

Evolutionary puzzle: discussing the evolution of sentience in Metazoa through a phylogenetic perspective

Sentience is the capacity of organisms to feel and experience through subjective states. During the last years, several investigations have indicated that response mechanisms to harmful stimuli can be highly conserved among the Metazoa. However, there is a research bias towards vertebrates in the available studies. Here we discuss the evolution of the nervous and sensory system, pain and nociception in animals through a phylogenetic perspective testing the hypothesis of common ancestry of sentience. Our results indicate that characteristics related to sentience - morphological and molecular and behavioural -, were already present in the common ancestors of Metazoa, Eumetazoa and Bilateria. Our phylogenetic hypotheses positioned Porifera as the sister-group to all the other Metazoa, corroborating the hypothesis of a single origin of the nervous system. Our results also depict Urbilateria as the ancestor of the metazoan toolkit related to the sentience. These scenarios suggest that some attributes of the sensory system may have appeared even before the emergence of the nervous system, through possible cooptations of sensory modules of the first Metazoa.