Essay Check-List

This simple essay check-list encourages students to evaluate their own work before handing a paper in. The worksheeet also serves as a reminder for what needs to be included

Plant biomass and prediction of debarking caused by rodents in artificial regeneration of forest stands

Homolka, M., Heroldová, M., Kamler, J

Synchronous population fluctuations of forest and field voles: implications for population management

Tkadlec, E., Suchomel, J., Purchart, L., Heroldová, M., Čepelka, L., Homolka, M

Effects of drying procedures on chemical composition and nutritive value of alfalfa forage

The effects of various drying procedures of alfalfa forage were evaluated on chemical composition, in vitro neutral detergent fibre (NDF) and dry matter (DM) digestibility, in situ DM, organic matter and crude protein (CP) degradability. The alfalfa had been harvested in the spring growth (early bud and flowering) and first regrowth (late bud and late flowering) periods. The samples were dried at 30 °C (T30), 40 °C (T40), 50 °C (T50), 60 °C (T60) and 100 °C (T100) in a forced-air oven or frozen for one month and then freeze-dried (TFD) or oven-dried at 50 °C (TFREE). Another drying procedure included pre-treatment by heating in a microwave oven (TMO) or in a forced-air oven at 100 °C for 1 hour (T100+50) and then oven-dried at 50 °C. The freeze-drying method was chosen as a reference method. Freeze-dried samples had the lowest NDF, acid detergent fibre (ADF), acid detergent lignin (ADL), neutral detergent insoluble protein (NDIP) and acid detergent insoluble protein contents (P <0.05). Additionally, freeze-dried products had the highest CP, in vitro true digestibility of DM and CP degradability values (P <0.05). There was no added benefit of the TMO in the chemical composition, in vitro digestibility or in situ degradation compared with T50. This study showed that T50 can yield chemical composition, in vitro and in situ results that are similar to those obtained with the freeze-drying method and that this procedure is useful for forage analyses and evaluation.Keywords: freeze-drying, insoluble nitrogen, in vitro digestibility, oven-drying, ruminant

Soil Amplification at Treasure Island During the Loma Prieta Earthquake

The Loma Prieta Earthquake ground motions recorded on Treasure Island, a man-made fill in San Francisco Bay were considerably greater than on the adjacent Yerba Buena rock outcrop. The Yerba Buena motions were used as input to the computer program SHAKE90 for computing soil amplification at Treasure Island. Shear wave propagation velocities were obtained by seismic cone penetration testing. Reasonable agreement was observed between the computed and recorded accelerations at the strong motion recording station. The maximum computed accelerations around the island ranged from 0.13 to 0.20 g\u27s. The degree of damage at various locations on the island correlated somewhat with the maximum computed accelerations

Vole impact on tree regeneration: insights into forest management

Heroldová, M., Homolka, M., Tkadlec, E., Kamler, J., Suchomel, J., Purchart, L., Krojerová, J., Barančeková, M., Turek, K., Baňař, M

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

Biogeochemistry of upland to wetland soils, sediments, and surface waters across Mid-Atlantic and Great Lakes coastal interfaces

Transferable and mechanistic understanding of cross-scale interactions is necessary to predict how coastal systems respond to global change. Cohesive datasets across geographically distributed sites can be used to examine how transferable a mechanistic understanding of coastal ecosystem control points is. To address the above research objectives, data were collected by the EXploration of Coastal Hydrobiogeochemistry Across a Network of Gradients and Experiments (EXCHANGE) Consortium – a regionally distributed network of researchers that collaborated on experimental design, methodology, collection, analysis, and publication. The EXCHANGE Consortium collected samples from 52 coastal terrestrial-aquatic interfaces (TAIs) during Fall of 2021. At each TAI, samples collected include soils from across a transverse elevation gradient (i.e., coastal upland forest, transitional forest, and wetland soils), surface waters, and nearshore sediments across research sites in the Great Lakes and Mid-Atlantic regions (Chesapeake and Delaware Bays) of the continental USA. The first campaign measures surface water quality parameters, bulk geochemical parameters on water, soil, and sediment samples, and physicochemical parameters of sediment and soil

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis

Recoil-Ion Detection System

This research was sponsored by the National Science Foundation Grant NSF PHY-931478