Big Scrub: A cleared landscape in transition back to forest?

Restoring the rainforests of the Big Scrub is a powerful restoration symbol for the regional communities of far north coast New South Wales, but it is only a partly realized aspiration. What progress has been made in 35 years and to what extent is the aspiration achievable?     

Relationships among somatic cell count, California mastitis test, impedance and bacteriological status of milk in goats and sheep in early lactation

The objectives of this trial were to evaluate and compare the test characteristics of a number of indirect tests of bacteriological status of the milk from goats and sheep and to assess the affect of varying levels of prevalence of infection on the performance of those tests.The somatic cell count, California mastitis test (CMT) score, electrical impedance and the bacteriological status of 220 and 262 milk samples from the glands of lactating dairy goats and sheep, respectively, were determined. The sensitivity and specificity of indirect tests in predicting the bacteriological status were compared by analyzing the areas under the receiver operating characteristic curve and calculating the likelihood ratio at various cut-off values.Bacteria were isolated from 17.7 and 4.6% of glands from goats and sheep, respectively. Somatic cell count was a better predictor of bacteriological status than either the CMT score or impedance in both goats and sheep. However, knowledge of the CMT score in both sheep and goats and the impedance in goats increases the likelihood of predicting the presence of a bacterial pathogen compared to no testing at all (P<0.05). Knowledge of the age and days postpartum of the animals at the time of testing did not increase the probability that infection status could be predicted. Variation in cut-off levels to predict infection status reported in the literature may be due to variation in the prevalence of infection in the populations studied. Use of likelihood ratio allows comparison of tests over a range of prevalence’s as likelihood ratios are independent of prevalence. The prevalence of infection within a herd should be considered when selecting a cut-off value for indirect testing for the presence of bacteria in milk of small ruminants.     

In situ biological particle analyzer based on digital inline holography

Obtaining in situ measurements of biological microparticles is crucial for both scientific research and numerous industrial applications (e.g., early detection of harmful algal blooms, monitoring yeast during fermentation). However, existing methods are limited to offer timely diagnostics of these particles with sufficient accuracy and information. Here, we introduce a novel method for real-time, in situ analysis using machine learning (ML)-assisted digital inline holography (DIH). Our ML model uses a customized YOLOv5 architecture specialized for the detection and classification of small biological particles. We demonstrate the effectiveness of our method in the analysis of 10 plankton species with equivalent high accuracy and significantly reduced processing time compared to previous methods. We also applied our method to differentiate yeast cells under four metabolic states and from two strains. Our results show that the proposed method can accurately detect and differentiate cellular and subcellular features related to metabolic states and strains. This study demonstrates the potential of ML-driven DIH approach as a sensitive and versatile diagnostic tool for real-time, in situ analysis of both biotic and abiotic particles. This method can be readily deployed in a distributive manner for scientific research and manufacturing on an industrial scale.     

Does consumer injury modify invasion impact?

Predicting the impacts of an invasive species solely by its abundance is common, yet it ignores other potentially important moderating factors. One such factor is injury. Severe injury can lead to mortality, which can directly reduce the abundance of the invader. However, more moderate, sublethal injury can also temper the impact of invasive species. Therefore, to predict impacts, it may be useful to examine not only abundance, but also moderating factors (e.g., injury) and predictors of these factors (e.g., density, size). We documented the density, injury (i.e., limb loss), and size of two conspicuous invaders, the European green crab (Carcinus maenas) and the Asian shore crab (Hemigrapsus sanguineus), at thirty sites from Shinnecock County Park, New York to Lubec, Maine. In addition, we used a field experiment to determine how injury influenced the consumption rate of mussels (Mytilus edulis) by each crab species. 31.6% of all C. maenas (1,493/4,721) and 30.7% of H. sanguineus (2,003/6,523) were missing appendage(s). Of the crabs injured, 38.4% (573/1,493) and 30.5% (611/2,003) were missing cheliped(s) for C. maenas and H. sanguineus, respectively. In our experiments, cheliped loss reduced consumption of both species on M. edulis. Injured C. maenas consumed 21% fewer mussels than uninjured crabs. Injury completely eliminated mussel consumption by H. sanguineus. Previous studies have highlighted the detrimental impacts of these two invaders on native bivalve prey. While the loss of a single cheliped can greatly reduce or even eliminate the ability of C. maenas and H. sanguineus to consume M. edulis, our results suggest that injury has a relatively minor role in reducing overall population-level impacts on prey such as mussels. However, injury on an individual-level can play a role in moderating the consumptive impacts of these invaders.     

Genes coding for valine transfer ribonucleic acid-3b in Drosophila melanogaster.

The genes for tRNA_3b^val were localized to 84D and 92B on the polytene chromosomes of Drosophila melanogaster with a possible minor site at 90B-C by hybridization in situ and autoradiography with ¹²⁵I-labeled tRNA_3b^val. Flies carrying a duplication of the 84D region had increased amounts (30%) of tRNA_3b^val in proportion to the increased number of genes. While a proportional decrease in the amount of tRNA^val_3b in flies bearing a deletion of the same region was found, the total acceptance of valine remained at the level found in the wild type.     

Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress

Real-time RT-PCR is a powerful technique for the measurement of gene expression, but its accuracy depends on the stability of the internal reference gene(s) used for data normalization. Tobacco (Nicotiana tabacum) is an important model in studies of plant gene expression, but stable reference genes have not been well-studied in the tobacco system. We address this problem by analysing the expression stability of eight potential tobacco reference genes. Primers targeting each gene (18S rRNA, EF-1α, Ntubc2, α- and β-tubulin, PP2A, L25 and actin) were developed and optimized. The expression of each gene was then measured by real-time PCR in a diverse set of 22 tobacco cDNA samples derived from developmentally distinct tissues and from plants exposed to several abiotic stresses. L25 and EF-1α demonstrated the highest expression stability, followed by Ntubc2. Measurement of L25 and EF-1α was sufficient for accurate normalization in either the developmental or stress-treated samples, but Ntubc2 was also required when considering the entire sample set. Analysis of a tobacco circadian gene (NTCP-23) verified these reference genes in an additional context, and all techniques were optimized to enable a high-throughput approach. These results provide a foundation for the more accurate and widespread use of real-time RT-PCR in tobacco.     

Changes in the activity of enzymes involved with primary nitrogen metabolism due to ectomycorrhizal symbiosis on jack pine seedlings

Jack pine (Pinus banksiana Lamb.) seedlings were inoculated with either one of the ectomycorrhizal (ECM) fungi, Laccaria bicolor (Maire) Orton or Pisolithus tinctorius (Pers.) Coker and Couch, and grown for 16 weeks in a growth chamber along with non-ECM controls. Five enzymes involved with the assimilation of nitrogen or the synthesis of amino acids were measured in the 3 jack pine root systems as well as in the pure fungal cultures. Pisolithus tinctorius in pure culture had no detectable activity of nitrate reductase (NR. EC 1.6.6.1), glutamate dehydrogenase (GDH. EC 1.4.1.2), glutamate decarboxylase (GDCO. EC 4.1.1.15) or glutamate oxoglutarate aminotransferase (GOGAT, EC 1.4.1.13) but did have some glutamine synthetase (GS, EC 6.3.1.2) activity. Laccaria bicolor in pure culture had no NR activity, small levels of GDCO activity, and high GS, GDH and GOGAT activity. The high levels of enzymatic activity present in L. bicolor indicate that it may play a greater role in the nitrogen metabolism of its host plant than P. tinctorius. ECM infection clearly altered the enzymatic activity in jack pine roots but the nature of these changes depended on the fungal associate. Non-ECM root systems had higher specific activities than ECM root systems for NR, GS, GDH and GDCO but GOGAT activites were the same for both the ECM and non-ECM roots. Root systems infected with L. bicolor had significantly greater NR and GDCO activity than those infected with P. tinctorius. Differences in the GS activity of the two fungi in pure culture corresponded to the GS activity of jack pine roots in symbiotic association with these fungi. While the free amino acid profiles in roots were significantly affected by ECM infection, the profile of free amino acids exported to the stem was the same for all treatments. High asparagine and low glutamine in roots infected with P. tinctorius indicates that asparagine synthetase (EC x.x.x.x) activity should be higher within this symbiotic association than in the L. bicolor association or in the non-mycorrhizal roots.