Opening the black box: explainable deep-learning classification of wood microscopic image of endangered tree species.

BACKGROUND: Traditional method of wood species identification involves the use of hand lens by wood anatomists, which is a time-consuming method that usually identifies only at the genetic level. Computer vision method can achieve "species" level identification but cannot provide an explanation on what features are used for the identification. Thus, in this study, we used computer vision methods coupled with deep learning to reveal interspecific differences between closely related tree species. RESULT: A total of 850 images were collected from the cross and tangential sections of 15 wood species. These images were used to construct a deep-learning model to discriminate wood species, and a classification accuracy of 99.3% was obtained. The key features between species in machine identification were targeted by feature visualization methods, mainly the axial parenchyma arrangements and vessel in cross section and the wood ray in tangential section. Moreover, the degree of importance of the vessels of different tree species in the cross-section images was determined by the manual feature labeling method. The results showed that vessels play an important role in the identification of Dalbergia, Pterocarpus, Swartzia, Carapa, and Cedrela, but exhibited limited resolutions on discriminating Swietenia species. CONCLUSION: The research results provide a computer-assisted tool for identifying endangered tree species in laboratory scenarios, which can be used to combat illegal logging and related trade and contribute to the implementation of CITES convention and the conservation of global biodiversity.

Retrieving complete plastid genomes of endangered Guibourtia timber using hybridization capture for forensic identification and phylogenetic analysis.

The high economic value and increased demand for timber have led to illegal logging and overexploitation, threatening wild populations. In this context, there is an urgent need to develop effective and accurate forensic tools for identifying endangered Guibourtia timber species to protect forest ecosystem resources and regulate their trade. In this study, a hybridization capture method was developed and applied to explore the feasibility of retrieving complete plastid genomes from Guibourtia sapwood and heartwood specimens stored in a xylarium (wood collection). We then carried out forensic identification and phylogenetic analyses of Guibourtia within the subfamily Detarioideae. This study is the first to successfully retrieve high-quality plastid genomes from xylarium specimens, with 76.95-99.97% coverage. The enrichment efficiency, sequence depth, and coverage of plastid genomes from sapwood were 16.73 times, 70.47 times and 1.14 times higher, respectively, than those from heartwood. Although the DNA capture efficiency of heartwood was lower than that of sapwood, the hybridization capture method used in this study is still suitable for heartwood DNA analysis. Based on the complete plastid genome, we identified six endangered or commonly traded Guibourtia woods at the species level. This technique also has the potential for geographical traceability, especially for Guibourtia demeusei and Guibourtia ehie. Meanwhile, Bayesian phylogenetic analysis suggested that these six Guibourtia species diverged from closely related species within the subfamily Detarioideae ca. 18 Ma during the Miocene. The DNA reference database established based on the xylarium specimens provides admissible evidence for diversity conservation and evolutionary analyses of endangered Guibourtia species.

Non-destructive preservation state estimation of waterlogged archaeological wooden artifacts.

Non-destructive preservation state estimation is an essential prerequisite for the preservation and conservation of waterlogged archaeological wooden artifacts. Herein, Near Infrared (NIR) spectroscopy coupled with orthogonal partial least squares discriminant analysis (OPLS-DA) were applied to assess sixty-four waterlogged archaeological woods collected from seven excavation sites in the period range of 2900 BCE-1912 CE, aiming at developing a non-destructive, accurate and rapid preservation state estimation methodology. The role of non-decayed recent wood of relevant species on preservation state estimation was studied in prior, showing the use of non-decayed recent wood could not improve the predictive ability. Besides, the high variability in terms of chemical structure between archaeological softwoods and archaeological hardwoods did affect the preservation state estimation. Thus, a simple OPLS-DA model of non-destructively distinguishing archaeological hardwoods from softwoods, R2Xcum of 0.659, R2Ycum of 0.836 and Q2cum of 0.763, was established to avoid and overcome destructive approach for wood identification. Then, the well-defined three grouped separations of slightly-decayed, moderately-decayed and severely-decayed waterlogged archaeological woods were revealed in OPLS-DA models, providing R2Xcum of 0.793, R2Ycum of 0.738, Q2cum of 0.680, and R2Xcum of 0.780, R2Ycum of 0.901, Q2cum of 0.870, for waterlogged archaeological hardwoods and waterlogged archaeological softwoods respectively. Potential predictive wood spectral bands were screened and tentatively identified as hydroxyls of crystalline cellulose, acetyl groups of hemicelluloses, C-H bands of lignin, which guaranteed the elimination of non-structural compounds, such as water and inorganic components interference. Furthermore, the developed NIR methodology was validated by an extensively used destructive method consisting of anatomical characteristics, maximum water content and basic density analyses. The results indicated that NIR coupled to chemometrics could non-destructively and accurately predict the preservation states of waterlogged archaeological wooden artifacts and avoid the interference of water and inorganic deposits.

Anatomical adaptions of pits in two types of ray parenchyma cells in Populus tomentosa during the xylem differentiation.

Pits in ray parenchyma cells are important to understand the functional anatomy of the ray parenchyma network in the xylem but have been less studied. Herein, pits in two types of ray parenchyma cells, contact cells and isolation cells, across different developmental stages were qualitatively studied using 48-year-old Populus tomentosa trees. The timing of differentiation and death was determined by histochemical staining and polarized light microscopy. The dimension, shape and density of pits as well as cell wall thickness were measured using SEM and optical microscopy images of semi-thin radial sections and macerated ray parenchyma cells, and analyzed by multi-factor analyses of variance. Results showed that secondary wall thickening and lignification of contact cells begun near the cambium, contrarily those of isolation cells have started until the transition zone. But even in the sapwood, contact cell walls were still much thinner than isolation cell walls. Moreover, district anatomical adaptions of pits during the xylem differentiation were present between horizontal walls and tangential walls, between contact cells and isolation cells. Ray pits were simple to slightly bordered, whereas sieve-like pits were only shown on tangential walls of isolation cells. Pit density of horizontal walls was similar between contact cells and isolation cells, nevertheless greater pits were present on tangential walls, especially for isolation cells. In addition, pits of ray parenchyma cells in the heartwood were smaller and more bordered than those in the sapwood, particularly on the horizontal walls. Moreover, isolation cells had pits with the smaller dimensions, greater pits on the tangential walls, more bordered pits on horizontal walls, as well as longer and narrower cell morphology with much thicker cell walls than contact cells. To a certain extent, all these anatomical adaptations were developed to ensure distinct functions of the two types of ray parenchyma cells in the xylem and finally to support tree growth in demand.

Salutaxel, a Conjugate of Docetaxel and a Muramyl Dipeptide (MDP) Analogue, Acts as Multifunctional Prodrug That Inhibits Tumor Growth and Metastasis.

Salutaxel (3) is a conjugate of docetaxel (7) and a muramyl dipeptide (MDP) analogue. Docetaxel (7) has been recognized as a highly active chemotherapeutic agent against various cancers. MDP and its analogues are powerful potentiators of the antitumor actions of various tumor-necrotizing agents. This article documents the discovery of compound 3 and presents pharmacological proof of its biological function in tumor-bearing mice. Drug candidate 3 was superior to compound 7 in its ability to prevent tumor growth and metastasis. Compound 3 suppressed myeloid-derived suppressor cell (MDSC) accumulation in the spleens of tumor-bearing mice and decreased various serum inflammatory cytokines levels. Furthermore, compound 3 antagonized the nucleotide-binding oligomerization domain-like receptor 1 (NOD1) signaling pathway both in vitro and in vivo.

Characterization of three positive regulators for tetramycin biosynthesis in Streptomyces ahygroscopicus.

Three putative regulatory genes, namely ttmRI, ttmRII and ttmRIII, which are present in the tetramycin (ttm) biosynthetic gene cluster, were found in Streptomyces ahygroscopicus Disruption of ttmRI, ttmRII or ttmRIII reduced tetramycin production, and their complementation restored production to varying degrees. Gene expression analysis of the wild-type (WT) and mutant strains through reverse transcriptase-polymerase chain reaction (RT-PCR) of the ttm gene cluster showed that the expression levels of most of the biosynthetic genes were reduced in ΔttmRI, ΔttmRII and ΔttmRIII Electrophoretic mobility shift assays demonstrated that TtmRI, TtmRII and TtmRIII bound the promoters of several genes in the ttm gene cluster. This study found that these three proteins are a group of positive regulators that activate the transcription of the ttm gene cluster in S. ahygroscopicus In addition, ΔttmRII had a reduced degree of grey pigmentation. Thus, TtmRII has a pleiotropic regulatory function in the tetramycin biosynthetic pathway and in development.

[Effect of TGRJ on blood press, NO and Ang II in renal hypertensive rats].

OBJECTIVE: To study the effect of total glycosides of Ranunculus japoniucus (TGRJ) on blood pressure, nitric oxide (NO) calcium and angiotensin II (Ang II) in renal hypertensive rats (RHR). METHODS: 1) RHR were established by two kidney one clip (2K1C) and drugs were given by intragastric administration for 5 week, the blood pressure were measured at the end of 5 week,detected the concentration of NO in the serum and Ang II in the blood plasma,heart and kidney tissue. 2) Used a new generations of Ca2+ fluorescent probe (Fluo-3/AM) to mark calcium in vascular smooth muscle cells. Observed the fluorescence imaging by inverted fluorescence microscope and measured the fluorescence intensity of calcium by fluorescence spectrophotometer in vascular smooth muscle cells. RESULTS: 1) The high, medium doses of TGRJ could decrease blood pressure of RHR (P<0.05), TGRJ could significantly increase the concentration of NO in the serum (P<0.01), but it showed no significant effect on the concentration of Ang II (P>0.05); 2) The Ang II could significantly promote the calcium ions in extracellular inner flow. The different doses of TGRJ could reduce the calcium ions in cells which were mediated by Ang II. CONCLUSION: TGRJ could decrease blood pressure in RHR. the mechanism might be related to increasing the rats' NO level and reducing the calcium ions level in cells which are increased by Ang II.